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Search Results: 1 - 10 of 335844 matches for " R. B. Cook "
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The Unified North American Soil Map and its implication on the soil organic carbon stock in North America
S. Liu,Y. Wei,W. M. Post,R. B. Cook
Biogeosciences Discussions , 2012, DOI: 10.5194/bgd-9-15175-2012
Abstract: The Unified North American Soil Map (UNASM) was developed to provide more accurate regional soil information for terrestrial biosphere modeling. The UNASM combines information from state-of-the-art US STATSGO2 and Soil Landscape of Canada (SLCs) databases. The area not covered by these datasets is filled with the Harmonized World Soil Database version 1.1 (HWSD1.1). The UNASM contains maximum soil depth derived from the data source as well as seven soil attributes (including sand, silt, and clay content, gravel content, organic carbon content, pH, and bulk density) for the top soil layer (0–30 cm) and the sub soil layer (30–100 cm) respectively, of the spatial resolution of 0.25° in latitude and longitude. There are pronounced differences in the spatial distributions of soil properties and soil organic carbon between UNASM and HWSD, but the UNASM overall provides more detailed and higher-quality information particularly in Alaska and Central Canada. To provide more accurate and up-to-date estimate of soil organic carbon stock in North America, we incorporated Northern Circumpolar Soil Carbon Database (NCSCD) into the UNASM. The estimate of total soil organic carbon mass in the upper 100 cm soil profile based on the improved UNASM is 347.70 Pg, of which 24.7% is under trees, 14.2% is under shrubs, and 1.3% is under grasses and 3.8% under crops. This UNASM data will provide a resource for use in land surface and terrestrial biogeochemistry modeling both for input of soil characteristics and for benchmarking model output.
Competition between Multiple Totally Asymmetric Simple Exclusion Processes for a Finite Pool of Resources
L. Jonathan Cook,R. K. P. Zia,B. Schmittmann
Physics , 2009, DOI: 10.1103/PhysRevE.80.031142
Abstract: Using Monte Carlo simulations and a domain wall theory, we discuss the effect of coupling several totally asymmetric simple exclusion processes (TASEPs) to a finite reservoir of particles. This simple model mimics directed biological transport processes in the presence of finite resources, such as protein synthesis limited by a finite pool of ribosomes. If all TASEPs have equal length, we find behavior which is analogous to a single TASEP coupled to a finite pool. For the more generic case of chains with different lengths, several unanticipated new regimes emerge. A generalized domain wall theory captures our findings in good agreement with simulation results.
Contrasting carbon dioxide fluxes between a drying shrub wetland in Northern Wisconsin, USA, and nearby forests
B. N. Sulman, A. R. Desai, B. D. Cook, N. Saliendra,D. S. Mackay
Biogeosciences (BG) & Discussions (BGD) , 2009,
Abstract: Wetland biogeochemistry is strongly influenced by water and temperature dynamics, and these interactions are currently poorly represented in ecosystem and climate models. A decline in water table of approximately 30 cm was observed at a wetland in Northern Wisconsin, USA over a period from 2001–2007, which was highly correlated with an increase in daily soil temperature variability. Eddy covariance measurements of carbon dioxide exchange were compared with measured CO2 fluxes at two nearby forests in order to distinguish wetland effects from regional trends. As wetland water table declined, both ecosystem respiration and ecosystem production increased by over 20% at the wetland, while forest CO2 fluxes had no significant trends. Net ecosystem exchange of carbon dioxide at the wetland was not correlated with water table, but wetland evapotranspiration decreased substantially as the water table declined. These results suggest that changes in hydrology may not have a large impact on shrub wetland carbon balance over inter-annual time scales due to opposing responses in both ecosystem respiration and productivity.
The impact of a declining water table on observed carbon fluxes at a northern temperate wetland
B. N. Sulman,A. R. Desai,B. D. Cook,N. Saliendra
Biogeosciences Discussions , 2009,
Abstract: Wetland biogeochemistry is strongly influenced by water and temperature dynamics, and these interactions are currently poorly represented in ecosystem and climate models. A decline in water table of approximately 6 cm/year was observed at a wetland in northern Wisconsin, USA over a period from 2001–2007. Eddy covariance measurements of carbon dioxide exchange in conjunction with the declining water table revealed an increase in ecosystem respiration of over 20% as water table depth fell through a range between 5 and 35 cm below the surface. Ecosystem respiration was not correlated with water table outside of this range. The limits of the range were dependent on temperature, with the effect of water table penetrating deeper at higher temperatures. Yearly average ecosystem production was approximately 20% higher in years with low water table than in years with high water table. As the water table declined, evapotranspiration decreased and ecosystem water use efficiency increased. Wetland net ecosystem exchange was not correlated with water table, but in 2007, a year with an exceptionally dry growing season, the wetland site was a net carbon source. These results suggest that changes in hydrology may not have a large impact on wetland carbon flux over inter-annual time scales due to opposing responses in both ecosystem respiration and productivity. However, this balance appears to be sensitive to changes in the seasonal distribution of precipitation.
Opposing Effects of Omega-3 and Omega-6 Long Chain Polyunsaturated Fatty Acids on the Expression of Lipogenic Genes in Omental and Retroperitoneal Adipose Depots in the Rat
B. S. Muhlhausler,R. Cook-Johnson,M. James,D. Miljkovic,E. Duthoit,R. Gibson
Journal of Nutrition and Metabolism , 2010, DOI: 10.1155/2010/927836
Abstract: This study aimed to determine the effect of varying dietary intake of the major n-3 PUFA in human diets, -linolenic acid (ALA; 18 : 3n-3), on expression of lipogenic genes in adipose tissue. Rats were fed diets containing from 0.095%en to 6.3%en ALA and a constant n-6 PUFA level for 3 weeks. Samples from distinct adipose depots (omental and retroperitoneal) were collected and mRNA expression of the pro-lipogenic transcription factors Sterol-Retinoid-Element-Binding-Protein1c (SREBP1c) and Peroxisome Proliferator Activated Receptor- (PPAR), lipogenic enzymes Sterol-coenzyme Desaturase1 (SCD-1), Fatty Acid Synthase (FAS), lipoprotein lipase (LPL) and glycerol-3-phosphate dehydrogenase (G3PDH) and adipokines leptin and adiponectin determined by qRT-PCR. Increasing dietary ALA content resulted in altered expression of SREBP1c, FAS and G3PDH mRNA in both adipose depots. SREBP1c mRNA expression was related directly to n-6 PUFA concentrations (omental, 2=.71; <.001; Retroperitoneal, 2=.20; <.002), and inversely to n-3 PUFA concentrations (omental, 2=.59; <.001; Retroperitoneal, 2=.19; <.005) independent of diet. The relationship between total n-6 PUFA and SREBP1c mRNA expression persisted when the effects of n-3 PUFA were controlled for. Altering red blood cell concentrations of n-3 PUFA is thus associated with altered expression of lipogenic genes in a depot-specific manner and this effect is modulated by prevailing n-6 PUFA concentrations.
Opposing Effects of Omega-3 and Omega-6 Long Chain Polyunsaturated Fatty Acids on the Expression of Lipogenic Genes in Omental and Retroperitoneal Adipose Depots in the Rat
B. S. Muhlhausler,R. Cook-Johnson,M. James,D. Miljkovic,E. Duthoit,R. Gibson
Journal of Nutrition and Metabolism , 2010, DOI: 10.1155/2010/927836
Abstract: This study aimed to determine the effect of varying dietary intake of the major n-3 PUFA in human diets, -linolenic acid (ALA; 18?:?3n-3), on expression of lipogenic genes in adipose tissue. Rats were fed diets containing from 0.095%en to 6.3%en ALA and a constant n-6 PUFA level for 3 weeks. Samples from distinct adipose depots (omental and retroperitoneal) were collected and mRNA expression of the pro-lipogenic transcription factors Sterol-Retinoid-Element-Binding-Protein1c (SREBP1c) and Peroxisome Proliferator Activated Receptor- (PPAR ), lipogenic enzymes Sterol-coenzyme Desaturase1 (SCD-1), Fatty Acid Synthase (FAS), lipoprotein lipase (LPL) and glycerol-3-phosphate dehydrogenase (G3PDH) and adipokines leptin and adiponectin determined by qRT-PCR. Increasing dietary ALA content resulted in altered expression of SREBP1c, FAS and G3PDH mRNA in both adipose depots. SREBP1c mRNA expression was related directly to n-6 PUFA concentrations (omental, ; ; Retroperitoneal, ; ), and inversely to n-3 PUFA concentrations (omental, ; ; Retroperitoneal, ; ) independent of diet. The relationship between total n-6 PUFA and SREBP1c mRNA expression persisted when the effects of n-3 PUFA were controlled for. Altering red blood cell concentrations of n-3 PUFA is thus associated with altered expression of lipogenic genes in a depot-specific manner and this effect is modulated by prevailing n-6 PUFA concentrations. 1. Introduction In adults, changes in the patterns of expression of key regulatory and functional genes within adipose tissue are important determinants of fat accumulation and can profoundly influence the ability of an individual to maintain energy balance and resist weight gain [1–4]. The transcription factors Sterol Retinoid Binding Protein-1c (SREBP1c) and Peroxisome Proliferator Activated Receptor- (PPAR ) regulate lipid storage and adipose tissue mass by regulating the expression of genes in the lipogenic pathway. Specifically, activation of SREBP1c and PPAR increases the expression of a series of enzymes which increase the synthesis and storage of triglycerides in adipose tissue, including lipoprotein lipase (LPL), which increases uptake of fatty acids from the circulation, and Fatty Acid Synthase (FAS) and glycerol-3-phosphate dehydrogenase (G3PDH), which both promote triglyceride synthesis [5]. While the cause of the current global obesity epidemic includes excessive food consumption and reduced exercise, there is increasing evidence that both the quantity and the type of fats in the diet have a major role in defining the propensity of an individual to
Classification of Northern Hemisphere stratospheric ozone and water vapor profiles by meteorological regime
M. B. Follette-Cook, R. D. Hudson,G. E. Nedoluha
Atmospheric Chemistry and Physics (ACP) & Discussions (ACPD) , 2009,
Abstract: The subtropical and polar upper troposphere fronts and the polar vortex serve as the boundaries to divide the Northern Hemisphere into four meteorological regimes. These regimes are defined as (1) the arctic regime – within the polar vortex, (2) the polar regime – between the polar front and the polar vortex, or when the latter is not present, the pole, (3) the midlatitude regime – between the subtropical and polar fronts, and (4) the tropical regime – between the equator and the subtropical front. Data from the Halogen Occultation Experiment (HALOE) and the Stratospheric Aerosol and Gas Experiment II (SAGE II) were used to show that within each meteorological regime, ozone and water profiles are characterized by unique ozonepause and hygropause heights. Daily measurements and seven-year (1997–2003) monthly climatologies showed that, within each meteorological regime, both constituents exhibited distinct profile shapes from the tropopause up to approximately 20 km. This distinction was most pronounced in the winter and spring months, and weak in the summer and fall. Despite differences in retrieval techniques and sampling between the SAGE and HALOE instruments, the seven-year monthly climatologies calculated for each regime agreed well for both species below ~22 km. Given that profiles of ozone and water vapor exhibit unique profiles shapes within each regime in the UTLS, trends in this region will therefore be the result of both changes within each meteorological regime, and changes in the relative contribution of each regime to a given zonal band over time.
Efficacy of a Commercial Post-Chill Whole Carcass Cecure Antimicrobial1 Application for Extending the Shelf-Life of Various Broiler Products
R.A. Baker,K.L. Beers,P.E. Cook,B.A. Smith
International Journal of Poultry Science , 2010,
Abstract: The objective of the following study was to determine if a post-chill whole carcass Cecure (Safe Foods Corporation, N. Little Rock, AR) treatment (0.3% @ 0.5 gallon/carcass) would extend the shelf-life of various further processed broiler products which were produced from Cecure -treated whole carcasses. Cecure is an FDA and USDA/FSIS approved, patented formulation containing the active ingredient cetylpyridinium chloride. Cecure is approved by FDA and USDA/FSIS for application to pre-immersion chilled, post-immersion chilled and air-chilled whole carcasses and to skin-on carcass parts. For this study, a commercially available, fully automated, post-chill Cecure rinse cabinet was installed and operated in a USDA-inspected broiler processing facility several months prior to initiation of the study. On the day the shelf-life study was to be conducted, a single flock of birds was utilized. Control samples were collected during a 2-hour period prior to turning on the Cecure post-chill whole carcass system. Six different types of broiler products were collected for evaluation including boneless skinless breast meat, thighs, wings, split breasts, leg quarters and whole carcasses. After all control samples were collected (n=70 per product type) the Cecure system was turned on and allowed to run for 2 hours after which similar product samples were collected for products produced from Cecure -treated whole carcasses. All broiler parts were tray-packed and whole carcasses were bagged individually. On Day 0, all samples were held at 28o F for approximately 6 hours after which they were held at 32oF for 3 days. For the remainder of the study, all samples were held at 34oF. On Days 0, 5 and 10 and Days 14 through 22, each of the six product types was microbiologically evaluated using Aerobic Plate Count Petrifilm 3 until the products were considered spoiled (7 logs colony forming units per mL). Regardless of product type, the Cecure whole carcass post-chill treatment (0.3%) resulted in initial reductions in Aerobic Plate Count on Day 0 from 0.5 to > 1 log. These initial Day 0 microbial reductions led to increases in product shelf-life as follows: boneless skinless breast meat and whole carcasses (1.5-day extension), thighs, split breasts and wings (2-day extension) and leg quarters (1-day extension). It should be noted that the slope and the shape of the bacterial growth curves for all Cecure -treated products were almost identical to those for the control products with the exception of a lower initial (Day 0) level of bacteria; hence, increasing the days to
The Growth and Survival of Mycobacterium smegmatis Is Enhanced by Co-Metabolism of Atmospheric H2
Chris Greening, Silas G. Villas-B?as, Jennifer R. Robson, Michael Berney, Gregory M. Cook
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0103034
Abstract: The soil bacterium Mycobacterium smegmatis is able to scavenge the trace concentrations of H2 present in the atmosphere, but the physiological function and importance of this activity is not understood. We have shown that atmospheric H2 oxidation in this organism depends on two phylogenetically and kinetically distinct high-affinity hydrogenases, Hyd1 (MSMEG_2262-2263) and Hyd2 (MSMEG_2720-2719). In this study, we explored the effect of deleting Hyd2 on cellular physiology by comparing the viability, energetics, transcriptomes, and metabolomes of wild-type vs. Δhyd2 cells. The long-term survival of the Δhyd2 mutant was significantly reduced compared to the wild-type. The mutant additionally grew less efficiently in a range of conditions, most notably during metabolism of short-chain fatty acids; there was a twofold reduction in growth rate and growth yield of the Δhyd2 strain when acetate served as the sole carbon source. Hyd1 compensated for loss of Hyd2 when cells were grown in a high H2 atmosphere. Analysis of cellular parameters showed that Hyd2 was not necessary to generate the membrane potential, maintain intracellular pH homeostasis, or sustain redox balance. However, microarray analysis indicated that Δhyd2 cells were starved for reductant and compensated by rewiring central metabolism; transcripts encoding proteins responsible for oxidative decarboxylation pathways, the urea cycle, and ABC transporter-mediated import were significantly more abundant in the Δhyd2 mutant. Metabolome profiling consistently revealed an increase in intracellular amino acids in the Δhyd2 mutant. We propose that atmospheric H2 oxidation has two major roles in mycobacterial cells: to generate reductant during mixotrophic growth and to sustain the respiratory chain during dormancy.
Estimation of effective connectivity via data-driven neural modeling
Dean R. Freestone,Philippa J. Karoly,Parham Aram,Mark J. Cook,David B. Grayden
Frontiers in Neuroscience , 2014, DOI: 10.3389/fnins.2014.00383
Abstract: This research introduces a new method for functional brain imaging via a process of model inversion. By estimating parameters of a computational model, we are able to track effective connectivity and mean membrane potential dynamics that cannot be directly measured using electrophysiological measurements alone. The ability to track the hidden aspects of neurophysiology will have a profound impact on the way we understand and treat epilepsy. For example, under the assumption the model captures the key features of the cortical circuits of interest, the framework will provide insights into seizure initiation and termination on a patient-specific basis. It will enable investigation into the effect a particular drug has on specific neural populations and connectivity structures using minimally invasive measurements. The method is based on approximating brain networks using an interconnected neural population model. The neural population model is based on a neural mass model that describes the functional activity of the brain, capturing the mesoscopic biophysics and anatomical structure. The model is made subject-specific by estimating the strength of intra-cortical connections within a region and inter-cortical connections between regions using a novel Kalman filtering method. We demonstrate through simulation how the framework can be used to track the mechanisms involved in seizure initiation and termination.
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