Comparison of environmental DNA and underwater visual count surveys for detecting juvenile coho salmon (Oncorhynchus kisutch) in rivers

Environmental DNA (eDNA) has developed into a useful tool for determining the distribution of rare aquatic species, but relatively few studies have directly compared the detection probabilities of this method with other conventional survey techniques. These comparisons can inform which method may be better suited to address study objectives. In this study, the overall goal was to compare the ability of eDNA and underwater visual count (UVC) surveys to detect juvenile coho salmon (Oncorhynchus kisutch), a species of conservation concern at the southern extent of its geographic range. Specifically, I address two objectives: (1) compare the ability of eDNA and UVC surveys to detect coho salmon and the influence of environmental covariates on detectability and (2) evaluate the utility of eDNA concentrations and habitat covariates to predict the count of coho salmon within small pools. Water samples for eDNA analysis and snorkel surveys were conducted at 96 pools across 25 stream reaches in the Smith River basin, California. I used multi-scale occupancy models to estimate method-specific detection probabilities (p) and the effect of habitat covariates, including basin area (as a proxy for discharge), residual pool depth, and large woody debris. Results showed that eDNA and UVC surveys had a high degree of agreement in detecting the presence of coho salmon at both the pool scale (93% agreement) and reach scale (80% agreement), however there were several occasions where only one method detected coho salmon. The top occupancy model, identified using Akaike’s information criterion, indicated that the detection probabilities were best predicted by method, basin area, residual pool depth, and an interaction between method and basin area. Under median habitat conditions, detection probabilities were similar and high for both methods (peDNA=91%, pUVC=89%). Residual pool depth had a slight positive effect on peDNA and pUVC. Detection probabilities for both methods were affected negatively by increasing basin size, but p declined more substantially for eDNA; at the highest basin areas, peDNA =40% compared to pUVC=78%. Finally, eDNA concentrations were a poor predictor of coho salmon count in small pools. The absence of a relationship between eDNA concentrations and fish counts is contrary to other studies and may have resulted as a consequence of the relatively small differences in counts observed between pools, which ranged from 0 to 210 individuals. Overall, this study illustrates that eDNA methods were as sensitive as UVC surveys for detecting coho presence under most conditions but could not be used to produce reliable estimates of the average observed count of the target species in this system. Therefore, these findings support the use of eDNA methods for monitoring the distributions of a rare species but indicate that implementation should be guided by study objectives and local environmental conditions

Observation of blue-shifted ultralong-range Cs2_{2} Rydberg molecules

We observe ultralong-range blue-shifted Cs$_{2}$ molecular states near $ns_{1/2}$ Rydberg states in an optical dipole trap, where $31\leq n\leq34$. The accidental near degeneracy of $(n-4)l$ and $ns$ Rydberg states for $l>2$ in Cs, due to the small fractional $ns$ quantum defect, leads to non-adiabatic coupling among these states, producing potential wells above the $ns$ thresholds. Two important consequences of admixing high angular momentum states with $ns$ states are the formation of large permanent dipole moments, $\sim 15-100\,$Debye, and accessibility of these states via two-photon association. The observed states are in excellent agreement with theory. Both projections of the total angular momentum on the internuclear axis are visible in the experiment

Parallel Load Balancing Strategies for Ensembles of Stochastic Biochemical Simulations

The evolution of biochemical systems where some chemical species are present with only a small number of molecules, is strongly influenced by discrete and stochastic effects that cannot be accurately captured by continuous and deterministic models. The budding yeast cell cycle provides an excellent example of the need to account for stochastic effects in biochemical reactions. To obtain statistics of the cell cycle progression, a stochastic simulation algorithm must be run thousands of times with different initial conditions and parameter values. In order to manage the computational expense involved, the large ensemble of runs needs to be executed in parallel. The CPU time for each individual task is unknown before execution, so a simple strategy of assigning an equal number of tasks per processor can lead to considerable work imbalances and loss of parallel efficiency. Moreover, deterministic analysis approaches are ill suited for assessing the effectiveness of load balancing algorithms in this context. Biological models often require stochastic simulation. Since generating an ensemble of simulation results is computationally intensive, it is important to make efficient use of computer resources. This paper presents a new probabilistic framework to analyze the performance of dynamic load balancing algorithms when applied to large ensembles of stochastic biochemical simulations. Two particular load balancing strategies (point-to-point and all-redistribution) are discussed in detail. Simulation results with a stochastic budding yeast cell cycle model confirm the theoretical analysis. While this work is motivated by cell cycle modeling, the proposed analysis framework is general and can be directly applied to any ensemble simulation of biological systems where many tasks are mapped onto each processor, and where the individual compute times vary considerably among tasks

A Framework to Analyze the Performance of Load Balancing Schemes for Ensembles of Stochastic Simulations

Ensembles of simulations are employed to estimate the statistics of possible future states of a system, and are widely used in important applications such as climate change and biological modeling. Ensembles of runs can naturally be executed in parallel. However, when the CPU times of individual simulations vary considerably, a simple strategy of assigning an equal number of tasks per processor can lead to serious work imbalances and low parallel efficiency. This paper presents a new probabilistic framework to analyze the performance of dynamic load balancing algorithms for ensembles of simulations where many tasks are mapped onto each processor, and where the individual compute times vary considerably among tasks. Four load balancing strategies are discussed: most-dividing, all-redistribution, random-polling, and neighbor-redistribution. Simulation results with a stochastic budding yeast cell cycle model is consistent with the theoretical analysis. It is especially significant that there is a provable global decrease in load imbalance for the local rebalancing algorithms due to scalability concerns for the global rebalancing algorithms. The overall simulation time is reduced by up to 25%, and the total processor idle time by 85%

Photoionization Rates of Cs Rydberg Atoms in a 1064 nm Far Off-Resonance Trap

Experimental measurements of photoionization rates of $nD_{5/2}$ Rydberg states of Cs ($50 \leq n \leq 75$) in a 1064 nm far off-resonance dipole trap are presented. The photoionization rates are obtained by measuring the lifetimes of Rydberg atoms produced inside of a 1064 nm far off-resonance trap and comparing the lifetimes to corresponding control experiments in a magneto-optical trap. Experimental results for the control experiments agree with recent theoretical predictions for Rydberg state lifetimes and measured photoionization rates are in agreement with transition rates calculated from a model potential.Comment: 12 pages, 4 figure

Three Proposals for Rewarding Novel Health Technologies Benefiting People Living in Poverty. A Comparative Analysis of Prize Funds, Health Impact Funds and a Cost-Effectiveness/Competitive Tender Treaty

This paper sets out to analyse three different academic proposals for addressing the needs of the poor in relation to new, rather than ‘essential’ medicines. It focuses particularly on (1) research and development (R&D) prize funds, (2) a health impact fund (HIF) system and (3) a multilateral treaty on health technology cost-effectiveness evaluation and competitive tender. It compares the extent to which each responds to the ‘market fundamentalist’ philosophy (that we maintain forms a loose theoretical background for the patent-driven approach to pharmaceutical R&D) and begins to analyse their respective strengths and weaknesses

Unilateral and Exclusionary/Strategic Effects of Common Agency: Price Impacts in a Repeated Common Value English Auction

The business justification for multiple principals to hire a common agent is efficiency. Our empirical study demonstrates that the creation of the common agent unilaterally depresses winning bids. Additionally, the common agent was not only observed to be the dominant bidder but also paid significantly lower prices than fringe competitors (price/quantity differential). The observed price/quantity differential is consistent with the almost common value English auction theory developed by Rose and Kagel (2008) in which a cost advantaged bidder is able to reduce competition by credibly raising the costs of disadvantaged rivals associated with the winner’s curse.Common Value Auctions, Common Agency, Antitrust, Industrial Organization, D44, K21, K23,

Lung Rest During Extracorporeal Membrane Oxygenation for Neonatal Respiratory Failure-Practice Variations and Outcomes.

OBJECTIVE: Describe practice variations in ventilator strategies used for lung rest during extracorporeal membrane oxygenation for respiratory failure in neonates, and assess the potential impact of various lung rest strategies on the duration of extracorporeal membrane oxygenation and the duration of mechanical ventilation after decannulation. DATA SOURCES: Retrospective cohort analysis from the Extracorporeal Life Support Organization registry database during the years 2008-2013. STUDY SELECTION: All extracorporeal membrane oxygenation runs for infants less than or equal to 30 days of life for pulmonary reasons were included. DATA EXTRACTION: Ventilator type and ventilator settings used for lung rest at 24 hours after extracorporeal membrane oxygenation initiation were obtained. DATA SYNTHESIS: A total of 3,040 cases met inclusion criteria. Conventional mechanical ventilation was used for lung rest in 88% of cases and high frequency ventilation was used in 12%. In the conventional mechanical ventilation group, 32% used positive end-expiratory pressure strategy of 4-6 cm H2O (low), 22% used 7-9 cm H2O (mid), and 43% used 10-12 cm H2O (high). High frequency ventilation was associated with an increased mean (SEM) hours of extracorporeal membrane oxygenation (150.2 [0.05] vs 125 [0.02]; p \u3c 0.001) and an increased mean (SEM) hours of mechanical ventilation after decannulation (135 [0.09] vs 100.2 [0.03]; p = 0.002), compared with conventional mechanical ventilation among survivors. Within the conventional mechanical ventilation group, use of higher positive end-expiratory pressure was associated with a decreased mean (SEM) hours of extracorporeal membrane oxygenation (high vs low: 136 [1.06] vs 156 [1.06], p = 0.001; mid vs low: 141 [1.06] vs 156 [1.06]; p = 0.04) but increased duration of mechanical ventilation after decannulation in the high positive end-expiratory pressure group compared with low positive end-expiratory pressure (p = 0.04) among survivors. CONCLUSIONS: Wide practice variation exists with regard to ventilator settings used for lung rest during neonatal respiratory extracorporeal membrane oxygenation. Use of high frequency ventilation when compared with conventional mechanical ventilation and use of low positive end-expiratory pressure strategy when compared with mid positive end-expiratory pressure and high positive end-expiratory pressure strategy is associated with longer duration of extracorporeal membrane oxygenation. Further research to provide evidence to drive optimization of pulmonary management during neonatal respiratory extracorporeal membrane oxygenation is warranted