Free-surface turbulence and air-water gas exchange

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2000This thesis investigates the physical mechanisms of air-water gas transfer through direct measurements of turbulence at the air--water interface. To enable this study, a new approach to the particle image velocimetry (PIV) technique is developed in order to quantify free-surface flows. Two aspects of this work are innovative. First, the use of a three-dimensional laser light cone and optical filtering of the camera allow for the motion of fluorescent flow tracers at the water surface to be isolated and measured. Validation experiments indicate that this measurement reflects the fluid motion within the upper few hundred microns. A key benefit to this approach is the ability to deal with deforming surfaces, provided the amplitudes are not prohibitively large. This feature was used in this thesis to explore the surface flow induced by mechanically generated waves. Second, a new hybrid PIV image processing algorithm was developed that provides high accuracy velocity estimation with improved computational efficiency. This algorithm combines the concepts of dynamic Fourier-domain cross-correlation with a localized direct multiplicative correlation. In order to explore relationships between free-surface hydrodynamics and air-water gas transfer, an oscillating grid-stirred tank was constructed. By its design, this tank can be managed for chemical cleanliness, offers an unobstructed free surface, and is suited for turbulent mixing and air--water gas-exchange studies. A series of acoustic Doppler velocimeter, PIV, and infrared imaging experiments are presented that characterize the flow for the grid forcing conditions studied. Results indicate that the flows are stationary and reasonably repeatable. In addition, the flows exhibit near-isotropic turbulence and are quasi-homogeneous in horizontal planes. Secondary circulations are revealed and investigated. Finally, PIV measurements of free-surface turbulence are performed with concurrent measurements of gas transfer in the grid tank for a range of turbulent mixing and surface conditions. Surface turbulence, vorticity, and divergence are all affected by the presence of a surface film, with significant effects realized for relatively small surface pressures. Results show that while a relationship between surface turbulence and the gas-transfer velocity is an obvious improvement over that found using an estimate of the bulk flow turbulence, this relationship is dependent on the flow regime. This is revealed through additional surface wave studies. However, the data from both the wave experiments and the grid turbulence experiments can be reconciled by a single relationship between the gas-transfer velocity and the 1/2-power of the surface divergence, which agrees with previous conceptual models. These results (1) further our understanding of interfacial transport processes, (2) demonstrate the important role of surface divergence in air-water gas exchange, and (3) relate, in a physically meaningful way, the interactions between surface renewal, surfactants, and gas transfer.I was supported as an Office of Naval Research Graduate Fellow. This assistance was the impetus for my pursuit of a doctoral degree and is gratefully acknowledged. Very special thanks also to the WHOI Ocean Ventures Fund Program, Mr. F. Thomas Westcott, and the WHOI Education Department for generous financial support over the past several years

Gait Characteristics and Cognitive Function in Middle-Aged Adults With and Without Type 2 Diabetes Mellitus: Data from ENBIND

Type 2 Diabetes Mellitus (T2DM) in midlife is associated with a greater risk of dementia in later life. Both gait speed and spatiotemporal gait characteristics have been associated with later cognitive decline in community-dwelling older adults. Thus, the assessment of gait characteristics in uncomplicated midlife T2DM may be important in selecting-out those with T2DM at greatest risk of later cognitive decline. We assessed the relationship between Inertial Motion Unit (IMUs)- derived gait characteristics and cognitive function assessed via Montreal Cognitive Assessment (MOCA)/detailed neuropsychological assessment battery (CANTAB) in middle-aged adults with and without uncomplicated T2DM using both multivariate linear regression and a neural network approach. Gait was assessed under (i) normal walking, (ii) fast (maximal) walking and (iii) cognitive dual-task walking (reciting alternate letters of the alphabet) conditions. Overall, 138 individuals were recruited (n = 94 with T2DM; 53% female, 52.8 8.3 years; n = 44 healthy controls, 43% female, 51.9 8.1 years). Midlife T2DM was associated with significantly slower gait velocity on both slow and fast walks (both p \u3c 0.01) in addition to a longer stride time and greater gait complexity during normal walk (both p \u3c 0.05). Findings persisted following covariate adjustment. In analyzing cognitive performance, the strongest association was observed between gait velocity and global cognitive function (MOCA). Significant associations were also observed between immediate/delayed memory performance and gait velocity. Analysis using a neural network approach did not outperform multivariate linear regression in predicting cognitive function (MOCA) from gait velocity. Our study demonstrates the impact of uncomplicated T2DM on gait speed and gait characteristics in midlife, in addition to the striking relationship between gait characteristics and global cognitive function/memory performance in midlife. Further studies are needed to evaluate the longitudinal relationship between midlife gait characteristics and later cognitive decline, which may aid in selecting-out those with T2DM at greatest-risk for preventative interventions

Impact of the structural integrity of the three-way junction of adenovirus VAI RNA on PKR inhibition

Sherpa Romeo green journal. Open access article. Creative Commons Attribution License applies.Highly structured RNA derived from viral genomes is a key cellular indicator of viral infection. In response, cells produce the interferon inducible RNA-dependent protein kinase (PKR) that, when bound to viral dsRNA, phosphorylates eukaryotic initiation factor 2αand attenuates viral protein translation. Adenovirus can evade this line of defence through transcription of a non-coding RNA, VAI, an inhibitor of PKR. VAI consists of three base-paired regions that meet at a three-way junction; an apical stem responsible for the interaction with PKR, a central stem required for inhibition, and a terminal stem. Recent studies have highlighted the potential importance of the tertiary structure of the three-way junction to PKR inhibition by enabling interaction between regions of the central and terminal stems. To further investigate the role of the three-way junction, we characterized the binding affinity and inhibitory potential of central stem mutants designed to introduce subtle alterations. These results were then correlated with small-angle X-ray scattering solution studies and computational tertiary structural models. Our results demonstrate that while mutations to the central stem have no observable effect on binding affinity to PKR, mutations that appear to disrupt the structure of the three-way junction prevent inhibition of PKR. Therefore, we propose that instead of simply sequestering PKR, a specific structural conformation of the PKR-VAI complex may be required for inhibition

Gene content evolution in the arthropods

Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity

Activation of 2′ 5′-oligoadenylate synthetase by stem loops at the 5′-end of the West Nile virus genome

West Nile virus (WNV) has a positive sense RNA genome with conserved structural elements in the 5′ and 3′ -untranslated regions required for polyprotein production. Antiviral immunity to WNV is partially mediated through the production of a cluster of proteins known as the interferon stimulated genes (ISGs). The 2′ 5′-oligoadenylate synthetases (OAS) are key ISGs that help to amplify the innate immune response. Upon interaction with viral double stranded RNA, OAS enzymes become activated and enable the host cell to restrict viral propagation. Studies have linked mutations in the OAS1 gene to increased susceptibility to WNV infection, highlighting the importance of OAS1 enzyme. Here we report that the region at the 5′-end of the WNV genome comprising both the 5′-UTR and initial coding region is capable of OAS1 activation in vitro. This region contains three RNA stem loops (SLI, SLII, and SLIII) whose relative contribution to OAS1 binding affinity and activation were investigated using electrophoretic mobility shift assays and enzyme kinetics experiments. Stem loop I, comprising nucleotides 1-73, is dispensable for maximum OAS1 activation, as a construct containing only SLII and SLIII was capable of enzymatic activation. Mutations to the RNA binding site of OAS1 confirmed the specificity of the interaction. The purity, monodispersity and homogeneity of the 5′-end (SLI/II/III) and OAS1 were evaluated using dynamic light scattering and analytical ultra-centrifugation. Solution conformations of both the 5′-end RNA of WNV and OAS1 were then elucidated using small-angle x-ray scattering. In the context of purified components in vitro, these data demonstrate the recognition of conserved secondary structural elements of the WNV genome by a member of the interferon-mediated innate immune response

Air-sea CO2 exchange in the equatorial Pacific

Author Posting. © American Geophysical Union, 2004. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 109 (2004): C08S02, doi:10.1029/2003JC002256.GasEx-2001, a 15-day air-sea carbon dioxide (CO2) exchange study conducted in the equatorial Pacific, used a combination of ships, buoys, and drifters equipped with ocean and atmospheric sensors to assess variability and surface mechanisms controlling air-sea CO2 fluxes. Direct covariance and profile method air-sea CO2 fluxes were measured together with the surface ocean and marine boundary layer processes. The study took place in February 2001 near 125°W, 3°S in a region of high CO2. The diurnal variation in the air-sea CO2 difference was 2.5%, driven predominantly by temperature effects on surface solubility. The wind speed was 6.0 ± 1.3 m s−1, and the atmospheric boundary layer was unstable with conditions over the range −1 < z/L < 0. Diurnal heat fluxes generated daytime surface ocean stratification and subsequent large nighttime buoyancy fluxes. The average CO2 flux from the ocean to the atmosphere was determined to be 3.9 mol m−2 yr−1, with nighttime CO2 fluxes increasing by 40% over daytime values because of a strong nighttime increase in (vertical) convective velocities. The 15 days of air-sea flux measurements taken during GasEx-2001 demonstrate some of the systematic environmental trends of the eastern equatorial Pacific Ocean. The fact that other physical processes, in addition to wind, were observed to control the rate of CO2 transfer from the ocean to the atmosphere indicates that these processes need to be taken into account in local and global biogeochemical models. These local processes can vary on regional and global scales. The GasEx-2001 results show a weak wind dependence but a strong variability in processes governed by the diurnal heating cycle. This implies that any changes in the incident radiation, including atmospheric cloud dynamics, phytoplankton biomass, and surface ocean stratification may have significant feedbacks on the amount and variability of air-sea gas exchange. This is in sharp contrast with previous field studies of air-sea gas exchange, which showed that wind was the dominating forcing function. The results suggest that gas transfer parameterizations that rely solely on wind will be insufficient for regions with low to intermediate winds and strong insolation.This work was performed with the support of the National Science Foundation Grant OCE-9986724 and the NOAA Global Carbon Cycle Program Grants NA06GP048, NA17RJ1223, and NA87RJ0445 in the Office of Global Programs

Conducting Online Expert panels: a feasibility and experimental replicability study

<p>Abstract</p> <p>Background</p> <p>This paper has two goals. First, we explore the feasibility of conducting online expert panels to facilitate consensus finding among a large number of geographically distributed stakeholders. Second, we test the replicability of panel findings across four panels of different size.</p> <p>Method</p> <p>We engaged 119 panelists in an iterative process to identify definitional features of Continuous Quality Improvement (CQI). We conducted four parallel online panels of different size through three one-week phases by using the RAND's ExpertLens process. In Phase I, participants rated potentially definitional CQI features. In Phase II, they discussed rating results online, using asynchronous, anonymous discussion boards. In Phase III, panelists re-rated Phase I features and reported on their experiences as participants.</p> <p>Results</p> <p>66% of invited experts participated in all three phases. 62% of Phase I participants contributed to Phase II discussions and 87% of them completed Phase III. Panel disagreement, measured by the mean absolute deviation from the median (MAD-M), decreased after group feedback and discussion in 36 out of 43 judgments about CQI features. Agreement between the four panels after Phase III was fair (four-way kappa = 0.36); they agreed on the status of five out of eleven CQI features. Results of the post-completion survey suggest that participants were generally satisfied with the online process. Compared to participants in smaller panels, those in larger panels were more likely to agree that they had debated each others' view points.</p> <p>Conclusion</p> <p>It is feasible to conduct online expert panels intended to facilitate consensus finding among geographically distributed participants. The online approach may be practical for engaging large and diverse groups of stakeholders around a range of health services research topics and can help conduct multiple parallel panels to test for the reproducibility of panel conclusions.</p

Self-Organization of Muscle Cell Structure and Function

The organization of muscle is the product of functional adaptation over several length scales spanning from the sarcomere to the muscle bundle. One possible strategy for solving this multiscale coupling problem is to physically constrain the muscle cells in microenvironments that potentiate the organization of their intracellular space. We hypothesized that boundary conditions in the extracellular space potentiate the organization of cytoskeletal scaffolds for directed sarcomeregenesis. We developed a quantitative model of how the cytoskeleton of neonatal rat ventricular myocytes organizes with respect to geometric cues in the extracellular matrix. Numerical results and in vitro assays to control myocyte shape indicated that distinct cytoskeletal architectures arise from two temporally-ordered, organizational processes: the interaction between actin fibers, premyofibrils and focal adhesions, as well as cooperative alignment and parallel bundling of nascent myofibrils. Our results suggest that a hierarchy of mechanisms regulate the self-organization of the contractile cytoskeleton and that a positive feedback loop is responsible for initiating the break in symmetry, potentiated by extracellular boundary conditions, is required to polarize the contractile cytoskeleton

On the climate impacts of blue hydrogen production

Natural gas based hydrogen production with carbon capture and storage is referred to as blue hydrogen. If substantial amounts of CO2 from natural gas reforming are captured and permanently stored, such hydrogen could be a low-carbon energy carrier. However, recent research raises questions about the effective climate impacts of blue hydrogen from a life cycle perspective. Our analysis sheds light on the relevant issues and provides a balanced perspective on the impacts on climate change associated with blue hydrogen. We show that such impacts may indeed vary over large ranges and depend on only a few key parameters: the methane emission rate of the natural gas supply chain, the CO2 removal rate at the hydrogen production plant, and the global warming metric applied. State-of-the-art reforming with high CO2 capture rates combined with natural gas supply featuring low methane emissions does indeed allow for substantial reduction of greenhouse gas emissions compared to both conventional natural gas reforming and direct combustion of natural gas. Under such conditions, blue hydrogen is compatible with low-carbon economies and exhibits climate change impacts at the upper end of the range of those caused by hydrogen production from renewable-based electricity. However, neither current blue nor green hydrogen production pathways render fully “net-zero” hydrogen without additional CO2 removal

Air-sea gas transfer : its dependence on wind stress, small-scale roughness, and surface films

Author Posting. © American Geophysical Union, 2004. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 109 (2004): C08S17, doi:10.1029/2003JC002131.The influence of wind stress, small-scale waves, and surface films on air-sea gas exchange at low to moderate wind speeds (<10 m s−1) is examined. Coincident observations of wind stress, heat transfer velocity, surface wave slope, and surface film enrichments were made in coastal and offshore waters south of Cape Cod, New England, in July 1997 as part of the NSF-CoOP Coastal Air-Sea Chemical Fluxes study. Gas transfer velocities have been extrapolated from aqueous heat transfer velocities derived from infrared imagery and direct covariance and bulk heat flux estimates. Gas transfer velocity is found to follow a quadratic relationship with wind speed, which accounts for ~75–77% of the variance but which overpredicts transfer velocity in the presence of surface films. The dependence on wind stress as represented by the friction velocity is also nonlinear, reflecting a wave field-dependent transition between limiting transport regimes. In contrast, the dependence on mean square slope computed for the wave number range of 40–800 rad m−1 is found to be linear and in agreement with results from previous laboratory wind wave studies. The slope spectrum of the small-scale waves and the gas transfer velocity are attenuated in the presence of surface films. Observations over large-scale gradients of biological productivity and dissolved organic matter show that the reduction in slope and transfer velocity are more clearly correlated with surface film enrichments than with bulk organic matter concentrations. The mean square slope parameterization explains ~89–95% of the observed variance in the data and does not overpredict transfer velocities where films are present. While the specific relationships between gas transfer velocity and wind speed or mean square slope vary slightly with the choice of Schmidt number exponent used to scale the heat transfer velocities to gas transfer velocities, the correlation of heat or gas transfer velocity with mean square slope is consistently better than with wind speed.Funding for this work was provided by the NSF Coastal Ocean Processes (CoOP) program (OCE-9410534, OCE- 9711285 (WHOI) and OCE-9409222, OCE-9711391(URI)). Additional support for data analysis was provided by NASA (NAGW-2431, JPL Contract 961425). Partial funding was also provided by the German Science Foundation (DFG) through the DFG research unit FOR240: Image Sequence Analysis to Investigate Dynamic Processes