A novel drifter designed for use with a mounted Acoustic Doppler Current Profiler in shallow environments

We present a novel design for a surface drifter, mounted with a pulse-coherent Acoustic Doppler Current Profiler (ADCP) for measuring near-surface (depths 0.18-1 m) flows. During repeated drifter deployments over the tidal flats of Skagit Bay, the mounted ADCP recorded high quality and high resolution profiles of velocity in depths as shallow as 0.4 m. Depth-dependent velocities revealed regions of vertically sheared currents and wave motions not resolved by surface drifters alone. Although the cost of ADCPs is substantial, the drifter bodies were low cost, robust, and of simple construction

Lagrangian measurements of turbulent dissipation over a shallow tidal flat from pulse coherent Acoustic Doppler Profilers

We present high resolution (25 mm spatial, 8 Hz temporal) profiles of velocity measured over a shallow tidal flat using pulse-coherent Acoustic Doppler Profilers mounted on surface drifters. The use of Lagrangian measurements mitigated the problem of resolving velocity ambiguities, a problem which often limits the application of high-resolution pulse-coherent profilers. Turbulent dissipation rates were estimated from second-order structure functions of measured velocity. Drifters were advected towards, and subsequently trapped on, a convergent surface front which marked the edge of a freshwater plume. Measured dissipation rates increased as a drifter deployed within the plume approached the front. A drifter then propagated with and along the front as the fresh plume spread across the tidal flats. Near-surface turbulent dissipation measured at the front roughly matched a theoretical mean-shear-cubed relationship, whereas dissipation measured in the stratified plume behind the front was suppressed. After removal of estimates affected by surface waves, near-bed dissipation matched the velocity cubed relationship, although scatter was substantial. Dissipation rates appeared to be enhanced when the drifter propagated across small subtidal channels

Comment on “Breaking wave induced cross‐shore tracer dispersion in the surf zone: Model results and scaling”

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94805/1/jgrc10792.pd

The SISO CSPI PDG standard for commercial off-the-shelf simulation package interoperability reference models

For many years discrete-event simulation has been used to analyze production and logistics problems in manufactur-ing and defense. Commercial-off-the-shelf Simulation Packages (CSPs), visual interactive modelling environ-ments such as Arena, Anylogic, Flexsim, Simul8, Witness, etc., support the development, experimentation and visua-lization of simulation models. There have been various attempts to create distributed simulations with these CSPs and their tools, some with the High Level Architecture (HLA). These are complex and it is quite difficult to assess how a set of models/CSP are actually interoperating. As the first in a series of standards aimed at standardizing how the HLA is used to support CSP distributed simula-tions, the Simulation Interoperability Standards Organiza-tion’s (SISO) CSP Interoperability Product Development Group (CSPI PDG) has developed and standardized a set of Interoperability Reference Models (IRM) that are in-tended to clearly identify the interoperability capabilities of CSP distributed simulations

Fine-suspended sediment and water budgets for a large, seasonally dry tropical catchment: Burdekin River catchment, Queensland, Australia

The Burdekin River catchment (~130,400 km2) is a seasonally dry tropical catchment located in north-east Queensland, Australia. It is the single largest source of suspended sediment to the Great Barrier Reef (GBR). Fine sediments are a threat to ecosystems on the GBR where they contribute to elevated turbidity (reduced light), sedimentation stress, and potential impacts from the associated nutrients. Suspended sediment data collected over a 5 year period were used to construct a catchment-wide sediment source and transport budget. The Bowen River tributary was identified as the major source of end-of-river suspended sediment export, yielding an average of 530 t km−2 yr−1 during the study period. Sediment trapping within a large reservoir (1.86 million ML) and the preferential transport of clays and fine silts downstream of the structure were also examined. The data reveal that the highest clay and fine silt loads—which are of most interest to environmental managers of the GBR—are not always sourced from areas that yield the largest total suspended sediment load (i.e., all size fractions). Our results demonstrate the importance of incorporating particle size into catchment sediment budget studies undertaken to inform management decisions to reduce downstream turbidity and sedimentation. Our data on sediment source, reservoir influence, and subcatchment and catchment yields will improve understandings of sediment dynamics in other tropical catchments, particularly those located in seasonally wet-dry tropical savannah/semiarid climates. The influence of climatic variability (e.g., drought/wetter periods) on annual sediment loads within large seasonally dry tropical catchments is also demonstrated by our data

The effect of ageing on human lymphocyte subsets: comparison of males and females

There is reported to be a decline in immune function and an alteration in the frequency of circulating lymphocytes with advancing age. There are also differences in ageing and lifespan between males and females. We performed this study to see if there were differences between males and females in the frequency of the different lymphocyte subsets with age.Using flow cytometry we have examined different populations of peripheral blood leukocytes purified from healthy subjects with age ranging from the third to the tenth decade. We used linear regression analysis to determine if there is a linear relationship between age and cell frequencies. For the whole group, we find that with age there is a significant decline in the percentage of naïve T cells and CD8(+) T cells, and an increase in the percentage of effector memory cells, CD4(+)foxp3(+) T cells and NK cells. For all cells where there was an effect of ageing, the slope of the curve was greater for men than for women and this was statistically significant for CD8(+)alphabeta(+) T cells and CD3(+)CD45RA(-)CCR7(-) effector memory cells. There was also a difference for naïve cells but this was not significant.The cause of the change in percentage of lymphocyte subsets with age, and the different effects on males and females is not fully understood but warrants further study

Menthol stereoisomers exhibit different effects on α4β2 nAChR upregulation and dopamine neuron spontaneous firing

Menthol contributes to poor cessation rates among smokers, in part because menthol enhances nicotine reward and reinforcement. Mentholated tobacco products contain (−)-menthol and (+)-menthol, in varying proportions. We examined these two menthol stereoisomers for their ability to upregulate α4β2 nAChRs and to alter dopamine neuron firing frequency using long-term, low-dose (≤ 500 nM) exposure that is pharmacologically relevant to smoking. We found that (−)-menthol upregulates α4β2 nAChRs while (+)-menthol does not. We also found that (−)-menthol decreases dopamine neuron baseline firing and dopamine neuron excitability, while (+)-menthol exhibits no effect. We then examined both stereoisomers for their ability to inhibit α4β2 nAChR function at higher concentrations (>10 µM) using the Xenopus oocyte expression system. To probe for the potential binding site of menthol, we conducted flooding simulations and site-directed mutagenesis. We found that menthol likely binds to the 9’ position on the TM2 helix. We found that menthol inhibition is dependent on the end-to-end distance of the side chain at the 9’ residue. Additionally, we have found that (−)-menthol is only modestly (∼25%) more potent than (+)-menthol at inhibiting wildtype α4β2 nAChRs and a series of L9’ mutant nAChRs. These data reveal that menthol exhibits a stereoselective effect on nAChRs and that the stereochemical effect is much greater for long-term, sub µM exposure in mice than for acute, higher level exposure. We hypothesize that of the two menthol stereoisomers, only (−)-menthol plays a role in enhancing nicotine reward through nAChRs on dopamine neurons

Nearshore sandbar migration predicted by an eddy-diffusive boundary layer model

We simulated the erosion and accretion of a natural beach using a wave-resolving eddy-diffusive model of water and suspended sediment motion in the bottom boundary layer. Nonlinear advection was included in this one-dimensional (vertical profile) model by assuming that waves propagated almost without change of form. Flows were forced by fluctuating pressure gradients chosen to reproduce the velocity time series measured during the Duck94 field experiment. The cross-shore flux of suspended sediment beneath each field-deployed current meter was estimated, and beach erosion (accretion) was calculated from the divergence (convergence) of this flux. Horizontal pressure forces on sediment particles were neglected. The model successfully predicted two bar migration events (one shoreward bar migration and one seaward) but failed to predict a third (seaward migration) event. Simulated seaward sediment transport was due to seaward mean currents. Simulated shoreward sediment transport was due to covariance between wave-frequency fluctuations in velocity and sediment concentration and was mostly confined to the wave boundary layer. Predicted seaward (shoreward) bar migration was driven by a maximum in the current-generated (wave-generated) flux over the sandbar. A wave-generated downward flux of shoreward momentum into the wave boundary layer contributed to shoreward sediment transport and often had a local maximum over the bar crest. Second-order nonlinear advection of sediment, mostly representing shoreward advection by the Stokes drift, also often had a local maximum over the bar crest. Together, wave-generated momentum fluxes and the Stokes drift substantially increased shoreward transport and were essential to predictions of shoreward bar migration

Improved Imputation of Common and Uncommon Single Nucleotide Polymorphisms (SNPs) with a New Reference Set

Statistical imputation of genotype data is an important technique for analysis of genome-wide association studies (GWAS). We have built a reference dataset to improve imputation accuracy for studies of individuals of primarily European descent using genotype data from the Hap1, Omni1, and Omni2.5 human SNP arrays (Illumina). Our dataset contains 2.5-3.1 million variants for 930 European, 157 Asian, and 162 African/African-American individuals. Imputation accuracy of European data from Hap660 or OmniExpress array content, measured by the proportion of variants imputed with R^2^>0.8, improved by 34%, 23% and 12% for variants with MAF of 3%, 5% and 10%, respectively, compared to imputation using publicly available data from 1,000 Genomes and International HapMap projects. The improved accuracy with the use of the new dataset could increase the power for GWAS by as much as 8% relative to genotyping all variants. This reference dataset is available to the scientific community through the NCBI dbGaP portal. Future versions will include additional genotype data as well as non-European populations