Mean and Turbulent Flow Statistics in a Trellised Agricultural Canopy

Flow physics is investigated in a two-dimensional trellised agricultural canopy to examine that architecture’s unique signature on turbulent transport. Analysis of meteorological data from an Oregon vineyard demonstrates that the canopy strongly influences the flow by channelling the mean flow into the vine-row direction regardless of the above-canopy wind direction. Additionally, other flow statistics in the canopy sub-layer show a dependance on the difference between the above-canopy wind direction and the vine-row direction. This includes an increase in the canopy displacement height and a decrease in the canopy-top shear length scale as the above-canopy flow rotates from row-parallel towards row-orthogonal. Distinct wind-direction-based variations are also observed in the components of the stress tensor, turbulent kinetic energy budget, and the energy spectra. Although spectral results suggest that sonic anemometry is insufficient for resolving all of the important scales of motion within the canopy, the energy spectra peaks still exhibit dependencies on the canopy and the wind direction. These variations demonstrate that the trellised-canopy’s effect on the flow during periods when the flow is row-aligned is similar to that seen by sparse canopies, and during periods when the flow is row-orthogonal, the effect is similar to that seen by dense canopies.     

Optical dating and soil micromorphology at MacCauley's Beach,New South Wales,Australia

The ability to position landscapes in a context of time and space is a particular goal of Quaternary science research. The lack of context for dating samples published previously for MacCauley's Beach, an important site for the reconstruction of Australian sea levels, warranted a re‐evaluation of both the site stratigraphy and chronology. In this study, we combined optically stimulated luminescence (OSL) dating of sedimentary quartz grains and soil micromorphology of the same samples to improve our understanding of the depositional history and chronology of the sediments. This combination allowed the contextualization of samples not only in time and space, but also in terms of their depositional histories. The latter is important in OSL dating, where pre‐, syn‐ and post‐depositional processes can all influence the accuracy and precision of the final age estimates. The sediment profile at MacCauley's Beach is made up of three major units. The basal mottled mud layer has undergone extensive pedogenesis since deposition, and only a minimum age of 14.7 ± 2.7 ka could be calculated. The overlying grey mud, with OSL ages from the bottom and top of the unit of 10.0 ± 0.7 and 7.7 ± 0.5 ka, respectively, shows evidence of soil structure collapse. This unit correspond to the onset of the mid‐Holocene sea‐level high stand for this region. The overlying sand layer was first deposited at 7.5 ± 0.4 ka, with deposition continuing beyond 6.6 ± 0.4 ka. Not only does the chronology presented constrain the timing of deposition (and the extent of post‐depositional processes) at MacCauley's Beach, but the methodological approach used here can be applied to any site to aid in the interpretation of formation processes and assess their influence on OSL age determination. Copyright © 2014 John Wiley & Sons, Ltd.     

Evaluating local population dynamics of the American lobster,Homarus americanus,with trap‐based mark‐recapture methods and seabed mapping

Seabed mapping, spatially referenced trapping, and mark‐recapture methods have all been useful tools in ecological studies of lobsters and other benthic animals. Here we integrate the three methods to evaluate local population dynamics and movements of American lobsters, Homarus americanus, in coastal fishing grounds in Maine, United States. The study was conducted on five study areas of different size, and used two different sampling protocols. At one site (1 km² in area) we used a monthly mark‐recapture sampling interval over a 6‐month period, only tagging a subsample of the catch. At four smaller sites (0.3 km²) we used a shorter‐term approach, sampling at 3–4‐day intervals for a 2‐week duration, tagging the entire catch. Tagging data were analysed with a modified Jolly‐Seber model adapted for continuous sampling to estimate population abundance, gains (immigration), and losses (emigration and mortality). Side‐scan sonar surveys of the seabed combined with diver‐based population surveys, stratified by substrate type, provided an independent comparison to mark‐recapture‐based estimates of abundance over the same areas. Spatial referencing of trap catch also allowed us to relate catch rates and lobster movements directly to seabed features. The longer‐term tagging data on the larger study area provided abundance estimates that were more consistent with the diver observations, and estimates of gains and losses statistically more robust, than those derived from the shorter‐term effort on the smaller sites. The flux of lobsters followed the well known seasonal movements on these fishing grounds, with gains and losses from the larger study area ranging over 1000 individuals per day, and an estimated mid‐summer peak density of >65 000 lobsters per km² (individuals >50 mm carapace length). This approach may lend itself to broader application with the American lobster.     

Biofilm Detection in a Model Well‐Bore Environment Using Low‐Field NMR

This research addresses the challenges of the lack of non‐invasive methods and poor spatiotemporal resolution associated with monitoring biogeochemical activity central to bioremediation of subsurface contaminants. Remediation efforts often include growth of biofilm to contain or degrade chemical contaminants, such as nitrates, hydrocarbons, heavy metals, and some chlorinated solvents. Previous research indicates that nuclear magnetic resonance (NMR) is sensitive to the biogeochemical processes of biofilm accumulation. The current research focuses on developing methods to use low‐cost NMR technology to support in situ monitoring of biofilm growth and geochemical remediation processes in the subsurface. Biofilm was grown in a lab‐scale radial flow bioreactor designed to model the near wellbore subsurface environment. The Vista Clara Javelin NMR logging device, a slim down‐the‐borehole probe, collected NMR measurements over the course of eight days while biofilm was cultivated in the sand‐packed reactor. Measured NMR mean log T₂ relaxation times decreased from approximately 710 to 389 ms, indicating that the pore environment and bulk fluid properties were changing due to biofilm growth. Destructive sampling employing drop plate microbial population analysis and scanning electron and stereoscopic microscopy confirmed biofilm formation. Our findings demonstrate that the NMR logging tool can detect small to moderate changes in T₂ distribution associated with environmentally relevant quantities of biofilm in quartz sand.     

A changing nutrient regime in the Gulf of Maine

Recent oceanographic observations and a retrospective analysis of nutrients and hydrography over the past five decades have revealed that the principal source of nutrients to the Gulf of Maine, the deep, nutrient-rich continental slope waters that enter at depth through the Northeast Channel, may have become less important to the Gulf's nutrient load. Since the 1970s, the deeper waters in the interior Gulf of Maine (>100 m) have become fresher and cooler, with lower nitrate (NO₃) but higher silicate (Si(OH)₄) concentrations. Prior to this decade, nitrate concentrations in the Gulf normally exceeded silicate by 4–5 μM, but now silicate and nitrate are nearly equal. These changes only partially correspond with that expected from deep slope water fluxes correlated with the North Atlantic Oscillation, and are opposite to patterns in freshwater discharges from the major rivers in the region. We suggest that accelerated melting in the Arctic and concomitant freshening of the Labrador Sea in recent decades have likely increased the equatorward baroclinic transport of the inner limb of the Labrador Current that flows over the broad continental shelf from the Grand Banks of Newfoundland to the Gulf of Maine. That current system now brings a greater fraction of colder and fresher deep shelf waters into the Gulf than warmer and saltier offshore slope waters which were previously thought to dominate the flux of nutrients. Those deep shelf waters reflect nitrate losses from sediment denitrification and silicate accumulations from rivers and in situ regeneration, which together are altering the nutrient regime and potentially the structure of the planktonic ecosystem.     

Fluvial seed dispersal of riparian trees: transport and depositional processes

Fluvial seed dispersal considers both the transport and deposition of seeds where channel geomorphic structures, hydrology and seed dispersal traits contribute to transport times and depositional locations. This study examines the influence of stream flow patterns on fluvial seed dispersal of buoyant white alder (Alnus rhombifolia) seeds by applying a one‐dimensional transport model. Conceptually, the model separates the stream into two components: (i) the main channel where the seeds are transported downstream; and (ii) the transient storage zone where seeds are temporarily detained or deposited on the river bank. Transport processes are characterized by an advection–dispersion equation which is coupled to a transient storage model using an exponential decay term. The model parameters: longitudinal dispersion (D_L), exchange coefficient (α), main channel area (A) and storage zone (A_s) are estimated based on field experiments conducted in a confined, bedrock‐gravel bed river with pool‐riffle morphology located in coastal northern California. The riparian zone is inhabited by Alnus rhombifolia that disperse buoyant seeds in mid‐spring coinciding with the end of the wet, Mediterranean season. Artificial seeds, with similar traits of buoyancy and density to alder seeds, were used to quantify transport times and depositional locations. Preferential deposition resulted in stream reaches with larger A_s, high A_s/A ratios, and faster exchange coefficients corresponding to divergent stream flow (back‐eddies, re‐circulating flow, flow expansions) caused by geomorphic structures such as the ends of bar/riffle features and bends in the stream. The results demonstrate the importance of transient storage for seed transport and depositional processes. Morphological features that increase a channel's complexity create complex flow structures that detain seeds and provide a greater opportunity for deposition to occur. The model provides a simplification of river hydraulics to represent dispersal dynamics and lends itself to further understanding of hydrochory processes and associated population structure. Copyright © 2015 John Wiley & Sons, Ltd.     

Does geographic location impact the survival differential between screen- and interval-detected breast cancers?

Although mammography screening programs aim to diagnose breast cancer at an early stage, not all tumours are detected during the regular screening examination. This study examines the influence of various characteristics, including geographical residence, on the survival between screen- and interval-detected breast cancers among participants of a public population-based breast screening program in Queensland, Australia. The investigation was performed using the linked population-based datasets from BreastScreen Queensland and the Queensland Cancer Registry for the period of 1997–2008 for women aged 40–89 years at diagnosis. A Bayesian spatial relative survival modelling approach that accommodates rare outcomes in small geographic regions was adopted, with the use of Markov chain Monte Carlo computation, to evaluate the relative excess risk of breast cancer. In the multivariate Bayesian spatial model, higher relative excess risk of mortality was observed in interval-detected cancer (RER = 1.59, 95 % credible interval = [1.33, 1.89]) compared to screen-detected cancer. Higher cancer survival among the study cohort was also observed among younger women (40–59 years), those of non-Indigenous ethnicity, with localised (stage I) tumour stage as well as those not in the work force. There was no independent association with marital status. Moreover, there was no substantive evidence of either measured geographical or latent random spatial inequalities in survival among screening participants across Queensland, meaning the higher survival for screen-detected breast cancer patients compared to interval-detected women was consistent across the state. These results provide suggestive evidence supporting the effectiveness of the BreastScreen Queensland screening program in reaching socio-economically disadvantaged women as well as those living in rural and remote areas of the state, but also highlights the need for any interval cancer awareness programs to be geographically widespread.