Estimating changes in urban ozone concentrations due to life cycle emissions from hydrogen transportation systems

NASA Astrophysics Data System (ADS)

Wang, Guihua; Ogden, Joan M.; Chang, Daniel P. Y.

Hydrogen has been proposed as a low polluting alternative transportation fuel that could help improve urban air quality. This paper examines the potential impact of introducing a hydrogen-based transportation system on urban ambient ozone concentrations. This paper considers two scenarios, where significant numbers of new hydrogen vehicles are added to a constant number of gasoline vehicles. In our scenarios hydrogen fuel cell vehicles (HFCVs) are introduced in Sacramento, California at market penetrations of 9% and 20%. From a life cycle analysis (LCA) perspective, considering all the emissions involved in producing, transporting, and using hydrogen, this research compares three hypothetical natural gas to hydrogen pathways: (1) on-site hydrogen production; (2) central hydrogen production with pipeline delivery; and (3) central hydrogen production with liquid hydrogen truck delivery. Using a regression model, this research shows that the daily maximum temperature correlates well with atmospheric ozone formation. However, increases in initial VOC and NO x concentrations do not necessarily increase the peak ozone concentration, and may even cause it to decrease. It is found that ozone formation is generally limited by NO x in the summer and is mostly limited by VOC in the fall in Sacramento. Of the three hydrogen pathways, the truck delivery pathway contributes the most to ozone precursor emissions. Ozone precursor emissions from the truck pathway at 9% market penetration can cause additional 3-h average VOC (or NO x) concentrations up to approximately 0.05% (or 1%) of current pollution levels, and at 20% market penetration up to approximately 0.1% (or 2%) of current pollution levels. However, all of the hydrogen pathways would result in very small (either negative or positive) changes in ozone air quality. In some cases they will result in worse ozone air quality (mostly in July, August, and September), and in some cases they will result in better ozone air quality (mostly in October). The truck pathway tends to cause a much wider fluctuation in degradation or improvement of ozone air quality: percentage changes in peak ozone concentrations are approximately -0.01% to 0.04% for the assumed 9% market penetration, and approximately -0.03% to 0.1% for the 20% market penetration. Moreover, the 20% on-site pathway occasionally results in a decrease of about -0.1% of baseline ozone pollution. Compared to the current ambient pollution level, all three hydrogen pathways are unlikely to cause a serious ozone problem for market penetration levels of HFCVs in the 9-20% range.

The effect of long-range air mass transport pathways on PM10 and NO2 concentrations at urban and rural background sites in Ireland: Quantification using clustering techniques.

PubMed

Donnelly, Aoife A; Broderick, Brian M; Misstear, Bruce D

2015-01-01

The specific aims of this paper are to: (i) quantify the effects of various long range transport pathways nitrogen dioxide (NO2) and particulate matter with diameter less than 10μm (PM10) concentrations in Ireland and identify air mass movement corridors which may lead to incidences poor air quality for application in forecasting; (ii) compare the effects of such pathways at various sites; (iii) assess pathways associated with a period of decreased air quality in Ireland. The origin of and the regions traversed by an air mass 96h prior to reaching a receptor is modelled and k-means clustering is applied to create air-mass groups. Significant differences in air pollution levels were found between air mass cluster types at urban and rural sites. It was found that easterly or recirculated air masses lead to higher NO2 and PM10 levels with average NO2 levels varying between 124% and 239% of the seasonal mean and average PM10 levels varying between 103% and 199% of the seasonal mean at urban and rural sites. Easterly air masses are more frequent during winter months leading to higher overall concentrations. The span in relative concentrations between air mass clusters is highest at the rural site indicating that regional factors are controlling concentration levels. The methods used in this paper could be applied to assist in modelling and forecasting air quality based on long range transport pathways and forecast meteorology without the requirement for detailed emissions data over a large regional domain or the use of computationally demanding modelling techniques.

Results of a long-term study of vapor intrusion at four large buildings at the NASA Ames Research Center.

PubMed

Brenner, David

2010-06-01

Most of the published empirical data on indoor air concentrations resulting from vapor intrusion of contaminants from underlying groundwater are for residential structures. The National Aeronautics and Space Administration (NASA) Research Park site, located in Moffett Field, CA, and comprised of 213 acres, is being planned for redevelopment as a collaborative research and educational campus with associated facilities. Groundwater contaminated with hydrocarbon and halogenated hydrocarbon volatile organic compounds (VOCs) is the primary environmental medium of concern at the site. Over a 15-month period, approximately 1000 indoor, outdoor ambient, and outdoor ambient background samples were collected from four buildings designated as historical landmarks using Summa canisters and analyzed by the U.S. Environmental Protection Agency TO-15 selective ion mode. Both 24-hr and sequential 8-hr samples were collected. Comparison of daily sampling results relative to daily background results indicates that the measured trichloroethylene (TCE) concentrations were primarily due to the subsurface vapor intrusion pathway, although there is likely some contribution due to infiltration of TCE from the outdoor ambient background concentrations. Analysis of the cis-1,2-dichloroethylene concentrations relative to TCE concentrations with respect to indoor air concentrations and the background air support this hypothesis; however, this indicates that relative contributions of the vapor intrusion and infiltration pathways vary with each building. Indoor TCE concentrations were also compared with indoor benzene and background benzene concentrations. These data indicate significant correlation between background benzene concentrations and the concentration of benzene in the indoor air, indicating benzene was present in the indoor air primarily through infiltration of outdoor air into the indoor space. By comparison, measured TCE indoor air concentrations showed a significantly different relationship to background concentrations. Analysis of the results show that indoor air samples can be used to definitively define the source of the TCE present in the indoor air space of large industrial buildings.

Comparative International Air Cargo Solutions: The Pathway to a Resilient, Adaptable, Balanced and Sustainable Secure Global Air Cargo Supply Chain

DTIC Science & Technology

2013-12-01

NUMBERS 6. AUTHOR(S) Thomas P. Guglielmo 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Naval Postgraduate School Monterey, CA 93943-5000 8... PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING /MONITORING AGENCY NAME(S) AND ADDRESS(ES) N/A 10. SPONSORING/MONITORING AGENCY REPORT...improvised explosive devices (IEDs). In an analysis conducted by the Homeland Security News Wire after the Boston Marathon bombings, it was

Special Analysis for the Disposal of the Sandia National Laboratory Classified Macroencapsulated Mixed Waste at the Area 5 Radioactive Waste Management Site, Nevada National Security Site, Nye County, Nevada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gregory, Louis B.

This special analysis evaluates whether the Sandia National Laboratory (SNL) Classified Macroencapsulated Mixed Waste stream (ASLA000001007, Revision 4) is suitable for disposal by shallow land burial (SLB) at the Area 5 Radioactive Waste Management Site (RWMS) at the Nevada National Security Site (NNSS). The SNL Classified Macroencapsulated Mixed Waste stream consists of debris from classified nuclear weapons components (SNL 2015). The SNL Classified Macroencapsulated Mixed Waste stream required a special analysis due to tritium (3H) exceeding the NNSS Waste Acceptance Criteria (WAC) Action Levels (U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office [NNSA/NFO] 2015). The SNL Classifiedmore » Macroencapsulated Mixed Waste stream had no significant effect on the maximum mean and 95th percentile results for the resident air pathway and all-pathways annual total effective dose (TED). The SNL Classified Macroencapsulated Mixed Waste stream increases the mean air pathway and all-pathways annual TED from approximately 100 to 200 years after closure. Addition of the SNL Classified Macroencapsulated Mixed Waste stream inventory shifts the maximum TED to approximately 100 years after closure and increases the TED for several alternative exposure scenarios. The maximum mean and the 95th percentile 222Rn flux density remain less than the performance objective throughout the compliance period. The SNL Classified Macroencapsulated Mixed Waste stream is suitable for disposal by SLB at the Area 5 RWMS. The waste stream is recommended for approval without conditions.« less

First report of Legionella pneumophila in car cabin air filters. Are these a potential exposure pathway for professional drivers?

PubMed

Alexandropoulou, Ioanna G; Konstantinidis, Theocharis G; Parasidis, Theodoros A; Nikolaidis, Christos; Panopoulou, Maria; Constantinidis, Theodoros C

2013-12-01

Recent findings have identified professional drivers as being at an increased risk of Legionnaires' disease. Our hypothesis was that used car cabin air filters represent a reservoir of Legionella bacteria, and thus a potential pathway for contamination. We analysed used cabin air filters from various types of car. The filters were analysed by culture and by molecular methods. Our findings indicated that almost a third of air filters were colonized with Legionella pneumophila. Here, we present the first finding of Legionella spp. in used car cabin air filters. Further investigations are needed in order to confirm this exposure pathway. The presence of Legionella bacteria in used cabin air filters may have been an unknown source of infection until now.

Relation of pediatric blood lead levels to lead in gasoline.

PubMed Central

Billick, I H; Curran, A S; Shier, D R

1980-01-01

Analysis of a large data set of pediatric blood lead levels collected in New York City (1970-1976) shows a highly significant association between geometric mean blood lead levels and the amount of lead present in gasoline sold during the same period. This association was observed for all age and ethnic groups studied, and it suggests that possible exposure pathways other than ambient air should be considered. Even without detailed knowledge of the exact exposure pathways, sufficient information now exists for policy analysis and decisions relevant to controls and standards related to lead in gasoline and its effect on subsets of the population. PMID:7389685

Influence of Rack Design and Disease Prevalence on Detection of Rodent Pathogens in Exhaust Debris Samples from Individually Ventilated Caging Systems.

PubMed

Bauer, Beth A; Besch-Williford, Cynthia; Livingston, Robert S; Crim, Marcus J; Riley, Lela K; Myles, Matthew H

2016-11-01

Sampling of bedding debris within the exhaust systems of ventilated racks may be a mechanism for detecting murine pathogens in colony animals. This study examined the effectiveness of detecting pathogens by PCR analysis of exhaust debris samples collected from ventilated racks of 2 different rack designs, one with unfiltered air flow from within the cage to the air-exhaust pathway, and the other had a filter between the cage and the air-exhaust pathway. For 12 wk, racks were populated with either 1 or 5 cages of mice (3 mice per cage) infected with one of the following pathogens: mouse norovirus (MNV), mouse parvovirus (MPV), mouse hepatitis virus (MHV), Helicobacter spp., Pasteurella pneumotropica, pinworms, Entamoeba muris, Tritrichomonas muris, and fur mites. Pathogen shedding by infected mice was monitored throughout the study. In the filter-containing rack, PCR testing of exhaust plenums yielded negative results for all pathogens at all time points of the study. In the rack with open air flow, pathogens detected by PCR analysis of exhaust debris included MHV, Helicobacter spp., P. pneumotropica, pinworms, enteric protozoa, and fur mites; these pathogens were detected in racks housing either 1 or 5 cages of infected mice. Neither MPV nor MNV was detected in exhaust debris, even though prolonged viral shedding was confirmed. These results demonstrate that testing rack exhaust debris from racks with unfiltered air flow detected MHV, enteric bacteria and parasites, and fur mites. However, this method failed to reliably detect MNV or MPV infection of colony animals.

Influence of Rack Design and Disease Prevalence on Detection of Rodent Pathogens in Exhaust Debris Samples from Individually Ventilated Caging Systems

PubMed Central

Bauer, Beth A; Besch-Williford, Cynthia; Livingston, Robert S; Crim, Marcus J; Riley, Lela K; Myles, Matthew H

2016-01-01

Sampling of bedding debris within the exhaust systems of ventilated racks may be a mechanism for detecting murine pathogens in colony animals. This study examined the effectiveness of detecting pathogens by PCR analysis of exhaust debris samples collected from ventilated racks of 2 different rack designs, one with unfiltered air flow from within the cage to the air-exhaust pathway, and the other had a filter between the cage and the air-exhaust pathway. For 12 wk, racks were populated with either 1 or 5 cages of mice (3 mice per cage) infected with one of the following pathogens: mouse norovirus (MNV), mouse parvovirus (MPV), mouse hepatitis virus (MHV), Helicobacter spp., Pasteurella pneumotropica, pinworms, Entamoeba muris, Tritrichomonas muris, and fur mites. Pathogen shedding by infected mice was monitored throughout the study. In the filter-containing rack, PCR testing of exhaust plenums yielded negative results for all pathogens at all time points of the study. In the rack with open air flow, pathogens detected by PCR analysis of exhaust debris included MHV, Helicobacter spp., P. pneumotropica, pinworms, enteric protozoa, and fur mites; these pathogens were detected in racks housing either 1 or 5 cages of infected mice. Neither MPV nor MNV was detected in exhaust debris, even though prolonged viral shedding was confirmed. These results demonstrate that testing rack exhaust debris from racks with unfiltered air flow detected MHV, enteric bacteria and parasites, and fur mites. However, this method failed to reliably detect MNV or MPV infection of colony animals. PMID:27931317

Modelling the bioaccumulation of persistent organic pollutants in agricultural food chains for regulatory exposure assessment.

PubMed

Takaki, Koki; Wade, Andrew J; Collins, Chris D

2017-02-01

New models for estimating bioaccumulation of persistent organic pollutants in the agricultural food chain were developed using recent improvements to plant uptake and cattle transfer models. One model named AgriSim was based on K OW regressions of bioaccumulation in plants and cattle, while the other was a steady-state mechanistic model, AgriCom. The two developed models and European Union System for the Evaluation of Substances (EUSES), as a benchmark, were applied to four reported food chain (soil/air-grass-cow-milk) scenarios to evaluate the performance of each model simulation against the observed data. The four scenarios considered were as follows: (1) polluted soil and air, (2) polluted soil, (3) highly polluted soil surface and polluted subsurface and (4) polluted soil and air at different mountain elevations. AgriCom reproduced observed milk bioaccumulation well for all four scenarios, as did AgriSim for scenarios 1 and 2, but EUSES only did this for scenario 1. The main causes of the deviation for EUSES and AgriSim were the lack of the soil-air-plant pathway and the ambient air-plant pathway, respectively. Based on the results, it is recommended that soil-air-plant and ambient air-plant pathway should be calculated separately and the K OW regression of transfer factor to milk used in EUSES be avoided. AgriCom satisfied the recommendations that led to the low residual errors between the simulated and the observed bioaccumulation in agricultural food chain for the four scenarios considered. It is therefore recommended that this model should be incorporated into regulatory exposure assessment tools. The model uncertainty of the three models should be noted since the simulated concentration in milk from 5th to 95th percentile of the uncertainty analysis often varied over two orders of magnitude. Using a measured value of soil organic carbon content was effective to reduce this uncertainty by one order of magnitude.

SPATIO-TEMPORAL ANALYSIS OF TOTAL NITRATE CONCENTRATIONS USING DYNAMIC STATISTICAL MODELS

EPA Science Inventory

Atmospheric concentrations of total nitrate (TNO₃), defined here as gas-phase nitric acid plus particle-phase nitrate, are difficult to simulate in numerical air quality models due to the presence of a variety of formation pathways and loss mechanisms, some of which ar...

Assessment of inter-city transport of particulate matter in the Beijing-Tianjin-Hebei region

NASA Astrophysics Data System (ADS)

Chang, Xing; Wang, Shuxiao; Zhao, Bin; Cai, Siyi; Hao, Jiming

2018-04-01

The regional transport of particulate matter with diameter less than 2.5 µm (PM2.5) plays an important role in the air pollution of the Beijing-Tianjin-Hebei (BTH) region in China. However, previous studies on regional transport of PM2.5 mainly aim at province level, which is insufficient for the development of an optimal joint PM2.5 control strategy. In this study, we calculate PM2.5 inflows and outflows through the administrative boundaries of three major cities in the BTH region, i.e., Beijing, Tianjin and Shijiazhuang, using the WRF (Weather Research and Forecasting model)-CMAQ (Community Multiscale Air Quality) modeling system. The monthly average inflow fluxes indicate the major directions of PM2.5 transport. For Beijing, the PM2.5 inflow fluxes from Zhangjiakou (in the northwest) and Baoding (in the southwest) constitute 57 % of the total in winter, and Langfang (in the southeast) and Baoding constitute 73 % in summer. Based on the net PM2.5 fluxes and their vertical distributions, we find there are three major transport pathways in the BTH region: the northwest-southeast pathway in winter (at all levels below 1000 m), the northwest-southeast pathway in summer (at all levels below 1000 m), and the southwest-northeast pathway in both winter and in summer (mainly at 300-1000 m). In winter, even if surface wind speeds are low, the transport at above 300 m can still be strong. Among the three pathways, the southwest-northeast happens along with PM2.5 concentrations 30 and 55 % higher than the monthly average in winter and summer, respectively. Analysis of two heavy pollution episodes in January and July in Beijing show a much (8-16 times) stronger transport than the monthly average, emphasizing the joint air pollution control of the cities located on the transport pathways, especially during heavy pollution episodes.

Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations

PubMed Central

Levicán, Gloria; Ugalde, Juan A; Ehrenfeld, Nicole; Maass, Alejandro; Parada, Pilar

2008-01-01

Background Carbon and nitrogen fixation are essential pathways for autotrophic bacteria living in extreme environments. These bacteria can use carbon dioxide directly from the air as their sole carbon source and can use different sources of nitrogen such as ammonia, nitrate, nitrite, or even nitrogen from the air. To have a better understanding of how these processes occur and to determine how we can make them more efficient, a comparative genomic analysis of three bioleaching bacteria isolated from mine sites in Chile was performed. This study demonstrated that there are important differences in the carbon dioxide and nitrogen fixation mechanisms among bioleaching bacteria that coexist in mining environments. Results In this study, we probed that both Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans incorporate CO2 via the Calvin-Benson-Bassham cycle; however, the former bacterium has two copies of the Rubisco type I gene whereas the latter has only one copy. In contrast, we demonstrated that Leptospirillum ferriphilum utilizes the reductive tricarboxylic acid cycle for carbon fixation. Although all the species analyzed in our study can incorporate ammonia by an ammonia transporter, we demonstrated that Acidithiobacillus thiooxidans could also assimilate nitrate and nitrite but only Acidithiobacillus ferrooxidans could fix nitrogen directly from the air. Conclusion The current study utilized genomic and molecular evidence to verify carbon and nitrogen fixation mechanisms for three bioleaching bacteria and provided an analysis of the potential regulatory pathways and functional networks that control carbon and nitrogen fixation in these microorganisms. PMID:19055775

Potential Air Pollutant Emissions and Permitting Classifications for Two Biorefinery Process Designs in the United States

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eberle, Annika; Bhatt, Arpit; Zhang, Yimin

Advanced biofuel production facilities (biorefineries), such as those envisioned by the United States (U.S.) Renewable Fuel Standard and U.S. Department of Energy's research and development programs, often lack historical air pollutant emissions data, which can pose challenges for obtaining air emission permits that are required for construction and operation. To help fill this knowledge gap, we perform a thorough regulatory analysis and use engineering process designs to assess the applicability of federal air regulations and quantify air pollutant emissions for two feasibility-level biorefinery designs. We find that without additional emission-control technologies both biorefineries would likely be required to obtain majormore » source permits under the Clean Air Act's New Source Review program. The permitting classification (so-called 'major' or 'minor') has implications for the time and effort required for permitting and therefore affects the cost of capital and the fuel selling price. Consequently, we explore additional technically feasible emission-control technologies and process modifications that have the potential to reduce emissions to achieve a minor source permitting classification. Finally, our analysis of air pollutant emissions and controls can assist biorefinery developers with the air permitting process and inform regulatory agencies about potential permitting pathways for novel biorefinery designs.« less

Potential Air Pollutant Emissions and Permitting Classifications for Two Biorefinery Process Designs in the United States

DOE PAGES

Eberle, Annika; Bhatt, Arpit; Zhang, Yimin; ...

2017-04-26

Advanced biofuel production facilities (biorefineries), such as those envisioned by the United States (U.S.) Renewable Fuel Standard and U.S. Department of Energy's research and development programs, often lack historical air pollutant emissions data, which can pose challenges for obtaining air emission permits that are required for construction and operation. To help fill this knowledge gap, we perform a thorough regulatory analysis and use engineering process designs to assess the applicability of federal air regulations and quantify air pollutant emissions for two feasibility-level biorefinery designs. We find that without additional emission-control technologies both biorefineries would likely be required to obtain majormore » source permits under the Clean Air Act's New Source Review program. The permitting classification (so-called 'major' or 'minor') has implications for the time and effort required for permitting and therefore affects the cost of capital and the fuel selling price. Consequently, we explore additional technically feasible emission-control technologies and process modifications that have the potential to reduce emissions to achieve a minor source permitting classification. Finally, our analysis of air pollutant emissions and controls can assist biorefinery developers with the air permitting process and inform regulatory agencies about potential permitting pathways for novel biorefinery designs.« less

Potential Air Pollutant Emissions and Permitting Classifications for Two Biorefinery Process Designs in the United States.

PubMed

Eberle, Annika; Bhatt, Arpit; Zhang, Yimin; Heath, Garvin

2017-06-06

Advanced biofuel production facilities (biorefineries), such as those envisioned by the United States (U.S.) Renewable Fuel Standard and U.S. Department of Energy's research and development programs, often lack historical air pollutant emissions data, which can pose challenges for obtaining air emission permits that are required for construction and operation. To help fill this knowledge gap, we perform a thorough regulatory analysis and use engineering process designs to assess the applicability of federal air regulations and quantify air pollutant emissions for two feasibility-level biorefinery designs. We find that without additional emission-control technologies both biorefineries would likely be required to obtain major source permits under the Clean Air Act's New Source Review program. The permitting classification (so-called "major" or "minor") has implications for the time and effort required for permitting and therefore affects the cost of capital and the fuel selling price. Consequently, we explore additional technically feasible emission-control technologies and process modifications that have the potential to reduce emissions to achieve a minor source permitting classification. Our analysis of air pollutant emissions and controls can assist biorefinery developers with the air permitting process and inform regulatory agencies about potential permitting pathways for novel biorefinery designs.

Integrated turbomachine oxygen plant

DOEpatents

Anand, Ashok Kumar; DePuy, Richard Anthony; Muthaiah, Veerappan

2014-06-17

An integrated turbomachine oxygen plant includes a turbomachine and an air separation unit. One or more compressor pathways flow compressed air from a compressor through one or more of a combustor and a turbine expander to cool the combustor and/or the turbine expander. An air separation unit is operably connected to the one or more compressor pathways and is configured to separate the compressed air into oxygen and oxygen-depleted air. A method of air separation in an integrated turbomachine oxygen plant includes compressing a flow of air in a compressor of a turbomachine. The compressed flow of air is flowed through one or more of a combustor and a turbine expander of the turbomachine to cool the combustor and/or the turbine expander. The compressed flow of air is directed to an air separation unit and is separated into oxygen and oxygen-depleted air.

Implied Maximum Dose Analysis of Standard Values of 25 Pesticides Based on Major Human Exposure Pathways

PubMed Central

Li, Zijian; Jennings, Aaron A.

2017-01-01

Worldwide jurisdictions are making efforts to regulate pesticide standard values in residential soil, drinking water, air, and agricultural commodity to lower the risk of pesticide impacts on human health. Because human may exposure to pesticides from many ways, such as ingestion, inhalation, and dermal contact, it is important to examine pesticide standards by considering all major exposure pathways. Analysis of implied maximum dose limits for commonly historical and current used pesticides was adopted in this study to examine whether worldwide pesticide standard values are enough to prevent human health impact or not. Studies show that only U.S. has regulated pesticides standard in the air. Only 4% of the total number of implied maximum dose limits is based on three major exposures. For Chlorpyrifos, at least 77.5% of the total implied maximum dose limits are above the acceptable daily intake. It also shows that most jurisdictions haven't provided pesticide standards in all major exposures yet, and some of the standards are not good enough to protect human health. PMID:29546224

Health risks of energy systems.

PubMed

Krewitt, W; Hurley, F; Trukenmüller, A; Friedrich, R

1998-08-01

Health risks from fossil, renewable and nuclear reference energy systems are estimated following a detailed impact pathway approach. Using a set of appropriate air quality models and exposure-effect functions derived from the recent epidemiological literature, a methodological framework for risk assessment has been established and consistently applied across the different energy systems, including the analysis of consequences from a major nuclear accident. A wide range of health impacts resulting from increased air pollution and ionizing radiation is quantified, and the transferability of results derived from specific power plants to a more general context is discussed.

The Impacts of Policies To Meet The UK Climate Change Act Target on Air Quality - An Explicit Modelling Study

NASA Astrophysics Data System (ADS)

Williams, M.; Beevers, S.; Lott, M. C.; Kitwiroon, N.

2016-12-01

This paper presents a preliminary analysis of different pathways to meet the UK Climate Change Act target for 2050, of an 80% reduction in carbon dioxide equivalent emissions on a base year of 1990. The pathways can result in low levels of air pollution emissions through the use of renewables and nuclear power. But large increases in biomass burning and the continued use of diesel cars they can result in larger air quality impacts. The work evaluated the air quality impacts in several pathways using an energy system optimisation model (UK TIMES) and a chemical transport model (CMAQ). The work described in this paper goes beyond the `damage cost' approach where only emissions in each are assessed. In this work we used scenarios produced by the UK TIMES model which we converted into air pollution emissions. Emissions of ammonia from agriculture are not attributed to the energy system and are thus not captured by energy system models, yet are crucial in forming PM2.5, acknowledged to be currently the most important pollutant associated with premature deaths. Our model includes these emissions and other non-energy sources of hydrocarbons which lead to the formation of ozone, another significant cause of air pollution health impacts. A key policy issue is how much biogenic hydrocarbons contribute to ozone formation compared with man-made emissions. We modelled pollution concentrations at a resolution of 7 km across the UK and at 2km in urban areas. These results allow us to estimate changes in premature mortality and morbidity associated with the changes in air pollution and subsequently the economic cost of the impacts on public health. The work shows that in the `clean' scenario, urban exposures to particles (PM2.5) and NO2 could decrease by very large amounts, but ozone exposures are likely to increase without further significant reductions world-wide. Large increases in biomass use however could lead to increases in urban levels of carcinogens and primary PM.

Pathways of inhalation exposure to manganese in children ...

EPA Pesticide Factsheets

Manganese (Mn) is both essential element and neurotoxicant. Exposure to Mn can occur from various sources and routes. Structural equation modeling was used to examine routes of exposure to Mn among children residing near a ferromanganese refinery in Marietta, Ohio. An inhalation pathway model to ambient air Mn was hypothesized. Data for model evaluation were obtained from participants in the Communities Actively Researching Exposure Study (CARES). These data were collected in 2009 and included levels of Mn in residential soil and dust, levels of Mn in children's hair, information on the amount of time the child spent outside, heat and air conditioning in the home and level of parent education. Hair Mn concentration was the primary endogenous variable used to assess the theoretical inhalation exposure pathways. The model indicated that household dust Mn was a significant contributor to child hair Mn (0.37). Annual ambient air Mn concentration (0.26), time children spent outside (0.24) and soil Mn (0.24) significantly contributed to the amount of Mn in household dust. These results provide a potential framework for understanding the inhalation exposure pathway for children exposed to ambient air Mn who live in proximity to an industrial emission source. The purpose of this study was to use a structural equations modeling approach combined with exposure estimates derived from air-dispersion modeling to assess potential inhalation exposure pathways for children to a

Distribution pathways of hexachlorocyclohexane isomers in a soil-plant-air system. A case study with Cynara scolymus L. and Erica sp. plants grown in a contaminated site.

PubMed

Pereira, R Calvelo; Monterroso, C; Macías, F; Camps-Arbestain, M

2008-09-01

This study focuses on the main routes of distribution and accumulation of different hexachlorocyclohexane (HCH) isomers (mainly alpha-, beta-, gamma- and delta-HCH) in a soil-plant-air system. A field assay was carried out with two plant species, Cynara scolymus L. and Erica sp., which were planted either: (i) directly in the HCH-contaminated soil; or (ii) in pots filled with uncontaminated soil, which were placed in the HCH-contaminated soil. Both plant species accumulated HCH in their tissues, with relatively higher accumulation in above-ground biomass than in roots. The beta-HCH isomer was the main isomer in all plant tissues. Adsorption of HCH by the roots from contaminated soil (soil-->root pathway) and adsorption through the aerial biomass from either the surrounding air, following volatilization of the contaminant (soil-->air-->shoot pathway), and/or contact with air-suspended particles contaminated with HCH (soil particles-->shoot pathway) were the main mechanisms of accumulation. These results may have important implications for the use of plants for reducing the transfer of contaminants via the atmosphere.

Migration of Beryllium via Multiple Exposure Pathways among Work Processes in Four Different Facilities

PubMed Central

Armstrong, Jenna L.; Day, Gregory A.; Park, Ji Young; Stefaniak, Aleksandr B.; Stanton, Marcia L.; Deubner, David C.; Kent, Michael S.; Schuler, Christine R.; Virji, M. Abbas

2016-01-01

Inhalation of beryllium is associated with the development of sensitization; however, dermal exposure may also be important. The primary aim of this study was to elucidate relationships among exposure pathways in four different manufacturing and finishing facilities. Secondary aims were to identify jobs with increased levels of beryllium in air, on skin, and on surfaces; identify potential discrepancies in exposure pathways, and determine if these are related to jobs with previously identified risk. Beryllium was measured in air, on cotton gloves, and on work surfaces. Summary statistics were calculated and correlations among all three measurement types were examined at the facility and job level. Exposure ranking strategies were used to identify jobs with higher exposures. The highest air, glove, and surface measurements were observed in beryllium metal production and beryllium oxide ceramics manufacturing jobs that involved hot processes and handling powders. Two finishing and distribution facilities that handle solid alloy products had lower exposures than the primary production facilities, and there were differences observed among jobs. For all facilities combined, strong correlations were found between air-surface (rp ≥ 0.77), glove-surface (rp ≥ 0.76), and air-glove measurements (rp ≥ 0.69). In jobs where higher risk of beryllium sensitization or disease has been reported, exposure levels for all three measurement types were higher than in jobs with lower risk, though they were not the highest. Some jobs with low air concentrations had higher levels of beryllium on glove and surface wipe samples, suggesting a need to further evaluate the causes of the discrepant levels. Although such correlations provide insight on where beryllium is located throughout the workplace, they cannot identify the direction of the pathways between air, surface, or skin. Ranking strategies helped to identify jobs with the highest combined air, glove, and/or surface exposures. All previously identified high-risk jobs had high air concentrations, dermal mass loading, or both, and none had low dermal and air. We have found that both pathways are relevant. PMID:25357184

A Techno-Economic Analysis of Emission Controls on Hydrocarbon Biofuel Production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhatt, Arpit; Zhang, Yimin; Davis, Ryan

Biofuels have the potential to reduce our dependency on petroleum-derived transportation fuels and decrease greenhouse gas (GHG) emissions. Although the overall GHG emissions from biofuels are expected to be lower when compared to those of petroleum fuels, the process of converting biomass feedstocks into biofuels emits various air pollutants, which may be subject to federal air quality regulation or emission limits. While prior research has evaluated the technical and economic feasibility of biofuel technologies, gaps still exist in understanding the regulatory issues associated with the biorefineries and their economic implications on biofuel production costs (referred to as minimum fuel sellingmore » price (MFSP) in this study). The aim of our research is to evaluate the economic impact of implementing emission reduction technologies at biorefineries and estimate the cost effectiveness of two primary control technologies that may be required for air permitting purposes. We analyze a lignocellulosic sugars-to-hydrocarbon biofuel production pathway developed by the National Renewable Energy Laboratory (NREL) and implement air emission controls in Aspen Plus to evaluate how they affect the MFSP. Results from this analysis can help inform decisions about biorefinery siting and sizing, as well as mitigate the risks associated with air permitting.« less

A rapid response air quality analysis system for use in projects having stringent quality assurance requirements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowman, A.W.

1990-04-01

This paper describes an approach to solve air quality problems which frequently occur during iterations of the baseline change process. From a schedule standpoint, it is desirable to perform this evaluation in as short a time as possible while budgetary pressures limit the size of the staff available to do the work. Without a method in place to deal with baseline change proposal requests the environment analysts may not be able to produce the analysis results in the time frame expected. Using a concept called the Rapid Response Air Quality Analysis System (RAAS), the problems of timing and cost becomemore » tractable. The system could be adapted to assess other atmospheric pathway impacts, e.g., acoustics or visibility. The air quality analysis system used to perform the EA analysis (EA) for the Salt Repository Project (part of the Civilian Radioactive Waste Management Program), and later to evaluate the consequences of proposed baseline changes, consists of three components: Emission source data files; Emission rates contained in spreadsheets; Impact assessment model codes. The spreadsheets contain user-written codes (macros) that calculate emission rates from (1) emission source data (e.g., numbers and locations of sources, detailed operating schedules, and source specifications including horsepower, load factor, and duty cycle); (2) emission factors such as those published by the U.S. Environmental Protection Agency, and (3) control efficiencies.« less

Influence of long-range atmospheric transport pathways and climate teleconnection patterns on the variability of surface 210Pb and 7Be concentrations in southwestern Europe.

PubMed

Grossi, C; Ballester, J; Serrano, I; Galmarini, S; Camacho, A; Curcoll, R; Morguí, J A; Rodò, X; Duch, M A

2016-12-01

The variability of the atmospheric concentration of the 7 Be and 210 Pb radionuclides is strongly linked to the origin of air masses, the strength of their sources and the processes of wet and dry deposition. It has been shown how these processes and their variability are strongly affected by climate change. Thus, a deeper knowledge of the relationship between the atmospheric radionuclides variability measured close to the ground and these atmospheric processes could help in the analysis of climate scenarios. In the present study, we analyze the atmospheric variability of a 14-year time series of 7 Be and 210 Pb in a Mediterranean coastal city using a synergy of different indicators and tools such as: the local meteorological conditions, global and regional climate indexes and a lagrangian atmospheric transport model. We particularly focus on the relationships between the main pathways of air masses and sun spots occurrence, the variability of the local relative humidity and temperature conditions, and the main modes of regional climate variability, such as the North Atlantic Oscillation (NAO) and the Western Mediterranean Oscillation (WeMO). The variability of the observed atmospheric concentrations of both 7 Be and 210 Pb radionuclides was found to be mainly positively associated to the local climate conditions of temperature and to the pathways of air masses arriving at the station. Measured radionuclide concentrations significantly increase when air masses travel at low tropospheric levels from central Europe and the western part of the Iberian Peninsula, while low concentrations are associated with westerly air masses. We found a significant negative correlation between the WeMO index and the atmospheric variability of both radionuclides and no significant association was observed for the NAO index. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thinking outside of the lungs: systemic stress response as a pathway and modifier of air pollution health effects

EPA Science Inventory

This poster will describe the effects of non-chemical stressors (e.g. noise) on the physiological response to air pollution, as well as the role of systemic stress pathways in the mediating the adverse health effects. The findings presented here are important because they elucida...

Impacts of Lowered Urban Air Temperatures on Precursor Emission and Ozone Air Quality.

PubMed

Taha, Haider; Konopacki, Steven; Akbari, Hashem

1998-09-01

Meteorological, photochemical, building-energy, and power plant simulations were performed to assess the possible precursor emission and ozone air quality impacts of decreased air temperatures that could result from implementing the "cool communities" concept in California's South Coast Air Basin (SoCAB). Two pathways are considered. In the direct pathway, a reduction in cooling energy use translates into reduced demand for generation capacity and, thus, reduced precursor emissions from electric utility power plants. In the indirect pathway, reduced air temperatures can slow the atmospheric production of ozone as well as precursor emission from anthropogenic and biogenic sources. The simulations suggest small impacts on emissions following implementation of cool communities in the SoCAB. In summer, for example, there can be reductions of up to 3% in NO x emissions from in-basin power plants. The photochemical simulations suggest that the air quality impacts of these direct emission reductions are small. However, the indirect atmospheric effects of cool communities can be significant. For example, ozone peak concentrations can decrease by up to 11% in summer and population-weighted exceedance exposure to ozone above the California and National Ambient Air Quality Standards can decrease by up to 11 and 17%, respectively. The modeling suggests that if these strategies are combined with others, such as mobile-source emission control, the improvements in ozone air quality can be substantial.

Migration of Beryllium via Multiple Exposure Pathways among Work Processes in Four Different Facilities.

PubMed

Armstrong, Jenna L; Day, Gregory A; Park, Ji Young; Stefaniak, Aleksandr B; Stanton, Marcia L; Deubner, David C; Kent, Michael S; Schuler, Christine R; Virji, M Abbas

2014-01-01

Inhalation of beryllium is associated with the development of sensitization; however, dermal exposure may also be important. The primary aim of this study was to elucidate relationships among exposure pathways in four different manufacturing and finishing facilities. Secondary aims were to identify jobs with increased levels of beryllium in air, on skin, and on surfaces; identify potential discrepancies in exposure pathways, and determine if these are related to jobs with previously identified risk. Beryllium was measured in air, on cotton gloves, and on work surfaces. Summary statistics were calculated and correlations among all three measurement types were examined at the facility and job level. Exposure ranking strategies were used to identify jobs with higher exposures. The highest air, glove, and surface measurements were observed in beryllium metal production and beryllium oxide ceramics manufacturing jobs that involved hot processes and handling powders. Two finishing and distribution facilities that handle solid alloy products had lower exposures than the primary production facilities, and there were differences observed among jobs. For all facilities combined, strong correlations were found between air-surface (rp ≥ 0.77), glove-surface (rp ≥ 0.76), and air-glove measurements (rp ≥ 0.69). In jobs where higher risk of beryllium sensitization or disease has been reported, exposure levels for all three measurement types were higher than in jobs with lower risk, though they were not the highest. Some jobs with low air concentrations had higher levels of beryllium on glove and surface wipe samples, suggesting a need to further evaluate the causes of the discrepant levels. Although such correlations provide insight on where beryllium is located throughout the workplace, they cannot identify the direction of the pathways between air, surface, or skin. Ranking strategies helped to identify jobs with the highest combined air, glove, and/or surface exposures. All previously identified high-risk jobs had high air concentrations, dermal mass loading, or both, and none had low dermal and air. We have found that both pathways are relevant. [Supplementary materials are available for this article. Go to the publisher's online edition of Journal of Occupational and Environmental Hygiene for the following free supplemental resource: a file describing the forms of beryllium materials encountered during production and characteristics of the aerosols by process areas.].

The effect of the indoor environment on the fate of organic chemicals in the urban landscape.

PubMed

Cousins, Anna Palm

2012-11-01

To assess the effect of the indoor environment on the urban fate of organic chemicals, an 8-compartment indoor-inclusive steady state multimedia chemical fate model was developed. The model includes typical urban compartments (air, soil, water, sediment, and urban film) and a novel module representing a generic indoor environment. The model was parameterized to the municipality of Stockholm, Sweden and applied to four organic chemicals with different physical-chemical characteristics and use patterns: formaldehyde, 2,4,6-tribromophenol, di-ethylhexylphthalate and decabromodiphenyl ether. The results show that emissions to indoor air may increase the steady state mass and residence time in the urban environment by a factor of 1.1 to 22 for the four chemicals, compared to if emissions are assigned to outdoor air. This is due to the nested nature of the indoor environment, which creates a physical barrier that prevents chemicals from leaving the urban system with outflowing air. For DEHP and BDE 209, the additional partitioning to indoor surfaces results in a greater importance of the indoor removal pathways from surfaces. The outdoor environmental concentrations of these chemicals are predicted to be lower if emitted to indoor air than if emitted to outdoor air because of the additional indoor removal pathways of dust and indoor film, leading to loss of chemical from the system. For formaldehyde and 2,4,6-TBP outdoor environmental concentrations are not affected by whether the release occurs indoors or outdoors because of the limited partitioning to indoor surfaces. A sensitivity analysis revealed that there appears to be a relationship between logK(OA) and the impact of the ventilation rate on the urban fate of organic chemicals. Copyright © 2012 Elsevier B.V. All rights reserved.

Clinging to the Past: The Air Force’s War on Dual-Career Families

DTIC Science & Technology

2014-06-01

combines existing research on stress and work-family conflict with new primary research on current USAF dual-career families in the form of a case...incompatibilities between the Air Force family schema (conceptions of, and practices relating to, USAF families). The study combines existing research on stress ... Stress Pathways ..................................................... 74 Figure 5, Civilian Dual-Career Stress Pathways

Environmental assessments on schools located on or near former industrial facilities: Feedback on attenuation factors for the prediction of indoor air quality.

PubMed

Derycke, Virginie; Coftier, Aline; Zornig, Clément; Léprond, Hubert; Scamps, Mathilde; Gilbert, Dominique

2018-06-01

One of the goals of the French national campaign called "Etablissements Sensibles (Sensitive Establishments)" is to evaluate indoor air degradation in schools because of vapor intrusion of volatile compounds from soil gases towards the indoor air, related to the presence of former industrial sites on or near the establishment. During this campaign, as recommended by the United States of Environmental Protection Agency (US EPA), indoor air quality was evaluated from soil gas concentrations using generic attenuation factors, and extra investigations into soil gases and indoor air were performed when the estimated values exceeded target indoor air concentrations. This study exploits matched data on subsurface soil gases and indoor air that came from the "Sensitive Establishments" campaign. It aims to consolidate and refine the use of attenuation factors as a function of environmental variables acquired routinely during environmental assessments. We have been able to select the measured environmental variables that have the most influence on vapor intrusion using Principal Components Analysis and hypotheses tests. Since the collected data are mainly related to weak sources (only 15% schools required risk management measures related to vapor intrusion), halogenated volatile organic compounds (HVOC) were selected as tracer compounds for vapor intrusion for this study. This choice enables the exclusion or minimization of background sources contributions. From the results we have calculated the descriptive statistics of the attenuation factors distribution for the subslab-to-indoor air pathway and refined the attenuation factors for this pathway through an easily obtained parameter, building age. Qualitative comparison of attenuation factors according to the building age shows that attenuation factors observed for building less than 50 years are lower than attenuation factors for buildings 50 years old and above. These results show the utility of creating databases for consolidating and refining attenuation factors and therefore improving their use. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Temporal variability of indoor air concentrations under natural conditions in a house overlying a dilute chlorinated solvent groundwater plume.

PubMed

Holton, Chase; Luo, Hong; Dahlen, Paul; Gorder, Kyle; Dettenmaier, Erik; Johnson, Paul C

2013-01-01

Current vapor intrusion (VI) pathway assessment heavily weights concentrations from infrequent (monthly-seasonal) 24 h indoor air samples. This study collected a long-term and high-frequency data set that can be used to assess indoor air sampling strategies for answering key pathway assessment questions like: "Is VI occurring?", and "Will VI impacts exceed thresholds of concern?". Indoor air sampling was conducted for 2.5 years at 2-4 h intervals in a house overlying a dilute chlorinated solvent plume (10-50 μg/L TCE). Indoor air concentrations varied by 3 orders of magnitude (<0.01-10 ppbv TCE) with two recurring behaviors. The VI-active behavior, which was prevalent in fall, winter, and spring involved time-varying impacts intermixed with sporadic periods of inactivity; the VI-dormant behavior, which was prevalent in the summer, involved long periods of inactivity with sporadic VI impacts. These data were used to study outcomes of three simple sparse data sampling plans; the probabilities of false-negative and false-positive decisions were dependent on the ratio of the (action level/true mean of the data), the number of exceedances needed, and the sampling strategy. The analysis also suggested a significant potential for poor characterization of long-term mean concentrations with sparse sampling plans. The results point to a need for additional dense data sets and further investigation into the robustness of possible VI assessment paradigms. As this is the first data set of its kind, it is unknown if the results are representative of other VI-sites.

Air quality and passenger comfort in an air-conditioned bus micro-environment.

PubMed

Zhu, Xiaoxuan; Lei, Li; Wang, Xingshen; Zhang, Yinghui

2018-04-12

In this study, passenger comfort and the air pollution status of the micro-environmental conditions in an air-conditioned bus were investigated through questionnaires, field measurements, and a numerical simulation. As a subjective analysis, passengers' perceptions of indoor environmental quality and comfort levels were determined from questionnaires. As an objective analysis, a numerical simulation was conducted using a discrete phase model to determine the diffusion and distribution of pollutants, including particulate matter with a diameter < 10 μm (PM 10 ), which were verified by experimental results. The results revealed poor air quality and dissatisfactory thermal comfort conditions in Jinan's air-conditioned bus system. To solve these problems, three scenarios (schemes A, B, C) were designed to alter the ventilation parameters. According to the results of an improved simulation of these scenarios, reducing or adding air outputs would shorten the time taken to reach steady-state conditions and weaken the airflow or lower the temperature in the cabin. The airflow pathway was closely related to the layout of the air conditioning. Scheme B lowered the temperature by 0.4 K and reduced the airflow by 0.01 m/s, while scheme C reduced the volume concentration of PM 10 to 150 μg/m 3 . Changing the air supply angle could further improve the airflow and reduce the concentration of PM 10 . With regard to the perception of airflow and thermal comfort, the scheme with an airflow provided by a 60° nozzle was considered better, and the concentration of PM 10 was reduced to 130 μg/m 3 .

Particulate matter triggers depressive-like response associated with modulation of inflammatory cytokine homeostasis and brain-derived neurotrophic factor signaling pathway in mice.

PubMed

Liu, Xuemei; Qian, Xin; Xing, Jing; Wang, Jinhua; Sun, Yixuan; Wang, Qin'geng; Li, Huiming

2018-04-23

Particulate matter (PM) exposure may contribute to depressive-like response in mice. However, few studies have evaluated the adaptive impacts of long-term PM exposure on depressive-like response associated with systemic inflammation and brain-derived neurotrophic factor (BDNF) signaling pathway. We studied the association among depressive-like behaviors, mRNA levels of pro- and anti-inflammatory cytokines, and the expression of BDNF signaling pathway in mice by long-term PM exposure. C57BL/6 male mice were exposed to ambient air alongside control mice breathing air filtered through a high-efficiency air PM (HEPA) filter. Depressive-like behaviors were assessed together with pro-inflammatory, anti-inflammatory cytokine mRNA levels and the modulation of BDNF pathway in hippocampus and olfactory-bulb of mice exposed to PM for 4, 8, and 12 weeks. Exposure to HEPA filtered air for 4 weeks may exert antidepressant like effects in mice. Pro-inflammatory cytokines were up-regulated while the expression of BDNF, its high-affinity receptor tropomyosin-related kinase B (TrkB), and the transcription factor cAMP-response-element binding protein (CREB) were down-regulated in ambient air mice. However, after 8 weeks, there was no significant difference in the rate of depressive-like behaviors between the two groups. After 12 weeks, mice exposed to ambient air again had a higher rate of depressive-like behaviors, significant up-regulation of pro-inflammatory cytokines, down-regulation of interleukin-10 (IL-10), BDNF, TrkB, and CREB than HEPA mice. Ultrafine PM in brain tissues of mice exposed to ambient air was observed. Our results suggest continuous high-level PM exposure alters the depressive-like response in mice and induces a damage-repair-imbalance reaction.

FGF coordinates air sac development by activation of the EGF ligand Vein through the transcription factor PntP2.

PubMed

Cruz, Josefa; Bota-Rabassedas, Neus; Franch-Marro, Xavier

2015-12-03

How several signaling pathways are coordinated to generate complex organs through regulation of tissue growth and patterning is a fundamental question in developmental biology. The larval trachea of Drosophila is composed of differentiated functional cells and groups of imaginal tracheoblasts that build the adult trachea during metamorphosis. Air sac primordium cells (ASP) are tracheal imaginal cells that form the dorsal air sacs that supply oxygen to the flight muscles of the Drosophila adult. The ASP emerges from the tracheal branch that connects to the wing disc by the activation of both Bnl-FGF/Btl and EGFR signaling pathways. Together, these pathways promote cell migration and proliferation. In this study we demonstrate that Vein (vn) is the EGF ligand responsible for the activation of the EGFR pathway in the ASP. We also find that the Bnl-FGF/Btl pathway regulates the expression of vn through the transcription factor PointedP2 (PntP2). Furthermore, we show that the FGF target gene escargot (esg) attenuates EGFR signaling at the tip cells of the developing ASP, reducing their mitotic rate to allow proper migration. Altogether, our results reveal a link between Bnl-FGF/Btl and EGFR signaling and provide novel insight into how the crosstalk of these pathways regulates migration and growth.

FGF coordinates air sac development by activation of the EGF ligand Vein through the transcription factor PntP2

PubMed Central

Cruz, Josefa; Bota-Rabassedas, Neus; Franch-Marro, Xavier

2015-01-01

How several signaling pathways are coordinated to generate complex organs through regulation of tissue growth and patterning is a fundamental question in developmental biology. The larval trachea of Drosophila is composed of differentiated functional cells and groups of imaginal tracheoblasts that build the adult trachea during metamorphosis. Air sac primordium cells (ASP) are tracheal imaginal cells that form the dorsal air sacs that supply oxygen to the flight muscles of the Drosophila adult. The ASP emerges from the tracheal branch that connects to the wing disc by the activation of both Bnl-FGF/Btl and EGFR signaling pathways. Together, these pathways promote cell migration and proliferation. In this study we demonstrate that Vein (vn) is the EGF ligand responsible for the activation of the EGFR pathway in the ASP. We also find that the Bnl-FGF/Btl pathway regulates the expression of vn through the transcription factor PointedP2 (PntP2). Furthermore, we show that the FGF target gene escargot (esg) attenuates EGFR signaling at the tip cells of the developing ASP, reducing their mitotic rate to allow proper migration. Altogether, our results reveal a link between Bnl-FGF/Btl and EGFR signaling and provide novel insight into how the crosstalk of these pathways regulates migration and growth. PMID:26632449

Conceptual Model for Assessing Criteria Air Pollutants in a Multipollutant Context: A Modified Adverse Outcome Pathway Approach

EPA Science Inventory

Background: Air pollution consists of a complex mixture of particulate and gaseous components. Individual criteria and other hazardous air pollutants have been linked to adverse respiratory and cardiovascular health outcomes. However, assessing risk of air pollutant mixtures is d...

Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution

PubMed Central

Moretti, Stefano; van Leeuwen, Danitsja; Gmuender, Hans; Bonassi, Stefano; van Delft, Joost; Kleinjans, Jos; Patrone, Fioravante; Merlo, Domenico Franco

2008-01-01

Background In gene expression analysis, statistical tests for differential gene expression provide lists of candidate genes having, individually, a sufficiently low p-value. However, the interpretation of each single p-value within complex systems involving several interacting genes is problematic. In parallel, in the last sixty years, game theory has been applied to political and social problems to assess the power of interacting agents in forcing a decision and, more recently, to represent the relevance of genes in response to certain conditions. Results In this paper we introduce a Bootstrap procedure to test the null hypothesis that each gene has the same relevance between two conditions, where the relevance is represented by the Shapley value of a particular coalitional game defined on a microarray data-set. This method, which is called Comparative Analysis of Shapley value (shortly, CASh), is applied to data concerning the gene expression in children differentially exposed to air pollution. The results provided by CASh are compared with the results from a parametric statistical test for testing differential gene expression. Both lists of genes provided by CASh and t-test are informative enough to discriminate exposed subjects on the basis of their gene expression profiles. While many genes are selected in common by CASh and the parametric test, it turns out that the biological interpretation of the differences between these two selections is more interesting, suggesting a different interpretation of the main biological pathways in gene expression regulation for exposed individuals. A simulation study suggests that CASh offers more power than t-test for the detection of differential gene expression variability. Conclusion CASh is successfully applied to gene expression analysis of a data-set where the joint expression behavior of genes may be critical to characterize the expression response to air pollution. We demonstrate a synergistic effect between coalitional games and statistics that resulted in a selection of genes with a potential impact in the regulation of complex pathways. PMID:18764936

Health assessment of future PM2.5 exposures from indoor, outdoor, and secondhand tobacco smoke concentrations under alternative policy pathways in Ulaanbaatar, Mongolia

PubMed Central

Edwards, Rufus; Turner, Jay R.; Argo, Yuma D.; Olkhanud, Purevdorj B.; Odsuren, Munkhtuul; Guttikunda, Sarath; Ochir, Chimedsuren; Smith, Kirk R.

2017-01-01

Introduction Winter air pollution in Ulaanbaatar, Mongolia is among the worst in the world. The health impacts of policy decisions affecting air pollution exposures in Ulaanbaatar were modeled and evaluated under business as usual and two more-strict alternative emissions pathways through 2024. Previous studies have relied on either outdoor or indoor concentrations to assesses the health risks of air pollution, but the burden is really a function of total exposure. This study combined projections of indoor and outdoor concentrations of PM2.5 with population time-activity estimates to develop trajectories of total age-specific PM2.5 exposure for the Ulaanbaatar population. Indoor PM2.5 contributions from secondhand tobacco smoke (SHS) were estimated in order to fill out total exposures, and changes in population and background disease were modeled. The health impacts were derived using integrated exposure-response curves from the Global Burden of Disease Study. Results Annual average population-weighted PM2.5 exposures at baseline (2014) were estimated at 59 μg/m3. These were dominated by exposures occurring indoors, influenced considerably by infiltrated outdoor pollution. Under current control policies, exposures increased slightly to 60 μg/m3 by 2024; under moderate emissions reductions and under a switch to clean technologies, exposures were reduced from baseline levels by 45% and 80%, respectively. The moderate improvement pathway decreased per capita annual disability-adjusted life year (DALY) and death burdens by approximately 40%. A switch to clean fuels decreased per capita annual DALY and death burdens by about 85% by 2024 with the relative SHS contribution increasing substantially. Conclusion This study demonstrates a way to combine estimated changes in total exposure, background disease and population levels, and exposure-response functions to project the health impacts of alternative policy pathways. The resulting burden analysis highlights the need for aggressive action, including the elimination of residential coal burning and the reduction of current smoking rates. PMID:29088256

Age and Pathway Diagnostics for a Stratospheric General Circulation Model

NASA Technical Reports Server (NTRS)

Schoeberl, Mark R.; Douglass, Anne R.; Polansky, Brian

2004-01-01

Using a variety of age diagnostic experiments we examine the stratospheric age spectrum of the Goddard Finite Volume Generd Circulation Model. Pulse tracer release age-of-air computations are compared to forward and backward trajectory computations. These comparisons show good agreement, and the age-of-air also compares well with observed long lived tracers. Pathway diagnostics show how air arrives in the lowermost stratosphere and the age structure of that region. Using tracers with different lifetimes we can estimate the age spectrum - this technique should be useful in diagnosing transport from various trace gas observations.

INDIRECT EXPOSURE ASSESSMENT AT THE U.S. EPA

EPA Science Inventory

In the early 1980s, exposures and subsequent health impact assessments from contaminants emitted into the air from stationary sources focused on the inhalation pathway. This 'direct' pathway of exposure was thought to be the most critical pathway, as it is for many contaminants. ...

Study of atmospheric dynamics and pollution in the coastal area of English Channel using clustering technique

NASA Astrophysics Data System (ADS)

Sokolov, Anton; Dmitriev, Egor; Delbarre, Hervé; Augustin, Patrick; Gengembre, Cyril; Fourmenten, Marc

2016-04-01

The problem of atmospheric contamination by principal air pollutants was considered in the industrialized coastal region of English Channel in Dunkirk influenced by north European metropolitan areas. MESO-NH nested models were used for the simulation of the local atmospheric dynamics and the online calculation of Lagrangian backward trajectories with 15-minute temporal resolution and the horizontal resolution down to 500 m. The one-month mesoscale numerical simulation was coupled with local pollution measurements of volatile organic components, particulate matter, ozone, sulphur dioxide and nitrogen oxides. Principal atmospheric pathways were determined by clustering technique applied to backward trajectories simulated. Six clusters were obtained which describe local atmospheric dynamics, four winds blowing through the English Channel, one coming from the south, and the biggest cluster with small wind speeds. This last cluster includes mostly sea breeze events. The analysis of meteorological data and pollution measurements allows relating the principal atmospheric pathways with local air contamination events. It was shown that contamination events are mostly connected with a channelling of pollution from local sources and low-turbulent states of the local atmosphere.

Aerosols in Northern Morocco: Input pathways and their chemical fingerprint

NASA Astrophysics Data System (ADS)

Benchrif, A.; Guinot, B.; Bounakhla, M.; Cachier, H.; Damnati, B.; Baghdad, B.

2018-02-01

The Mediterranean basin is one of the most sensitive regions in the world regarding climate change and air quality. Deserts and marine aerosols combine with combustion aerosols from maritime traffic, large urban centers, and at a larger scale from populated industrialized regions in Europe. From Tetouan city located in the North of Morocco, we attempted to better figure out the main aerosol transport pathways and their respective aerosol load and chemical profile by examining air mass back trajectory patterns and aerosol chemical compositions from May 2011 to April 2012. The back trajectory analysis throughout the sampling period led to four clusters, for which meteorological conditions and aerosol chemical characteristics have been investigated. The most frequent cluster (CL3: 39%) corresponds to polluted air masses coming from the Mediterranean Basin, characterized by urban and marine vessels emissions out of Spain and of Northern Africa. Two other polluted clusters were characterized. One is of local origin (CL1: 22%), with a marked contribution from urban aerosols (Rabat, Casablanca) and from biomass burning aerosols. The second (CL2: 32%) defines air masses from the near Atlantic Ocean, affected by pollutants emitted from the Iberian coast. A fourth cluster (CL4: 7%) is characterized by rather clean, fast and rainy oceanic air masses, influenced during their last 24 h before reaching Tetouan by similar sources with those affecting CL2, but to a lesser extent. The chemical data show that carbonaceous species are found in the fine aerosols fraction and are generally from local primary sources (low OC/EC) rather than long-range transported. In addition to fresh traffic and maritime vessel aerosols, our results suggest the contribution of local biomass burning.

Textile Inspired Lithium-Oxygen Battery Cathode with Decoupled Oxygen and Electrolyte Pathways.

PubMed

Xu, Shaomao; Yao, Yonggang; Guo, Yuanyuan; Zeng, Xiaoqiao; Lacey, Steven D; Song, Huiyu; Chen, Chaoji; Li, Yiju; Dai, Jiaqi; Wang, Yanbin; Chen, Yanan; Liu, Boyang; Fu, Kun; Amine, Khalil; Lu, Jun; Hu, Liangbing

2018-01-01

The lithium-air (Li-O 2 ) battery has been deemed one of the most promising next-generation energy-storage devices due to its ultrahigh energy density. However, in conventional porous carbon-air cathodes, the oxygen gas and electrolyte often compete for transport pathways, which limit battery performance. Here, a novel textile-based air cathode is developed with a triple-phase structure to improve overall battery performance. The hierarchical structure of the conductive textile network leads to decoupled pathways for oxygen gas and electrolyte: oxygen flows through the woven mesh while the electrolyte diffuses along the textile fibers. Due to noncompetitive transport, the textile-based Li-O 2 cathode exhibits a high discharge capacity of 8.6 mAh cm -2 , a low overpotential of 1.15 V, and stable operation exceeding 50 cycles. The textile-based structure can be applied to a range of applications (fuel cells, water splitting, and redox flow batteries) that involve multiple phase reactions. The reported decoupled transport pathway design also spurs potential toward flexible/wearable Li-O 2 batteries. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling.

PubMed

Liston, Adrian; Hardy, Kristine; Pittelkow, Yvonne; Wilson, Susan R; Makaroff, Lydia E; Fahrer, Aude M; Goodnow, Christopher C

2007-01-01

T cells in the thymus undergo opposing positive and negative selection processes so that the only T cells entering circulation are those bearing a T cell receptor (TCR) with a low affinity for self. The mechanism differentiating negative from positive selection is poorly understood, despite the fact that inherited defects in negative selection underlie organ-specific autoimmune disease in AIRE-deficient people and the non-obese diabetic (NOD) mouse strain Here we use homogeneous populations of T cells undergoing either positive or negative selection in vivo together with genome-wide transcription profiling on microarrays to identify the gene expression differences underlying negative selection to an Aire-dependent organ-specific antigen, including the upregulation of a genomic cluster in the cytogenetic band 2F. Analysis of defective negative selection in the autoimmune-prone NOD strain demonstrates a global impairment in the induction of the negative selection response gene set, but little difference in positive selection response genes. Combining expression differences with genetic linkage data, we identify differentially expressed candidate genes, including Bim, Bnip3, Smox, Pdrg1, Id1, Pdcd1, Ly6c, Pdia3, Trim30 and Trim12. The data provide a molecular map of the negative selection response in vivo and, by analysis of deviations from this pathway in the autoimmune susceptible NOD strain, suggest that susceptibility arises from small expression differences in genes acting at multiple points in the pathway between the TCR and cell death.

Impairment of organ-specific T cell negative selection by diabetes susceptibility genes: genomic analysis by mRNA profiling

PubMed Central

Liston, Adrian; Hardy, Kristine; Pittelkow, Yvonne; Wilson, Susan R; Makaroff, Lydia E; Fahrer, Aude M; Goodnow, Christopher C

2007-01-01

Background T cells in the thymus undergo opposing positive and negative selection processes so that the only T cells entering circulation are those bearing a T cell receptor (TCR) with a low affinity for self. The mechanism differentiating negative from positive selection is poorly understood, despite the fact that inherited defects in negative selection underlie organ-specific autoimmune disease in AIRE-deficient people and the non-obese diabetic (NOD) mouse strain Results Here we use homogeneous populations of T cells undergoing either positive or negative selection in vivo together with genome-wide transcription profiling on microarrays to identify the gene expression differences underlying negative selection to an Aire-dependent organ-specific antigen, including the upregulation of a genomic cluster in the cytogenetic band 2F. Analysis of defective negative selection in the autoimmune-prone NOD strain demonstrates a global impairment in the induction of the negative selection response gene set, but little difference in positive selection response genes. Combining expression differences with genetic linkage data, we identify differentially expressed candidate genes, including Bim, Bnip3, Smox, Pdrg1, Id1, Pdcd1, Ly6c, Pdia3, Trim30 and Trim12. Conclusion The data provide a molecular map of the negative selection response in vivo and, by analysis of deviations from this pathway in the autoimmune susceptible NOD strain, suggest that susceptibility arises from small expression differences in genes acting at multiple points in the pathway between the TCR and cell death. PMID:17239257

INDIRECT EXPOSURE ASSESSMENT AT THE UNITED STATES ENRONMENTAL PROTECTION AGENCY

EPA Science Inventory

In the early 1980s, expousres and subsequent health impact assessments from contaminants emitted into the air from stationary sources focused on the inhalation pathway. This 'direct' pathway of exposure was thought to be the most critical pathway, as it is for many contaminants. ...

A multi-model assessment of the co-benefits of climate mitigation for global air quality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Shilpa; Klimont, Zbigniew; Leitao, Joana

The recent International Panel on Climate change (IPCC) report identifies significant co-benefits from climate policies on near-term ambient air pollution and related human health outcomes [1]. This is increasingly relevant for policy making as the health impacts of air pollution are a major global concern- the Global Burden of Disease (GBD) study identifies outdoor air pollution as the sixth major cause of death globally [2]. Integrated assessment models (IAMs) are an effective tool to evaluate future air pollution outcomes across a wide range of assumptions on socio-economic development and policy regimes. The Representative Concentration Pathways (RCPs) [3] were the firstmore » set of long-term global scenarios developed across multiple integrated assessment models that provided detailed estimates of a number of air pollutants until 2100. However these scenarios were primarily designed to cover a defined range of radiative forcing outcomes and thus did not specifically focus on the interactions of long-term climate goals on near-term air pollution impacts. More recently, [4] used the RCP4.5 scenario to evaluate the co-benefits of global GHG reductions on air quality and human health in 2030. [5-7] have further examined the interactions of more diverse pollution control regimes with climate policies. This paper extends the listed studies in a number of ways. Firstly it uses multiple IAMs to look into the co-benefits of a global climate policy for ambient air pollution under harmonized assumptions on near-term air pollution control. Multi-model frameworks have been extensively used in the analysis of climate change mitigation pathways, and the structural uncertainties regarding the underlying mechanisms (see for example [8-10]. This is to our knowledge the first time that a multi-model evaluation has been specifically designed and applied to analyze the co-benefits of climate change policy on ambient air quality, thus enabling a better understanding of at a detailed sector and region level. A second methodological advancement is a quantification of the co-benefits in terms of the associated atmospheric concentrations of fine particulate matter (PM2.5) and consequent mortality related outcomes across different models. This is made possible by the use of state-of the art simplified atmospheric model that allows for the first time a computationally feasible multi-model evaluation of such outcomes.« less

Catalytic wet air oxidation of phenol with functionalized carbon materials as catalysts: reaction mechanism and pathway.

PubMed

Wang, Jianbing; Fu, Wantao; He, Xuwen; Yang, Shaoxia; Zhu, Wanpeng

2014-08-01

The development of highly active carbon material catalysts in catalytic wet air oxidation (CWAO) has attracted a great deal of attention. In this study different carbon material catalysts (multi-walled carbon nanotubes, carbon fibers and graphite) were developed to enhance the CWAO of phenol in aqueous solution. The functionalized carbon materials exhibited excellent catalytic activity in the CWAO of phenol. After 60 min reaction, the removal of phenol was nearly 100% over the functionalized multi-walled carbon, while it was only 14% over the purified multi-walled carbon under the same reaction conditions. Carboxylic acid groups introduced on the surface of the functionalized carbon materials play an important role in the catalytic activity in CWAO. They can promote the production of free radicals, which act as strong oxidants in CWAO. Based on the analysis of the intermediates produced in the CWAO reactions, a new reaction pathway for the CWAO of phenol was proposed in this study. There are some differences between the proposed reaction pathway and that reported in the literature. First, maleic acid is transformed directly into malonic acid. Second, acetic acid is oxidized into an unknown intermediate, which is then oxidized into CO2 and H2O. Finally, formic acid and oxalic acid can mutually interconvert when conditions are favorable. Copyright © 2014. Published by Elsevier B.V.

Estimating environmental co-benefits of U.S. low-carbon pathways using an integrated assessment model with state-level resolution

EPA Science Inventory

There are many technological pathways that can lead to reduced carbon dioxide emissions. However, these pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. This study uses an integrated assessmen...

Estimating Environmental Co-benefits of U.S. CO2 Reduction Pathways Using the GCAM-USA Integrated Assessment Model

EPA Science Inventory

Various technological pathways can lead to reduced CO2 emissions. However, different pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. The Global Change Assessment Model (GCAM) is a high resolu...

Estimating environmental co-benefits of U.S. low-carbon pathways using an integrated assessment model with state-level resolution.

PubMed

Ou, Yang; Shi, Wenjing; Smith, Steven J; Ledna, Catherine M; West, J Jason; Nolte, Christopher G; Loughlin, Daniel H

2018-04-15

There are many technological pathways that can lead to reduced carbon dioxide emissions. However, these pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. This study uses an integrated assessment model with state-level resolution of the energy system to compare environmental impacts of alternative low-carbon pathways for the United States. One set of pathways emphasizes nuclear energy and carbon capture and storage, while another set emphasizes renewable energy, including wind, solar, geothermal power, and bioenergy. These are compared with pathways in which all technologies are available. Air pollutant emissions, mortality costs attributable to particulate matter smaller than 2.5 μm in diameter, and energy-related water demands are evaluated for 50% and 80% carbon dioxide reduction targets in 2050. The renewable low-carbon pathways require less water withdrawal and consumption than the nuclear and carbon capture pathways. However, the renewable low-carbon pathways modeled in this study produce higher particulate matter-related mortality costs due to greater use of biomass in residential heating. Environmental co-benefits differ among states because of factors such as existing technology stock, resource availability, and environmental and energy policies.

Transcriptome sequencing reveals e-cigarette vapor and mainstream-smoke from tobacco cigarettes activate different gene expression profiles in human bronchial epithelial cells

PubMed Central

Shen, Yifei; Wolkowicz, Michael J.; Kotova, Tatyana; Fan, Lonjiang; Timko, Michael P.

2016-01-01

Electronic cigarettes (e-cigarettes) generate an aerosol vapor (e-vapor) thought to represent a less risky alternative to main stream smoke (MSS) of conventional tobacco cigarettes. RNA-seq analysis was used to examine the transcriptomes of differentiated human bronchial epithelial (HBE) cells exposed to air, MSS from 1R5F tobacco reference cigarettes, and e-vapor with and without added nicotine in an in vitro air-liquid interface model for cellular exposure. Our results indicate that while e-vapor does not elicit many of the cell toxicity responses observed in MSS-exposed HBE cells, e-vapor exposure is not benign, but elicits discrete transcriptomic signatures with and without added nicotine. Among the cellular pathways with the most significantly enriched gene expression following e-vapor exposure are the phospholipid and fatty acid triacylglycerol metabolism pathways. Our data suggest that alterations in cellular glycerophopholipid biosynthesis are an important consequences of e-vapor exposure. Moreover, the presence of nicotine in e-vapor elicits a cellular response distinct from e-vapor alone including alterations of cytochrome P450 function, retinoid metabolism, and nicotine catabolism. These studies establish a baseline for future analysis of e-vapor and e-vapor additives that will better inform the FDA and other governmental bodies in discussions of the risks and future regulation of these products. PMID:27041137

7. Survivable low frequency communication system pathway, looking east ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

7. Survivable low frequency communication system pathway, looking east - Ellsworth Air Force Base, Delta Flight, Launch Control Facility, County Road CS23A, North of Exit 127, Interior, Jackson County, SD

Global transcriptomic profiling of aspen trees under elevated [CO2] to identify potential molecular mechanisms responsible for enhanced radial growth.

PubMed

Wei, Hairong; Gou, Jiqing; Yordanov, Yordan; Zhang, Huaxin; Thakur, Ramesh; Jones, Wendy; Burton, Andrew

2013-03-01

Aspen (Populus tremuloides) trees growing under elevated [CO(2)] at a free-air CO(2) enrichment (FACE) site produced significantly more biomass than control trees. We investigated the molecular mechanisms underlying the observed increase in biomass by producing transcriptomic profiles of the vascular cambium zone (VCZ) and leaves, and then performed a comparative study to identify significantly changed genes and pathways after 12 years exposure to elevated [CO(2)]. In leaves, elevated [CO(2)] enhanced expression of genes related to Calvin cycle activity and linked pathways. In the VCZ, the pathways involved in cell growth, cell division, hormone metabolism, and secondary cell wall formation were altered while auxin conjugation, ABA synthesis, and cytokinin glucosylation and degradation were inhibited. Similarly, the genes involved in hemicellulose and pectin biosynthesis were enhanced, but some genes that catalyze important steps in lignin biosynthesis pathway were inhibited. Evidence from systemic analysis supported the functioning of multiple molecular mechanisms that underpin the enhanced radial growth in response to elevated [CO(2)].

Estimating environmental co-benefits of U.S. GHG reduction pathways using the GCAM-USA Integrated Assessment Model (A&WMA Presentation)

EPA Science Inventory

A variety of technological pathways lead to reduced greenhouse gas (GHG) emissions. However, different pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. In this study we use the Global Change ...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Renhui; Sun, Yuanyuan; Song, Kai

Recent experimental studies have shown that the vibrational dynamics of free OH groups at the water-air interface is significantly different from that in bulk water. In this work, by performing molecular dynamics simulations and mixed quantum/classical calculations, we investigate different vibrational energy transfer pathways of free OH groups at the water-air interface. The calculated intramolecular vibrational energy transfer rate constant and the free OH bond reorientation time scale agree well with the experiment. It is also found that, due to the small intermolecular vibrational couplings, the intermolecular vibrational energy transfer pathway that is very important in bulk water plays amore » much less significant role in the vibrational energy relaxation of the free OH groups at the water-air interface.« less

The Pathway for Oxygen: Tutorial Modelling on Oxygen Transport from Air to Mitochondrion: The Pathway for Oxygen.

PubMed

Bassingthwaighte, James B; Raymond, Gary M; Dash, Ranjan K; Beard, Daniel A; Nolan, Margaret

2016-01-01

The 'Pathway for Oxygen' is captured in a set of models describing quantitative relationships between fluxes and driving forces for the flux of oxygen from the external air source to the mitochondrial sink at cytochrome oxidase. The intervening processes involve convection, membrane permeation, diffusion of free and heme-bound O2 and enzymatic reactions. While this system's basic elements are simple: ventilation, alveolar gas exchange with blood, circulation of the blood, perfusion of an organ, uptake by tissue, and consumption by chemical reaction, integration of these pieces quickly becomes complex. This complexity led us to construct a tutorial on the ideas and principles; these first PathwayO2 models are simple but quantitative and cover: (1) a 'one-alveolus lung' with airway resistance, lung volume compliance, (2) bidirectional transport of solute gasses like O2 and CO2, (3) gas exchange between alveolar air and lung capillary blood, (4) gas solubility in blood, and circulation of blood through the capillary syncytium and back to the lung, and (5) blood-tissue gas exchange in capillaries. These open-source models are at Physiome.org and provide background for the many respiratory models there.

The Role of AIRE in the Immunity Against Candida Albicans in a Model of Human Macrophages.

PubMed

de Albuquerque, Jose Antonio Tavares; Banerjee, Pinaki Prosad; Castoldi, Angela; Ma, Royce; Zurro, Nuria Bengala; Ynoue, Leandro Hideki; Arslanian, Christina; Barbosa-Carvalho, Marina Uchoa Wall; Correia-Deur, Joya Emilie de Menezes; Weiler, Fernanda Guimarães; Dias-da-Silva, Magnus Regios; Lazaretti-Castro, Marise; Pedroza, Luis Alberto; Câmara, Niels Olsen Saraiva; Mace, Emily; Orange, Jordan Scott; Condino-Neto, Antonio

2018-01-01

Autoimmune-polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a primary immunodeficiency caused by mutations in the autoimmune regulator gene ( AIRE ). Patients with AIRE mutations are susceptible to Candida albicans infection and present with autoimmune disorders. We previously demonstrated that cytoplasmic AIRE regulates the Syk-dependent Dectin-1 pathway. In this study, we further evaluated direct contact with fungal elements, synapse formation, and the response of macrophage-like THP-1 cells to C. albicans hyphae to determine the role of AIRE upon Dectin receptors function and signaling. We examined the fungal synapse (FS) formation in wild-type and AIRE-knockdown THP-1 cells differentiated to macrophages, as well as monocyte-derived macrophages from APECED patients. We evaluated Dectin-2 receptor signaling, phagocytosis, and cytokine secretion upon hyphal stimulation. AIRE co-localized with Dectin-2 and Syk at the FS upon hyphal stimulation of macrophage-like THP-1 cells. AIRE-knockdown macrophage-like THP-1 cells exhibited less Dectin-1 and Dectin-2 receptors accumulation, decreased signaling pathway activity at the FS, lower C. albicans phagocytosis, and less lysosome formation. Furthermore, IL-1β, IL-6, or TNF-α secretion by AIRE-knockdown macrophage-like THP-1 cells and AIRE-deficient patient macrophages was decreased compared to control cells. Our results suggest that AIRE modulates the FS formation and hyphal recognition and help to orchestrate an effective immune response against C. albicans .

Impacts of Four SO2 Oxidation Pathways on Wintertime Sulfate Concentrations

NASA Astrophysics Data System (ADS)

Sarwar, G.; Fahey, K.; Zhang, Y.; Kang, D.; Mathur, R.; Xing, J.; Wei, C.; Cheng, Y.

2017-12-01

Air quality models tend to under-estimate winter-time sulfate concentrations compared to observed data. Such under-estimations are particularly acute in China where very high concentrations of sulfate have been measured. Sulfate is produced by oxidation of sulfur dioxide (SO2) in gas-phase by hydroxyl radical and in aqueous-phase by hydrogen peroxide, ozone, etc. and most air quality models employ such typical reactions. Several additional SO2 oxidation pathways have recently been proposed. Heterogeneous reaction on dust has been suggested to be an important sink for SO2. Oxidation of SO2 on fine particles in presence of nitrogen dioxide (NO2) and ammonia (NH3) at high relative humidity has been implicated for sulfate formation in Chinese haze and London fog. Reactive nitrogen chemistry in aerosol water has also been suggested to produce winter-time sulfate in China. Specifically, high aerosol water can trap SO2 which can be subsequently oxidized by NO2 to form sulfate. Aqueous-phase (in-cloud) oxidation of SO2 by NO2 can also produce sulfate. Here, we use the hemispheric Community Multiscale Air Quality (CMAQ) modeling system to examine the potential impacts of these SO2 oxidation pathways on sulfate formation. We use anthropogenic emissions from the Emissions Database for Global Atmospheric Research and biogenic emissions from Global Emissions InitiAtive. We performed simulations without and with these SO2 oxidation pathways for October-December of 2014 using meteorological fields obtained from the Weather Research and Forecasting model. The standard CMAQ model contains one gas-phase chemical reaction and five aqueous-phase chemical reactions for SO2 oxidation. We implement four additional SO2 oxidation pathways into the CMAQ model. Our preliminary results suggest that the dust chemistry enhances mean sulfate over parts of China and Middle-East, the in-cloud SO2 oxidation by NO2 enhances sulfate over parts of western Europe, oxidation of SO2 by NO2 and NH3 on fine particles enhances sulfate only over parts of China, and SO2 oxidation by NO2 in aerosol water enhances sulfate only over parts of China by >5%. We will present a detailed analysis of the results and a comparison of model predictions with available observed data.

A risk assessment of direct and indirect exposure to emissions from a proposed hazardous waste incinerator in Puerto Rico

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hallinger, K.; Huggins, A.; Warner, L.

1995-12-31

An Indirect Exposure Assessment (IEA) was conducted, under USEPA`s RCRA Combustion Strategy, as part of the Part B permitting process for a proposed hazardous waste incinerator. The IEA involved identification of constituents of concern, emissions estimations, air dispersion and deposition modeling, evaluation of site-specific exposure pathways/scenarios, and food chain modeling in order to evaluate potential human health and environmental risks. The COMPDEP model was used to determine ambient ground level concentrations and dry and wet deposition rates of constituents of concern. The air modeling results were input into 50th percentile (Central) and 95th percentile (High-End) exposure scenarios which evaluated directmore » exposure via inhalation, dermal contact, and soil ingestion pathways, and indirect exposure through the food chain. The indirect pathway analysis considered the accumulation of constituents in plants and animals used as food sources by local inhabitants. Local food consumption data obtained from the Puerto Rico USDA were combined with realistic present-day and future-use exposure scenarios such as residential use, pineapple farming, and subsistence farming to obtain a comprehensive evaluation of risk, Overall risk was calculated using constituent doses and toxicity factors associated with the various routes of exposure. Risk values for each exposure pathway were summed to determine total carcinogenic and non-carcinogenic hazard to exposed individuals. A population risk assessment was also conducted in order to assess potential risks to the population surrounding the facility. Results of the assessment indicated no acute effects from constituents of concern, and a high-end excess lifetime cancer risk of approximately 6 in a million with dioxins (as 2,3,7,8-TCDD) and arsenic dominating the risk estimate.« less

Numerical modelling of the effect of dry air traces in a helium parallel plate dielectric barrier discharge

NASA Astrophysics Data System (ADS)

Lazarou, C.; Belmonte, T.; Chiper, A. S.; Georghiou, G. E.

2016-10-01

A validated numerical model developed for the study of helium barrier discharges in the presence of dry air impurities is presented in this paper. The model was used to numerically investigate the influence of air traces on the evolution of the helium dielectric barrier discharge (DBD). The level of dry air used as impurity was in the range from 0 to 1500 ppm, which corresponds to the most commonly encountered range in atmospheric pressure discharge experiments. The results presented in this study clearly show that the plasma chemistry and consequently the discharge evolution is highly affected by the concentration level of impurities in the mixture. In particular, it was observed that air traces assist the discharge ignition at low concentration levels (~55 ppm), while on the other hand, they increase the burning voltage at higher concentration levels (~1000 ppm). Furthermore, it was found that the discharge symmetry during the voltage cycle highly depends on the concentration of air. For the interpretation of the results, a detailed analysis of the processes that occur in the discharge gap is performed and the main reaction pathways of ion production are described. Thanks to this approach, useful insight into the physics behind the evolution of the discharge is obtained.

Changes in gene expression in chronic allergy mouse model exposed to natural environmental PM2.5-rich ambient air pollution.

PubMed

Ouyang, Yuhui; Xu, Zhaojun; Fan, Erzhong; Li, Ying; Miyake, Kunio; Xu, Xianyan; Zhang, Luo

2018-04-20

Particulate matter (PM) air pollution has been associated with an increase in the incidence of chronic allergic diseases; however, the mechanisms underlying the effect of exposure to natural ambient air pollution in chronic allergic diseases have not been fully elucidated. In the present study, we aimed to investigate the cellular responses induced by exposure to natural ambient air pollution, employing a mouse model of chronic allergy. The results indicated that exposure to ambient air pollution significantly increased the number of eosinophils in the nasal mucosa. The modulation of gene expression profile identified a set of regulated genes, and the Triggering Receptor Expressed on Myeloid cells1(TREM1) signaling canonical pathway was increased after exposure to ambient air pollution. In vitro, PM2.5 increased Nucleotide-binding oligomerization domain-containing protein 1 (Nod1) and nuclear factor (NF)-κB signaling pathway activation in A549 and HEK293 cell cultures. These results suggest a novel mechanism by which, PM2.5 in ambient air pollution may stimulate the innate immune system through the PM2.5-Nod1-NF-κB axis in chronic allergic disease.

Criegee intermediate-hydrogen sulfide chemistry at the air/water interface.

PubMed

Kumar, Manoj; Zhong, Jie; Francisco, Joseph S; Zeng, Xiao C

2017-08-01

We carry out Born-Oppenheimer molecular dynamic simulations to show that the reaction between the smallest Criegee intermediate, CH 2 OO, and hydrogen sulfide (H 2 S) at the air/water interface can be observed within few picoseconds. The reaction follows both concerted and stepwise mechanisms with former being the dominant reaction pathway. The concerted reaction proceeds with or without the involvement of one or two nearby water molecules. An important implication of the simulation results is that the Criegee-H 2 S reaction can provide a novel non-photochemical pathway for the formation of a C-S linkage in clouds and could be a new oxidation pathway for H 2 S in terrestrial, geothermal and volcanic regions.

Malaria infection, poor nutrition and indoor air pollution mediate socioeconomic differences in adverse pregnancy outcomes in Cape Coast, Ghana.

PubMed

Amegah, Adeladza K; Damptey, Obed K; Sarpong, Gideon A; Duah, Emmanuel; Vervoorn, David J; Jaakkola, Jouni J K

2013-01-01

The epidemiological evidence linking socioeconomic deprivation with adverse pregnancy outcomes has been conflicting mainly due to poor measurement of socioeconomic status (SES). Studies have also failed to evaluate the plausible pathways through which socioeconomic disadvantage impacts on pregnancy outcomes. We investigated the importance of maternal SES as determinant of birth weight and gestational duration in an urban area and evaluated main causal pathways for the influence of SES. A population-based cross-sectional study was conducted among 559 mothers accessing postnatal services at the four main health facilities in Cape Coast, Ghana in 2011. Information on socioeconomic characteristics of the mothers was collected in a structured questionnaire. In multivariate linear regression adjusting for maternal age, parity and gender of newborn, low SES resulted in 292 g (95% CI: 440-145) reduction in birth weight. Important SES-related determinants were neighborhood poverty (221 g; 95% CI: 355-87), low education (187 g; 95% CI: 355-20), studentship during pregnancy (291 g; 95% CI: 506-76) and low income (147 g; 95% CI: 277-17). In causal pathway analysis, malaria infection (6-20%), poor nutrition (2-51%) and indoor air pollution (10-62%) mediated substantial proportions of the observed effects of socioeconomic deprivation on birth weight. Generalized linear models adjusting for confounders indicated a 218% (RR: 3.18; 95% CI: 1.41-7.21) risk increase of LBW and 83% (RR: 1.83; 95% CI: 1.31-2.56) of PTB among low income mothers. Low and middle SES was associated with 357% (RR: 4.57; 95% CI: 1.67-12.49) and 278% (RR: 3.78; 95% CI: 1.39-10.27) increased risk of LBW respectively. Malaria infection, poor nutrition and indoor air pollution respectively mediated 10-21%, 16-44% and 31-52% of the observed effects of socioeconomic disadvantage on LBW risk. We provide evidence of the effects of socioeconomic deprivation, substantially mediated by malaria infection, poor nutrition and indoor air pollution, on pregnancy outcomes in a developing country setting.

Transport pathway and source area for Artemisia pollen in Beijing, China

NASA Astrophysics Data System (ADS)

Qin, Xiaoxin; Li, Yiyin; Sun, Xu; Meng, Ling; Wang, Xiaoke

2017-12-01

Artemisia pollen is an important allergen responsible for allergic rhinitis in Beijing, China. To explore the transport pathways and source areas of Artemisia pollen, we used Burkard 7-day traps to monitor daily pollen concentrations in 2016 in an urban and suburban locality. Backward trajectories of 24- and 96-h and their cluster analysis were performed to identify transport pathways of Artemisia pollen using the HYSPLIT model on 0.5° × 0.5° GADS meteorological data. The potential source contribution function (PSCF) and concentration weighted trajectory (CWT) were calculated to further identify the major potential source areas at local, regional, and long-range scales. Our results showed significant differences in Artemisia pollen concentration between urban and suburban areas, attributed to differences in plant distribution and altitude of the sampling locality. Such differences arisen from both pollen emission and air mass movements, hence pollen dispersal. At local or regional scales, source area of northwestern parts of Beijing City, Hebei Province and northern and northwestern parts of Inner Mongolia influenced the major transport pathways of Artemisia pollen. Transport pathway at a long-range scale and its corresponding source area extended to northwestern parts of Mongolia. The regional-scale transport affected by wind and altitude is more profound for Artemisia pollen at the suburban than at the urban station.

Recommended Henry’s Law Constants for Non-Groundwater Pathways Models in GoldSim

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dyer, J.

This memorandum documents the source and numerical value of Henry’s law constants for volatile radionuclides of interest used in the non-groundwater (air and radon) pathways models for the 2018 E-Area Performance Assessment.

Conceptual model for assessing criteria air pollutants in a multipollutant context: A modified adverse outcome pathway approach.

PubMed

Buckley, Barbara; Farraj, Aimen

2015-09-01

Air pollution consists of a complex mixture of particulate and gaseous components. Individual criteria and other hazardous air pollutants have been linked to adverse respiratory and cardiovascular health outcomes. However, assessing risk of air pollutant mixtures is difficult since components are present in different combinations and concentrations in ambient air. Recent mechanistic studies have limited utility because of the inability to link measured changes to adverse outcomes that are relevant to risk assessment. New approaches are needed to address this challenge. The purpose of this manuscript is to describe a conceptual model, based on the adverse outcome pathway approach, which connects initiating events at the cellular and molecular level to population-wide impacts. This may facilitate hazard assessment of air pollution mixtures. In the case reports presented here, airway hyperresponsiveness and endothelial dysfunction are measurable endpoints that serve to integrate the effects of individual criteria air pollutants found in inhaled mixtures. This approach incorporates information from experimental and observational studies into a sequential series of higher order effects. The proposed model has the potential to facilitate multipollutant risk assessment by providing a framework that can be used to converge the effects of air pollutants in light of common underlying mechanisms. This approach may provide a ready-to-use tool to facilitate evaluation of health effects resulting from exposure to air pollution mixtures. Published by Elsevier Ireland Ltd.

The evaluation of stack metal emissions from hazardous waste incinerators: assessing human exposure through noninhalation pathways.

PubMed Central

Sedman, R M; Polisini, J M; Esparza, J R

1994-01-01

Potential public health effects associated with exposure to metal emissions from hazardous waste incinerators through noninhalation pathways were evaluated. Instead of relying on modeling the movement of toxicants through various environmental media, an approach based on estimating changes from baseline levels of exposure was employed. Changes in soil and water As, Cd, Hg, Pb, Cr, and Be concentrations that result from incinerator emissions were first determined. Estimates of changes in human exposure due to direct contact with shallow soil or the ingestion of surface water were then ascertained. Projected changes in dietary intakes of metals due to incinerator emissions were estimated based on changes from baseline dietary intakes that are monitored in U.S. Food and Drug Administration total diet studies. Changes from baseline intake were deemed to be proportional to the projected changes in soil or surface water metal concentrations. Human exposure to metals emitted from nine hazardous waste incinerators were then evaluated. Metal emissions from certain facilities resulted in tangible human exposure through noninhalation pathways. However, the analysis indicated that the deposition of metals from ambient air would result in substantially greater human exposure through noninhalation pathways than the emissions from most of the facilities. PMID:7925180

Long-term measurements (2010-2014) of carbonaceous aerosol and carbon monoxide at the Zotino Tall Tower Observatory (ZOTTO) in central Siberia

NASA Astrophysics Data System (ADS)

Mikhailov, Eugene F.; Mironova, Svetlana; Mironov, Gregory; Vlasenko, Sergey; Panov, Alexey; Chi, Xuguang; Walter, David; Carbone, Samara; Artaxo, Paulo; Heimann, Martin; Lavric, Jost; Pöschl, Ulrich; Andreae, Meinrat O.

2017-12-01

We present long-term (5-year) measurements of particulate matter with an upper diameter limit of ˜ 10 µm (PM10), elemental carbon (EC), organic carbon (OC), and water-soluble organic carbon (WSOC) in aerosol filter samples collected at the Zotino Tall Tower Observatory in the middle-taiga subzone (Siberia). The data are complemented with carbon monoxide (CO) measurements. Air mass back trajectory analysis and satellite image analysis were used to characterise potential source regions and the transport pathway of haze plumes. Polluted and background periods were selected using a non-parametric statistical approach and analysed separately. In addition, near-pristine air masses were selected based on their EC concentrations being below the detection limit of our thermal-optical instrument. Over the entire sampling campaign, 75 and 48 % of air masses in winter and in summer, respectively, and 42 % in spring and fall are classified as polluted. The observed background concentrations of CO and EC showed a sine-like behaviour with a period of 365 ± 4 days, mostly due to different degrees of dilution and the removal of polluted air masses arriving at the Zotino Tall Tower Observatory (ZOTTO) from remote sources. Our analysis of the near-pristine conditions shows that the longest periods with clean air masses were observed in summer, with a frequency of 17 %, while in wintertime only 1 % can be classified as a clean. Against a background of low concentrations of CO, EC, and OC in the near-pristine summertime, it was possible to identify pollution plumes that most likely came from crude-oil production sites located in the oil-rich regions of Western Siberia. Overall, our analysis indicates that most of the time the Siberian region is impacted by atmospheric pollution arising from biomass burning and anthropogenic emissions. A relatively clean atmosphere can be observed mainly in summer, when polluted species are removed by precipitation and the aerosol burden returns to near-pristine conditions.

Radioecological indexes of fallout measurements from the Fukushima nuclear accident

NASA Astrophysics Data System (ADS)

Manolopoulou, Metaxia; Stoulos, Stylianos; Ioannidou, Alexandra; Vagena, Eleni

2014-05-01

Fallout from the Fukushima nuclear accident has been monitored for about 1 month in Thessaloniki, Northern Greece. Three different radionuclides, one short-lived, one relatively long-lived and one long- lived fission product were identified in air, grass and milk samples. The 131I, 137Cs and 134Cs activity concentrations in air reached 497, 145 and 126 μBqm-3, respectively on 4 April, 2011. These radionuclides are of particular concern regarding their transfer from the environment to population through the ingestion pathways for the assessment of the Fukushima accident consequences. Radioecological indexes (eco-indexes) of fallout measurements in the air-grass-cow-milk-man pathway for 131I were determined, as they are related to radiological impact of the Fukushima derived radionuclides on the public and environment.

A prospective study (SCOPE) comparing the cardiometabolic and respiratory effects of air pollution exposure on healthy and pre-diabetic individuals.

PubMed

Wang, Yanwen; Han, Yiqun; Zhu, Tong; Li, Weiju; Zhang, Hongyin

2018-01-01

Air pollution is known to be a major risk factor for cardiopulmonary disease, but this is unclear for cardiometabolic disease (e.g. diabetes). This is of considerable public health importance, given the nationwide epidemic of diabetes, accompanied by severe air pollution, in China. The evidence so far remained inadequate to answer questions of whether individuals with cardiometabolic dysfunctions are susceptible to air pollution and whether air pollution exacerbates diabetes development via certain biological pathways. In this manuscript, we summarize the results and limitations of studies exploring these two topics and elaborate our design of a prospective panel study (SCOPE) as a solution. We assessed and compared the health effect of air pollution among pre-diabetic individuals and matched healthy controls through four repeated clinical visits over 1 year. Comprehensive evaluation was made to both health endpoints and exposure. The primary biomarkers were assessed to reveal the impact on multiple biological pathways, including glycolipid metabolism and insulin resistance, endothelial function, and inflammation. Detailed chemical and size fractional components of particulate matter were measured in this study, along with the application of personal monitors. The work should increase our understanding of how air pollution affects individuals with cardiometabolic dysfunction and the underlying mechanisms.

Estimating environmental co-benefits of U.S. low-carbon pathways using an integrated assessment model with state-level resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ou, Yang; Shi, Wenjing; Smith, Steven J.

There are many technological pathways that can lead to reduced carbon dioxide (CO 2) emissions. However, these pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. This study uses an integrated assessment model with state-level resolution of the U.S. energy system to compare environmental impacts of alternative low-carbon pathways. One set of pathways emphasizes nuclear energy and carbon capture and storage (NUC/CCS), while another set emphasizes renewable energy (RE). These are compared with pathways in which all technologies are available. Air pollutant emissions, mortality costs attributable to particulate matter less thanmore » 2.5 microns in diameter (PM2.5), and energy-related water demands are evaluated for 50% and 80% CO 2 reduction targets in the U.S. in 2050. The RE low-carbon pathways require less water withdrawal and consumption than the NUC/CCS pathways because of the large cooling demands of nuclear power and CCS. However, the NUC/CCS low-carbon pathways produce greater health benefits, mainly because the NUC/CCS assumptions result in less primary PM2.5 emissions from residential wood combustion. Environmental co-benefits differ among states because of factors such as existing technology stock, resource availability, and environmental and energy policies. An important finding is that biomass in the building sector can offset some of the health co-benefits of the low-carbon pathways even though it plays only a minor role in reducing CO 2 emissions.« less

Next-generation sequencing analysis of gene regulation in the rat model of retinopathy of prematurity.

PubMed

Griffith, Rachel M; Li, Hu; Zhang, Nan; Favazza, Tara L; Fulton, Anne B; Hansen, Ronald M; Akula, James D

2013-08-01

The purpose of this study was to identify the genes, biochemical signaling pathways, and biological themes involved in the pathogenesis of retinopathy of prematurity (ROP). Next-generation sequencing (NGS) was performed on the RNA transcriptome of rats with the Penn et al. (Pediatr Res 36:724-731, 1994) oxygen-induced retinopathy model of ROP at the height of vascular abnormality, postnatal day (P) 19, and normalized to age-matched, room-air-reared littermate controls. Eight custom-developed pathways with potential relevance to known ROP sequelae were evaluated for significant regulation in ROP: The three major Wnt signaling pathways, canonical, planar cell polarity (PCP), and Wnt/Ca(2+); two signaling pathways mediated by the Rho GTPases RhoA and Cdc42, which are, respectively, thought to intersect with canonical and non-canonical Wnt signaling; nitric oxide signaling pathways mediated by two nitric oxide synthase (NOS) enzymes, neuronal (nNOS) and endothelial (eNOS); and the retinoic acid (RA) signaling pathway. Regulation of other biological pathways and themes was detected by gene ontology using the Kyoto Encyclopedia of Genes and Genomes and the NIH's Database for Annotation, Visualization, and Integrated Discovery's GO terms databases. Canonical Wnt signaling was found to be regulated, but the non-canonical PCP and Wnt/Ca(2+) pathways were not. Nitric oxide signaling, as measured by the activation of nNOS and eNOS, was also regulated, as was RA signaling. Biological themes related to protein translation (ribosomes), neural signaling, inflammation and immunity, cell cycle, and cell death were (among others) highly regulated in ROP rats. These several genes and pathways identified by NGS might provide novel targets for intervention in ROP.

Next Generation Sequencing Analysis of Gene Regulation in the Rat Model of Retinopathy of Prematurity

PubMed Central

Griffith, Rachel M.; Li, Hu; Zhang, Nan; Favazza, Tara L.; Fulton, Anne B.; Hansen, Ronald M.; Akula, James D.

2013-01-01

Purpose To identify the genes, biochemical signaling pathways and biological themes involved in the pathogenesis of retinopathy of prematurity (ROP). Methods Next-generation sequencing (NGS) was performed on the RNA transcriptome of rats with the Penn et al. (1994) oxygen-induced retinopathy (OIR) model of ROP at the height of vascular abnormality, postnatal day (P) 19, and normalized to age-matched, room-air-reared littermate controls. Eight custom developed pathways with potential relevance to known ROP sequelae were evaluated for significant regulation in ROP: The three major Wnt signaling pathways, canonical, planar cell polarity (PCP), and Wnt/Ca2+, two signaling pathways mediated by the Rho GTPases RhoA and Cdc42, which are respectively thought to intersect with canonical and noncanonical Wnt signaling, nitric oxide signaling pathways mediated by two nitrox oxide synthase (NOS) enzymes, neuronal (nNOS) and endothelial (eNOS), and the retinoic acid (RA) signaling pathway. Regulation of other biological pathways and themes were detected by gene ontology using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the NIH's Database for Annotation, Visualization and Integrated Discovery (DAVID)'s GO terms databases. Results Canonical Wnt signaling was found to be regulated, but the non-canonical PCP and Wnt/Ca2+ pathways were not. Nitric oxide (NO) signaling, as measured by the activation of nNOS eNOS, was also regulated, as was RA signaling. Biological themes related to protein translation (ribosomes), neural signaling, inflammation and immunity, cell cycle and cell death, were (among others) highly regulated in ROP rats. Conclusions These several genes and pathways identified by NGS might provide novel targets for intervention in ROP. PMID:23775346

Interrelationships among Grain Size, Surface Composition, Air Stability, and Interfacial Resistance of Al-Substituted Li7La3Zr2O12 Solid Electrolytes.

PubMed

Cheng, Lei; Wu, Cheng Hao; Jarry, Angelique; Chen, Wei; Ye, Yifan; Zhu, Junfa; Kostecki, Robert; Persson, Kristin; Guo, Jinghua; Salmeron, Miquel; Chen, Guoying; Doeff, Marca

2015-08-19

The interfacial resistances of symmetrical lithium cells containing Al-substituted Li7La3Zr2O12 (LLZO) solid electrolytes are sensitive to their microstructures and histories of exposure to air. Air exposure of LLZO samples with large grain sizes (∼150 μm) results in dramatically increased interfacial impedances in cells containing them, compared to those with pristine large-grained samples. In contrast, a much smaller difference is seen between cells with small-grained (∼20 μm) pristine and air-exposed LLZO samples. A combination of soft X-ray absorption (sXAS) and Raman spectroscopy, with probing depths ranging from nanometer to micrometer scales, revealed that the small-grained LLZO pellets are more air-stable than large-grained ones, forming far less surface Li2CO3 under both short- and long-term exposure conditions. Surface sensitive X-ray photoelectron spectroscopy (XPS) indicates that the better chemical stability of the small-grained LLZO is related to differences in the distribution of Al and Li at sample surfaces. Density functional theory calculations show that LLZO can react via two different pathways to form Li2CO3. The first, more rapid, pathway involves a reaction with moisture in air to form LiOH, which subsequently absorbs CO2 to form Li2CO3. The second, slower, pathway involves direct reaction with CO2 and is favored when surface lithium contents are lower, as with the small-grained samples. These observations have important implications for the operation of solid-state lithium batteries containing LLZO because the results suggest that the interfacial impedances of these devices is critically dependent upon specific characteristics of the solid electrolyte and how it is prepared.

Computer simulations show that Neanderthal facial morphology represents adaptation to cold and high energy demands, but not heavy biting.

PubMed

Wroe, Stephen; Parr, William C H; Ledogar, Justin A; Bourke, Jason; Evans, Samuel P; Fiorenza, Luca; Benazzi, Stefano; Hublin, Jean-Jacques; Stringer, Chris; Kullmer, Ottmar; Curry, Michael; Rae, Todd C; Yokley, Todd R

2018-04-11

Three adaptive hypotheses have been forwarded to explain the distinctive Neanderthal face: (i) an improved ability to accommodate high anterior bite forces, (ii) more effective conditioning of cold and/or dry air and, (iii) adaptation to facilitate greater ventilatory demands. We test these hypotheses using three-dimensional models of Neanderthals, modern humans, and a close outgroup ( Homo heidelbergensis ), applying finite-element analysis (FEA) and computational fluid dynamics (CFD). This is the most comprehensive application of either approach applied to date and the first to include both. FEA reveals few differences between H. heidelbergensis , modern humans, and Neanderthals in their capacities to sustain high anterior tooth loadings. CFD shows that the nasal cavities of Neanderthals and especially modern humans condition air more efficiently than does that of H. heidelbergensis , suggesting that both evolved to better withstand cold and/or dry climates than less derived Homo We further find that Neanderthals could move considerably more air through the nasal pathway than could H. heidelbergensis or modern humans, consistent with the propositions that, relative to our outgroup Homo , Neanderthal facial morphology evolved to reflect improved capacities to better condition cold, dry air, and, to move greater air volumes in response to higher energetic requirements. © 2018 The Author(s).

Air quality and climate impacts due to CNG conversion of motor vehicles in Dhaka, Bangladesh.

PubMed

Wadud, Zia; Khan, Tanzila

2013-12-17

Dhaka had recently experienced rapid conversion of its motor vehicle fleet to run on compressed natural gas (CNG). This paper quantifies ex-post the air quality and climate benefits of the CNG conversion policy, including monetary valuations, through an impact pathway approach. Around 2045 (1665) avoided premature deaths in greater Dhaka (City Corporation) can be attributed to air quality improvements from the CNG conversion policy in 2010, resulting in a saving of around USD 400 million. Majority of these health benefits resulted from the conversion of high-emitting diesel vehicles. CNG conversion was clearly detrimental from climate change perspective using the changes in CO2 and CH4 only (CH4 emissions increased); however, after considering other global pollutants (especially black carbon), the climate impact was ambiguous. Uncertainty assessment using input distributions and Monte Carlo simulation along with a sensitivity analysis show that large uncertainties remain for climate impacts. For our most likely estimate, there were some climate costs, valued at USD 17.7 million, which is an order of magnitude smaller than the air quality benefits. This indicates that such policies can and should be undertaken on the grounds of improving local air pollution alone and that precautions should be taken to reduce the potentially unintended increases in GHG emissions or other unintended effects.

Open-loop heat-recovery dryer

DOEpatents

TeGrotenhuis, Ward Evan

2013-11-05

A drying apparatus is disclosed that includes a drum and an open-loop airflow pathway originating at an ambient air inlet, passing through the drum, and terminating at an exhaust outlet. A passive heat exchanger is included for passively transferring heat from air flowing from the drum toward the exhaust outlet to air flowing from the ambient air inlet toward the drum. A heat pump is also included for actively transferring heat from air flowing from the passive heat exchanger toward the exhaust outlet to air flowing from the passive heat exchanger toward the drum. A heating element is also included for further heating air flowing from the heat pump toward the drum.

Developmental transcriptome analysis and identification of genes involved in formation of intestinal air-breathing function of Dojo loach, Misgurnus anguillicaudatus

PubMed Central

Luo, Weiwei; Cao, Xiaojuan; Xu, Xiuwen; Huang, Songqian; Liu, Chuanshu; Tomljanovic, Tea

2016-01-01

Dojo loach, Misgurnus anguillicaudatus is a freshwater fish species of the loach family Cobitidae, using its posterior intestine as an accessory air-breathing organ. Little is known about the molecular regulatory mechanisms in the formation of intestinal air-breathing function of M. anguillicaudatus. Here high-throughput sequencing of mRNAs was performed from six developmental stages of posterior intestine of M. anguillicaudatus: 4-Dph (days post hatch) group, 8-Dph group, 12-Dph group, 20-Dph group, 40-Dph group and Oyd (one-year-old) group. These six libraries were assembled into 81300 unigenes. Totally 40757 unigenes were annotated. Subsequently, 35291 differentially expressed genes (DEGs) were scanned among different developmental stages and clustered into 20 gene expression profiles. Finally, 15 key pathways and 25 key genes were mined, providing potential targets for candidate gene selection involved in formation of intestinal air-breathing function in M. anguillicaudatus. This is the first report of developmental transcriptome of posterior intestine in M. anguillicaudatus, offering a substantial contribution to the sequence resources for this species and providing a deep insight into the formation mechanism of its intestinal air-breathing function. This report demonstrates that M. anguillicaudatus is a good model for studies to identify and characterize the molecular basis of accessory air-breathing organ development in fish. PMID:27545457

Cell cycle pathway dysregulation in human keratinocytes during chronic exposure to low arsenite.

PubMed

Al-Eryani, Laila; Waigel, Sabine; Jala, Venkatakrishna; Jenkins, Samantha F; States, J Christopher

2017-09-15

Arsenic is naturally prevalent in the earth's crust and widely distributed in air and water. Chronic low arsenic exposure is associated with several cancers in vivo, including skin cancer, and with transformation in vitro of cell lines including immortalized human keratinocytes (HaCaT). Arsenic also is associated with cell cycle dysregulation at different exposure levels in multiple cell lines. In this work, we analyzed gene expression in HaCaT cells to gain an understanding of gene expression changes contributing to transformation at an early time point. HaCaT cells were exposed to 0 or 100nM NaAsO 2 for 7weeks. Total RNA was purified and analyzed by microarray hybridization. Differential expression with fold change≥|1.5| and p-value≤0.05 was determined using Partek Genomic Suite™ and pathway and network analyses using MetaCore™ software (FDR≤0.05). Cell cycle analysis was performed using flow cytometry. 644 mRNAs were differentially expressed. Cell cycle/cell cycle regulation pathways predominated in the list of dysregulated pathways. Genes involved in replication origin licensing were enriched in the network. Cell cycle assay analysis showed an increase in G2/M compartment in arsenite-exposed cells. Arsenite exposure induced differential gene expression indicating dysregulation of cell cycle control, which was confirmed by cell cycle analysis. The results suggest that cell cycle dysregulation is an early event in transformation manifested in cells unable to transit G2/M efficiently. Further study at later time points will reveal additional changes in gene expression related to transformation processes. Copyright © 2017 Elsevier Inc. All rights reserved.

Genetic susceptibility for air pollution-induced airway inflammation in the SALIA study.

PubMed

Hüls, Anke; Krämer, Ursula; Herder, Christian; Fehsel, Karin; Luckhaus, Christian; Stolz, Sabine; Vierkötter, Andrea; Schikowski, Tamara

2017-01-01

Long-term air pollution exposure has been associated with chronic inflammation providing a link to the development of chronic health effects. Furthermore, there is evidence that pathways activated by endoplasmatic reticulum (ER) stress induce airway inflammation and thereby play an important role in the pathogenesis of inflammatory diseases. We investigated the role of genetic variation of the ER stress pathway on air pollution-induced inflammation. We used the follow-up examination of the German SALIA study (N=402, age 68-79 years). Biomarkers of inflammation were determined in induced sputum. We calculated biomarker-specific weighted genetic risk scores (GRS) out of eight ER stress related single nucleotide polymorphisms and tested their interaction with PM 2.5 , PM 2.5 absorbance, PM 10 and NO 2 exposure on inflammation by adjusted linear regression. Genetic variation of the ER stress pathway was associated with higher concentration of inflammation-related biomarkers (levels of leukotriene (LT)B 4 , tumor necrosis factor-α (TNF-α), the total number of cells and nitric oxide (NO) derivatives). Furthermore, we observed a significant interaction between air pollution exposure and the ER stress risk score on the concentration of inflammation-related biomarkers. The strongest gene-environment interaction was found for LTB 4 (PM 2.5 : p-value=0.002, PM 2.5 absorbance: p-value=0.002, PM 10 : p-value=0.001 and NO 2 : p-value=0.004). Women with a high GRS had a 38% (95%-CI: 16-64%) higher LTB 4 level for an increase of 2.06μg/m³(IQR) in PM 2.5 (no associations in women with a low GRS). These results indicate that genetic variation in the ER stress pathway might play a role in air pollution induced inflammation in the lung. Copyright © 2016 Elsevier Inc. All rights reserved.

Hypercholesterolemia potentiates aortic endothelial response to inhaled diesel exhaust

PubMed Central

Maresh, J. Gregory; Campen, Matthew J.; Reed, Matthew D.; Darrow, April L.; Shohet, Ralph V.

2012-01-01

Background Inhalation of diesel exhaust induces vascular effects including impaired endothelial function and increased atherosclerosis. Objective To examine the in vivo effects of subchronic diesel exhaust exposure on endothelial cell transcriptional responses in the presence of hypercholesterolemia. Methods ApoE (−/−) and ApoE (+/+) mice inhaled diesel exhaust diluted to particulate matter levels of 300 or 1000 μg/m3 vs. filtered air. After 30 days, endothelial cells were harvested from dispersed aortic cells by fluorescent-activated cell sorting (FACS). Relative mRNA abundance was evaluated by microarray analysis to measure strain-specific transcriptional responses in mice exposed to dilute diesel exhaust vs. filtered air. Results Forty-nine transcripts were significantly dysregulated by >2.8-fold in the endothelium of ApoE (−/−) mice receiving diesel exhaust at 300 or 1000 μg/m3. These included transcripts with roles in plasminogen activation, endothelial permeability, inflammation, genomic stability, and atherosclerosis; similar responses were not observed in ApoE (+/+) mice. Conclusions The potentiation of diesel exhaust-related endothelial gene regulation by hypercholesterolemia helps to explain air pollution-induced vascular effects in animals and humans. The observed regulated transcripts implicate pathways important in the acceleration of atherosclerosis by air pollution. PMID:21222557

Modeling the oxidative capacity of the atmosphere of the south coast air basin of California. 2. HOx radical production.

PubMed

Griffin, Robert J

2004-02-01

The production of HOx radicals in the South Coast Air Basin of California is investigated during the smog episode of September 9, 1993 using the California Institute of Technology (CIT) air-quality model. Sources of HOx(hydroxyl, hydroperoxy, and organic peroxy radicals) incorporated into the associated gas-phase chemical mechanism include the combination of excited-state singlet oxygen (formed from ozone (O3) photolysis (hv)) with water, the photolysis of nitrous acid, hydrogen peroxide (H2O2), and carbonyl compounds (formaldehyde (HCHO) or higher aldehydes and ketones), the consumption of aldehydes and alkenes (ALK) by the nitrate radical, and the consumption of alkenes by O3 and the oxygen atom (O). At a given time or location for surface cells and vertical averages, each route of HOx formation may be the greatest contributor to overall formation except HCHO-hv, H2O2-hv, and ALK-O, the latter two of which are insignificant pathways in general. The contribution of the ALK-O3 pathway is dependent on the stoichiometric yield of OH, but this pathway, at least for the studied smog episode, may not be as generally significant as previous research suggests. Future emissions scenarios yield lower total HOx production rates and a shift in the relative importance of individual pathways.

Hot air injection for removal of dense, non-aqueous-phase liquid contaminants from low-permeability soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Payne, F.C.

1996-08-01

The performance of soil vapor extraction systems for the recovery of volatile and semi-volatile organic compounds is potentially enhanced by the injection of heated air to increase soil temperatures. The soil temperature increase is expected to improve soil vapor extraction (SVE) performance by increasing target compound vapor pressures and by increasing soil permeability through drying. The vapor pressure increase due to temperature rise relieves the vapor pressure limit on the feasibility of soil vapor extraction. However, the system still requires an air flow through the soil system to deliver heat and to recover mobilized contaminants. Although the soil permeability canmore » be increased through drying, very low permeability soils and low permeability soils adjacent to high permeability air flow pathways will be treated slowly, if at all. AR thermal enhancement methods face this limitation. Heated air injection offers advantages relative to other thermal techniques, including low capital and operation costs. Heated air injection is at a disadvantage relative to other thermal techniques due to the low heat capacity of air. To be effective, heated air injection requires that higher air flows be established than for steam injection or radio frequency heating. Heated air injection is not economically feasible for the stratified soil system developed as a standard test for this document. This is due to the inability to restrict heated air flow to the clay stratum when a low-resistance air flow pathway is available in the adjoining sand. However, the technology should be especially attractive, both technically and economically, for low-volatile contaminant recovery from relatively homogeneous soil formations. 16 refs., 2 tabs.« less

Summary of the BIOMOVS A4 scenario: Testing models of the air-pasture-cow milk pathway using Chernobyl fallout data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peterson, S.R.; Hoffman, F.O.; Koehler, H.

1996-08-01

A unique opportunity to test dose assessment models arose after the Chernobyl reactor accident. During the passage of the contaminated plume, concentrations of {sup 131}I and {sup 137}Cs in air, pasture, and cow`s milk were collected at various sites in the northern hemisphere. Afterwards, contaminated pasture and milk samples were analyzed over time. Under the auspices of the Biospheric Model Validation Study (BIOMOVS), data from 13 sites for {sup 131}I and 10 sites for {sup 137}Cs were used to test model predictions for the air-pasture-cow milk pathway. Calculations were submitted for 23 models, 10 of which were quasi-steady state. Themore » others were time-dependent. Daily predictions and predictions of time-integrated concentration of {sup 131}I and {sup 137}Cs in pasture grass and milk for six months post-accident were calculated and compared with observed data. Testing against data from several locations over time for several steps in the air-to-milk pathway resulted in a better understanding of important processes and how they should be modeled. This model testing exercise showed both the strengths and weaknesses of the models and revealed the importance of testing all parts of dose assessment models whenever possible. 19 refs., 14 figs., 4 tabs.« less

Air pathway effects of nuclear materials production at the Hanford Site, 1983 to 1992

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patton, G.W.; Cooper, A.T.

1993-10-01

This report describes the air pathway effects of Hanford Site operations from 1983 to 1992 on the local environment by summarizing the air concentrations of selected radionuclides at both onsite and offsite locations, comparing trends in environment concentrations to changing facility emissions, and briefly describing trends in the radiological dose to the hypothetical maximally exposed member of the public. The years 1983 to 1992 represent the last Hanford Site plutonium production campaign, and this report deals mainly with the air pathway effects from the 200 Areas, in which the major contributors to radiological emissions were located. An additional purpose formore » report was to review the environmental data for a long period of time to provide insight not available in an annual report format. The sampling and analytical systems used by the Surface Environmental Surveillance Project (SESP) to collect air samples during the period of this report were sufficiently sensitive to observe locally elevated concentrations of selected radionuclides near onsite source of emission as well as observing elevated levels, compared to distant locations, of some radionuclides at the down wind perimeter. The US DOE Derived Concentration Guides (DCGs) for airborne radionuclides were not exceeded for any air sample collected during 1983 to 1992, with annual average concentrations of all radionuclides at the downwind perimeter being considerably below the DCG values. Air emissions at the Hanford Site during the period of this report were dominated by releases from the PUREX Plant, with {sup 85}Kr being the major release on a curie basis and {sup 129}I being the major release on a radiological dose basis. The estimated potential radiological dose from Hanford Site point source emissions to the hypothetical maximally exposed individual (MEI) ranged from 0. 02 to 0.22 mrem/yr (effective dose equivalent), which is well below the DOE radiation limit to the public of 100 mrem/yr.« less

76 FR 14660 - Public Comment on the Development of Final Guidance for Evaluating the Vapor Intrusion to Indoor...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-17

... Groundwater and Soils (Subsurface Vapor Intrusion Guidance) AGENCY: Environmental Protection Agency (EPA... Pathway from Contaminated Groundwater and Soil (Subsurface Vapor Intrusion Guidance). A draft of the... Evaluating Vapor Intrusion to Indoor Air Pathway from Contaminated Groundwater and Soil (Subsurface Vapor...

Can Erythrocytes Transmit Oxidative Stress Beyond the Lungs? An Adverse Outcome Pathway for the Cardiovascular Effects of Air Pollution.

EPA Science Inventory

Adverse outcome pathways (AOPs) are systems biology roadmaps with potential utility in xenobiotic exposure risk assessment. AOPs connect molecular initiating events (MIEs) to population-level adverse outcomes (AOs) via cellular, organ, and organism key events (KE) and KE relatio...

Estimating Environmental Co-benefits of U.S. GHG Reduction Pathways Using the GCAM-USA Integrated Assessment Model

EPA Science Inventory

Previous studies have shown that mitigating climate change through curbing greenhouse gas (GHG) emissions can bring about substantial environmental co-benefits, such as for air quality and reductions in energy-related water demand. A variety of pathways are available for reducing...

A review of chamber experiments for determining specific emission rates and investigating migration pathways of flame retardants

NASA Astrophysics Data System (ADS)

Rauert, Cassandra; Lazarov, Borislav; Harrad, Stuart; Covaci, Adrian; Stranger, Marianne

2014-01-01

The widespread use of flame retardants (FRs) in indoor products has led to their ubiquitous distribution within indoor microenvironments with many studies reporting concentrations in indoor air and dust. Little information is available however on emission of these compounds to air, particularly the measurement of specific emission rates (SERs), or the migration pathways leading to dust contamination. Such knowledge gaps hamper efforts to develop understanding of human exposure. This review summarizes published data on SERs of the following FRs released from treated products: polybrominated diphenyl ethers (PBDEs), hexabromocyclododecanes (HBCDs), tetrabromobisphenol-A (TBBPA), novel brominated flame retardants (NBFRs) and organophosphate flame retardants (PFRs), including a brief discussion of the methods used to derive these SERs. Also reviewed are published studies that utilize emission chambers for investigations/measurements of mass transfer of FRs to dust, discussing the chamber configurations and methods used for these experiments. A brief review of studies investigating correlations between concentrations detected in indoor air/dust and possible sources in the microenvironment is included along with efforts to model contamination of indoor environments. Critical analysis of the literature reveals that the major limitations with utilizing chambers to derive SERs for FRs arise due to the physicochemical properties of FRs. In particular, increased partitioning to chamber surfaces, airborne particles and dust, causes loss through “sink” effects and results in long times to reach steady state conditions inside the chamber. The limitations of chamber experiments are discussed as well as their potential for filling gaps in knowledge in this area.

Human primordial germ cell formation is diminished by exposure to environmental toxicants acting through the AHR signaling pathway.

PubMed

Kee, Kehkooi; Flores, Martha; Cedars, Marcelle I; Reijo Pera, Renee A

2010-09-01

Historically, effects of environmental toxicants on human development have been deduced via epidemiological studies because direct experimental analysis has not been possible. However, in recent years, the derivation of human pluripotent stem cells has provided a potential experimental system to directly probe human development. Here, we used human embryonic stem cells (hESCs) to study the effect of environmental toxicants on human germ cell development, with a focus on differentiation of the founding population of primordial germ cells (PGCs), which will go on to form the oocytes of the adult. We demonstrate that human PGC numbers are specifically reduced by exposure to polycyclic aromatic hydrocarbons (PAHs), a group of toxicants common in air pollutants released from gasoline combustion or tobacco smoke. Further, we demonstrate that the adverse effects of PAH exposure are mediated through the aromatic hydrocarbon receptor (AHR) and BAX pathway. This study demonstrates the utility of hESCs as a model system for direct examination of the molecular and genetic pathways of environmental toxicants on human germ cell development.

Toward Understanding the Genetic Basis of Yak Ovary Reproduction: A Characterization and Comparative Analyses of Estrus Ovary Transcriptiome in Yak and Cattle.

PubMed

Lan, Daoliang; Xiong, Xianrong; Huang, Cai; Mipam, Tserang Donko; Li, Jian

2016-01-01

Yaks (Bos grunniens) are endemic species that can adapt well to thin air, cold temperatures, and high altitude. These species can survive in harsh plateau environments and are major source of animal production for local residents, being an important breed in the Qinghai-Tibet Plateau. However, compared with ordinary cattle that live in the plains, yaks generally have lower fertility. Investigating the basic physiological molecular features of yak ovary and identifying the biological events underlying the differences between the ovaries of yak and plain cattle is necessary to understand the specificity of yak reproduction. Therefore, RNA-seq technology was applied to analyze transcriptome data comparatively between the yak and plain cattle estrous ovaries. After deep sequencing, 3,653,032 clean reads with a total of 4,828,772,880 base pairs were obtained from yak ovary library. Alignment analysis showed that 16992 yak genes mapped to the yak genome, among which, 12,731 and 14,631 genes were assigned to Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, comparison of yak and cattle ovary transcriptome data revealed that 1307 genes were significantly and differentially expressed between the two libraries, wherein 661 genes were upregulated and 646 genes were downregulated in yak ovary. Functional analysis showed that the differentially expressed genes were involved in various Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. GO annotations indicated that the genes related to "cell adhesion," "hormonal" biological processes, and "calcium ion binding," "cation transmembrane transport" molecular events were significantly active. KEGG pathway analysis showed that the "complement and coagulation cascade" pathway was the most enriched in yak ovary transcriptome data, followed by the "cytochrome P450" related and "ECM-receptor interaction" pathways. Moreover, several novel pathways, such as "circadian rhythm," were significantly enriched despite having no evident associations with the reproductive function. Our findings provide a molecular resource for further investigation of the general molecular mechanism of yak ovary and offer new insights to understand comprehensively the specificity of yak reproduction.

Automated retinofugal visual pathway reconstruction with multi-shell HARDI and FOD-based analysis.

PubMed

Kammen, Alexandra; Law, Meng; Tjan, Bosco S; Toga, Arthur W; Shi, Yonggang

2016-01-15

Diffusion MRI tractography provides a non-invasive modality to examine the human retinofugal projection, which consists of the optic nerves, optic chiasm, optic tracts, the lateral geniculate nuclei (LGN) and the optic radiations. However, the pathway has several anatomic features that make it particularly challenging to study with tractography, including its location near blood vessels and bone-air interface at the base of the cerebrum, crossing fibers at the chiasm, somewhat-tortuous course around the temporal horn via Meyer's Loop, and multiple closely neighboring fiber bundles. To date, these unique complexities of the visual pathway have impeded the development of a robust and automated reconstruction method using tractography. To overcome these challenges, we develop a novel, fully automated system to reconstruct the retinofugal visual pathway from high-resolution diffusion imaging data. Using multi-shell, high angular resolution diffusion imaging (HARDI) data, we reconstruct precise fiber orientation distributions (FODs) with high order spherical harmonics (SPHARM) to resolve fiber crossings, which allows the tractography algorithm to successfully navigate the complicated anatomy surrounding the retinofugal pathway. We also develop automated algorithms for the identification of ROIs used for fiber bundle reconstruction. In particular, we develop a novel approach to extract the LGN region of interest (ROI) based on intrinsic shape analysis of a fiber bundle computed from a seed region at the optic chiasm to a target at the primary visual cortex. By combining automatically identified ROIs and FOD-based tractography, we obtain a fully automated system to compute the main components of the retinofugal pathway, including the optic tract and the optic radiation. We apply our method to the multi-shell HARDI data of 215 subjects from the Human Connectome Project (HCP). Through comparisons with post-mortem dissection measurements, we demonstrate the retinotopic organization of the optic radiation including a successful reconstruction of Meyer's loop. Then, using the reconstructed optic radiation bundle from the HCP cohort, we construct a probabilistic atlas and demonstrate its consistency with a post-mortem atlas. Finally, we generate a shape-based representation of the optic radiation for morphometry analysis. Copyright © 2015 Elsevier Inc. All rights reserved.

Mathematical Model of HIF-1 alpha Pathway, Oxygen Transport and Hypoxia

DTIC Science & Technology

2017-09-01

interpret experimental data in terms of underlying mechanisms. Such experiments, if quantitative , can also be used to calibrate and further parameterize...Wing Air Force Research Laboratory Wright-Patterson AFB OH 45433-5707 STINFO COPY Work Unit Manager MATTIE.DAV ID.R.123010 1880 Digitally signed by...MONITORING AGENCY NAME(S) AND ADDRESS(ES) Air Force Materiel Command* Air Force Research Laboratory 711th Human Performance Wing Human Effectiveness

Field Testing of Compartmentalization Methods for Multifamily Construction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ueno, K.; Lstiburek, J.

The 2012 IECC has an airtightness requirement of 3 air changes per hour at 50 Pascals test pressure for both single-family and multifamily construction in Climate Zones 3-8. Other programs (LEED, ASHRAE 189, ASHRAE 62.2) have similar or tighter compartmentalization requirements, driving the need for easier and more effective methods of compartmentalization in multifamily buildings. Builders and practitioners have found that fire-resistance rated wall assemblies are a major source of difficulty in air sealing/compartmentalization, particularly in townhouse construction. This problem is exacerbated when garages are “tucked in” to the units and living space is located over the garages. In thismore » project, Building Science Corporation examined the taping of exterior sheathing details to improve air sealing results in townhouse and multifamily construction, when coupled with a better understanding of air leakage pathways. Current approaches are cumbersome, expensive, time consuming, and ineffective; these details were proposed as a more effective and efficient method. The effectiveness of these air sealing methods was tested with blower door testing, including “nulled” or “guarded” testing (adjacent units run at equal test pressure to null out inter-unit air leakage, or “pressure neutralization”). Pressure diagnostics were used to evaluate unit-to-unit connections and series leakage pathways (i.e., air leakage from exterior, into the fire-resistance rated wall assembly, and to the interior).« less

Air pollution, inflammation and preterm birth: a potential mechanistic link.

PubMed

Vadillo-Ortega, Felipe; Osornio-Vargas, Alvaro; Buxton, Miatta A; Sánchez, Brisa N; Rojas-Bracho, Leonora; Viveros-Alcaráz, Martin; Castillo-Castrejón, Marisol; Beltrán-Montoya, Jorge; Brown, Daniel G; O'Neill, Marie S

2014-02-01

Preterm birth is a public health issue of global significance, which may result in mortality during the perinatal period or may lead to major health and financial consequences due to lifelong impacts. Even though several risk factors for preterm birth have been identified, prevention efforts have failed to halt the increasing rates of preterm birth. Epidemiological studies have identified air pollution as an emerging potential risk factor for preterm birth. However, many studies were limited by study design and inadequate exposure assessment. Due to the ubiquitous nature of ambient air pollution and the potential public health significance of any role in causing preterm birth, a novel focus investigating possible causal mechanisms influenced by air pollution is therefore a global health priority. We hypothesize that air pollution may act together with other biological factors to induce systemic inflammation and influence the duration of pregnancy. Evaluation and testing of this hypothesis is currently being conducted in a prospective cohort study in Mexico City and will provide an understanding of the pathways that mediate the effects of air pollution on preterm birth. The important public health implication is that crucial steps in this mechanistic pathway can potentially be acted on early in pregnancy to reduce the risk of preterm birth. Copyright © 2013 Elsevier Ltd. All rights reserved.

AIR POLLUTION, INFLAMMATION AND PRETERM BIRTH: A POTENTIAL MECHANISTIC LINK

PubMed Central

Vadillo-Ortega, Felipe; Osornio-Vargas, Alvaro; Buxton, Miatta A.; Sánchez, Brisa N.; Rojas-Bracho, Leonora; Viveros-Alcaráz, Martin; Castillo-Castrejón, Marisol; Beltrán-Montoya, Jorge; Brown, Daniel G.; O´Neill, Marie S.

2014-01-01

Preterm birth is a public health issue of global significance, which may result in mortality during the perinatal period or may lead to major health and financial consequences due to lifelong impacts. Even though several risk factors for preterm birth have been identified, prevention efforts have failed to halt the increasing rates of preterm birth. Epidemiological studies have identified air pollution as an emerging potential risk factor for preterm birth. However, many studies were limited by study design and inadequate exposure assessment. Due to the ubiquitous nature of ambient air pollution and the potential public health significance of any role in causing preterm birth, a novel focus investigating possible causal mechanisms influenced by air pollution is therefore a global health priority. We hypothesize that air pollution may act together with other biological factors to induce systemic inflammation and influence the duration of pregnancy. Evaluation and testing of this hypothesis is currently being conducted in a prospective cohort study in Mexico City and will provide an understanding of the pathways that mediate the effects of air pollution on preterm birth. The important public health implication is that crucial steps in this mechanistic pathway can potentially be acted on early in pregnancy to reduce the risk of preterm birth. PMID:24382337

The impact of ambient air pollution on the human blood metabolome.

PubMed

Vlaanderen, J J; Janssen, N A; Hoek, G; Keski-Rahkonen, P; Barupal, D K; Cassee, F R; Gosens, I; Strak, M; Steenhof, M; Lan, Q; Brunekreef, B; Scalbert, A; Vermeulen, R C H

2017-07-01

Biological perturbations caused by air pollution might be reflected in the compounds present in blood originating from air pollutants and endogenous metabolites influenced by air pollution (defined here as part of the blood metabolome). We aimed to assess the perturbation of the blood metabolome in response to short term exposure to air pollution. We exposed 31 healthy volunteers to ambient air pollution for 5h. We measured exposure to particulate matter, particle number concentrations, absorbance, elemental/organic carbon, trace metals, secondary inorganic components, endotoxin content, gaseous pollutants, and particulate matter oxidative potential. We collected blood from the participants 2h before and 2 and 18h after exposure. We employed untargeted metabolite profiling to monitor 3873 metabolic features in 493 blood samples from these volunteers. We assessed lung function using spirometry and six acute phase proteins in peripheral blood. We assessed the association of the metabolic features with the measured air pollutants and with health markers that we previously observed to be associated with air pollution in this study. We observed 89 robust associations between air pollutants and metabolic features two hours after exposure and 118 robust associations 18h after exposure. Some of the metabolic features that were associated with air pollutants were also associated with acute health effects, especially changes in forced expiratory volume in 1s. We successfully identified tyrosine, guanosine, and hypoxanthine among the associated features. Bioinformatics approach Mummichog predicted enriched pathway activity in eight pathways, among which tyrosine metabolism. This study demonstrates for the first time the application of untargeted metabolite profiling to assess the impact of air pollution on the blood metabolome. Copyright © 2017 Elsevier Inc. All rights reserved.

Assessment of health benefits related to air quality improvement strategies in urban areas: An Impact Pathway Approach.

PubMed

Silveira, Carlos; Roebeling, Peter; Lopes, Myriam; Ferreira, Joana; Costa, Solange; Teixeira, João P; Borrego, Carlos; Miranda, Ana I

2016-12-01

Air pollution is, increasingly, a concern to our society given the threats to human health and the environment. Concerted actions to improve air quality have been taken at different levels, such as through the development of Air Quality Plans (AQPs). However, air quality impacts associated with the implementation of abatement measures included in AQPs are often neglected. In order to identify the major gaps and strengths in current knowledge, a literature review has been performed on existing methodologies to estimate air pollution-related health impacts and subsequent external costs. Based on this review, the Impact Pathway Approach was adopted and applied within the context of the MAPLIA research project to assess the health impacts and benefits (or avoided external costs) derived from improvements in air quality. Seven emission abatement scenarios, based on individual and combined abatement measures, were tested for the major activity sectors (traffic, residential and industrial combustion and production processes) of a Portuguese urban area (Grande Porto) with severe particular matter (PM10) air pollution problems. Results revealed a strong positive correlation between population density and health benefits obtained from the assessed reduction scenarios. As a consequence, potential health benefits from reduction scenarios are largest in densely populated areas with high anthropic activity and, thus, where air pollution problems are most alarming. Implementation of all measures resulted in a reduction in PM10 emissions by almost 8%, improving air quality by about 1% and contributing to a benefit of 8.8 million €/year for the entire study domain. The introduction of PM10 reduction technologies in industrial units was the most beneficial abatement measure. This study intends to contribute to policy support for decision-making on air quality management. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genome-Wide Analysis of DNA Methylation and Fine Particulate Matter Air Pollution in Three Study Populations: KORA F3, KORA F4, and the Normative Aging Study.

PubMed

Panni, Tommaso; Mehta, Amar J; Schwartz, Joel D; Baccarelli, Andrea A; Just, Allan C; Wolf, Kathrin; Wahl, Simone; Cyrys, Josef; Kunze, Sonja; Strauch, Konstantin; Waldenberger, Melanie; Peters, Annette

2016-07-01

Epidemiological studies have reported associations between particulate matter (PM) concentrations and cancer and respiratory and cardiovascular diseases. DNA methylation has been identified as a possible link but so far it has only been analyzed in candidate sites. We studied the association between DNA methylation and short- and mid-term air pollution exposure using genome-wide data and identified potential biological pathways for additional investigation. We collected whole blood samples from three independent studies-KORA F3 (2004-2005) and F4 (2006-2008) in Germany, and the Normative Aging Study (1999-2007) in the United States-and measured genome-wide DNA methylation proportions with the Illumina 450k BeadChip. PM concentration was measured daily at fixed monitoring stations and three different trailing averages were considered and regressed against DNA methylation: 2-day, 7-day and 28-day. Meta-analysis was performed to pool the study-specific results. Random-effect meta-analysis revealed 12 CpG (cytosine-guanine dinucleotide) sites as associated with PM concentration (1 for 2-day average, 1 for 7-day, and 10 for 28-day) at a genome-wide Bonferroni significance level (p ≤ 7.5E-8); 9 out of these 12 sites expressed increased methylation. Through estimation of I2 for homogeneity assessment across the studies, 4 of these sites (annotated in NSMAF, C1orf212, MSGN1, NXN) showed p > 0.05 and I2 < 0.5: the site from the 7-day average results and 3 for the 28-day average. Applying false discovery rate, p-value < 0.05 was observed in 8 and 1,819 additional CpGs at 7- and 28-day average PM2.5 exposure respectively. The PM-related CpG sites found in our study suggest novel plausible systemic pathways linking ambient PM exposure to adverse health effect through variations in DNA methylation. Panni T, Mehta AJ, Schwartz JD, Baccarelli AA, Just AC, Wolf K, Wahl S, Cyrys J, Kunze S, Strauch K, Waldenberger M, Peters A. 2016. A genome-wide analysis of DNA methylation and fine particulate matter air pollution in three study populations: KORA F3, KORA F4, and the Normative Aging Study. Environ Health Perspect 124:983-990; http://dx.doi.org/10.1289/ehp.1509966.

Environmental public health dimensions of shale and tight gas development.

PubMed

Shonkoff, Seth B C; Hays, Jake; Finkel, Madelon L

2014-08-01

The United States has experienced a boom in natural gas production due to recent technological innovations that have enabled this resource to be produced from shale formations. We reviewed the body of evidence related to exposure pathways in order to evaluate the potential environmental public health impacts of shale gas development. We highlight what is currently known and identify data gaps and research limitations by addressing matters of toxicity, exposure pathways, air quality, and water quality. There is evidence of potential environmental public health risks associated with shale gas development. Several studies suggest that shale gas development contributes to ambient air concentrations of pollutants known to be associated with increased risk of morbidity and mortality. Similarly, an increasing body of studies suggest that water contamination risks exist through a variety of environmental pathways, most notably during wastewater transport and disposal, and via poor zonal isolation of gases and fluids due to structural integrity impairment of cement in gas wells. Despite a growing body of evidence, data gaps persist. Most important, there is a need for more epidemiological studies to assess associations between risk factors, such as air and water pollution, and health outcomes among populations living in close proximity to shale gas operations.

The Pathway for Oxygen: Tutorial Modelling on Oxygen Transport from Air to Mitochondrion

PubMed Central

Bassingthwaighte, James B.; Raymond, Gary M.; Dash, Ranjan K.; Beard, Daniel A.; Nolan, Margaret

2016-01-01

The ‘Pathway for Oxygen’ is captured in a set of models describing quantitative relationships between fluxes and driving forces for the flux of oxygen from the external air source to the mitochondrial sink at cytochrome oxidase. The intervening processes involve convection, membrane permeation, diffusion of free and heme-bound O2 and enzymatic reactions. While this system’s basic elements are simple: ventilation, alveolar gas exchange with blood, circulation of the blood, perfusion of an organ, uptake by tissue, and consumption by chemical reaction, integration of these pieces quickly becomes complex. This complexity led us to construct a tutorial on the ideas and principles; these first PathwayO2 models are simple but quantitative and cover: 1) a ‘one-alveolus lung’ with airway resistance, lung volume compliance, 2) bidirectional transport of solute gasses like O2 and CO2, 3) gas exchange between alveolar air and lung capillary blood, 4) gas solubility in blood, and circulation of blood through the capillary syncytium and back to the lung, and 5) blood-tissue gas exchange in capillaries. These open-source models are at Physiome.org and provide background for the many respiratory models there. PMID:26782201

Mediation pathways and effects of green structures on respiratory mortality via reducing air pollution

NASA Astrophysics Data System (ADS)

Shen, Yu-Sheng; Lung, Shih-Chun Candice

2017-02-01

Previous studies have shown both health and environmental benefits of green spaces, especially in moderating temperature and reducing air pollution. However, the characteristics of green structures have been overlooked in previous investigations. In addition, the mediation effects of green structures on respiratory mortality have not been assessed. This study explores the potential mediation pathways and effects of green structure characteristics on respiratory mortality through temperature, primary and secondary air pollutants separately using partial least squares model with data from Taiwan. The measurable characteristics of green structure include the largest patch percentage, landscape proportion, aggregation, patch distance, and fragmentation. The results showed that mortality of pneumonia and chronic lower respiratory diseases could be reduced by minimizing fragmentation and increasing the largest patch percentage of green structure, and the mediation effects are mostly through reducing air pollutants rather than temperature. Moreover, a high proportion of but fragmented green spaces would increase secondary air pollutants and enhance health risks; demonstrating the deficiency of traditional greening policy with primary focus on coverage ratio. This is the first research focusing on mediation effects of green structure characteristics on respiratory mortality, revealing that appropriate green structure planning can be a useful complementary strategy in environmental health management.

Mediation pathways and effects of green structures on respiratory mortality via reducing air pollution.

PubMed

Shen, Yu-Sheng; Lung, Shih-Chun Candice

2017-02-23

Previous studies have shown both health and environmental benefits of green spaces, especially in moderating temperature and reducing air pollution. However, the characteristics of green structures have been overlooked in previous investigations. In addition, the mediation effects of green structures on respiratory mortality have not been assessed. This study explores the potential mediation pathways and effects of green structure characteristics on respiratory mortality through temperature, primary and secondary air pollutants separately using partial least squares model with data from Taiwan. The measurable characteristics of green structure include the largest patch percentage, landscape proportion, aggregation, patch distance, and fragmentation. The results showed that mortality of pneumonia and chronic lower respiratory diseases could be reduced by minimizing fragmentation and increasing the largest patch percentage of green structure, and the mediation effects are mostly through reducing air pollutants rather than temperature. Moreover, a high proportion of but fragmented green spaces would increase secondary air pollutants and enhance health risks; demonstrating the deficiency of traditional greening policy with primary focus on coverage ratio. This is the first research focusing on mediation effects of green structure characteristics on respiratory mortality, revealing that appropriate green structure planning can be a useful complementary strategy in environmental health management.

Understanding Potential Air Emissions from a Cellulosic Biorefinery Producing Renewable Diesel Blendstock.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yimin; Heath, Garvin A.; Renzaglia, Jason

2015-06-22

The Energy Independence and Security Act of 2007, through the Renewable Fuel Standard (RFS), mandates increased use of biofuels, including cellulosic biofuels. The RFS is expected to spur the development of advanced biofuel technologies (e.g., new and innovative biofuel conversion pathways) as well as the construction of biorefineries (refineries that produce biofuels) using these technologies. To develop sustainable cellulosic biofuels, one of the goals of the Bioenergy Technologies Office (BETO) at the Department of Energy is to minimize air pollutants from the entire biofuel supply chain, as stated in their 2014 Multi-Year Program Plan (2014). Although biofuels in general havemore » been found to have lower life cycle greenhouse gas (GHG) emissions compared to petroleum fuels on an energy basis, biomass feedstock production, harvesting, transportation, processing and conversion are expected to emit a wide range of other air pollutants (e.g., criteria air pollutants, hazardous air pollutants), which could affect the environmental benefits of biofuels when displacing petroleum fuels. While it is important for policy makers, air quality planners and regulators, biofuel developers, and investors to understand the potential implications on air quality from a growing biofuel industry, there is a general lack of information and knowledge about the type, fate and magnitude of potential air pollutant emissions from the production of cellulosic biofuels due to the nascent stage of this emerging industry. This analysis assesses potential air pollutant emissions from a hypothetical biorefinery, selected by BETO for further research and development, which uses a biological conversion process of sugars to hydrocarbons to produce infrastructural-compatible renewable diesel blendstock from cellulosic biomass.« less

Impact of cercal air currents on singing motor pattern generation in the cricket (Gryllus bimaculatus DeGeer)

PubMed Central

2015-01-01

The cercal system of crickets detects low-frequency air currents produced by approaching predators and self-generated air currents during singing, which may provide sensory feedback to the singing motor network. We analyzed the effect of cercal stimulation on singing motor pattern generation to reveal the response of a singing interneuron to predator-like signals and to elucidate the possible role of self-generated air currents during singing. In fictive singing males, we recorded an interneuron of the singing network while applying air currents to the cerci; additionally, we analyzed the effect of abolishing the cercal system in freely singing males. In fictively singing crickets, the effect of short air stimuli is either to terminate prematurely or to lengthen the interchirp interval, depending on their phase in the chirp cycle. Within our stimulation paradigm, air stimuli of different velocities and durations always elicited an inhibitory postsynaptic potential in the singing interneuron. Current injection in the singing interneuron elicited singing motor activity, even during the air current-evoked inhibitory input from the cercal pathway. The disruptive effects of air stimuli on the fictive singing pattern and the inhibitory response of the singing interneuron point toward the cercal system being involved in initiating avoidance responses in singing crickets, according to the established role of cerci in a predator escape pathway. After abolishing the activity of the cercal system, the timing of natural singing activity was not significantly altered. Our study provides no evidence that self-generated cercal sensory activity has a feedback function for singing motor pattern generation. PMID:26334014

Impact of ambient air pollution on obesity: a systematic review.

PubMed

An, Ruopeng; Ji, Mengmeng; Yan, Hai; Guan, Chenghua

2018-05-24

Over 80% of the global populations living in urban areas are exposed to air quality levels that exceed the World Health Organization limits. Air pollution may lead to unhealthy body weight through metabolic dysfunction, chronic disease onset, and disruption of regular physical activity. A literature search was conducted in the PubMed and Web of Science for peer-reviewed articles published until September 2017 that assessed the relationship between air pollution and body weight status. A standardized data extraction form was used to collect methodological and outcome variables from each eligible study. Sixteen studies met the selection criteria and were included in the review. They were conducted in seven countries, including the US (n = 9), China (n = 2), Canada (n = 1), Italy (n = 1), The Netherlands (n = 1), Serbia (n = 1), and South Korea (n = 1). Half of them adopted a longitudinal study design, and the rest adopted a cross-sectional study design. Commonly examined air pollutants included PM, NO 2 , SO 2 , O 3 , and overall air quality index. Among a total of 66 reported associations between air pollution and body weight status, 29 (44%) found air pollution to be positively associated with body weight, 29 (44%) reported a null finding, and the remaining eight (12%) found air pollution to be negatively associated with body weight. The reported associations between air pollution and body weight status varied by sex, age group, and type of air pollutant. Three pathways hypothesized in the selected studies were through increased oxidative stress and adipose tissue inflammation, elevated risk for chronic comorbidities, and insufficient physical activity. Concurrent evidence regarding the impact of air pollution on body weight status remains mixed. Future studies should assess the impact of severe air pollution on obesity in developing countries, focus on a homogenous population subgroup, and elucidate the biomedical and psychosocial pathways linking air pollution to body weight.

Analysis of organophosphate hydraulic fluids in U.S. Air force base soils

PubMed

David; Seiber

1999-04-01

Tri-aryl and tri-alkyl organophosphates (TAPs) have been used extensively as flame-retardant hydraulic fluids and fluid additives in commercial and military aircraft. Up to 80% of the consumption of these fluids has been estimated to be lost to unrecovered leakage. Tri-aryl phosphate components of these fluids are resistant to volatilization and solubilization in water, thus, their primary environmental fate pathway is sorption to soils. Environmental audits of military air bases generally do not include quantification of these compounds in soils. We have determined the presence and extent of TAP contamination in soil samples from several U.S. Air Force bases. Soils were collected, extracted, and analyzed using GC/FPD and GC/MS. Tricresyl phosphate was the most frequently found TAP in soil, ranging from 0.02 to 130 ppm. Other TAPs in soils included triphenyl phosphate and isopropylated triphenyl phosphate. Observations are made regarding the distribution, typical concentrations, persistence, and need for further testing of TAPs in soils at military installations. Additionally, GC and mass spectral data for these TAPs are presented, along with methods for their extraction, sample clean-up, and quantification.

The performance of spinel bulk-like oxygen-deficient CoGa2O4 as an air-cathode catalyst in microbial fuel cell

NASA Astrophysics Data System (ADS)

Liu, Di; Mo, Xiaoping; Li, Kexun; Liu, Yi; Wang, Junjie; Yang, Tingting

2017-08-01

Nano spinel bulk-like CoGa2O4 prepared via a facile hydrothermal method is used as a high efficient electrochemical catalyst in activated carbon (AC) air-cathode microbial fuel cell (MFC). The maximum power density of the modified MFC is 1911 ± 49 mW m-2, 147% higher than the MFC of untreated AC cathode. Transmission electron microscope (TEM) and X-ray diffraction (XRD) exhibit the morphology and crystal structure of CoGa2O4. Rotating disk electrode (RDE) confirms the four-electron pathway at the cathode during the oxygen reduction reaction (ORR). Thermogravimetric analysis (TGA) and X-ray photoelectron spectroscopy (XPS) illustrate that the high rate oxygen vacancy exist in the CoGa2O4. The oxygen vacancy of CoGa2O4 plays an important role in catalytic activity. In a word, the prepared nano spinel bulk-like CoGa2O4 provides an alternative to the costly Pt in air-cathode for power output.

Differential Expression of pro-inflammatory and oxidative stress mediators induced by nitrogen dioxide and ozone in primary human bronchial epithelial cells

EPA Science Inventory

CONTEXT: N02 and 03 are ubiquitous air toxicants capable of inducing lung damage to the respiratory epithelium. Due to their oxidizing capabilities, these pollutants have been proposed to target specific biological pathways, but few publications have compared the pathways activat...

PATHWAYS OF MERCURY EVASION FROM CONTAMINATED WETLANDS: A GLOBALLY IMPORTANT SOURCE OF ATMOSPHERIC MERCURY?

EPA Science Inventory

Mercury (Hg) is a globally occurring pollutant that bioaccumulates and persists in the environment. The global Hg cycle is highly dependant on air/water exchange, as it is one of the primary pathways to deliver Hg to the atmosphere. Although open water systems appear to be net...

Middle Latency Auditory Evoked Potential (MLAEP) in Workers with and without Tinnitus who are Exposed to Occupational Noise.

PubMed

dos Santos Filha, Valdete Alves Valentins; Samelli, Alessandra Giannella; Matas, Carla Gentile

2015-09-11

Tinnitus is an important occupational health concern, but few studies have focused on the central auditory pathways of workers with a history of occupational noise exposure. Thus, we analyzed the central auditory pathways of workers with a history of occupational noise exposure who had normal hearing threshold, and compared middle latency auditory evoked potential in those with and without noise-induced tinnitus. Sixty individuals (30 with and 30 without tinnitus) underwent the following procedures: anamnesis, immittance measures, pure-tone air conduction thresholds at all frequencies between 0.25-8 kHz, and middle latency auditory evoked potentials. Quantitative analysis of latencies and amplitudes of middle latency auditory evoked potential showed no significant differences between the groups with and without tinnitus. In the qualitative analysis, we found that both groups showed increased middle latency auditory evoked potential latencies. The study group had more alterations of the "both" type regarding the Na-Pa amplitude, while the control group had more "electrode effect" alterations, but these alterations were not significantly different when compared to controls. Individuals with normal hearing with or without tinnitus who are exposed to occupational noise have altered middle latency auditory evoked potential, suggesting impairment of the auditory pathways in cortical and subcortical regions. Although differences did not reach significance, individuals with tinnitus seemed to have more abnormalities in components of the middle latency auditory evoked potential when compared to individuals without tinnitus, suggesting alterations in the generation and transmission of neuroelectrical impulses along the auditory pathway.

Characterization of Changes in Gene Expression and Biochemical Pathways at Low Levels of Benzene Exposure

PubMed Central

Thomas, Reuben; Hubbard, Alan E.; McHale, Cliona M.; Zhang, Luoping; Rappaport, Stephen M.; Lan, Qing; Rothman, Nathaniel; Vermeulen, Roel; Guyton, Kathryn Z.; Jinot, Jennifer; Sonawane, Babasaheb R.; Smith, Martyn T.

2014-01-01

Benzene, a ubiquitous environmental pollutant, causes acute myeloid leukemia (AML). Recently, through transcriptome profiling of peripheral blood mononuclear cells (PBMC), we reported dose-dependent effects of benzene exposure on gene expression and biochemical pathways in 83 workers exposed across four airborne concentration ranges (from <1 ppm to >10 ppm) compared with 42 subjects with non-workplace ambient exposure levels. Here, we further characterize these dose-dependent effects with continuous benzene exposure in all 125 study subjects. We estimated air benzene exposure levels in the 42 environmentally-exposed subjects from their unmetabolized urinary benzene levels. We used a novel non-parametric, data-adaptive model selection method to estimate the change with dose in the expression of each gene. We describe non-parametric approaches to model pathway responses and used these to estimate the dose responses of the AML pathway and 4 other pathways of interest. The response patterns of majority of genes as captured by mean estimates of the first and second principal components of the dose-response for the five pathways and the profiles of 6 AML pathway response-representative genes (identified by clustering) exhibited similar apparent supra-linear responses. Responses at or below 0.1 ppm benzene were observed for altered expression of AML pathway genes and CYP2E1. Together, these data show that benzene alters disease-relevant pathways and genes in a dose-dependent manner, with effects apparent at doses as low as 100 ppb in air. Studies with extensive exposure assessment of subjects exposed in the low-dose range between 10 ppb and 1 ppm are needed to confirm these findings. PMID:24786086

Implications of alternative assumptions regarding future air pollution control in scenarios similar to the Representative Concentration Pathways

NASA Astrophysics Data System (ADS)

Chuwah, Clifford; van Noije, Twan; van Vuuren, Detlef P.; Hazeleger, Wilco; Strunk, Achim; Deetman, Sebastiaan; Beltran, Angelica Mendoza; van Vliet, Jasper

2013-11-01

The uncertain, future development of emissions of short-lived trace gases and aerosols forms a key factor for future air quality and climate forcing. The Representative Concentration Pathways (RCPs) only explore part of this range as they all assume that worldwide ambitious air pollution control policies will be implemented. In this study, we explore how different assumptions on future air pollution policy and climate policy lead to different concentrations of air pollutants for a set of RCP-like scenarios developed using the IMAGE model. These scenarios combine low and high air pollution variants of the scenarios with radiative forcing targets in 2100 of 2.6 W m-2 and 6.0 W m-2. Simulations using the global atmospheric chemistry and transport model TM5 for the present-day climate show that both climate mitigation and air pollution control policies have large-scale effects on pollutant concentrations, often of similar magnitude. If no further air pollution policies would be implemented, pollution levels could be considerably higher than in the RCPs, especially in Asia. Air pollution control measures could significantly reduce the warming by tropospheric ozone and black carbon and the cooling by sulphate by 2020, and in the longer term contribute to enhanced warming by methane. These effects tend to cancel each other on a global scale. According to our estimates the effect of the worldwide implementation of air pollution control measures on the total global mean direct radiative forcing in 2050 is +0.09 W m-2 in the 6.0 W m-2 scenario and -0.16 W m-2 in the 2.6 W m-2 scenario.

VOC SAMPLING IN THE WATER TABLE/CAPILLARY FRINGE AREA FOR ASSESSING IMPACT ON VAPOR INTRUSION AND INDOOR AIR QUALITY

EPA Science Inventory

Vapor intrusion has been determined to be a major pathway for increased indoor air contamination from volatile organic contaminants (VOCs) at certain contaminated sites. In order to properly assess vapor intrusion, it is important to adequately evaluate VOC concentrations in the...

Relationships between drought, heat and air humidity responses revealed by transcriptome-metabolome co-analysis.

PubMed

Georgii, Elisabeth; Jin, Ming; Zhao, Jin; Kanawati, Basem; Schmitt-Kopplin, Philippe; Albert, Andreas; Winkler, J Barbro; Schäffner, Anton R

2017-07-10

Elevated temperature and reduced water availability are frequently linked abiotic stresses that may provoke distinct as well as interacting molecular responses. Based on non-targeted metabolomic and transcriptomic measurements from Arabidopsis rosettes, this study aims at a systematic elucidation of relevant components in different drought and heat scenarios as well as relationships between molecular players of stress response. In combined drought-heat stress, the majority of single stress responses are maintained. However, interaction effects between drought and heat can be discovered as well; these relate to protein folding, flavonoid biosynthesis and growth inhibition, which are enhanced, reduced or specifically induced in combined stress, respectively. Heat stress experiments with and without supplementation of air humidity for maintenance of vapor pressure deficit suggest that decreased relative air humidity due to elevated temperature is an important component of heat stress, specifically being responsible for hormone-related responses to water deprivation. Remarkably, this "dry air effect" is the primary trigger of the metabolomic response to heat. In contrast, the transcriptomic response has a substantial temperature component exceeding the dry air component and including up-regulation of many transcription factors and protein folding-related genes. Data level integration independent of prior knowledge on pathways and condition labels reveals shared drought and heat responses between transcriptome and metabolome, biomarker candidates and co-regulation between genes and metabolic compounds, suggesting novel players in abiotic stress response pathways. Drought and heat stress interact both at transcript and at metabolite response level. A comprehensive, non-targeted view of this interaction as well as non-interacting processes is important to be taken into account when improving tolerance to abiotic stresses in breeding programs. Transcriptome and metabolome may respond with different extent to individual stress components. Their contrasting behavior in response to temperature stress highlights that the protein folding machinery effectively shields the metabolism from stress. Disentangling the complex relationships between transcriptome and metabolome in response to stress is an enormous challenge. As demonstrated by case studies with supporting evidence from additional data, the large dataset provided in this study may assist in determining linked genetic and metabolic features as candidates for future mechanistic analyses.

Role of oxidative stress in cardiovascular disease outcomes following exposure to ambient air pollution.

PubMed

Kelly, Frank J; Fussell, Julia C

2017-09-01

Exposure to ambient air pollution is associated with adverse cardiovascular outcomes. These are manifested through several, likely overlapping, pathways including at the functional level, endothelial dysfunction, atherosclerosis, pro-coagulation and alterations in autonomic nervous system balance and blood pressure. At numerous points within each of these pathways, there is potential for cellular oxidative imbalances to occur. The current review examines epidemiological, occupational and controlled exposure studies and research employing healthy and diseased animal models, isolated organs and cell cultures in assessing the importance of the pro-oxidant potential of air pollution in the development of cardiovascular disease outcomes. The collective body of data provides evidence that oxidative stress (OS) is not only central to eliciting specific cardiac endpoints, but is also implicated in modulating the risk of succumbing to cardiovascular disease, sensitivity to ischemia/reperfusion injury and the onset and progression of metabolic disease following ambient pollution exposure. To add to this large research effort conducted to date, further work is required to provide greater insight into areas such as (a) whether an oxidative imbalance triggers and/or worsens the effect and/or is representative of the consequence of disease progression, (b) OS pathways and cardiac outcomes caused by individual pollutants within air pollution mixtures, or as a consequence of inter-pollutant interactions and (c) potential protection provided by nutritional supplements and/or pharmacological agents with antioxidant properties, in susceptible populations residing in polluted urban cities. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

A mechanistic study of limonene oxidation products and pathways following cleaning activities

NASA Astrophysics Data System (ADS)

Carslaw, Nicola

2013-12-01

Indoor air pollution has caused increasing concern since the 1970s, when the advent of stricter energy efficiency measures lead to increased reports of building related symptoms. Cleaning activities have been linked to adverse health effects indoors, although it is unclear which of the components of cleaning products cause these reported health effects. This paper uses a detailed chemical model for indoor air chemistry, to identify the species formed at the highest concentrations following use of a limonene-based cleaning product. The explicit nature of the chemical mechanism also permits the key pathways to their formation to be identified. The results show that the key species in terms of gas-phase concentration are multi-functional carbonyl species including limonaldehyde, 4-acetyl-1-methyl-1-cyclohexene and other dicarbonyl species. The particle-phase was dominated by peroxide species. The predicted gas-phase concentrations for three limonene-oxidation products were compared to recently published human reference values, but found not to be high enough to cause concern for typical indoor conditions, or under high indoor ozone conditions. However, cleaning products contain a range of terpenes other than limonene, which could also produce some of the secondary products identified here, as well as more common species such as formaldehyde, glyoxal and hydrogen peroxide. A mechanistic pathway analysis shows that the secondary products formed through limonene oxidation indoors depend critically on the competition between ozone and hydroxyl radicals, such that indoor pollutant concentrations and composition could vary widely in different locations for a nominally similar residence and indoor activities. Future studies should focus on aiming to measure multi-functional carbonyl species indoors to help validate models, whilst human reference values are needed for many more relevant species indoors.

Maternal smoke exposure decreases mesenchymal proliferation and modulates Rho-GTPase-dependent actin cytoskeletal signaling in fetal lungs.

PubMed

Unachukwu, Uchenna; Trischler, Jordis; Goldklang, Monica; Xiao, Rui; D'Armiento, Jeanine

2017-06-01

The present study tested the hypothesis that maternal smoke exposure results in fetal lung growth retardation due to dysregulation in various signaling pathways, including the Wnt (wingless-related integration site)/β-catenin pathway. Pregnant female C57BL/6J mice were exposed to cigarette smoke (100-150 mg/m 3 ) or room air, and offspring were humanely killed on 12.5, 14.5, 16.5, and 18.5 d post coitum (dpc). We assessed lung stereology with Cavalieri estimation; apoptosis with proliferating cell nuclear antigen, TUNEL, and caspase assays; and gene expression with quantitative PCR (qPCR) and RNA sequencing on lung epithelium and mesenchyme retrieved by laser capture microdissection. Results demonstrated a significant decrease in body weight and lung volume of smoke-exposed embryos. At 16.5 dpc, the reduction in lung volume was due to loss of lung mesenchymal tissue correlating with a decrease in cell proliferation ( n = 10; air: 61.65% vs. smoke: 44.21%, P < 0.05). RNA sequence analysis demonstrated an alteration in the Wnt pathway, and qPCR confirmed an increased expression of secreted frizzled-related protein 1 (sFRP-1) [ n = 12; relative quantification (RQ) 1 vs. 2.33, P < 0.05] and down-regulation of Cyclin D1 ( n = 7; RQ 1 vs. 0.61, P < 0.05) in mesenchymal tissue. Furthermore, genome expression studies revealed a smoke-induced up-regulation of Rho-GTPase-dependent actin cytoskeletal signaling that can lead to loss of tissue integrity.-Unachukwu, U., Trischler, J., Goldklang, M., Xiao, R., D'Armiento, J. Maternal smoke exposure decreases mesenchymal proliferation and modulates Rho-GTPase-dependent actin cytoskeletal signaling in fetal lungs. © FASEB.

Risk-based indicators of Canadians' exposures to environmental carcinogens.

PubMed

Setton, Eleanor; Hystad, Perry; Poplawski, Karla; Cheasley, Roslyn; Cervantes-Larios, Alejandro; Keller, C Peter; Demers, Paul A

2013-02-12

Tools for estimating population exposures to environmental carcinogens are required to support evidence-based policies to reduce chronic exposures and associated cancers. Our objective was to develop indicators of population exposure to selected environmental carcinogens that can be easily updated over time, and allow comparisons and prioritization between different carcinogens and exposure pathways. We employed a risk assessment-based approach to produce screening-level estimates of lifetime excess cancer risk for selected substances listed as known carcinogens by the International Agency for Research on Cancer. Estimates of lifetime average daily intake were calculated using population characteristics combined with concentrations (circa 2006) in outdoor air, indoor air, dust, drinking water, and food and beverages from existing monitoring databases or comprehensive literature reviews. Intake estimates were then multiplied by cancer potency factors from Health Canada, the United States Environmental Protection Agency, and the California Office of Environmental Health Hazard Assessment to estimate lifetime excess cancer risks associated with each substance and exposure pathway. Lifetime excess cancer risks in excess of 1 per million people are identified as potential priorities for further attention. Based on data representing average conditions circa 2006, a total of 18 carcinogen-exposure pathways had potential lifetime excess cancer risks greater than 1 per million, based on varying data quality. Carcinogens with moderate to high data quality and lifetime excess cancer risk greater than 1 per million included benzene, 1,3-butadiene and radon in outdoor air; benzene and radon in indoor air; and arsenic and hexavalent chromium in drinking water. Important data gaps were identified for asbestos, hexavalent chromium and diesel exhaust in outdoor and indoor air, while little data were available to assess risk for substances in dust, food and beverages. The ability to track changes in potential population exposures to environmental carcinogens over time, as well as to compare between different substances and exposure pathways, is necessary to support comprehensive, evidence-based prevention policy. We used estimates of lifetime excess cancer risk as indicators that, although based on a number of simplifying assumptions, help to identify important data gaps and prioritize more detailed data collection and exposure assessment needs.

Implications of alternative assumptions regarding future air pollution control in RCP-like scenarios

NASA Astrophysics Data System (ADS)

Chuwah, Clifford; van Noije, Twan; van Vuuren, Detlef; Hazeleger, Wilco; Strunk, Achim; Deetman, Sebastiaan; Mendoza Beltran, Angelica; van Vliet, Jasper

2013-04-01

Estimation of future emissions of short-lived trace gases and aerosols from human activities is a main source of uncertainty in projections of future air quality and climate forcing. The Representative Concentration Pathways (RCPs), however, all assume that worldwide ambitious air pollution control policies will be implemented in the coming decades. In this study, we therefore explore the consequences of four alternative emission scenarios generated using the IMAGE integrated assessment model following the methods used to generate the RCPs. These scenarios combine low and high air pollution variants of the scenarios with radiative forcing targets in 2100 of 2.6 W/m2 and 6.0 W/m2 (the high air pollution variants assume no improvement in emission factors, representing a hypothetical upper end of emission levels). Analysis using the global atmospheric chemistry and transport model TM5 shows that climate mitigation and air pollution control policy variants studied here have similar large-scale effects on the concentrations of ozone and black carbon; the impact of climate policy, however, has a stronger impact on sulphate concentrations. Air pollution control measures could significantly reduce the warming by tropospheric ozone and black carbon and the cooling by sulphate already in 2020, and on the longer term contribute to enhanced warming by methane. These effects tend to cancel each other at the global scale. According to our estimates the effect of the worldwide implementation of air pollution control measures on the total global mean direct radiative forcing in 2050 is +0.09 W/m2 in the 6.0 W/m2 scenario and -0.16 W/m2 in the 2.6 W/m2 scenario.

Airline Baggage as a Pathway for Alien Insect Species Invading the United States

Treesearch

Andrew M. Liebhold; Timothy T. Work; Deborah G. McCullough; Joseph F. Cavey; Joseph F. Cavey

2006-01-01

Invasions by non-indigenous species are a problem of increasing magnitude and threaten the stability of the world's ecosystems and economies. Despite the enormity of this problem, relatively little is known about the importance of various invasion pathways. Using historical records of interceptions of alien insects in air passenger baggage by USDA inspectors, we...

Asthmatics exhibit altered oxylipin profiles compared to healthy individuals after subway air exposure.

PubMed

Lundström, Susanna L; Levänen, Bettina; Nording, Malin; Klepczynska-Nyström, Anna; Sköld, Magnus; Haeggström, Jesper Z; Grunewald, Johan; Svartengren, Magnus; Hammock, Bruce D; Larsson, Britt-Marie; Eklund, Anders; Wheelock, Åsa M; Wheelock, Craig E

2011-01-01

Asthma is a chronic inflammatory lung disease that causes significant morbidity and mortality worldwide. Air pollutants such as particulate matter (PM) and oxidants are important factors in causing exacerbations in asthmatics, and the source and composition of pollutants greatly affects pathological implications. This randomized crossover study investigated responses of the respiratory system to Stockholm subway air in asthmatics and healthy individuals. Eicosanoids and other oxylipins were quantified in the distal lung to provide a measure of shifts in lipid mediators in association with exposure to subway air relative to ambient air. Sixty-four oxylipins representing the cyclooxygenase (COX), lipoxygenase (LOX) and cytochrome P450 (CYP) metabolic pathways were screened using liquid chromatography-tandem mass spectrometry (LC-MS/MS) of bronchoalveolar lavage (BAL)-fluid. Validations through immunocytochemistry staining of BAL-cells were performed for 15-LOX-1, COX-1, COX-2 and peroxisome proliferator-activated receptor gamma (PPARγ). Multivariate statistics were employed to interrogate acquired oxylipin and immunocytochemistry data in combination with patient clinical information. Asthmatics and healthy individuals exhibited divergent oxylipin profiles following exposure to ambient and subway air. Significant changes were observed in 8 metabolites of linoleic- and α-linolenic acid synthesized via the 15-LOX pathway, and of the COX product prostaglandin E(2) (PGE(2)). Oxylipin levels were increased in healthy individuals following exposure to subway air, whereas asthmatics evidenced decreases or no change. Several of the altered oxylipins have known or suspected bronchoprotective or anti-inflammatory effects, suggesting a possible reduced anti-inflammatory response in asthmatics following exposure to subway air. These observations may have ramifications for sensitive subpopulations in urban areas.

Strategie de commande pour un systeme hybride eolien diesel avec stockage d'air comprime =

NASA Astrophysics Data System (ADS)

Perron, Francois

The electrical energy provisioning of isolated sites requires a steady supply of diesel fuel which represents a significant logistical and economic burden. The main objective of this project is to propose a control strategy for an air storage wind diesel hybrid system (SHEDAC) and to evaluate its fuel reduction potential for a given site. This research is conducted within a result validation context. It encompasses the combination of a wind speed and load modeling on an isolated village including a SHEDAC model and the results are tailored to this specific site. Because the pneumatic hybridation of an otherwise unmodified diesel engine is at the core of the suggested approach, a detailed thermodynamic model of the engine behavior as well as a comprehensive friction analysis of its components is presented. Simulation results show that the energy recovery from the pneumatic pathway of the motor is counter productive and an alternative configuration involving an air turbine is proposed. The study of this modified SHEDAC is performed with a specific focus on the efficiency of the compressed air recovery path in an effort to make it as general as possible. Fuel consumption reductions of 49% could be achieved with this system while the recovery efficiency was etaair = 0.5.

DIDEM - An integrated model for comparative health damage costs calculation of air pollution

NASA Astrophysics Data System (ADS)

Ravina, Marco; Panepinto, Deborah; Zanetti, Maria Chiara

2018-01-01

Air pollution represents a continuous hazard to human health. Administration, companies and population need efficient indicators of the possible effects given by a change in decision, strategy or habit. The monetary quantification of health effects of air pollution through the definition of external costs is increasingly recognized as a useful indicator to support decision and information at all levels. The development of modelling tools for the calculation of external costs can provide support to analysts in the development of consistent and comparable assessments. In this paper, the DIATI Dispersion and Externalities Model (DIDEM) is presented. The DIDEM model calculates the delta-external costs of air pollution comparing two alternative emission scenarios. This tool integrates CALPUFF's advanced dispersion modelling with the latest WHO recommendations on concentration-response functions. The model is based on the impact pathway method. It was designed to work with a fine spatial resolution and a local or national geographic scope. The modular structure allows users to input their own data sets. The DIDEM model was tested on a real case study, represented by a comparative analysis of the district heating system in Turin, Italy. Additional advantages and drawbacks of the tool are discussed in the paper. A comparison with other existing models worldwide is reported.

Structural equation modeling of PAHs in ambient air, dust fall, soil, and cabbage in vegetable bases of Northern China.

PubMed

Zhang, YunHui; Hou, DeYi; Xiong, GuanNan; Duan, YongHong; Cai, ChuanYang; Wang, Xin; Li, JingYa; Tao, Shu; Liu, WenXin

2018-08-01

A series of field samples including ambient air (gaseous and particulate phases), dust fall, surface soil, rhizosphere soil and cabbage tissues (leaf, root and core), were collected in vegetable bases near a large coking manufacturer in Shanxi Province, Northern China, during a harvest season. A factor analysis was employed to apportion the emission sources of polycyclic aromatic hydrocarbons (PAHs), and the statistical results indicated coal combustion was the dominant emission source that accounted for different environmental media and cabbage tissues, while road traffic, biomass burning and the coking industry contributed to a lesser extent. A structural equation model was first developed to quantitatively explore the transport pathways of PAHs from surrounding media to cabbage tissues. The modeling results showed that PAHs in ambient air were positively associated with those in dust fall, and a close relationship was also true for PAHs in dust fall and in surface soil due to air-soil exchange process. Furthermore, PAHs in surface soil were correlated with those in rhizosphere soil and in the cabbage leaf with the path coefficients of 0.83 and 0.39, respectively. PAHs in the cabbage leaf may dominantly contribute to the accumulation of PAHs in the edible part of cabbages. Copyright © 2018 Elsevier Ltd. All rights reserved.

Identification of aerosol types over an urban site based on air-mass trajectory classification

NASA Astrophysics Data System (ADS)

Pawar, G. V.; Devara, P. C. S.; Aher, G. R.

2015-10-01

Columnar aerosol properties retrieved from MICROTOPS II Sun Photometer measurements during 2010-2013 over Pune (18°32‧N; 73°49‧E, 559 m amsl), a tropical urban station in India, are analyzed to identify aerosol types in the atmospheric column. Identification/classification is carried out on the basis of dominant airflow patterns, and the method of discrimination of aerosol types on the basis of relation between aerosol optical depth (AOD500 nm) and Ångström exponent (AE, α). Five potential advection pathways viz., NW/N, SW/S, N, SE/E and L have been identified over the observing site by employing the NOAA-HYSPLIT air mass back trajectory analysis. Based on AE against AOD500 nm scatter plot and advection pathways followed five major aerosol types viz., continental average (CA), marine continental average (MCA), urban/industrial and biomass burning (UB), desert dust (DD) and indeterminate or mixed type (MT) have been identified. In winter, sector SE/E, a representative of air masses traversed over Bay of Bengal and Eastern continental Indian region has relatively small AOD (τpλ = 0.43 ± 0.13) and high AE (α = 1.19 ± 0.15). These values imply the presence of accumulation/sub-micron size anthropogenic aerosols. During pre-monsoon, aerosols from the NW/N sector have high AOD (τpλ = 0.61 ± 0.21), and low AE (α = 0.54 ± 0.14) indicating an increase in the loading of coarse-mode particles over Pune. Dominance of UB type in winter season for all the years (i.e. 2010-2013) may be attributed to both local/transported aerosols. During pre-monsoon seasons, MT is the dominant aerosol type followed by UB and DD, while the background aerosols are insignificant.

Potential Impacts of Future Climate Change on Regional Air Quality and Public Health over China

NASA Astrophysics Data System (ADS)

Hong, C.; Zhang, Q.; Zhang, Y.; He, K.

2017-12-01

Future climate change would affect public health through changing air quality. Climate extremes and poor weather conditions are likely to occur at a higher frequency in China under a changing climate, but the air pollution-related health impacts due to future climate change remain unclear. Here the potential impacts of future climate change on regional air quality and public health over China is projected using a coupling of climate, air quality and epidemiological models. We present the first assessment of China's future air quality in a changing climate under the Representative Concentration Pathway 4.5 (RCP4.5) scenario using the dynamical downscaling technique. In RCP4.5 scenario, we estimate that climate change from 2006-2010 to 2046-2050 is likely to adversely affect air quality covering more than 86% of population and 55% of land area in China, causing an average increase of 3% in O3 and PM2.5 concentrations, which are found to be associated with the warmer climate and the more stable atmosphere. Our estimate of air pollution-related mortality due to climate change in 2050 is 26,000 people per year in China. Of which, the PM2.5-related mortality is 18,700 people per year, and the O3-related mortality is 7,300 people per year. The climate-induced air pollution and health impacts vary spatially. The climate impacts are even more pronounced on the urban areas where is densely populated and polluted. 90% of the health loss is concentrated in 20% of land areas in China. We use a simple statistical analysis method to quantify the contributions of climate extremes and find more intense climate extremes play an important role in climate-induced air pollution-related health impacts. Our results indicate that global climate change will likely alter the level of pollutant management required to meet future air quality targets as well as the efforts to protect public health in China.

TEMPORAL-SPATIAL ANALYSIS OF U.S.- MEXICO BORDER ENVIRONMENTAL FINE AND COARSE PM AIR SAMPLE EXTRACT ACTIVITY IN HUMAN BRONCHIAL EPITHELIAL CELLS

PubMed Central

Lauer, Fredine T.; Mitchell, Leah A.; Bedrick, Edward; McDonald, Jacob D.; Lee, Wen-Yee; Li, Wen-Whai; Olvera, Hector; Amaya, Maria A.; Berwick, Marianne; Gonzales, Melissa; Currey, Robert; Pingitore, Nicholas E.; Burchiel, Scott W.

2009-01-01

Particulate matter less than 10 μm (PM10) has been shown to be associated with aggravation of asthma and respiratory and cardiopulmonary morbidity. There is also great interest in the potential health effects of PM 2.5. Particulate matter (PM) varies in composition both spatially and temporally depending on the source, location and seasonal condition. El Paso County which lies in the Paso del Norte airshed is a unique location to study ambient air pollution due to three major points: the geological land formation, the relatively large population and the various sources of PM. In this study, dichotomous filters were collected from various sites in El Paso County every seven days for a period of one year. The sampling sites were both distant and near border crossings, which are near heavily populated areas with high traffic volume. Fine (PM2.5) and Coarse (PM10-2.5) PM filter samples were extracted using dichloromethane and were assessed for biologic activity and polycyclic aromatic (PAH) content. Three sets of marker genes human BEAS2B bronchial epithelial cells were utilized to assess the effects of airborne PAHs on biologic activities associated with specific biological pathways associated with airway diseases. These pathways included in inflammatory cytokine production (IL-6, IL-8), oxidative stress (HMOX-1, NQO-1, ALDH3A1, AKR1C1), and aryl hydrocarbon receptor (AhR)-dependent signaling (CYP1A1). Results demonstrated interesting temporal and spatial patterns of gene induction for all pathways, particularly those associated with oxidative stress, and significant differences in the PAHs detected in the PM10-2.5 and PM 2.5 fractions. Temporally, the greatest effects on gene induction were observed in winter months, which appeared to correlate with inversions that are common in the air basin. Spatially, the greatest gene expression increases were seen in extracts collected from the central most areas of El Paso which are also closest to highways and border crossings. PMID:19410595

NO2 inhalation causes tauopathy by disturbing the insulin signaling pathway.

PubMed

Yan, Wei; Ku, Tingting; Yue, Huifeng; Li, Guangke; Sang, Nan

2016-12-01

Air pollution has been evidenced as a risk factor for neurodegenerative tauopathies. NO 2 , a primary component of air pollution, is negatively linked to neurodegenerative disorders, but its independent and direct association with tau lesion remains to be elucidated. Considering the fact that the insulin signaling pathway can be targeted by air pollutants and regulate tau function, this study focused on the role of insulin signaling in this NO 2 -induced tauopathy. Using a dynamic inhalation treatment, we demonstrated that exposure to NO 2 induced a disruption of insulin signaling in skeletal muscle, liver, and brain, with associated p38 MAPK and/or JNK activation. We also found that in parallel with these kinase signaling cascades, the compensatory hyperinsulinemia triggered by whole-body insulin resistance (IR) further attenuated the IRS-1/AKT/GSK-3β signaling pathway in the central nervous system, which consequently increased the phosphorylation of tau and reduced the expression of synaptic proteins that contributed to the development of the tau pathology. These findings provide new insight into the possible mechanisms involved in the etiopathogenesis of NO 2 -induced tauopathy, suggesting that the targeting of insulin signaling may be a promising therapeutic strategy to prevent this disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

Installation Restoration Program. Preliminary Assessment for the 153rd Tactical Airlift Group, Wyoming Air National Guard, Cheyenne Municipal Airport, Cheyenne, Wyoming

DTIC Science & Technology

1988-03-01

Cheyenne area is characterized by semi-arid conditions and large diurnal and annual temperature changes. The summers are generally warm with humidity...contaminants through pathways (groundwater, surface water, soil, and air). MIOCENE - An epoch of the upper Tertiary period, after the Oligocene and before the

The injury of fine particulate matter from cooking oil fumes on umbilical cord blood vessels in vitro.

PubMed

Hou, Lijuan; Zhang, Jian; Zhang, Chao; Xu, Yachun; Zhu, Xiaoxia; Yao, Cijiang; Liu, Ying; Li, Tao; Cao, Jiyu

2017-01-01

Cooking oil fumes (COFs) derived PM 2.5 is the major source of indoor air pollution in Asia. For this, a pregnant rat model within different doses of cooking oil fumes (COFs) derived PM 2.5 was established in pregnancy in our research. Our previous studies have showed that exposure to COFs-derived PM 2.5 was related to adverse pregnancy outcomes. However, the mechanisms of signaling pathways remain unknown. Therefore, this study aimed to investigate the underlying mechanisms induced by COFs-derived PM2.5 injury on umbilical cord blood vessels (UCs) in vitro. Exposure to COFs-derived PM 2.5 resulted in changing the expression of eNOS, ET-1, ETRA, and ETRB. In additions, western blot analysis indicated that the HIF-1α/iNOS/NO signaling pathway and VEGF/VEGFR1/iNOS signaling pathway were involved in UCs injury triggered by COFs-derived PM 2.5 . In conclusion, our data suggested that exposure to COFs-derived PM 2.5 resulted in increasing of oxidative stress and inflammation, as well as dysfunction of UCs. Copyright © 2016 Elsevier B.V. All rights reserved.

Evidence for non-linear metabolism at low benzene exposures? A reanalysis of data.

PubMed

McNally, K; Sams, C; Loizou, G D; Jones, K

2017-12-25

The presence of a high-affinity metabolic pathway for low level benzene exposures of less than one part per million (ppm) has been proposed although a pathway has not been identified. The variation of metabolite molar fractions with increasing air benzene concentrations was suggested as evidence of significantly more efficient benzene metabolism at concentrations <0.1 ppm The evidence for this pathway is predicated on a rich data set from a study of Chinese shoe workers exposed to a wide range of benzene concentrations (not just "low level"). In this work we undertake a further independent re-analysis of this data with a focus on the evidence for an increase in the rate of metabolism of benzene exposures of less than 1 ppm. The analysis dataset consisted of measurements of benzene and toluene from personal air samplers, and measurements of unmetabolised benzene and toluene and five metabolites (phenol hydroquinone, catechol, trans, trans-muconic acid and s-phenylmercapturic acid) from post-shift urine samples for 213 workers with an occupational exposure to benzene (and toluene) and 139 controls. Measurements from control subjects were used to estimate metabolite concentrations resulting from non-occupational sources, including environmental sources of benzene. Data from occupationally exposed subjects were used to estimate metabolite concentrations as a function of benzene exposure. Correction for background (environmental exposure) sources of metabolites was achieved through a comparison of geometric means in occupationally exposed and control populations. The molar fractions of the five metabolites as a function of benzene exposure were computed. A supra-linear relationship between metabolite concentrations and benzene exposure was observed over the range 0.1-10 ppm benzene, however over the range benzene exposures of between 0.1 and 1 ppm only a modest departure from linearity was observed. The molar fractions estimated in this work were near constant over the range 0.1-10 ppm. No evidence of high affinity metabolism at these low level exposures was observed. Our reanalysis brings in to question the appropriateness of the dataset for commenting on low dose exposures and the use of a purely statistical approach to the analysis. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Potential Impacts of two SO2 oxidation pathways on regional sulfate concentrations: acqueous-hase oxidation by NO2 and gas-phase oxidation by Stabilized Criegee Intermediates

EPA Science Inventory

We examine the potential impacts of two additional sulfate production pathways using the Community Multiscale Air Quality modeling system. First we evaluate the impact of the aqueous-phase oxidation of S(IV) by nitrogen dioxide using two published rate constants, differing by 1-2...

Evaluating officially reported polycyclic aromatic hydrocarbon emissions in the Athabasca oil sands region with a multimedia fate model.

PubMed

Parajulee, Abha; Wania, Frank

2014-03-04

Emissions of organic substances with potential toxicity to humans and the environment are a major concern surrounding the rapid industrial development in the Athabasca oil sands region (AOSR). Although concentrations of polycyclic aromatic hydrocarbons (PAHs) in some environmental samples have been reported, a comprehensive picture of organic contaminant sources, pathways, and sinks within the AOSR has yet to be elucidated. We sought to use a dynamic multimedia environmental fate model to reconcile the emissions and residue levels reported for three representative PAHs in the AOSR. Data describing emissions to air compiled from two official sources result in simulated concentrations in air, soil, water, and foliage that tend to fall close to or below the minimum measured concentrations of phenanthrene, pyrene, and benzo(a)pyrene in the environment. Accounting for evaporative emissions (e.g., from tailings pond disposal) provides a more realistic representation of PAH distribution in the AOSR. Such indirect emissions to air were found to be a greater contributor of PAHs to the AOSR atmosphere relative to reported direct emissions to air. The indirect pathway transporting uncontrolled releases of PAHs to aquatic systems via the atmosphere may be as significant a contributor of PAHs to aquatic systems as other supply pathways. Emission density estimates for the three PAHs that account for tailings pond disposal are much closer to estimated global averages than estimates based on the available emissions datasets, which fall close to the global minima. Our results highlight the need for improved accounting of PAH emissions from oil sands operations, especially in light of continued expansion of these operations.

Signaling Pathways Involved in Lunar Dust Induced Cytotoxicity

NASA Technical Reports Server (NTRS)

Zhang, Ye; Lam, Chiu-Wing; Scully, Robert R.; Williams, Kyle; Zalesak, Selina; Wu, Honglu; James, John T.

2014-01-01

The Moon's surface is covered by a layer of fine, reactive dust. Lunar dust contain about 1-2% of very fine dust (< 3 micron), that is respirable. The habitable area of any lunar landing vehicle and outpost would inevitably be contaminated with lunar dust that could pose a health risk. The purpose of the study is to evaluate the toxicity of Apollo moon dust in rodents to assess the health risk of dust exposures to humans. One of the particular interests in the study is to evaluate dust-induced changes of the expression of fibrosis-related genes, and to identify specific signaling pathways involved in lunar dust-induced toxicity. F344 rats were exposed for 4 weeks (6h/d; 5d/wk) in nose-only inhalation chambers to concentrations of 0 (control air), 2.1, 6.1, 21, and 61 mg/m(exp 3) of lunar dust. Five rats per group were euthanized 1 day, 1 week, 1 month, and 3 months after the last inhalation exposure. The total RNAs were isolated from the blood or lung tissue after being lavaged, using the Qigen RNeasy kit. The Rat Fibrosis RT2 Profile PCR Array was used to profile the expression of 84 genes relevant to fibrosis. The genes with significant expression changes are identified and the gene expression data were further analyzed using IPA pathway analysis tool to determine the signaling pathways with significant changes.

Toward Understanding the Genetic Basis of Yak Ovary Reproduction: A Characterization and Comparative Analyses of Estrus Ovary Transcriptiome in Yak and Cattle

PubMed Central

Huang, Cai; Mipam, Tserang Donko; Li, Jian

2016-01-01

Background Yaks (Bos grunniens) are endemic species that can adapt well to thin air, cold temperatures, and high altitude. These species can survive in harsh plateau environments and are major source of animal production for local residents, being an important breed in the Qinghai–Tibet Plateau. However, compared with ordinary cattle that live in the plains, yaks generally have lower fertility. Investigating the basic physiological molecular features of yak ovary and identifying the biological events underlying the differences between the ovaries of yak and plain cattle is necessary to understand the specificity of yak reproduction. Therefore, RNA-seq technology was applied to analyze transcriptome data comparatively between the yak and plain cattle estrous ovaries. Results After deep sequencing, 3,653,032 clean reads with a total of 4,828,772,880 base pairs were obtained from yak ovary library. Alignment analysis showed that 16992 yak genes mapped to the yak genome, among which, 12,731 and 14,631 genes were assigned to Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, comparison of yak and cattle ovary transcriptome data revealed that 1307 genes were significantly and differentially expressed between the two libraries, wherein 661 genes were upregulated and 646 genes were downregulated in yak ovary. Functional analysis showed that the differentially expressed genes were involved in various Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. GO annotations indicated that the genes related to “cell adhesion,” “hormonal” biological processes, and “calcium ion binding,” “cation transmembrane transport” molecular events were significantly active. KEGG pathway analysis showed that the “complement and coagulation cascade” pathway was the most enriched in yak ovary transcriptome data, followed by the “cytochrome P450” related and “ECM–receptor interaction” pathways. Moreover, several novel pathways, such as “circadian rhythm,” were significantly enriched despite having no evident associations with the reproductive function. Conclusion Our findings provide a molecular resource for further investigation of the general molecular mechanism of yak ovary and offer new insights to understand comprehensively the specificity of yak reproduction. PMID:27044040

Low-temperature, mineral-catalyzed air oxidation: a possible new pathway for PAH stabilization in sediments and soils.

PubMed

Ghislain, Thierry; Faure, Pierre; Biache, Coralie; Michels, Raymond

2010-11-15

Reactivity of polycyclic aromatic hydrocarbons (PAHs) in the subsurface is of importance to environmental assessment, as they constitute a highly toxic hazard. Understanding their reactivity in the long term in natural recovering systems is thus a key issue. This article describes an experimental investigation on the air oxidation of fluoranthene (a PAH abundant in natural systems polluted by industrial coal use) at 100°C on different mineral substrates commonly found in soils and sediments (quartz sand, limestone, and clay). Results demonstrate that fluoranthene is readily oxidized in the presence of limestone and clay, leading to the formation of high molecular weight compounds and a carbonaceous residue as end product especially for clay experiments. As demonstrated elsewhere, the experimental conditions used permitted the reproduction of the geochemical pathway of organic matter observed under natural conditions. It is therefore suggested that low-temperature, mineral-catalyzed air oxidation is a mechanism relevant to the stabilization of PAHs in sediments and soils.

Role of air on local water retention behavior in the shallow heterogeneous vadose zone

NASA Astrophysics Data System (ADS)

Sakaki, T.; Limsuwat, A.; Illangasekare, T. H.

2009-12-01

In the presence of a subsurface source, air flowing through the unsaturated soil can transport toxic vapor into subsurface structures due to pressure gradients created by, e.g., a pressure drop within the building. Development of dynamic air pathways in the subsurface are largely controlled by the geological heterogeneity and the spatial and temporal distribution of soil moisture. To better understand how these air pathways are developed, it is crucial to know how water is retained in heterogeneous medium at spatial resolutions that are finer than those adopted in typical hydrologic and soil physics applications. Although methods for soil water pressure measurement can be readily found in literature, a technique for measuring “air pressure” in wet soil is not well-established or documented. Hydrophobic porous ceramic cups have been used to measure non-wetting NAPL phase pressure in two-phase systems. However, our preliminary tests using the hydrophobic ceramic cups installed in highly wet soil showed that under conditions of fast drainage of the wetting fluid that is replaced by air, it typically took some time before the cups responded to register the air pressure. Therefore, an attempt was made to develop a more robust method where the time lag is minimized. The tested materials were; 1) ceramic porous cups, 2) sintered stainless steel cups, 3) porous glass discs, and 4) non-woven PTFE fabric. The ceramic cups, sintered stainless steel cups and sintered porous glass discs required hydrophobic treatment, whereas the non-woven PTFE fabric is hydrophobic by itself. To treat the ceramic porous cups, the method proposed by Parker and Lenhard [1988] was adopted. The sintered porous stainless steel cups and porous glass discs were treated by a commercially available water repellant compound. For those four materials, contact angle, water entry pressure, and time lag to respond to an imposed pressure were measured. The best performing material was then tested in a simple heterogeneous column. The column was packed using two sands to form three layers where the coarser sand was sandwitched by two layers of a finer sand. In each layer, soil moisture, water pressure and air pressure were monitored. The soil was initially saturated and suction at the bottom was gradually increased to induce wetting fluid drainage, and followed by a wetting cycle. In the drainage cycle, the coarse middle layer did not drain until air front reached the bottom of the top fine layer. Once the air front reached the fine-coarse interface, air was quickly pulled into the coarse layer. The results showed that the newly developed hydrophobic material showed very small time lag and captured the abrupt air pressure change in the wet soil. In the wetting cycle, we observed positive air pressure which indicated entrapment of air and its compression as wetting proceeded. This behavior cannot be evaluated properly without the rapid measurement of air pressure. The method is currently being applied in a large 2D vertical aquifer with a structured heterogeneity to investigate how air pathways are formed under various flux/temperature conditions at the soil surface.

Asthmatics Exhibit Altered Oxylipin Profiles Compared to Healthy Individuals after Subway Air Exposure

PubMed Central

Nording, Malin; Klepczynska-Nyström, Anna; Sköld, Magnus; Haeggström, Jesper Z.; Grunewald, Johan; Svartengren, Magnus; Hammock, Bruce D.; Larsson, Britt-Marie; Eklund, Anders; Wheelock, Åsa M.; Wheelock, Craig E.

2011-01-01

Background Asthma is a chronic inflammatory lung disease that causes significant morbidity and mortality worldwide. Air pollutants such as particulate matter (PM) and oxidants are important factors in causing exacerbations in asthmatics, and the source and composition of pollutants greatly affects pathological implications. Objectives This randomized crossover study investigated responses of the respiratory system to Stockholm subway air in asthmatics and healthy individuals. Eicosanoids and other oxylipins were quantified in the distal lung to provide a measure of shifts in lipid mediators in association with exposure to subway air relative to ambient air. Methods Sixty-four oxylipins representing the cyclooxygenase (COX), lipoxygenase (LOX) and cytochrome P450 (CYP) metabolic pathways were screened using liquid chromatography-tandem mass spectrometry (LC-MS/MS) of bronchoalveolar lavage (BAL)-fluid. Validations through immunocytochemistry staining of BAL-cells were performed for 15-LOX-1, COX-1, COX-2 and peroxisome proliferator-activated receptor gamma (PPARγ). Multivariate statistics were employed to interrogate acquired oxylipin and immunocytochemistry data in combination with patient clinical information. Results Asthmatics and healthy individuals exhibited divergent oxylipin profiles following exposure to ambient and subway air. Significant changes were observed in 8 metabolites of linoleic- and α-linolenic acid synthesized via the 15-LOX pathway, and of the COX product prostaglandin E2 (PGE2). Oxylipin levels were increased in healthy individuals following exposure to subway air, whereas asthmatics evidenced decreases or no change. Conclusions Several of the altered oxylipins have known or suspected bronchoprotective or anti-inflammatory effects, suggesting a possible reduced anti-inflammatory response in asthmatics following exposure to subway air. These observations may have ramifications for sensitive subpopulations in urban areas. PMID:21897859

Mice exposed in situ to urban air pollution exhibit pulmonary alterations in gene expression in the lipid droplet synthesis pathways.

PubMed

Rowan-Carroll, Andrea; Halappanavar, Sabina; Williams, Andrew; Somers, Christophers M; Yauk, Carole L

2013-05-01

It is clear that particulate air pollution poses a serious risk to human health; however, the underlying mechanisms are not completely understood. We investigated pulmonary transcriptional responses in mice following in-situ exposure to ambient air in a heavily industrialized urban environment. Mature C57BL/CBA male mice were caged in sheds near two working steel mills and a major highway in Hamilton, Ontario, Canada in the spring/summer of 2004. Control mice were housed in the same environment, but received only high-efficiency particle filtered air (HEPA). Whole lung tissues were collected from mice exposed for 3, 10, or for 10 weeks followed by 6 weeks recovery in the laboratory (16 weeks). DNA microarrays were used to profile changes in pulmonary gene expression. Transcriptional profiling revealed changes in the expression of genes implicated in the lipid droplet synthesis (Plin I, Dgat2, Lpl, S3-12, and Agpat2), and antioxidant defense (Ucp1) pathways in mice breathing unfiltered air. We postulate that exposure to urban air, containing an abundance of particulate matter adsorbed with polycyclic aromatic hydrocarbons, triggers lipid droplet (holding depots for lipids and malformed/excess proteins tagged for degradation) synthesis in the lungs, which may act to sequester particulates. Increased lipid droplet synthesis could lead to endogenous/stressor-induced production of reactive oxygen species and activation of antioxidant mechanisms. Further investigation into the stimulation of lipid droplet synthesis in the lung in response to air pollution and the resulting health implications is warranted. Copyright © 2013 Wiley Periodicals, Inc.

Investigation of molecular metabolites in expired air of healthy man in condition of long-term isolation in hermetical confined environment

NASA Astrophysics Data System (ADS)

Tsarkov, Dmitriy; Mardanov, Robert; Markin, Andrey; Moukhamedieva, Lana

Investigation of intermediary metabolites, produced in cells, in expired air of healthy man is directed on determination of molecular markers which are reflecting normal physiological pro-cesses in an organism, as well as on determination and validation of biomarkers for objective screening and non-invasive prenosological diagnostics of disorders in metabolic processes caused by negative effect of live environment. Investigation of influence of long-term isolation in her-metical confined environment on composition of healthy human expired air was made during experiment with 105 days isolation in condition of controlled environment and standard food ra-tion. Expired air samples were analyzed on gas chromatograph associated with the quadrupole mass spectrometer. The investigation results show that at rest hydroxy ketones, mostly 1-hydroxy-prorapanone-2 (acetol), aldehydes (decenal, benzaldehyde), acetophenone, phenol and fatty acids were determined. After physical performance (oxidative stress) the content of ke-tones (heptanone-2, heptanone-3), phenol, determined aldehydes (decenal, octadecenal) and acetol in expired air of volunteers decreased. It can be concerned with prevailing of alternative -methylglyoxalic metabolic pathway and caused by oxidative stress. Analysis of expired air samples taken on 30, 60 and 90 day of isolation showed that in conditions of long-term iso-lation concentration of heptanone-2, heptanone-3, 2,3-butadione, acetol, furanones, aldehydes (decenal, benzaldehyde) and acetophenone is increasing while concentration of phenol and fatty acids is decreasing as compared to samples taken before isolation. It was shown that dynamics of concentration of saturated hydrocarbons in expired air can be informative marker for estima-tion of organism response to oxidative stress, while the level of acetol can be used as indicator of man's training status, validity of exercise load and as a marker of hypoxic state.

Genome-Wide Analysis of DNA Methylation and Fine Particulate Matter Air Pollution in Three Study Populations: KORA F3, KORA F4, and the Normative Aging Study

PubMed Central

Panni, Tommaso; Mehta, Amar J.; Schwartz, Joel D.; Baccarelli, Andrea A.; Just, Allan C.; Wolf, Kathrin; Wahl, Simone; Cyrys, Josef; Kunze, Sonja; Strauch, Konstantin; Waldenberger, Melanie; Peters, Annette

2016-01-01

Background: Epidemiological studies have reported associations between particulate matter (PM) concentrations and cancer and respiratory and cardiovascular diseases. DNA methylation has been identified as a possible link but so far it has only been analyzed in candidate sites. Objectives: We studied the association between DNA methylation and short- and mid-term air pollution exposure using genome-wide data and identified potential biological pathways for additional investigation. Methods: We collected whole blood samples from three independent studies—KORA F3 (2004–2005) and F4 (2006–2008) in Germany, and the Normative Aging Study (1999–2007) in the United States—and measured genome-wide DNA methylation proportions with the Illumina 450k BeadChip. PM concentration was measured daily at fixed monitoring stations and three different trailing averages were considered and regressed against DNA methylation: 2-day, 7-day and 28-day. Meta-analysis was performed to pool the study-specific results. Results: Random-effect meta-analysis revealed 12 CpG (cytosine-guanine dinucleotide) sites as associated with PM concentration (1 for 2-day average, 1 for 7-day, and 10 for 28-day) at a genome-wide Bonferroni significance level (p ≤ 7.5E-8); 9 out of these 12 sites expressed increased methylation. Through estimation of I2 for homogeneity assessment across the studies, 4 of these sites (annotated in NSMAF, C1orf212, MSGN1, NXN) showed p > 0.05 and I2 < 0.5: the site from the 7-day average results and 3 for the 28-day average. Applying false discovery rate, p-value < 0.05 was observed in 8 and 1,819 additional CpGs at 7- and 28-day average PM2.5 exposure respectively. Conclusion: The PM-related CpG sites found in our study suggest novel plausible systemic pathways linking ambient PM exposure to adverse health effect through variations in DNA methylation. Citation: Panni T, Mehta AJ, Schwartz JD, Baccarelli AA, Just AC, Wolf K, Wahl S, Cyrys J, Kunze S, Strauch K, Waldenberger M, Peters A. 2016. A genome-wide analysis of DNA methylation and fine particulate matter air pollution in three study populations: KORA F3, KORA F4, and the Normative Aging Study. Environ Health Perspect 124:983–990; http://dx.doi.org/10.1289/ehp.1509966 PMID:26731791

Distribution of apparent activation energy counterparts during thermo - And thermo-oxidative degradation of Aronia melanocarpa (black chokeberry).

PubMed

Janković, Bojan; Marinović-Cincović, Milena; Janković, Marija

2017-09-01

Kinetics of degradation for Aronia melanocarpa fresh fruits in argon and air atmospheres were investigated. The investigation was based on probability distributions of apparent activation energy of counterparts (ε a ). Isoconversional analysis results indicated that the degradation process in an inert atmosphere was governed by decomposition reactions of esterified compounds. Also, based on same kinetics approach, it was assumed that in an air atmosphere, the primary compound in degradation pathways could be anthocyanins, which undergo rapid chemical reactions. A new model of reactivity demonstrated that, under inert atmospheres, expectation values for ε a occured at levels of statistical probability. These values corresponded to decomposition processes in which polyphenolic compounds might be involved. ε a values obeyed laws of binomial distribution. It was established that, for thermo-oxidative degradation, Poisson distribution represented a very successful approximation for ε a values where there was additional mechanistic complexity and the binomial distribution was no longer valid. Copyright © 2017 Elsevier Ltd. All rights reserved.

Accounting for cyanide and its degradation products at three Nevada gold mines; constraints from stable C- and N-isotopes

USGS Publications Warehouse

Johnson, C.A.; Grimes, D.J.; Rye, R.O.

1998-01-01

An understanding of the fate of cyanide (CN-) in mine process waters is important for addressing environmental concerns and for taking steps to minimize reagent costs. The utility of stable isotope methods in identifying cyanide loss pathways has been investigated in case studies at three Nevada gold mines. Freshly prepared barren solutions at the mines have cyanide d15N and d13C values averaging -4 ? and -36 ?, respectively, reflecting the nitrogen and carbon sources used by commercial manufacturers, air and natural gas methane. Pregnant solutions returning from ore heaps display small isotopic shifts to lower d15N and d13C values. The shifts are similar to those observed in laboratory experiments where cyanide was progressively precipitated as a cyanometallic compound, and are opposite in sign and much smaller in magnitude than the shifts observed in experiments where HCN was offgassed. Offgassing is inferred to be a minor cyanide loss mechanism in the heap leach operations at the three mines, and precipitation as cyanometallic compounds, and possibly coprecipitation with ferric oxides, is inferred to be an important loss mechanism. Isotopic analysis of dissolved inorganic carbon (DIC) shows that uptake of high d13C air CO2 has been important in many barren and pregnant solutions. However, DIC in reclaim pond waters at all three mines has low d13C values of -28 to -34 ? indicating cyanide breakdown either by hydrolysis or by other chemical pathways that break the C-N bond. Isotope mass balance calculations indicate that about 40 % of the DIC load in the ponds, at a minimum, was derived from cyanide breakdown. This level of cyanide hydrolysis accounts for 14-100 % of the dissolved inorganic nitrogen species present in the ponds. Overall, isotope data provide quantitative evidence that only minor amounts of cyanide are lost via offgassing and that significant amounts are destroyed via hydrolysis and related pathways. The data also highlight the possibility that significant cyanide may be either retained in the ore heaps or destroyed via other chemical pathways.

A study of impact of Asian dusts and their transport pathways to Hong Kong using multiple AERONET data, trajectory, and in-situ measurements

NASA Astrophysics Data System (ADS)

Wong, Man Sing; Nichol, Janet Elizabeth; Lee, Kwon Ho

2010-10-01

Hong Kong, a commercial and financial city located in south-east China has suffered serious air pollution for the last decade due largely to rapid urban and industrial expansion of the cities of mainland China. However, the potential sources and pathways of aerosols transported to Hong Kong have not been well researched due to the lack of air quality monitoring stations in southern China. Here, an integrated method combining the AErosol RObotic NETwork (AERONET) data, trajectory and Potential Source Contribution Function (PSCF) modeling is used to identify the potential transport pathways and contribution of sources from four characteristic aerosol types. Four characteristic aerosol types were defined using a total of 730 AERONET data measurements between 2005 and 2008. They are coastal urban, polluted urban, dust (likely to be long distance desert dust), and heavy pollution. Results show that the sources of polluted urban and heavy pollution are associated with industrial emissions in southern China, whereas coastal urban aerosols have been affected both from natural marine aerosol and emissions. The PSCF map of dust shows a wide range of pathways followed by east- and south-eastwards trajectories from northwest China to Hong Kong. Although the contribution from dust sources is small compared to the anthropogenic aerosols, a serious recent dust outbreak has been observed in Hong Kong with an elevation of the Air Pollution Index to 500, compared with 50-100 on normal days. Therefore, the combined use of clustered AERONET data, trajectory and the PSCF models can help to resolve the longstanding issue about source regions and characteristics of pollutants carried to Hong Kong.

Health co-benefits from air pollution and mitigation costs of the Paris Agreement: a modelling study.

PubMed

Markandya, Anil; Sampedro, Jon; Smith, Steven J; Van Dingenen, Rita; Pizarro-Irizar, Cristina; Arto, Iñaki; González-Eguino, Mikel

2018-03-01

Although the co-benefits from addressing problems related to both climate change and air pollution have been recognised, there is not much evidence comparing the mitigation costs and economic benefits of air pollution reduction for alternative approaches to meeting greenhouse gas targets. We analysed the extent to which health co-benefits would compensate the mitigation cost of achieving the targets of the Paris climate agreement (2°C and 1·5°C) under different scenarios in which the emissions abatement effort is shared between countries in accordance with three established equity criteria. Our study had three stages. First, we used an integrated assessment model, the Global Change Assessment Model (GCAM), to investigate the emission (greenhouse gases and air pollutants) pathways and abatement costs of a set of scenarios with varying temperature objectives (nationally determined contributions, 2°C, or 1·5°C) and approaches to the distribution of climate change methods (capability, constant emission ratios, and equal per capita). The resulting emissions pathways were transferred to an air quality model (TM5-FASST) to estimate the concentrations of particulate matter and ozone in the atmosphere and the resulting associated premature deaths and morbidity. We then applied a monetary value to these health impacts by use of a term called the value of statistical life and compared these values with those of the mitigation costs calculated from GCAM, both globally and regionally. Our analysis looked forward to 2050 in accordance with the socioeconomic narrative Shared Socioeconomic Pathways 2. The health co-benefits substantially outweighed the policy cost of achieving the target for all of the scenarios that we analysed. In some of the mitigation strategies, the median co-benefits were double the median costs at a global level. The ratio of health co-benefit to mitigation cost ranged from 1·4 to 2·45, depending on the scenario. At the regional level, the costs of reducing greenhouse gas emissions could be compensated with the health co-benefits alone for China and India, whereas the proportion the co-benefits covered varied but could be substantial in the European Union (7-84%) and USA (10-41%), respectively. Finally, we found that the extra effort of trying to pursue the 1·5°C target instead of the 2°C target would generate a substantial net benefit in India (US$3·28-8·4 trillion) and China ($0·27-2·31 trillion), although this positive result was not seen in the other regions. Substantial health gains can be achieved from taking action to prevent climate change, independent of any future reductions in damages due to climate change. Some countries, such as China and India, could justify stringent mitigation efforts just by including health co-benefits in the analysis. Our results also suggest that the statement in the Paris Agreement to pursue efforts to limit temperature increase to 1·5°C could make economic sense in some scenarios and countries if health co-benefits are taken into account. European Union's Horizon 2020 research and innovation programme. Copyright © 2018 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND 4.0 license. Published by Elsevier Ltd.. All rights reserved.

Toll-like receptor 4 in glial inflammatory responses to air pollution in vitro and in vivo.

PubMed

Woodward, Nicholas C; Levine, Morgan C; Haghani, Amin; Shirmohammadi, Farimah; Saffari, Arian; Sioutas, Constantinos; Morgan, Todd E; Finch, Caleb E

2017-04-14

Exposure to traffic-related air pollution (TRAP) is associated with accelerated cognitive aging and higher dementia risk in human populations. Rodent brains respond to TRAP with activation of astrocytes and microglia, increased inflammatory cytokines, and neurite atrophy. A role for Toll-like receptor 4 (TLR4) was suggested in mouse TLR4-knockouts, which had attenuated lung macrophage responses to air pollution. To further analyze these mechanisms, we examined mixed glial cultures (astrocytes and microglia) for RNA responses to nanoscale particulate matter (nPM; diameter <0.2 μm), a well-characterized nanoscale particulate matter subfraction of TRAP collected from a local freeway (Morgan et al. Environ Health Perspect 2011; 119,1003-1009, 2011). The nPM was compared with responses to the endotoxin lipopolysaccharide (LPS), a classic TLR4 ligand, using Affymetrix whole genome microarray in rats. Expression patterns were analyzed by significance analysis of microarrays (SAM) for fold change and by weighted gene co-expression network analysis (WGCNA) to identify modules of shared responses between nPM and LPS. Finally, we examined TLR4 activation in hippocampal tissue from mice chronically exposed to nPM. SAM and WGCNA analyses showed strong activation of TLR4 and NF-κB by both nPM and LPS. TLR4 siRNA attenuated TNFα and other inflammatory responses to nPM in vitro, via the MyD88-dependent pathway. In vivo, mice chronically exposed to nPM showed increased TLR4, MyD88, TNFα, and TNFR2 RNA, and decreased NF-κB and TRAF6 RNA TLR4 and NF-κB responses in the hippocampus. These results show TLR4 activation is integral in brain inflammatory responses to air pollution, and warrant further study of TLR4 in accelerated cognitive aging by air pollution.

Air pollution and stroke - an overview of the evidence base.

PubMed

Maheswaran, Ravi

2016-08-01

Air pollution is being increasingly recognized as a significant risk factor for stroke. There are numerous sources of air pollution including industry, road transport and domestic use of biomass and solid fuels. Early reports of the association between air pollution and stroke come from studies investigating health effects of severe pollution episodes. Several daily time series and case-crossover studies have reported associations with stroke. There is also evidence linking chronic air pollution exposure with stroke and with reduced survival after stroke. A conceptual framework linking air pollution exposure and stroke is proposed. It links acute and chronic exposure to air pollution with pathways to acute and chronic effects on stroke risk. Current evidence regarding potential mechanisms mainly relate to particulate air pollution. Whilst further evidence would be useful, there is already sufficient evidence to support consideration of reduction in air pollution as a preventative measure to reduce the stroke burden globally. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluating officially reported polycyclic aromatic hydrocarbon emissions in the Athabasca oil sands region with a multimedia fate model

PubMed Central

Parajulee, Abha; Wania, Frank

2014-01-01

Emissions of organic substances with potential toxicity to humans and the environment are a major concern surrounding the rapid industrial development in the Athabasca oil sands region (AOSR). Although concentrations of polycyclic aromatic hydrocarbons (PAHs) in some environmental samples have been reported, a comprehensive picture of organic contaminant sources, pathways, and sinks within the AOSR has yet to be elucidated. We sought to use a dynamic multimedia environmental fate model to reconcile the emissions and residue levels reported for three representative PAHs in the AOSR. Data describing emissions to air compiled from two official sources result in simulated concentrations in air, soil, water, and foliage that tend to fall close to or below the minimum measured concentrations of phenanthrene, pyrene, and benzo(a)pyrene in the environment. Accounting for evaporative emissions (e.g., from tailings pond disposal) provides a more realistic representation of PAH distribution in the AOSR. Such indirect emissions to air were found to be a greater contributor of PAHs to the AOSR atmosphere relative to reported direct emissions to air. The indirect pathway transporting uncontrolled releases of PAHs to aquatic systems via the atmosphere may be as significant a contributor of PAHs to aquatic systems as other supply pathways. Emission density estimates for the three PAHs that account for tailings pond disposal are much closer to estimated global averages than estimates based on the available emissions datasets, which fall close to the global minima. Our results highlight the need for improved accounting of PAH emissions from oil sands operations, especially in light of continued expansion of these operations. PMID:24596429

Comprehensive gene and microRNA expression profiling on cardiovascular system in zebrafish co-exposured of SiNPs and MeHg.

PubMed

Hu, Hejing; Shi, Yanfeng; Zhang, Yannan; Wu, Jing; Asweto, Collins Otieno; Feng, Lin; Yang, Xiaozhe; Duan, Junchao; Sun, Zhiwei

2017-12-31

Air pollution has been shown to increase cardiovascular diseases. However, little attention has been paid to the combined effects of PM and air pollutants on the cardiovascular system. To explore this, a high-throughput sequencing technology was used to determine combined effects of silica nanoparticles (SiNPs) and MeHg in zebrafish. Our study demonstrated that SiNPs and MeHg co-exposure could cause significant changes in mRNA and miRNA expression patterns in zebrafish. The differentially expressed (DE) genes in profiles 17 and 26 of STC analysis suggest that SiNPs and MeHg co-exposure had more proinflammatory and cardiovascular toxicity in zebrafish than single exposure. Major gene functions associated with cardiovascular system in the co-exposed zebrafish were discerned from the dynamic-gene-network, including stxbp1a, celf4, ahr1b and bai2. In addition, the prominently expressed pathway of cardiac muscle contraction was targeted by 3 DE miRNAs identified by the miRNA-pathway-network (dre-miR-7147, dre-miR-26a and dre-miR-375), which included 23 DE genes. This study presents a global view of the combined SiNPs and MeHg toxicity on the dynamic expression of both mRNAs and miRNAs in zebrafish, and could serve as fundamental research clues for future studies, especially on cardiovascular system toxicity. Copyright © 2017 Elsevier B.V. All rights reserved.

On the Right Path: The Higher Education Study of One Generation. AIR 2001 Annual Forum Paper.

ERIC Educational Resources Information Center

Cabrera, Alberto A.; La Nasa, Steven, M.; Burkum, Kurt, R.

Data from the High School and Beyond Study were used to study the pathways taken by members of the High School Class of 1982 to a college degree. The class of 1982 followed nine different pathways to a 4-year degree, paths formed by a combination of academic resources secured in high school and the first type of postsecondary institution attended.…

Long-range pollution transport during the MILAGRO-2006 campaign: a case study of a major Mexico City outflow event using free-floating altitude-controlled balloons

NASA Astrophysics Data System (ADS)

Voss, P. B.; Zaveri, R. A.; Flocke, F. M.; Mao, H.; Hartley, T. P.; Deamicis, P.; Deonandan, I.; Contreras-Jiménez, G.; Martínez-Antonio, O.; Figueroa Estrada, M.; Greenberg, D.; Campos, T. L.; Weinheimer, A. J.; Knapp, D. J.; Montzka, D. D.; Crounse, J. D.; Wennberg, P. O.; Apel, E.; Madronich, S.; de Foy, B.

2010-02-01

One of the major objectives of the Megacities Initiative: Local And Global Research Observations (MILAGRO-2006) campaign was to investigate the long-range transport of polluted Mexico City Metropolitan Area (MCMA) outflow and determine its downwind impacts on air quality and climate. Six research aircraft, including the National Center for Atmospheric Research (NCAR) C-130, made extensive chemical, aerosol, and radiation measurements above MCMA and more than 1000 km downwind in order to characterize the evolution of the outflow as it aged and dispersed over the Mesa Alta and Gulf of Mexico. As part of this effort, free-floating Controlled-Meteorological (CMET) balloons, commanded to change altitude via satellite, made repeated profile measurements of winds and state variables within the advecting outflow. In this paper, we present an analysis based on the data from two CMET balloons that were launched near Mexico City on the afternoon of 18 March 2006 and floated downwind with the MCMA pollution for nearly 30 h. The repeating profile measurements show the evolving structure of the outflow in considerable detail: its stability and stratification, interaction with other air masses, mixing episodes, and dispersion into the regional background. Air parcel trajectories, computed directly from the balloon wind profiles, show three different transport pathways on 18-19 March: (a) high-altitude advection of the top of the MCMA mixed layer, (b) mid-level outflow over the Sierra Madre Oriental followed by decoupling and isolated transport over the Gulf, and (c) low-altitude outflow with entrainment into a cleaner westerly jet below the plateau. The C-130 aircraft intercepted the balloon-based trajectories three times on 19 March, once along each of these pathways. In all three cases, distinct peaks in the urban tracer signatures and LIDAR backscatter imagery were consistent with MCMA pollution. The coherence of the high-altitude outflow was well preserved after one day whereas that lower in the atmosphere was more widely dispersed over the same time period. Other C-130 intercepts of polluted air are shown to have likely originated outside of MCMA. These findings, and the aircraft intercepts in particular, should prove useful in answering a range of scientific questions pertaining to the transport, transformation, and downwind impacts of megacity air pollution.

Time-resolved measurements of PM2.5 carbonaceous aerosols at Gosan, Korea.

PubMed

Batmunkh, T; Kim, Y J; Lee, K Y; Cayetano, M G; Jung, J S; Kim, S Y; Kim, K C; Lee, S J; Kim, J S; Chang, L S; An, J Y

2011-11-01

In order to better understand the characteristics of atmospheric carbonaceous aerosol at a background site in Northeast Asia, semicontinuous organic carbon (OC) and elemental carbon (EC), and time-resolved water-soluble organic carbon (WSOC) were measured by a Sunset OC/ EC and a PILS-TOC (particle-into-liquid sampler coupled with an online total organic carbon) analyzer, respectively, at the Gosan supersite on Jeju Island, Korea, in the summer (May 28-June 17) and fall (August 24-September 30) of 2009. Hourly average OC concentration varied in the range of approximately 0.87-28.38 microgC m-3, with a mean of 4.07+/- 2.60 microgC m-3, while the hourly average EC concentration ranged approximately from 0.04 to 8.19 .microgC m-3, with a mean of 1.35 +/- 0.71 microgC m-3, from May 28 to June 17, 2009. During the fall season, OC varied in the approximate range 0.9-9.6 microgC m-3, with a mean of 2.30 +/-0.80 microgC m-3, whereas EC ranged approximately from 0.01 to 5.40 microgC m-3, with a mean of 0.66 +/- 0.38 microgC m-3. Average contributions of EC to TC and WSOC to OC were 26.0% +/- 9.7% and 20.6% +/-7.4%, and 37.6% +/- 23.5% and 57.2% +/- 22.2% during summer and fall seasons, respectively. As expected, clear diurnal variation of WSOC/OC was found in summer, varying from 0.22 during the nighttime up to 0.72 during the daytime, mainly due to the photo-oxidation process. In order to investigate the effect of air mass pathway on the characteristics of carbonaceous aerosol, 5-day back-trajectory analysis was conducted using the HYSPLIT model. The air mass pathways were classified into four types: Continental (CC), Marine (M), East Sea (ES) and Korean Peninsula (KP). The highest OC/EC ratio of 3.63 was observed when air mass originated from the Continental area (CC). The lowest OC/EC ratio of 0.79 was measured when air mass originated from the Marine area (M). A high OC concentration was occasionally observed at Gosan due to local biomass burning activities. The contribution of secondary OC to total OC varied approximately between 8.4% and 32.2% and depended on air mass type.

Aminoimidazole Carboxamide Ribotide Exerts Opposing Effects on Thiamine Synthesis in Salmonella enterica

PubMed Central

Bazurto, Jannell V.; Heitman, Nicholas J.

2015-01-01

ABSTRACT In Salmonella enterica, the thiamine biosynthetic intermediate 5-aminoimidazole ribotide (AIR) can be synthesized de novo independently of the early purine biosynthetic reactions. This secondary route to AIR synthesis is dependent on (i) 5-amino-4-imidazolecarboxamide ribotide (AICAR) accumulation, (ii) a functional phosphoribosylaminoimidazole-succinocarboxamide (SAICAR) synthetase (PurC; EC 6.3.2.6), and (iii) methionine and lysine in the growth medium. Studies presented here show that AICAR is a direct precursor to AIR in vivo. PurC-dependent conversion of AICAR to AIR was recreated in vitro. Physiological studies showed that exogenous nutrients (e.g., methionine and lysine) antagonize the inhibitory effects of AICAR on the ThiC reaction and decreased the cellular thiamine requirement. Finally, genetic results identified multiple loci that impacted the effect of AICAR on thiamine synthesis and implicated cellular aspartate levels in AICAR-dependent AIR synthesis. Together, the data here clarify the mechanism that allows conditional growth of a strain lacking the first five biosynthetic enzymes, and they provide additional insights into the complexity of the metabolic network and its plasticity. IMPORTANCE In bacteria, the pyrimidine moiety of thiamine is derived from aminoimidazole ribotide (AIR), an intermediate in purine biosynthesis. A previous study described conditions under which AIR synthesis is independent of purine biosynthesis. This work is an extension of that previous study and describes a new synthetic pathway to thiamine that depends on a novel thiamine precursor and a secondary activity of the biosynthetic enzyme PurC. These findings provide mechanistic details of redundancy in the synthesis of a metabolite that is essential for nucleotide and coenzyme biosynthesis. Metabolic modifications that allow the new pathway to function or enhance it are also described. PMID:26100042

Ambient air pollution and thrombosis.

PubMed

Robertson, Sarah; Miller, Mark R

2018-01-03

Air pollution is a growing public health concern of global significance. Acute and chronic exposure is known to impair cardiovascular function, exacerbate disease and increase cardiovascular mortality. Several plausible biological mechanisms have been proposed for these associations, however, at present, the pathways are incomplete. A seminal review by the American Heart Association (2010) concluded that the thrombotic effects of particulate air pollution likely contributed to their effects on cardiovascular mortality and morbidity. The aim of the current review is to appraise the newly accumulated scientific evidence (2009-2016) on contribution of haemostasis and thrombosis towards cardiovascular disease induced by exposure to both particulate and gaseous pollutants.Seventy four publications were reviewed in-depth. The weight of evidence suggests that acute exposure to fine particulate matter (PM 2.5 ) induces a shift in the haemostatic balance towards a pro-thrombotic/pro-coagulative state. Insufficient data was available to ascertain if a similar relationship exists for gaseous pollutants, and very few studies have addressed long-term exposure to ambient air pollution. Platelet activation, oxidative stress, interplay between interleukin-6 and tissue factor, all appear to be potentially important mechanisms in pollution-mediated thrombosis, together with an emerging role for circulating microvesicles and epigenetic changes.Overall, the recent literature supports, and arguably strengthens, the contention that air pollution contributes to cardiovascular morbidity by promoting haemostasis. The volume and diversity of the evidence highlights the complexity of the pathophysiologic mechanisms by which air pollution promotes thrombosis; multiple pathways are plausible and it is most likely they act in concert. Future research should address the role gaseous pollutants play in the cardiovascular effects of air pollution mixture and direct comparison of potentially susceptible groups to healthy individuals.

Microarray Analysis of Gene Expression Alteration in Human Middle Ear Epithelial Cells Induced by Asian Sand Dust.

PubMed

Go, Yoon Young; Park, Moo Kyun; Kwon, Jee Young; Seo, Young Rok; Chae, Sung-Won; Song, Jae-Jun

2015-12-01

The primary aim of this study is to evaluate the gene expression profile of Asian sand dust (ASD)-treated human middle ear epithelial cell (HMEEC) using microarray analysis. The HMEEC was treated with ASD (400 µg/mL) and total RNA was extracted for microarray analysis. Molecular pathways among differentially expressed genes were further analyzed. For selected genes, the changes in gene expression were confirmed by real-time polymerase chain reaction. A total of 1,274 genes were differentially expressed by ASD. Among them, 1,138 genes were 2 folds up-regulated, whereas 136 genes were 2 folds down-regulated. Up-regulated genes were mainly involved in cellular processes, including apoptosis, cell differentiation, and cell proliferation. Down-regulated genes affected cellular processes, including apoptosis, cell cycle, cell differentiation, and cell proliferation. The 10 genes including ADM, CCL5, EDN1, EGR1, FOS, GHRL, JUN, SOCS3, TNF, and TNFSF10 were identified as main modulators in up-regulated genes. A total of 11 genes including CSF3, DKK1, FOSL1, FST, TERT, MMP13, PTHLH, SPRY2, TGFBR2, THBS1, and TIMP1 acted as main components of pathway associated with 2-fold down regulated genes. We identified the differentially expressed genes in ASD-treated HMEEC. Our work indicates that air pollutant like ASD, may play an important role in the pathogenesis of otitis media.

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.

PubMed

Bohler, Anwesha; Eijssen, Lars M T; van Iersel, Martijn P; Leemans, Christ; Willighagen, Egon L; Kutmon, Martina; Jaillard, Magali; Evelo, Chris T

2015-08-23

Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary data analysis, such as quality control, normalisation, and statistical analysis, is often performed in scripting languages like R, Perl, and Python. Subsequent pathway analysis is usually performed using dedicated external applications. Workflows involving manual use of multiple environments are time consuming and error prone. Therefore, tools are needed that enable pathway analysis directly within the same scripting languages used for primary data analyses. Existing tools have limited capability in terms of available pathway content, pathway editing and visualisation options, and export file formats. Consequently, making the full-fledged pathway analysis tool PathVisio available from various scripting languages will benefit researchers. We developed PathVisioRPC, an XMLRPC interface for the pathway analysis software PathVisio. PathVisioRPC enables creating and editing biological pathways, visualising data on pathways, performing pathway statistics, and exporting results in several image formats in multiple programming environments. We demonstrate PathVisioRPC functionalities using examples in Python. Subsequently, we analyse a publicly available NCBI GEO gene expression dataset studying tumour bearing mice treated with cyclophosphamide in R. The R scripts demonstrate how calls to existing R packages for data processing and calls to PathVisioRPC can directly work together. To further support R users, we have created RPathVisio simplifying the use of PathVisioRPC in this environment. We have also created a pathway module for the microarray data analysis portal ArrayAnalysis.org that calls the PathVisioRPC interface to perform pathway analysis. This module allows users to use PathVisio functionality online without having to download and install the software and exemplifies how the PathVisioRPC interface can be used by data analysis pipelines for functional analysis of processed genomics data. PathVisioRPC enables data visualisation and pathway analysis directly from within various analytical environments used for preliminary analyses. It supports the use of existing pathways from WikiPathways or pathways created using the RPC itself. It also enables automation of tasks performed using PathVisio, making it useful to PathVisio users performing repeated visualisation and analysis tasks. PathVisioRPC is freely available for academic and commercial use at http://projects.bigcat.unimaas.nl/pathvisiorpc.

Pathway enrichment analysis approach based on topological structure and updated annotation of pathway.

PubMed

Yang, Qian; Wang, Shuyuan; Dai, Enyu; Zhou, Shunheng; Liu, Dianming; Liu, Haizhou; Meng, Qianqian; Jiang, Bin; Jiang, Wei

2017-08-16

Pathway enrichment analysis has been widely used to identify cancer risk pathways, and contributes to elucidating the mechanism of tumorigenesis. However, most of the existing approaches use the outdated pathway information and neglect the complex gene interactions in pathway. Here, we first reviewed the existing widely used pathway enrichment analysis approaches briefly, and then, we proposed a novel topology-based pathway enrichment analysis (TPEA) method, which integrated topological properties and global upstream/downstream positions of genes in pathways. We compared TPEA with four widely used pathway enrichment analysis tools, including database for annotation, visualization and integrated discovery (DAVID), gene set enrichment analysis (GSEA), centrality-based pathway enrichment (CePa) and signaling pathway impact analysis (SPIA), through analyzing six gene expression profiles of three tumor types (colorectal cancer, thyroid cancer and endometrial cancer). As a result, we identified several well-known cancer risk pathways that could not be obtained by the existing tools, and the results of TPEA were more stable than that of the other tools in analyzing different data sets of the same cancer. Ultimately, we developed an R package to implement TPEA, which could online update KEGG pathway information and is available at the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/TPEA/. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Long-range transport pathways of tropospheric source gases originating in Asia into the northern lower stratosphere during the Asian monsoon season 2012

NASA Astrophysics Data System (ADS)

Vogel, Bärbel; Günther, Gebhard; Müller, Rolf; Grooß, Jens-Uwe; Afchine, Armin; Bozem, Heiko; Hoor, Peter; Krämer, Martina; Müller, Stefan; Riese, Martin; Rolf, Christian; Spelten, Nicole; Stiller, Gabriele P.; Ungermann, Jörn; Zahn, Andreas

2016-12-01

Global simulations with the Chemical Lagrangian Model of the Stratosphere (CLaMS) using artificial tracers of air mass origin are used to analyze transport mechanisms from the Asian monsoon region into the lower stratosphere. In a case study, the transport of air masses from the Asian monsoon anticyclone originating in India/China by an eastward-migrating anticyclone which broke off from the main anticyclone on 20 September 2012 and filaments separated at the northeastern flank of the anticyclone are analyzed. Enhanced contributions of young air masses (younger than 5 months) are found within the separated anticyclone confined at the top by the thermal tropopause. Further, these air masses are confined by the anticyclonic circulation and, on the polar side, by the subtropical jet such that the vertical structure resembles a bubble within the upper troposphere. Subsequently, these air masses are transported eastwards along the subtropical jet and enter the lower stratosphere by quasi-horizontal transport in a region of double tropopauses most likely associated with Rossby wave breaking events. As a result, thin filaments with enhanced signatures of tropospheric trace gases were measured in the lower stratosphere over Europe during the TACTS/ESMVal campaign in September 2012 in very good agreement with CLaMS simulations. Our simulations demonstrate that source regions in Asia and in the Pacific Ocean have a significant impact on the chemical composition of the lower stratosphere of the Northern Hemisphere. Young, moist air masses, in particular at the end of the monsoon season in September/October 2012, flooded the extratropical lower stratosphere in the Northern Hemisphere with contributions of up to ≈ 30 % at 380 K (with the remaining fraction being aged air). In contrast, the contribution of young air masses to the Southern Hemisphere is much lower. At the end of October 2012, approximately 1.5 ppmv H2O is found in the lower Northern Hemisphere stratosphere (at 380 K) from source regions both in Asia and in the tropical Pacific compared to a mean water vapor content of ≈ 5 ppmv. In addition to this main transport pathway from the Asian monsoon anticyclone to the east along the subtropical jet and subsequent transport into the northern lower stratosphere, a second horizontal transport pathway out of the anticyclone to the west into the tropics (TTL) is found in agreement with MIPAS HCFC-22 measurements.

Conceptual Model Scenarios for the Vapor Intrusion Pathway

EPA Pesticide Factsheets

This report provides simplified simulation examples to illustrate graphically how subsurface conditions and building-specific characteristics determine the distribution chemical distribution and indoor air concentration relative to a source concentration.

Role of Science at EPA

EPA Pesticide Factsheets

Decision-making is driven by research with the highest standards for integrity, peer review, transparency, and ethics. Ongoing positive impacts include reducing pollution, improving air quality, defining exposure pathways, and protecting water sources.

Genetic analysis of conidiation regulatory pathways in koji-mold Aspergillus oryzae.

PubMed

Ogawa, Masahiro; Tokuoka, Masafumi; Jin, Feng Jie; Takahashi, Tadashi; Koyama, Yasuji

2010-01-01

Conidia of koji-mold Aspergillus oryzae are often used as starters in the fermented food industry. However, little is known about conidiation regulation in A. oryzae. To improve the productivity of conidia in A. oryzae, it is necessary to understand conidiation regulation in the strain. Therefore, we analyzed the conidiation regulatory system in A. oryzae using 10 kinds of conidiation regulatory gene disruptants. The phenotypes of AorfluG, AorflbA, AorflbB, AorflbC, AorflbD, AorflbE, AorbrlA, AorabaA, AorwetA, and AorfadA mutants are almost identical to those of the corresponding mutants in Aspergillus nidulans. The results indicated that the functions of conidiation regulatory genes are almost conserved between A. oryzae and A. nidulans. However, the severely reduced conidiation phenotype of the AorfluG disruptant in A. oryzae differs from the phenotype of the corresponding mutant in Aspergillus fumigatus in air-exposed culture conditions. These results suggest that A. oryzae, A. nidulans, and A. fumigatus have a G-protein signaling pathway and brlA orthologs in common, and only A. fumigatus has particular brlA activation pathways that are independent of the fluG ortholog. Furthermore, the analyses of AorflbA disruptant and AorfadA dominant-active mutants implicated that AorFadA-mediated G-protein signaling suppresses vegetative growth of A. oryzae.

Geospatial Analysis of Oil and Gas Wells in California

NASA Astrophysics Data System (ADS)

Riqueros, N. S.; Kang, M.; Jackson, R. B.

2015-12-01

California currently ranks third in oil production by U.S. state and more than 200,000 wells have been drilled in the state. Oil and gas wells provide a potential pathway for subsurface migration, leading to groundwater contamination and emissions of methane and other fluids to the atmosphere. Here we compile available public databases on oil and gas wells from the California Department of Conservation's Division of Oil, Gas, and Geothermal Resources, the U.S. Geological Survey, and other state and federal sources. We perform geospatial analysis at the county and field levels to characterize depths, producing formations, spud/completion/abandonment dates, land cover, population, and land ownership of active, idle, buried, abandoned, and plugged wells in California. The compiled database is designed to serve as a quantitative platform for developing field-based groundwater and air emission monitoring plans.

The Shared Pathoetiological Effects of Particulate Air Pollution and the Social Environment on Fetal-Placental Development

PubMed Central

2014-01-01

Exposure to particulate air pollution and socioeconomic risk factors are shown to be independently associated with adverse pregnancy outcomes; however, their confounding relationship is an epidemiological challenge that requires understanding of their shared etiologic pathways affecting fetal-placental development. The purpose of this paper is to explore the etiological mechanisms associated with exposure to particulate air pollution in contributing to adverse pregnancy outcomes and how these mechanisms intersect with those related to socioeconomic status. Here we review the role of oxidative stress, inflammation and endocrine modification in the pathoetiology of deficient deep placentation and detail how the physical and social environments can act alone and collectively to mediate the established pathology linked to a spectrum of adverse pregnancy outcomes. We review the experimental and epidemiological literature showing that diet/nutrition, smoking, and psychosocial stress share similar pathways with that of particulate air pollution exposure to potentially exasperate the negative effects of either insult alone. Therefore, socially patterned risk factors often treated as nuisance parameters should be explored as potential effect modifiers that may operate at multiple levels of social geography. The degree to which deleterious exposures can be ameliorated or exacerbated via community-level social and environmental characteristics needs further exploration. PMID:25574176

Pathway cross-talk network analysis identifies critical pathways in neonatal sepsis.

PubMed

Meng, Yu-Xiu; Liu, Quan-Hong; Chen, Deng-Hong; Meng, Ying

2017-06-01

Despite advances in neonatal care, sepsis remains a major cause of morbidity and mortality in neonates worldwide. Pathway cross-talk analysis might contribute to the inference of the driving forces in bacterial sepsis and facilitate a better understanding of underlying pathogenesis of neonatal sepsis. This study aimed to explore the critical pathways associated with the progression of neonatal sepsis by the pathway cross-talk analysis. By integrating neonatal transcriptome data with known pathway data and protein-protein interaction data, we systematically uncovered the disease pathway cross-talks and constructed a disease pathway cross-talk network for neonatal sepsis. Then, attract method was employed to explore the dysregulated pathways associated with neonatal sepsis. To determine the critical pathways in neonatal sepsis, rank product (RP) algorithm, centrality analysis and impact factor (IF) were introduced sequentially, which synthetically considered the differential expression of genes and pathways, pathways cross-talks and pathway parameters in the network. The dysregulated pathways with the highest IF values as well as RP<0.01 were defined as critical pathways in neonatal sepsis. By integrating three kinds of data, only 6919 common genes were included to perform the pathway cross-talk analysis. By statistic analysis, a total of 1249 significant pathway cross-talks were selected to construct the pathway cross-talk network. Moreover, 47 dys-regulated pathways were identified via attract method, 20 pathways were identified under RP<0.01, and the top 10 pathways with the highest IF were also screened from the pathway cross-talk network. Among them, we selected 8 common pathways, i.e. critical pathways. In this study, we systematically tracked 8 critical pathways involved in neonatal sepsis by integrating attract method and pathway cross-talk network. These pathways might be responsible for the host response in infection, and of great value for advancing diagnosis and therapy of neonatal sepsis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Assessment of air quality and climate co-benefits of decarbonisation of the UK energy system using remote sensing and model simulations - the case for prioritizing end uses in urban areas

NASA Astrophysics Data System (ADS)

Sobral Mourao, Zenaida; Konadu, Daniel Dennis; Damoah, Richard; Li, Pei-hao

2017-04-01

The UK has a binding obligation to reduce GHG emission by 80% (based on 1990 levels) by 2050. Meeting this target requires extensive decarbonisation of the UK energy system. Different pathways that achieve this target at the lowest system costs are being explored at different levels of policy and decisions on future energy infrastructure. Whilst benefits of decarbonisation are mainly focused on the impacts on climate change, there are other potential environmental and health impacts such as air-quality. In particular, a decrease in fossil fuel use by directly substituting current systems with low-carbon technologies could lead to significant reductions in the concentrations of SO2, NOX, CO and other atmospheric pollutants. So far, the proposed decarbonisation pathways tend to target the electricity sector first, followed by a transition in transport and heating technologies and use. However, the spatial dimension of where short term changes in the energy sector occur in relation to high density population areas is not taken into account when defining the energy transition strategies. This may lead to limited short-term improvements in air quality within urban areas, where use of fossil fuels for heating and transport is the main contribution to overall atmospheric pollutant levels. It is therefore imperative to explore decarbonisation strategies that prioritise transition in sectors of the energy system that produce immediate improvements in air quality in key regions of the UK. This study aims to use a combination of Remote Sensing observations and atmospheric chemistry/transport modelling approaches to estimate and map the impact on NOx of the traditional approach of decarbonising electricity first compared to a slower transition in the electricity sector, but faster change in the transport sector. This is done by generating a set of alternative energy system pathways with a higher share of zero emissions vehicles in 2030 than the energy system optimization model would choose if the only goal was the 80% GHG emissions reduction. Our overarching goal is to provide an additional standard to compare future energy system pathways beyond the traditional metrics of cost and GHG emissions reductions.

Prioritizing biological pathways by recognizing context in time-series gene expression data.

PubMed

Lee, Jusang; Jo, Kyuri; Lee, Sunwon; Kang, Jaewoo; Kim, Sun

2016-12-23

The primary goal of pathway analysis using transcriptome data is to find significantly perturbed pathways. However, pathway analysis is not always successful in identifying pathways that are truly relevant to the context under study. A major reason for this difficulty is that a single gene is involved in multiple pathways. In the KEGG pathway database, there are 146 genes, each of which is involved in more than 20 pathways. Thus activation of even a single gene will result in activation of many pathways. This complex relationship often makes the pathway analysis very difficult. While we need much more powerful pathway analysis methods, a readily available alternative way is to incorporate the literature information. In this study, we propose a novel approach for prioritizing pathways by combining results from both pathway analysis tools and literature information. The basic idea is as follows. Whenever there are enough articles that provide evidence on which pathways are relevant to the context, we can be assured that the pathways are indeed related to the context, which is termed as relevance in this paper. However, if there are few or no articles reported, then we should rely on the results from the pathway analysis tools, which is termed as significance in this paper. We realized this concept as an algorithm by introducing Context Score and Impact Score and then combining the two into a single score. Our method ranked truly relevant pathways significantly higher than existing pathway analysis tools in experiments with two data sets. Our novel framework was implemented as ContextTRAP by utilizing two existing tools, TRAP and BEST. ContextTRAP will be a useful tool for the pathway based analysis of gene expression data since the user can specify the context of the biological experiment in a set of keywords. The web version of ContextTRAP is available at http://biohealth.snu.ac.kr/software/contextTRAP .

Added value of stress related gene inductions in HepG2 cells as effect measurement in monitoring of air pollution

NASA Astrophysics Data System (ADS)

Nobels, Ingrid; Vanparys, Caroline; Van den Heuvel, Rosette; Vercauteren, Jordy; Blust, Ronny

2012-08-01

In this study we studied the effects of particulate matter samples (PM) through gene expression analysis in a routine air quality monitoring campaign by the Flemish Environment Agency (VMM, Belgium). We selected a human hepatoma (HepG2) multiple endpoint reporter assay for targeted stress related endpoint screening. Organic extracts of air samples (total suspended particles, TSP) were collected during one year in an industrial, urban and background location in Flanders, Belgium. Simultaneously, meteorological conditions (temperature, wind speed and precipitation) and particulate matter size ≤ 10 μM (PM10), organic (OC), elemental (EC) and total (TC) carbon were monitored and air samples were collected for chemical analysis (11 PAHs). Correlations between the induction of the different stress genes and the chemical pollutants were analysed. Exposure of HepG2 cells to daily air equivalents (20 m3) of organic TSP extracts revealed the dominant induction of the xenobiotic response element (Xre) and phase I (Cyp1A1) and phase II (GstYa) biotransformation enzymes. Additional effects were the induction of c-Fos, a proto-oncogen and Gadd45, a marker for cell cycle disturbance and responsive to genotoxic compounds. Inductions of other relevant pathways, such as sequestration of heavy metals, retinoids response, protein misfolding and increased cAMP levels were measured occasionally. A significant correlation was found between the genes Cyp1A1 (a typical marker for presence of PAHs and dioxin like compounds), c-Fos, Gadd45, (responsive to DNA damaging compounds) and the amount of PM10 and elemental carbon (EC) whereas no correlation was found between these genes and total PAHs content. This may suggest that the observed induction of Cyp1A1 and DNA damage related genes was provoked (partially) by other particle bound compounds (e.g. pesticides, PCBs, brominated flame retardants, dioxins, …), than PAHs. The contribution of particle bound compounds, other than PAHs might be important to take into account in risk evaluation of air pollution.

Control of gill ventilation and air-breathing in the bowfin amia calva

PubMed

Hedrick; Jones

1999-01-01

The purpose of this study was to investigate the roles of branchial and gas bladder reflex pathways in the control of gill ventilation and air-breathing in the bowfin Amia calva. We have previously determined that bowfin use two distinct air-breathing mechanisms to ventilate the gas bladder: type I air breaths are characterized by exhalation followed by inhalation, are stimulated by aquatic or aerial hypoxia and appear to regulate O2 gas exchange; type II air breaths are characterized by inhalation alone and possibly regulate gas bladder volume and buoyancy. In the present study, we test the hypotheses (1) that gill ventilation and type I air breaths are controlled by O2-sensitive chemoreceptors located in the branchial region, and (2) that type II air breaths are controlled by gas bladder mechanosensitive stretch receptors. Hypothesis 1 was tested by examining the effects of partial or complete branchial denervation of cranial nerves IX and X to the gill arches on gill ventilation frequency (fg) and the proportion of type I air breaths during normoxia and hypoxia; hypothesis II was tested by gas bladder inflation and deflation. Following complete bilateral branchial denervation, fg did not differ from that of sham-operated control fish; in addition, fg was not significantly affected by aquatic hypoxia in sham-operated or denervated fish. In sham-operated fish, aquatic hypoxia significantly increased overall air-breathing frequency (fab) and the percentage of type I breaths. In fish with complete IX-X branchial denervation, fab was also significantly increased during aquatic hypoxia, but there were equal percentages of type I and type II air breaths. Branchial denervation did not affect the frequency of type I air breaths during aquatic hypoxia. Gas bladder deflation via an indwelling catheter resulted in type II breaths almost exclusively; furthermore, fab was significantly correlated with the volume removed from the gas bladder, suggesting a volume-regulating function for type II air breaths. These results indicate that chronic (3-4 weeks) branchial denervation does not significantly affect fg or type I air-breathing responses to aquatic hypoxia. Because type I air-breathing responses to aquatic hypoxia persist after IX-X cranial nerve denervation, O2-sensitive chemoreceptors that regulate air-breathing may be carried in other afferent pathways, such as the pseudobranch. Gas bladder deflation reflexly stimulates type II breaths, suggesting that gas bladder volume-sensitive stretch receptors control this particular air-breathing mechanism. It is likely that type II air breaths function to regulate buoyancy when gas bladder volume declines during the inter-breath interval.

Possible Exposure Pathways During Emergencies

EPA Pesticide Factsheets

There are three basic ways a person may be exposed to a hazardous substance: inhalation, ingestion, or direct contact. Points of contact include groundwater or surface water; soil, sediment, or dust; air; or food.

Feasibility Study of Endo- and Exo-skeletal Framed Structures with Envelopes for LTA Platforms

DTIC Science & Technology

2011-02-15

pathway for design and fabrication of Endo- and Exoskeleton framed elliptical envelopes was demonstrated. Envelope sizes of 2 ft x 0.5 ft and 5 ft x...Lighter than air, Endoskeleton, Exoskeleton , Helium filled envelope, Design, Fabrication Robert Sadler and Raghu Panduranga ARIS Inc 115-C, South...Structures with Envelopes for LTA Platforms Report Title ABSTRACT A pathway for design and fabrication of Endo- and Exoskeleton framed elliptical envelopes

Laser Ablation Molecular Isotopic Spectrometry for Molecules Formation Chemistry in Femtosecond-Laser Ablated Plasmas.

PubMed

Hou, Huaming; Mao, Xianglei; Zorba, Vassilia; Russo, Richard E

2017-07-18

Recently, laser ablated molecular isotopic spectrometry (LAMIS) has expanded its capability to explore molecules formation mechanism in laser-induced plasma in addition to isotope analysis. LAMIS is a powerful tool for tracking the origination of atoms that is involved in formation of investigated molecules by labeling atoms with their isotopic substitution. The evolutionary formation pathways of organic molecules, especially of C 2 dimers and CN radicals, were frequently reported. However, very little is known about the formation pathways for metallic radicals and heterodimers in laser ablated plasma. This research focuses on elucidating the formation pathways of AlO radicals in femtosecond laser ablated plasma from 18 O-labeled Al 2 O 3 pellet. Plasmas expanding with strong forward bias in the direction normal to the sample surface were generated in the wake of a weakly ionized channel created by a femtosecond laser. The formation mechanism of AlO and influence of air were investigated with multiple plasma diagnostic methods such as monochromatic fast gating imaging, spatiotemporal resolved optical emission spectroscopy, and LAMIS. An advanced LAMIS fitting procedure was used to deduce the spatiotemporal distributions of Al 18 O and Al 16 O number densities and also their ratios. We found that the Al 16 O/Al 18 O number density ratio is higher for plasma portion closer to the sample surface, which suggests that chemical reactions between the plasma plume and ambient air are more intense at the tail of the plasma. The results also reveals that direct association of free Al and O atoms is the main mechanism for the formation of AlO at the early stage of the plasma. To the contrast, chemical reactions between plasma materials and ambient oxygen molecules and the isotope exchange effect are the dominant mechanisms of the formation of AlO and evolution of Al 16 O/Al 18 O number density ratio at the late stage of the plasma.

Metabolic Profiling as Well as Stable Isotope Assisted Metabolic and Proteomic Analysis of RAW 264.7 Macrophages Exposed to Ship Engine Aerosol Emissions: Different Effects of Heavy Fuel Oil and Refined Diesel Fuel

PubMed Central

Sapcariu, Sean C.; Kanashova, Tamara; Dilger, Marco; Diabaté, Silvia; Oeder, Sebastian; Passig, Johannes; Radischat, Christian; Buters, Jeroen; Sippula, Olli; Streibel, Thorsten; Paur, Hanns-Rudolf; Schlager, Christoph; Mülhopt, Sonja; Stengel, Benjamin; Rabe, Rom; Harndorf, Horst; Krebs, Tobias; Karg, Erwin; Gröger, Thomas; Weiss, Carsten; Dittmar, Gunnar; Hiller, Karsten; Zimmermann, Ralf

2016-01-01

Exposure to air pollution resulting from fossil fuel combustion has been linked to multiple short-term and long term health effects. In a previous study, exposure of lung epithelial cells to engine exhaust from heavy fuel oil (HFO) and diesel fuel (DF), two of the main fuels used in marine engines, led to an increased regulation of several pathways associated with adverse cellular effects, including pro-inflammatory pathways. In addition, DF exhaust exposure was shown to have a wider response on multiple cellular regulatory levels compared to HFO emissions, suggesting a potentially higher toxicity of DF emissions over HFO. In order to further understand these effects, as well as to validate these findings in another cell line, we investigated macrophages under the same conditions as a more inflammation-relevant model. An air-liquid interface aerosol exposure system was used to provide a more biologically relevant exposure system compared to submerged experiments, with cells exposed to either the complete aerosol (particle and gas phase), or the gas phase only (with particles filtered out). Data from cytotoxicity assays were integrated with metabolomics and proteomics analyses, including stable isotope-assisted metabolomics, in order to uncover pathways affected by combustion aerosol exposure in macrophages. Through this approach, we determined differing phenotypic effects associated with the different components of aerosol. The particle phase of diluted combustion aerosols was found to induce increased cell death in macrophages, while the gas phase was found more to affect the metabolic profile. In particular, a higher cytotoxicity of DF aerosol emission was observed in relation to the HFO aerosol. Furthermore, macrophage exposure to the gas phase of HFO leads to an induction of a pro-inflammatory metabolic and proteomic phenotype. These results validate the effects found in lung epithelial cells, confirming the role of inflammation and cellular stress in the response to combustion aerosols. PMID:27348622

Environmental Public Health Dimensions of Shale and Tight Gas Development

PubMed Central

Hays, Jake; Finkel, Madelon L.

2014-01-01

Background: The United States has experienced a boom in natural gas production due to recent technological innovations that have enabled this resource to be produced from shale formations. Objectives: We reviewed the body of evidence related to exposure pathways in order to evaluate the potential environmental public health impacts of shale gas development. We highlight what is currently known and identify data gaps and research limitations by addressing matters of toxicity, exposure pathways, air quality, and water quality. Discussion: There is evidence of potential environmental public health risks associated with shale gas development. Several studies suggest that shale gas development contributes to ambient air concentrations of pollutants known to be associated with increased risk of morbidity and mortality. Similarly, an increasing body of studies suggest that water contamination risks exist through a variety of environmental pathways, most notably during wastewater transport and disposal, and via poor zonal isolation of gases and fluids due to structural integrity impairment of cement in gas wells. Conclusion: Despite a growing body of evidence, data gaps persist. Most important, there is a need for more epidemiological studies to assess associations between risk factors, such as air and water pollution, and health outcomes among populations living in close proximity to shale gas operations. Citation: Shonkoff SB, Hays J, Finkel ML. 2014. Environmental public health dimensions of shale and tight gas development. Environ Health Perspect 122:787–795; http://dx.doi.org/10.1289/ehp.1307866 PMID:24736097

Measurement of inflammation and oxidative stress following drastic changes in air pollution during the Beijing Olympics: a panel study approach

PubMed Central

Kipen, Howard; Rich, David; Huang, Wei; Zhu, Tong; Wang, Guangfa; Hu, Min; Lu, Shou-en; Ohman-Strickland, Pamela; Zhu, Ping; Wang, Yuedan; Zhang, Jim (Junfeng)

2014-01-01

Ambient air pollution has been linked to cardiovascular and respiratory morbidity and mortality in epidemiology studies. Frequently, oxidative and nitrosative stress are hypothesized to mediate these pollution effects, however precise mechanisms remain unclear. This paper describes the methodology for a major panel study to examine air pollution effects on these and other mechanistic pathways. The study took place during the drastic air pollution changes accompanying the 2008 Olympics in Beijing, China. After a general description of air pollution health effects, we provide a discussion of panel studies and describe the unique features of this study that make it likely to provide compelling results. This study should lead to a clearer and more precise definition of the role of oxidative and nitrosative stress, as well as other mechanisms, in determining acute morbidity and mortality from air pollution exposure. PMID:20716299

Impact of typhoons on the composition of the upper troposphere within the Asian summer monsoon anticyclone: the SWOP campaign in Lhasa 2013

NASA Astrophysics Data System (ADS)

Li, Dan; Vogel, Bärbel; Bian, Jianchun; Müller, Rolf; Pan, Laura L.; Günther, Gebhard; Bai, Zhixuan; Li, Qian; Zhang, Jinqiang; Fan, Qiujun; Vömel, Holger

2017-04-01

In the frame of the SWOP (sounding water vapour, ozone, and particle) campaign during the Asian summer monsoon (ASM), ozone and water vapour profiles were measured by balloon-borne sensors launched from Lhasa (29.66° N, 91.14° E, elevation 3650 m), China, in August 2013. In total, 24 soundings were launched, nearly half of which show strong variations in the relationship between ozone and water vapour in the tracer-tracer correlation in the upper troposphere and lower stratosphere (UTLS). For each sounding, 20-day backward trajectories were calculated using the trajectory module of the Chemical Lagrangian Model of the Stratosphere (CLaMS) to analyse these variations. The trajectory calculations demonstrate that three tropical cyclones (tropical storm Jebi, typhoons Utor and Trami), which occurred over the western Pacific Ocean during August 2013, had a considerable impact on the vertical distribution of ozone and water vapour by uplifting marine air masses to altitudes of the ASM anticyclone. Air parcels subsequently arrived at the observation site via two primary pathways: firstly via direct horizontal transport from the location of the typhoon to the station within approximately 3 days, and secondly via transport following the clockwise wind flow of the ASM within a timescale of 1 week. Furthermore, the interplay between the spatial position of the ASM anticyclone and tropical cyclones plays a key role in controlling the transport pathways of air parcels from the boundary layer of the western Pacific to Lhasa in horizontal and vertical transport. Moreover, the statistical analysis shows that the strongest impact by typhoons is found at altitudes between 14.5 and 17 km (365-375 K). Low ozone values (50-80 ppbv) were observed between 370 and 380 K due to the strong vertical transport within tropical cyclones.

Extracellular vesicle-driven information mediates the long-term effects of particulate matter exposure on coagulation and inflammation pathways.

PubMed

Pavanello, Sofia; Bonzini, Matteo; Angelici, Laura; Motta, Valeria; Pergoli, Laura; Hoxha, Mirjam; Cantone, Laura; Pesatori, Angela Cecilia; Apostoli, Pietro; Tripodi, Armando; Baccarelli, Andrea; Bollati, Valentina

2016-09-30

Continuous exposure to particulate air pollution (PM) is a serious worldwide threat to public health as it coherently links with increased morbidity and mortality of cardiorespiratory diseases (CRD), and of type 2 diabetes (T2D). Extracellular vesicles (EVs) are circular plasma membrane fragments released from human cells that transfer microRNAs between tissues. In the present work it was explored the hypothesis that EVs with their encapsulated microRNAs (EVmiRNAs) contents might mediate PM effects by triggering key pathways in CRD and T2D. Expression of EVmiRNAs analyzed by real-time PCR was correlated with oxidative stress, coagulation and inflammation markers, from healthy steel plant workers (n=55) with a well-characterized exposure to PM and PM-associated metals. All p-values were adjusted for multiple comparisons. In-silico Ingenuity Pathway Analysis (IPA) was performed to identify biological pathways regulated by PM-associated EVmiRNAs. Increased expression in 17 EVmiRNAs is associated with PM and metal exposure (p<0.01). Mir-196b that tops the list, being related to 9 different metals, is fundamental in insulin biosynthesis, however three (miR-302b, miR-200c, miR-30d) out of these 17 EVmiRNAs are in turn also related to disruptions (p<0.01) in inflammatory and coagulation markers. The study's findings support the hypothesis that adverse cardiovascular and metabolic effects stemming from inhalation exposures in particular to PM metallic component may be mediated by EVmiRNAs that target key factors in the inflammation, coagulation and glucose homeostasis pathways. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A new conceptual model for quantifying transboundary contribution of atmospheric pollutants in the East Asian Pacific rim region.

PubMed

Lai, I-Chien; Lee, Chon-Lin; Huang, Hu-Ching

2016-03-01

Transboundary transport of air pollution is a serious environmental concern as pollutant affects both human health and the environment. Many numerical approaches have been utilized to quantify the amounts of pollutants transported to receptor regions, based on emission inventories from possible source regions. However, sparse temporal-spatial observational data and uncertainty in emission inventories might make the transboundary transport contribution difficult to estimate. This study presents a conceptual quantitative approach that uses transport pathway classification in combination with curve fitting models to simulate an air pollutant concentration baseline for pollution background concentrations. This approach is used to investigate the transboundary transport contribution of atmospheric pollutants to a metropolitan area in the East Asian Pacific rim region. Trajectory analysis categorized pollution sources for the study area into three regions: East Asia, Southeast Asia, and Taiwan cities. The occurrence frequency and transboundary contribution results suggest the predominant source region is the East Asian continent. This study also presents an application to evaluate heavy pollution cases for health concerns. This new baseline construction model provides a useful tool for the study of the contribution of transboundary pollution delivered to receptors, especially for areas deficient in emission inventories and regulatory monitoring data for harmful air pollutants. Copyright © 2015 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paton, Ian

The Rocky Flats Environmental Technology Site (RFETS) is a Department of Energy facility located approximately 16 miles northwest of Denver, Colorado. Processing and fabrication of nuclear weapons components occurred at Rocky Flats from 1952 through 1989. Operations at the Site included the use of several radionuclides, including plutonium-239/240 (Pu), americium-241 (Am), and various uranium (U) isotopes, as well as several types of chlorinated solvents. The historic operations resulted in legacy contamination, including contaminated facilities, process waste lines, buried wastes and surface soil contamination. Decontamination and removal of buildings at the site was completed in late 2005, culminating more than tenmore » years of active environmental remediation work. The Corrective Action Decision/Record of Decision was subsequently approved in 2006, signifying regulatory approval and closure of the site. The use of RFETS as a National Wildlife Refuge is scheduled to be in full operation by 2012. To develop a plan for remediating different types of radionuclide contaminants present in the RFETS environment required understanding the different environmental transport pathways for the various actinides. Developing this understanding was the primary objective of the Actinide Migration Evaluation (AME) project. Findings from the AME studies were used in the development of RFETS remediation strategies. The AME project focused on issues of actinide behavior and mobility in surface water, groundwater, air, soil and biota at RFETS. For the purposes of the AME studies, actinide elements addressed included Pu, Am, and U. The AME program, funded by DOE, brought together personnel with a broad range of relevant expertise in technical investigations. The AME advisory panel identified research investigations and approaches that could be used to solve issues related to actinide migration at the Site. An initial step of the AME was to develop a conceptual model to provide a qualitative description of the relationships among potential actinide sources and transport pathways at RFETS. One conceptual model was developed specifically for plutonium and americium, because of their similar geochemical and transport properties. A separate model was developed for uranium because of its different properties and mobility in the environment. These conceptual models were guidelines for quantitative analyses described in the RFETS Pathway Analysis Report, which used existing data from the literature as well as site-specific analyses, including field, laboratory and modeling studies to provide quantitative estimates of actinide migration in the RFETS environment. For pathways where more than one method was used to estimate offsite loads for a specific pathway, the method yielding the highest estimated off-site was used for comparison purposes. For all actinides studied, for pre-remediation conditions, air and surface water were identified to be the dominant transport mechanisms. The estimated annual airborne plutonium-239/240 load transported off site exceeded the surface water load by roughly a factor of 40. However, despite being the largest transport pathway, airborne radionuclide concentrations at the monitoring location with the highest measurements during the period studied were less than two percent of the allowable 10 milli-rem standard governing DOE facilities. Estimated actinide loads for other pathways were much less. Shallow groundwater was approximately two orders of magnitude lower, or 1/100 of the load conveyed in surface water. The estimated biological pathway load for plutonium was approximately five orders of magnitude less, or 1/100,000, of the load estimated for surface-water. The pathway analysis results were taken into consideration during subsequent remediation activities that occurred at the site. For example, when the 903 Pad area was remediated to address elevated concentrations of Pu and Am in the surface soil, portable tent structures were constructed to prevent wind and water erosion from occurring while remediation activities took place. Following remediation of the 903 Pad and surrounding area, coconut erosion blankets were installed to mitigate erosion effects while vegetation was reestablished [2]. These measures were effective tools to address the primary transport mechanisms identified, coupling the scientific understanding of the site with the remediation strategy.« less

Clinical effects of air pollution on the central nervous system; a review.

PubMed

Babadjouni, Robin M; Hodis, Drew M; Radwanski, Ryan; Durazo, Ramon; Patel, Arati; Liu, Qinghai; Mack, William J

2017-09-01

The purpose of this review is to describe recent clinical and epidemiological studies examining the adverse effects of urban air pollution on the central nervous system (CNS). Air pollution and particulate matter (PM) are associated with neuroinflammation and reactive oxygen species (ROS). These processes affect multiple CNS pathways. The conceptual framework of this review focuses on adverse effects of air pollution with respect to neurocognition, white matter disease, stroke, and carotid artery disease. Both children and older individuals exposed to air pollution exhibit signs of cognitive dysfunction. However, evidence on middle-aged cohorts is lacking. White matter injury secondary to air pollution exposure is a putative mechanism for neurocognitive decline. Air pollution is associated with exacerbations of neurodegenerative conditions such as Alzheimer's and Parkinson's diseases. Increases in stroke incidences and mortalities are seen in the setting of air pollution exposure and CNS pathology is robust. Large populations living in highly polluted environments are at risk. This review aims to outline current knowledge of air pollution exposure effects on neurological health. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of alternative pathways for reducing nitrogen oxide emissions.

PubMed

Loughlin, Daniel H; Kaufman, Katherine R; Lenox, Carol S; Hubbell, Bryan J

2015-09-01

Strategies for reducing tropospheric ozone (O3) typically include modifying combustion processes to reduce the formation of nitrogen oxides (NOx) and applying control devices that remove NOx from the exhaust gases of power plants, industrial sources and vehicles. For portions of the U.S., these traditional controls may not be sufficient to achieve the National Ambient Air Quality Standard for ozone. We apply the MARKet ALlocation (MARKAL) energy system model in a sensitivity analysis to explore whether additional NOx reductions can be achieved through extensive electrification of passenger vehicles, adoption of energy efficiency and conservation measures within buildings, and deployment of wind and solar power in the electric sector. Nationally and for each region of the country, we estimate the NOx implications of these measures. Energy efficiency and renewable electricity are shown to reduce NOx beyond traditional controls. Wide-spread light duty vehicle electrification produces varied results, with NOx increasing in some regions and decreasing in others. However, combining vehicle electrification with renewable electricity reduces NOx in all regions. State governments are charged with developing plans that demonstrate how air quality standards will be met and maintained. The results presented here provide an indication of the national and regional NOx reductions available beyond traditional controls via extensive adoption of energy efficiency, renewable electricity, and vehicle electrification.

Investigation of Ruthenium Dissolution in Advanced Membrane Electrode Assemblies for Direct Methanol Based Fuel Cell Stacks

NASA Technical Reports Server (NTRS)

Valdez, Thomas I.; Firdosy, S.; Koel, B. E.; Narayanan, S. R.

2005-01-01

Dissolution of ruthenium was observed in the 80-cell stack. Duration testing was performed in single cell MEAs to determine the pathway of cell degradation. EDAX analysis on each of the single cell MEAs has shown that the Johnson Matthey commercial catalyst is stable in DMFC operation for 250 hours, no ruthenium dissolution was observed. Changes in the hydrophobicity of the cathode backing papers was minimum. Electrode polarization analysis revealed that the MEA performance loss is attributed to changes in the cathode catalyst layer. Ruthenium migration does not seem to occur during cell operation but can occur when methanol is absent from the anode compartment, the cathode compartment has access to air, and the cells in the stack are electrically connected to a load (Shunt Currents). The open-to-air cathode stack design allowed for: a) The MEAs to have continual access to oxygen; and b) The stack to sustain shunt currents. Ruthenium dissolution in a DMFC stack can be prevented by: a) Developing an internally manifolded stacks that seal reactant compartments when not in operation; b) Bringing the cell voltages to zero quickly when not in operation; and c) Limiting the total number of cells to 25 in an effort to limit shunt currents.

Global Air Quality and Climate

NASA Technical Reports Server (NTRS)

Fiore, Arlene M.; Naik, Vaishali; Steiner, Allison; Unger, Nadine; Bergmann, Dan; Prather, Michael; Righi, Mattia; Rumbold, Steven T.; Shindell, Drew T.; Skeie, Ragnhild B.;

Challenges and Opportunities of Airborne Metagenomics

PubMed Central

Behzad, Hayedeh; Gojobori, Takashi; Mineta, Katsuhiko

2015-01-01

Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles. PMID:25953766

Alternative Methods for Assessing Contaminant Transport from the Vadose Zone to Indoor Air

NASA Astrophysics Data System (ADS)

Baylor, K. J.; Lee, A.; Reddy, P.; Plate, M.

2010-12-01

Vapor intrusion, which is the transport of contaminant vapors from groundwater and the vadose zone to indoor air, has emerged as a significant human health risk near hazardous waste sites. Volatile organic compounds (VOCs) such as trichloroethylene (TCE) and tetrachloroethylene (PCE) can volatilize from groundwater and from residual sources in the vadose zone and enter homes and commercial buildings through cracks in the slab, plumbing conduits, or other preferential pathways. Assessment of the vapor intrusion pathway typically requires collection of groundwater, soil gas, and indoor air samples, a process which can be expensive and time-consuming. We evaluated three alternative vapor intrusion assessment methods, including 1) use of radon as a surrogate for vapor intrusion, 2) use of pressure differential measurements between indoor/outdoor and indoor/subslab to assess the potential for vapor intrusion, and 3) use of passive, longer-duration sorbent methods to measure indoor air VOC concentrations. The primary test site, located approximately 30 miles south of San Francisco, was selected due to the presence of TCE (10 - 300 ug/L) in shallow groundwater (5 to 10 feet bgs). At this test site, we found that radon was not a suitable surrogate to asses vapor intrusion and that pressure differential measurements are challenging to implement and equipment-intensive. More significantly, we found that the passive, longer-duration sorbent methods are easy to deploy and compared well quantitatively with standard indoor air sampling methods. The sorbent technique is less than half the cost of typical indoor air methods, and also provides a longer duration sample, typically 3 to 14 days rather than 8 to 24 hours for standard methods. The passive sorbent methods can be a reliable, cost-effective, and easy way to sample for TCE, PCE and other VOCs as part of a vapor intrusion investigation.

The Characteristics of Long-range Transboundary Inorganic Secondary Aerosols in Northeast Asia

NASA Astrophysics Data System (ADS)

Kim, Y. J.; Carmichael, G. R.; Woo, J. H.; Qiang, Z.

2014-12-01

Recurrent particle matter episodes greatly influence air quality in Northeast Asia. According to many studies, a major reason is long-range transport of air pollutant. Large amount of emission of chemical compounds aggravate air pollution in the region. Emitted air pollutants mainly come from industrialized regions along the East China coast. It can be transported over downwind region by the prevailing westerlies. The long-rang transported fine particle certainly attributes to air quality in downwind region, but there are many unknowns on the quantity, transport pattern, and secondary aerosol production mechanism despite the fact with many studies have been performed. Major contributors of PM2.5 are inorganic secondary aerosols, sulfate, nitrate and ammonium, in Korea. Especially high relative contributions of inorganic secondary aerosols appear for westerly wind cases. The main pathway of production of inorganic secondary aerosols is produced by converting from SO2 and NOx during the long-range transport but the contribution varies dramatically depending on season and wind pattern. Sulfate is consistently the primary contributor of PM2.5 still now but we should more concern nitrate because that NOx emissions of China is increasing steeply since 2000 by leading powerplant, industry, and transport, despite downward trend of SO2. In order to better understand regional air quality modeling of the long-range transport, international study, MICS-Asia phase III, has been initiated with many researchers. We will present chemical characteristics of PM2.5 long-range transport during westerly wind cases focused on secondary aerosol, tracking their transport pattern, and production pathway. Results using CMAQ with the modeling domain covering Northeast and Southeast China, Korea, and Japan with 15km resolution will be discussed.

A multi-model assessment of the co-benefits of climate mitigation for global air quality

NASA Astrophysics Data System (ADS)

Rao, Shilpa; Klimont, Zbigniew; Leitao, Joana; Riahi, Keywan; van Dingenen, Rita; Aleluia Reis, Lara; Calvin, Katherine; Dentener, Frank; Drouet, Laurent; Fujimori, Shinichiro; Harmsen, Mathijs; Luderer, Gunnar; Heyes, Chris; Strefler, Jessica; Tavoni, Massimo; van Vuuren, Detlef P.

2016-12-01

We present a model comparison study that combines multiple integrated assessment models with a reduced-form global air quality model to assess the potential co-benefits of global climate mitigation policies in relation to the World Health Organization (WHO) goals on air quality and health. We include in our assessment, a range of alternative assumptions on the implementation of current and planned pollution control policies. The resulting air pollution emission ranges significantly extend those in the Representative Concentration Pathways. Climate mitigation policies complement current efforts on air pollution control through technology and fuel transformations in the energy system. A combination of stringent policies on air pollution control and climate change mitigation results in 40% of the global population exposed to PM levels below the WHO air quality guideline; with the largest improvements estimated for India, China, and Middle East. Our results stress the importance of integrated multisector policy approaches to achieve the Sustainable Development Goals.

AIRE-induced apoptosis is associated with nuclear translocation of stress sensor protein GAPDH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liiv, Ingrid, E-mail: ingrid.liiv@ut.ee; Haljasorg, Uku; Kisand, Kai

2012-06-22

Highlights: Black-Right-Pointing-Pointer AIRE induces apoptosis in epithelial cells. Black-Right-Pointing-Pointer CARD domain of AIRE is sufficient for apoptosis induction. Black-Right-Pointing-Pointer AIRE induced apoptosis involves GAPDH translocation to the nuclei. Black-Right-Pointing-Pointer Deprenyl inhibits AIRE induced apoptosis. -- Abstract: AIRE (Autoimmune Regulator) has a central role in the transcriptional regulation of self-antigens in medullary thymic epithelial cells, which is necessary for negative selection of autoreactive T cells. Recent data have shown that AIRE can also induce apoptosis, which may be linked to cross-presentation of these self-antigens. Here we studied AIRE-induced apoptosis using AIRE over-expression in a thymic epithelial cell line as well asmore » doxycycline-inducible HEK293 cells. We show that the HSR/CARD domain in AIRE together with a nuclear localization signal is sufficient to induce apoptosis. In the nuclei of AIRE-positive cells, we also found an increased accumulation of a glycolytic enzyme, glyceraldehyde-3-phosphate (GAPDH) reflecting cellular stress and apoptosis. Additionally, AIRE-induced apoptosis was inhibited with an anti-apoptotic agent deprenyl that blocks GAPDH nitrosylation and nuclear translocation. We propose that the AIRE-induced apoptosis pathway is associated with GAPDH nuclear translocation and induction of NO-induced cellular stress in AIRE-expressing cells.« less

Visualizing the intercity correlation of PM2.5 time series in the Beijing-Tianjin-Hebei region using ground-based air quality monitoring data.

PubMed

Liu, Jianzheng; Li, Weifeng; Wu, Jiansheng; Liu, Yonghong

2018-01-01

The Beijing-Tianjin-Hebei area faces a severe fine particulate matter (PM2.5) problem. To date, considerable progress has been made toward understanding the PM2.5 problem, including spatial-temporal characterization, driving factors, and health effects. However, little research has been done on the dynamic interactions and relationships between PM2.5 concentrations in different cities in this area. To address the research gap, this study discovered a phenomenon of time-lagged intercity correlations of PM2.5 time series and proposed a visualization framework based on this phenomenon to visualize the interaction in PM2.5 concentrations between cities. The visualizations produced using the framework show that there are significant time-lagged correlations between the PM2.5 time series in different cities in this area. The visualizations also show that the correlations are more significant in colder months and between cities that are closer, and that there are seasonal changes in the temporal order of the correlated PM2.5 time series. Further analysis suggests that the time-lagged intercity correlations of PM2.5 time series are most likely due to synoptic meteorological variations. We argue that the visualizations demonstrate the interactions of air pollution between cities in the Beijing-Tianjin-Hebei area and the significant effect of synoptic meteorological conditions on PM2.5 pollution. The visualization framework could help determine the pathway of regional transportation of air pollution and may also be useful in delineating the area of interaction of PM2.5 pollution for impact analysis.

Visualizing the intercity correlation of PM2.5 time series in the Beijing-Tianjin-Hebei region using ground-based air quality monitoring data

PubMed Central

Li, Weifeng; Wu, Jiansheng; Liu, Yonghong

2018-01-01

The Beijing-Tianjin-Hebei area faces a severe fine particulate matter (PM2.5) problem. To date, considerable progress has been made toward understanding the PM2.5 problem, including spatial-temporal characterization, driving factors, and health effects. However, little research has been done on the dynamic interactions and relationships between PM2.5 concentrations in different cities in this area. To address the research gap, this study discovered a phenomenon of time-lagged intercity correlations of PM2.5 time series and proposed a visualization framework based on this phenomenon to visualize the interaction in PM2.5 concentrations between cities. The visualizations produced using the framework show that there are significant time-lagged correlations between the PM2.5 time series in different cities in this area. The visualizations also show that the correlations are more significant in colder months and between cities that are closer, and that there are seasonal changes in the temporal order of the correlated PM2.5 time series. Further analysis suggests that the time-lagged intercity correlations of PM2.5 time series are most likely due to synoptic meteorological variations. We argue that the visualizations demonstrate the interactions of air pollution between cities in the Beijing-Tianjin-Hebei area and the significant effect of synoptic meteorological conditions on PM2.5 pollution. The visualization framework could help determine the pathway of regional transportation of air pollution and may also be useful in delineating the area of interaction of PM2.5 pollution for impact analysis. PMID:29438417

Transcriptome-wide analyses indicate mitochondrial responses to particulate air pollution exposure.

PubMed

Winckelmans, Ellen; Nawrot, Tim S; Tsamou, Maria; Den Hond, Elly; Baeyens, Willy; Kleinjans, Jos; Lefebvre, Wouter; Van Larebeke, Nicolas; Peusens, Martien; Plusquin, Michelle; Reynders, Hans; Schoeters, Greet; Vanpoucke, Charlotte; de Kok, Theo M; Vrijens, Karen

2017-08-18

Due to their lack of repair capacity mitochondria are critical targets for environmental toxicants. We studied genes and pathways reflecting mitochondrial responses to short- and medium-term PM 10 exposure. Whole genome gene expression was measured in peripheral blood of 98 adults (49% women). We performed linear regression analyses stratified by sex and adjusted for individual and temporal characteristics to investigate alterations in gene expression induced by short-term (week before blood sampling) and medium-term (month before blood sampling) PM 10 exposure. Overrepresentation analyses (ConsensusPathDB) were performed to identify enriched mitochondrial associated pathways and gene ontology sets. Thirteen Human MitoCarta genes were measured by means of quantitative real-time polymerase chain reaction (qPCR) along with mitochondrial DNA (mtDNA) content in an independent validation cohort (n = 169, 55.6% women). Overrepresentation analyses revealed significant pathways (p-value <0.05) related to mitochondrial genome maintenance and apoptosis for short-term exposure and to the electron transport chain (ETC) for medium-term exposure in women. For men, medium-term PM 10 exposure was associated with the Tri Carbonic Acid cycle. In an independent study population, we validated several ETC genes, including UQCRH and COX7C (q-value <0.05), and some genes crucial for the maintenance of the mitochondrial genome, including LONP1 (q-value: 0.07) and POLG (q-value: 0.04) in women. In this exploratory study, we identified mitochondrial genes and pathways associated with particulate air pollution indicating upregulation of energy producing pathways as a potential mechanism to compensate for PM-induced mitochondrial damage.

ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis

PubMed Central

Han, Junwei; Shi, Xinrui; Zhang, Yunpeng; Xu, Yanjun; Jiang, Ying; Zhang, Chunlong; Feng, Li; Yang, Haixiu; Shang, Desi; Sun, Zeguo; Su, Fei; Li, Chunquan; Li, Xia

2015-01-01

Pathway analyses are playing an increasingly important role in understanding biological mechanism, cellular function and disease states. Current pathway-identification methods generally focus on only the changes of gene expression levels; however, the biological relationships among genes are also the fundamental components of pathways, and the dysregulated relationships may also alter the pathway activities. We propose a powerful computational method, Edge Set Enrichment Analysis (ESEA), for the identification of dysregulated pathways. This provides a novel way of pathway analysis by investigating the changes of biological relationships of pathways in the context of gene expression data. Simulation studies illustrate the power and performance of ESEA under various simulated conditions. Using real datasets from p53 mutation, Type 2 diabetes and lung cancer, we validate effectiveness of ESEA in identifying dysregulated pathways. We further compare our results with five other pathway enrichment analysis methods. With these analyses, we show that ESEA is able to help uncover dysregulated biological pathways underlying complex traits and human diseases via specific use of the dysregulated biological relationships. We develop a freely available R-based tool of ESEA. Currently, ESEA can support pathway analysis of the seven public databases (KEGG; Reactome; Biocarta; NCI; SPIKE; HumanCyc; Panther). PMID:26267116

Effect of gamma radiation on sugars and vitamin C: Radiolytic pathways.

PubMed

Ramírez-Cahero, Hiram F; Valdivia-López, Ma Angeles

2018-04-15

The radiolytic decomposition of glucose, fructose, sucrose, ascorbic acid (H 2 A) and dehydroascorbic acid (DHAA), induced by ionizing radiation, was investigated. Aqueous solutions of these compounds were gamma-irradiated at doses of 0.5, 0.7 and 1 kGy, with a dose rate of 0.04 kGy/min, in the presence of air, followed by HPLC, HPLC-MS, EPR, and UV-VIS spectroscopy analysis of the resulting mixtures. Carboxylic acids, 2-furaldehyde, 5-hydroxymethyl-2-furaldehyde, furfuryl alcohol, 2-furoic acid and 2(5H)-furanone were identified in solutions of sugars and vitamin C, by comparing with standards. EPR studies exhibited a higher amount of free radicals for fructose than the other sugars, and more for DHAA than H 2 A. Additionally, spectroscopic determinations showed a typical UV-VIS absorption for furans during the storage of irradiated solutions. Formation and decomposition routes for furanoids and aliphatic carboxylic acids, and mechanistic pathways for the radiolytic induced rupture of glucose, fructose, sucrose and vitamin C have been proposed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Elementary Mode Analysis: A Useful Metabolic Pathway Analysis Tool for Characterizing Cellular Metabolism

PubMed Central

Trinh, Cong T.; Wlaschin, Aaron; Srienc, Friedrich

2010-01-01

Elementary Mode Analysis is a useful Metabolic Pathway Analysis tool to identify the structure of a metabolic network that links the cellular phenotype to the corresponding genotype. The analysis can decompose the intricate metabolic network comprised of highly interconnected reactions into uniquely organized pathways. These pathways consisting of a minimal set of enzymes that can support steady state operation of cellular metabolism represent independent cellular physiological states. Such pathway definition provides a rigorous basis to systematically characterize cellular phenotypes, metabolic network regulation, robustness, and fragility that facilitate understanding of cell physiology and implementation of metabolic engineering strategies. This mini-review aims to overview the development and application of elementary mode analysis as a metabolic pathway analysis tool in studying cell physiology and as a basis of metabolic engineering. PMID:19015845

Caffeic acid phenethyl ester inhibits diesel exhaust particle-induced inflammation of human middle ear epithelial cells via NOX4 inhibition.

PubMed

Jo, Sun-Young; Lee, Naree; Hong, Sung-Moon; Jung, Hak Hyun; Chae, Sung-Won

2013-09-01

Otitis media is one of the most common diseases in pediatric populations. Recent research on its pathogenesis has focused on air pollution. Chronic exposure to particulate air pollution is associated with the impairment of middle ear function. However, the mechanisms and the underlying inhibitory pathways, especially in the human middle ear, remain unknown. Caffeic acid phenethyl ester (CAPE) is a biologically active ingredient of propolis, a product of honeybee hives, which has anti-oxidative and anti-inflammatory activities. The aim of this study was to evaluate the inhibitory effect of CAPE on diesel exhaust particle (DEP)-induced inflammation of human middle ear epithelial cells and to determine the underlying pathway of the action of CAPE. The inflammatory damage caused by DEPs and the anti-inflammatory effects of CAPE were determined by measuring the levels of tumor necrosis factor alpha and nicotinamide adenine dinucleotide phosphate oxidase (NOX) 4 with real-time reverse transcription polymerase chain reaction and Western blot analysis. The oxidative stress induced by DEPs and the anti-oxidative effects of CAPE were directly evaluated by measuring reactive oxygen species production by use of flow cytometric analysis of 2',7'-dichlorofluorescein diacetate. The effects of CAPE were compared with those of N-acetyl-L-cysteine, which has anti-oxidative and anti-inflammatory effects. Use of CAPE significantly inhibited DEP-induced up-regulation of tumor necrosis factor alpha and NOX4 expression in a dose- and time-dependent manner. The accumulation of reactive oxygen species induced by DEPs was decreased by pretreatment with CAPE. The anti-inflammatory and anti-oxidative effects of CAPE were similar to those of N-acetyl-L-cysteine. The inflammation induced by DEP is reduced by CAPE via the inhibition of NOX4 expression. These findings suggest that CAPE might be used as a therapeutic agent against DEP-induced inflammation of human middle ear epithelial cells.

Integrative Analysis of the Physical Transport Network into Australia.

PubMed

Cope, Robert C; Ross, Joshua V; Wittmann, Talia A; Prowse, Thomas A A; Cassey, Phillip

2016-01-01

Effective biosecurity is necessary to protect nations and their citizens from a variety of threats, including emerging infectious diseases, agricultural or environmental pests and pathogens, and illegal wildlife trade. The physical pathways by which these threats are transported internationally, predominantly shipping and air traffic, have undergone significant growth and changes in spatial distributions in recent decades. An understanding of the specific pathways and donor-traffic hotspots created by this integrated physical transport network is vital for the development of effective biosecurity strategies into the future. In this study, we analysed the physical transport network into Australia over the period 1999-2012. Seaborne and air traffic were weighted to calculate a "weighted cumulative impact" score for each source region worldwide, each year. High risk source regions, and those source regions that underwent substantial changes in risk over the study period, were determined. An overall risk ranking was calculated by integrating across all possible weighting combinations. The source regions having greatest overall physical connectedness with Australia were Singapore, which is a global transport hub, and the North Island of New Zealand, a close regional trading partner with Australia. Both those regions with large amounts of traffic across multiple vectors (e.g., Hong Kong), and those with high levels of traffic of only one type (e.g., Bali, Indonesia with respect to passenger flights), were represented among high risk source regions. These data provide a baseline model for the transport of individuals and commodities against which the effectiveness of biosecurity controls may be assessed, and are a valuable tool in the development of future biosecurity policy.

Integrative Analysis of the Physical Transport Network into Australia

PubMed Central

Cope, Robert C.; Ross, Joshua V.; Wittmann, Talia A.; Prowse, Thomas A. A.; Cassey, Phillip

2016-01-01

Effective biosecurity is necessary to protect nations and their citizens from a variety of threats, including emerging infectious diseases, agricultural or environmental pests and pathogens, and illegal wildlife trade. The physical pathways by which these threats are transported internationally, predominantly shipping and air traffic, have undergone significant growth and changes in spatial distributions in recent decades. An understanding of the specific pathways and donor-traffic hotspots created by this integrated physical transport network is vital for the development of effective biosecurity strategies into the future. In this study, we analysed the physical transport network into Australia over the period 1999–2012. Seaborne and air traffic were weighted to calculate a “weighted cumulative impact” score for each source region worldwide, each year. High risk source regions, and those source regions that underwent substantial changes in risk over the study period, were determined. An overall risk ranking was calculated by integrating across all possible weighting combinations. The source regions having greatest overall physical connectedness with Australia were Singapore, which is a global transport hub, and the North Island of New Zealand, a close regional trading partner with Australia. Both those regions with large amounts of traffic across multiple vectors (e.g., Hong Kong), and those with high levels of traffic of only one type (e.g., Bali, Indonesia with respect to passenger flights), were represented among high risk source regions. These data provide a baseline model for the transport of individuals and commodities against which the effectiveness of biosecurity controls may be assessed, and are a valuable tool in the development of future biosecurity policy. PMID:26881782

Uncertainty, Sensitivity Analysis, and Causal Identification in the Arctic using a Perturbed Parameter Ensemble of the HiLAT Climate Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunke, Elizabeth Clare; Urrego Blanco, Jorge Rolando; Urban, Nathan Mark

Coupled climate models have a large number of input parameters that can affect output uncertainty. We conducted a sensitivity analysis of sea ice proper:es and Arc:c related climate variables to 5 parameters in the HiLAT climate model: air-ocean turbulent exchange parameter (C), conversion of water vapor to clouds (cldfrc_rhminl) and of ice crystals to snow (micro_mg_dcs), snow thermal conduc:vity (ksno), and maximum snow grain size (rsnw_mlt). We used an elementary effect (EE) approach to rank their importance for output uncertainty. EE is an extension of one-at-a-time sensitivity analyses, but it is more efficient in sampling multi-dimensional parameter spaces. We lookedmore » for emerging relationships among climate variables across the model ensemble, and used causal discovery algorithms to establish potential pathways for those relationships.« less

Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production.

PubMed

George, Kevin W; Chen, Amy; Jain, Aakriti; Batth, Tanveer S; Baidoo, Edward E K; Wang, George; Adams, Paul D; Petzold, Christopher J; Keasling, Jay D; Lee, Taek Soon

2014-08-01

The ability to rapidly assess and optimize heterologous pathway function is critical for effective metabolic engineering. Here, we develop a systematic approach to pathway analysis based on correlations between targeted proteins and metabolites and apply it to the microbial production of isopentenol, a promising biofuel. Starting with a seven-gene pathway, we performed a correlation analysis to reduce pathway complexity and identified two pathway proteins as the primary determinants of efficient isopentenol production. Aided by the targeted quantification of relevant pathway intermediates, we constructed and subsequently validated a conceptual model of isopentenol pathway function. Informed by our analysis, we assembled a strain which produced isopentenol at a titer 1.5 g/L, or 46% of theoretical yield. Our engineering approach allowed us to accurately identify bottlenecks and determine appropriate pathway balance. Paired with high-throughput cloning techniques and analytics, this strategy should prove useful for the analysis and optimization of increasingly complex heterologous pathways. © 2014 Wiley Periodicals, Inc.

Analysis of the nicotinamide phosphoribosyltransferase family provides insight into vertebrate adaptation to different oxygen levels during the water-to-land transition.

PubMed

Fang, Chengchi; Guan, Lihong; Zhong, Zaixuan; Gan, Xiaoni; He, Shunping

2015-08-01

One of the most important events in vertebrate evolutionary history is the water-to-land transition, during which some morphological and physiological changes occurred in concert with the loss of specific genes in tetrapods. However, the molecular mechanisms underlying this transition have not been well explored. To explore vertebrate adaptation to different oxygen levels during the water-to-land transition, we performed comprehensive bioinformatics and experimental analysis aiming to investigate the NAMPT family in vertebrates. NAMPT, a rate-limiting enzyme in the salvage pathway of NAD+ biosynthesis, is critical for cell survival in a hypoxic environment, and a high level of NAMPT significantly augments oxidative stress in normoxic environments. Phylogenetic analysis showed that NAMPT duplicates arose from a second round whole-genome duplication event. NAMPTA existed in all classes of vertebrates, whereas NAMPTB was only found in fishes and not tetrapods. Asymmetric evolutionary rates and purifying selection were the main evolutionary forces involved. Although functional analysis identified several functionally divergent sites during NAMPT family evolution, in vitro experimental data demonstrated that NAMPTA and NAMPTB were functionally conserved for NAMPT enzymatic function in the NAD+ salvage pathway. In situ hybridization revealed broad NAMPTA and NAMPTB expression patterns, implying regulatory functions over a wide range of developmental processes. The morpholino-mediated knockdown data demonstrated that NAMPTA was more essential than NAMPTB for vertebrate embryo development. We propose that the retention of NAMPTB in water-breathing fishes and its loss in air-breathing tetrapods resulted from vertebrate adaptation to different oxygen levels during the water-to-land transition. © 2015 FEBS.

Global Mercury Pathways in the Arctic Ecosystem

NASA Astrophysics Data System (ADS)

Lahoutifard, N.; Lean, D.

2003-12-01

The sudden depletions of atmospheric mercury which occur during the Arctic spring are believed to involve oxidation of gaseous elemental mercury, Hg(0), rendering it less volatile and more soluble. The Hg(II) oxidation product(s) are more susceptible to deposition, consistent with the observation of dramatic increases in snow mercury levels during depletion events. Temporal correlations with ozone depletion events and the proliferation of BrO radicals support the hypothesis that oxidation of Hg(0) occurs in the gas phase and results in its conversion to RGM (Reactive Gaseous Mercury). The mechanisms of Hg(0) oxidation and particularly Hg(II) reduction are as yet unproven. In order to evaluate the feasibility of proposed chemical processes involving mercury in the Arctic atmosphere and its pathway after deposition on the snow from the air, we investigated mercury speciation in air and snow pack at Resolute, Nunavut, Canada (latitude 75° N) prior to and during snow melt during spring 2003. Quantitative, real-time information on emission, air transport and deposition were combined with experimental studies of the distribution and concentrations of different mercury species, methyl mercury, anions, total organic carbon and total inorganic carbon in snow samples. The effect of solar radiation and photoreductants on mercury in snow samples was also investigated. In this work, we quantify mercury removed from the air, and deposited on the snow and the transformation to inorganic and methyl mercury.

Summer 2015 measurements of total OH reactivity at a UK coastal site

NASA Astrophysics Data System (ADS)

Woodward-Massey, R.; Cryer, D. R.; Whalley, L. K.; Ingham, T.; Crilley, L.; Kramer, L. J.; Reeves, C.; Forster, G.; Oram, D.; Bandy, B.; Reed, C.; Lee, J. D.; Bloss, W.; Heard, D. E.

2015-12-01

The hydroxyl radical (OH) plays a central role in the day time oxidative removal of pollutants and greenhouse gases in the atmosphere. It is essential that all production and loss pathways of OH are understood and included in computer models in order to accurately predict OH concentrations for a range of environments, and in turn the rate of production of secondary products, for example ozone and organic aerosol. Direct measurement of total OH reactivity, the pseudo first order rate coefficient for OH loss by reaction with its sinks, is a very useful tool to test how complete our knowledge is of OH loss pathways. Comparison with values of total OH reactivity calculated by computer models using concentrations of simultaneously measured OH 'sinks' and unmeasured intermediates enables environments to be identified where there are unidentified 'missing' OH sinks. Total OH reactivity was measured using the laser flash photolysis combined with time-resolved laser-induced fluorescence technique during the ICOZA (Integrated Chemistry of OZone in the Atmosphere) campaign in July 2015 at the Weybourne Atmospheric Observatory (WAO), Norfolk, UK. Air masses sampled ranged from polluted air from the UK or Europe containing processed urban emissions to very clean air of marine origin. Data for measured and calculated OH reactivity will be presented in addition to a discussion of the magnitude of the 'missing' OH sink determined for each type of air mass.

Aqueous organic chemistry in the atmosphere: sources and chemical processing of organic aerosols.

PubMed

McNeill, V Faye

2015-02-03

Over the past decade, it has become clear that aqueous chemical processes occurring in cloud droplets and wet atmospheric particles are an important source of organic atmospheric particulate matter. Reactions of water-soluble volatile (or semivolatile) organic gases (VOCs or SVOCs) in these aqueous media lead to the formation of highly oxidized organic particulate matter (secondary organic aerosol; SOA) and key tracer species, such as organosulfates. These processes are often driven by a combination of anthropogenic and biogenic emissions, and therefore their accurate representation in models is important for effective air quality management. Despite considerable progress, mechanistic understanding of some key aqueous processes is still lacking, and these pathways are incompletely represented in 3D atmospheric chemistry and air quality models. In this article, the concepts, historical context, and current state of the science of aqueous pathways of SOA formation are discussed.

Characterization of cookstove emissions from various stoves, fuels, and cycles; intervention pathways and implications for climate

NASA Astrophysics Data System (ADS)

DeCarlo, P. F.; Jetter, J.; Khan, B.; Zhao, Y.; Yelverton, T.; Hays, M. D.

2011-12-01

Nearly half of the world's population relies on inefficient open fire or rudimentary cookstoves to prepare their food. Combustion of biomass or other fuels results in not only high indoor air pollution, but is also a large source of climate forcing species such as black and organic carbon species to the earth's atmosphere. Large-scale intervention programs are now underway to replace inefficient cooking methods with newer technologies. These intervention programs have as a goal the improvement of indoor air pollution and reduction of negative climate impacts. To characterize the current available alternatives, a major cookstove testing program was conducted at the US EPA. This presentation will focus on the characterization of the emission measurements for a variety of different cookstoves, fuels and cooking cycles. The work will focus on the aerosol optical properties measured with a PASS-3, and the climate impacts of various intervention pathways will be discussed.

Bourdieu does environmental justice? Probing the linkages between population health and air pollution epidemiology.

PubMed

Buzzelli, Michael

2007-03-01

The environmental justice literature faces a number of conceptual and methodological shortcomings. The purpose of this paper is to probe ways in which these shortcomings can be remedied via recent developments in related literatures: population health and air pollution epidemiology. More sophisticated treatment of social structure, particularly if based on Pierre Bourdieu's relational approach to forms of capital, can be combined with the methodological rigour and established biological pathways of air pollution epidemiology. The aim is to reformulate environmental justice research in order to make further meaningful contributions to the wider movement concerned with issues of social justice and equity in health research.

Air-soil exchange of organochlorine pesticides in a sealed chamber.

PubMed

Yang, Bing; Han, Baolu; Xue, Nandong; Zhou, Lingli; Li, Fasheng

2015-01-01

So far little is known about air-soil exchange under any sealed circumstances (e.g., in plastic and glass sheds), which however has huge implications for the soil-air-plant pathways of persistent organic pollutants including organochlorine pesticides (OCPs). A newly designed passive air sampler was tested in a sealed chamber for measuring the vertical concentration profiles of gaseous phase OCPs (hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethanes (DDTs)). Air was sampled at 5, 15, and 30 cm above ground level every 10th day during a 60-day period by deploying polyurethane foam cylinders housed in acrylonitrile butadiene styrene-covered cartridges. Concentrations and compositions of OCPs along the vertical sections indicated a clear relationship with proximity to the mixture of HCHs and DDTs which escapes from the soils. In addition, significant positive correlations were found between air temperatures and concentrations of HCHs and DDTs. These results indicated revolatilization and re-deposition being at or close to dynamic pseudo-equilibrium with the overlying air. The sampler used for addressing air-soil exchange of persistent organic pollutants in any sealed conditions is discussed. Copyright © 2014. Published by Elsevier B.V.

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms.

PubMed

Bianco, Luca; Riccadonna, Samantha; Lavezzo, Enrico; Falda, Marco; Formentin, Elide; Cavalieri, Duccio; Toppo, Stefano; Fontana, Paolo

2017-02-01

Pathway Inspector is an easy-to-use web application helping researchers to find patterns of expression in complex RNAseq experiments. The tool combines two standard approaches for RNAseq analysis: the identification of differentially expressed genes and a topology-based analysis of enriched pathways. Pathway Inspector is equipped with ad hoc interactive graphical interfaces simplifying the discovery of modulated pathways and the integration of the differentially expressed genes in the corresponding pathway topology. Pathway Inspector is available at the website http://admiral.fmach.it/PI and has been developed in Python, making use of the Django Web Framework. Contact:paolo.fontana@fmach.it

Air and radon pathways screenings methodologies for the next revision of the E-area PA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dyer, J. A.

The strategic plan for the next E-Area Low-Level Waste Facility Performance Assessment includes recommended changes to the screening criteria used to reduce the number of radioisotopes that are to be considered in the air and radon pathways incorporated into the GoldSim® atmospheric release model (ARM). For the air pathway, a revised screening methodology was developed based on refinement of previous E-Area PA screening approaches and consideration of the strategic plan recommendations. The revised methodology has three sequential screening steps for each radioisotope: (1) volatility test using the Periodic Table of the Elements, (2) stability test based on half-life, and (3)more » stability test based on volatility as measured by the Henry’s Law constant for the assumed dominant gaseous species or vapor pressure in the case of tritiated water. Of the 1252 radioisotopes listed in the International Commission on Radiological Protection Publication 107, only the 10 that satisfied all three steps of the revised screening methodology will be included in the ARM. They are: Ar-37, Ar-39, Ar-42, C-14, H-3, Hg-194, Hg-203, Kr-81, Kr-85, and Xe-127. For the radon pathway, a revised screening methodology was developed that also has three sequential steps: (1) identify all decay chains that terminate at Rn-222, (2) screen out parents that decay through U-238 because of its 4.5-billion-year primordial half-life, and (3) eliminate remaining parents whose half-life is shorter than one day. Of the 86 possible decay chains leading to Rn-222, six decay chains consist of 15 unique radioisotopes that will be incorporated into the ARM. The 15 radioisotopes are: U-238, Th-234, Pa-234m, Pu-238, U-234, Th-230, Ra-226, Cf-246, Cm-242, Am-242m, Am-242, Np-238, Np-234, Pa-230, and Rn-222.« less

A review of models for near-field exposure pathways of chemicals in consumer products.

PubMed

Huang, Lei; Ernstoff, Alexi; Fantke, Peter; Csiszar, Susan A; Jolliet, Olivier

2017-01-01

Exposure to chemicals in consumer products has been gaining increasing attention, with multiple studies showing that near-field exposures from products is high compared to far-field exposures. Regarding the numerous chemical-product combinations, there is a need for an overarching review of models able to quantify the multiple transfers of chemicals from products used near-field to humans. The present review therefore aims at an in-depth overview of modeling approaches for near-field chemical release and human exposure pathways associated with consumer products. It focuses on lower-tier, mechanistic models suitable for life cycle assessments (LCA), chemical alternative assessment (CAA) and high-throughput screening risk assessment (HTS). Chemicals in a product enter the near-field via a defined "compartment of entry", are transformed or transferred to adjacent compartments, and eventually end in a "human receptor compartment". We first focus on models of physical mass transfers from the product to 'near-field' compartments. For transfers of chemicals from article interior, adequate modeling of in-article diffusion and of partitioning between article surface and air/skin/food is key. Modeling volatilization and subsequent transfer to the outdoor is crucial for transfers of chemicals used in the inner space of appliances, on object surfaces or directly emitted to indoor air. For transfers from skin surface, models need to reflect the competition between dermal permeation, volatilization and fraction washed-off. We then focus on transfers from the 'near-field' to 'human' compartments, defined as respiratory tract, gastrointestinal tract and epidermis, for which good estimates of air concentrations, non-dietary ingestion parameters and skin permeation are essential, respectively. We critically characterize for each exposure pathway the ability of models to estimate near-field transfers and to best inform LCA, CAA and HTS, summarizing the main characteristics of the potentially best-suited models. This review identifies large knowledge gaps for several near-field pathways and suggests research needs and future directions. Copyright © 2016 Elsevier B.V. All rights reserved.

Colorado air quality impacted by long-range-transported aerosol: a set of case studies during the 2015 Pacific Northwest fires

NASA Astrophysics Data System (ADS)

Creamean, Jessie M.; Neiman, Paul J.; Coleman, Timothy; Senff, Christoph J.; Kirgis, Guillaume; Alvarez, Raul J.; Yamamoto, Atsushi

2016-09-01

Biomass burning plumes containing aerosols from forest fires can be transported long distances, which can ultimately impact climate and air quality in regions far from the source. Interestingly, these fires can inject aerosols other than smoke into the atmosphere, which very few studies have evidenced. Here, we demonstrate a set of case studies of long-range transport of mineral dust aerosols in addition to smoke from numerous fires (including predominantly forest fires and a few grass/shrub fires) in the Pacific Northwest to Colorado, US. These aerosols were detected in Boulder, Colorado, along the Front Range using beta-ray attenuation and energy-dispersive X-ray fluorescence spectroscopy, and corroborated with satellite-borne lidar observations of smoke and dust. Further, we examined the transport pathways of these aerosols using air mass trajectory analysis and regional- and synoptic-scale meteorological dynamics. Three separate events with poor air quality and increased mass concentrations of metals from biomass burning (S and K) and minerals (Al, Si, Ca, Fe, and Ti) occurred due to the introduction of smoke and dust from regional- and synoptic-scale winds. Cleaner time periods with good air quality and lesser concentrations of biomass burning and mineral metals between the haze events were due to the advection of smoke and dust away from the region. Dust and smoke present in biomass burning haze can have diverse impacts on visibility, health, cloud formation, and surface radiation. Thus, it is important to understand how aerosol populations can be influenced by long-range-transported aerosols, particularly those emitted from large source contributors such as wildfires.

Pathway modeling of microarray data: A case study of pathway activity changes in the testis following in utero exposure to dibutyl phthalate (DBP)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ovacik, Meric A.; Sen, Banalata; Euling, Susan Y.

Pathway activity level analysis, the approach pursued in this study, focuses on all genes that are known to be members of metabolic and signaling pathways as defined by the KEGG database. The pathway activity level analysis entails singular value decomposition (SVD) of the expression data of the genes constituting a given pathway. We explore an extension of the pathway activity methodology for application to time-course microarray data. We show that pathway analysis enhances our ability to detect biologically relevant changes in pathway activity using synthetic data. As a case study, we apply the pathway activity level formulation coupled with significancemore » analysis to microarray data from two different rat testes exposed in utero to Dibutyl Phthalate (DBP). In utero DBP exposure in the rat results in developmental toxicity of a number of male reproductive organs, including the testes. One well-characterized mode of action for DBP and the male reproductive developmental effects is the repression of expression of genes involved in cholesterol transport, steroid biosynthesis and testosterone synthesis that lead to a decreased fetal testicular testosterone. Previous analyses of DBP testes microarray data focused on either individual gene expression changes or changes in the expression of specific genes that are hypothesized, or known, to be important in testicular development and testosterone synthesis. However, a pathway analysis may inform whether there are additional affected pathways that could inform additional modes of action linked to DBP developmental toxicity. We show that Pathway activity analysis may be considered for a more comprehensive analysis of microarray data.« less

Assessment of environmental co-benefits of energy system decarbonisation - the case of UK air quality using Remote Sensing and Model simulations

NASA Astrophysics Data System (ADS)

Sobral Mourao, Z.; Konadu, D. D.; Damoah, R.

2016-12-01

The UK has a binding obligation to reduce GHG emission by 80% (based on 1990 levels) by 2050. Meeting this target requires extensive decarbonisation of the UK energy system. Different pathways that achieve this target at the lowest system costs are being explored at different levels of policy and decisions on future energy infrastructure. Whilst benefits of decarbonisation are mainly focused on the impacts on climate change, there are other potential environmental and health impacts such as air-quality. In particular, a decrease in fossil fuel use by directly substituting current systems with low-carbon technologies could lead to significant reductions in the concentrations of SO2, NOX, CO and other atmospheric pollutants. So far, the proposed decarbonisation pathways tend to target the electricity sector first, followed by a transition in transport and heating technologies and use. However, the spatial dimension of where short term changes in the energy sector occur in relation to high density population areas is not taken into account when defining the energy transition strategies. This may lead to limited short-term improvements in air quality within urban areas, where use of fossil fuels for heating and transport is the main contribution to overall atmospheric pollutant levels. It is therefore imperative to explore decarbonisation strategies that prioritise transition in sectors of the energy system that produce immediate improvements in air quality in key regions of the UK. This study aims to use a combination of Remote Sensing observations and atmospheric chemistry/transport modelling approaches to estimate and map the atmospheric pollutants impact of the traditional approach of decarbonising electricity first compared to a slower transition in the electricity sector, but faster change in end use sectors (heating and transport). This would provide an additional standard to compare future energy system pathways beyond the traditional metrics of cost and GHG emissions reductions.

Building upon the Great Waters Initiative: Scoping study for potential polyaromatic hydrocarbon deposition into San Diego Bay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koehler, J.; Sylte, W.W.

1997-12-31

The deposition of atmospheric polyaromatic hydrocarbons (PAHs) into San Diego Bay was evaluated at an initial study level. This study was part of an overall initial estimate of PAH waste loading to San Diego Bay from all environmental pathways. The study of air pollutant deposition to water bodies has gained increased attention both as a component of Total Maximum Daily Load (TMDL) determinations required under the Clean Water Act and pursuant to federal funding authorized by the 1990 Clean Air Act Amendments to study the atmospheric deposition of hazardous air pollutants to the Great Waters, which includes coastal waters. Tomore » date, studies under the Clean Air Act have included the Great Lakes, Chesapeake Bay, Lake Champlain, and Delaware Bay. Given the limited resources of this initial study for San Diego Bay, the focus was on maximizing the use of existing data and information. The approach developed included the statistical evaluation of measured atmospheric PAH concentrations in the San Diego area, the extrapolation of EPA study results of atmospheric PAH concentrations above Lake Michigan to supplement the San Diego data, the estimation of dry and wet deposition with published calculation methods considering local wind and rainfall data, and the comparison of resulting PAH deposition estimates for San Diego Bay with estimated PAH emissions from ship and commercial boat activity in the San Diego area. The resulting PAH deposition and ship emission estimates were within the same order of magnitude. Since a significant contributor to the atmospheric deposition of PAHs to the Bay is expected to be from shipping traffic, this result provides a check on the order of magnitude on the PAH deposition estimate. Also, when compared against initial estimates of PAH loading to San Diego Bay from other environmental pathways, the atmospheric deposition pathway appears to be a significant contributor.« less

Modulation of the cyclooxygenase pathway via inhibition of nitric oxide production contributes to the anti-inflammatory activity of kaempferol.

PubMed

Mahat, Mahamad Yunnus A; Kulkarni, Nagaraj M; Vishwakarma, Santosh L; Khan, Farhin R; Thippeswamy, B S; Hebballi, Vijay; Adhyapak, Anjana A; Benade, Vijay S; Ashfaque, Saudagar Mohammad; Tubachi, Suraj; Patil, Basangouda M

2010-09-10

Kaempferol has been reported to inhibit nitric oxide synthase and cyclooxygenase enzymes in animal models. The present study was designed to investigate whether kaempferol modulates the cyclooxygenase pathway via inhibition of nitric oxide production, which in turn contributes to its anti-inflammatory activity. Investigations were performed using carrageenan induced rat air pouch model. Inflammation was assessed by measurement of nitrites (nitrite, a breakdown product of nitric oxide), prostaglandin-E(2) levels and cellular infiltration in the pouch fluid exudates. To assess the anti-inflammatory effect of the extract, rat air pouch linings were examined histologically. The levels of nitrite and prostaglandin-E(2) in pouch fluid were measured by using Griess assay and ELISA respectively. Cell counts and differential counts were performed using a Coulter counter and Wright-Giemsa stain respectively. Kaempferol when administered orally at 50 and 100mg/kg dose showed significant inhibition of carrageenan induced production of nitrite (40.12 and 59.74%, respectively) and prostaglandin-E(2) generation (64.23 and 78.55%, respectively). Infiltration of the cells into the rat granuloma air pouch was also significantly inhibited by kaempferol. Modulation of cyclooxygenase pathway via inhibition of nitric oxide synthesis significantly contributes to kaempferol's anti-inflammatory activity. The present study characterizes the effects and mechanisms of naturally occurring phenolic flavonoid kaempferol, on inducible nitric oxide synthase expression and nitric oxide production. These results partially explain the pharmacological efficacy of flavonoids in general and kaempferol in particular as anti-inflammatory compounds. Copyright (c) 2010 Elsevier B.V. All rights reserved.

PathFinder: reconstruction and dynamic visualization of metabolic pathways.

PubMed

Goesmann, Alexander; Haubrock, Martin; Meyer, Folker; Kalinowski, Jörn; Giegerich, Robert

2002-01-01

Beyond methods for a gene-wise annotation and analysis of sequenced genomes new automated methods for functional analysis on a higher level are needed. The identification of realized metabolic pathways provides valuable information on gene expression and regulation. Detection of incomplete pathways helps to improve a constantly evolving genome annotation or discover alternative biochemical pathways. To utilize automated genome analysis on the level of metabolic pathways new methods for the dynamic representation and visualization of pathways are needed. PathFinder is a tool for the dynamic visualization of metabolic pathways based on annotation data. Pathways are represented as directed acyclic graphs, graph layout algorithms accomplish the dynamic drawing and visualization of the metabolic maps. A more detailed analysis of the input data on the level of biochemical pathways helps to identify genes and detect improper parts of annotations. As an Relational Database Management System (RDBMS) based internet application PathFinder reads a list of EC-numbers or a given annotation in EMBL- or Genbank-format and dynamically generates pathway graphs.

[Association of Inorganics Accumulation with the Activation of NF-κB Signaling Pathway and the iNOS Expression of Lung Tissue in Xuanwei Lung Cancer Patients].

PubMed

Yang, Jiapeng; Li, Guangjian; Huang, Yunchao; Ye, Lianhua; Zhou, Yongchun; Zhao, Guangqiang; Lei, Yujie; Chen, Xiaobo; Wang, Kun; Chen, Ying; Dai, Chun; Zhang, Yanjun

2016-01-01

Indoor air pollution induces asthma, leads to chronic obstructive pulmonary disease, and may promote lung cancer. Our previous studies found that the accumulation of inorganic particulate matter that is due to indoor air pollution can lead to damage to alveolar cells and activation of signaling pathway, and ultimately provoke tumorigenesis. The aim of this study is to explore the accumulation of inorganics and activation of nuclear factor κB (NF-κB)-inducible nitric oxide synthase (iNOS) signaling pathway of lung tissue in Xuanwei lung cancer patients. From December 2013 to November 2014, 48 cases Xuanwei patients with lung cancer who underwent surgical treatment from the Third Affiliated Hospital of Kunming Medical University were enrolled in this study and compared with lung cancer patients from other regions. The ultrastructure of postoperative specimens was observed by transmission electron microscopy (TEM) to explore the occurrence of inorganic particles. Serum cytokines were analyzed. Then, the expression levels of NF-κB-p65 protein and iNOS protein in postoperative specimens was explored by immunohistochemistry and Western blot. Finally, 8-OHdG accumulation in lung cancer tissues and urine was measured. A large number of nanoscale inorganics were observed in alveolar type II cells and macrophages located in adjacent tissues of lung cancer with Xuanwei patients. Silicon (Si) content was found in inorganic elemental analysis. The serum interleukin (IL)-1β levels (31.50 ± 19.16) pg/mL of Xuanwei lung-cancer patients were remarkably higher than those from other regions (11.33 ± 6.94) pg/mL (P<0.01), with statistically significant difference. The pathological tissues of Xuanwei lung-cancer patients express NF-κB-p65, and iNOS expression were significantly higher than those of patients from non-Xuanwei regions. No significant difference was found between cancerous and normal adjacent tissues. Xuanwei lung-cancer tissues and urine 8-OHdG level (40.124 ± 8.597) ng/mgCr were significantly higher than those of patients from other regions (25.673 ± 7.986) ng/mg Cr (P<0.05), with statistically significant difference. The accumulation of inorganics and the activation of NF-κB-iNOS signaling pathway may contribute to Xuanwei lung cancer.
.

Urban Form, Air Pollution, and Health.

PubMed

Hankey, Steve; Marshall, Julian D

2017-12-01

Urban form can impact air pollution and public health. We reviewed health-related articles that assessed (1) the relationships among urban form, air pollution, and health as well as (2) aspects of the urban environment (i.e., green space, noise, physical activity) that may modify those relationships. Simulation and empirical studies demonstrate an association between compact growth, improved regional air quality, and health. Most studies are cross-sectional and focus on connections between transportation emissions and land use. The physical and mental health impacts of green space, public spaces that promote physical activity, and noise are well-studied aspects of the urban environment and there is evidence that these factors may modify the relationship between air pollution and health. Urban form can support efforts to design clean, health-promoting cities. More work is needed to operationalize specific strategies and to elucidate the causal pathways connecting various aspects of health.

EPA EcoBox Tools by Exposure Pathways - Air

EPA Pesticide Factsheets

Eco-Box is a toolbox for exposure assessors. Its purpose is to provide a compendium of exposure assessment and risk characterization tools that will present comprehensive step-by-step guidance and links to relevant exposure assessment data bases

Regulation of L-ascorbic acid content in strawberry fruits

PubMed Central

Cruz-Rus, Eduardo; Amaya, Iraida; Sánchez-Sevilla, José F.; Botella, Miguel A.; Valpuesta, Victoriano

2011-01-01

Plants have several L-ascorbic acid (AsA) biosynthetic pathways, but the contribution of each one to the synthesis of AsA varyies between different species, organs, and developmental stages. Strawberry (Fragaria×ananassa) fruits are rich in AsA. The pathway that uses D-galacturonate as the initial substrate is functional in ripe fruits, but the contribution of other pathways to AsA biosynthesis has not been studied. The transcription of genes encoding biosynthetic enzymes such as D-galacturonate reductase (FaGalUR) and myo-inositol oxygenase (FaMIOX), and the AsA recycling enzyme monodehydroascorbate reductase (FaMDHAR) were positively correlated with the increase in AsA during fruit ripening. Fruit storage for 72 h in a cold room reduced the AsA content by 30%. Under an ozone atmosphere, this reduction was 15%. Ozone treatment increased the expression of the FaGalUR, FaMIOX, and L-galactose-1-phosphate phosphatase (FaGIPP) genes, and transcription of the L-galactono-1,4-lactone dehydrogenase (FaGLDH) and FAMDHAR genes was higher in the ozone-stored than in the air-stored fruits. Analysis of AsA content in a segregating population from two strawberry cultivars showed high variability, which did not correlate with the transcription of any of the genes studied. Study of GalUR protein in diverse cultivars of strawberry and different Fragaria species showed that a correlation between GalUR and AsA content was apparent in most cases, but it was not general. Three alleles were identified in strawberry, but any sequence effect on the AsA variability was eliminated by analysis of the allele-specific expression. Taken together, these results indicate that FaGalUR shares the control of AsA levels with other enzymes and regulatory elements in strawberry fruit. PMID:21561953

Microarray analysis of gene expression alteration in human middle ear epithelial cells induced by micro particle.

PubMed

Song, Jae-Jun; Kwon, Jee Young; Park, Moo Kyun; Seo, Young Rok

2013-10-01

The primary aim of this study is to reveal the effect of particulate matter (PM) on the human middle ear epithelial cell (HMEEC). The HMEEC was treated with PM (300 μg/ml) for 24 h. Total RNA was extracted and used for microarray analysis. Molecular pathways among differentially expressed genes were further analyzed by using Pathway Studio 9.0 software. For selected genes, the changes in gene expression were confirmed by real-time PCR. A total of 611 genes were regulated by PM. Among them, 366 genes were up-regulated, whereas 245 genes were down-regulated. Up-regulated genes were mainly involved in cellular processes, including reactive oxygen species generation, cell proliferation, apoptosis, cell differentiation, inflammatory response and immune response. Down-regulated genes affected several cellular processes, including cell differentiation, cell cycle, proliferation, apoptosis and cell migration. A total of 21 genes were discovered as crucial components in potential signaling networks containing 2-fold up regulated genes. Four genes, VEGFA, IL1B, CSF2 and HMOX1 were revealed as key mediator genes among the up-regulated genes. A total of 25 genes were revealed as key modulators in the signaling pathway associated with 2-fold down regulated genes. Four genes, including IGF1R, TIMP1, IL6 and FN1, were identified as the main modulator genes. We identified the differentially expressed genes in PM-treated HMEEC, whose expression profile may provide a useful clue for the understanding of environmental pathophysiology of otitis media. Our work indicates that air pollution, like PM, plays an important role in the pathogenesis of otitis media. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Respiratory effects of air pollution on children.

PubMed

Goldizen, Fiona C; Sly, Peter D; Knibbs, Luke D

2016-01-01

A substantial proportion of the global burden of disease is directly or indirectly attributable to exposure to air pollution. Exposures occurring during the periods of organogenesis and rapid lung growth during fetal development and early post-natal life are especially damaging. In this State of the Art review, we discuss air toxicants impacting on children's respiratory health, routes of exposure with an emphasis on unique pathways relevant to young children, methods of exposure assessment and their limitations and the adverse health consequences of exposures. Finally, we point out gaps in knowledge and research needs in this area. A greater understanding of the adverse health consequences of exposure to air pollution in early life is required to encourage policy makers to reduce such exposures and improve human health. © 2015 Wiley Periodicals, Inc.

Air/Superfund national technical guidance study series, Volume 2. Estimation of baseline air emission at Superfund sites. Interim report(Final)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1989-01-01

This volume is one in a series of manuals prepared for EPA to assist its Remedial Project Managers in the assessment of the air contaminant pathway and developing input data for risk assessment. The manual provides guidance on developing baseline-emission estimates from hazardous waste sites. Baseline-emission estimates (BEEs) are defined as emission rates estimated for a site in its undisturbed state. Specifically, the manual is intended to: Present a protocol for selecting the appropriate level of effort to characterize baseline air emissions; Assist site managers in designing an approach for BEEs; Describe useful technologies for developing site-specific baseline emission estimatesmore » (BEEs); Help site managers select the appropriate technologies for generating site-specific BEEs.« less

Exploring pathway interactions in insulin resistant mouse liver

PubMed Central

2011-01-01

Background Complex phenotypes such as insulin resistance involve different biological pathways that may interact and influence each other. Interpretation of related experimental data would be facilitated by identifying relevant pathway interactions in the context of the dataset. Results We developed an analysis approach to study interactions between pathways by integrating gene and protein interaction networks, biological pathway information and high-throughput data. This approach was applied to a transcriptomics dataset to investigate pathway interactions in insulin resistant mouse liver in response to a glucose challenge. We identified regulated pathway interactions at different time points following the glucose challenge and also studied the underlying protein interactions to find possible mechanisms and key proteins involved in pathway cross-talk. A large number of pathway interactions were found for the comparison between the two diet groups at t = 0. The initial response to the glucose challenge (t = 0.6) was typed by an acute stress response and pathway interactions showed large overlap between the two diet groups, while the pathway interaction networks for the late response were more dissimilar. Conclusions Studying pathway interactions provides a new perspective on the data that complements established pathway analysis methods such as enrichment analysis. This study provided new insights in how interactions between pathways may be affected by insulin resistance. In addition, the analysis approach described here can be generally applied to different types of high-throughput data and will therefore be useful for analysis of other complex datasets as well. PMID:21843341

Separate enrichment analysis of pathways for up- and downregulated genes.

PubMed

Hong, Guini; Zhang, Wenjing; Li, Hongdong; Shen, Xiaopei; Guo, Zheng

2014-03-06

Two strategies are often adopted for enrichment analysis of pathways: the analysis of all differentially expressed (DE) genes together or the analysis of up- and downregulated genes separately. However, few studies have examined the rationales of these enrichment analysis strategies. Using both microarray and RNA-seq data, we show that gene pairs with functional links in pathways tended to have positively correlated expression levels, which could result in an imbalance between the up- and downregulated genes in particular pathways. We then show that the imbalance could greatly reduce the statistical power for finding disease-associated pathways through the analysis of all-DE genes. Further, using gene expression profiles from five types of tumours, we illustrate that the separate analysis of up- and downregulated genes could identify more pathways that are really pertinent to phenotypic difference. In conclusion, analysing up- and downregulated genes separately is more powerful than analysing all of the DE genes together.

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis.

PubMed

Yi, Ming; Mudunuri, Uma; Che, Anney; Stephens, Robert M

2009-06-29

One of the challenges in the analysis of microarray data is to integrate and compare the selected (e.g., differential) gene lists from multiple experiments for common or unique underlying biological themes. A common way to approach this problem is to extract common genes from these gene lists and then subject these genes to enrichment analysis to reveal the underlying biology. However, the capacity of this approach is largely restricted by the limited number of common genes shared by datasets from multiple experiments, which could be caused by the complexity of the biological system itself. We now introduce a new Pathway Pattern Extraction Pipeline (PPEP), which extends the existing WPS application by providing a new pathway-level comparative analysis scheme. To facilitate comparing and correlating results from different studies and sources, PPEP contains new interfaces that allow evaluation of the pathway-level enrichment patterns across multiple gene lists. As an exploratory tool, this analysis pipeline may help reveal the underlying biological themes at both the pathway and gene levels. The analysis scheme provided by PPEP begins with multiple gene lists, which may be derived from different studies in terms of the biological contexts, applied technologies, or methodologies. These lists are then subjected to pathway-level comparative analysis for extraction of pathway-level patterns. This analysis pipeline helps to explore the commonality or uniqueness of these lists at the level of pathways or biological processes from different but relevant biological systems using a combination of statistical enrichment measurements, pathway-level pattern extraction, and graphical display of the relationships of genes and their associated pathways as Gene-Term Association Networks (GTANs) within the WPS platform. As a proof of concept, we have used the new method to analyze many datasets from our collaborators as well as some public microarray datasets. This tool provides a new pathway-level analysis scheme for integrative and comparative analysis of data derived from different but relevant systems. The tool is freely available as a Pathway Pattern Extraction Pipeline implemented in our existing software package WPS, which can be obtained at http://www.abcc.ncifcrf.gov/wps/wps_index.php.

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms

PubMed Central

Bianco, Luca; Riccadonna, Samantha; Lavezzo, Enrico; Falda, Marco; Formentin, Elide; Cavalieri, Duccio; Toppo, Stefano

2017-01-01

Abstract Summary: Pathway Inspector is an easy-to-use web application helping researchers to find patterns of expression in complex RNAseq experiments. The tool combines two standard approaches for RNAseq analysis: the identification of differentially expressed genes and a topology-based analysis of enriched pathways. Pathway Inspector is equipped with ad hoc interactive graphical interfaces simplifying the discovery of modulated pathways and the integration of the differentially expressed genes in the corresponding pathway topology. Availability and Implementation: Pathway Inspector is available at the website http://admiral.fmach.it/PI and has been developed in Python, making use of the Django Web Framework. Contact: paolo.fontana@fmach.it PMID:28158604

Graphene-based battery electrodes having continuous flow paths

DOEpatents

Zhang, Jiguang; Xiao, Jie; Liu, Jun; Xu, Wu; Li, Xiaolin; Wang, Deyu

2014-05-24

Some batteries can exhibit greatly improved performance by utilizing electrodes having randomly arranged graphene nanosheets forming a network of channels defining continuous flow paths through the electrode. The network of channels can provide a diffusion pathway for the liquid electrolyte and/or for reactant gases. Metal-air batteries can benefit from such electrodes. In particular Li-air batteries show extremely high capacities, wherein the network of channels allow oxygen to diffuse through the electrode and mesopores in the electrode can store discharge products.

United States Air Force Summer Faculty Research Program (1987). Program Management Report.

DTIC Science & Technology

1987-12-01

lllllll~hEEEI ,II .2 I. 1.25u 11111 1 1 MICROCOP RESOLUTION TES CHART 1% 0., :: nb- l q1 120 I iI UNITED STATES AIR FORCE SUMMER FACULTY RESEARCH...certain chemical compound , its pharmacological properties and the pathways of metabolism, absorption, distribution and excretion must be investigated, the...criteria can be recommended for personnel who handle or are otherwise in contact with such compounds . 5.0. r ,r,. -,&5 N The Toxic Hazards Division

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways

PubMed Central

Koumakis, Lefteris; Kartsaki, Evgenia; Chatzimina, Maria; Zervakis, Michalis; Vassou, Despoina; Marias, Kostas; Moustakis, Vassilis; Potamias, George

2016-01-01

Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system (www.minepath.org) offering dynamic and rich pathway visualization functionality, with the unique characteristic to color regulatory relations between genes and reveal their phenotype inclination. This unique characteristic makes MinePath a valuable tool for in silico molecular biology experimentation as it serves the biomedical researchers’ exploratory needs to reveal and interpret the regulatory mechanisms that underlie and putatively govern the expression of target phenotypes. PMID:27832067

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways.

PubMed

Koumakis, Lefteris; Kanterakis, Alexandros; Kartsaki, Evgenia; Chatzimina, Maria; Zervakis, Michalis; Tsiknakis, Manolis; Vassou, Despoina; Kafetzopoulos, Dimitris; Marias, Kostas; Moustakis, Vassilis; Potamias, George

2016-11-01

Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system (www.minepath.org) offering dynamic and rich pathway visualization functionality, with the unique characteristic to color regulatory relations between genes and reveal their phenotype inclination. This unique characteristic makes MinePath a valuable tool for in silico molecular biology experimentation as it serves the biomedical researchers' exploratory needs to reveal and interpret the regulatory mechanisms that underlie and putatively govern the expression of target phenotypes.

Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures

PubMed Central

Foroushani, Amir B.K.; Brinkman, Fiona S.L.

2013-01-01

Motivation. Predominant pathway analysis approaches treat pathways as collections of individual genes and consider all pathway members as equally informative. As a result, at times spurious and misleading pathways are inappropriately identified as statistically significant, solely due to components that they share with the more relevant pathways. Results. We introduce the concept of Pathway Gene-Pair Signatures (Pathway-GPS) as pairs of genes that, as a combination, are specific to a single pathway. We devised and implemented a novel approach to pathway analysis, Signature Over-representation Analysis (SIGORA), which focuses on the statistically significant enrichment of Pathway-GPS in a user-specified gene list of interest. In a comparative evaluation of several published datasets, SIGORA outperformed traditional methods by delivering biologically more plausible and relevant results. Availability. An efficient implementation of SIGORA, as an R package with precompiled GPS data for several human and mouse pathway repositories is available for download from http://sigora.googlecode.com/svn/. PMID:24432194

A System-Level Pathway-Phenotype Association Analysis Using Synthetic Feature Random Forest

PubMed Central

Pan, Qinxin; Hu, Ting; Malley, James D.; Andrew, Angeline S.; Karagas, Margaret R.; Moore, Jason H.

2015-01-01

As the cost of genome-wide genotyping decreases, the number of genome-wide association studies (GWAS) has increased considerably. However, the transition from GWAS findings to the underlying biology of various phenotypes remains challenging. As a result, due to its system-level interpretability, pathway analysis has become a popular tool for gaining insights on the underlying biology from high-throughput genetic association data. In pathway analyses, gene sets representing particular biological processes are tested for significant associations with a given phenotype. Most existing pathway analysis approaches rely on single-marker statistics and assume that pathways are independent of each other. As biological systems are driven by complex biomolecular interactions, embracing the complex relationships between single-nucleotide polymorphisms (SNPs) and pathways needs to be addressed. To incorporate the complexity of gene-gene interactions and pathway-pathway relationships, we propose a system-level pathway analysis approach, synthetic feature random forest (SF-RF), which is designed to detect pathway-phenotype associations without making assumptions about the relationships among SNPs or pathways. In our approach, the genotypes of SNPs in a particular pathway are aggregated into a synthetic feature representing that pathway via Random Forest (RF). Multiple synthetic features are analyzed using RF simultaneously and the significance of a synthetic feature indicates the significance of the corresponding pathway. We further complement SF-RF with pathway-based Statistical Epistasis Network (SEN) analysis that evaluates interactions among pathways. By investigating the pathway SEN, we hope to gain additional insights into the genetic mechanisms contributing to the pathway-phenotype association. We apply SF-RF to a population-based genetic study of bladder cancer and further investigate the mechanisms that help explain the pathway-phenotype associations using SEN. The bladder cancer associated pathways we found are both consistent with existing biological knowledge and reveal novel and plausible hypotheses for future biological validations. PMID:24535726

Quantification of vapor intrusion pathways into a slab-on-ground building under varying environmental conditions.

PubMed

Patterson, Bradley M; Davis, Greg B

2009-02-01

Potential hydrocarbon-vapor intrusion pathways into a building through a concrete slab-on-ground were investigated and quantified under a variety of environmental conditions to elucidate the potential mechanisms for indoor air contamination. Vapor discharge from the uncovered open ground soil adjacent to the building and subsequent advection into the building was unlikely due to the low soil-gas concentrations at the edge of the building as a result of aerobic biodegradation of hydrocarbon vapors. When the building's interior was under ambient pressure, a flux of vapors into the building due to molecular diffusion of vapors through the building's concrete slab (cyclohexane 11 and methylcyclohexane 31 mg m(-2) concrete slab day(-1)) and short-term (up to 8 h) cyclical pressure-driven advection of vapors through an artificial crack (cyclohexane 4.2 x 10(3) and methylcyclohexane 1.2 x 10(4) mg m(-2) cracks day(-1)) was observed. The average subslab vapor concentration under the center of the building was 25,000 microg L(-1). Based on the measured building's interiorvapor concentrations and the building's air exchange rate of 0.66 h(-1), diffusion of vapors through the concrete slab was the dominantvapor intrusion pathway and cyclical pressure exchanges resulted in a near zero advective flux. When the building's interior was under a reduced pressure (-12 Pa), advective transport through cracks or gaps in the concrete slab (cyclohexane 340 and methylcyclohexane 1100 mg m(-2) cracks day(-1)) was the dominant vapor intrusion pathway.

Stress-tolerance of baker's-yeast (Saccharomyces cerevisiae) cells: stress-protective molecules and genes involved in stress tolerance.

PubMed

Shima, Jun; Takagi, Hiroshi

2009-05-29

During the fermentation of dough and the production of baker's yeast (Saccharomyces cerevisiae), cells are exposed to numerous environmental stresses (baking-associated stresses) such as freeze-thaw, high sugar concentrations, air-drying and oxidative stresses. Cellular macromolecules, including proteins, nucleic acids and membranes, are seriously damaged under stress conditions, leading to the inhibition of cell growth, cell viability and fermentation. To avoid lethal damage, yeast cells need to acquire a variety of stress-tolerant mechanisms, for example the induction of stress proteins, the accumulation of stress protectants, changes in membrane composition and repression of translation, and by regulating the corresponding gene expression via stress-triggered signal-transduction pathways. Trehalose and proline are considered to be critical stress protectants, as is glycerol. It is known that these molecules are effective for providing protection against various types of environmental stresses. Modifications of the metabolic pathways of trehalose and proline by self-cloning methods have significantly increased tolerance to baking-associated stresses. To clarify which genes are required for stress tolerance, both a comprehensive phenomics analysis and a functional genomics analysis were carried out under stress conditions that simulated those occurring during the commercial baking process. These analyses indicated that many genes are involved in stress tolerance in yeast. In particular, it was suggested that vacuolar H+-ATPase plays important roles in yeast cells under stress conditions.

Aliphatic hydrocarbons recovered in vegetables from soils based on their in-situ distribution in various soil humus fractions using a successive extraction method.

PubMed

Zhang, Juan; Fan, Shu-Kai; Zhang, Ming-Hua; Grieneisen, Michael L; Zhang, Jian-Feng

2018-03-15

Aliphatic hydrocarbons (AHs) are major petroleum contaminants in the environment. In this study, the AHs bound to various soil endogenetic humus fractions were separated through successive extraction. Most of the AHs (46.1%) in soils were adsorbed onto/into humic acids (HA) and a small quantity of AHs (9.6%) were organic solvent extractable. AHs in B. chinensis were also analyzed since their potential risks to the residents through ingestion. AHs from C 21 to C 34 , so called high molecular weight AHs (HMWAHs), were dominant AHs in B. chinensis (85.5%) and soils (70.4%), followed by AHs from C 16 to C 21, whose mobility can be enhanced via binding to fulvic acids and then can be taken up by plant root lipids (soil-plant pathway). HMWAHs were mainly HA-bound and then were detained in the top soil layers. HMWAHs associated with fine topsoil particles could be transported to B. chinensis via the soil-air-plant pathway, including resuspension and aboveground plant cuticle capture. Results from Principal Component Analysis combined with Regression Analysis supported this assumption due to the positive correlations between HMWAHs concentration in B. chinensis and fine particle contents in soils. This work presents the distributions of petroleum contaminants that result from previously described behavior mechanisms. Copyright © 2017 Elsevier B.V. All rights reserved.

FUGACITY-BASED INDOOR RESIDENTIAL PESTICIDE FATE MODEL

EPA Science Inventory

Dermal and non-dietary pathways are possibly important for exposure to pesticides used in residences. Limited data have been collected on pesticide concentrations in residential air and surfaces following application. Models may be useful for interpreting these data and to make...

NEAR ROADWAYS EXPOSURE TO URBAN AIR POLLUTANTS STUDY (NEXUS)

EPA Science Inventory

The proposed research addresses both the effects and the mechanisms by which traffic-associated exposures induce exaggerated airway responses in children with asthma, and how these exposures cause biologic responses on inflammatory pathways, oxidative stress, and the frequ...

INDOOR AIR VAPOR INTRUSION SEMINAR INTRODUCTION

EPA Science Inventory

This seminar is sponsored by the ORD in collaboration with the Office of Solid Waste and Emergency Response. The goal of this seminar is to present information and guidance to evaluate, assess and characterize chemical vapor pathways migrating into structures resulting from conta...

Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways

PubMed Central

Kaushik, Abhinav; Ali, Shakir; Gupta, Dinesh

2017-01-01

Gene connection rewiring is an essential feature of gene network dynamics. Apart from its normal functional role, it may also lead to dysregulated functional states by disturbing pathway homeostasis. Very few computational tools measure rewiring within gene co-expression and its corresponding regulatory networks in order to identify and prioritize altered pathways which may or may not be differentially regulated. We have developed Altered Pathway Analyzer (APA), a microarray dataset analysis tool for identification and prioritization of altered pathways, including those which are differentially regulated by TFs, by quantifying rewired sub-network topology. Moreover, APA also helps in re-prioritization of APA shortlisted altered pathways enriched with context-specific genes. We performed APA analysis of simulated datasets and p53 status NCI-60 cell line microarray data to demonstrate potential of APA for identification of several case-specific altered pathways. APA analysis reveals several altered pathways not detected by other tools evaluated by us. APA analysis of unrelated prostate cancer datasets identifies sample-specific as well as conserved altered biological processes, mainly associated with lipid metabolism, cellular differentiation and proliferation. APA is designed as a cross platform tool which may be transparently customized to perform pathway analysis in different gene expression datasets. APA is freely available at http://bioinfo.icgeb.res.in/APA. PMID:28084397

Analysis of Organizational Architectures for the Air Force Tuition Assistance Program

DTIC Science & Technology

2003-03-01

FORCE TUITION ASSISTANCE PROGRAM THESIS Krista Zimmerman LaPietra AFIT/GOR/ENS/03-15 DEPARTMENT OF THE AIR FORCE AIR UNIVERSITY AIR...ANALYSIS OF ORGANIZATIONAL ARCHITECTURES FOR THE AIR FORCE TUITION ASSISTANCE PROGRAM THESIS Presented to the Faculty Department...ANALYSIS OF ORGANIZATIONAL ARCHITECTURES FOR THE AIR FORCE TUITION ASSISTANCE PROGRAM Krista Zimmerman LaPietra, BS

Global air quality and climate.

PubMed

Fiore, Arlene M; Naik, Vaishali; Spracklen, Dominick V; Steiner, Allison; Unger, Nadine; Prather, Michael; Bergmann, Dan; Cameron-Smith, Philip J; Cionni, Irene; Collins, William J; Dalsøren, Stig; Eyring, Veronika; Folberth, Gerd A; Ginoux, Paul; Horowitz, Larry W; Josse, Béatrice; Lamarque, Jean-François; MacKenzie, Ian A; Nagashima, Tatsuya; O'Connor, Fiona M; Righi, Mattia; Rumbold, Steven T; Shindell, Drew T; Skeie, Ragnhild B; Sudo, Kengo; Szopa, Sophie; Takemura, Toshihiko; Zeng, Guang

2012-10-07

Emissions of air pollutants and their precursors determine regional air quality and can alter climate. Climate change can perturb the long-range transport, chemical processing, and local meteorology that influence air pollution. We review the implications of projected changes in methane (CH(4)), ozone precursors (O(3)), and aerosols for climate (expressed in terms of the radiative forcing metric or changes in global surface temperature) and hemispheric-to-continental scale air quality. Reducing the O(3) precursor CH(4) would slow near-term warming by decreasing both CH(4) and tropospheric O(3). Uncertainty remains as to the net climate forcing from anthropogenic nitrogen oxide (NO(x)) emissions, which increase tropospheric O(3) (warming) but also increase aerosols and decrease CH(4) (both cooling). Anthropogenic emissions of carbon monoxide (CO) and non-CH(4) volatile organic compounds (NMVOC) warm by increasing both O(3) and CH(4). Radiative impacts from secondary organic aerosols (SOA) are poorly understood. Black carbon emission controls, by reducing the absorption of sunlight in the atmosphere and on snow and ice, have the potential to slow near-term warming, but uncertainties in coincident emissions of reflective (cooling) aerosols and poorly constrained cloud indirect effects confound robust estimates of net climate impacts. Reducing sulfate and nitrate aerosols would improve air quality and lessen interference with the hydrologic cycle, but lead to warming. A holistic and balanced view is thus needed to assess how air pollution controls influence climate; a first step towards this goal involves estimating net climate impacts from individual emission sectors. Modeling and observational analyses suggest a warming climate degrades air quality (increasing surface O(3) and particulate matter) in many populated regions, including during pollution episodes. Prior Intergovernmental Panel on Climate Change (IPCC) scenarios (SRES) allowed unconstrained growth, whereas the Representative Concentration Pathway (RCP) scenarios assume uniformly an aggressive reduction, of air pollutant emissions. New estimates from the current generation of chemistry-climate models with RCP emissions thus project improved air quality over the next century relative to those using the IPCC SRES scenarios. These two sets of projections likely bracket possible futures. We find that uncertainty in emission-driven changes in air quality is generally greater than uncertainty in climate-driven changes. Confidence in air quality projections is limited by the reliability of anthropogenic emission trajectories and the uncertainties in regional climate responses, feedbacks with the terrestrial biosphere, and oxidation pathways affecting O(3) and SOA.

A novel approach to select differential pathways associated with hypertrophic cardiomyopathy based on gene co‑expression analysis.

PubMed

Chen, Xiao-Min; Feng, Ming-Jun; Shen, Cai-Jie; He, Bin; Du, Xian-Feng; Yu, Yi-Bo; Liu, Jing; Chu, Hui-Min

2017-07-01

The present study was designed to develop a novel method for identifying significant pathways associated with human hypertrophic cardiomyopathy (HCM), based on gene co‑expression analysis. The microarray dataset associated with HCM (E‑GEOD‑36961) was obtained from the European Molecular Biology Laboratory‑European Bioinformatics Institute database. Informative pathways were selected based on the Reactome pathway database and screening treatments. An empirical Bayes method was utilized to construct co‑expression networks for informative pathways, and a weight value was assigned to each pathway. Differential pathways were extracted based on weight threshold, which was calculated using a random model. In order to assess whether the co‑expression method was feasible, it was compared with traditional pathway enrichment analysis of differentially expressed genes, which were identified using the significance analysis of microarrays package. A total of 1,074 informative pathways were screened out for subsequent investigations and their weight values were also obtained. According to the threshold of weight value of 0.01057, 447 differential pathways, including folding of actin by chaperonin containing T‑complex protein 1 (CCT)/T‑complex protein 1 ring complex (TRiC), purine ribonucleoside monophosphate biosynthesis and ubiquinol biosynthesis, were obtained. Compared with traditional pathway enrichment analysis, the number of pathways obtained from the co‑expression approach was increased. The results of the present study demonstrated that this method may be useful to predict marker pathways for HCM. The pathways of folding of actin by CCT/TRiC and purine ribonucleoside monophosphate biosynthesis may provide evidence of the underlying molecular mechanisms of HCM, and offer novel therapeutic directions for HCM.

Challenges and opportunities of airborne metagenomics.

PubMed

Behzad, Hayedeh; Gojobori, Takashi; Mineta, Katsuhiko

2015-05-06

Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Pathway analysis of genome-wide association datasets of personality traits.

PubMed

Kim, H-N; Kim, B-H; Cho, J; Ryu, S; Shin, H; Sung, J; Shin, C; Cho, N H; Sung, Y A; Choi, B-O; Kim, H-L

2015-04-01

Although several genome-wide association (GWA) studies of human personality have been recently published, genetic variants that are highly associated with certain personality traits remain unknown, due to difficulty reproducing results. To further investigate these genetic variants, we assessed biological pathways using GWA datasets. Pathway analysis using GWA data was performed on 1089 Korean women whose personality traits were measured with the Revised NEO Personality Inventory for the 5-factor model of personality. A total of 1042 pathways containing 8297 genes were included in our study. Of these, 14 pathways were highly enriched with association signals that were validated in 1490 independent samples. These pathways include association of: Neuroticism with axon guidance [L1 cell adhesion molecule (L1CAM) interactions]; Extraversion with neuronal system and voltage-gated potassium channels; Agreeableness with L1CAM interaction, neurotransmitter receptor binding and downstream transmission in postsynaptic cells; and Conscientiousness with the interferon-gamma and platelet-derived growth factor receptor beta polypeptide pathways. Several genes that contribute to top-ranked pathways in this study were previously identified in GWA studies or by pathway analysis in schizophrenia or other neuropsychiatric disorders. Here we report the first pathway analysis of all five personality traits. Importantly, our analysis identified novel pathways that contribute to understanding the etiology of personality traits. © 2015 The Authors. Genes, Brain and Behavior published by International Behavioural and Neural Genetics Society and John Wiley & Sons Ltd.

Development of Future Scenario Emission Inventories for East Asia in Support of Multiple Modeling Studies

NASA Astrophysics Data System (ADS)

Kim, Y.; Woo, J. H.; Choi, K. C.; Lee, J. B.; Song, C. K.; Kim, S. K.; Hong, J.; Hong, S. C.; Zhang, Q.; Hong, C.; Tong, D.

2015-12-01

Future emission scenarios based on up-to-date regional socio-economic and control policy information were developed in support of climate-air quality integrated modeling research over East Asia. Two IPCC-participated Integrated Assessment Models(IAMs) were used to developed those scenario pathways. The two emission processing systems, KU-EPS and SMOKE-Asia, were used to convert these future scenario emissions to comprehensive chemical transport model-ready form. The NIER/KU-CREATE (Comprehensive Regional Emissions inventory for Atmospheric Transport Experiment) served as the regional base-year emission inventory. For anthropogenic emissions, it has 54 fuel classes, 201 sub-sectors and 13 pollutants, including CO2, CH4, N2O, SO2, NOx, CO, NMVOC, NH3, OC, BC, PM10, PM2.5, and mercury. Fast energy growth and aggressive penetration of the control measures make emissions projection very active for East Asia. Despite of more stringent air pollution control policies by the governments, however, air quality over the region seems not been improved as much - even worse in many cases. The needs of more scientific understanding of inter-relationship among emissions, transport, chemistry over the region are very high to effectively protect public health and ecosystems against ozone, fine particles, and other toxic pollutants in the air. After developing these long-term future emissions, therefore, we also tried to apply our future scenarios to develop the present emissions inventory for chemical weather forecasting and aircraft field campaign. On site, we will present; 1) the future scenario development framework and process methodologies, 2) initial development results of the future emission pathways, 3) present emission inventories from short-term projection, and 4) air quality modeling performance improvements over the region.

The degree of bacterial contamination while performing spine surgery.

PubMed

Ahn, Dong Ki; Park, Hoon Seok; Kim, Tae Woo; Yang, Jong Hwa; Boo, Kyung Hwan; Kim, In Ja; Lee, Hye Jin

2013-03-01

Prospective experimental study. To evaluate bacterial contamination during surgery. The participants of surgery and ventilation system have been known as the most significant sources of contamination. Two pairs of air culture blood agar plate for G(+) bacteria and MacConkey agar plate for G(-) bacteria were placed at 3 different locations in a conventional operation room: in the surgical field, under the airflow of local air conditioner, and pathway to door while performing spine surgeries. One pair of culture plates was retrieved after one hour and the other pair was retrieved after 3 hours. The cultured bacteria were identified and number of colonies was counted. There was no G(-) bacteria identified. G(+) bacteria grew on all 90 air culture blood agar plates. The colony count of one hour group was 14.5±5.4 in the surgical field, 11.3±6.6 under the local air conditioner, and 13.1±8.7 at the pathway to the door. There was no difference among the 3 locations. The colony count of 3 hours group was 46.4±19.5, 30.3±12.9, and 39.7±15.2, respectively. It was more at the surgical field than under the air conditioner (p=0.03). The number of colonies of one hour group was 13.0±7.0 and 3 hours group was 38.8±17.1. There was positive correlation between the time and the number of colonies (r=0.76, p=0.000). Conventional operation room was contaminated by G(+) bacteria. The degree of contamination was most high at the surgical field. The number of bacteria increased right proportionally to the time.

The Degree of Bacterial Contamination While Performing Spine Surgery

PubMed Central

Ahn, Dong Ki; Park, Hoon Seok; Yang, Jong Hwa; Boo, Kyung Hwan; Kim, In Ja; Lee, Hye Jin

2013-01-01

Study Design Prospective experimental study. Purpose To evaluate bacterial contamination during surgery. Overview of Literature The participants of surgery and ventilation system have been known as the most significant sources of contamination. Methods Two pairs of air culture blood agar plate for G(+) bacteria and MacConkey agar plate for G(-) bacteria were placed at 3 different locations in a conventional operation room: in the surgical field, under the airflow of local air conditioner, and pathway to door while performing spine surgeries. One pair of culture plates was retrieved after one hour and the other pair was retrieved after 3 hours. The cultured bacteria were identified and number of colonies was counted. Results There was no G(-) bacteria identified. G(+) bacteria grew on all 90 air culture blood agar plates. The colony count of one hour group was 14.5±5.4 in the surgical field, 11.3±6.6 under the local air conditioner, and 13.1±8.7 at the pathway to the door. There was no difference among the 3 locations. The colony count of 3 hours group was 46.4±19.5, 30.3±12.9, and 39.7±15.2, respectively. It was more at the surgical field than under the air conditioner (p=0.03). The number of colonies of one hour group was 13.0±7.0 and 3 hours group was 38.8±17.1. There was positive correlation between the time and the number of colonies (r=0.76, p=0.000). Conclusions Conventional operation room was contaminated by G(+) bacteria. The degree of contamination was most high at the surgical field. The number of bacteria increased right proportionally to the time. PMID:23508998

Risk assessment of heavy metals in air, water, vegetables, grains, and related soils irrigated with biogas slurry in Taihu Basin, China.

PubMed

Bian, Bo; Zhou, Ling Jun; Li, Lei; Lv, Lin; Fan, Ya Min

2015-05-01

Metal contamination in farmlands irrigated with biogas slurry is of great concern because of its potential health risks to local inhabitants. Health risks that depend heavily on multi-pathway exposure to heavy metals (e.g., Pb, Cd, Cr, Zn, Cu, and As) in water, soil, air, and local food were studied through field sampling in Taihu Basin, China. Results show that Zn, Pb, and Cd in soils irrigated with biogas slurry exceed the soil quality standard values, and grown vegetables and grains contaminated with Pb and Cd exceed the permissible limits. Food ingestion plays an important role in the total average daily dose of metals, especially for Cu and Zn, which account for 94 and 91%, respectively. Non-carcinogenic risks posed to adults mainly result from Cu, Zn, Pb, Cd, and As through food ingestion and from Cr through soil ingestion. The highest non-carcinogenic risk was determined from food ingestion, followed by soil ingestion, air inhalation, air ingestion, and dermal contact with air. Carcinogenic risks to adults are 6.68 to 7.00 times higher than the safe level and can be attributed to Cr, As, and Cd pollution. The estimated risks mainly result from As and Cd through food ingestion and from Cr through soil ingestion. Both cancer and non-cancer risks through dermal contact can be ignored. Therefore, attention should be paid to health risks imposed by adults' multi-pathway exposure to heavy metals in vegetables, grains, and related soils irrigated with biogas slurry in Taihu Basin. Effective measures should be implemented to control heavy metal pollution and protect potentially exposed adults.

Integrating genome-wide association studies and gene expression data highlights dysregulated multiple sclerosis risk pathways.

PubMed

Liu, Guiyou; Zhang, Fang; Jiang, Yongshuai; Hu, Yang; Gong, Zhongying; Liu, Shoufeng; Chen, Xiuju; Jiang, Qinghua; Hao, Junwei

2017-02-01

Much effort has been expended on identifying the genetic determinants of multiple sclerosis (MS). Existing large-scale genome-wide association study (GWAS) datasets provide strong support for using pathway and network-based analysis methods to investigate the mechanisms underlying MS. However, no shared genetic pathways have been identified to date. We hypothesize that shared genetic pathways may indeed exist in different MS-GWAS datasets. Here, we report results from a three-stage analysis of GWAS and expression datasets. In stage 1, we conducted multiple pathway analyses of two MS-GWAS datasets. In stage 2, we performed a candidate pathway analysis of the large-scale MS-GWAS dataset. In stage 3, we performed a pathway analysis using the dysregulated MS gene list from seven human MS case-control expression datasets. In stage 1, we identified 15 shared pathways. In stage 2, we successfully replicated 14 of these 15 significant pathways. In stage 3, we found that dysregulated MS genes were significantly enriched in 10 of 15 MS risk pathways identified in stages 1 and 2. We report shared genetic pathways in different MS-GWAS datasets and highlight some new MS risk pathways. Our findings provide new insights on the genetic determinants of MS.

The oxidized low-density lipoprotein receptor mediates vascular effects of inhaled vehicle emissions

EPA Science Inventory

Rationale: To determine vascular signaling pathways involved in air pollution (vehicular engine emission) exposure -induced exacerbation of atherosclerosis, associated with onset of clinical cardiovascular events. Objective: To elucidate the role of oxidized LDL (oxLDL) and its ...

EVALUATION OF ANALYTICAL METHODS FOR DETERMINING PESTICIDES IN FOODS

EPA Science Inventory

Children can be exposed to pesticides by inhaling contaminated air, ingesting tainted food or non-dietary substances, or absorbing them through the skin from contaminated media. Earlier pilot-scale exposure studies suggest that dietary ingestion is an important pathway for chi...

Data Sources for Prioritizing Human Exposure to Chemicals

EPA Science Inventory

Humans may be exposed to thousands of chemicals through contact in the workplace, home, and via air, water, food, and soil. A major challenge is estimating chemical exposures, which requires understanding potential exposure pathways directly related to how chemicals are used. Wit...

REVIEW OF RECENT RESEARCH ON VAPOR INTRUSTION

EPA Science Inventory

This report reviews current and recent research in the area of vapor intrusion of organic compounds into residential buildings. We begin with a description of the challenges in evaluating the subsurface-to-indoor air pathway. A discussion of the fate and transport mechanisms affe...

Understanding pathways to organic aerosol: How the sweat and communications of plants influence our air quality

EPA Science Inventory

Isoprene and monoterpenes are major contributors to organic aerosol in in the southeastern U.S. This work presents results from 4 years of work improving the CMAQ model representation of aerosol from these precursors.

Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome

PubMed Central

Shen, Haoran; Liang, Zhou; Zheng, Saihua; Li, Xuelian

2017-01-01

The purpose of this study was to identify promising candidate genes and pathways in polycystic ovary syndrome (PCOS). Microarray dataset GSE345269 obtained from the Gene Expression Omnibus database includes 7 granulosa cell samples from PCOS patients, and 3 normal granulosa cell samples. Differentially expressed genes (DEGs) were screened between PCOS and normal samples. Pathway enrichment analysis was conducted for DEGs using ClueGO and CluePedia plugin of Cytoscape. A Reactome functional interaction (FI) network of the DEGs was built using ReactomeFIViz, and then network modules were extracted, followed by pathway enrichment analysis for the modules. Expression of DEGs in granulosa cell samples was measured using quantitative RT-PCR. A total of 674 DEGs were retained, which were significantly enriched with inflammation and immune-related pathways. Eight modules were extracted from the Reactome FI network. Pathway enrichment analysis revealed significant pathways of each module: module 0, Regulation of RhoA activity and Signaling by Rho GTPases pathways shared ARHGAP4 and ARHGAP9; module 2, GlycoProtein VI-mediated activation cascade pathway was enriched with RHOG; module 3, Thromboxane A2 receptor signaling, Chemokine signaling pathway, CXCR4-mediated signaling events pathways were enriched with LYN, the hub gene of module 3. Results of RT-PCR confirmed the finding of the bioinformatic analysis that ARHGAP4, ARHGAP9, RHOG and LYN were significantly upregulated in PCOS. RhoA-related pathways, GlycoProtein VI-mediated activation cascade pathway, ARHGAP4, ARHGAP9, RHOG and LYN may be involved in the pathogenesis of PCOS. PMID:28949383

SPECIAL ANALYSIS AIR PATHWAY MODELING OF E-AREA LOW-LEVEL WASTE FACILITY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hiergesell, R.; Taylor, G.

This Special Analysis (SA) was initiated to address a concern expressed by the Department of Energy's Low Level Waste Disposal Facility Federal Review Group (LFRG) Review Team during their review of the 2008 E-Area Performance Assessment (PA) (WSRC, 2008). Their concern was the potential for overlapping of atmospheric plumes, emanating from the soil surface above SRS LLW disposal facilities within the E-Area, to contribute to the dose received by a member of the public during the Institutional Control (IC) period. The implication of this concern was that the dose to the maximally-exposed individual (MEI) located at the SRS boundary mightmore » be underestimated during this time interval. To address this concern a re-analysis of the atmospheric pathway releases from E-Area was required. In the process of developing a new atmospheric release model (ARM) capable of addressing the LFRG plume overlap concern, it became obvious that new and better atmospheric pathway disposal limits should be developed for each of the E-Area disposal facilities using the new ARM. The scope of the SA was therefore expanded to include the generation of these new limits. The initial work conducted in this SA was to develop a new ARM using the GoldSim{reg_sign} program (GTG, 2009). The model simulates the subsurface vapor diffusion of volatile radionuclides as they release from E-Area disposal facility waste zones and migrate to the land surface. In the process of this work, many new features, including several new physical and chemical transport mechanisms, were incorporated into the model. One of the most important improvements was to incorporate a mechanism to partition volatile contaminants across the water-air interface within the partially saturated pore space of the engineered and natural materials through which vapor phase transport occurs. A second mechanism that was equally important was to incorporate a maximum concentration of 1.9E-07 Ci/m{sup 3} of {sup 14}CO{sub 2} in the air-filled pores of cementitious materials. The ARM also combines the individual transport models constructed for each E-Area disposal facility into a single model, and was ultimately used to analyze the LFRG concern regarding the potential for atmospheric plume overlap at the SRS boundary during the IC period. To evaluate the plume overlap issue, a conservative approach was adopted whereby the MEI at the SRS boundary was exposed to the releases from all E-Area disposal facilities simultaneously. This is equivalent to a 100% overlap of all atmospheric plumes emanating from E-Area. Should the dose received from this level of atmospheric plume overlap still fall below the permissible exposure level of 10 mrem/yr, then the LFRG concern would be alleviated. The structuring of the ARM enables this evaluation to be easily performed. During the IC period, the peak of the 'total plume overlap dose' was computed to be 1.9E-05 mrem/yr, which is five orders of magnitude lower than the 10 mrem/yr PA performance objective for the atmospheric release pathway. The main conclusion of this study is that for atmospheric releases from the E-Area disposal facilities, plume overlap does not cause the total dose to the MEI at the SRS boundary during the IC to exceed the Performance Assessment (PA) performance objective. Additionally, the potential for plume overlap was assessed in the post-Institutional Control period. Atmospheric plume overlap is less likely to occur during this period but conceivably could occur if the prevailing wind direction shifted so as to pass directly over all EArea disposal facilities and transport airborne radionuclides to the MEI at the 100 m point of compliance (POC). This concern was also demonstrated of little concern, as the maximum plume overlap dose was found to be 1.45E+00 mrem/yr (or {approx}15% of the performance measure) during this period and under these unlikely conditions.« less

Pathway analysis of high-throughput biological data within a Bayesian network framework.

PubMed

Isci, Senol; Ozturk, Cengizhan; Jones, Jon; Otu, Hasan H

2011-06-15

Most current approaches to high-throughput biological data (HTBD) analysis either perform individual gene/protein analysis or, gene/protein set enrichment analysis for a list of biologically relevant molecules. Bayesian Networks (BNs) capture linear and non-linear interactions, handle stochastic events accounting for noise, and focus on local interactions, which can be related to causal inference. Here, we describe for the first time an algorithm that models biological pathways as BNs and identifies pathways that best explain given HTBD by scoring fitness of each network. Proposed method takes into account the connectivity and relatedness between nodes of the pathway through factoring pathway topology in its model. Our simulations using synthetic data demonstrated robustness of our approach. We tested proposed method, Bayesian Pathway Analysis (BPA), on human microarray data regarding renal cell carcinoma (RCC) and compared our results with gene set enrichment analysis. BPA was able to find broader and more specific pathways related to RCC. Accompanying BPA software (BPAS) package is freely available for academic use at http://bumil.boun.edu.tr/bpa.

Comparative study on gene set and pathway topology-based enrichment methods.

PubMed

Bayerlová, Michaela; Jung, Klaus; Kramer, Frank; Klemm, Florian; Bleckmann, Annalen; Beißbarth, Tim

2015-10-22

Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions. In contrast, the new group of so called pathway topology-based methods integrates the topological structure of a pathway into the analysis. We comparatively investigated gene set and pathway topology-based enrichment approaches, considering three gene set and four topological methods. These methods were compared in two extensive simulation studies and on a benchmark of 36 real datasets, providing the same pathway input data for all methods. In the benchmark data analysis both types of methods showed a comparable ability to detect enriched pathways. The first simulation study was conducted with KEGG pathways, which showed considerable gene overlaps between each other. In this study with original KEGG pathways, none of the topology-based methods outperformed the gene set approach. Therefore, a second simulation study was performed on non-overlapping pathways created by unique gene IDs. Here, methods accounting for pathway topology reached higher accuracy than the gene set methods, however their sensitivity was lower. We conducted one of the first comprehensive comparative works on evaluating gene set against pathway topology-based enrichment methods. The topological methods showed better performance in the simulation scenarios with non-overlapping pathways, however, they were not conclusively better in the other scenarios. This suggests that simple gene set approach might be sufficient to detect an enriched pathway under realistic circumstances. Nevertheless, more extensive studies and further benchmark data are needed to systematically evaluate these methods and to assess what gain and cost pathway topology information introduces into enrichment analysis. Both types of methods for enrichment analysis require further improvements in order to deal with the problem of pathway overlaps.

Public health assessment for Garden State Cleaners, Cerclis No. NJD053280160 and South Jersey Clothing Company, Minotola, Atlantic County, New Jersey, Region 2. Cerclis No. NJD980766828. addendum. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-04-21

The Garden State Cleaners (GSC) and South Jersey Clothing Company (SJCC) sites are located in Buena Borough, Atlantic County, New Jersey. Completed human exposure pathway existed in the past at the site and were associated with groundwater, and ambient air (SJCC). Potential exposure pathways are associated with groundwater and on site soils (SJCC). Based upon the likelihood of past exposure, ATSDR and NJDOH consider this site to have posed a public health hazard.

Human Exposure Pathways of Heavy Metals in a Lead-Zinc Mining Area, Jiangsu Province, China

PubMed Central

Qu, Chang-Sheng; Ma, Zong-Wei; Yang, Jin; Liu, Yang; Bi, Jun; Huang, Lei

2012-01-01

Heavy metal pollution is becoming a serious issue in developing countries such as China, and the public is increasingly aware of its adverse health impacts in recent years. We assessed the potential health risks in a lead-zinc mining area and attempted to identify the key exposure pathways. We evaluated the spatial distributions of personal exposure using indigenous exposure factors and field monitoring results of water, soil, food, and indoor and outdoor air samples. The risks posed by 10 metals and the contribution of inhalation, ingestion and dermal contact pathways to these risks were estimated. Human hair samples were also analyzed to indicate the exposure level in the human body. Our results show that heavy metal pollution may pose high potential health risks to local residents, especially in the village closest to the mine (V1), mainly due to Pb, Cd and Hg. Correspondingly, the residents in V1 had higher Pb (8.14 mg/kg) levels in hair than those in the other two villages. Most of the estimated risks came from soil, the intake of self-produced vegetables and indoor air inhalation. This study highlights the importance of site-specific multipathway health risk assessments in studying heavy-metal exposures in China. PMID:23152752

Hydrothermal Synthesis of Nanostructured Manganese Oxide as Cathodic Catalyst in a Microbial Fuel Cell Fed with Leachate

PubMed Central

Haoran, Yuan; Lifang, Deng; Tao, Lu; Yong, Chen

2014-01-01

Much effort has been devoted to the synthesis of novel nanostructured MnO2 materials because of their unique properties and potential applications as cathode catalyst in Microbial fuel cell. Hybrid MnO2 nanostructures were fabricated by a simple hydrothermal method in this study. Their crystal structures, morphology, and electrochemical characters were carried out by FESEM, N2-adsorption-desorption, and CV, indicating that the hydrothermally synthesized MnO2 (HSM) was structured by nanorods of high aspect ratio and multivalve nanoflowers and more positive than the naturally synthesized MnO2 (NSM), accompanied by a noticeable increase in oxygen reduction peak current. When the HSM was employed as the cathode catalyst in air-cathode MFC which fed with leachate, a maximum power density of 119.07 mW/m2 was delivered, 64.68% higher than that with the NSM as cathode catalyst. Furthermore, the HSM via a 4-e pathway, but the NSM via a 2-e pathway in alkaline solution, and as 4-e pathway is a more efficient oxygen reduction reaction, the HSM was more positive than NSM. Our study provides useful information on facile preparation of cost-effective cathodic catalyst in air-cathode MFC for wastewater treatment. PMID:24723824

Note of the methodological flaws in the paper entitled "Polymorphisms in IL-4/IL-13 pathway genes and glioma risk: an updated meta-analysis".

PubMed

Wang, Ting-Ting; Li, Jin-Mei; Zhou, Dong

2016-01-01

With great interest, we read the paper "Polymorphisms in IL-4/IL-13 pathway genes and glioma risk: an updated meta-analysis" (by Chen PQ et al.) [1], which has reached important conclusions about the relationship between polymorphisms in interleukin (IL)-4/IL-13 pathway genes and glioma risk. Through quantitative analysis, the meta-analysis found no association between IL-4/IL-13 pathway genetic polymorphisms and glioma risk (Chen et al. in Tumor Biol 36:121-127, 2015). The meta-analysis is the most comprehensive study of polymorphisms in the IL-4/IL-13 pathway and glioma risk. Nevertheless, some deficiencies still exist in this meta-analysis that we would like to raise.

Ventilation Rates and Airflow Pathways in Patient Rooms: A Case Study of Bioaerosol Containment and Removal.

PubMed

Mousavi, Ehsan S; Grosskopf, Kevin R

2015-11-01

Most studies on the transmission of infectious airborne disease have focused on patient room air changes per hour (ACH) and how ACH provides pathogen dilution and removal. The logical but mostly unproven premise is that greater air change rates reduce the concentration of infectious particles and thus, the probability of airborne disease transmission. Recently, a growing body of research suggests pathways between pathogenic source (patient) and control (exhaust) may be the dominant environmental factor. While increases in airborne disease transmission have been associated with ventilation rates below 2 ACH, comparatively less data are available to quantify the benefits of higher air change rates in clinical spaces. As a result, a series of tests were conducted in an actual hospital to observe the containment and removal of respirable aerosols (0.5-10 µm) with respect to ventilation rate and directional airflow in a general patient room, and, an airborne infectious isolation room. Higher ventilation rates were not found to be proportionately effective in reducing aerosol concentrations. Specifically, increasing mechanical ventilation from 2.5 to 5.5 ACH reduced aerosol concentrations only 30% on average. However, particle concentrations were more than 40% higher in pathways between the source and exhaust as was the suspension and migration of larger particles (3-10 µm) throughout the patient room(s). Computational analyses were used to validate the experimental results, and, to further quantify the effect of ventilation rate on exhaust and deposition removal in patient rooms as well as other particle transport phenomena. © The Author 2015. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

Potential transport pathways of dust emanating from the playa of Ebinur Lake, Xinjiang, in arid northwest China

NASA Astrophysics Data System (ADS)

Ge, Yongxiao; Abuduwaili, Jilili; Ma, Long; Wu, Na; Liu, Dongwei

2016-09-01

In this paper, the HYSPLIT model, driven with reanalysis meteorological data from 1978 to 2013, was used to understand the potential transport characteristics of dust and salt dust emanating from the playa of Ebinur Lake in arid northwest China. Daily air parcel trajectories were computed forward for 8 days from an origin centered over Ebinur Lake at 100 m above ground level. Air parcel trajectory density plots were mapped for seven levels: 0-100 m agl., 100-500 m agl., 500-1000 m agl., 1000-1500 m agl., 1500-2000 m agl., 2000-3000 m agl., and 3000-5000 m agl. These show that potential dust transport pathways have clear seasonal differentiation. The potential transport distance of dust and salt dust is greatest in spring and summer. In autumn and winter, the potential transport of the high-density air trajectory is below 1000 m traveling a shorter distance. Potential dust transport pathways showed notifying directivity in different seasons and heights. Southeast in spring and summer, and north to northeast in autumn and winter are the two main potential transport channels of dust and salt dust. Accordingly, dust and salt dust from the playa of Ebinur Lake may influence the atmospheric processes and biogeochemical cycles of a vast region. The main area of influence of dust and salt dust is close to the source area, and will significantly accelerate the melting of snow and ice in the Tianshan Mountains. This highlights the urgent need to combine remote sensing, isotope and other methods to further research the transport characteristics of dust and salt dust from the playa of the Ebinur Lake.

In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development.

PubMed

Ozerov, Ivan V; Lezhnina, Ksenia V; Izumchenko, Evgeny; Artemov, Artem V; Medintsev, Sergey; Vanhaelen, Quentin; Aliper, Alexander; Vijg, Jan; Osipov, Andreyan N; Labat, Ivan; West, Michael D; Buzdin, Anton; Cantor, Charles R; Nikolsky, Yuri; Borisov, Nikolay; Irincheeva, Irina; Khokhlovich, Edward; Sidransky, David; Camargo, Miguel Luiz; Zhavoronkov, Alex

2016-11-16

Signalling pathway activation analysis is a powerful approach for extracting biologically relevant features from large-scale transcriptomic and proteomic data. However, modern pathway-based methods often fail to provide stable pathway signatures of a specific phenotype or reliable disease biomarkers. In the present study, we introduce the in silico Pathway Activation Network Decomposition Analysis (iPANDA) as a scalable robust method for biomarker identification using gene expression data. The iPANDA method combines precalculated gene coexpression data with gene importance factors based on the degree of differential gene expression and pathway topology decomposition for obtaining pathway activation scores. Using Microarray Analysis Quality Control (MAQC) data sets and pretreatment data on Taxol-based neoadjuvant breast cancer therapy from multiple sources, we demonstrate that iPANDA provides significant noise reduction in transcriptomic data and identifies highly robust sets of biologically relevant pathway signatures. We successfully apply iPANDA for stratifying breast cancer patients according to their sensitivity to neoadjuvant therapy.

In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development

PubMed Central

Ozerov, Ivan V.; Lezhnina, Ksenia V.; Izumchenko, Evgeny; Artemov, Artem V.; Medintsev, Sergey; Vanhaelen, Quentin; Aliper, Alexander; Vijg, Jan; Osipov, Andreyan N.; Labat, Ivan; West, Michael D.; Buzdin, Anton; Cantor, Charles R.; Nikolsky, Yuri; Borisov, Nikolay; Irincheeva, Irina; Khokhlovich, Edward; Sidransky, David; Camargo, Miguel Luiz; Zhavoronkov, Alex

2016-01-01

Signalling pathway activation analysis is a powerful approach for extracting biologically relevant features from large-scale transcriptomic and proteomic data. However, modern pathway-based methods often fail to provide stable pathway signatures of a specific phenotype or reliable disease biomarkers. In the present study, we introduce the in silico Pathway Activation Network Decomposition Analysis (iPANDA) as a scalable robust method for biomarker identification using gene expression data. The iPANDA method combines precalculated gene coexpression data with gene importance factors based on the degree of differential gene expression and pathway topology decomposition for obtaining pathway activation scores. Using Microarray Analysis Quality Control (MAQC) data sets and pretreatment data on Taxol-based neoadjuvant breast cancer therapy from multiple sources, we demonstrate that iPANDA provides significant noise reduction in transcriptomic data and identifies highly robust sets of biologically relevant pathway signatures. We successfully apply iPANDA for stratifying breast cancer patients according to their sensitivity to neoadjuvant therapy. PMID:27848968

A novel method to identify hub pathways of rheumatoid arthritis based on differential pathway networks.

PubMed

Wei, Shi-Tong; Sun, Yong-Hua; Zong, Shi-Hua

2017-09-01

The aim of the current study was to identify hub pathways of rheumatoid arthritis (RA) using a novel method based on differential pathway network (DPN) analysis. The present study proposed a DPN where protein‑protein interaction (PPI) network was integrated with pathway‑pathway interactions. Pathway data was obtained from background PPI network and the Reactome pathway database. Subsequently, pathway interactions were extracted from the pathway data by building randomized gene‑gene interactions and a weight value was assigned to each pathway interaction using Spearman correlation coefficient (SCC) to identify differential pathway interactions. Differential pathway interactions were visualized using Cytoscape to construct a DPN. Topological analysis was conducted to identify hub pathways that possessed the top 5% degree distribution of DPN. Modules of DPN were mined according to ClusterONE. A total of 855 pathways were selected to build pathway interactions. By filtrating pathway interactions of weight values >0.7, a DPN with 312 nodes and 791 edges was obtained. Topological degree analysis revealed 15 hub pathways, such as heparan sulfate/heparin‑glycosaminoglycan (HS‑GAG) degradation, HS‑GAG metabolism and keratan sulfate degradation for RA based on DPN. Furthermore, hub pathways were also important in modules, which validated the significance of hub pathways. In conclusion, the proposed method is a computationally efficient way to identify hub pathways of RA, which identified 15 hub pathways that may be potential biomarkers and provide insight to future investigation and treatment of RA.

Identification of metabolic pathways using pathfinding approaches: a systematic review.

PubMed

Abd Algfoor, Zeyad; Shahrizal Sunar, Mohd; Abdullah, Afnizanfaizal; Kolivand, Hoshang

2017-03-01

Metabolic pathways have become increasingly available for various microorganisms. Such pathways have spurred the development of a wide array of computational tools, in particular, mathematical pathfinding approaches. This article can facilitate the understanding of computational analysis of metabolic pathways in genomics. Moreover, stoichiometric and pathfinding approaches in metabolic pathway analysis are discussed. Three major types of studies are elaborated: stoichiometric identification models, pathway-based graph analysis and pathfinding approaches in cellular metabolism. Furthermore, evaluation of the outcomes of the pathways with mathematical benchmarking metrics is provided. This review would lead to better comprehension of metabolism behaviors in living cells, in terms of computed pathfinding approaches. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

SEE Action Guide for States: Energy Efficiency as a Least-Cost Strategy to Reduce Greenhouse Gases and Air Pollution and Meet Energy Needs in the Power Sector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwartz, Lisa; Leventis, Greg; Schiller, Steven R.

This guide is designed to provide information to state decision makers and staff on options to advance energy efficiency through strategies designed or implemented at the state and local levels of government and in the private sector.1 The information in this guide is intended to be useful to a wide variety of partners and stakeholders involved in energy-related discussions and decision-making at state and local levels. These energy efficiency options, or “pathways” as they are identified in this guide, can assist states in using energy efficiency to meet air pollution reduction and other policy objectives such as energy affordability andmore » reliability. A pathway is a set of interdependent actions that results in measurable energy savings streams and associated avoided air emissions and other benefits over a period of time. These activities can include state, local, or private sector regulations, policies, programs and other activities. For each of five broad pathways that offer sizable cost-effective energy savings, the guide addresses likely questions policy makers and regulators face when screening for the best opportunities to advance energy efficiency in their state.« less

Imaging Preferential Flow Pathways of Contaminants from Passive Acid Mine Drainage Mitigation Sites Using Electrical Resistivity

NASA Astrophysics Data System (ADS)

Kelley, N.; Mount, G.; Terry, N.; Herndon, E.; Singer, D. M.

2017-12-01

The Critical Zone represents the surficial and shallow layer of rock, air, water, and soil where most interactions between living organisms and the Earth occur. Acid mine drainage (AMD) resulting from coal extraction can influence both biological and geochemical processes across this zone. Conservative estimates suggest that more than 300 million gallons of AMD are released daily, making this acidic solution of water and contaminants a common issue in areas with legacy or current coal extraction. Electrical resistivity imaging (ERI) provides a rapid and minimally invasive method to identify and monitor contaminant pathways from AMD remediation systems in the subsurface of the Critical Zone. The technique yields spatially continuous data of subsurface resistivity that can be inverted to determine electrical conductivity as a function of depth. Since elevated concentrations of heavy metals can directly influence soil conductivity, ERI data can be used to trace the flow pathways or perhaps unknown mine conduits and transport of heavy metals through the subsurface near acid mine drainage sources. This study aims to examine preferential contaminant migration from those sources through substrate pores, fractures, and shallow mine workings in the near subsurface surrounding AMD sites in eastern Ohio and western Pennsylvania. We utilize time lapse ERI measures during different hydrologic conditions to better understand the variability of preferential flow pathways in relation to changes in stage and discharge within the remediation systems. To confirm ERI findings, and provide constraint to geochemical reactions occurring in the shallow subsurface, we conducted Inductively Coupled Plasma (ICP) spectrometry analysis of groundwater samples from boreholes along the survey transects. Through these combined methods, we can provide insight into the ability of engineered systems to contain and isolate metals in passive acid mine drainage treatment systems.

Characteristics of bacterial community in cloud water at Mt Tai: similarity and disparity under polluted and non-polluted cloud episodes

NASA Astrophysics Data System (ADS)

Wei, Min; Xu, Caihong; Chen, Jianmin; Zhu, Chao; Li, Jiarong; Lv, Ganglin

2017-04-01

Bacteria are widely distributed in atmospheric aerosols and are indispensable components of clouds, playing an important role in the atmospheric hydrological cycle. However, limited information is available about the bacterial community structure and function, especially for the increasing air pollution in the North China Plain. Here, we present a comprehensive characterization of bacterial community composition, function, variation, and environmental influence for cloud water collected at Mt Tai from 24 July to 23 August 2014. Using Miseq 16S rRNA gene sequencing, the highly diverse bacterial community in cloud water and the predominant phyla of Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes were investigated. Bacteria that survive at low temperature, radiation, and poor nutrient conditions were found in cloud water, suggesting adaption to an extreme environment. The bacterial gene functions predicted from the 16S rRNA gene using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that the pathways related to metabolism and disease infections were significantly correlated with the predominant genera. The abundant genera Acinetobacter, Stenotrophomonas, Pseudomonas, and Empedobacter originated from a wide range of habitats including cloud condensation nuclei and ice nuclei active species, opportunistic pathogens, and functional species, demonstrating the importance of ecology and health in cloud water. Cluster analysis including hierarchical cluster (Hcluster) and principal coordinate analysis (PCoA) indicated a significant disparity between polluted and non-polluted samples. Linear discriminant analysis effect size (LEfSe) demonstrated that potential pathogens were enriched in the polluted cloud samples, whereas the diverse ecological function groups were significant in the non-polluted samples. Discrepant community structure determined by redundancy analysis (RDA) indicated that the major ions in cloud water and PM2. 5 in the atmosphere have a negative impact on bacteria, playing a vital role in shaping microbial community structure. The major ions might provide nutrition to bacteria and directly influence the bacterial community, whereas PM2. 5 in air has an indirect impact on bacterial community structure. During wet deposition, soluble particulate matter was dissolved in water droplets resulting in elevated concentration in cloud water. PM2. 5 was possibly associated with different origins and pathways of air mass as determined using source tracking by the backward trajectory, mainly related to long-range transport. This work enhanced our understanding of the characteristics of bacterial ecology in the atmospheric aqueous phase, highlighting the potential influence of environmental variables on the bacterial community in cloud processes. It may provide fundamental information of the bacterial community response in cloud water under increasing pollution. However, due to the limited sample size (13 samples) collected at the summit of Mt Tai, these issues need in-depth discussion. Further studies based on an annual series of field observation experiments and laboratory simulations will continue to track these issues.

Temporary vs. Permanent Sub-slab Ports: A Comparative Performance Study

EPA Science Inventory

Vapor intrusion (VI) is the migration of subsurface vapors, including radon and volatile organic compounds (VOCs), from the subsurface to indoor air. The VI exposure pathway extends from the contaminant source, which can be impacted soil, non-aqueous phase liquid, or contaminated...

ACCURACY AND COST CONSIDERATIONS IN CHOOSING A CHEMICAL MECHANISM FOR OPERATIONAL USE IN AQ MODELS

EPA Science Inventory

There are several contemporary chemical kinetic mechanisms available for use in tropospheric air quality simulation models, with varying degrees of condensation of the chemical reaction pathways. Likewise, there are several different numerical solution methods available to use w...

Projecting state-level air pollutant emissions using an integrated assessment model: GCAM-USA.

EPA Science Inventory

Integrated Assessment Models (IAMs) characterize the interactions among human and earth systems. IAMs typically have been applied to investigate future energy, land use, and emission pathways at global to continental scales. Recent directions in IAM development include enhanced t...

MODELING INHALATION AND MULTIMEDIA MULTIPATHWAY HUMAN EXPOSURES TO ENVIRONMENTAL POLLUTANTS

EPA Science Inventory

Estimation of exposures of children and adults to air toxics or multimedia pollutants require careful consideration of sources and concentrations of pollutants that may be present in different media, as well as various routes and pathways of exposures associated with age-specif...

REFINED PBPK MODEL OF AGGREGATE EXPOSURE TO METHYL TERTIARY-BUTYL ETHER

EPA Science Inventory

Aggregate (multiple pathway) exposures to methyl tertiary-butyl ether (MTBE) in air and water occur via dermal, inhalation, and oral routes. Previously, physiologically-based pharmacokinetic (PBPK) models have been used to quantify the kinetic behavior of MTBE and its primary met...

Prolonged effect of the stratospheric pathway in linking Barents-Kara Sea sea ice variability to the midlatitude circulation in a simplified model

NASA Astrophysics Data System (ADS)

Zhang, Pengfei; Wu, Yutian; Smith, Karen L.

2018-01-01

To better understand the dynamical mechanism that accounts for the observed lead-lag correlation between the early winter Barents-Kara Sea (BKS) sea ice variability and the later winter midlatitude circulation response, a series of experiments are conducted using a simplified atmospheric general circulation model with a prescribed idealized near-surface heating over the BKS. A prolonged effect is found in the idealized experiments following the near-surface heating and can be explicitly attributed to the stratospheric pathway and the long time scale in the stratosphere. The analysis of the Eliassen-Palm flux shows that, as a result of the imposed heating and linear constructive interference, anomalous upward propagating planetary-scale waves are excited and weaken the stratospheric polar vortex. This stratospheric response persists for approximately 1-2 months accompanied by downward migration to the troposphere and the surface. This downward migration largely amplifies and extends the low-level jet deceleration in the midlatitudes and cold air advection over central Asia. The idealized model experiments also suggest that the BKS region is the most effective in affecting the midlatitude circulation than other regions over the Arctic.

Inactivation of virus in solution by cold atmospheric pressure plasma: identification of chemical inactivation pathways

NASA Astrophysics Data System (ADS)

Aboubakr, Hamada A.; Gangal, Urvashi; Youssef, Mohammed M.; Goyal, Sagar M.; Bruggeman, Peter J.

2016-05-01

Cold atmospheric pressure plasma (CAP) inactivates bacteria and virus through in situ production of reactive oxygen and nitrogen species (RONS). While the bactericidal and virucidal efficiency of plasmas is well established, there is limited knowledge about the chemistry leading to the pathogen inactivation. This article describes a chemical analysis of the CAP reactive chemistry involved in the inactivation of feline calicivirus. We used a remote radio frequency CAP produced in varying gas mixtures leading to different plasma-induced chemistries. A study of the effects of selected scavengers complemented with positive control measurements of relevant RONS reveal two distinctive pathways based on singlet oxygen and peroxynitrous acid. The first mechanism is favored in the presence of oxygen and the second in the presence of air when a significant pH reduction is induced in the solution by the plasma. Additionally, smaller effects of the H2O2, O3 and \\text{NO}2- produced were also found. Identification of singlet oxygen-mediated 2-imidazolone/2-oxo-His (His  +14 Da)—an oxidative modification of His 262 comprising the capsid protein of feline calicivirus links the plasma induced singlet oxygen chemistry to viral inactivation.

Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome.

PubMed

Shen, Haoran; Liang, Zhou; Zheng, Saihua; Li, Xuelian

2017-11-01

The purpose of this study was to identify promising candidate genes and pathways in polycystic ovary syndrome (PCOS). Microarray dataset GSE345269 obtained from the Gene Expression Omnibus database includes 7 granulosa cell samples from PCOS patients, and 3 normal granulosa cell samples. Differentially expressed genes (DEGs) were screened between PCOS and normal samples. Pathway enrichment analysis was conducted for DEGs using ClueGO and CluePedia plugin of Cytoscape. A Reactome functional interaction (FI) network of the DEGs was built using ReactomeFIViz, and then network modules were extracted, followed by pathway enrichment analysis for the modules. Expression of DEGs in granulosa cell samples was measured using quantitative RT-PCR. A total of 674 DEGs were retained, which were significantly enriched with inflammation and immune-related pathways. Eight modules were extracted from the Reactome FI network. Pathway enrichment analysis revealed significant pathways of each module: module 0, Regulation of RhoA activity and Signaling by Rho GTPases pathways shared ARHGAP4 and ARHGAP9; module 2, GlycoProtein VI-mediated activation cascade pathway was enriched with RHOG; module 3, Thromboxane A2 receptor signaling, Chemokine signaling pathway, CXCR4-mediated signaling events pathways were enriched with LYN, the hub gene of module 3. Results of RT-PCR confirmed the finding of the bioinformatic analysis that ARHGAP4, ARHGAP9, RHOG and LYN were significantly upregulated in PCOS. RhoA-related pathways, GlycoProtein VI-mediated activation cascade pathway, ARHGAP4, ARHGAP9, RHOG and LYN may be involved in the pathogenesis of PCOS.

Pathway Analysis of Metabolic Syndrome Using a Genome-Wide Association Study of Korea Associated Resource (KARE) Cohorts.

PubMed

Shim, Unjin; Kim, Han-Na; Sung, Yeon-Ah; Kim, Hyung-Lae

2014-12-01

Metabolic syndrome (MetS) is a complex disorder related to insulin resistance, obesity, and inflammation. Genetic and environmental factors also contribute to the development of MetS, and through genome-wide association studies (GWASs), important susceptibility loci have been identified. However, GWASs focus more on individual single-nucleotide polymorphisms (SNPs), explaining only a small portion of genetic heritability. To overcome this limitation, pathway analyses are being applied to GWAS datasets. The aim of this study is to elucidate the biological pathways involved in the pathogenesis of MetS through pathway analysis. Cohort data from the Korea Associated Resource (KARE) was used for analysis, which include 8,842 individuals (age, 52.2 ± 8.9 years; body mass index, 24.6 ± 3.2 kg/m(2)). A total of 312,121 autosomal SNPs were obtained after quality control. Pathway analysis was conducted using Meta-analysis Gene-Set Enrichment of Variant Associations (MAGENTA) to discover the biological pathways associated with MetS. In the discovery phase, SNPs from chromosome 12, including rs11066280, rs2074356, and rs12229654, were associated with MetS (p < 5 × 10(-6)), and rs11066280 satisfied the Bonferroni-corrected cutoff (unadjusted p < 1.38 × 10(-7), Bonferroni-adjusted p < 0.05). Through pathway analysis, biological pathways, including electron carrier activity, signaling by platelet-derived growth factor (PDGF), the mitogen-activated protein kinase kinase kinase cascade, PDGF binding, peroxisome proliferator-activated receptor (PPAR) signaling, and DNA repair, were associated with MetS. Through pathway analysis of MetS, pathways related with PDGF, mitogen-activated protein kinase, and PPAR signaling, as well as nucleic acid binding, protein secretion, and DNA repair, were identified. Further studies will be needed to clarify the genetic pathogenesis leading to MetS.

Redundancy control in pathway databases (ReCiPa): an application for improving gene-set enrichment analysis in Omics studies and "Big data" biology.

PubMed

Vivar, Juan C; Pemu, Priscilla; McPherson, Ruth; Ghosh, Sujoy

2013-08-01

Abstract Unparalleled technological advances have fueled an explosive growth in the scope and scale of biological data and have propelled life sciences into the realm of "Big Data" that cannot be managed or analyzed by conventional approaches. Big Data in the life sciences are driven primarily via a diverse collection of 'omics'-based technologies, including genomics, proteomics, metabolomics, transcriptomics, metagenomics, and lipidomics. Gene-set enrichment analysis is a powerful approach for interrogating large 'omics' datasets, leading to the identification of biological mechanisms associated with observed outcomes. While several factors influence the results from such analysis, the impact from the contents of pathway databases is often under-appreciated. Pathway databases often contain variously named pathways that overlap with one another to varying degrees. Ignoring such redundancies during pathway analysis can lead to the designation of several pathways as being significant due to high content-similarity, rather than truly independent biological mechanisms. Statistically, such dependencies also result in correlated p values and overdispersion, leading to biased results. We investigated the level of redundancies in multiple pathway databases and observed large discrepancies in the nature and extent of pathway overlap. This prompted us to develop the application, ReCiPa (Redundancy Control in Pathway Databases), to control redundancies in pathway databases based on user-defined thresholds. Analysis of genomic and genetic datasets, using ReCiPa-generated overlap-controlled versions of KEGG and Reactome pathways, led to a reduction in redundancy among the top-scoring gene-sets and allowed for the inclusion of additional gene-sets representing possibly novel biological mechanisms. Using obesity as an example, bioinformatic analysis further demonstrated that gene-sets identified from overlap-controlled pathway databases show stronger evidence of prior association to obesity compared to pathways identified from the original databases.

DOE Office of Scientific and Technical Information (OSTI.GOV)

LaFreniere, L. M.

The Commodity Credit Corporation of the U.S. Department of Agriculture (CCC/USDA) operated a grain storage facility at the western edge of Everest, Kansas, from the early 1950s to the early 1970s. Sampling by the Kansas Department of Health and Environment (KDHE) in 1997 resulted in the detection of carbon tetrachloride in one domestic well (the Nigh well) northwest of the former facility. On behalf of the CCC/USDA, Argonne National Laboratory subsequently conducted a series of investigations to characterize the contamination (Argonne 2003, 2006a,b,c). Automatic, continuous monitoring of groundwater levels began in 2002 and is ongoing at six locations. The resultsmore » have consistently indicated groundwater flow toward the north-northwest from the former CCC/USDA property to the Nigh property, then west-southwest from the Nigh property to the intermittent creek. Sitewide periodic groundwater and surface water sampling with analysis for volatile organic compounds (VOCs) began in 2008. Argonne's combined data indicate no significant downgradient extension of contamination since 2000. At present, the sampling is annual, as approved by the KDHE (2009) in response to a plan developed for the CCC/USDA (Argonne 2009). This document presents a plan for collecting indoor air samples in homes located along and adjacent to the defined extent of the carbon tetrachloride contamination. The plan was requested by the KDHE. Ambient air samples to represent the conditions along this pathway will also be taken. The purpose of the proposed work is to satisfy KDHE requirements and to collect additional data for assessing the risk to human health due to the potential upward migration of carbon tetrachloride and its primary degradation product (chloroform) into homes located in close proximity to the former grain storage facility, as well as along and within 100 ft laterally from the currently defined plume emanating from the former Everest facility. Investigation of the indoor air environment was not a defined objective during the previous investigations of the Everest site (Argonne 2003, 2006a,b,c) as they predated the more recent regulatory concern regarding potential health risks associated with the vapor contaminant pathway.« less

Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome.

PubMed

Johar, Angad S; Mastronardi, Claudio; Rojas-Villarraga, Adriana; Patel, Hardip R; Chuah, Aaron; Peng, Kaiman; Higgins, Angela; Milburn, Peter; Palmer, Stephanie; Silva-Lara, Maria Fernanda; Velez, Jorge I; Andrews, Dan; Field, Matthew; Huttley, Gavin; Goodnow, Chris; Anaya, Juan-Manuel; Arcos-Burgos, Mauricio

2015-06-02

Multiple autoimmune syndrome (MAS), an extreme phenotype of autoimmune disorders, is a very well suited trait to tackle genomic variants of these conditions. Whole exome sequencing (WES) is a widely used strategy for detection of protein coding and splicing variants associated with inherited diseases. The DNA of eight patients affected by MAS [all of whom presenting with Sjögren's syndrome (SS)], four patients affected by SS alone and 38 unaffected individuals, were subject to WES. Filters to identify novel and rare functional (pathogenic-deleterious) homozygous and/or compound heterozygous variants in these patients and controls were applied. Bioinformatics tools such as the Human gene connectome as well as pathway and network analysis were applied to test overrepresentation of genes harbouring these variants in critical pathways and networks involved in autoimmunity. Eleven novel and rare functional variants were identified in cases but not in controls, harboured in: MACF1, KIAA0754, DUSP12, ICA1, CELA1, LRP1/STAT6, GRIN3B, ANKLE1, TMEM161A, and FKRP. These were subsequently subject to network analysis and their functional relatedness to genes already associated with autoimmunity was evaluated. Notably, the LRP1/STAT6 novel mutation was homozygous in one MAS affected patient and heterozygous in another. LRP1/STAT6 disclosed the strongest plausibility for autoimmunity. LRP1/STAT6 are involved in extracellular and intracellular anti-inflammatory pathways that play key roles in maintaining the homeostasis of the immune system. Further; networks, pathways, and interaction analyses showed that LRP1 is functionally related to the HLA-B and IL10 genes and it has a substantial impact within immunological pathways and/or reaction to bacterial and other foreign proteins (phagocytosis, regulation of phospholipase A2 activity, negative regulation of apoptosis and response to lipopolysaccharides). Further, ICA1 and STAT6 were also closely related to AIRE and IRF5, two very well known autoimmunity genes. Novel and rare exonic mutations that may account for autoimmunity were identified. Among those, the LRP1/STAT6 novel mutation has the strongest case for being categorised as potentially causative of MAS given the presence of intriguing patterns of functional interaction with other major genes shaping autoimmunity.

Convergent evidence from systematic analysis of GWAS revealed genetic basis of esophageal cancer.

PubMed

Gao, Xue-Xin; Gao, Lei; Wang, Jiu-Qiang; Qu, Su-Su; Qu, Yue; Sun, Hong-Lei; Liu, Si-Dang; Shang, Ying-Li

2016-07-12

Recent genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with risk of esophageal cancer (EC). However, investigation of genetic basis from the perspective of systematic biology and integrative genomics remains scarce.In this study, we explored genetic basis of EC based on GWAS data and implemented a series of bioinformatics methods including functional annotation, expression quantitative trait loci (eQTL) analysis, pathway enrichment analysis and pathway grouped network analysis.Two hundred and thirteen risk SNPs were identified, in which 44 SNPs were found to have significantly differential gene expression in esophageal tissues by eQTL analysis. By pathway enrichment analysis, 170 risk genes mapped by risk SNPs were enriched into 38 significant GO terms and 17 significant KEGG pathways, which were significantly grouped into 9 sub-networks by pathway grouped network analysis. The 9 groups of interconnected pathways were mainly involved with muscle cell proliferation, cellular response to interleukin-6, cell adhesion molecules, and ethanol oxidation, which might participate in the development of EC.Our findings provide genetic evidence and new insight for exploring the molecular mechanisms of EC.

Air-liquid biofilm formation is dependent on ammonium depletion in a Saccharomyces cerevisiae flor strain.

PubMed

Zara, Giacomo; Budroni, Marilena; Mannazzu, Ilaria; Zara, Severino

2011-12-01

Air-liquid biofilm formation appears to be an adaptive mechanism that promotes foraging of Saccharomyces cerevisiae flor strains in response to nutrient starvation. The FLO11 gene plays a central role in this phenotype as its expression allows yeast cells to rise to the liquid surface. Here, we investigated the role of ammonium depletion in air-liquid biofilm formation and FLO11 expression in a S. cerevisiae flor strain. The data obtained show that increasing ammonium concentrations from 0 to 450 m m reduce air-liquid biofilm in terms of biomass and velum formation and correlate with a reduction of FLO11 expression. Rapamycin inhibition of the TOR pathway and deletion of RAS2 gene significantly reduced biofilm formation and FLO11 expression. Taken together, these data suggest that ammonium depletion is a key factor in the induction of air-liquid biofilm formation and FLO11 expression in S. cerevisiae flor strains. Copyright © 2011 John Wiley & Sons, Ltd.

Progress of ambient air pollution and cardiovascular disease research in Asia.

PubMed

Su, Ta-Chen; Chen, Szu-Ying; Chan, Chang-Chuan

2011-01-01

Asian countries are with deteriorating air quality accompanying the rapid economic and social development of the past decades, and the potential health impacts of air pollution have been noticed by researchers in the region. We reviewed the scientific literature on air pollution and cardiovascular diseases (CVD) published by Asian researchers in English since the 1980s to determine whether the findings in Europe and North America can be extrapolated to Asia. Epidemiological studies show that short-term particulate matter pollution is a strong predictor for CVD morbidity and mortality and suggestive on cerebrovascular morbidity and mortality in newly developed countries in Asia. Multicountry epidemiological studies are needed to fully appreciate the extent of air pollution on CVD in Asia, especially less developed Asian countries. New cohort studies should be initiated to improve our understanding of particulate matter's toxicological pathways, long-term exposure effects, and gene-environment interaction on CVD among the Asian population. Copyright © 2011 Elsevier Inc. All rights reserved.

Insights into significant pathways and gene interaction networks underlying breast cancer cell line MCF-7 treated with 17β-estradiol (E2).

PubMed

Huan, Jinliang; Wang, Lishan; Xing, Li; Qin, Xianju; Feng, Lingbin; Pan, Xiaofeng; Zhu, Ling

2014-01-01

Estrogens are known to regulate the proliferation of breast cancer cells and to alter their cytoarchitectural and phenotypic properties, but the gene networks and pathways by which estrogenic hormones regulate these events are only partially understood. We used global gene expression profiling by Affymetrix GeneChip microarray analysis, with KEGG pathway enrichment, PPI network construction, module analysis and text mining methods to identify patterns and time courses of genes that are either stimulated or inhibited by estradiol (E2) in estrogen receptor (ER)-positive MCF-7 human breast cancer cells. Of the genes queried on the Affymetrix Human Genome U133 plus 2.0 microarray, we identified 628 (12h), 852 (24h) and 880 (48 h) differentially expressed genes (DEGs) that showed a robust pattern of regulation by E2. From pathway enrichment analysis, we found out the changes of metabolic pathways of E2 treated samples at each time point. At 12h time point, the changes of metabolic pathways were mainly focused on pathways in cancer, focal adhesion, and chemokine signaling pathway. At 24h time point, the changes were mainly enriched in neuroactive ligand-receptor interaction, cytokine-cytokine receptor interaction and calcium signaling pathway. At 48 h time point, the significant pathways were pathways in cancer, regulation of actin cytoskeleton, cell adhesion molecules (CAMs), axon guidance and ErbB signaling pathway. Of interest, our PPI network analysis and module analysis found that E2 treatment induced enhancement of PRSS23 at the three time points and PRSS23 was in the central position of each module. Text mining results showed that the important genes of DEGs have relationship with signal pathways, such as ERbB pathway (AREG), Wnt pathway (NDP), MAPK pathway (NTRK3, TH), IP3 pathway (TRA@) and some transcript factors (TCF4, MAF). Our studies highlight the diverse gene networks and metabolic and cell regulatory pathways through which E2 operates to achieve its widespread effects on breast cancer cells. © 2013 Elsevier B.V. All rights reserved.

Trapping, chemistry, and export of trace gases in the South Asian summer monsoon observed during CARIBIC flights in 2008

NASA Astrophysics Data System (ADS)

Rauthe-Schöch, Armin; Baker, Angela K.; Schuck, Tanja J.; Brenninkmeijer, Carl A. M.; Zahn, Andreas; Hermann, Markus; Stratmann, Greta; Ziereis, Helmut; van Velthoven, Peter F. J.; Lelieveld, Jos

2016-03-01

The CARIBIC (Civil Aircraft for the Regular Investigation of the Atmosphere Based on an Instrument Container) passenger aircraft observatory performed in situ measurements at 10-12 km altitude in the South Asian summer monsoon anticyclone between June and September 2008. These measurements enable us to investigate this atmospheric region (which so far has mostly been observed from satellites) using the broad suite of trace gases and aerosol particles measured by CARIBIC. Elevated levels of a variety of atmospheric pollutants (e.g. carbon monoxide, total reactive nitrogen oxides, aerosol particles, and several volatile organic compounds) were recorded. The measurements provide detailed information about the chemical composition of air in different parts of the monsoon anticyclone, particularly of ozone precursors. While covering a range of 3500 km inside the monsoon anticyclone, CARIBIC observations show remarkable consistency, i.e. with distinct latitudinal patterns of trace gases during the entire monsoon period. Using the CARIBIC trace gas and aerosol particle measurements in combination with the Lagrangian particle dispersion model FLEXPART, we investigated the characteristics of monsoon outflow and the chemical evolution of air masses during transport. The trajectory calculations indicate that these air masses originated mainly from South Asia and mainland Southeast Asia. Estimated photochemical ages of the air were found to agree well with transport times from a source region east of 90-95° E. The photochemical ages of the air in the southern part of the monsoon anticyclone were systematically younger (less than 7 days) and the air masses were mostly in an ozone-forming chemical mode. In its northern part the air masses were older (up to 13 days) and had unclear ozone formation or destruction potential. Based on analysis of forward trajectories, several receptor regions were identified. In addition to predominantly westward transport, we found evidence for efficient transport (within 10 days) to the Pacific and North America, particularly during June and September, and also of cross-tropopause exchange, which was strongest during June and July. Westward transport to Africa and further to the Mediterranean was the main pathway during July.

Trapping, chemistry and export of trace gases in the South Asian summer monsoon observed during CARIBIC flights in 2008

NASA Astrophysics Data System (ADS)

Rauthe-Schöch, A.; Baker, A. K.; Schuck, T. J.; Brenninkmeijer, C. A. M.; Zahn, A.; Hermann, M.; Stratmann, G.; Ziereis, H.; van Velthoven, P. F. J.; Lelieveld, J.

2015-03-01

The CARIBIC (Civil Aircraft for the Regular Investigation of the Atmosphere Based on an Instrument Container) passenger aircraft observatory performed in situ measurements at 10-12 km altitude in the South Asian summer monsoon anticyclone between June and September 2008. These measurements enable us to investigate this atmospheric region, which so far has mostly been observed from satellites, using the broad suite of trace gases and aerosols measured by CARIBIC. Elevated levels of a range of atmospheric pollutants were recorded e.g. carbon monoxide, total reactive nitrogen oxides, aerosol particles and several volatile organic compounds. The measurements provide detailed information about the chemical composition of air in different parts of the monsoon anticyclone, particularly of ozone precursors. While covering a range of 3500 km inside the monsoon anticyclone, CARIBIC observations show remarkable consistency, i.e. with regular latitudinal patterns of trace gases during the entire monsoon period. Trajectory calculations indicate that these air masses originated mainly from South Asia and Mainland Southeast Asia. Using the CARIBIC trace gas and aerosol measurements in combination with the Lagrangian particle dispersion model FLEXPART we investigated the characteristics of monsoon outflow and the chemical evolution of air masses during transport. Estimated photochemical ages of the air were found to agree well with transport times from a source region east of 95° E. The photochemical ages of the air in the southern part of the monsoon anticyclone were consistently younger (less than 7 days) and the air masses mostly in an ozone forming chemical regime. In its northern part the air masses were older (up to 13 days) and had unclear ozone formation or destruction potential. Based on analysis of forward trajectories several receptor regions were identified. In addition to predominantly westward transport, we found evidence for efficient transport (within 10 days) to the Pacific and North America, particularly during June and September, and also of cross-tropopause exchange, which was strongest during June and July. Westward transport to Africa and further to the Mediterranean was the main pathway during July.

Modeled aerosol nitrate formation pathways during wintertime in the Great Lakes region of North America

NASA Astrophysics Data System (ADS)

Kim, Yoo Jung; Spak, Scott N.; Carmichael, Gregory R.; Riemer, Nicole; Stanier, Charles O.

2014-11-01

Episodic wintertime particle pollution by ammonium nitrate is an important air quality concern across the Midwest U.S. Understanding and accurately forecasting PM2.5 episodes are complicated by multiple pathways for aerosol nitrate formation, each with uncertain rate parameters. Here, the Community Multiscale Air Quality model (CMAQ) simulated regional atmospheric nitrate budgets during the 2009 LADCO Winter Nitrate Study, using integrated process rate (IPR) and integrated reaction rate (IRR) tools to quantify relevant processes. Total nitrate production contributing to PM2.5 episodes is a regional phenomenon, with peak production over the Ohio River Valley and southern Great Lakes. Total nitrate production in the lower troposphere is attributed to three pathways, with 57% from heterogeneous conversion of N2O5, 28% from the reaction of OH and NO2, and 15% from homogeneous conversion of N2O5. TNO3 formation rates varied day-to-day and on synoptic timescales. Rate-limited production does not follow urban-rural gradients and NOx emissions due, to counterbalancing of urban enhancement in daytime HNO3 production with nocturnal reductions. Concentrations of HNO3 and N2O5 and nighttime TNO3 formation rates have maxima aloft (100-500 m), leading to net total nitrate vertical flux during episodes, with substantial vertical gradients in nitrate partitioning. Uncertainties in all three pathways are relevant to wintertime aerosol modeling and highlight the importance of interacting transport and chemistry processes during ammonium nitrate episodes, as well as the need for additional constraint on the system through field and laboratory experiments.

Contribution of air pollution to COPD and small airway dysfunction.

PubMed

Berend, Norbert

2016-02-01

Although in many Western countries levels of ambient air pollution have been improving with the setting of upper limits and better urban planning, air pollution in developing countries and particularly those with rapid industrialization has become a major global problem. Together with increased motor vehicle ownership and traffic congestion, there is a growing issue with airborne particles of respirable size. These particles are thought responsible for respiratory and cardiovascular effects and have also been implicated in cancer pathogenesis. The pathologic effects in the lung are mediated via inflammatory pathways and involve oxidative stress similar to cigarette smoking. These effects are seen in the peripheral airways where the smaller particle fractions are deposited and lead to airway remodelling. However, emphysema and loss of bronchioles seen with cigarette smoking have not been described with ambient air pollution, and there are few studies specifically looking at peripheral airway function. Definitive evidence of air pollution causing COPD is lacking and a different study design is required to link air pollution and COPD. © 2015 Asian Pacific Society of Respirology.

The Paleo-ecology of C4 Evolution

NASA Astrophysics Data System (ADS)

Sage, R. F.; Khoshravesh, R.

2014-12-01

Molecular clock analysis of extant plant lineages consistently place the earliest appearance of the C4 photosynthetic pathway in the mid-to-late Oligocene, coincident with a decline in atmospheric CO2 and a spread of dry environments. Most of the approximately 70 known lineages of C4 photosynthesis, however, evolved over the subsequent 23 million years since the Oligocene. Examination of living C3-C4 intermediate species, and close C3 relatives of modern C4 lineages, indicate that the C4 pathway evolved in regions of high heat and episodic drought and/or salinity, usually in the drier ends of the monsoon belts of the subtropics. Soils associated with transitional species are typically sandy, rocky, or salinized, and have low vegetation density, which in combination with high air temperature allows for high surface heat loads that warm leaves to near 45°C. Under such conditions in low CO2 atmospheres, the rate of photorespiration is very high and would greatly impair C3 photosynthesis and establish conditions favoring C4 evolution. However, studies with modern taxa do not address whether the extreme habitats proposed to facilitate C4 evolution were actually present at the time when the C4 pathway evolved in any given lineage. Here, we examine the paleo-record to evaluate the environmental conditions present in the C4 centres of origin when the respective transitions from C3 to C4 photosynthesis are estimated to have occurred.

Identifying novel glioma associated pathways based on systems biology level meta-analysis.

PubMed

Hu, Yangfan; Li, Jinquan; Yan, Wenying; Chen, Jiajia; Li, Yin; Hu, Guang; Shen, Bairong

2013-01-01

With recent advances in microarray technology, including genomics, proteomics, and metabolomics, it brings a great challenge for integrating this "-omics" data to analysis complex disease. Glioma is an extremely aggressive and lethal form of brain tumor, and thus the study of the molecule mechanism underlying glioma remains very important. To date, most studies focus on detecting the differentially expressed genes in glioma. However, the meta-analysis for pathway analysis based on multiple microarray datasets has not been systematically pursued. In this study, we therefore developed a systems biology based approach by integrating three types of omics data to identify common pathways in glioma. Firstly, the meta-analysis has been performed to study the overlapping of signatures at different levels based on the microarray gene expression data of glioma. Among these gene expression datasets, 12 pathways were found in GeneGO database that shared by four stages. Then, microRNA expression profiles and ChIP-seq data were integrated for the further pathway enrichment analysis. As a result, we suggest 5 of these pathways could be served as putative pathways in glioma. Among them, the pathway of TGF-beta-dependent induction of EMT via SMAD is of particular importance. Our results demonstrate that the meta-analysis based on systems biology level provide a more useful approach to study the molecule mechanism of complex disease. The integration of different types of omics data, including gene expression microarrays, microRNA and ChIP-seq data, suggest some common pathways correlated with glioma. These findings will offer useful potential candidates for targeted therapeutic intervention of glioma.

Plasma Assisted Combustion Mechanism for Small Hydrocarbons

DTIC Science & Technology

2015-01-01

fast ionization wave. Combust.  Theory Modeling, 2001. V.5 pp.97‐129.  N.A.Popov. Effect of a  Pulsed  High‐Current  Discharge  on Hydrogen–Air  Mixtures... Discharge Tube Mono- chro- mator PM Pressure Gauge Electric Gauge Physics of Nonequilibrium  Systems Laboratory Hexane Oxidation by  Pulsed  Nanosecond...Pathways: C2H4‐air  Where PAC Experimental Data is Available Avalanche  to Streamer Transition in Uniform  Electric Field (air, 1 bar, 300 K, 1 cm

Survival Analysis of US Air Force Officer Retention Rate

DTIC Science & Technology

2017-03-23

Air Force Institute of Technology AFIT Scholar Theses and Dissertations 3-23-2017 Survival Analysis of US Air Force Officer Retention Rate Courtney N...AIR UNIVERSITY AIR FORCE INSTITUTE OF TECHNOLOGY Wright-Patterson Air Force Base, Ohio DISTRIBUTION STATEMENT A. APPROVED FOR PUBLIC RELEASE...to the Faculty Department of Operational Sciences Graduate School of Engineering and Management Air Force Institute of Technology Air University

Genome-wide pathway-based association analysis identifies risk pathways associated with Parkinson's disease.

PubMed

Zhang, Mingming; Mu, Hongbo; Shang, Zhenwei; Kang, Kai; Lv, Hongchao; Duan, Lian; Li, Jin; Chen, Xinren; Teng, Yanbo; Jiang, Yongshuai; Zhang, Ruijie

2017-01-06

Parkinson's disease (PD) is the second most common neurodegenerative disease. It is generally believed that it is influenced by both genetic and environmental factors, but the precise pathogenesis of PD is unknown to date. In this study, we performed a pathway analysis based on genome-wide association study (GWAS) to detect risk pathways of PD in three GWAS datasets. We first mapped all SNP markers to autosomal genes in each GWAS dataset. Then, we evaluated gene risk values using the minimum P-value of the tagSNPs. We took a pathway as a unit to identify the risk pathways based on the cumulative risks of the genes in the pathway. Finally, we combine the analysis results of the three datasets to detect the high risk pathways associated with PD. We found there were five same pathways in the three datasets. Besides, we also found there were five pathways which were shared in two datasets. Most of these pathways are associated with nervoussystem. Five pathways had been reported to be PD-related pathways in the previous literature. Our findings also implied that there was a close association between immune response and PD. Continued investigation of these pathways will further help us explain the pathogenesis of PD. Copyright © 2016. Published by Elsevier Ltd.

A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways

PubMed Central

Han, Junwei; Li, Chunquan; Yang, Haixiu; Xu, Yanjun; Zhang, Chunlong; Ma, Jiquan; Shi, Xinrui; Liu, Wei; Shang, Desi; Yao, Qianlan; Zhang, Yunpeng; Su, Fei; Feng, Li; Li, Xia

2015-01-01

Identifying dysregulated pathways from high-throughput experimental data in order to infer underlying biological insights is an important task. Current pathway-identification methods focus on single pathways in isolation; however, consideration of crosstalk between pathways could improve our understanding of alterations in biological states. We propose a novel method of pathway analysis based on global influence (PAGI) to identify dysregulated pathways, by considering both within-pathway effects and crosstalk between pathways. We constructed a global gene–gene network based on the relationships among genes extracted from a pathway database. We then evaluated the extent of differential expression for each gene, and mapped them to the global network. The random walk with restart algorithm was used to calculate the extent of genes affected by global influence. Finally, we used cumulative distribution functions to determine the significance values of the dysregulated pathways. We applied the PAGI method to five cancer microarray datasets, and compared our results with gene set enrichment analysis and five other methods. Based on these analyses, we demonstrated that PAGI can effectively identify dysregulated pathways associated with cancer, with strong reproducibility and robustness. We implemented PAGI using the freely available R-based and Web-based tools (http://bioinfo.hrbmu.edu.cn/PAGI). PMID:25551156

Meta-analysis of pathway enrichment: combining independent and dependent omics data sets.

PubMed

Kaever, Alexander; Landesfeind, Manuel; Feussner, Kirstin; Morgenstern, Burkhard; Feussner, Ivo; Meinicke, Peter

2014-01-01

A major challenge in current systems biology is the combination and integrative analysis of large data sets obtained from different high-throughput omics platforms, such as mass spectrometry based Metabolomics and Proteomics or DNA microarray or RNA-seq-based Transcriptomics. Especially in the case of non-targeted Metabolomics experiments, where it is often impossible to unambiguously map ion features from mass spectrometry analysis to metabolites, the integration of more reliable omics technologies is highly desirable. A popular method for the knowledge-based interpretation of single data sets is the (Gene) Set Enrichment Analysis. In order to combine the results from different analyses, we introduce a methodical framework for the meta-analysis of p-values obtained from Pathway Enrichment Analysis (Set Enrichment Analysis based on pathways) of multiple dependent or independent data sets from different omics platforms. For dependent data sets, e.g. obtained from the same biological samples, the framework utilizes a covariance estimation procedure based on the nonsignificant pathways in single data set enrichment analysis. The framework is evaluated and applied in the joint analysis of Metabolomics mass spectrometry and Transcriptomics DNA microarray data in the context of plant wounding. In extensive studies of simulated data set dependence, the introduced correlation could be fully reconstructed by means of the covariance estimation based on pathway enrichment. By restricting the range of p-values of pathways considered in the estimation, the overestimation of correlation, which is introduced by the significant pathways, could be reduced. When applying the proposed methods to the real data sets, the meta-analysis was shown not only to be a powerful tool to investigate the correlation between different data sets and summarize the results of multiple analyses but also to distinguish experiment-specific key pathways.

Tissue Non-Specific Genes and Pathways Associated with Diabetes: An Expression Meta-Analysis.

PubMed

Mei, Hao; Li, Lianna; Liu, Shijian; Jiang, Fan; Griswold, Michael; Mosley, Thomas

2017-01-21

We performed expression studies to identify tissue non-specific genes and pathways of diabetes by meta-analysis. We searched curated datasets of the Gene Expression Omnibus (GEO) database and identified 13 and five expression studies of diabetes and insulin responses at various tissues, respectively. We tested differential gene expression by empirical Bayes-based linear method and investigated gene set expression association by knowledge-based enrichment analysis. Meta-analysis by different methods was applied to identify tissue non-specific genes and gene sets. We also proposed pathway mapping analysis to infer functions of the identified gene sets, and correlation and independent analysis to evaluate expression association profile of genes and gene sets between studies and tissues. Our analysis showed that PGRMC1 and HADH genes were significant over diabetes studies, while IRS1 and MPST genes were significant over insulin response studies, and joint analysis showed that HADH and MPST genes were significant over all combined data sets. The pathway analysis identified six significant gene sets over all studies. The KEGG pathway mapping indicated that the significant gene sets are related to diabetes pathogenesis. The results also presented that 12.8% and 59.0% pairwise studies had significantly correlated expression association for genes and gene sets, respectively; moreover, 12.8% pairwise studies had independent expression association for genes, but no studies were observed significantly different for expression association of gene sets. Our analysis indicated that there are both tissue specific and non-specific genes and pathways associated with diabetes pathogenesis. Compared to the gene expression, pathway association tends to be tissue non-specific, and a common pathway influencing diabetes development is activated through different genes at different tissues.

Transcriptome and key genes expression related to carbon fixation pathways in Chlorella PY-ZU1 cells and their growth under high concentrations of CO2.

PubMed

Huang, Yun; Cheng, Jun; Lu, Hongxiang; He, Yong; Zhou, Junhu; Cen, Kefa

2017-01-01

The biomass yield of Chlorella PY-ZU1 drastically increased when cultivated under high CO 2 condition compared with that cultivated under air condition. However, less attention has been given to the microalgae photosynthetic mechanisms response to different CO 2 concentrations. The genetic reasons for the higher growth rate, CO 2 fixation rate, and photosynthetic efficiency of microalgal cells under higher CO 2 concentration have not been clearly defined yet. In this study, the Illumina sequencing and de novo transcriptome assembly of Chlorella PY-ZU1 cells cultivated under 15% CO 2 were performed and compared with those of cells grown under air. It was found that carbonic anhydrase (CAs, enzyme for interconversion of bicarbonate to CO 2 ) dramatically decreased to near 0 in 15% CO 2 -grown cells, which indicated that CO 2 molecules directly permeated into cells under high CO 2 stress without CO 2 -concentrating mechanism. Extrapolating from the growth conditions and quantitative Real-Time PCR of CCM-related genes, the K m (CO 2 ) (the minimum intracellular CO 2 concentration that rubisco required) of Chlorella PY-ZU1 might be in the range of 80-192 μM. More adenosine triphosphates was saved for carbon fixation-related pathways. The transcript abundance of rubisco (the most important enzyme of CO 2 fixation reaction) was 16.3 times higher in 15% CO 2 -grown cells than that under air. Besides, the transcript abundances of most key genes involved in carbon fixation pathways were also enhanced in 15% CO 2 -grown cells. Carbon fixation and nitrogen metabolism are the two most important metabolisms in the photosynthetic cells. These genes related to the two most metabolisms with significantly differential expressions were beneficial for microalgal growth (2.85 g L -1 ) under 15% CO 2 concentration. Considering the micro and macro growth phenomena of Chlorella PY-ZU1 under different concentrations of CO 2 (0.04-60%), CO 2 transport pathways responses to different CO 2 (0.04-60%) concentrations was reconstructed.

In vitro short-term exposure to air pollution PM{sub 2.5-0.3} induced cell cycle alterations and genetic instability in a human lung cell coculture model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abbas, Imane; EA4492-UCEIV, Université du Littoral-Côte d’Opale, Dunkerque; Lebanese Atomic Energy Commission – CNRS, Beirut

Although its adverse health effects of air pollution particulate matter (PM2.5) are well-documented and often related to oxidative stress and pro-inflammatory response, recent evidence support the role of the remodeling of the airway epithelium involving the regulation of cell death processes. Hence, the overarching goals of the present study were to use an in vitro coculture model, based on human AM and L132 cells to study the possible alteration of TP53-RB gene signaling pathways (i.e. cell cycle phases, gene expression of TP53, BCL2, BAX, P21, CCND1, and RB, and protein concentrations of their active forms), and genetic instability (i.e. LOHmore » and/or MSI) in the PM{sub 2.5-0.3}-exposed coculture model. PM{sub 2.5-0.3} exposure of human AM from the coculture model induced marked cell cycle alterations after 24 h, as shown by increased numbers of L132 cells in subG1 and S+G2 cell cycle phases, indicating apoptosis and proliferation. Accordingly, activation of the TP53-RB gene signaling pathways after the coculture model exposure to PM{sub 2.5-0.3} was reported in the L132 cells. Exposure of human AM from the coculture model to PM{sub 2.5-0.3} resulted in MS alterations in 3p chromosome multiple critical regions in L132 cell population. Hence, in vitro short-term exposure of the coculture model to PM{sub 2.5-0.3} induced cell cycle alterations relying on the sequential occurrence of molecular abnormalities from TP53-RB gene signaling pathway activation and genetic instability. - Highlights: • Better knowledge on health adverse effects of air pollution PM{sub 2.5}. • Human alveolar macrophage and normal human epithelial lung cell coculture. • Molecular abnormalities from TP53-RB gene signaling pathway. • Loss of heterozygosity and microsatellite instability. • Pathologic changes in morphology and number of cells in relation to airway remodeling.« less

Children’s Phthalate Intakes and Resultant Cumulative Exposures Estimated from Urine Compared with Estimates from Dust Ingestion, Inhalation and Dermal Absorption in Their Homes and Daycare Centers

PubMed Central

Bekö, Gabriel; Weschler, Charles J.; Langer, Sarka; Callesen, Michael; Toftum, Jørn; Clausen, Geo

2013-01-01

Total daily intakes of diethyl phthalate (DEP), di(n-butyl) phthalate (DnBP), di(isobutyl) phthalate (DiBP), butyl benzyl phthalate (BBzP) and di(2-ethylhexyl) phthalate (DEHP) were calculated from phthalate metabolite levels measured in the urine of 431 Danish children between 3 and 6 years of age. For each child the intake attributable to exposures in the indoor environment via dust ingestion, inhalation and dermal absorption were estimated from the phthalate levels in the dust collected from the child’s home and daycare center. Based on the urine samples, DEHP had the highest total daily intake (median: 4.42 µg/d/kg-bw) and BBzP the lowest (median: 0.49 µg/d/kg-bw). For DEP, DnBP and DiBP, exposures to air and dust in the indoor environment accounted for approximately 100%, 15% and 50% of the total intake, respectively, with dermal absorption from the gas-phase being the major exposure pathway. More than 90% of the total intake of BBzP and DEHP came from sources other than indoor air and dust. Daily intake of DnBP and DiBP from all exposure pathways, based on levels of metabolites in urine samples, exceeded the Tolerable Daily Intake (TDI) for 22 and 23 children, respectively. Indoor exposures resulted in an average daily DiBP intake that exceeded the TDI for 14 children. Using the concept of relative cumulative Tolerable Daily Intake (TDIcum), which is applicable for phthalates that have established TDIs based on the same health endpoint, we examined the cumulative total exposure to DnBP, DiBP and DEHP from all pathways; it exceeded the tolerable levels for 30% of the children. From the three indoor pathways alone, several children had a cumulative intake that exceeded TDIcum. Exposures to phthalates present in the air and dust indoors meaningfully contribute to a child’s total intake of certain phthalates. Such exposures, by themselves, may lead to intakes exceeding current limit values. PMID:23626820

COMPARISON OF MEASURED AND MODELED SURFACE FLUXES OF HEAT, MOISTURE, AND CHEMICAL DRY DEPOSITION

EPA Science Inventory

Realistic air quality modeling requires accurate simulation of both meteorological and chemical processes within the planetary boundary layer (PBL). n vegetated areas, the primary pathway for surface fluxes of moisture as well a many gaseous chemicals is through vegetative transp...

Exploring consumer pathways and patterns of use for chemicals in the environment

EPA Science Inventory

Background: Humans may be exposed to thousands of chemicals through contact in the workplace, home, and via air, water, food, and soil. A major challenge is estimating exposures to these chemicals, which requires understanding potential exposure routes directly related to how che...

Epoxide pathways improve model predictions of isoprene markers and reveal key role of acidity in aerosol formation

EPA Science Inventory

Isoprene significantly contributes to organic aerosol in the southeastern United States where biogenic hydrocarbons mix with anthropogenic emissions. In this work, the Community Multiscale Air Quality model is updated to predict isoprene aerosol from epoxides produced under both ...

GROUND WATER SAMPLING OF VOCS IN THE WATER/CAPILLARY FRINGE AREA FOR VAPOR INTRUSION ASSESSMENT

EPA Science Inventory

Vapor intrusion has recently been considered a major pathway for increased indoor air contamination from certain volatile organic contaminants (VOCs). The recent Draft EPA Subsurface Vapor Intrusion Guidance Document states that ground water samples should be obtained from the u...

Effects of elevated CO sub 2 concentrations on glycolysis in intact Bartlett pear fruit. [Pyrus communis L

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerbel, E.L.; Kader, A.A.; Romani, R.J.

1988-04-01

Mature intact Bartlett pear fruit (Pyrus communis L.) were stored under a continuous flow of air or air + 10% CO{sub 2} for 4 days at 20{degree}C. Fruit kept under elevated CO{sub 2} concentrations exhibited reduced respiration (O{sub 2} consumption) and ethylene evolution rates, and remained firmer and greener than fruit stored in air. Protein content, fructose 1,6-bisphosphate levels, and ATP:phosphofructokinase and PPi:phosphofructokinase activities declined, while levels of fructose 6-phosphate and fructose 2,6-bisphosphate increased in fruit exposed to air + 10% CO{sub 2}. These results are discussed in light of a possible inhibitory effect of CO{sub 2} at the sitemore » of action of both phosphofructokinases in the glycolytic pathway, which could account, at least in part, for the observed reduction in respiration.« less

Ag-Cu nanoalloyed film as a high-performance cathode electrocatalytic material for zinc-air battery

NASA Astrophysics Data System (ADS)

Lei, Yimin; Chen, Fuyi; Jin, Yachao; Liu, Zongwen

2015-04-01

A novel Ag50Cu50 film electrocatalyst for oxygen reduction reaction (ORR) was prepared by pulsed laser deposition (PLD) method. The electrocatalyst actually is Ag-Cu alloyed nanoparticles embedded in amorphous Cu film, based on transmission electron microscopy (TEM) characterization. The rotating disk electrode (RDE) measurements provide evidence that the ORR proceed via a four-electron pathway on the electrocatalysts in alkaline solution. And it is much more efficient than pure Ag catalyst. The catalytic layer has maximum power density of 67 mW cm-2 and an acceptable cell voltage at 0.863 V when current densities increased up to 100 mA cm-2 in the Ag50Cu50-based primary zinc-air battery. The resulting rechargeable zinc-air battery exhibits low charge-discharge voltage polarization of 1.1 V at 20 mAcm-2 and high durability over 100 cycles in natural air.

Migration history of air-breathing fishes reveals Neogene atmospheric circulation patterns

NASA Astrophysics Data System (ADS)

Böhme, M.

2004-05-01

The migration history of an air-breathing fish group (Channidae; snakehead fishes) is used for reconstructing Neogene Eurasian precipitation and atmospheric circulation patterns. The study shows that snakeheads are sensitive indicators of summer precipitation maxima in subtropical and temperate regions, and are present regularly if the wettest month exceeds 150 mm precipitation and 20 °C mean temperature. The analysis of 515 fossil freshwater fish deposits of the past 50 m.y. from Africa and Eurasia shows two continental-scale migration events from the snakeheads' center of origin in the south Himalayan region, events that can be related to changes in the Northern Hemisphere circulation pattern. The first migration, ca. 17.5 Ma, into western and central Eurasia may have been caused by a northward shift of the Intertropical Convergence Zone that brought western Eurasia under the influence of trade winds that produced a zonal and meridional precipitation gradient in Europe. During the second migration, between 8 and 4 Ma, into Africa and East Asia, snakeheads reached their present-day distribution. This migration could have been related to the intensification of the Asian monsoon that brought summer precipitation to their migratory pathways in East Africa Arabia and East Asia.

Multi-membership gene regulation in pathway based microarray analysis

PubMed Central

2011-01-01

Background Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway. Results We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency. Conclusions We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes. PMID:21939531

Multi-membership gene regulation in pathway based microarray analysis.

PubMed

Pavlidis, Stelios P; Payne, Annette M; Swift, Stephen M

2011-09-22

Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway. We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency. We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.

Long-range pollution transport during the MILAGRO-2006 campaign: a case study of a major Mexico City outflow event using free-floating altitude-controlled balloons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Voss, Paul B.; Zaveri, Rahul A.; Flocke, Frank M.

2010-08-04

One of the major objectives of the Megacities Initiative: Local And Global Research 3 Observations (MILAGRO 2006) campaign was to investigate the long-range transport of 4 Mexico City Metropolitan Area (MCMA) pollution outflow and its downwind impacts on air 5 quality and climate. Four aircraft (DOE G-1, NSF/NCAR C-130, NASA-J31, and NASA 6 DC-8) made extensive chemical, aerosol, and radiation measurements above MCMA and over 7 1000 km downwind in order to characterize the evolution of MCMA pollution as it aged and 8 dispersed over the central Mexican plateau and the Gulf of Mexico. As part of this effort, 9more » free-floating Controlled-Meteorological (CMET) balloons, capable of changing altitude on 10 command via satellite, characterized the MCMA outflow by performing repeated soundings 11 during the transit. In this paper, we present an analysis based on the data from two CMET 12 balloons that were launched near Mexico City on the afternoon of 18 March 2006 and floated 13 downwind with the outflow for nearly 30 hours. Continuous profile measurements made by 14 the balloons show the evolving structure of the MCMA outflow in considerable detail: its 15 stability and stratification, interaction with other air masses, mixing episodes, and dispersion 16 into the regional background. Air parcel trajectories, computed directly from the balloon 17 wind profiles, show three different transport pathways for Mexico City outflow on 18-19 18 March: (a) high-altitude advection of the top of the MCMA mixed layer, (b) low-altitude flow 19 over the Sierra Madre Oriental followed by decoupling and isolated transport over the Gulf, 20 and (c) the same decoupling scenario with entrainment into a cleaner westerly jet below the 21 plateau. The C-130 intercepted the balloon-based trajectories three times on 19 March, once 22 along each transport pathway. In all three cases, distinct peaks in the urban tracer signature 23 and LIDAR backscatter imagery provided evidence for Mexico City air. The coherence of the 24 high-altitude outflow was well preserved after 25 hours whereas that lower in the atmosphere 25 was more widely dispersed over the same time period. Other C-130 intercepts, previously 26 thought to be from Mexico City, are shown to have likely originated elsewhere. These 27 findings address key questions about the long-range transport of Mexico City pollution and its 28 impact on the regional background. The particular intercepts identified should prove useful in 29 answering a wide range scientific questions pertaining to the transport, transformation, and 30 downwind impacts of megacity air pollution. 31 32« less

Efficient photocatalytic degradation of gaseous N,N-dimethylformamide in tannery waste gas using doubly open-ended Ag/TiO2 nanotube array membranes

NASA Astrophysics Data System (ADS)

Zhao, Yang; Ma, Lin; Chang, Wenkai; Huang, Zhiding; Feng, Xugen; Qi, Xiaoxia; Li, Zenghe

2018-06-01

Gaseous N,N-dimethylformamide (DMF), typical volatile organic compound exhausted from manufacturing factories, may damage the health of workers under long-term exposure even at low levels. The defined geometry, porous surface and highly ordered channels make the free-standing anodic TiO2 nanotube (TiNT) arrays particularly suitable for applications of practical air purification by flow-through photocatalysis. In the present work, crystallized doubly open-ended Ag/TiNT array membranes were designed and prepared by employing a lift-off process based on an anodization-annealing-anodization-etching sequence, followed by uniform Ag nanoparticles decoration. For the photocatalytic degradation of gaseous DMF at low concentration levels close to that found in realistic pollutant air, an analytical methodology for the monitoring and determination of degradation process was developed based on the coupling of headspace sampling with gas chromatography mass spectrometry (HS-GC-MS). The doubly open-ended Ag/TiNT arrays exhibited higher removal efficiency of gaseous DMF from air compared with conventional bottom-closed Ag/TiNT arrays and pure bottomless TiNT arrays. These results indicated that the photocatalytic properties of TiNT arrays were improved with the open-bottom morphology and the Ag nanoparticles decoration. Based on the analysis with GC-MS and high performance ion chromatography (HPIC), it was found that demethylation is the main pathway of DMF degradation in photocatalytic reactions. Furthermore, decontamination of actual polluted tannery waste gas collected in leather factory proved that the photocatalysis on doubly open-ended Ag/TiNT array membrane is an efficient way and a promising application to treat air contaminated by DMF despite the complexity of various volatile organic compounds.

Morphology and vascular anatomy of the gills of a primitive air-breathing fish, the bowfin (Amia calva).

PubMed

Olson, K R

1981-01-01

The morphology of the gills of a primitive air breather (Amia calva) was examined by light microscopy of semithin sections of gill filaments, and gill perfusion pathways were identified by scanning-electron microscopic analysis of corrosion replicas prepared by intravascular injection of methyl methacrylate. The arrangement of gill filaments and respiratory lamellae is similar to that ot teleosts with the exception of an interfilamental support bar that is fused to the outer margins of lamellae on adjacent filaments. The prebranchial vasculature is also similar to that of teleosts, whereas the postbranchial circulation of arches III and IV is modified to permit selective perfusion of the air bladder. Gill filaments contain three distinct vascular systems: (1) the respiratory circulation which receives the entire cardiac output and perfuses the secondary lamellae; (2) a nutrient system that arises from the postlammelar circulation and perfuses filamental tissues; (3) a network of unknown function consisting of subepithelial sinusoids surrounding afferent and efferent margins of the filament and traversing the filament beneath the interlamellar epithelium. Prelamellar arteriovenous anastomoses (AVAs) are rare, postlammelar AVAs are common especially at the base of the filament where they form a dense network of small tortuous vessels before coalescing into a large filamental nutrient artery. Unlike in most teleosts, the outer vascular margins of the lamellae are embedded in the interfilamental support bar and become the sole vasculature of this tissue. Arterial-arterial lamellar bypass vessels were not observed. Previously observed decreases in oxygen transfer across the gills during air breathing can be explained only by redistribution of blood flow between or within the respiratory lamellae.

MTHFR Gene Polymorphism-Mutations and Air Pollution as Risk Factors for Breast Cancer

PubMed Central

Gonzales, Mildred C.; Yu, Pojui; Shiao, S. Pamela K.

2017-01-01

Background The methylenetetrahydrofolate reductase gene (MTHFR) is one of the most investigated genes associated with breast cancer for its role in epigenetic pathways. Objectives The objectives of this metaprediction study were to examine the polymorphism-mutation risk subtypes of MTHFR and air pollution as contributing factors for breast cancer. Methods For triangulation purposes in metapredictive analyses, we used a recursive partition tree, nonlinear association curve fit, and heat maps for data visualization, in addition to the conventional comparison procedure and pooled analyses. Results We included 36,683 breast cancer cases and 40,689 controls across 82 studies for MTHFR 677 and 23,252 cases and 27,094 controls across 50 studies for MTHFR 1298. MTHFR 677 TT was a risk genotype for breast cancer (p = .0004) and in the East Asian subgroup (p = .005). On global maps, the most polymorphism-mutations on MTHFR 677 TT were found in the Middle East, Europe, Asia, and the Americas, whereas the most mutations on MTHFR 1298 CC were located in Europe and the Middle East for the control group. The geographic information system maps further revealed that MTHFR 677 TT mutations yielded a higher risk of breast cancer for Australia, East Asia, the Middle East, South Europe, Morocco, and the Americas and that MTHFR 1298 CC mutations yielded a higher risk in Asia, the Middle East, South Europe, and South America. Metapredictive analysis revealed that air pollution level was significantly associated with MTHFR 677 TT polymorphism-mutation genotype. Discussion We present the most comprehensive analyses to date of MTHFR polymorphism-mutations and breast cancer risk. Future nursing studies are needed to investigate the health impact on breast cancer of epigenetics and air pollution across populations. PMID:28114181

MTHFR Gene Polymorphism-Mutations and Air Pollution as Risk Factors for Breast Cancer: A Metaprediction Study.

PubMed

Gonzales, Mildred C; Yu, Pojui; Shiao, S Pamela K

The methylenetetrahydrofolate reductase gene (MTHFR) is one of the most investigated genes associated with breast cancer for its role in epigenetic pathways. The objectives of this metaprediction study were to examine the polymorphism-mutation risk subtypes of MTHFR and air pollution as contributing factors for breast cancer. For triangulation purposes in metapredictive analyses, we used a recursive partition tree, nonlinear association curve fit, and heat maps for data visualization, in addition to the conventional comparison procedure and pooled analyses. We included 36,683 breast cancer cases and 40,689 controls across 82 studies for MTHFR 677 and 23,252 cases and 27,094 controls across 50 studies for MTHFR 1298. MTHFR 677 TT was a risk genotype for breast cancer (p = .0004) and in the East Asian subgroup (p = .005). On global maps, the most polymorphism-mutations on MTHFR 677 TT were found in the Middle East, Europe, Asia, and the Americas, whereas the most mutations on MTHFR 1298 CC were located in Europe and the Middle East for the control group. The geographic information system maps further revealed that MTHFR 677 TT mutations yielded a higher risk of breast cancer for Australia, East Asia, the Middle East, South Europe, Morocco, and the Americas and that MTHFR 1298 CC mutations yielded a higher risk in Asia, the Middle East, South Europe, and South America. Metapredictive analysis revealed that air pollution level was significantly associated with MTHFR 677 TT polymorphism-mutation genotype. We present the most comprehensive analyses to date of MTHFR polymorphism-mutations and breast cancer risk. Future nursing studies are needed to investigate the health impact on breast cancer of epigenetics and air pollution across populations.

Formaldehyde Column Density Measurements as a Suitable Pathway to Estimate Near-Surface Ozone Tendencies from Space

NASA Technical Reports Server (NTRS)

Schroeder, Jason R.; Crawford, James H.; Fried, Alan; Walega, James; Weinheimer, Andrew; Wisthaler, Armin; Mueller, Markus; Mikoviny, Tomas; Chen, Gao; Shook, Michael;

minepath.org: a free interactive pathway analysis web server.

PubMed

Koumakis, Lefteris; Roussos, Panos; Potamias, George

2017-07-03

( www.minepath.org ) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles. The highly ranked, and phenotype inclined sub-paths are kept. Apart from the pathway analysis algorithm, the fundamental innovation of the MinePath web-server concerns its advanced visualization and interactive capabilities. To our knowledge, this is the first pathway analysis server that introduces and offers visualization of the underlying and active pathway regulatory mechanisms instead of genes. Other features include live interaction, immediate visualization of functional sub-paths per phenotype and dynamic linked annotations for the engaged genes and molecular relations. The user can download not only the results but also the corresponding web viewer framework of the performed analysis. This feature provides the flexibility to immediately publish results without publishing source/expression data, and get all the functionality of a web based pathway analysis viewer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Predicting SVOC Emissions into Air and Foods in Support of High-Throughput Exposure Assessment

EPA Science Inventory

The release of semi-volatile organic compounds (SVOCs) from consumer articles may be a critical human exposure pathway. In addition, the migration of SVOCs from food packaging materials into foods may also be a dominant source of exposure for some chemicals. Here we describe re...

APPLICATION OF A MICROSCALE EMISSION FACTOR MODEL FOR PARTICULATE MATTER (MICROFACPM) IN CONJUNCTION WITH CALINE4-MODEL

EPA Science Inventory

The United States Environmental Protection Agency's (EPA) National Exposure Research Laboratory is developing improved methods for modeling the pollutant sources through the air pathway to human exposure in significant microenvironments of exposure. As a part of this project, w...

APPLICATION OF A MICROSCALE EMISSION FACTOR MODEL FOR PARTICULATE MATTER (MICROFACPM) TO CALCULATE VEHICLE GENERATED CONTRIBUTION PM 2.5 EMISSIONS

EPA Science Inventory

The United States Environmental Protection Agency's (EPA) National Exposure Research Laboratory is developing improved methods for modeling the source through the air pathway to human exposure in significant microenvironments of exposure. As a part of this project, we develope...

Installation Restoration Program Records Search for Dobbins Air Force Base, Georgia

DTIC Science & Technology

1982-04-01

migation Death to irond water ____________ lift ogaeiitation 1 . Subsurface flow_____I a _____________ Direct aess W 4round water______ j Submrs(10 x actr...potential pathways, surface water migation , flooding, and ground-water * migration. Select the highest rating, and proceed to C. f 1. Surface water migration

Effect of Mitochondrial Oxidative Stress and Age on the Signaling Pathway of Ultrafine Particulate Matter Exposure in Murine Aorta

EPA Science Inventory

Epidemiological studies have linked ultrafine particulate matter (PM) exposure and adverse cardiovascular events. PM-induced oxidative stress is believed to be a key mechanism contributing to the adverse short-term vascular effects of air pollution exposure. Advanced age is one ...

BRINGING SCIENCE AND PLANNING TOGETHER: A CASE STUDY ON PROTECTING HUMAN HEALTH, SAFETY, AND WELFARE FROM VAPOR INTRUSION

EPA Science Inventory

Vapor intrusion is the movement of volatile chemicals in the subsurface that eventually contaminate the indoor air that people breathe in overlaying buildings. This often overlooked exposure pathway of hazardous chemicals is a significant environmental health hazard. The USEPA ...

Adverse Outcome Pathways (AOPs) in Human Systems Biology: Gas-Phase Probes for Assessing In Vitro Enzyme System Perturbations

EPA Science Inventory

The Air, Climate, and Energy (ACE) and Chemical Safety for Sustainability (CSS) programs at the U.S. EnvironmentalProtection Agency (EPA) encompass broad-based research that includes assessment of the health and environmentalimpacts of anthropogenic and manufactured chemicals. On...

Pathway Interaction Network Analysis Identifies Dysregulated Pathways in Human Monocytes Infected by Listeria monocytogenes.

PubMed

Fan, Wufeng; Zhou, Yuhan; Li, Hao

2017-01-01

In our study, we aimed to extract dysregulated pathways in human monocytes infected by Listeria monocytogenes (LM) based on pathway interaction network (PIN) which presented the functional dependency between pathways. After genes were aligned to the pathways, principal component analysis (PCA) was used to calculate the pathway activity for each pathway, followed by detecting seed pathway. A PIN was constructed based on gene expression profile, protein-protein interactions (PPIs), and cellular pathways. Identifying dysregulated pathways from the PIN was performed relying on seed pathway and classification accuracy. To evaluate whether the PIN method was feasible or not, we compared the introduced method with standard network centrality measures. The pathway of RNA polymerase II pretranscription events was selected as the seed pathway. Taking this seed pathway as start, one pathway set (9 dysregulated pathways) with AUC score of 1.00 was identified. Among the 5 hub pathways obtained using standard network centrality measures, 4 pathways were the common ones between the two methods. RNA polymerase II transcription and DNA replication owned a higher number of pathway genes and DEGs. These dysregulated pathways work together to influence the progression of LM infection, and they will be available as biomarkers to diagnose LM infection.

A systematic analysis of a mi-RNA inter-pathway regulatory motif

PubMed Central

2013-01-01

Background The continuing discovery of new types and functions of small non-coding RNAs is suggesting the presence of regulatory mechanisms far more complex than the ones currently used to study and design Gene Regulatory Networks. Just focusing on the roles of micro RNAs (miRNAs), they have been found to be part of several intra-pathway regulatory motifs. However, inter-pathway regulatory mechanisms have been often neglected and require further investigation. Results In this paper we present the result of a systems biology study aimed at analyzing a high-level inter-pathway regulatory motif called Pathway Protection Loop, not previously described, in which miRNAs seem to play a crucial role in the successful behavior and activation of a pathway. Through the automatic analysis of a large set of public available databases, we found statistical evidence that this inter-pathway regulatory motif is very common in several classes of KEGG Homo Sapiens pathways and concurs in creating a complex regulatory network involving several pathways connected by this specific motif. The role of this motif seems also confirmed by a deeper review of other research activities on selected representative pathways. Conclusions Although previous studies suggested transcriptional regulation mechanism at the pathway level such as the Pathway Protection Loop, a high-level analysis like the one proposed in this paper is still missing. The understanding of higher-level regulatory motifs could, as instance, lead to new approaches in the identification of therapeutic targets because it could unveil new and “indirect” paths to activate or silence a target pathway. However, a lot of work still needs to be done to better uncover this high-level inter-pathway regulation including enlarging the analysis to other small non-coding RNA molecules. PMID:24152805

Spatial assessment of air quality patterns in Malaysia using multivariate analysis

NASA Astrophysics Data System (ADS)

Dominick, Doreena; Juahir, Hafizan; Latif, Mohd Talib; Zain, Sharifuddin M.; Aris, Ahmad Zaharin

2012-12-01

This study aims to investigate possible sources of air pollutants and the spatial patterns within the eight selected Malaysian air monitoring stations based on a two-year database (2008-2009). The multivariate analysis was applied on the dataset. It incorporated Hierarchical Agglomerative Cluster Analysis (HACA) to access the spatial patterns, Principal Component Analysis (PCA) to determine the major sources of the air pollution and Multiple Linear Regression (MLR) to assess the percentage contribution of each air pollutant. The HACA results grouped the eight monitoring stations into three different clusters, based on the characteristics of the air pollutants and meteorological parameters. The PCA analysis showed that the major sources of air pollution were emissions from motor vehicles, aircraft, industries and areas of high population density. The MLR analysis demonstrated that the main pollutant contributing to variability in the Air Pollutant Index (API) at all stations was particulate matter with a diameter of less than 10 μm (PM10). Further MLR analysis showed that the main air pollutant influencing the high concentration of PM10 was carbon monoxide (CO). This was due to combustion processes, particularly originating from motor vehicles. Meteorological factors such as ambient temperature, wind speed and humidity were also noted to influence the concentration of PM10.

Overexpression of PSP1 enhances growth of transgenic Arabidopsis plants under ambient air conditions.

PubMed

Han, Xiaofang; Peng, Keli; Wu, Haixia; Song, Shanshan; Zhu, Yerong; Bai, Yanling; Wang, Yong

2017-07-01

The importance of the phosphorylated pathway (PPSB) of L-serine (Ser) biosynthesis in plant growth and development has been demonstrated, but its specific role in leaves and interaction with photorespiration, the main leaf Ser biosynthetic pathway at daytime, are still unclear. To investigate whether changes in biosynthesis of Ser by the PPSB in leaves could have an impact on photorespiration and plant growth, we overexpressed PSP1, the last enzyme of this pathway, under control of the Cauliflower Mosaic Virus 35S promoter in Arabidopsis thaliana. Overexpressor plants grown in normal air displayed larger rosette diameter and leaf area as well as higher fresh and dry weight than the wild type. By contrast, no statistically significant differences to the wild type were observed when the overexpressor seedlings were transferred to elevated CO 2 , indicating a relationship between PSP1 overexpression and photorespiration. Additionally, the transgenic plants displayed higher photorespiration, an increase in CO 2 net-uptake and stronger expression in the light of genes encoding enzymes involved in photorespiration. We further demonstrated that expression of many genes involved in nitrogen assimilation was also promoted in leaves of transgenic plants and that leaf nitrate reductase activity increased in the light, too, although not in the dark. Our results suggest a close correlation between the function of PPSB and photorespiration, and also nitrogen metabolism in leaves.

Development and Performance of Alternative Electricity Sector Pathways Subject to Multiple Climate and Water Projections

NASA Astrophysics Data System (ADS)

Newmark, R. L.; Vorosmarty, C. J.; Miara, A.; Cohen, S.; Macknick, J.; Sun, Y.; Corsi, F.; Fekete, B. M.; Tidwell, V. C.

2017-12-01

Climate change impacts on air temperatures and water availability have the potential to alter future electricity sector investment decisions as well as the reliability and performance of the power sector. Different electricity sector configurations are more or less vulnerable to climate-induced changes. For example, once-through cooled thermal facilities are the most cost-effective and efficient technologies under cooler and wetter conditions, but can be substantially affected by and vulnerable to warmer and drier conditions. Non-thermal renewable technologies, such as PV and wind, are essentially "drought-proof" but have other integration and reliability challenges. Prior efforts have explored the impacts of climate change on electric sector development for a limited set of climate and electricity scenarios. Here, we provide a comprehensive suite of scenarios that evaluate how different electricity sector pathways could be affected by a range of climate and water resource conditions. We use four representative concentration pathway (RCP) scenarios under five global circulation models (GCM) as climate drivers to a Water Balance Model (WBM), to provide twenty separate future climate-water conditions. These climate-water conditions influence electricity sector development from present day to 2050 as determined using the Regional Energy Deployment Systems (ReEDS) model. Four unique electricity sector pathways will be considered, including business-as-usual, carbon cap, high renewable energy technology costs, and coal reliance scenarios. The combination of climate-water and electricity sector pathway scenarios leads to 80 potential future cases resulting in different national and regional electricity infrastructure configurations. The vulnerability of these configurations in relation to climate change (including in-stream thermal pollution impacts and environmental regulations) is evaluated using the Thermoelectric Power and Thermal Pollution (TP2M) model, providing quantitative estimates of the power sector's ability to meet loads, given changes in air temperature, water temperature, and water availability.

Prenatal exposure to residential air pollution and infant mental development: modulation by antioxidants and detoxification factors.

PubMed

Guxens, Mònica; Aguilera, Inmaculada; Ballester, Ferran; Estarlich, Marisa; Fernández-Somoano, Ana; Lertxundi, Aitana; Lertxundi, Nerea; Mendez, Michelle A; Tardón, Adonina; Vrijheid, Martine; Sunyer, Jordi

2012-01-01

Air pollution effects on children's neurodevelopment have recently been suggested to occur most likely through the oxidative stress pathway. We aimed to assess whether prenatal exposure to residential air pollution is associated with impaired infant mental development, and whether antioxidant/detoxification factors modulate this association. In the Spanish INfancia y Medio Ambiente (INMA; Environment and Childhood) Project, 2,644 pregnant women were recruited during their first trimester. Nitrogen dioxide (NO2) and benzene were measured with passive samplers covering the study areas. Land use regression models were developed for each pollutant to predict average outdoor air pollution levels for the entire pregnancy at each residential address. Maternal diet was obtained at first trimester through a validated food frequency questionnaire. Around 14 months, infant mental development was assessed using Bayley Scales of Infant Development. Among the 1,889 children included in the analysis, mean exposure during pregnancy was 29.0 μg/m3 for NO2 and 1.5 μg/m3 for benzene. Exposure to NO2 and benzene showed an inverse association with mental development, although not statistically significant, after adjusting for potential confounders [β (95% confidence interval) = -0.95 (-3.90, 1.89) and -1.57 (-3.69, 0.56), respectively, for a doubling of each compound]. Stronger inverse associations were estimated for both pollutants among infants whose mothers reported low intakes of fruits/vegetables during pregnancy [-4.13 (-7.06, -1.21) and -4.37 (-6.89, -1.86) for NO2 and benzene, respectively], with little evidence of associations in the high-intake group (interaction p-values of 0.073 and 0.047). Inverse associations were also stronger in non-breast-fed infants and infants with low maternal vitamin D, but effect estimates and interactions were not significant. Our findings suggest that prenatal exposure to residential air pollutants may adversely affect infant mental development, but potential effects may be limited to infants whose mothers report low antioxidant intakes.

Ozone and fine particle in the western Yangtze River Delta: an overview of 1 yr data at the SORPES station

NASA Astrophysics Data System (ADS)

Ding, A. J.; Fu, C. B.; Yang, X. Q.; Sun, J. N.; Zheng, L. F.; Xie, Y. N.; Herrmann, E.; Nie, W.; Petäjä, T.; Kerminen, V.-M.; Kulmala, M.

2013-06-01

This work presents an overview of 1 yr measurements of ozone (O3) and fine particular matter (PM2.5) and related trace gases at a recently developed regional background site, the Station for Observing Regional Processes of the Earth System (SORPES), in the western part of the Yangtze River Delta (YRD) in eastern China. Ozone and PM2.5 showed strong seasonal cycles but with contrast patterns: O3 reached a maximum in warm seasons but PM2.5 in cold seasons. Correlation analysis suggests a VOC-sensitive regime for O3 chemistry and a formation of secondary aerosols under conditions of high O3 in summer. Compared with the National Ambient Air Quality Standards in China, our measurements report 15 days of O3 exceedance and 148 days of PM2.5 exceedance during the 1 yr period, suggesting a severe air pollution situation in this region. Case studies for typical O3 and PM2.5 episodes demonstrated that these episodes were generally associated with an air mass transport pathway over the mid-YRD, i.e., along the Nanjing-Shanghai axis with its city clusters, and showed that synoptic weather played an important role in air pollution, especially for O3. Agricultural burning activities caused high PM2.5 and O3 pollution during harvest seasons, especially in June. A calculation of potential source contributions based on Lagrangian dispersion simulations suggests that emissions from the YRD contributed to over 70% of the O3 precursor CO, with a majority from the mid-YRD. North-YRD and the North China Plain are the main contributors to PM2.5 pollution in this region. This work shows an important environmental impact from industrialization and urbanization in the YRD region, and suggests an urgent need for improving air quality in these areas through collaborative control measures among different administrative regions.

Methods and approaches in the topology-based analysis of biological pathways

PubMed Central

Mitrea, Cristina; Taghavi, Zeinab; Bokanizad, Behzad; Hanoudi, Samer; Tagett, Rebecca; Donato, Michele; Voichiţa, Călin; Drăghici, Sorin

2013-01-01

The goal of pathway analysis is to identify the pathways significantly impacted in a given phenotype. Many current methods are based on algorithms that consider pathways as simple gene lists, dramatically under-utilizing the knowledge that such pathways are meant to capture. During the past few years, a plethora of methods claiming to incorporate various aspects of the pathway topology have been proposed. These topology-based methods, sometimes referred to as “third generation,” have the potential to better model the phenomena described by pathways. Although there is now a large variety of approaches used for this purpose, no review is currently available to offer guidance for potential users and developers. This review covers 22 such topology-based pathway analysis methods published in the last decade. We compare these methods based on: type of pathways analyzed (e.g., signaling or metabolic), input (subset of genes, all genes, fold changes, gene p-values, etc.), mathematical models, pathway scoring approaches, output (one or more pathway scores, p-values, etc.) and implementation (web-based, standalone, etc.). We identify and discuss challenges, arising both in methodology and in pathway representation, including inconsistent terminology, different data formats, lack of meaningful benchmarks, and the lack of tissue and condition specificity. PMID:24133454

LAND AND WATER USE CHARACTERISTICS AND HUMAN HEALTH INPUT PARAMETERS FOR USE IN ENVIRONMENTAL DOSIMETRY AND RISK ASSESSMENTS AT THE SAVANNAH RIVER SITE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jannik, T.; Karapatakis, D.; Lee, P.

2010-08-06

Operations at the Savannah River Site (SRS) result in releases of small amounts of radioactive materials to the atmosphere and to the Savannah River. For regulatory compliance purposes, potential offsite radiological doses are estimated annually using computer models that follow U.S. Nuclear Regulatory Commission (NRC) Regulatory Guides. Within the regulatory guides, default values are provided for many of the dose model parameters but the use of site-specific values by the applicant is encouraged. A detailed survey of land and water use parameters was conducted in 1991 and is being updated here. These parameters include local characteristics of meat, milk andmore » vegetable production; river recreational activities; and meat, milk and vegetable consumption rates as well as other human usage parameters required in the SRS dosimetry models. In addition, the preferred elemental bioaccumulation factors and transfer factors to be used in human health exposure calculations at SRS are documented. Based on comparisons to the 2009 SRS environmental compliance doses, the following effects are expected in future SRS compliance dose calculations: (1) Aquatic all-pathway maximally exposed individual doses may go up about 10 percent due to changes in the aquatic bioaccumulation factors; (2) Aquatic all-pathway collective doses may go up about 5 percent due to changes in the aquatic bioaccumulation factors that offset the reduction in average individual water consumption rates; (3) Irrigation pathway doses to the maximally exposed individual may go up about 40 percent due to increases in the element-specific transfer factors; (4) Irrigation pathway collective doses may go down about 50 percent due to changes in food productivity and production within the 50-mile radius of SRS; (5) Air pathway doses to the maximally exposed individual may go down about 10 percent due to the changes in food productivity in the SRS area and to the changes in element-specific transfer factors; and (6) Air pathway collective doses may go down about 30 percent mainly due to the decrease in the inhalation rate assumed for the average individual.« less

Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways

PubMed Central

Jo, Kyuri; Jung, Inuk; Moon, Ji Hwan; Kim, Sun

2016-01-01

Motivation: To understand the dynamic nature of the biological process, it is crucial to identify perturbed pathways in an altered environment and also to infer regulators that trigger the response. Current time-series analysis methods, however, are not powerful enough to identify perturbed pathways and regulators simultaneously. Widely used methods include methods to determine gene sets such as differentially expressed genes or gene clusters and these genes sets need to be further interpreted in terms of biological pathways using other tools. Most pathway analysis methods are not designed for time series data and they do not consider gene-gene influence on the time dimension. Results: In this article, we propose a novel time-series analysis method TimeTP for determining transcription factors (TFs) regulating pathway perturbation, which narrows the focus to perturbed sub-pathways and utilizes the gene regulatory network and protein–protein interaction network to locate TFs triggering the perturbation. TimeTP first identifies perturbed sub-pathways that propagate the expression changes along the time. Starting points of the perturbed sub-pathways are mapped into the network and the most influential TFs are determined by influence maximization technique. The analysis result is visually summarized in TF-Pathway map in time clock. TimeTP was applied to PIK3CA knock-in dataset and found significant sub-pathways and their regulators relevant to the PIP3 signaling pathway. Availability and Implementation: TimeTP is implemented in Python and available at http://biohealth.snu.ac.kr/software/TimeTP/. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: sunkim.bioinfo@snu.ac.kr PMID:27307609

Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers

PubMed Central

2013-01-01

Background Many large-scale studies analyzed high-throughput genomic data to identify altered pathways essential to the development and progression of specific types of cancer. However, no previous study has been extended to provide a comprehensive analysis of pathways disrupted by copy number alterations across different human cancers. Towards this goal, we propose a network-based method to integrate copy number alteration data with human protein-protein interaction networks and pathway databases to identify pathways that are commonly disrupted in many different types of cancer. Results We applied our approach to a data set of 2,172 cancer patients across 16 different types of cancers, and discovered a set of commonly disrupted pathways, which are likely essential for tumor formation in majority of the cancers. We also identified pathways that are only disrupted in specific cancer types, providing molecular markers for different human cancers. Analysis with independent microarray gene expression datasets confirms that the commonly disrupted pathways can be used to identify patient subgroups with significantly different survival outcomes. We also provide a network view of disrupted pathways to explain how copy number alterations affect pathways that regulate cell growth, cycle, and differentiation for tumorigenesis. Conclusions In this work, we demonstrated that the network-based integrative analysis can help to identify pathways disrupted by copy number alterations across 16 types of human cancers, which are not readily identifiable by conventional overrepresentation-based and other pathway-based methods. All the results and source code are available at http://compbio.cs.umn.edu/NetPathID/. PMID:23822816

PyPathway: Python Package for Biological Network Analysis and Visualization.

PubMed

Xu, Yang; Luo, Xiao-Chun

2018-05-01

Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

Mobile Air Monitoring: Measuring Change in Air Quality in the City of Hamilton, 2005-2010

ERIC Educational Resources Information Center

Adams, Matthew D.; DeLuca, Patrick F.; Corr, Denis; Kanaroglou, Pavlos S.

2012-01-01

This paper examines the change in air pollutant concentrations between 2005 and 2010 occurring in the City of Hamilton, Ontario, Canada. After analysis of stationary air pollutant concentration data, we analyze mobile air pollutant concentration data. Air pollutants included in the analysis are CO, PM[subscript 2.5], SO[subscript 2], NO,…

PathwaySplice: An R package for unbiased pathway analysis of alternative splicing in RNA-Seq data.

PubMed

Yan, Aimin; Ban, Yuguang; Gao, Zhen; Chen, Xi; Wang, Lily

2018-04-24

Pathway analysis of alternative splicing would be biased without accounting for the different number of exons or junctions associated with each gene, because genes with higher number of exons or junctions are more likely to be included in the "significant" gene list in alternative splicing. We present PathwaySplice, an R package that (1) Performs pathway analysis that explicitly adjusts for the number of exons or junctions associated with each gene; (2) Visualizes selection bias due to different number of exons or junctions for each gene and formally tests for presence of bias using logistic regression; (3) Supports gene sets based on the Gene Ontology terms, as well as more broadly defined gene sets (e.g. MSigDB) or user defined gene sets; (4) Identifies the significant genes driving pathway significance and (5) Organizes significant pathways with an enrichment map, where pathways with large number of overlapping genes are grouped together in a network graph. https://bioconductor.org/packages/release/bioc/html/PathwaySplice.html. lily.wangg@gmail.com, xi.steven.chen@gmail.com.

Exhaled methyl nitrate as a noninvasive marker of hyperglycemia in type 1 diabetes

PubMed Central

Novak, B. J.; Blake, D. R.; Meinardi, S.; Rowland, F. S.; Pontello, A.; Cooper, D. M.; Galassetti, P. R.

2007-01-01

Recent technical advances allow detection of several hundred volatile organic compounds (VOCs) in human exhaled air, many of which reflect unidentified endogenous pathways. Our group has previously estimated plasma glucose levels in healthy adults during a standard oral glucose tolerance test via exhaled VOC analysis. As a result of the metabolic characteristics of hyperglycemia in the diabetic (low insulin and increased free fatty acids and ketones), we hypothesized that different exhaled VOC profiles may be present in children with type 1 diabetes mellitus (T1DM) during spontaneous hyperglycemia. Exhaled methyl nitrate strongly correlated specifically with the acute, spontaneous hyperglycemia of T1DM children. Eighteen experiments were conducted among 10 T1DM children. Plasma glucose and exhaled gases were monitored during either constant euglycemia (n = 5) or initial hyperglycemia with gradual correction (n = 13); all subjects received i.v. insulin and glucose as needed. Gas analysis was performed on 1.9-liter breath samples via gas chromatography using electron capture, flame ionization, and mass selective detection. Among the ≈100 measured exhaled gases, the kinetic profile of exhaled methyl nitrate, commonly present in room air in the range of 5–10 parts per trillion, was most strongly statistically correlated with that of plasma glucose (P = 0.003–0.001). Indeed, the kinetic profiles of the two variables paralleled each other in 16 of 18 experiments, including repeat subjects who at different times displayed either euglycemia or hyperglycemia. PMID:17895380

Possible Mediation by Methylation in Acute Inflammation Following Personal Exposure to Fine Particulate Air Pollution

PubMed Central

Wang, Cuicui; Chen, Renjie; Shi, Min; Cai, Jing; Shi, Jingjin; Yang, Changyuan; Li, Huichu; Lin, Zhijing; Meng, Xia; Liu, Cong; Niu, Yue; Xia, Yongjie; Zhao, Zhuohui; Kan, Haidong; Weinberg, Clarice R

2018-01-01

Abstract Air pollution may increase cardiovascular and respiratory risk through inflammatory pathways, but evidence for acute effects has been weak and indirect. Between December 2014 and July 2015, we enrolled 36 healthy, nonsmoking college students for a panel study in Shanghai, China, a city with highly variable levels of air pollution. We measured personal exposure to particulate matter with an aerodynamic diameter less than or equal to 2.5 μm (PM2.5) continuously for 72 hours preceding each of 4 clinical visits that included phlebotomy. We measured 4 inflammation proteins and DNA methylation at nearby regulatory cytosine-phosphate-guanine (CpG) loci. We applied linear mixed-effect models to examine associations over various lag times. When results suggested mediation, we evaluated methylation as mediator. Increased PM2.5 concentration was positively associated with all 4 inflammation proteins and negatively associated with DNA methylation at regulatory loci for tumor necrosis factor alpha (TNF-α) and soluble intercellular adhesion molecule-1. A 10-μg/m3 increase in average PM2.5 during the 24 hours preceding blood draw corresponded to a 4.4% increase in TNF-α and a statistically significant decrease in methylation at one of the two studied candidate CpG loci for TNF-α. Epigenetics may play an important role in mediating effects of PM2.5 on inflammatory pathways. PMID:29020142

Enhancing the Oxidation Stability of Polydivinylbenzene Films via Residual Pendant Vinyl Passivation

DOE PAGES

Lepro, Xavier; Ehrmann, Paul; Rodriguez, Jennifer; ...

2018-01-11

Polydivinylbenzene (PDVB) is a thermally stable, optically transparent, crosslinked polymer that until recently has been difficult to synthesize as a thin film. With the recent demonstration of initiated chemical vapor deposition (iCVD) of thin PDVB films, a renewed interest in the material properties of PDVB has developed. In particular, attention is now focused on its oxidation pathways and long-term stability under the desired application use conditions. In this paper, we report on the thermal and environmental stability of PDVB films and show that unreacted pendant vinyl groups drive polymer oxidation upon exposure to either air or light. We demonstrate thatmore » such vinyls can be effectively passivated by a simple ex-situ thermal annealing at ca. 300 °C in inert atmosphere that induces an 87% reduction of the PDVB oxidation rate in air and slows light (λ=405 nm) induced oxidation by 56%. While the thermal annealing is less effective at preventing oxidation under higher energy (λ = 365 nm) UV light, we demonstrate that this aging pathway is based on the presence of reactive oxygen species rather than traditional photo-oxidation. Finally, vinyl removal through ex-situ thermal annealing improves the chemical stability of iCVD PDVB to continuous air (over 500 days) or light (70 hours) exposure and offers a simple option to improve its environmental aging resistance which is important for long-term protective applications.« less

40 CFR 60.2050 - What is a siting analysis?

Code of Federal Regulations, 2012 CFR

2012-07-01

... Analysis § 60.2050 What is a siting analysis? (a) The siting analysis must consider air pollution control... include the consideration of air pollution control alternatives specified in paragraph (a) of this section... Section 60.2050 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS...

Pathway Analysis in Attention Deficit Hyperactivity Disorder: An Ensemble Approach

PubMed Central

Mooney, Michael A.; McWeeney, Shannon K.; Faraone, Stephen V.; Hinney, Anke; Hebebrand, Johannes; Nigg, Joel T.; Wilmot, Beth

2016-01-01

Despite a wealth of evidence for the role of genetics in attention deficit hyperactivity disorder (ADHD), specific and definitive genetic mechanisms have not been identified. Pathway analyses, a subset of gene-set analyses, extend the knowledge gained from genome-wide association studies (GWAS) by providing functional context for genetic associations. However, there are numerous methods for association testing of gene sets and no real consensus regarding the best approach. The present study applied six pathway analysis methods to identify pathways associated with ADHD in two GWAS datasets from the Psychiatric Genomics Consortium. Methods that utilize genotypes to model pathway-level effects identified more replicable pathway associations than methods using summary statistics. In addition, pathways implicated by more than one method were significantly more likely to replicate. A number of brain-relevant pathways, such as RhoA signaling, glycosaminoglycan biosynthesis, fibroblast growth factor receptor activity, and pathways containing potassium channel genes, were nominally significant by multiple methods in both datasets. These results support previous hypotheses about the role of regulation of neurotransmitter release, neurite outgrowth and axon guidance in contributing to the ADHD phenotype and suggest the value of cross-method convergence in evaluating pathway analysis results. PMID:27004716

Analysis of Air Force Secondary Power Logistics Solution Contract

DTIC Science & Technology

2010-05-21

IL 62225 SUBJECT: Audit. Analysis of Air Force Secondary Power Logistics Solution Contract, 748th Supply Chain Management Group, Hill Air Fon:r... Power Logis.tics Solution Contnict. 748111 Supply Ch.,in Management Group. !-lill Air FOfC! BII.SI!, UT (Project 02009· DOOOCH·0213.000) I. AUlIctlcd...00-00-2010 to 00-00-2010 4. TITLE AND SUBTITLE Analysis of Air Force Secondary Power Logistics Solution Contract 5a. CONTRACT NUMBER 5b. GRANT

Decomposition of naphthalene by dc gliding arc gas discharge.

PubMed

Yu, Liang; Li, Xiaodong; Tu, Xin; Wang, Yu; Lu, Shengyong; Yan, Jianhua

2010-01-14

Gliding arc discharge has been proved to be effective in treatment of gas and liquid contaminants. In this study, physical characteristics of dc gliding arc discharge and its application to naphthalene destruction are investigated with different external resistances and carrier gases. The decomposition rate increases with increasing of oxygen concentration and decreases with external resistance. This value can be achieved up to 92.3% at the external resistance of 50 kOmega in the oxygen discharge, while the highest destruction energy efficiency reaches 3.6 g (kW h)(-1) with the external resistance of 93 kOmega. Possible reaction pathways and degradation mechanisms in the plasma with different gases are proposed by qualitative analysis of postdestructed products. In the air and oxygen gliding arc discharges, the naphthalene degradation is mainly governed by reactions with oxygen-derived radicals.

KEGGParser: parsing and editing KEGG pathway maps in Matlab.

PubMed

Arakelyan, Arsen; Nersisyan, Lilit

2013-02-15

KEGG pathway database is a collection of manually drawn pathway maps accompanied with KGML format files intended for use in automatic analysis. KGML files, however, do not contain the required information for complete reproduction of all the events indicated in the static image of a pathway map. Several parsers and editors of KEGG pathways exist for processing KGML files. We introduce KEGGParser-a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment. It also works with Scilab. The source code is available at http://www.mathworks.com/matlabcentral/fileexchange/37561.

The identification of key genes and pathways in hepatocellular carcinoma by bioinformatics analysis of high-throughput data.

PubMed

Zhang, Chaoyang; Peng, Li; Zhang, Yaqin; Liu, Zhaoyang; Li, Wenling; Chen, Shilian; Li, Guancheng

2017-06-01

Liver cancer is a serious threat to public health and has fairly complicated pathogenesis. Therefore, the identification of key genes and pathways is of much importance for clarifying molecular mechanism of hepatocellular carcinoma (HCC) initiation and progression. HCC-associated gene expression dataset was downloaded from Gene Expression Omnibus database. Statistical software R was used for significance analysis of differentially expressed genes (DEGs) between liver cancer samples and normal samples. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, based on R software, were applied for the identification of pathways in which DEGs significantly enriched. Cytoscape software was for the construction of protein-protein interaction (PPI) network and module analysis to find the hub genes and key pathways. Finally, weighted correlation network analysis (WGCNA) was conducted to further screen critical gene modules with similar expression pattern and explore their biological significance. Significance analysis identified 1230 DEGs with fold change >2, including 632 significantly down-regulated DEGs and 598 significantly up-regulated DEGs. GO term enrichment analysis suggested that up-regulated DEG significantly enriched in immune response, cell adhesion, cell migration, type I interferon signaling pathway, and cell proliferation, and the down-regulated DEG mainly enriched in response to endoplasmic reticulum stress and endoplasmic reticulum unfolded protein response. KEGG pathway analysis found DEGs significantly enriched in five pathways including complement and coagulation cascades, focal adhesion, ECM-receptor interaction, antigen processing and presentation, and protein processing in endoplasmic reticulum. The top 10 hub genes in HCC were separately GMPS, ACACA, ALB, TGFB1, KRAS, ERBB2, BCL2, EGFR, STAT3, and CD8A, which resulted from PPI network. The top 3 gene interaction modules in PPI network enriched in immune response, organ development, and response to other organism, respectively. WGCNA revealed that the confirmed eight gene modules significantly enriched in monooxygenase and oxidoreductase activity, response to endoplasmic reticulum stress, type I interferon signaling pathway, processing, presentation and binding of peptide antigen, cellular response to cadmium and zinc ion, cell locomotion and differentiation, ribonucleoprotein complex and RNA processing, and immune system process, respectively. In conclusion, we identified some key genes and pathways closely related with HCC initiation and progression by a series of bioinformatics analysis on DEGs. These screened genes and pathways provided for a more detailed molecular mechanism underlying HCC occurrence and progression, holding promise for acting as biomarkers and potential therapeutic targets.

Systematic analysis of signaling pathways using an integrative environment.

PubMed

Visvanathan, Mahesh; Breit, Marc; Pfeifer, Bernhard; Baumgartner, Christian; Modre-Osprian, Robert; Tilg, Bernhard

2007-01-01

Understanding the biological processes of signaling pathways as a whole system requires an integrative software environment that has comprehensive capabilities. The environment should include tools for pathway design, visualization, simulation and a knowledge base concerning signaling pathways as one. In this paper we introduce a new integrative environment for the systematic analysis of signaling pathways. This system includes environments for pathway design, visualization, simulation and a knowledge base that combines biological and modeling information concerning signaling pathways that provides the basic understanding of the biological system, its structure and functioning. The system is designed with a client-server architecture. It contains a pathway designing environment and a simulation environment as upper layers with a relational knowledge base as the underlying layer. The TNFa-mediated NF-kB signal trans-duction pathway model was designed and tested using our integrative framework. It was also useful to define the structure of the knowledge base. Sensitivity analysis of this specific pathway was performed providing simulation data. Then the model was extended showing promising initial results. The proposed system offers a holistic view of pathways containing biological and modeling data. It will help us to perform biological interpretation of the simulation results and thus contribute to a better understanding of the biological system for drug identification.

75 FR 60493 - Advisory Circular 120-79A, Developing and Implementing an Air Carrier Continuing Analysis and...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-30

... and Implementing an Air Carrier Continuing Analysis and Surveillance System AGENCY: Federal Aviation... Analysis and Surveillance System''. This new advisory circular (AC) updates AC 120-79 originally issued on... Analysis and Surveillance System (CASS) required for commercial operators and air carriers certificated...

Rapid ice drilling with continual air transport of cuttings and cores: General concept

NASA Astrophysics Data System (ADS)

Wang, Rusheng; An, Liu; Cao, Pinlu; Chen, Baoyi; Sysoev, Mikhail; Fan, Dayou; Talalay, Pavel G.

2017-12-01

This article describes the investigation of the feasibility of rapid drilling in ice sheets and glaciers to depths of up to 600 m, with cuttings and cores continually transported by air reverse circulation. The method employs dual wall drill rods. The inner tubes provide a continuous pathway for the chips and cores from the drill bit face to the surface. To modify air reverse circulation drilling technology according to the conditions of a specific glacier, original cutter drill bits and air processing devices (air-cooled aftercoolers, air receivers, coalescing filters, desiccant dryers) should be used. The airflow velocity for conveying a 60-mm diameter and 200-mm long ice core should not be lower than 22.5 m/s, and the minimal airflow rate for continual chip and cores transport is 6.8 m3/min at 2.3-2.6 MPa. Drilling of a 600-m deep hole can be accomplished within 1.5 days in the case of 24 h drilling operations. However, to avoid sticking while drilling through ice, the drilling depth should to be limited to 540 m at a temperature of -20 °C and to 418 m at a temperature of -10 °C.

Air-borne and tissue-borne sensitivities of bioacoustic sensors used on the skin surface.

PubMed

Zañartu, Matías; Ho, Julio C; Kraman, Steve S; Pasterkamp, Hans; Huber, Jessica E; Wodicka, George R

2009-02-01

Measurements of body sounds on the skin surface have been widely used in the medical field and continue to be a topic of current research, ranging from the diagnosis of respiratory and cardiovascular diseases to the monitoring of voice dosimetry. These measurements are typically made using light-weight accelerometers and/or air-coupled microphones attached to the skin. Although normally neglected, air-borne sounds generated by the subject or other sources of background noise can easily corrupt such recordings, which is particularly critical in the recording of voiced sounds on the skin surface. In this study, the sensitivity of commonly used bioacoustic sensors to air-borne sounds was evaluated and compared with their sensitivity to tissue-borne body sounds. To delineate the sensitivity to each pathway, the sensors were first tested in vitro and then on human subjects. The results indicated that, in general, the air-borne sensitivity is sufficiently high to significantly corrupt body sound signals. In addition, the air-borne and tissue-borne sensitivities can be used to discriminate between these components. Although the study is focused on the evaluation of voiced sounds on the skin surface, an extension of the proposed methods to other bioacoustic applications is discussed.

Investigating Solutions to Wind Washing Issues in Two-Story Florida Homes, Phase 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Withers, Charles R.; Kono, Jamie

2015-04-13

With U.S. Department of Energy goals of reducing existing home energy use by 30% and new home energy use by 50%, it is imperative to focus on several energy efficiency measures, including the quality of air and thermal barriers. This report provides results from a second-phase research study of a phenomenon generally referred to as wind washing. Wind washing is the movement of unconditioned air around or through building thermal barriers in such a way as to diminish or nullify the intended thermal performance. In some cases, thermal and air barriers are installed very poorly or not at all, andmore » air can readily move from unconditioned attic spaces into quasi-conditioned interstitial spaces. This study focused on the impact of poorly sealed and insulated floor cavities adjacent to attic spaces in Florida homes. In these cases, unconditioned attic air can be transferred into floor cavities through pathways driven by natural factors such as wind, or by thermal differences between the floor cavity and the attic. Air can also be driven into a floor cavity through mechanical forces imposed by return duct leakage in the floor cavity.« less

Oxidative stress and inflammation mediate the effect of air pollution on cardio- and cerebrovascular disease: A prospective study in nonsmokers.

PubMed

Fiorito, Giovanni; Vlaanderen, Jelle; Polidoro, Silvia; Gulliver, John; Galassi, Claudia; Ranzi, Andrea; Krogh, Vittorio; Grioni, Sara; Agnoli, Claudia; Sacerdote, Carlotta; Panico, Salvatore; Tsai, Ming-Yi; Probst-Hensch, Nicole; Hoek, Gerard; Herceg, Zdenko; Vermeulen, Roel; Ghantous, Akram; Vineis, Paolo; Naccarati, Alessio

2018-04-01

Air pollution is associated with a broad range of adverse health effects, including mortality and morbidity due to cardio- and cerebrovascular diseases (CCVD), but the molecular mechanisms involved are not entirely understood. This study aims to investigate the involvement of oxidative stress and inflammation in the causal chain, and to identify intermediate biomarkers that are associated retrospectively with the exposure and prospectively with the disease. We designed a case-control study on CCVD nested in a cohort of 18,982 individuals from the EPIC-Italy study. We measured air pollution, inflammatory biomarkers, and whole-genome DNA methylation in blood collected up to 17 years before the diagnosis. The study sample includes all the incident CCVD cases among former- and never-smokers, with available stored blood sample, that arose in the cohort during the follow-up. We identified enrichment of altered DNA methylation in "ROS/Glutathione/Cytotoxic granules" and "Cytokine signaling" pathways related genes, associated with both air pollution (multiple comparisons adjusted p for enrichment ranging from 0.01 to 0.03 depending on pollutant) and with CCVD risk (P = 0.04 and P = 0.03, respectively). Also, Interleukin-17 was associated with higher exposure to NO 2 (P = 0.0004), NO x (P = 0.0005), and CCVD risk (OR = 1.79; CI 1.04-3.11; P = 0.04 comparing extreme tertiles). Our findings indicate that chronic exposure to air pollution can lead to oxidative stress, which in turn activates a cascade of inflammatory responses mainly involving the "Cytokine signaling" pathway, leading to increased risk of CCVD. Inflammatory proteins and DNA methylation alterations can be detected several years before CCVD diagnosis in blood samples, being promising preclinical biomarkers. Environ. Mol. Mutagen. 59:234-246, 2018. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Assessment of Mitigation Systems on Vapor Intrusion ...

EPA Pesticide Factsheets

Vapor intrusion is the migration of subsurface vapors, including radon and volatile organic compounds (VOCs), in soil gas from the subsurface to indoor air. Vapor intrusion happens because there are pressure and concentration differentials between indoor air and soil gas. Indoor environments are often negatively pressurized with respect to outdoor air and soil gas (for example, from exhaust fans or the stack effect), and this pressure difference allows soil gas containing subsurface vapors to flow into indoor air through advection. In addition, concentration differentials cause VOCs and radon to migrate from areas of higher to lower concentrations through diffusion, which is another cause of vapor intrusion. Current practice for evaluating the vapor intrusion pathway involves a multiple line of evidence approach based on direct measurements in groundwater, external soil gas, subslab soil gas, and/or indoor air. No single line of evidence is considered definitive, and direct measurements of vapor intrusion can be costly, especially where significant spatial and temporal variability require repeated measurements at multiple locations to accurately assess the chronic risks of long-term exposure to volatile organic compounds (VOCs) like chloroform, perchloroethylene (PCE), and trichloroethylene (TCE).

The role of micronutrients in the response to ambient air pollutants: Potential mechanisms and suggestions for research design.

PubMed

Miller, Colette N; Rayalam, Srujana

2017-01-01

People living in regions of low socioeconomic status are thought to be prone to higher exposures to environmental pollutants, poor nutrition, and numerous preventable diseases and infections. Poverty correlates with pollution and malnutrition; however, limited studies examined their interrelationship. The well-studied, deleterious health effects attributed to environmental pollutants and poor nutrition may act in combination with produce more severe adverse health outcomes than any one factor alone. Deficiencies in specific nutrients render the body more susceptible to injury which may influence the pathways that serve as the mechanistic responses to ambient air pollutants. This review (1) explores specific micronutrients that are of global concern, (2) explains how these nutrients may impact the body's response to ambient air pollution, and (3) provides guidance on designing animal models of nutritional deficiency. It is likely that those individuals who reside in regions of high ambient air pollution are similarly malnourished. Therefore, it is important that research identifies specific nutrients of concern and their impact in identified regions of high ambient air pollution.

Fine particulate matter air pollution and atherosclerosis: Mechanistic insights.

PubMed

Bai, Yuntao; Sun, Qinghua

2016-12-01

Atherosclerosis is a progressive disease characterized by the accumulation of lipids and fibrous plaque in the arteries. Its etiology is very complicated and its risk factors primarily include genetic defects, smoking, hyperlipidemia, hypertension, lack of exercise, and infection. Recent studies suggest that fine particulate matter (PM2.5) air pollution may also contribute to the development of atherosclerosis. The present review integrates current experimental evidence with mechanistic pathways whereby PM2.5 exposure can promote the development of atherosclerosis. PM2.5-mediated enhancement of atherosclerosis is likely due to its pro-oxidant and pro-inflammatory effects, involving multiple organs, different cell types, and various molecular mediators. Studies about the effects of PM2.5inhalation on atherosclerosis may yield a better understanding of the link between air pollution and major cardiovascular diseases, and provide useful information for policy makers to determine acceptable levels of PM2.5 air quality. This article is part of a Special Issue entitled Air Pollution, edited by Wenjun Ding, Andrew J. Ghio and Weidong Wu. Copyright © 2016 Elsevier B.V. All rights reserved.

Research on Air Quality Evaluation based on Principal Component Analysis

NASA Astrophysics Data System (ADS)

Wang, Xing; Wang, Zilin; Guo, Min; Chen, Wei; Zhang, Huan

2018-01-01

Economic growth has led to environmental capacity decline and the deterioration of air quality. Air quality evaluation as a fundamental of environmental monitoring and air pollution control has become increasingly important. Based on the principal component analysis (PCA), this paper evaluates the air quality of a large city in Beijing-Tianjin-Hebei Area in recent 10 years and identifies influencing factors, in order to provide reference to air quality management and air pollution control.

Identification of key target genes and pathways in laryngeal carcinoma

PubMed Central

Liu, Feng; Du, Jintao; Liu, Jun; Wen, Bei

2016-01-01

The purpose of the present study was to screen the key genes associated with laryngeal carcinoma and to investigate the molecular mechanism of laryngeal carcinoma progression. The gene expression profile of GSE10935 [Gene Expression Omnibus (GEO) accession number], including 12 specimens from laryngeal papillomas and 12 specimens from normal laryngeal epithelia controls, was downloaded from the GEO database. Differentially expressed genes (DEGs) were screened in laryngeal papillomas compared with normal controls using Limma package in R language, followed by Gene Ontology (GO) enrichment analysis and pathway enrichment analysis. Furthermore, the protein-protein interaction (PPI) network of DEGs was constructed using Cytoscape software and modules were analyzed using MCODE plugin from the PPI network. Furthermore, significant biological pathway regions (sub-pathway) were identified by using iSubpathwayMiner analysis. A total of 67 DEGs were identified, including 27 up-regulated genes and 40 down-regulated genes and they were involved in different GO terms and pathways. PPI network analysis revealed that Ras association (RalGDS/AF-6) domain family member 1 (RASSF1) was a hub protein. The sub-pathway analysis identified 9 significantly enriched sub-pathways, including glycolysis/gluconeogenesis and nitrogen metabolism. Genes such as phosphoglycerate kinase 1 (PGK1), carbonic anhydrase II (CA2), and carbonic anhydrase XII (CA12) whose node degrees were >10 were identified in the disease risk sub-pathway. Genes in the sub-pathway, such as RASSF1, PGK1, CA2 and CA12 were presumed to serve critical roles in laryngeal carcinoma. The present study identified DEGs and their sub-pathways in the disease, which may serve as potential targets for treatment of laryngeal carcinoma. PMID:27446427

EVALUATING TERRESTRIAL FOOD CHAIN IMPACTS NEAR SOURCES OF DIOXIN RELEASE IN U.S. EPA RISK ASSESSMENTS

EPA Science Inventory

Prior to the mid 1980s, assessments of health impacts from dioxin-like compounds released into the air only evaluated the inhalation exposure pathway. In the latter 1980s it was demonstrated that consumption of animal food products is the principal source of exposure to dioxin...

A CASE STUDY DEMONSTRATING GUIDANCE FOR EVALUATING LANDFILL GAS EMISSIONS FROM CLOSED OR ABANDONED FACILITIES--SOUTH KINGSTOWN, RHODE ISLAND

EPA Science Inventory

The report describes a case study that applies EPA/600/R-05/123a, the guidance for conducting air pathway analyses of landfill gas emissions that are of interest to superfund remedial project managers, on-scene coordinators, facility owners, and potentially responsible parties. T...

Acute Toluene Exposure Alters Expression of Genes in the Central Nervous System Associated With Synaptic Structure and Function

EPA Science Inventory

Toluene is a volatile organic compound (VOC) and a ubiquitous air pollutant of interest to EPA regulatory programs. Whereas its acute functional effects are well described, several modes of action in the CNS have been proposed. Therefore, we sought to identify potential pathways ...

Room-Temperature C-H Functionalization Sequence under Benchtop Conditions for the Undergraduate Chemistry Laboratory

ERIC Educational Resources Information Center

Chen, Shuming

2018-01-01

An iridium(III)-mediated C-H functionalization sequence involving a concerted cyclometalation-deprotonation/migratory insertion pathway is reported for the undergraduate chemistry laboratory. The air- and water-stable iridacycle intermediates are readily isolated and characterized by NMR spectroscopy. Both steps of the experiment are performed at…

The Role of Monsoon-Like Zonally Asymmetric Heating in Interhemispheric Transport

NASA Technical Reports Server (NTRS)

Chen, Gang; Orbe, Clara; Waugh, Darryn

2017-01-01

While the importance of the seasonal migration of the zonally averaged Hadley circulation on interhemispheric transport of trace gases has been recognized, few studies have examined the role of the zonally asymmetric monsoonal circulation. This study investigates the role of monsoon-like zonally asymmetric heating on interhemispheric transport using a dry atmospheric model that is forced by idealized Newtonian relaxation to a prescribed radiative equilibrium temperature. When only the seasonal cycle of zonally symmetric heating is considered, the mean age of air in the Southern Hemisphere since last contact with the Northern Hemisphere midlatitude boundary layer, is much larger than the observations. The introduction of monsoon-like zonally asymmetric heating not only reduces the mean age of tropospheric air to more realistic values, but also produces an upper-tropospheric cross-equatorial transport pathway in boreal summer that resembles the transport pathway simulated in the NASA Global Modeling Initiative (GMI) Chemistry Transport Model driven with MERRA meteorological fields. These results highlight the monsoon-induced eddy circulation plays an important role in the interhemispheric transport of long-lived chemical constituents.

The air quality and health co-benefits of alternative post-2020 pathways for achieving peak carbon targets in Jiangsu, China

NASA Astrophysics Data System (ADS)

Liu, M.; Bi, J.; Huang, Y.; Kinney, P. L.

2016-12-01

Jiangsu, which has three national low-carbon pilot cities, is set to be a model province in China for achieving peak carbon targets before 2030. However, according to local planning of responding to climate change, carbon emissions are projected to keep going up before 2020 even the strictest measures are implemented. In other words, innovative measures must be in action after 2020. This work aimed at assessing the air quality and health co-benefits of alternative post-2020 measures to help remove barriers of policy implementation through tying it to local incentives for air quality improvement. To achieve the aim, we select 2010 as baseline year and develop Bussiness As Usual (BAU) and Traditional Carbon Reduction (TCR) scenarios before 2020. Under BAU, only existing climate and air pollution control policies are considered; under TCR, potential climate policies in local planning and existing air pollution control policies are considered. After 2020, integrated gasification combined cycle (IGCC) plant with carbon capture and storage (CCS) technology and large-scale substitution of renewable energy seem to be two promising pathways for achieving peak carbon targets. Therefore, two additional scenarios (TCR-IGCC and TCR-SRE) are set after 2020. Based on the projections of future energy balances and industrial productions, we estimate the pollutant emissions and simulate PM2.5 and ozone concentrations by 2017, 2020, 2030 and 2050 using CMAQ. Then using health impact assessment approach, the premature deaths are estimated and monetized. Results show that the carbon peak in Jiangsu will be achieved before 2030 only under TCR-IGCC and TCR-SRE scenarios. Under three policy scenarios, Jiangsu's carbon emission control targets would have substantial effects on primary air pollutant emissions far beyond those we estimate would be needed to meet the PM2.5 concentration targets in 2017. Compared with IGCC with CCS, large-scale substitutions of renewable energy bring comparable pollutant emission reductions but more health benefits because it reduces more emissions from traffic sources which are more harmful to health. However, large-scale substitution of renewable energy posed challenges on energy supply capacity, which need to be seriously considered in future policy decision.

Pathway-based factor analysis of gene expression data produces highly heritable phenotypes that associate with age.

PubMed

Anand Brown, Andrew; Ding, Zhihao; Viñuela, Ana; Glass, Dan; Parts, Leopold; Spector, Tim; Winn, John; Durbin, Richard

2015-03-09

Statistical factor analysis methods have previously been used to remove noise components from high-dimensional data prior to genetic association mapping and, in a guided fashion, to summarize biologically relevant sources of variation. Here, we show how the derived factors summarizing pathway expression can be used to analyze the relationships between expression, heritability, and aging. We used skin gene expression data from 647 twins from the MuTHER Consortium and applied factor analysis to concisely summarize patterns of gene expression to remove broad confounding influences and to produce concise pathway-level phenotypes. We derived 930 "pathway phenotypes" that summarized patterns of variation across 186 KEGG pathways (five phenotypes per pathway). We identified 69 significant associations of age with phenotype from 57 distinct KEGG pathways at a stringent Bonferroni threshold ([Formula: see text]). These phenotypes are more heritable ([Formula: see text]) than gene expression levels. On average, expression levels of 16% of genes within these pathways are associated with age. Several significant pathways relate to metabolizing sugars and fatty acids; others relate to insulin signaling. We have demonstrated that factor analysis methods combined with biological knowledge can produce more reliable phenotypes with less stochastic noise than the individual gene expression levels, which increases our power to discover biologically relevant associations. These phenotypes could also be applied to discover associations with other environmental factors. Copyright © 2015 Brown et al.

Pathway-Based Factor Analysis of Gene Expression Data Produces Highly Heritable Phenotypes That Associate with Age

PubMed Central

Anand Brown, Andrew; Ding, Zhihao; Viñuela, Ana; Glass, Dan; Parts, Leopold; Spector, Tim; Winn, John; Durbin, Richard

2015-01-01

Statistical factor analysis methods have previously been used to remove noise components from high-dimensional data prior to genetic association mapping and, in a guided fashion, to summarize biologically relevant sources of variation. Here, we show how the derived factors summarizing pathway expression can be used to analyze the relationships between expression, heritability, and aging. We used skin gene expression data from 647 twins from the MuTHER Consortium and applied factor analysis to concisely summarize patterns of gene expression to remove broad confounding influences and to produce concise pathway-level phenotypes. We derived 930 “pathway phenotypes” that summarized patterns of variation across 186 KEGG pathways (five phenotypes per pathway). We identified 69 significant associations of age with phenotype from 57 distinct KEGG pathways at a stringent Bonferroni threshold (P<5.38×10−5). These phenotypes are more heritable (h2=0.32) than gene expression levels. On average, expression levels of 16% of genes within these pathways are associated with age. Several significant pathways relate to metabolizing sugars and fatty acids; others relate to insulin signaling. We have demonstrated that factor analysis methods combined with biological knowledge can produce more reliable phenotypes with less stochastic noise than the individual gene expression levels, which increases our power to discover biologically relevant associations. These phenotypes could also be applied to discover associations with other environmental factors. PMID:25758824

Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.

PubMed

Naithani, Sushma; Jaiswal, Pankaj

2017-01-01

The species-specific plant Pathway Genome Databases (PGDBs) based on the BioCyc platform provide a conceptual model of the cellular metabolic network of an organism. Such frameworks allow analysis of the genome-scale expression data to understand changes in the overall metabolisms of an organism (or organs, tissues, and cells) in response to various extrinsic (e.g. developmental and differentiation) and/or extrinsic signals (e.g. pathogens and abiotic stresses) from the surrounding environment. Using FragariaCyc, a pathway database for the diploid strawberry Fragaria vesca, we show (1) the basic navigation across a PGDB; (2) a case study of pathway comparison across plant species; and (3) an example of RNA-Seq data analysis using Omics Viewer tool. The protocols described here generally apply to other Pathway Tools-based PGDBs.

Aircraft/Air Traffic Management Functional Analysis Model. Version 2.0; User's Guide

NASA Technical Reports Server (NTRS)

Etheridge, Melvin; Plugge, Joana; Retina, Nusrat

1998-01-01

The Aircraft/Air Traffic Management Functional Analysis Model, Version 2.0 (FAM 2.0), is a discrete event simulation model designed to support analysis of alternative concepts in air traffic management and control. FAM 2.0 was developed by the Logistics Management Institute (LMI) a National Aeronautics and Space Administration (NASA) contract. This document provides a guide for using the model in analysis. Those interested in making enhancements or modification to the model should consult the companion document, Aircraft/Air Traffic Management Functional Analysis Model, Version 2.0 Technical Description.

Unexpectedly high ultrafine aerosol concentrations above East Antarctic sea ice

NASA Astrophysics Data System (ADS)

Humphries, R. S.; Klekociuk, A. R.; Schofield, R.; Keywood, M.; Ward, J.; Wilson, S. R.

2016-02-01

Better characterisation of aerosol processes in pristine, natural environments, such as Antarctica, have recently been shown to lead to the largest reduction in uncertainties in our understanding of radiative forcing. Our understanding of aerosols in the Antarctic region is currently based on measurements that are often limited to boundary layer air masses at spatially sparse coastal and continental research stations, with only a handful of studies in the vast sea-ice region. In this paper, the first observational study of sub-micron aerosols in the East Antarctic sea ice region is presented. Measurements were conducted aboard the icebreaker Aurora Australis in spring 2012 and found that boundary layer condensation nuclei (CN3) concentrations exhibited a five-fold increase moving across the polar front, with mean polar cell concentrations of 1130 cm-3 - higher than any observed elsewhere in the Antarctic and Southern Ocean region. The absence of evidence for aerosol growth suggested that nucleation was unlikely to be local. Air parcel trajectories indicated significant influence from the free troposphere above the Antarctic continent, implicating this as the likely nucleation region for surface aerosol, a similar conclusion to previous Antarctic aerosol studies. The highest aerosol concentrations were found to correlate with low-pressure systems, suggesting that the passage of cyclones provided an accelerated pathway, delivering air masses quickly from the free troposphere to the surface. After descent from the Antarctic free troposphere, trajectories suggest that sea-ice boundary layer air masses travelled equatorward into the low-albedo Southern Ocean region, transporting with them emissions and these aerosol nuclei which, after growth, may potentially impact on the region's radiative balance. The high aerosol concentrations and their transport pathways described here, could help reduce the discrepancy currently present between simulations and observations of cloud and aerosol over the Southern Ocean.

Subterranean karst environments as a global sink for atmospheric methane

NASA Astrophysics Data System (ADS)

Webster, Kevin D.; Drobniak, Agnieszka; Etiope, Giuseppe; Mastalerz, Maria; Sauer, Peter E.; Schimmelmann, Arndt

2018-03-01

The air in subterranean karst cavities is often depleted in methane (CH4) relative to the atmosphere. Karst is considered a potential sink for the atmospheric greenhouse gas CH4 because its subsurface drainage networks and solution-enlarged fractures facilitate atmospheric exchange. Karst landscapes cover about 14% of earth's continental surface, but observations of CH4 concentrations in cave air are limited to localized studies in Gibraltar, Spain, Indiana (USA), Vietnam, Australia, and by incomplete isotopic data. To test if karst is acting as a global CH4 sink, we measured the CH4 concentrations, δ13CCH4, and δ2HCH4 values of cave air from 33 caves in the USA and three caves in New Zealand. We also measured CO2 concentrations, δ13CCO2, and radon (Rn) concentrations to support CH4 data interpretation by assessing cave air residence times and mixing processes. Among these caves, 35 exhibited subatmospheric CH4 concentrations in at least one location compared to their local atmospheric backgrounds. CH4 concentrations, δ13CCH4, and δ2HCH4 values suggest that microbial methanotrophy within caves is the primary CH4 consumption mechanism. Only 5 locations from 3 caves showed elevated CH4 concentrations compared to the atmospheric background and could be ascribed to local CH4 sources from sewage and outgassing swamp water. Several associated δ13CCH4 and δ2HCH4 values point to carbonate reduction and acetate fermentation as biochemical pathways of limited methanogenesis in karst environments and suggest that these pathways occur in the environment over large spatial scales. Our data show that karst environments function as a global CH4 sink.

N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes.

PubMed

Li, Qike; Schissler, A Grant; Gardeux, Vincent; Achour, Ikbel; Kenost, Colleen; Berghout, Joanne; Li, Haiquan; Zhang, Hao Helen; Lussier, Yves A

2017-05-24

Transcriptome analytic tools are commonly used across patient cohorts to develop drugs and predict clinical outcomes. However, as precision medicine pursues more accurate and individualized treatment decisions, these methods are not designed to address single-patient transcriptome analyses. We previously developed and validated the N-of-1-pathways framework using two methods, Wilcoxon and Mahalanobis Distance (MD), for personal transcriptome analysis derived from a pair of samples of a single patient. Although, both methods uncover concordantly dysregulated pathways, they are not designed to detect dysregulated pathways with up- and down-regulated genes (bidirectional dysregulation) that are ubiquitous in biological systems. We developed N-of-1-pathways MixEnrich, a mixture model followed by a gene set enrichment test, to uncover bidirectional and concordantly dysregulated pathways one patient at a time. We assess its accuracy in a comprehensive simulation study and in a RNA-Seq data analysis of head and neck squamous cell carcinomas (HNSCCs). In presence of bidirectionally dysregulated genes in the pathway or in presence of high background noise, MixEnrich substantially outperforms previous single-subject transcriptome analysis methods, both in the simulation study and the HNSCCs data analysis (ROC Curves; higher true positive rates; lower false positive rates). Bidirectional and concordant dysregulated pathways uncovered by MixEnrich in each patient largely overlapped with the quasi-gold standard compared to other single-subject and cohort-based transcriptome analyses. The greater performance of MixEnrich presents an advantage over previous methods to meet the promise of providing accurate personal transcriptome analysis to support precision medicine at point of care.

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites

PubMed Central

Zhang, Bofei; Hu, Senyang; Baskin, Elizabeth; Patt, Andrew; Siddiqui, Jalal K.

2018-01-01

The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentation analysis given a list of genes and/or metabolites of interest. For usability, we have developed a RaMP R package (https://github.com/Mathelab/RaMP-DB), including a user-friendly RShiny web application, that supports basic simple and batch queries, pathway overrepresentation analysis given a list of genes or metabolites of interest, and network visualization of gene-metabolite relationships. The package also includes the raw database file (mysql dump), thereby providing a stand-alone downloadable framework for public use and integration with other tools. In addition, the Python code needed to recreate the database on another system is also publicly available (https://github.com/Mathelab/RaMP-BackEnd). Updates for databases in RaMP will be checked multiple times a year and RaMP will be updated accordingly. PMID:29470400

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

PubMed

Zhang, Bofei; Hu, Senyang; Baskin, Elizabeth; Patt, Andrew; Siddiqui, Jalal K; Mathé, Ewy A

2018-02-22

The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentation analysis given a list of genes and/or metabolites of interest. For usability, we have developed a RaMP R package (https://github.com/Mathelab/RaMP-DB), including a user-friendly RShiny web application, that supports basic simple and batch queries, pathway overrepresentation analysis given a list of genes or metabolites of interest, and network visualization of gene-metabolite relationships. The package also includes the raw database file (mysql dump), thereby providing a stand-alone downloadable framework for public use and integration with other tools. In addition, the Python code needed to recreate the database on another system is also publicly available (https://github.com/Mathelab/RaMP-BackEnd). Updates for databases in RaMP will be checked multiple times a year and RaMP will be updated accordingly.

[Exploration of common biological pathways for attention deficit hyperactivity disorder and low birth weight].

PubMed

Xiang, Bo; Yu, Minglan; Liang, Xuemei; Lei, Wei; Huang, Chaohua; Chen, Jing; He, Wenying; Zhang, Tao; Li, Tao; Liu, Kezhi

2017-12-10

To explore common biological pathways for attention deficit hyperactivity disorder (ADHD) and low birth weight (LBW). Thei-Gsea4GwasV2 software was used to analyze the result of genome-wide association analysis (GWAS) for LBW (pathways were derived from Reactome), and nominally significant (P< 0.05, FDR< 0.25) pathways were tested for replication in ADHD.Significant pathways were analyzed with DAPPLE and Reatome FI software to identify genes involved in such pathways, with each cluster enriched with the gene ontology (GO). The Centiscape2.0 software was used to calculate the degree of genetic networks and the betweenness value to explore the core node (gene). Weighed gene co-expression network analysis (WGCNA) was then used to explore the co-expression of genes in these pathways.With gene expression data derived from BrainSpan, GO enrichment was carried out for each gene module. Eleven significant biological pathways was identified in association with LBW, among which two (Selenoamino acid metabolism and Diseases associated with glycosaminoglycan metabolism) were replicated during subsequent ADHD analysis. Network analysis of 130 genes in these pathways revealed that some of the sub-networksare related with morphology of cerebellum, development of hippocampus, and plasticity of synaptic structure. Upon co-expression network analysis, 120 genes passed the quality control and were found to express in 3 gene modules. These modules are mainly related to the regulation of synaptic structure and activity regulation. ADHD and LBW share some biological regulation processes. Anomalies of such proces sesmay predispose to ADHD.

Pathway analysis with next-generation sequencing data.

PubMed

Zhao, Jinying; Zhu, Yun; Boerwinkle, Eric; Xiong, Momiao

2015-04-01

Although pathway analysis methods have been developed and successfully applied to association studies of common variants, the statistical methods for pathway-based association analysis of rare variants have not been well developed. Many investigators observed highly inflated false-positive rates and low power in pathway-based tests of association of rare variants. The inflated false-positive rates and low true-positive rates of the current methods are mainly due to their lack of ability to account for gametic phase disequilibrium. To overcome these serious limitations, we develop a novel statistic that is based on the smoothed functional principal component analysis (SFPCA) for pathway association tests with next-generation sequencing data. The developed statistic has the ability to capture position-level variant information and account for gametic phase disequilibrium. By intensive simulations, we demonstrate that the SFPCA-based statistic for testing pathway association with either rare or common or both rare and common variants has the correct type 1 error rates. Also the power of the SFPCA-based statistic and 22 additional existing statistics are evaluated. We found that the SFPCA-based statistic has a much higher power than other existing statistics in all the scenarios considered. To further evaluate its performance, the SFPCA-based statistic is applied to pathway analysis of exome sequencing data in the early-onset myocardial infarction (EOMI) project. We identify three pathways significantly associated with EOMI after the Bonferroni correction. In addition, our preliminary results show that the SFPCA-based statistic has much smaller P-values to identify pathway association than other existing methods.

The competition between the liquid-liquid dewetting and the liquid-solid dewetting.

PubMed

Xu, Lin; Shi, Tongfei; An, Lijia

2009-05-14

We investigate the dewetting behavior of the bilayer of air/PS/PMMA/silanized Si wafer and find the two competing dewetting pathways in the dewetting process. The upper layer dewets on the lower layer (dewetting pathway 1, the liquid-liquid dewetting) and the two layers rupture on the solid substrate (dewetting pathway 2, the liquid-solid dewetting). To the two competing dewetting pathways, the process of forming holes and the process of hole growth, influence their competing relation. In the process of forming holes, the time of forming holes is a main factor that influences their competing relation. During the process of hole growth, the dewetting velocity is a main factor that influences their competing relation. The liquid-liquid interfacial tension, the film thickness of the polymer, and the viscosity of the polymer are important factors that influence the time of forming holes and the dewetting velocity. When the liquid-liquid dewetting pathway and the liquid-solid dewetting pathway compete in the dewetting process, the competing relation can be controlled by changing the molecular weight of the polymer, the film thickness, and the annealing temperature. In addition, it is also found that the rim growth on the solid substrate is by a rolling mechanism in the process of hole growth.

Model framework for integrating multiple exposure pathways to chemicals in household cleaning products.

PubMed

Shin, H-M; McKone, T E; Bennett, D H

2017-07-01

We present a screening-level exposure-assessment method which integrates exposure from all plausible exposure pathways as a result of indoor residential use of cleaning products. The exposure pathways we considered are (i) exposure to a user during product use via inhalation and dermal, (ii) exposure to chemical residues left on clothing, (iii) exposure to all occupants from the portion released indoors during use via inhalation and dermal, and (iv) exposure to the general population due to down-the-drain disposal via inhalation and ingestion. We use consumer product volatilization models to account for the chemical fractions volatilized to air (f volatilized ) and disposed down the drain (f down-the-drain ) during product use. For each exposure pathway, we use a fate and exposure model to estimate intake rates (iR) in mg/kg/d. Overall, the contribution of the four exposure pathways to the total exposure varies by the type of cleaning activities and with chemical properties. By providing a more comprehensive exposure model and by capturing additional exposures from often-overlooked exposure pathways, our method allows us to compare the relative contribution of various exposure routes and could improve high-throughput exposure assessment for chemicals in cleaning products. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Polybrominated diphenyl ethers in indoor dust in Ottawa, Canada: implications for sources and exposure.

PubMed

Wilford, Bryony H; Shoeib, Mahiba; Harner, Tom; Zhu, Jiping; Jones, Kevin C

2005-09-15

Polybrominated diphenyl ethers (PBDEs) are widely used as additive flame retardants in plastics, soft furnishings, electrical and electronic equipment, and insulation in the indoor environment, and may be released indoors via volatilization or as dusts. The penta-and octa-brominated mixes are now banned in most parts of Europe, and phasing out of their use has recently begun in North America. This study follows a previous investigation into indoor air levels of PBDEs. House dust was analyzed from the family vacuum cleaners of 68 of the same 74 randomly selected homes, in Ottawa, Canada during the winter of 2002-2003. PBDEs, comprising on average 42% BDE-209, were found in all samples. The levels were log-normally distributed with a geometric mean sigmaPBDE of 2000 ng g(-1), and a median of 1800 ng g(-1) dust. The levels in dust did not correlate with questionnaire information on house characteristics. Correlations were found between pentamix congener levels in dust and in air from the same homes, but not for congeners of the more highly brominated mixes. Exposure scenarios are presented for mean and high dust ingestion rates, and compared against exposures from other pathways, for both adults and toddlers (6 months-2 years). Assuming a mean dust ingestion rate and median dust and air concentrations, adults would be exposed to ca. 7.5 ng sigmaPBDE d(-1) via the dust ingestion pathway, which represents approximately 14% of total daily exposure when compared to diet (82%) and inhalation (4%). However, for toddlers the equivalent intakes would be 99 ng d(-1), representing 80% of their daily PBDE exposure. At high dust ingestion rates these values increase to 180 ng d(-1) (80% daily intake) for adults and 360 ng d(-1) (89% daily intake) for toddlers. The data give a clearer picture of sources of PBDE exposure in the home environment and suggest that dust could be a significant exposure pathway for some individuals, particularly children.

Source regions and transport pathways of PM2.5 at a regional background site in East China

NASA Astrophysics Data System (ADS)

Zhang, Yanru; Zhang, Hongliang; Deng, Junjun; Du, Wenjiao; Hong, Youwei; Xu, Lingling; Qiu, Yuqing; Hong, Zhenyu; Wu, Xin; Ma, Qianli; Yao, Jie; Chen, Jinsheng

2017-10-01

PM2.5 samples were collected daily at the Lin'an regional background station (LA) in Zhejiang, China during 2014-2015 and the major chemical components including organic carbon (OC), elemental carbon (EC) and water-soluble inorganic ions (WSII) were determined. Backward trajectory clustering and potential source contribution function (PSCF) were adopted for identifying the transport pathways and potential source regions of PM2.5 at LA. The annual mean concentration was 68.9 ± 28.3 μg m-3, indicating severe pollution in East China. Obvious seasonal variations were found, with highest level in winter and lowest in summer. Carbonaceous aerosols and WSII were the predominant compositions, accounting for 30.7% and 53.5% of PM2.5, respectively. Secondary inorganic ions (SO42-, NO3-, and NH4+) made a total contribution of 45.2% to PM2.5. Heterogeneous formation played a dominant role in SO42- formation and NH4+ formation promoted NO3- formation. Stationary sources played a more important role than mobile sources based on NO3-/SO42- ratio of 0.53. Aerosol environment at LA was ammonium-poor and SO42- was only neutralized sufficiently by NH4+ with the predominant production of (NH4)2SO4 in winter. Four major transport pathways of air masses at LA were found based on trajectory clustering. Air masses from the northwest Gobi areas passing over the heavily polluted regions in North and Central China had the highest levels of PM2.5, followed by the air masses from Central China. PSCF results suggested that surrounding areas in the Yangtze River Delta region were major regional origins of PM2.5 and its major components. Northern region was an important origin for carbonaceous components, and southwestern region was significant for secondary inorganic ions. This study helps understand PM2.5 characteristics, identify potential source regions and effectively control PM2.5 in East China.

Computer Analysis of Air Pollution from Highways, Streets, and Complex Interchanges

DOT National Transportation Integrated Search

1974-03-01

A detailed computer analysis of air quality for a complex highway interchange was prepared, using an in-house version of the Environmental Protection Agency's Gaussian Highway Line Source Model. This analysis showed that the levels of air pollution n...

Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated "Knowledge-Based" Platform.

PubMed

Dubovenko, Alexey; Nikolsky, Yuri; Rakhmatulin, Eugene; Nikolskaya, Tatiana

2017-01-01

Analysis of NGS and other sequencing data, gene variants, gene expression, proteomics, and other high-throughput (OMICs) data is challenging because of its biological complexity and high level of technical and biological noise. One way to deal with both problems is to perform analysis with a high fidelity annotated knowledgebase of protein interactions, pathways, and functional ontologies. This knowledgebase has to be structured in a computer-readable format and must include software tools for managing experimental data, analysis, and reporting. Here, we present MetaCore™ and Key Pathway Advisor (KPA), an integrated platform for functional data analysis. On the content side, MetaCore and KPA encompass a comprehensive database of molecular interactions of different types, pathways, network models, and ten functional ontologies covering human, mouse, and rat genes. The analytical toolkit includes tools for gene/protein list enrichment analysis, statistical "interactome" tool for the identification of over- and under-connected proteins in the dataset, and a biological network analysis module made up of network generation algorithms and filters. The suite also features Advanced Search, an application for combinatorial search of the database content, as well as a Java-based tool called Pathway Map Creator for drawing and editing custom pathway maps. Applications of MetaCore and KPA include molecular mode of action of disease research, identification of potential biomarkers and drug targets, pathway hypothesis generation, analysis of biological effects for novel small molecule compounds and clinical applications (analysis of large cohorts of patients, and translational and personalized medicine).

Synoptic controls on precipitation pathways and snow delivery to high-accumulation ice core sites in the Ross Sea region, Antarctica

NASA Astrophysics Data System (ADS)

Sinclair, K. E.; Bertler, N. A. N.; Trompetter, W. J.

2010-11-01

Dominant storm tracks to two ice core sites on the western margin of the Ross Sea, Antarctica (Skinner Saddle (SKS) and Evans Piedmont Glacier), are investigated to establish key synoptic controls on snow accumulation. This is critical in terms of understanding the seasonality, source regions, and transport pathways of precipitation delivered to these sites. In situ snow depth and meteorological observations are used to identify major accumulation events in 2007-2008, which differ considerably between sites in terms of their magnitude and seasonal distribution. While snowfall at Evans Piedmont Glacier occurs almost exclusively during summer and spring, Skinner Saddle receives precipitation year round with a lull during the months of April and May. Cluster analysis of daily back trajectories reveals that the highest-accumulation days at both sites result from fast-moving air masses, associated with synoptic-scale low-pressure systems. There is evidence that short-duration pulses of snowfall at SKS also originate from mesocyclone development over the Ross Ice Shelf and local moisture sources. Changes in the frequency and seasonal distribution of these mechanisms of precipitation delivery will have a marked impact on annual accumulation over time and will therefore need careful consideration during the interpretation of stable isotope and geochemical records from these ice cores.

Plant Reactome: a resource for plant pathways and comparative analysis

PubMed Central

Naithani, Sushma; Preece, Justin; D'Eustachio, Peter; Gupta, Parul; Amarasinghe, Vindhya; Dharmawardhana, Palitha D.; Wu, Guanming; Fabregat, Antonio; Elser, Justin L.; Weiser, Joel; Keays, Maria; Fuentes, Alfonso Munoz-Pomer; Petryszak, Robert; Stein, Lincoln D.; Ware, Doreen; Jaiswal, Pankaj

2017-01-01

Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX. PMID:27799469

Integrated Assessment of Air Pollution Control Measures for Megacities

NASA Astrophysics Data System (ADS)

Friedrich, R.; Theloke, J.; Denier-van-der-Gon, H.; Kugler, U.; Kampffmeyer, T.; Roos, J.; Torras, S.

2012-04-01

Air pollution in large cities is still a matter of concern. Especially the concentration of fine particles (PM10 and PM2.5) is largest in large cities leading to severe health impacts. Furthermore the PM10 thresholds of the EU Air Quality Directive are frequently exceeded. Thus the question arises, whether the initiated policies and measures for mitigating air pollution are sufficient to meet the air quality targets and - if not - which efficient further pollution mitigation measures exist. These questions have been addressed in the EU research project MEGAPOLI for the four European megacities respectively agglomerations London, Paris, Rhine-Ruhr area and Po valley. Firstly, a reference scenario of future activities and emissions has been compiled for the megacities for the years 2020, 2030 and 2050 for all relevant air pollutants (CO, NH3, NMVOC, NOx, PM10, PM2.5 and SO2) and greenhouse gases (CO2, CH4 and N2O). The reference scenario takes into account as well population changes as technical progress and economic growth. As pollution flowing in from outside the city is about as important as pollution caused by emissions in the city, the analysis covers the whole of Europe and not only the city area. Emissions are then transformed into concentrations using atmospheric models. The higher concentrations in cities were estimated with a newly developed 'urban increment' model. Results show, that in the megacities the limits of the Air Quality Directive (2008/50/EC) will be exceeded. Thus additional efforts are necessary to reduce emissions further. Thus, a number of further measures (not implemented in current legislation) were selected and assessed. These included mitigation options for road transport, other mobile sources, large combustion plants, small and medium combustion plants and industry. For each measure and in addition for various bundles of measures a cost-benefit analysis has been carried out. Benefits (avoided health risks and climate change risks) have been calculated for each measure using the impact pathway or full chain approach. First the changes of emissions - compared with the reference scenario - are estimated, that occur, if the different options are implemented. Then, for each policy scenario the concentrations of pollutants are estimated. Using concentration-response-relationships, impacts, especially risks to human health, are calculated. These impact are then converted into DALYs (disability adjusted life years) and further into monetary values using contingent valuation methods (willingness to pay approach). The most efficient measures are the use of solar energy for heating,insulation of buildings combined with a mechanical ventilation system, wind energy for electricity production, use of more efficient combustion techniques and low and later zero emission zones for vehicles in cities. However, even if all available options are implemented, the air quality requirements for PM10 will not be met under all meteorological conditions.

Health risk assessment of air emissions from a municipal solid waste incineration plant--a case study.

PubMed

Cangialosi, Federico; Intini, Gianluca; Liberti, Lorenzo; Notarnicola, Michele; Stellacci, Paolo

2008-01-01

A health risk assessment of long-term emissions of carcinogenic and non-carcinogenic air pollutants has been carried out for the municipal solid waste incinerator (MSWI) of the city of Taranto, Italy. Ground level air concentrations and soil deposition of carcinogenic (Polychlorinated Dibenzo-p-Dioxins/Furans and Cd) and non-carcinogenic (Pb and Hg) pollutants have been estimated using a well documented atmospheric dispersion model. Health risk values for air inhalation, dermal contact, soil and food ingestion have been calculated based on a combination of these concentrations and a matrix of environmental exposure factors. Exposure of the surrounding population has been addressed for different release scenarios based on four pollutants, four exposure pathways and two receptor groups (children and adults). Spatial risk distribution and cancer excess cases projected from plant emissions have been compared with background mortality records. Estimated results based on the MSWI emissions show: (1) individual risks well below maximum acceptable levels, (2) very small incremental cancer risk compared with background level.

Linking Low-Frequency Large-Scale Circulation Patterns to Cold Air Outbreak Formation in the Northeastern North Atlantic

NASA Astrophysics Data System (ADS)

Papritz, L.; Grams, C. M.

2018-03-01

The regional variability of wintertime marine cold air outbreaks (CAOs) in the northeastern North Atlantic is studied focusing on the role of weather regimes in modulating the large-scale circulation. Each regime is characterized by a typical CAO frequency anomaly pattern and a corresponding imprint in air-sea heat fluxes. Cyclonically dominated regimes, Greenland blocking and the Atlantic ridge regime are found to provide favorable conditions for CAO formation in at least one major sea of the study region; CAO occurrence is suppressed, however, by blocked regimes whose associated anticyclones are centered over northern Europe (European / Scandinavian blocking). Kinematic trajectories reveal that strength and location of the storm tracks are closely linked to the pathways of CAO air masses and, thus, CAO occurrence. Finally, CAO frequencies are also linked to the strength of the stratospheric polar vortex, which is understood in terms of associated variations in the frequency of weather regimes.

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data

PubMed Central

Yi, Ming; Horton, Jay D; Cohen, Jonathan C; Hobbs, Helen H; Stephens, Robert M

2006-01-01

Background Analysis of High Throughput (HTP) Data such as microarray and proteomics data has provided a powerful methodology to study patterns of gene regulation at genome scale. A major unresolved problem in the post-genomic era is to assemble the large amounts of data generated into a meaningful biological context. We have developed a comprehensive software tool, WholePathwayScope (WPS), for deriving biological insights from analysis of HTP data. Result WPS extracts gene lists with shared biological themes through color cue templates. WPS statistically evaluates global functional category enrichment of gene lists and pathway-level pattern enrichment of data. WPS incorporates well-known biological pathways from KEGG (Kyoto Encyclopedia of Genes and Genomes) and Biocarta, GO (Gene Ontology) terms as well as user-defined pathways or relevant gene clusters or groups, and explores gene-term relationships within the derived gene-term association networks (GTANs). WPS simultaneously compares multiple datasets within biological contexts either as pathways or as association networks. WPS also integrates Genetic Association Database and Partial MedGene Database for disease-association information. We have used this program to analyze and compare microarray and proteomics datasets derived from a variety of biological systems. Application examples demonstrated the capacity of WPS to significantly facilitate the analysis of HTP data for integrative discovery. Conclusion This tool represents a pathway-based platform for discovery integration to maximize analysis power. The tool is freely available at . PMID:16423281

A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations.

PubMed

Zhang, Han; Wheeler, William; Hyland, Paula L; Yang, Yifan; Shi, Jianxin; Chatterjee, Nilanjan; Yu, Kai

2016-06-01

Meta-analysis of multiple genome-wide association studies (GWAS) has become an effective approach for detecting single nucleotide polymorphism (SNP) associations with complex traits. However, it is difficult to integrate the readily accessible SNP-level summary statistics from a meta-analysis into more powerful multi-marker testing procedures, which generally require individual-level genetic data. We developed a general procedure called Summary based Adaptive Rank Truncated Product (sARTP) for conducting gene and pathway meta-analysis that uses only SNP-level summary statistics in combination with genotype correlation estimated from a panel of individual-level genetic data. We demonstrated the validity and power advantage of sARTP through empirical and simulated data. We conducted a comprehensive pathway-based meta-analysis with sARTP on type 2 diabetes (T2D) by integrating SNP-level summary statistics from two large studies consisting of 19,809 T2D cases and 111,181 controls with European ancestry. Among 4,713 candidate pathways from which genes in neighborhoods of 170 GWAS established T2D loci were excluded, we detected 43 T2D globally significant pathways (with Bonferroni corrected p-values < 0.05), which included the insulin signaling pathway and T2D pathway defined by KEGG, as well as the pathways defined according to specific gene expression patterns on pancreatic adenocarcinoma, hepatocellular carcinoma, and bladder carcinoma. Using summary data from 8 eastern Asian T2D GWAS with 6,952 cases and 11,865 controls, we showed 7 out of the 43 pathways identified in European populations remained to be significant in eastern Asians at the false discovery rate of 0.1. We created an R package and a web-based tool for sARTP with the capability to analyze pathways with thousands of genes and tens of thousands of SNPs.

A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations

PubMed Central

Zhang, Han; Wheeler, William; Hyland, Paula L.; Yang, Yifan; Shi, Jianxin; Chatterjee, Nilanjan; Yu, Kai

2016-01-01

Meta-analysis of multiple genome-wide association studies (GWAS) has become an effective approach for detecting single nucleotide polymorphism (SNP) associations with complex traits. However, it is difficult to integrate the readily accessible SNP-level summary statistics from a meta-analysis into more powerful multi-marker testing procedures, which generally require individual-level genetic data. We developed a general procedure called Summary based Adaptive Rank Truncated Product (sARTP) for conducting gene and pathway meta-analysis that uses only SNP-level summary statistics in combination with genotype correlation estimated from a panel of individual-level genetic data. We demonstrated the validity and power advantage of sARTP through empirical and simulated data. We conducted a comprehensive pathway-based meta-analysis with sARTP on type 2 diabetes (T2D) by integrating SNP-level summary statistics from two large studies consisting of 19,809 T2D cases and 111,181 controls with European ancestry. Among 4,713 candidate pathways from which genes in neighborhoods of 170 GWAS established T2D loci were excluded, we detected 43 T2D globally significant pathways (with Bonferroni corrected p-values < 0.05), which included the insulin signaling pathway and T2D pathway defined by KEGG, as well as the pathways defined according to specific gene expression patterns on pancreatic adenocarcinoma, hepatocellular carcinoma, and bladder carcinoma. Using summary data from 8 eastern Asian T2D GWAS with 6,952 cases and 11,865 controls, we showed 7 out of the 43 pathways identified in European populations remained to be significant in eastern Asians at the false discovery rate of 0.1. We created an R package and a web-based tool for sARTP with the capability to analyze pathways with thousands of genes and tens of thousands of SNPs. PMID:27362418

TabPath: interactive tables for metabolic pathway analysis.

PubMed

Moraes, Lauro Ângelo Gonçalves de; Felestrino, Érica Barbosa; Assis, Renata de Almeida Barbosa; Matos, Diogo; Lima, Joubert de Castro; Lima, Leandro de Araújo; Almeida, Nalvo Franco; Setubal, João Carlos; Garcia, Camila Carrião Machado; Moreira, Leandro Marcio

2018-03-15

Information about metabolic pathways in a comparative context is one of the most powerful tool to help the understanding of genome-based differences in phenotypes among organisms. Although several platforms exist that provide a wealth of information on metabolic pathways of diverse organisms, the comparison among organisms using metabolic pathways is still a difficult task. We present TabPath (Tables for Metabolic Pathway), a web-based tool to facilitate comparison of metabolic pathways in genomes based on KEGG. From a selection of pathways and genomes of interest on the menu, TabPath generates user-friendly tables that facilitate analysis of variations in metabolism among the selected organisms. TabPath is available at http://200.239.132.160:8686. lmmorei@gmail.com.

40 CFR 60.2895 - What is a siting analysis?

Code of Federal Regulations, 2014 CFR

2014-07-01

... What is a siting analysis? (a) The siting analysis must consider air pollution control alternatives... consideration of air pollution control alternatives specified in paragraph (a) of this section. (c) You must... Section 60.2895 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS...

40 CFR 60.2895 - What is a siting analysis?

Code of Federal Regulations, 2013 CFR

2013-07-01

... What is a siting analysis? (a) The siting analysis must consider air pollution control alternatives... consideration of air pollution control alternatives specified in paragraph (a) of this section. (c) You must... Section 60.2895 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS...

40 CFR 60.2895 - What is a siting analysis?

Code of Federal Regulations, 2012 CFR

2012-07-01

... What is a siting analysis? (a) The siting analysis must consider air pollution control alternatives... consideration of air pollution control alternatives specified in paragraph (a) of this section. (c) You must... Section 60.2895 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS...

Rapid Evolution of piRNA Pathway in the Teleost Fish: Implication for an Adaptation to Transposon Diversity

PubMed Central

Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

2014-01-01

The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi–piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. PMID:24846630

Air pollution and public health: emerging hazards and improved understanding of risk.

PubMed

Kelly, Frank J; Fussell, Julia C

2015-08-01

Despite past improvements in air quality, very large parts of the population in urban areas breathe air that does not meet European standards let alone the health-based World Health Organisation Air Quality Guidelines. Over the last 10 years, there has been a substantial increase in findings that particulate matter (PM) air pollution is not only exerting a greater impact on established health endpoints, but is also associated with a broader number of disease outcomes. Data strongly suggest that effects have no threshold within the studied range of ambient concentrations, can occur at levels close to PM2.5 background concentrations and that they follow a mostly linear concentration-response function. Having firmly established this significant public health problem, there has been an enormous effort to identify what it is in ambient PM that affects health and to understand the underlying biological basis of toxicity by identifying mechanistic pathways-information that in turn will inform policy makers how best to legislate for cleaner air. Another intervention in moving towards a healthier environment depends upon the achieving the right public attitude and behaviour by the use of optimal air pollution monitoring, forecasting and reporting that exploits increasingly sophisticated information systems. Improving air quality is a considerable but not an intractable challenge. Translating the correct scientific evidence into bold, realistic and effective policies undisputedly has the potential to reduce air pollution so that it no longer poses a damaging and costly toll on public health.

Active Salt/Silica-Templated 2D Mesoporous FeCo-Nx -Carbon as Bifunctional Oxygen Electrodes for Zinc-Air Batteries.

PubMed

Li, Shuang; Cheng, Chong; Zhao, Xiaojia; Schmidt, Johannes; Thomas, Arne

2018-02-12

Two types of templates, an active metal salt and silica nanoparticles, are used concurrently to achieve the facile synthesis of hierarchical meso/microporous FeCo-N x -carbon nanosheets (meso/micro-FeCo-N x -CN) with highly dispersed metal sites. The resulting meso/micro-FeCo-N x -CN shows high and reversible oxygen electrocatalytic performances for both ORR and OER, thus having potential for applications in rechargeable Zn-air battery. Our approach creates a new pathway to fabricate 2D meso/microporous structured carbon architectures for bifunctional oxygen electrodes in rechargeable Zn-air battery as well as opens avenues to the scale-up production of rationally designed heteroatom-doped catalytic materials for a broad range of applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Meta-analysis of human gene expression in response to Mycobacterium tuberculosis infection reveals potential therapeutic targets.

PubMed

Wang, Zhang; Arat, Seda; Magid-Slav, Michal; Brown, James R

2018-01-10

With the global emergence of multi-drug resistant strains of Mycobacterium tuberculosis, new strategies to treat tuberculosis are urgently needed such as therapeutics targeting potential human host factors. Here we performed a statistical meta-analysis of human gene expression in response to both latent and active pulmonary tuberculosis infections from nine published datasets. We found 1655 genes that were significantly differentially expressed during active tuberculosis infection. In contrast, no gene was significant for latent tuberculosis. Pathway enrichment analysis identified 90 significant canonical human pathways, including several pathways more commonly related to non-infectious diseases such as the LRRK2 pathway in Parkinson's disease, and PD-1/PD-L1 signaling pathway important for new immuno-oncology therapies. The analysis of human genome-wide association studies datasets revealed tuberculosis-associated genetic variants proximal to several genes in major histocompatibility complex for antigen presentation. We propose several new targets and drug-repurposing opportunities including intravenous immunoglobulin, ion-channel blockers and cancer immuno-therapeutics for development as combination therapeutics with anti-mycobacterial agents. Our meta-analysis provides novel insights into host genes and pathways important for tuberculosis and brings forth potential drug repurposing opportunities for host-directed therapies.

Critical radionuclide/critical pathway analysis for the U.S. Department of Energy's Savannah River Site.

PubMed

Jannik, G T

1999-06-01

Many different radionuclides have been released to the environment from the Savannah River Site (SRS) during the facility's operational history. However, as shown by this analysis, only a small number of the released radionuclides have been significant contributors to potential doses and risks to off-site people. This article documents the radiological critical contaminant/critical pathway analysis performed for SRS. If site missions and operations remain constant over the next 30 years, only tritium oxide releases are projected to exceed a maximally exposed individual (MEI) risk of 1.0E-06 for either the airborne or liquid pathways. The critical exposure pathways associated with site airborne releases are inhalation and vegetation consumption, whereas the critical exposure pathways associated with liquid releases are drinking water and fish consumption. For the SRS-specific, nontypical exposure pathways (i.e., recreational fishing and deer and hog hunting), cesium-137 is the critical radionuclide.

Flux analysis of cholesterol biosynthesis in vivo reveals multiple tissue and cell-type specific pathways

PubMed Central

Mitsche, Matthew A; McDonald, Jeffrey G; Hobbs, Helen H; Cohen, Jonathan C

2015-01-01

Two parallel pathways produce cholesterol: the Bloch and Kandutsch-Russell pathways. Here we used stable isotope labeling and isotopomer analysis to trace sterol flux through the two pathways in mice. Surprisingly, no tissue used the canonical K–R pathway. Rather, a hybrid pathway was identified that we call the modified K–R (MK–R) pathway. Proportional flux through the Bloch pathway varied from 8% in preputial gland to 97% in testes, and the tissue-specificity observed in vivo was retained in cultured cells. The distribution of sterol isotopomers in plasma mirrored that of liver. Sterol depletion in cultured cells increased flux through the Bloch pathway, whereas overexpression of 24-dehydrocholesterol reductase (DHCR24) enhanced usage of the MK–R pathway. Thus, relative use of the Bloch and MK–R pathways is highly variable, tissue-specific, flux dependent, and epigenetically fixed. Maintenance of two interdigitated pathways permits production of diverse bioactive sterols that can be regulated independently of cholesterol. DOI: http://dx.doi.org/10.7554/eLife.07999.001 PMID:26114596

Genome-wide pathway analysis of memory impairment in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort implicates gene candidates, canonical pathways, and networks.

PubMed

Ramanan, Vijay K; Kim, Sungeun; Holohan, Kelly; Shen, Li; Nho, Kwangsik; Risacher, Shannon L; Foroud, Tatiana M; Mukherjee, Shubhabrata; Crane, Paul K; Aisen, Paul S; Petersen, Ronald C; Weiner, Michael W; Saykin, Andrew J

2012-12-01

Memory deficits are prominent features of mild cognitive impairment (MCI) and Alzheimer's disease (AD). The genetic architecture underlying these memory deficits likely involves the combined effects of multiple genetic variants operative within numerous biological pathways. In order to identify functional pathways associated with memory impairment, we performed a pathway enrichment analysis on genome-wide association data from 742 Alzheimer's Disease Neuroimaging Initiative (ADNI) participants. A composite measure of memory was generated as the phenotype for this analysis by applying modern psychometric theory to item-level data from the ADNI neuropsychological test battery. Using the GSA-SNP software tool, we identified 27 canonical, expertly-curated pathways with enrichment (FDR-corrected p-value < 0.05) against this composite memory score. Processes classically understood to be involved in memory consolidation, such as neurotransmitter receptor-mediated calcium signaling and long-term potentiation, were highly represented among the enriched pathways. In addition, pathways related to cell adhesion, neuronal differentiation and guided outgrowth, and glucose- and inflammation-related signaling were also enriched. Among genes that were highly-represented in these enriched pathways, we found indications of coordinated relationships, including one large gene set that is subject to regulation by the SP1 transcription factor, and another set that displays co-localized expression in normal brain tissue along with known AD risk genes. These results 1) demonstrate that psychometrically-derived composite memory scores are an effective phenotype for genetic investigations of memory impairment and 2) highlight the promise of pathway analysis in elucidating key mechanistic targets for future studies and for therapeutic interventions.

Pathview: an R/Bioconductor package for pathway-based data integration and visualization.

PubMed

Luo, Weijun; Brouwer, Cory

2013-07-15

Pathview is a novel tool set for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines. The package is freely available under the GPLv3 license through Bioconductor and R-Forge. It is available at http://bioconductor.org/packages/release/bioc/html/pathview.html and at http://Pathview.r-forge.r-project.org/. luo_weijun@yahoo.com Supplementary data are available at Bioinformatics online.

40 CFR 60.1125 - What must I include in my siting analysis?

Code of Federal Regulations, 2014 CFR

2014-07-01

... waste combustion unit affects four areas: (1) Ambient air quality. (2) Visibility. (3) Soils. (4) Vegetation. (b) Include an analysis of alternatives for controlling air pollution that minimize potential... analysis? 60.1125 Section 60.1125 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR...

40 CFR 60.1125 - What must I include in my siting analysis?

Code of Federal Regulations, 2011 CFR

2011-07-01

... waste combustion unit affects four areas: (1) Ambient air quality. (2) Visibility. (3) Soils. (4) Vegetation. (b) Include an analysis of alternatives for controlling air pollution that minimize potential... analysis? 60.1125 Section 60.1125 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR...

40 CFR 60.1125 - What must I include in my siting analysis?

Code of Federal Regulations, 2013 CFR

2013-07-01

... waste combustion unit affects four areas: (1) Ambient air quality. (2) Visibility. (3) Soils. (4) Vegetation. (b) Include an analysis of alternatives for controlling air pollution that minimize potential... analysis? 60.1125 Section 60.1125 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR...

40 CFR 60.1125 - What must I include in my siting analysis?

Code of Federal Regulations, 2012 CFR

2012-07-01

... waste combustion unit affects four areas: (1) Ambient air quality. (2) Visibility. (3) Soils. (4) Vegetation. (b) Include an analysis of alternatives for controlling air pollution that minimize potential... analysis? 60.1125 Section 60.1125 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR...

Result Summary for the Area 5 Radioactive Waste Management Site Performance Assessment Model Version 4.110

DOE Office of Scientific and Technical Information (OSTI.GOV)

NSTec Environmental Management

2011-07-20

Results for Version 4.110 of the Area 5 Radioactive Waste Management Site (RWMS) performance assessment (PA) model are summarized. Version 4.110 includes the fiscal year (FY) 2010 inventory estimate, including a future inventory estimate. Version 4.110 was implemented in GoldSim 10.11(SP4). The following changes have been implemented since the last baseline model, Version 4.105: (1) Updated the inventory and disposal unit configurations with data through the end of FY 2010. (1) Implemented Federal Guidance Report 13 Supplemental CD dose conversion factors (U.S. Environmental Protection Agency, 1999). Version 4.110 PA results comply with air pathway and all-pathways annual total effective dosemore » (TED) performance objectives (Tables 2 and 3, Figures 1 and 2). Air pathways results decrease moderately for all scenarios. The time of the maximum for the air pathway open rangeland scenario shifts from 1,000 to 100 years (y). All-pathways annual TED increases for all scenarios except the resident scenario. The maximum member of public all-pathways dose occurs at 1,000 y for the resident farmer scenario. The resident farmer dose was predominantly due to technetium-99 (Tc-99) (82 percent) and lead-210 (Pb-210) (13 percent). Pb-210 present at 1,000 y is produced predominantly by radioactive decay of uranium-234 (U-234) present at the time of disposal. All results for the postdrilling and intruder-agriculture scenarios comply with the performance objectives (Tables 4 and 5, Figures 3 and 4). The postdrilling intruder results are similar to Version 4.105 results. The intruder-agriculture results are similar to Version 4.105, except for the Pit 6 Radium Disposal Unit (RaDU). The intruder-agriculture result for the Shallow Land Burial (SLB) disposal units is a significant fraction of the performance objective and exceeds the performance objective at the 95th percentile. The intruder-agriculture dose is due predominantly to Tc-99 (75 percent) and U-238 (9.5 percent). The acute intruder scenario results comply with all performance objectives (Tables 6 and 7, Figures 5 and 6). The acute construction result for the SLB disposal units decreases significantly with this version. The maximum acute intruder dose occurs at 1,000 y for the SLB disposal units under the acute construction scenario. The acute intruder dose is caused by multiple radionuclides including U-238 (31 percent), Th-229 (28 percent), plutonium-239 (8.6 percent), U-233 (7.8 percent), and U-234 (6.7 percent). All results for radon-222 (Rn-222) flux density comply with the performance objective (Table 8, Figure 7). The mean Pit 13 RaDU flux density is close to the 0.74 Bq m{sup -2} s{sup -1} limit.« less

Information technology equipment cooling system

DOEpatents

Schultz, Mark D.

2014-06-10

According to one embodiment, a system for removing heat from a rack of information technology equipment may include a sidecar indoor air to liquid heat exchanger that cools warm air generated by the rack of information technology equipment. The system may also include a liquid to liquid heat exchanger and an outdoor heat exchanger. The system may further include configurable pathways to connect and control fluid flow through the sidecar heat exchanger, the liquid to liquid heat exchanger, the rack of information technology equipment, and the outdoor heat exchanger based upon ambient temperature and/or ambient humidity to remove heat from the rack of information technology equipment.

Significance of independent radon entry rate and air exchange rate assessment for the purpose of radon mitigation effectiveness proper evaluation: case studies.

PubMed

Froňka, A; Jílek, K; Moučka, L; Brabec, M

2011-05-01

Two new single-family houses identified as insufficient with regard to existing radon barrier efficiency, have been selected for further examination. A complex set of radon diagnosis procedures has been applied in order to localise and quantify radon entry pathways into the indoor environment. Independent assessment of radon entry rate and air exchange rate has been carried out using the continuous indoor radon measurement and a specific tracer gas application. Simultaneous assessment of these key determining factors has turned out to be absolutely crucial in the context of major cause identification of elevated indoor radon concentration.

AXAOTHER XL -- A spreadsheet for determining doses for incidents caused by tornadoes or high-velocity straight winds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simpkins, A.A.

1996-09-01

AXAOTHER XL is an Excel Spreadsheet used to determine dose to the maximally exposed offsite individual during high-velocity straight winds or tornado conditions. Both individual and population doses may be considered. Potential exposure pathways are inhalation and plume shine. For high-velocity straight winds the spreadsheet has the capability to determine the downwind relative air concentration, however for the tornado conditions, the user must enter the relative air concentration. Theoretical models are discussed and hand calculations are performed to ensure proper application of methodologies. A section has also been included that contains user instructions for the spreadsheet.

Sources of Virginia meteorological and air quality data for use in highway air quality analysis with comments on their usefulness.

DOT National Transportation Integrated Search

1975-01-01

The preparation of accurate air quality analysis portions of highway environmental impact statements requires valid meteorological and air quality data. These data are needed, in part, to determine the regional and local wind patterns on which pollut...

Environmental Assessment: General Plan-Based Environmental Impact Analysis Process, Laughlin Air Force Base

DTIC Science & Technology

2007-05-01

BASED ENVIROMENTAL IMPACT ANALYSIS PROCESS LAUGHLIN AIR FORCE BASE, TEXAS AGENCY: 47th Flying Training Wing (FTW), Laughlin Air Force Base (AFB), Texas...8217\\ \\ \\ \\ \\\\ \\ ~ >(- \\ , ~ AOC01 \\ PS018 / WP002 \\ DP008 // WP006 \\ ~ ,/ ’----- -----·-------------~--/·/ LAUGHLIN AIR FORCE BASE ENVIROMENTAL RESTORATION

Computing The No-Escape Envelope Of A Short-Range Missile

NASA Technical Reports Server (NTRS)

Neuman, Frank

1991-01-01

Method for computing no-escape envelope of short-range air-to-air missile devised. Useful for analysis of both strategies for avoidance and strategies for attack. With modifications, also useful in analysis of control strategies for one-on-one air-to-air combat, or wherever multiple control strategies considered.

Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress.

PubMed

Jo, Kyuri; Kwon, Hawk-Bin; Kim, Sun

2014-06-01

Measuring expression levels of genes at the whole genome level can be useful for many purposes, especially for revealing biological pathways underlying specific phenotype conditions. When gene expression is measured over a time period, we have opportunities to understand how organisms react to stress conditions over time. Thus many biologists routinely measure whole genome level gene expressions at multiple time points. However, there are several technical difficulties for analyzing such whole genome expression data. In addition, these days gene expression data is often measured by using RNA-sequencing rather than microarray technologies and then analysis of expression data is much more complicated since the analysis process should start with mapping short reads and produce differentially activated pathways and also possibly interactions among pathways. In addition, many useful tools for analyzing microarray gene expression data are not applicable for the RNA-seq data. Thus a comprehensive package for analyzing time series transcriptome data is much needed. In this article, we present a comprehensive package, Time-series RNA-seq Analysis Package (TRAP), integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment. In addition to implementing useful algorithms that are not available for RNA-seq data, we extended existing pathway analysis methods, ORA and SPIA, for time series analysis and estimates statistical values for combined dataset by an advanced metric. TRAP also produces visual summary of pathway interactions. Gene expression change labeling, a practical clustering method used in TRAP, enables more accurate interpretation of the data when combined with pathway analysis. We applied our methods on a real dataset for the analysis of rice (Oryza sativa L. Japonica nipponbare) upon drought stress. The result showed that TRAP was able to detect pathways more accurately than several existing methods. TRAP is available at http://biohealth.snu.ac.kr/software/TRAP/. Copyright © 2014 Elsevier Inc. All rights reserved.

Metabolomics Coupled with Multivariate Data and Pathway Analysis on Potential Biomarkers in Gastric Ulcer and Intervention Effects of Corydalis yanhusuo Alkaloid

PubMed Central

Shuai, Wang; Yongrui, Bao; Shanshan, Guan; Bo, Liu; Lu, Chen; Lei, Wang; Xiaorong, Ran

2014-01-01

Metabolomics, the systematic analysis of potential metabolites in a biological specimen, has been increasingly applied to discovering biomarkers, identifying perturbed pathways, measuring therapeutic targets, and discovering new drugs. By analyzing and verifying the significant difference in metabolic profiles and changes of metabolite biomarkers, metabolomics enables us to better understand substance metabolic pathways which can clarify the mechanism of Traditional Chinese Medicines (TCM). Corydalis yanhusuo alkaloid (CA) is a major component of Qizhiweitong (QZWT) prescription which has been used for treating gastric ulcer for centuries and its mechanism remains unclear completely. Metabolite profiling was performed by high-performance liquid chromatography combined with time-of-flight mass spectrometry (HPLC/ESI-TOF-MS) and in conjunction with multivariate data analysis and pathway analysis. The statistic software Mass Profiller Prossional (MPP) and statistic method including ANOVA and principal component analysis (PCA) were used for discovering novel potential biomarkers to clarify mechanism of CA in treating acid injected rats with gastric ulcer. The changes in metabolic profiling were restored to their base-line values after CA treatment according to the PCA score plots. Ten different potential biomarkers and seven key metabolic pathways contributing to the treatment of gastric ulcer were discovered and identified. Among the pathways, sphingophospholipid metabolism and fatty acid metabolism related network were acutely perturbed. Quantitative real time polymerase chain reaction (RT-PCR) analysis were performed to evaluate the expression of genes related to the two pathways for verifying the above results. The results show that changed biomarkers and pathways may provide evidence to insight into drug action mechanisms and enable us to increase research productivity toward metabolomics drug discovery. PMID:24454691

A fast and simple LC-MS-based characterization of the flavonoid biosynthesis pathway for few seed(ling)s.

PubMed

Jaegle, Benjamin; Uroic, Miran Kalle; Holtkotte, Xu; Lucas, Christina; Termath, Andreas Ole; Schmalz, Hans-Günther; Bucher, Marcel; Hoecker, Ute; Hülskamp, Martin; Schrader, Andrea

2016-09-01

(Pro)anthocyanidins are synthesized by the flavonoid biosynthesis pathway with multi-layered regulatory control. Methods for the analysis of the flavonoid composition in plants are well established for different purposes. However, they typically compromise either on speed or on depth of analysis. In this work we combined and optimized different protocols to enable the analysis of the flavonoid biosynthesis pathway with as little as possible biological material. We chose core substances of this metabolic pathway that serve as a fingerprint to recognize alterations in the main branches of the pathway. We used a simplified sample preparation, two deuterated internal standards, a short and efficient LC separation, highly sensitive detection with tandem MS in multiple reaction monitoring (MRM) mode and hydrolytic release of the core substances to reduce complexity. The method was optimized for Arabidopsis thaliana seeds and seedlings. We demonstrate that one Col-0 seed/seedling is sufficient to obtain a fingerprint of the core substances of the flavonoid biosynthesis pathway. For comparative analysis of different genotypes, we suggest the use of 10 seed(lings). The analysis of Arabidopsis thaliana mutants affecting steps in the pathway revealed foreseen and unexpected alterations of the pathway. For example, HY5 was found to differentially regulate kaempferol in seeds vs. seedlings. Furthermore, our results suggest that COP1 is a master regulator of flavonoid biosynthesis in seedlings but not of flavonoid deposition in seeds. When sample numbers are high and the plant material is limited, this method effectively facilitates metabolic fingerprinting with one seed(ling), revealing shifts and differences in the pathway. Moreover the combination of extracted non-hydrolysed, extracted hydrolysed and non-extracted hydrolysed samples proved useful to deduce the class of derivative from which the individual flavonoids have been released.

Health risk assessment of PCDD/F emissions from a hazardous and medical waste incinerator in Turkey.

PubMed

Karademir, Aykan

2004-10-01

A multimedia risk assessment procedure was conducted to determine the fate and transport of polychlorinated dibenzo-p-dioxin and polychlorinated dibenzofuran (PCDD/F) emissions from the Izmit Hazardous and Medical Waste Incinerator (IZAYDAS) in Turkey and their potential health risks. Congener concentrations in ambient air and their deposition rates were determined by an air dispersion model (ISCST3). Their transfer to some plant groups and animal tissues was predicted by food chain modeling. Exposure scenarios were produced based on three receptor groups (urban, semiurban, and rural) and five subgroups determined according to ages. Daily intakes of PCDD/Fs via exposure pathways were determined based on three different emission scenarios for each group and subgroup. Estimated incremental PCDD/F doses caused by the incinerator emissions in central-tendency scenario were computed as between 2.31 x 10(-6) and 0.008 pg TEQ kg(-1) bodyweight (bw) day(-1) on average for all the receptors other than infants in all the settings, while the range was 3.01 x 10(-5)-0.081 pg TEQ kg(-1) bw day(-1) for infants. Sensitivity analysis showed that the consumption of vegetal products and their locally grown fractions are the most significant parameters in the exposure to PCDD/Fs in the area.

The effect of ventilation on indoor exposure to semivolatile organic compounds.

PubMed

Liu, C; Zhang, Y; Benning, J L; Little, J C

2015-06-01

A mechanistic model was developed to examine how natural ventilation influences residential indoor exposure to semivolatile organic compounds (SVOCs) via inhalation, dermal sorption, and dust ingestion. The effect of ventilation on indoor particle mass concentration and mass transfer at source/sink surfaces, and the enhancing effect of particles on mass transfer at source/sink surfaces are included. When air exchange rate increases from 0.6/h to 1.8/h, the steady-state SVOC (gas-phase plus particle phase with log KOA varying from 9 to 13) concentration in the idealized model decreases by about 60%. In contrast, for the same change in ventilation, the simulated indoor formaldehyde (representing volatile organic compounds) gas-phase concentration decreases by about 70%. The effect of ventilation on exposure via each pathway has a relatively insignificant association with the KOA of the SVOCs: a change of KOA from 10(9) to 10(13) results in a change of only 2-30%. Sensitivity analysis identifies the deposition rate of PM2.5 as a primary factor influencing the relationship between ventilation and exposure for SVOCs with log KOA = 13. The relationship between ventilation rate and air speed near surfaces needs to be further substantiated. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Three Dimensional Vapor Intrusion Modeling: Model Validation and Uncertainty Analysis

NASA Astrophysics Data System (ADS)

Akbariyeh, S.; Patterson, B.; Rakoczy, A.; Li, Y.

2013-12-01

Volatile organic chemicals (VOCs), such as chlorinated solvents and petroleum hydrocarbons, are prevalent groundwater contaminants due to their improper disposal and accidental spillage. In addition to contaminating groundwater, VOCs may partition into the overlying vadose zone and enter buildings through gaps and cracks in foundation slabs or basement walls, a process termed vapor intrusion. Vapor intrusion of VOCs has been recognized as a detrimental source for human exposures to potential carcinogenic or toxic compounds. The simulation of vapor intrusion from a subsurface source has been the focus of many studies to better understand the process and guide field investigation. While multiple analytical and numerical models were developed to simulate the vapor intrusion process, detailed validation of these models against well controlled experiments is still lacking, due to the complexity and uncertainties associated with site characterization and soil gas flux and indoor air concentration measurement. In this work, we present an effort to validate a three-dimensional vapor intrusion model based on a well-controlled experimental quantification of the vapor intrusion pathways into a slab-on-ground building under varying environmental conditions. Finally, a probabilistic approach based on Monte Carlo simulations is implemented to determine the probability distribution of indoor air concentration based on the most uncertain input parameters.

Adaptation Pathway of Low Impact Development Planning under Climate Change for a Sustainable Rural Community

NASA Astrophysics Data System (ADS)

Chen, P. Y.; Tung, C. P.

2016-12-01

The study focuses on developing the methodology of adaptation pathway for storm water management in a community scale. Following previous results on adaptation procedures including problem and goal setup, current risk assessment and analysis, future risk assessment and analysis, and adaptation options identification and evaluation, the study aims at analyzing adaptation pathway planning and implementation, namely the fifth step, for applying low impact development (LID). Based on the efficacy analyses of the feasible adaptation options, an adaptation pathway map can be build. Each pathway is a combination of the adaptation measures arranged in certain order. The developed adaptation pathway map visualizes the relative effectiveness and the connection of the adaptation measures. In addition, the tipping points of the system can be clearly identified and the triggers can be defined accordingly. There are multiple choices of pathways in an adaptation pathway map, which can be referred as pathway candidates. To ensure the applicability and operability, the methodology of adaptation pathway analysis is applied to a case study. Required information for developing an adaptation pathway map includes the scores of the adaptation options on the criteria, namely the effects, costs, immediacy, and side effect. Feasible adaptation options for the design case are dredging, pipeline expansion, pumping station, LID and detention pond. By ranking the options according to the criteria, LID is found dominating dredging and pumping station in this case. The information of the pathway candidates can be further used by the stakeholders to select the most suitable and promising pathway.

Algorithms on Flag Manifolds for Knowledge Discovery in N-way Arrays

DTIC Science & Technology

2015-11-20

that three of 18 subjects will become symptomatic after only 8 hours. Host pathway analysis of a human endotoxin gene expression data set revealed a 14...pathway analysis of a human endotoxin gene expression data set revealed a 14 pathway signature that identified symptomatic subjects within 2-3 hours post

A fugacity-based indoor residential pesticide fate model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bennett, Deborah H.; Furtaw, Edward J.; McKone, Thomas E.

Dermal and non-dietary pathways are potentially significant exposure pathways to pesticides used in residences. Exposure pathways include dermal contact with residues on surfaces, ingestion from hand- and object-to-mouth activities, and absorption of pesticides into food. A limited amount of data has been collected on pesticide concentrations in various residential compartments following an application. But models are needed to interpret this data and make predictions about other pesticides based on chemical properties. In this paper, we propose a mass-balance compartment model based on fugacity principles. We include air (both gas phase and aerosols), carpet, smooth flooring, and walls as model compartments.more » Pesticide concentrations on furniture and toys, and in food, are being added to the model as data becomes available. We determine the compartmental fugacity capacity and mass transfer-rate coefficient for wallboard as an example. We also present the framework and equations needed for a dynamic mass-balance model.« less

Mercury emission and plant uptake of trace elements during early stage of soil amendment using flue gas desulfurization materials.

USDA-ARS?s Scientific Manuscript database

A pilot-scale field study was carried out to investigate the distribution of Hg and other selected elements in the three potential mitigation pathways, i.e., emission to ambient air, uptake by surface vegetation (i.e., grass), and rainfall infiltration, after flue gas desulfurization (FGD) material ...

Role of photoexcited nitrogen dioxide chemistry on ozone formation and emission control strategy over the Pearl River Delta, China

EPA Science Inventory

A new hydroxyl radical formation pathway via photo-excited nitrogen dioxide chemistry is incorporated into a chemistry-only box model as well as a 3D air quality model to examine its potential role on ozone formation and emission control strategy over the Pearl River Delta region...

Variation in isotopologues of atmospheric nitric acid in passively collected samples along an air pollution gradient in southern California

Treesearch

Michael D. Bell; James O. Sickman; Andrzej Bytnerowicz; Pamela E. Padgett; Edith B. Allen

2014-01-01

The sources and oxidation pathways of atmospheric nitric acid (HNO3) can be evaluated using the isotopic signatures of oxygen (O) and nitrogen (N). This study evaluated the ability of Nylasorb nylon filters to passively collect unbiased isotopologues of atmospheric HNO3 under controlled and field conditions. Filters...

Defusing the Toxics Threat: Controlling Pesticides and Industrial Waste. Worldwatch Paper 79.

ERIC Educational Resources Information Center

Postel, Sandra

The use of pesticides in agriculture and the discarding of industrial chemical waste into the air, soil, and water constitute two major pathways of human exposure to toxic substances. It is argued that these practices release hundreds of millions of tons of potentially hazardous substances into the environment each year. Speculation continues into…

In vitro systems toxicology approach to investigate the effects of repeated cigarette smoke exposure on human buccal and gingival organotypic epithelial tissue cultures.

PubMed

Schlage, Walter K; Iskandar, Anita R; Kostadinova, Radina; Xiang, Yang; Sewer, Alain; Majeed, Shoaib; Kuehn, Diana; Frentzel, Stefan; Talikka, Marja; Geertz, Marcel; Mathis, Carole; Ivanov, Nikolai; Hoeng, Julia; Peitsch, Manuel C

2014-10-01

Smoking has been associated with diseases of the lung, pulmonary airways and oral cavity. Cytologic, genomic and transcriptomic changes in oral mucosa correlate with oral pre-neoplasia, cancer and inflammation (e.g. periodontitis). Alteration of smoking-related gene expression changes in oral epithelial cells is similar to that in bronchial and nasal epithelial cells. Using a systems toxicology approach, we have previously assessed the impact of cigarette smoke (CS) seen as perturbations of biological processes in human nasal and bronchial organotypic epithelial culture models. Here, we report our further assessment using in vitro human oral organotypic epithelium models. We exposed the buccal and gingival organotypic epithelial tissue cultures to CS at the air-liquid interface. CS exposure was associated with increased secretion of inflammatory mediators, induction of cytochrome P450s activity and overall weak toxicity in both tissues. Using microarray technology, gene-set analysis and a novel computational modeling approach leveraging causal biological network models, we identified CS impact on xenobiotic metabolism-related pathways accompanied by a more subtle alteration in inflammatory processes. Gene-set analysis further indicated that the CS-induced pathways in the in vitro buccal tissue models resembled those in the in vivo buccal biopsies of smokers from a published dataset. These findings support the translatability of systems responses from in vitro to in vivo and demonstrate the applicability of oral organotypical tissue models for an impact assessment of CS on various tissues exposed during smoking, as well as for impact assessment of reduced-risk products.

Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach

PubMed Central

Alaimo, Salvatore; Marceca, Gioacchino Paolo; Ferro, Alfredo; Pulvirenti, Alfredo

2017-01-01

In the era of network medicine, pathway analysis methods play a central role in the prediction of phenotype from high throughput experiments. In this paper, we present a network-based systems biology approach capable of extracting disease-perturbed subpathways within pathway networks in connection with expression data taken from The Cancer Genome Atlas (TCGA). Our system extends pathways with missing regulatory elements, such as microRNAs, and their interactions with genes. The framework enables the extraction, visualization, and analysis of statistically significant disease-specific subpathways through an easy to use web interface. Our analysis shows that the methodology is able to fill the gap in current techniques, allowing a more comprehensive analysis of the phenomena underlying disease states. PMID:29657291

Airport landside operations and air service

NASA Astrophysics Data System (ADS)

Mandle, P. B.; Whitlock, E. M.; Lamagna, F.; Mundy, R. A.; Oberhausen, P. J.

The following areas are discussed: airport curbside planning and design; analysis of New Orleans airport ground transportation system; time series analysis of intercity air travel volume; economic justification of air service to small communities; and general aviation and the airport and airway system (an analysis of cost allocation and recovery).

LIFE CYCLE DESIGN OF AIR INTAKE MANIFOLDS; PHASE I: 2.0 L FORD CONTOUR AIR INTAKE MANIFOLD

EPA Science Inventory

The project team applied the life cycle design methodology to the design analysis of three alternative air intake manifolds: a sand cast aluminum, brazed aluminum tubular, and nylon composite. The design analysis included a life cycle inventory analysis, environmental regulatory...

ARL Support and Analysis to the Army Public Health Command Kabul Air Quality Data Collection (Spring 2014)

DTIC Science & Technology

2016-05-01

ARL-TR-7692•MAY 2016 US Army Research Laboratory ARL Support and Analysis to the Army Public Health Command Kabul Air Quality Data Collection (Spring...return it to the originator. ARL-TR-7692•MAY 2016 US Army Research Laboratory ARL Support and Analysis to the Army Public Health Command Kabul Air Quality ...and Analysis to the Army Public Health Command Kabul Air Quality Data Collection (Spring 2014) Alan Wetmore and Thomas DeFelice ARL-TR-7692 Approved

The Influence of Summertime Convection Over Southeast Asia on Water Vapor in the Tropical Stratosphere

NASA Technical Reports Server (NTRS)

Wright, J. S.; Fu, R.; Fueglistaler, S.; Liu, Y. S.; Zhang, Y.

2011-01-01

The relative contributions of Southeast Asian convective source regions during boreal summer to water vapor in the tropical stratosphere are examined using Lagrangian trajectories. Convective sources are identified using global observations of infrared brightness temperature at high space and time resolution, and water vapor transport is simulated using advection-condensation. Trajectory simulations are driven by three different reanalysis data sets, GMAO MERRA, ERA-Interim, and NCEP/NCAR, to establish points of consistency and evaluate the sensitivity of the results to differences in the underlying meteorological fields. All ensembles indicate that Southeast Asia is a prominent boreal summer source of tropospheric air to the tropical stratosphere. Three convective source domains are identified within Southeast Asia: the Bay of Bengal and South Asian subcontinent (MON), the South China and Philippine Seas (SCS), and the Tibetan Plateau and South Slope of the Himalayas (TIB). Water vapor transport into the stratosphere from these three domains exhibits systematic differences that are related to differences in the bulk characteristics of transport. We find air emanating from SCS to be driest, from MON slightly moister, and from TIB moistest. Analysis of pathways shows that air detrained from convection over TIB is most likely to bypass the region of minimum absolute saturation mixing ratio over the equatorial western Pacific; however, the impact of this bypass mechanism on mean water vapor in the tropical stratosphere at 68 hPa is small 0.1 ppmv). This result contrasts with previously published hypotheses, and it highlights the challenge of properly quantifying fluxes of atmospheric humidity.

Reconstruction of metabolic pathways for the cattle genome

PubMed Central

Seo, Seongwon; Lewin, Harris A

2009-01-01

Background Metabolic reconstruction of microbial, plant and animal genomes is a necessary step toward understanding the evolutionary origins of metabolism and species-specific adaptive traits. The aims of this study were to reconstruct conserved metabolic pathways in the cattle genome and to identify metabolic pathways with missing genes and proteins. The MetaCyc database and PathwayTools software suite were chosen for this work because they are widely used and easy to implement. Results An amalgamated cattle genome database was created using the NCBI and Ensembl cattle genome databases (based on build 3.1) as data sources. PathwayTools was used to create a cattle-specific pathway genome database, which was followed by comprehensive manual curation for the reconstruction of metabolic pathways. The curated database, CattleCyc 1.0, consists of 217 metabolic pathways. A total of 64 mammalian-specific metabolic pathways were modified from the reference pathways in MetaCyc, and two pathways previously identified but missing from MetaCyc were added. Comparative analysis of metabolic pathways revealed the absence of mammalian genes for 22 metabolic enzymes whose activity was reported in the literature. We also identified six human metabolic protein-coding genes for which the cattle ortholog is missing from the sequence assembly. Conclusion CattleCyc is a powerful tool for understanding the biology of ruminants and other cetartiodactyl species. In addition, the approach used to develop CattleCyc provides a framework for the metabolic reconstruction of other newly sequenced mammalian genomes. It is clear that metabolic pathway analysis strongly reflects the quality of the underlying genome annotations. Thus, having well-annotated genomes from many mammalian species hosted in BioCyc will facilitate the comparative analysis of metabolic pathways among different species and a systems approach to comparative physiology. PMID:19284618

Long-range pollution transport during the MILAGRO-2006 campaign: a case study of a major Mexico City outflow event using free-floating altitude-controlled balloons

NASA Astrophysics Data System (ADS)

Voss, P. B.; Zaveri, R. A.; Flocke, F. M.; Mao, H.; Hartley, T. P.; Deamicis, P.; Deonandan, I.; Contreras-Jiménez, G.; Martínez-Antonio, O.; Figueroa Estrada, M.; Greenberg, D.; Campos, T. L.; Weinheimer, A. J.; Knapp, D. J.; Montzka, D. D.; Crounse, J. D.; Wennberg, P. O.; Apel, E.; Madronich, S.; de Foy, B.

2010-08-01

One of the major objectives of the Megacities Initiative: Local And Global Research Observations (MILAGRO-2006) campaign was to investigate the long-range transport of polluted Mexico City Metropolitan Area (MCMA) outflow and determine its downwind impacts on air quality and climate. Six research aircraft, including the National Center for Atmospheric Research (NCAR) C-130, made extensive chemical, aerosol, and radiation measurements above MCMA and more than 1000 km downwind in order to characterize the evolution of the outflow as it aged and dispersed over the Mesa Alta, Sierra Madre Oriental, Coastal Plain, and Gulf of Mexico. As part of this effort, free-floating Controlled-Meteorological (CMET) balloons, commanded to change altitude via satellite, made repeated profile measurements of winds and state variables within the advecting outflow. In this paper, we present an analysis of the data from two CMET balloons that were launched near Mexico City on the afternoon of 18 March 2006 and floated downwind with the MCMA pollution for nearly 30 h. The repeating profile measurements show the evolving structure of the outflow in considerable detail: its stability and stratification, interaction with other air masses, mixing episodes, and dispersion into the regional background. Air parcel trajectories, computed directly from the balloon wind profiles, show three transport pathways on 18-19 March: (a) high-altitude advection of the top of the MCMA mixed layer, (b) mid-level outflow over the Sierra Madre Oriental followed by decoupling and isolated transport over the Gulf of Mexico, and (c) low-level outflow with entrainment into a cleaner northwesterly jet above the Coastal Plain. The C-130 aircraft intercepted the balloon-based trajectories three times on 19 March, once along each of these pathways; in all three cases, peaks in urban tracer concentrations and LIDAR backscatter are consistent with MCMA pollution. In comparison with the transport models used in the campaign, the balloon-based trajectories appear to shear the outflow far more uniformly and decouple it from the surface, thus forming a thin but expansive polluted layer over the Gulf of Mexico that is well aligned with the aircraft observations. These results provide critical context for the extensive aircraft measurements made during the 18-19 March MCMA outflow event and may have broader implications for modelling and understanding long-range transport.

Exposure to air pollution interacts with obesogenic nutrition to induce tissue-specific response patterns.

PubMed

Pardo, Michal; Kuperman, Yael; Levin, Liron; Rudich, Assaf; Haim, Yulia; Schauer, James J; Chen, Alon; Rudich, Yinon

2018-04-20

Obesity and exposure to particular matter (PM) have become two leading global threats to public health. However, the exact mechanisms and tissue-specificity of their health effects are largely unknown. Here we investigate whether a metabolic challenge (early nutritional obesity) synergistically interacts with an environmental challenge (PM exposure) to alter genes representing key response pathways, in a tissue-specific manner. Mice subjected to 7 weeks obesogenic nutrition were exposed every other day during the final week and a half to aqueous extracts of PM collected in the city of London (UK). The expression of 61 selected genes representing key response pathways were investigated in lung, liver, white and brown adipose tissues. Principal component analysis (PCA) revealed distinct patterns of expression changes between the 4 tissues, particularly in the lungs and the liver. Surprisingly, the lung responded to the nutrition challenge. The response of these organs to the PM challenge displayed opposite patterns for some key genes, in particular, those related to the Nrf2 pathway. While the contribution to the variance in gene expression changes in mice exposed to the combined challenge were largely similar among the tissues in PCA1, PCA2 exhibited predominant contribution of inflammatory and oxidative stress responses to the variance in the lungs, and a greater contribution of autophagy genes and MAP kinases in adipose tissues. Possible involvement of alterations in DNA methylation was demonstrated by cell-type-specific responses to a methylation inhibitor. Correspondingly, the DNA methyltransferase Dnmt3a2 increased in the lungs but decreased in the liver, demonstrating potential tissue-differential synergism between nutritional and PM exposure. The results suggest that urban PM, containing dissolved metals, interacts with obesogenic nutrition to regulate diverse response pathways including inflammation and oxidative stress, in a tissue-specific manner. Tissue-differential effects on DNA methylation may underlie tissue-specific responses to key stress-response genes such as catalase and Nrf2. Copyright © 2018 Elsevier Ltd. All rights reserved.

Text mining-based in silico drug discovery in oral mucositis caused by high-dose cancer therapy.

PubMed

Kirk, Jon; Shah, Nirav; Noll, Braxton; Stevens, Craig B; Lawler, Marshall; Mougeot, Farah B; Mougeot, Jean-Luc C

2018-08-01

Oral mucositis (OM) is a major dose-limiting side effect of chemotherapy and radiation used in cancer treatment. Due to the complex nature of OM, currently available drug-based treatments are of limited efficacy. Our objectives were (i) to determine genes and molecular pathways associated with OM and wound healing using computational tools and publicly available data and (ii) to identify drugs formulated for topical use targeting the relevant OM molecular pathways. OM and wound healing-associated genes were determined by text mining, and the intersection of the two gene sets was selected for gene ontology analysis using the GeneCodis program. Protein interaction network analysis was performed using STRING-db. Enriched gene sets belonging to the identified pathways were queried against the Drug-Gene Interaction database to find drug candidates for topical use in OM. Our analysis identified 447 genes common to both the "OM" and "wound healing" text mining concepts. Gene enrichment analysis yielded 20 genes representing six pathways and targetable by a total of 32 drugs which could possibly be formulated for topical application. A manual search on ClinicalTrials.gov confirmed no relevant pathway/drug candidate had been overlooked. Twenty-five of the 32 drugs can directly affect the PTGS2 (COX-2) pathway, the pathway that has been targeted in previous clinical trials with limited success. Drug discovery using in silico text mining and pathway analysis tools can facilitate the identification of existing drugs that have the potential of topical administration to improve OM treatment.

Plant Reactome: a resource for plant pathways and comparative analysis.

PubMed

Naithani, Sushma; Preece, Justin; D'Eustachio, Peter; Gupta, Parul; Amarasinghe, Vindhya; Dharmawardhana, Palitha D; Wu, Guanming; Fabregat, Antonio; Elser, Justin L; Weiser, Joel; Keays, Maria; Fuentes, Alfonso Munoz-Pomer; Petryszak, Robert; Stein, Lincoln D; Ware, Doreen; Jaiswal, Pankaj

2017-01-04

Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Analysis of Differentially Expressed Genes and Signaling Pathways Related to Intramuscular Fat Deposition in Skeletal Muscle of Sex-Linked Dwarf Chickens

PubMed Central

Ye, Yaqiong; Lin, Shumao; Mu, Heping; Tang, Xiaohong; Ou, Yangdan; Chen, Jian; Ma, Yongjiang; Li, Yugu

2014-01-01

Intramuscular fat (IMF) plays an important role in meat quality. However, the molecular mechanisms underlying IMF deposition in skeletal muscle have not been addressed for the sex-linked dwarf (SLD) chicken. In this study, potential candidate genes and signaling pathways related to IMF deposition in chicken leg muscle tissue were characterized using gene expression profiling of both 7-week-old SLD and normal chickens. A total of 173 differentially expressed genes (DEGs) were identified between the two breeds. Subsequently, 6 DEGs related to lipid metabolism or muscle development were verified in each breed based on gene ontology (GO) analysis. In addition, KEGG pathway analysis of DEGs indicated that some of them (GHR, SOCS3, and IGF2BP3) participate in adipocytokine and insulin signaling pathways. To investigate the role of the above signaling pathways in IMF deposition, the gene expression of pathway factors and other downstream genes were measured by using qRT-PCR and Western blot analyses. Collectively, the results identified potential candidate genes related to IMF deposition and suggested that IMF deposition in skeletal muscle of SLD chicken is regulated partially by pathways of adipocytokine and insulin and other downstream signaling pathways (TGF-β/SMAD3 and Wnt/catenin-β pathway). PMID:24757673

Screening for Key Pathways Associated with the Development of Osteoporosis by Bioinformatics Analysis

PubMed Central

Liu, Yanqing; Wang, Yueqiu; Zhang, Yanxia; Liu, Zhiyong; Xiang, Hongfei; Peng, Xianbo

2017-01-01

Objectives. We aimed to find the key pathways associated with the development of osteoporosis. Methods. We downloaded expression profile data of GSE35959 and analyzed the differentially expressed genes (DEGs) in 3 comparison groups (old_op versus middle, old_op versus old, and old_op versus senescent). KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses were carried out. Besides, Venn diagram analysis and gene functional interaction (FI) network analysis were performed. Results. Totally 520 DEGs, 966 DEGs, and 709 DEGs were obtained in old_op versus middle, old_op versus old, and old_op versus senescent groups, respectively. Lysosome pathway was the significantly enriched pathways enriched by intersection genes. The pathways enriched by subnetwork modules suggested that mitotic metaphase and anaphase and signaling by Rho GTPases in module 1 had more proteins from module. Conclusions. Lysosome pathway, mitotic metaphase and anaphase, and signaling by Rho GTPases may be involved in the development of osteoporosis. Furthermore, Rho GTPases may regulate the balance of bone resorption and bone formation via controlling osteoclast and osteoblast. These 3 pathways may be regarded as the treatment targets for osteoporosis. PMID:28466021

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hill, David P.; D’Eustachio, Peter; Berardini, Tanya Z.

The concept of a biological pathway, an ordered sequence of molecular transformations, is used to collect and represent molecular knowledge for a broad span of organismal biology. Representations of biomedical pathways typically are rich but idiosyncratic presentations of organized knowledge about individual pathways. Meanwhile, biomedical ontologies and associated annotation files are powerful tools that organize molecular information in a logically rigorous form to support computational analysis. The Gene Ontology (GO), representing Molecular Functions, Biological Processes and Cellular Components, incorporates many aspects of biological pathways within its ontological representations. Here we present a methodology for extending and refining the classes inmore » the GO for more comprehensive, consistent and integrated representation of pathways, leveraging knowledge embedded in current pathway representations such as those in the Reactome Knowledgebase and MetaCyc. With carbohydrate metabolic pathways as a use case, we discuss how our representation supports the integration of variant pathway classes into a unified ontological structure that can be used for data comparison and analysis.« less

Mining disease fingerprints from within genetic pathways.

PubMed

Nabhan, Ahmed Ragab; Sarkar, Indra Neil

2012-01-01

Mining biological networks can be an effective means to uncover system level knowledge out of micro level associations, such as encapsulated in genetic pathways. Analysis of human disease genetic pathways can lead to the identification of major mechanisms that may underlie disorders at an abstract functional level. The focus of this study was to develop an approach for structural pattern analysis and classification of genetic pathways of diseases. A probabilistic model was developed to capture characteristic components ('fingerprints') of functionally annotated pathways. A probability estimation procedure of this model searched for fingerprints in each disease pathway while improving probability estimates of model parameters. The approach was evaluated on data from the Kyoto Encyclopedia of Genes and Genomes (consisting of 56 pathways across seven disease categories). Based on the achieved average classification accuracy of up to ~77%, the findings suggest that these fingerprints may be used for classification and discovery of genetic pathways.

Mining Disease Fingerprints From Within Genetic Pathways

PubMed Central

Nabhan, Ahmed Ragab; Sarkar, Indra Neil

2012-01-01

Mining biological networks can be an effective means to uncover system level knowledge out of micro level associations, such as encapsulated in genetic pathways. Analysis of human disease genetic pathways can lead to the identification of major mechanisms that may underlie disorders at an abstract functional level. The focus of this study was to develop an approach for structural pattern analysis and classification of genetic pathways of diseases. A probabilistic model was developed to capture characteristic components (‘fingerprints’) of functionally annotated pathways. A probability estimation procedure of this model searched for fingerprints in each disease pathway while improving probability estimates of model parameters. The approach was evaluated on data from the Kyoto Encyclopedia of Genes and Genomes (consisting of 56 pathways across seven disease categories). Based on the achieved average classification accuracy of up to ∼77%, the findings suggest that these fingerprints may be used for classification and discovery of genetic pathways. PMID:23304411

Influence of firebed temperature on inorganic particle emissions in a residential wood pellet boiler

NASA Astrophysics Data System (ADS)

Gehrig, Matthias; Jaeger, Dirk; Pelz, Stefan K.; Weissinger, Alexander; Groll, Andreas; Thorwarth, Harald; Haslinger, Walter

2016-07-01

The temperature-dependent release of inorganic elements is the first step of the main formation pathway of particle emissions in automatically fired biomass burners. To investigate this step, a residential pellet boiler with an underfeed-burner was equipped with a direct firebed cooling. This test setup enabled decreased firebed temperatures without affecting further parameters like air flow rates or oxygen content in the firebed. A reduction of particle emissions in PM1-fraction at activated firebed cooling was found by impactor measurement and by optical particle counter. The affected particles were found in the size range <0.3 μm and have been composed mainly of potassium chloride (KCl). The chemical analysis of PM1 and boiler ash showed no statistically significant differences due to the firebed cooling. Therefore, our results indicate that the direct firebed cooling influenced the release of potassium (K) without affecting other chemical reactions.

pyhector: A Python interface for the simple climate model Hector

DOE PAGES

Willner, Sven N.; Hartin, Corinne; Gieseke, Robert

2017-04-01

Here, pyhector is a Python interface for the simple climate model Hector (Hartin et al. 2015) developed in C++. Simple climate models like Hector can, for instance, be used in the analysis of scenarios within integrated assessment models like GCAM1, in the emulation of complex climate models, and in uncertainty analyses. Hector is an open-source, object oriented, simple global climate carbon cycle model. Its carbon cycle consists of a one pool atmosphere, three terrestrial pools which can be broken down into finer biomes or regions, and four carbon pools in the ocean component. The terrestrial carbon cycle includes primary productionmore » and respiration fluxes. The ocean carbon cycle circulates carbon via a simplified thermohaline circulation, calculating air-sea fluxes as well as the marine carbonate system. The model input is time series of greenhouse gas emissions; as example scenarios for these the Pyhector package contains the Representative Concentration Pathways (RCPs)2.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Willner, Sven N.; Hartin, Corinne; Gieseke, Robert

Here, pyhector is a Python interface for the simple climate model Hector (Hartin et al. 2015) developed in C++. Simple climate models like Hector can, for instance, be used in the analysis of scenarios within integrated assessment models like GCAM1, in the emulation of complex climate models, and in uncertainty analyses. Hector is an open-source, object oriented, simple global climate carbon cycle model. Its carbon cycle consists of a one pool atmosphere, three terrestrial pools which can be broken down into finer biomes or regions, and four carbon pools in the ocean component. The terrestrial carbon cycle includes primary productionmore » and respiration fluxes. The ocean carbon cycle circulates carbon via a simplified thermohaline circulation, calculating air-sea fluxes as well as the marine carbonate system. The model input is time series of greenhouse gas emissions; as example scenarios for these the Pyhector package contains the Representative Concentration Pathways (RCPs)2.« less

Systems Genetics Analysis of GWAS reveals Novel Associations between Key Biological Processes and Coronary Artery Disease

PubMed Central

Ghosh, Sujoy; Vivar, Juan; Nelson, Christopher P; Willenborg, Christina; Segrè, Ayellet V; Mäkinen, Ville-Petteri; Nikpay, Majid; Erdmann, Jeannette; Blankenberg, Stefan; O'Donnell, Christopher; März, Winfried; Laaksonen, Reijo; Stewart, Alexandre FR; Epstein, Stephen E; Shah, Svati H; Granger, Christopher B; Hazen, Stanley L; Kathiresan, Sekar; Reilly, Muredach P; Yang, Xia; Quertermous, Thomas; Samani, Nilesh J; Schunkert, Heribert; Assimes, Themistocles L; McPherson, Ruth

2016-01-01

Objective Genome-wide association (GWA) studies have identified multiple genetic variants affecting the risk of coronary artery disease (CAD). However, individually these explain only a small fraction of the heritability of CAD and for most, the causal biological mechanisms remain unclear. We sought to obtain further insights into potential causal processes of CAD by integrating large-scale GWA data with expertly curated databases of core human pathways and functional networks. Approaches and Results Employing pathways (gene sets) from Reactome, we carried out a two-stage gene set enrichment analysis strategy. From a meta-analyzed discovery cohort of 7 CADGWAS data sets (9,889 cases/11,089 controls), nominally significant gene-sets were tested for replication in a meta-analysis of 9 additional studies (15,502 cases/55,730 controls) from the CARDIoGRAM Consortium. A total of 32 of 639 Reactome pathways tested showed convincing association with CAD (replication p<0.05). These pathways resided in 9 of 21 core biological processes represented in Reactome, and included pathways relevant to extracellular matrix integrity, innate immunity, axon guidance, and signaling by PDRF, NOTCH, and the TGF-β/SMAD receptor complex. Many of these pathways had strengths of association comparable to those observed in lipid transport pathways. Network analysis of unique genes within the replicated pathways further revealed several interconnected functional and topologically interacting modules representing novel associations (e.g. semaphorin regulated axonal guidance pathway) besides confirming known processes (lipid metabolism). The connectivity in the observed networks was statistically significant compared to random networks (p<0.001). Network centrality analysis (‘degree’ and ‘betweenness’) further identified genes (e.g. NCAM1, FYN, FURIN etc.) likely to play critical roles in the maintenance and functioning of several of the replicated pathways. Conclusions These findings provide novel insights into how genetic variation, interpreted in the context of biological processes and functional interactions among genes, may help define the genetic architecture of CAD. PMID:25977570

Coherent changes of wintertime surface air temperatures over North Asia and North America.

PubMed

Yu, Bin; Lin, Hai

2018-03-29

The surface temperature variance and its potential change with global warming are most prominent in winter over Northern Hemisphere mid-high latitudes. Consistent wintertime surface temperature variability has been observed over large areas in Eurasia and North America on a broad range of time scales. However, it remains a challenge to quantify where and how the coherent change of temperature anomalies occur over the two continents. Here we demonstrate the coherent change of wintertime surface temperature anomalies over North Asia and the central-eastern parts of North America for the period from 1951 to 2015. This is supported by the results from the empirical orthogonal function analysis of surface temperature and temperature trend anomalies over the Northern Hemisphere extratropical lands and the timeseries analysis of the regional averaged temperature anomalies over North Asia and the Great Plains and Great Lakes. The Asian-Bering-North American (ABNA) teleconnection provides a pathway to connect the regional temperature anomalies over the two continents. The ABNA is also responsible for the decadal variation of the temperature relationship between North Asia and North America.

How does the wetting dynamics affect capillary trapping in heterogeneous soil: Neutron imaging study

NASA Astrophysics Data System (ADS)

Sacha, Jan; Snehota, Michal; Trtik, Pavel; Vontobel, Peter

2017-04-01

The wetting dynamics of the water infiltration into a porous soil system has a strong influence on the amount of entrapped air inside the soil. Simultaneously, a higher volume of entrapped air obstructs a water flow in the medium. This effect is more noticeable in soils with preferential pathways because the soil matrix has a higher capillary forces and therefore the air is accumulated in preferential pathways. In the presented study, two experiments were conducted on the same sample. The first experiment was performed under the constant water level condition (CWL) and the second experiment was carried out under the constant water flux condition (CWF) at the top of the sample. The sample was composed of coarse and medium coarse fractions of sand and fine porous ceramics. Materials were packed into the quartz glass column of the inner diameter of 29 mm. The coarse sand represented a highly conductive region connected from the top to the bottom of the sample with the exception of three thin (2-3 mm) separation layers made up of the medium coarse sand. Three discs of fine ceramics formed slow flow regions. Infiltration experiments were monitored by neutron radiography at two different beamlines to produce two-dimensional (2D) projections. The CWL experiment was monitored at NEUTRA station with an acquisition time of 16 seconds per projection and the CWF experiment was visualized at BOA station with an acquisition time of 0.25 seconds per projection. Both stations are located at the Paul Scherrer Institut, Switzerland. The acquired radiograms of the dry sample were subtracted from all subsequent radiograms to determine the water thickness in projections. From series of corrected radiograms taken at the different angles three-dimensional (3D) image was reconstructed for steady state stage of the CWL experiment and for the entire CWF experiment. Then the series of 3D images mapped the wetting of the porous system over the corresponding phase of infiltration process. The results show a higher steady state infiltration rate during the CWL experiment. In this case, the air was mostly pushed out from the sample by the moving wetting front. The infiltration rate was continuously decreasing during the infiltration up to the value of steady state infiltration rate. When the wetting front has reached the bottom of the sample the air was moving from matrix domain to preferential domain. Infiltration rate was still higher than during CWF. On the contrary, during the CWF the water infiltrated into the fine ceramics first and then into the medium coarse sand attracted by forces that were stronger in comparison to the coarse sand. Due to this effect a significant amount of air was trapped in preferential pathways, and consequently blocked the water flow primarily due to the presence of medium coarse sand regions.

Climate change impacts on human health over Europe through its effect on air quality.

PubMed

Doherty, Ruth M; Heal, Mathew R; O'Connor, Fiona M

2017-12-05

This review examines the current literature on the effects of future emissions and climate change on particulate matter (PM) and O 3 air quality and on the consequent health impacts, with a focus on Europe. There is considerable literature on the effects of climate change on O 3 but fewer studies on the effects of climate change on PM concentrations. Under the latest Intergovernmental Panel on Climate Change (IPCC) 5th assessment report (AR5) Representative Concentration Pathways (RCPs), background O 3 entering Europe is expected to decrease under most scenarios due to higher water vapour concentrations in a warmer climate. However, under the extreme pathway RCP8.5 higher (more than double) methane (CH 4 ) abundances lead to increases in background O 3 that offset the O 3 decrease due to climate change especially for the 2100 period. Regionally, in polluted areas with high levels of nitrogen oxides (NO x ), elevated surface temperatures and humidities yield increases in surface O 3 - termed the O 3 climate penalty - especially in southern Europe. The O 3 response is larger for metrics that represent the higher end of the O 3 distribution, such as daily maximum O 3 . Future changes in PM concentrations due to climate change are much less certain, although several recent studies also suggest a PM climate penalty due to high temperatures and humidity and reduced precipitation in northern mid-latitude land regions in 2100.A larger number of studies have examined both future climate and emissions changes under the RCP scenarios. Under these pathways the impact of emission changes on air quality out to the 2050s will be larger than that due to climate change, because of large reductions in emissions of O 3 and PM pollutant precursor emissions and the more limited climate change response itself. Climate change will also affect climate extreme events such as heatwaves. Air pollution episodes are associated with stagnation events and sometimes heat waves. Air quality during the 2003 heatwave over Europe has been examined in numerous studies and mechanisms for enhancing O 3 have been identified.There are few studies on health effects associated with climate change impacts alone on air quality, but these report higher O 3 -related health burdens in polluted populated regions and greater PM 2.5 health burdens in these emission regions. Studies that examine the combined impacts of climate change and anthropogenic emissions change under the RCP scenarios report reductions in global and European premature O 3 -respiratory related and PM mortalities arising from the large decreases in precursor emissions. Under RCP 8.5 the large increase in CH 4 leads to global and European excess O 3 -respiratory related mortalities in 2100. For future health effects, besides uncertainty in future O 3 and particularly PM concentrations, there is also uncertainty in risk estimates such as effect modification by temperature on pollutant-response relationships and potential future adaptation that would alter exposure risk.

[Design and implementation of online statistical analysis function in information system of air pollution and health impact monitoring].

PubMed

Lü, Yiran; Hao, Shuxin; Zhang, Guoqing; Liu, Jie; Liu, Yue; Xu, Dongqun

2018-01-01

To implement the online statistical analysis function in information system of air pollution and health impact monitoring, and obtain the data analysis information real-time. Using the descriptive statistical method as well as time-series analysis and multivariate regression analysis, SQL language and visual tools to implement online statistical analysis based on database software. Generate basic statistical tables and summary tables of air pollution exposure and health impact data online; Generate tendency charts of each data part online and proceed interaction connecting to database; Generate butting sheets which can lead to R, SAS and SPSS directly online. The information system air pollution and health impact monitoring implements the statistical analysis function online, which can provide real-time analysis result to its users.

Vertically uniform formation pathways of tropospheric sulfate aerosols in East China detected from triple stable oxygen and radiogenic sulfur isotopes

NASA Astrophysics Data System (ADS)

Lin, Mang; Biglari, Saman; Zhang, Zhisheng; Crocker, Daniel; Tao, Jun; Su, Binbin; Liu, Lanzhong; Thiemens, Mark H.

2017-05-01

Sulfate aerosols (SO42-) in the continental outflow from East China significantly alter the atmospheric sulfur budget across the Pacific Rim, but its formation pathways, especially in the free troposphere (FT), remain poorly understood. Here we analyze stable oxygen (δ17O and δ18O) and radiogenic sulfur (35S) isotopes in SO42- collected at a mountain site in East China to investigate SO42- formation pathways at varying altitudes. We find that Δ17O (=δ17O-0.52 × δ18O) in SO42- is not correlated with 35S (a direct measure of high-altitude air masses). This pattern notably differs from the currently known 35S-Δ17O relation. The result implies that the formation pathway of tropospheric SO42- in East China is vertically uniform, likely due to large emissions and active convection in this region. Our measurements provide unambiguous isotopic constraints for reducing uncertainties in modeling SO42- in the FT over East China, which greatly affects regional climate but current models fail to accurately estimate.

Modeling the optimal central carbon metabolic pathways under feedback inhibition using flux balance analysis.

PubMed

De, Rajat K; Tomar, Namrata

2012-12-01

Metabolism is a complex process for energy production for cellular activity. It consists of a cascade of reactions that form a highly branched network in which the product of one reaction is the reactant of the next reaction. Metabolic pathways efficiently produce maximal amount of biomass while maintaining a steady-state behavior. The steady-state activity of such biochemical pathways necessarily incorporates feedback inhibition of the enzymes. This observation motivates us to incorporate feedback inhibition for modeling the optimal activity of metabolic pathways using flux balance analysis (FBA). We demonstrate the effectiveness of the methodology on a synthetic pathway with and without feedback inhibition. Similarly, for the first time, the Central Carbon Metabolic (CCM) pathways of Saccharomyces cerevisiae and Homo sapiens have been modeled and compared based on the above understanding. The optimal pathway, which maximizes the amount of the target product(s), is selected from all those obtained by the proposed method. For this, we have observed the concentration of the product inhibited enzymes of CCM pathway and its influence on its corresponding metabolite/substrate. We have also studied the concentration of the enzymes which are responsible for the synthesis of target products. We further hypothesize that an optimal pathway would opt for higher flux rate reactions. In light of these observations, we can say that an optimal pathway should have lower enzyme concentration and higher flux rates. Finally, we demonstrate the superiority of the proposed method by comparing it with the extreme pathway analysis.

Rapid evolution of piRNA pathway in the teleost fish: implication for an adaptation to transposon diversity.

PubMed

Yi, Minhan; Chen, Feng; Luo, Majing; Cheng, Yibin; Zhao, Huabin; Cheng, Hanhua; Zhou, Rongjia

2014-05-19

The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This article unveils evolutionary scene of piRNA pathway and its association with diverse transposons by systematically comparative analysis on diverse teleost fish genomes. Selective pressure analysis on piRNA pathway and miRNA/siRNA (microRNA/small interfering RNA) pathway genes between teleosts and mammals showed an accelerated evolution of piRNA pathway genes in the teleost lineages, and positive selection on functional PAZ (Piwi/Ago/Zwille) and Tudor domains involved in the Piwi-piRNA/Tudor interaction, suggesting that the amino acid substitutions are adaptive to their functions in piRNA pathway in the teleost fish species. Notably five piRNA pathway genes evolved faster in the swamp eel, a kind of protogynous hermaphrodite fish, than the other teleosts, indicating a differential evolution of piRNA pathway between the swamp eel and other gonochoristic fishes. In addition, genome-wide analysis showed higher diversity of transposons in the teleost fish species compared with mammals. Our results suggest that rapidly evolved piRNA pathway in the teleost fish is likely to be involved in the adaption to transposon diversity. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A Method for Gene-Based Pathway Analysis Using Genomewide Association Study Summary Statistics Reveals Nine New Type 1 Diabetes Associations

PubMed Central

Evangelou, Marina; Smyth, Deborah J; Fortune, Mary D; Burren, Oliver S; Walker, Neil M; Guo, Hui; Onengut-Gumuscu, Suna; Chen, Wei-Min; Concannon, Patrick; Rich, Stephen S; Todd, John A; Wallace, Chris

2014-01-01

Pathway analysis can complement point-wise single nucleotide polymorphism (SNP) analysis in exploring genomewide association study (GWAS) data to identify specific disease-associated genes that can be candidate causal genes. We propose a straightforward methodology that can be used for conducting a gene-based pathway analysis using summary GWAS statistics in combination with widely available reference genotype data. We used this method to perform a gene-based pathway analysis of a type 1 diabetes (T1D) meta-analysis GWAS (of 7,514 cases and 9,045 controls). An important feature of the conducted analysis is the removal of the major histocompatibility complex gene region, the major genetic risk factor for T1D. Thirty-one of the 1,583 (2%) tested pathways were identified to be enriched for association with T1D at a 5% false discovery rate. We analyzed these 31 pathways and their genes to identify SNPs in or near these pathway genes that showed potentially novel association with T1D and attempted to replicate the association of 22 SNPs in additional samples. Replication P-values were skewed () with 12 of the 22 SNPs showing . Support, including replication evidence, was obtained for nine T1D associated variants in genes ITGB7 (rs11170466, ), NRP1 (rs722988, ), BAD (rs694739, ), CTSB (rs1296023, ), FYN (rs11964650, ), UBE2G1 (rs9906760, ), MAP3K14 (rs17759555, ), ITGB1 (rs1557150, ), and IL7R (rs1445898, ). The proposed methodology can be applied to other GWAS datasets for which only summary level data are available. PMID:25371288

Pathway-Based Kernel Boosting for the Analysis of Genome-Wide Association Studies

PubMed Central

Manitz, Juliane; Burger, Patricia; Amos, Christopher I.; Chang-Claude, Jenny; Wichmann, Heinz-Erich; Kneib, Thomas; Bickeböller, Heike

2017-01-01

The analysis of genome-wide association studies (GWAS) benefits from the investigation of biologically meaningful gene sets, such as gene-interaction networks (pathways). We propose an extension to a successful kernel-based pathway analysis approach by integrating kernel functions into a powerful algorithmic framework for variable selection, to enable investigation of multiple pathways simultaneously. We employ genetic similarity kernels from the logistic kernel machine test (LKMT) as base-learners in a boosting algorithm. A model to explain case-control status is created iteratively by selecting pathways that improve its prediction ability. We evaluated our method in simulation studies adopting 50 pathways for different sample sizes and genetic effect strengths. Additionally, we included an exemplary application of kernel boosting to a rheumatoid arthritis and a lung cancer dataset. Simulations indicate that kernel boosting outperforms the LKMT in certain genetic scenarios. Applications to GWAS data on rheumatoid arthritis and lung cancer resulted in sparse models which were based on pathways interpretable in a clinical sense. Kernel boosting is highly flexible in terms of considered variables and overcomes the problem of multiple testing. Additionally, it enables the prediction of clinical outcomes. Thus, kernel boosting constitutes a new, powerful tool in the analysis of GWAS data and towards the understanding of biological processes involved in disease susceptibility. PMID:28785300

Pathway-Based Kernel Boosting for the Analysis of Genome-Wide Association Studies.

PubMed

Friedrichs, Stefanie; Manitz, Juliane; Burger, Patricia; Amos, Christopher I; Risch, Angela; Chang-Claude, Jenny; Wichmann, Heinz-Erich; Kneib, Thomas; Bickeböller, Heike; Hofner, Benjamin

2017-01-01

The analysis of genome-wide association studies (GWAS) benefits from the investigation of biologically meaningful gene sets, such as gene-interaction networks (pathways). We propose an extension to a successful kernel-based pathway analysis approach by integrating kernel functions into a powerful algorithmic framework for variable selection, to enable investigation of multiple pathways simultaneously. We employ genetic similarity kernels from the logistic kernel machine test (LKMT) as base-learners in a boosting algorithm. A model to explain case-control status is created iteratively by selecting pathways that improve its prediction ability. We evaluated our method in simulation studies adopting 50 pathways for different sample sizes and genetic effect strengths. Additionally, we included an exemplary application of kernel boosting to a rheumatoid arthritis and a lung cancer dataset. Simulations indicate that kernel boosting outperforms the LKMT in certain genetic scenarios. Applications to GWAS data on rheumatoid arthritis and lung cancer resulted in sparse models which were based on pathways interpretable in a clinical sense. Kernel boosting is highly flexible in terms of considered variables and overcomes the problem of multiple testing. Additionally, it enables the prediction of clinical outcomes. Thus, kernel boosting constitutes a new, powerful tool in the analysis of GWAS data and towards the understanding of biological processes involved in disease susceptibility.

Systems Genetics Analysis of Genome-Wide Association Study Reveals Novel Associations Between Key Biological Processes and Coronary Artery Disease.

PubMed

Ghosh, Sujoy; Vivar, Juan; Nelson, Christopher P; Willenborg, Christina; Segrè, Ayellet V; Mäkinen, Ville-Petteri; Nikpay, Majid; Erdmann, Jeannette; Blankenberg, Stefan; O'Donnell, Christopher; März, Winfried; Laaksonen, Reijo; Stewart, Alexandre F R; Epstein, Stephen E; Shah, Svati H; Granger, Christopher B; Hazen, Stanley L; Kathiresan, Sekar; Reilly, Muredach P; Yang, Xia; Quertermous, Thomas; Samani, Nilesh J; Schunkert, Heribert; Assimes, Themistocles L; McPherson, Ruth

2015-07-01

Genome-wide association studies have identified multiple genetic variants affecting the risk of coronary artery disease (CAD). However, individually these explain only a small fraction of the heritability of CAD and for most, the causal biological mechanisms remain unclear. We sought to obtain further insights into potential causal processes of CAD by integrating large-scale GWA data with expertly curated databases of core human pathways and functional networks. Using pathways (gene sets) from Reactome, we carried out a 2-stage gene set enrichment analysis strategy. From a meta-analyzed discovery cohort of 7 CAD genome-wide association study data sets (9889 cases/11 089 controls), nominally significant gene sets were tested for replication in a meta-analysis of 9 additional studies (15 502 cases/55 730 controls) from the Coronary ARtery DIsease Genome wide Replication and Meta-analysis (CARDIoGRAM) Consortium. A total of 32 of 639 Reactome pathways tested showed convincing association with CAD (replication P<0.05). These pathways resided in 9 of 21 core biological processes represented in Reactome, and included pathways relevant to extracellular matrix (ECM) integrity, innate immunity, axon guidance, and signaling by PDRF (platelet-derived growth factor), NOTCH, and the transforming growth factor-β/SMAD receptor complex. Many of these pathways had strengths of association comparable to those observed in lipid transport pathways. Network analysis of unique genes within the replicated pathways further revealed several interconnected functional and topologically interacting modules representing novel associations (eg, semaphoring-regulated axonal guidance pathway) besides confirming known processes (lipid metabolism). The connectivity in the observed networks was statistically significant compared with random networks (P<0.001). Network centrality analysis (degree and betweenness) further identified genes (eg, NCAM1, FYN, FURIN, etc) likely to play critical roles in the maintenance and functioning of several of the replicated pathways. These findings provide novel insights into how genetic variation, interpreted in the context of biological processes and functional interactions among genes, may help define the genetic architecture of CAD. © 2015 American Heart Association, Inc.

Impact of air exposure and surface chemistry on Li-Li 7La 3Zr 2O 12 interfacial resistance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharafi, Asma; Yu, Seungho; Naguib, Michael

Li 7La 3Zr 2O 12 (LLZO) is a promising solid-state electrolyte that could enable solid-state-batteries (SSB) employing metallic Li anodes. For a SSB to be viable, the stability and charge transfer kinetics at the Li–LLZO interface should foster facile plating and stripping of Li. Contrary to these goals, recent studies have reported high Li–LLZO interfacial resistance which was attributed to a contamination layer that forms upon exposure of LLZO to air. This study clarifies the mechanisms and consequences associated with air exposure of LLZO; additionally, strategies to minimize these effects are described. First-principles calculations reveal that LLZO readily reacts withmore » humid air; the most favorable reaction pathway involves protonation of LLZO and formation of Li2CO3. X-ray photoelectron spectroscopy, scanning electron microscopy, Raman spectroscopy, and transmission electron microscopy were used to characterize the surface and subsurface chemistry of LLZO as a function of relative humidity and exposure time. Additionally, electrochemical impedance spectroscopy was used to measure the Li–LLZO interfacial resistance as a function of surface contamination. These data indicate that air exposure-induced contamination impacts the interfacial resistance significantly, when exposure time exceeds 24 h. The results of this study provide valuable insight into the sensitivity of LLZO to air and how the effects of air contamination can be reversed.« less

Chronic effects of air pollution on respiratory health in Southern California children: findings from the Southern California Children's Health Study.

PubMed

Chen, Zhanghua; Salam, Muhammad T; Eckel, Sandrah P; Breton, Carrie V; Gilliland, Frank D

2015-01-01

Outdoor air pollution is one of the leading contributors to adverse respiratory health outcomes in urban areas around the world. Children are highly sensitive to the adverse effects of air pollution due to their rapidly growing lungs, incomplete immune and metabolic functions, patterns of ventilation and high levels of outdoor activity. The Children's Health Study (CHS) is a continuing series of longitudinal studies that first began in 1993 and has focused on demonstrating the chronic impacts of air pollution on respiratory illnesses from early childhood through adolescence. A large body of evidence from the CHS has documented that exposures to both regional ambient air and traffic-related pollutants are associated with increased asthma prevalence, new-onset asthma, risk of bronchitis and wheezing, deficits of lung function growth, and airway inflammation. These associations may be modulated by key genes involved in oxidative-nitrosative stress pathways via gene-environment interactions. Despite successful efforts to reduce pollution over the past 40 years, air pollution at the current levels still brings many challenges to public health. To further ameliorate adverse health effects attributable to air pollution, many more toxic pollutants may require regulation and control of motor vehicle emissions and other combustion sources may need to be strengthened. Individual interventions based on personal susceptibility may be needed to protect children's health while control measures are being implemented.

How Will Air Quality Change in South Asia by 2050?

NASA Astrophysics Data System (ADS)

Kumar, Rajesh; Barth, Mary C.; Pfister, G. G.; Delle Monache, L.; Lamarque, J. F.; Archer-Nicholls, S.; Tilmes, S.; Ghude, S. D.; Wiedinmyer, C.; Naja, M.; Walters, S.

2018-02-01

Exposure to unhealthy air causes millions of premature deaths and damages crops sufficient to feed a large portion of the South Asian population every year. However, little is known about how future air quality in South Asia will respond to changing human activities. Here we examine the combined effect of changes in climate and air pollutant emissions projected by the Representative Concentration Pathways (RCP) 8.5 and RCP6.0 on air quality of South Asia in 2050 using a state-of-the-science Nested Regional Climate model with Chemistry (NRCM-Chem). RCP8.5 and RCP6.0 are selected to represent scenarios of highest and lowest air pollution in South Asia by 2050. NRCM-Chem shows the ability to capture observed key features of variability in meteorological parameters, ozone and related gases, and aerosols. NRCM-Chem results show that surface ozone and particulate matter of less than 2.5 μm in diameter will increase significantly by midcentury in South Asia under the RCP8.5 but remain similar to present day under RCP6.0. No RCP suggest an improvement in air pollution in South Asia by midcentury. Under RCP8.5, the frequency of air pollution events is predicted to increase by 20-120 days per year in 2050 compared to the present-day conditions, with particulate matter of less than 2.5 μm in diameter predicted to breach the World Health Organization ambient air quality guidelines on an almost daily basis in many parts of South Asia. These results indicate that while the RCP scenarios project a global improvement in air quality, they generally result in degrading air quality in South Asia.

Identification of Significant Gene Signatures and Prognostic Biomarkers for Patients With Cervical Cancer by Integrated Bioinformatic Methods

PubMed Central

Li, Xiaofang; Tian, Run; Gao, Hugh; Yan, Feng; Ying, Le; Yang, Yongkang; Yang, Pei

2018-01-01

Cervical cancer is the leading cause of death with gynecological malignancies. We aimed to explore the molecular mechanism of carcinogenesis and biomarkers for cervical cancer by integrated bioinformatic analysis. We employed RNA-sequencing details of 254 cervical squamous cell carcinomas and 3 normal samples from The Cancer Genome Atlas. To explore the distinct pathways, messenger RNA expression was submitted to a Gene Set Enrichment Analysis. Kyoto Encyclopedia of Genes and Genomes and protein–protein interaction network analysis of differentially expressed genes were performed. Then, we conducted pathway enrichment analysis for modules acquired in protein–protein interaction analysis and obtained a list of pathways in every module. After intersecting the results from the 3 approaches, we evaluated the survival rates of both mutual pathways and genes in the pathway, and 5 survival-related genes were obtained. Finally, Cox hazards ratio analysis of these 5 genes was performed. DNA replication pathway (P < .001; 12 genes included) was suggested to have the strongest association with the prognosis of cervical squamous cancer. In total, 5 of the 12 genes, namely, minichromosome maintenance 2, minichromosome maintenance 4, minichromosome maintenance 5, proliferating cell nuclear antigen, and ribonuclease H2 subunit A were significantly correlated with survival. Minichromosome maintenance 5 was shown as an independent prognostic biomarker for patients with cervical cancer. This study identified a distinct pathway (DNA replication). Five genes which may be prognostic biomarkers and minichromosome maintenance 5 were identified as independent prognostic biomarkers for patients with cervical cancer. PMID:29642758

40 CFR 93.158 - Criteria for determining conformity of general Federal actions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... requirements: (i) Specified in paragraph (b) of this section, based on areawide air quality modeling analysis and local air quality modeling analysis; or (ii) Meet the requirements of paragraph (a)(5) of this section and, for local air quality modeling analysis, the requirement of paragraph (b) of this section; (4...

40 CFR 93.158 - Criteria for determining conformity of general Federal actions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... requirements: (i) Specified in paragraph (b) of this section, based on areawide air quality modeling analysis and local air quality modeling analysis; or (ii) Meet the requirements of paragraph (a)(5) of this section and, for local air quality modeling analysis, the requirement of paragraph (b) of this section; (4...

40 CFR 93.158 - Criteria for determining conformity of general Federal actions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... requirements: (i) Specified in paragraph (b) of this section, based on areawide air quality modeling analysis and local air quality modeling analysis; or (ii) Meet the requirements of paragraph (a)(5) of this section and, for local air quality modeling analysis, the requirement of paragraph (b) of this section; (4...

Investigating ego modules and pathways in osteosarcoma by integrating the EgoNet algorithm and pathway analysis.

PubMed

Chen, X Y; Chen, Y H; Zhang, L J; Wang, Y; Tong, Z C

2017-02-16

Osteosarcoma (OS) is the most common primary bone malignancy, but current therapies are far from effective for all patients. A better understanding of the pathological mechanism of OS may help to achieve new treatments for this tumor. Hence, the objective of this study was to investigate ego modules and pathways in OS utilizing EgoNet algorithm and pathway-related analysis, and reveal pathological mechanisms underlying OS. The EgoNet algorithm comprises four steps: constructing background protein-protein interaction (PPI) network (PPIN) based on gene expression data and PPI data; extracting differential expression network (DEN) from the background PPIN; identifying ego genes according to topological features of genes in reweighted DEN; and collecting ego modules using module search by ego gene expansion. Consequently, we obtained 5 ego modules (Modules 2, 3, 4, 5, and 6) in total. After applying the permutation test, all presented statistical significance between OS and normal controls. Finally, pathway enrichment analysis combined with Reactome pathway database was performed to investigate pathways, and Fisher's exact test was conducted to capture ego pathways for OS. The ego pathway for Module 2 was CLEC7A/inflammasome pathway, while for Module 3 a tetrasaccharide linker sequence was required for glycosaminoglycan (GAG) synthesis, and for Module 6 was the Rho GTPase cycle. Interestingly, genes in Modules 4 and 5 were enriched in the same pathway, the 2-LTR circle formation. In conclusion, the ego modules and pathways might be potential biomarkers for OS therapeutic index, and give great insight of the molecular mechanism underlying this tumor.

Investigating ego modules and pathways in osteosarcoma by integrating the EgoNet algorithm and pathway analysis

PubMed Central

Chen, X.Y.; Chen, Y.H.; Zhang, L.J.; Wang, Y.; Tong, Z.C.

2017-01-01

Osteosarcoma (OS) is the most common primary bone malignancy, but current therapies are far from effective for all patients. A better understanding of the pathological mechanism of OS may help to achieve new treatments for this tumor. Hence, the objective of this study was to investigate ego modules and pathways in OS utilizing EgoNet algorithm and pathway-related analysis, and reveal pathological mechanisms underlying OS. The EgoNet algorithm comprises four steps: constructing background protein-protein interaction (PPI) network (PPIN) based on gene expression data and PPI data; extracting differential expression network (DEN) from the background PPIN; identifying ego genes according to topological features of genes in reweighted DEN; and collecting ego modules using module search by ego gene expansion. Consequently, we obtained 5 ego modules (Modules 2, 3, 4, 5, and 6) in total. After applying the permutation test, all presented statistical significance between OS and normal controls. Finally, pathway enrichment analysis combined with Reactome pathway database was performed to investigate pathways, and Fisher's exact test was conducted to capture ego pathways for OS. The ego pathway for Module 2 was CLEC7A/inflammasome pathway, while for Module 3 a tetrasaccharide linker sequence was required for glycosaminoglycan (GAG) synthesis, and for Module 6 was the Rho GTPase cycle. Interestingly, genes in Modules 4 and 5 were enriched in the same pathway, the 2-LTR circle formation. In conclusion, the ego modules and pathways might be potential biomarkers for OS therapeutic index, and give great insight of the molecular mechanism underlying this tumor. PMID:28225867

Literature mining, gene-set enrichment and pathway analysis for target identification in Behçet's disease.

PubMed

Wilson, Paul; Larminie, Christopher; Smith, Rona

2016-01-01

To use literature mining to catalogue Behçet's associated genes, and advanced computational methods to improve the understanding of the pathways and signalling mechanisms that lead to the typical clinical characteristics of Behçet's patients. To extend this technique to identify potential treatment targets for further experimental validation. Text mining methods combined with gene enrichment tools, pathway analysis and causal analysis algorithms. This approach identified 247 human genes associated with Behçet's disease and the resulting disease map, comprising 644 nodes and 19220 edges, captured important details of the relationships between these genes and their associated pathways, as described in diverse data repositories. Pathway analysis has identified how Behçet's associated genes are likely to participate in innate and adaptive immune responses. Causal analysis algorithms have identified a number of potential therapeutic strategies for further investigation. Computational methods have captured pertinent features of the prominent disease characteristics presented in Behçet's disease and have highlighted NOD2, ICOS and IL18 signalling as potential therapeutic strategies.

Modeling biochemical pathways in the gene ontology

DOE PAGES

Hill, David P.; D’Eustachio, Peter; Berardini, Tanya Z.; ...

2016-09-01

The concept of a biological pathway, an ordered sequence of molecular transformations, is used to collect and represent molecular knowledge for a broad span of organismal biology. Representations of biomedical pathways typically are rich but idiosyncratic presentations of organized knowledge about individual pathways. Meanwhile, biomedical ontologies and associated annotation files are powerful tools that organize molecular information in a logically rigorous form to support computational analysis. The Gene Ontology (GO), representing Molecular Functions, Biological Processes and Cellular Components, incorporates many aspects of biological pathways within its ontological representations. Here we present a methodology for extending and refining the classes inmore » the GO for more comprehensive, consistent and integrated representation of pathways, leveraging knowledge embedded in current pathway representations such as those in the Reactome Knowledgebase and MetaCyc. With carbohydrate metabolic pathways as a use case, we discuss how our representation supports the integration of variant pathway classes into a unified ontological structure that can be used for data comparison and analysis.« less

Causal mediation analysis for longitudinal data with exogenous exposure

PubMed Central

Bind, M.-A. C.; Vanderweele, T. J.; Coull, B. A.; Schwartz, J. D.

2016-01-01

Mediation analysis is a valuable approach to examine pathways in epidemiological research. Prospective cohort studies are often conducted to study biological mechanisms and often collect longitudinal measurements on each participant. Mediation formulae for longitudinal data have been developed. Here, we formalize the natural direct and indirect effects using a causal framework with potential outcomes that allows for an interaction between the exposure and the mediator. To allow different types of longitudinal measures of the mediator and outcome, we assume two generalized mixed-effects models for both the mediator and the outcome. The model for the mediator has subject-specific random intercepts and random exposure slopes for each cluster, and the outcome model has random intercepts and random slopes for the exposure, the mediator, and their interaction. We also expand our approach to settings with multiple mediators and derive the mediated effects, jointly through all mediators. Our method requires the absence of time-varying confounding with respect to the exposure and the mediator. This assumption is achieved in settings with exogenous exposure and mediator, especially when exposure and mediator are not affected by variables measured at earlier time points. We apply the methodology to data from the Normative Aging Study and estimate the direct and indirect effects, via DNA methylation, of air pollution, and temperature on intercellular adhesion molecule 1 (ICAM-1) protein levels. Our results suggest that air pollution and temperature have a direct effect on ICAM-1 protein levels (i.e. not through a change in ICAM-1 DNA methylation) and that temperature has an indirect effect via a change in ICAM-1 DNA methylation. PMID:26272993

A Combined Pathway and Regional Heritability Analysis Indicates NETRIN1 Pathway Is Associated With Major Depressive Disorder.

PubMed

Zeng, Yanni; Navarro, Pau; Fernandez-Pujals, Ana M; Hall, Lynsey S; Clarke, Toni-Kim; Thomson, Pippa A; Smith, Blair H; Hocking, Lynne J; Padmanabhan, Sandosh; Hayward, Caroline; MacIntyre, Donald J; Wray, Naomi R; Deary, Ian J; Porteous, David J; Haley, Chris S; McIntosh, Andrew M

2017-02-15

Genome-wide association studies (GWASs) of major depressive disorder (MDD) have identified few significant associations. Testing the aggregation of genetic variants, in particular biological pathways, may be more powerful. Regional heritability analysis can be used to detect genomic regions that contribute to disease risk. We integrated pathway analysis and multilevel regional heritability analyses in a pipeline designed to identify MDD-associated pathways. The pipeline was applied to two independent GWAS samples [Generation Scotland: The Scottish Family Health Study (GS:SFHS, N = 6455) and Psychiatric Genomics Consortium (PGC:MDD) (N = 18,759)]. A polygenic risk score (PRS) composed of single nucleotide polymorphisms from the pathway most consistently associated with MDD was created, and its accuracy to predict MDD, using area under the curve, logistic regression, and linear mixed model analyses, was tested. In GS:SFHS, four pathways were significantly associated with MDD, and two of these explained a significant amount of pathway-level regional heritability. In PGC:MDD, one pathway was significantly associated with MDD. Pathway-level regional heritability was significant in this pathway in one subset of PGC:MDD. For both samples the regional heritabilities were further localized to the gene and subregion levels. The NETRIN1 signaling pathway showed the most consistent association with MDD across the two samples. PRSs from this pathway showed competitive predictive accuracy compared with the whole-genome PRSs when using area under the curve statistics, logistic regression, and linear mixed model. These post-GWAS analyses highlight the value of combining multiple methods on multiple GWAS data for the identification of risk pathways for MDD. The NETRIN1 signaling pathway is identified as a candidate pathway for MDD and should be explored in further large population studies. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Biomarkers of the Hedgehog/Smoothened pathway in healthy volunteers

PubMed Central

Kadam, Sunil K; Patel, Bharvin K R; Jones, Emma; Nguyen, Tuan S; Verma, Lalit K; Landschulz, Katherine T; Stepaniants, Sergey; Li, Bin; Brandt, John T; Brail, Leslie H

2012-01-01

The Hedgehog (Hh) pathway is involved in oncogenic transformation and tumor maintenance. The primary objective of this study was to select surrogate tissue to measure messenger ribonucleic acid (mRNA) levels of Hh pathway genes for measurement of pharmacodynamic effect. Expression of Hh pathway specific genes was measured by quantitative real time polymerase chain reaction (qRT-PCR) and global gene expression using Affymetrix U133 microarrays. Correlations were made between the expression of specific genes determined by qRT-PCR and normalized microarray data. Gene ontology analysis using microarray data for a broader set of Hh pathway genes was performed to identify additional Hh pathway-related markers in the surrogate tissue. RNA extracted from blood, hair follicle, and skin obtained from healthy subjects was analyzed by qRT-PCR for 31 genes, whereas 8 samples were analyzed for a 7-gene subset. Twelve sample sets, each with ≤500 ng total RNA derived from hair, skin, and blood, were analyzed using Affymetrix U133 microarrays. Transcripts for several Hh pathway genes were undetectable in blood using qRT-PCR. Skin was the most desirable matrix, followed by hair follicle. Whether processed by robust multiarray average or microarray suite 5 (MAS5), expression patterns of individual samples showed co-clustered signals; both normalization methods were equally effective for unsupervised analysis. The MAS5- normalized probe sets appeared better suited for supervised analysis. This work provides the basis for selection of a surrogate tissue and an expression analysis-based approach to evaluate pathway-related genes as markers of pharmacodynamic effect with novel inhibitors of the Hh pathway. PMID:22611475

Plasmonic Hotspots in Air: An Omnidirectional Three-Dimensional Platform for Stand-Off In-Air SERS Sensing of Airborne Species.

PubMed

Phan-Quang, Gia Chuong; Lee, Hiang Kwee; Teng, Hao Wen; Koh, Charlynn Sher Lin; Yim, Barnabas Qinwei; Tan, Eddie Khay Ming; Tok, Wee Lee; Phang, In Yee; Ling, Xing Yi

2018-05-14

Molecular-level airborne sensing is critical for early prevention of disasters, diseases, and terrorism. Currently, most 2D surface-enhanced Raman spectroscopy (SERS) substrates used for air sensing have only one functional surface and exhibit poor SERS-active depth. "Aerosolized plasmonic colloidosomes" (APCs) are introduced as airborne plasmonic hotspots for direct in-air SERS measurements. APCs function as a macroscale 3D and omnidirectional plasmonic cloud that receives laser irradiation and emits signals in all directions. Importantly, it brings about an effective plasmonic hotspot in a length scale of approximately 2.3 cm, which affords 100-fold higher tolerance to laser misalignment along the z-axis compared with 2D SERS substrates. APCs exhibit an extraordinary omnidirectional property and demonstrate consistent SERS performance that is independent of the laser and analyte introductory pathway. Furthermore, the first in-air SERS detection is demonstrated in stand-off conditions at a distance of 200 cm, highlighting the applicability of 3D omnidirectional plasmonic clouds for remote airborne sensing in threatening or inaccessible areas. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study of Regional Downscaled Climate and Air Quality in the United States

NASA Astrophysics Data System (ADS)

Gao, Y.; Fu, J. S.; Drake, J.; Lamarque, J.; Lam, Y.; Huang, K.

2011-12-01

Due to the increasing anthropogenic greenhouse gas emissions, the global and regional climate patterns have significantly changed. Climate change has exerted strong impact on ecosystem, air quality and human life. The global model Community Earth System Model (CESM v1.0) was used to predict future climate and chemistry under projected emission scenarios. Two new emission scenarios, Representative Community Pathways (RCP) 4.5 and RCP 8.5, were used in this study for climate and chemistry simulations. The projected global mean temperature will increase 1.2 and 1.7 degree Celcius for the RCP 4.5 and RCP 8.5 scenarios in 2050s, respectively. In order to take advantage of local detailed topography, land use data and conduct local climate impact on air quality, we downscaled CESM outputs to 4 km by 4 km Eastern US domain using Weather Research and Forecasting (WRF) Model and Community Multi-scale Air Quality modeling system (CMAQ). The evaluations between regional model outputs and global model outputs, regional model outputs and observational data were conducted to verify the downscaled methodology. Future climate change and air quality impact were also examined on a 4 km by 4 km high resolution scale.

Targeting Cancer Cells with Reactive Oxygen and Nitrogen Species Generated by Atmospheric-Pressure Air Plasma

PubMed Central

Hoan, Nguyen Ngoc; Kim, Churl Ho; Moon, Eunpyo; Choi, Kyeong Sook; Yang, Sang Sik; Lee, Jong-Soo

2014-01-01

The plasma jet has been proposed as a novel therapeutic method for cancer. Anticancer activity of plasma has been reported to involve mitochondrial dysfunction. However, what constituents generated by plasma is linked to this anticancer process and its mechanism of action remain unclear. Here, we report that the therapeutic effects of air plasma result from generation of reactive oxygen/nitrogen species (ROS/RNS) including H2O2, Ox, OH−, •O2, NOx, leading to depolarization of mitochondrial membrane potential and mitochondrial ROS accumulation. Simultaneously, ROS/RNS activate c-Jun NH2-terminal kinase (JNK) and p38 kinase. As a consequence, treatment with air plasma jets induces apoptotic death in human cervical cancer HeLa cells. Pretreatment of the cells with antioxidants, JNK and p38 inhibitors, or JNK and p38 siRNA abrogates the depolarization of mitochondrial membrane potential and impairs the air plasma-induced apoptotic cell death, suggesting that the ROS/RNS generated by plasma trigger signaling pathways involving JNK and p38 and promote mitochondrial perturbation, leading to apoptosis. Therefore, administration of air plasma may be a feasible strategy to eliminate cancer cells. PMID:24465942

Environmental pollution and lung effects in children.

PubMed

Searing, Daniel A; Rabinovitch, Nathan

2011-06-01

Studies over the last 2 years have added important new information on the relationship between air pollution and asthma incidence and severity. Outdoor air pollution has been associated with asthma exacerbations, including emergency department visits and hospitalizations, as well as with the onset of asthma. Possible mechanisms mediating both incidence and severity effects include the induction of oxidative stress, and/or allergic sensitization, as well as increased susceptibility to viral infections. Some of these mechanisms may be occurring in utero including epigenetic changes that may increase risk for development of asthma. Factors related to increased susceptibility for air pollution-related asthma severity include age, season and genetic polymorphisms related to antioxidant enzymes. Ambient pollution levels may be associated with both asthma incidence and severity. Susceptibility to air pollution may be higher in children with genetic polymorphisms related to the 'oxidant stress pathways'. Potential interventions for susceptible children at risk for asthma development and/or severity include decreased exposure on high air pollution days, especially in the summer months, and antioxidant supplementation. On the population level, changes in school and home zoning to increase distance from busy roadways may help reduce both asthma incidence and severity.

Techno-economic analysis of biofuel production considering logistic configurations.

PubMed

Li, Qi; Hu, Guiping

2016-04-01

In the study, a techno-economic analysis method considering logistic configurations is proposed. The economic feasibility of a low temperature biomass gasification pathway and an integrated pathway with fast pyrolysis and bio-oil gasification are evaluated and compared with the proposed method in Iowa. The results show that both pathways are profitable, biomass gasification pathway could achieve an Internal Rate of Return (IRR) of 10.00% by building a single biorefinery and integrated bio-oil gasification pathway could achieve an IRR of 3.32% by applying decentralized supply chain structure. A Monte-Carlo simulation considering interactions among parameters is also proposed and conducted, which indicates that both pathways are at high risk currently. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis

DOE PAGES

Wang, Jack P.; Matthews, Megan L.; Williams, Cranos M.; ...

2018-04-20

A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in wood formation of Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 reactions on 24 metabolites, leading to lignin and affecting wood properties. We perturb these 21 pathway genes and integrate transcriptomic, proteomic, fluxomic and phenomic data from 221 lines selected from ~2000 transgenics (6-month-old). The integrative analysis estimates how changing expression of pathway gene or gene combination affects protein abundance, metabolic-flux,more » metabolite concentrations, and 25 wood traits, including lignin, tree-growth, density, strength, and saccharification. The analysis then predicts improvements in any of these 25 traits individually or in combinations, through engineering expression of specific monolignol genes. The analysis may lead to greater understanding of other pathways for improved growth and adaptation.« less