Brett G. Amidan

Survival Estimates for Juvenile Fish Subjected to a Laboratory-Generated Shear Environment

Abstract Juvenile rainbow trout Oncorhynchus mykiss and steelhead (anadromous rainbow trout), fall (age-0 and age-1) and spring Chinook salmon O. tshawytscha, and American shad Alosa sapidissima were exposed to shear environments in the laboratory to establish injury–mortality thresholds based on estimates of strain rate. Fish were exposed to a submerged jet having exit velocities of 0 to 21.3 m/s, providing estimated exposure strain rates up to 1,185/s. Turbulence intensity in the area of the jet where fish were subjected to shear was minimal, varying from 3% to 6% of the estimated exposure strain rate. Injuries and mortalities increased for all species of fish at strain rates greater than 495/s. American shad were the most susceptible to injury after being subjected headfirst to a shear environment, while steelhead and rainbow trout were the most resistant. There was no apparent size-related trend in susceptibility to high shear except that age-0 fall Chinook salmon were more resistant to shear environm...

In vivo MRI of altered proton signal intensity and T2 relaxation in a bleomycin model of pulmonary inflammation and fibrosis

To investigate the ability of proton (1H) magnetic resonance imaging (MRI) to distinguish between pulmonary inflammation and fibrosis.

Laboratory Studies of the Effects of Pressure and Dissolved Gas Supersaturation on Turbine-Passed Fish

The objective of this study was to examine the relative importance of pressure changes as a source of turbine-passage injury and mortality. Specific tests were designed to quantify the response of fish to rapid pressure changes typical of turbine passage, with and without the complication of the fish being acclimated to gas supersaturated water. We investigated the responses of rainbow trout (Oncorhynchus mykiss), chinook salmon (O. tshawytscha), and bluegill sunfish (Lepomis macrochirus) to these two stresses, both singly and in combination.

Comparison of two quantitative methods of discerning airspace enlargement in smoke-exposed mice.

In this work, we compare two methods for evaluating and quantifying pulmonary airspace enlargement in a mouse model of chronic cigarette smoke exposure. Standard stereological sample preparation, sectioning, and imaging of mouse lung tissues were performed for semi-automated acquisition of mean linear intercept (Lm) data. After completion of the Lm measurements, D2, a metric of airspace enlargement, was measured in a blinded manner on the same lung images using a fully automated technique developed in-house. An analysis of variance (ANOVA) shows that although Lm was able to separate the smoke-exposed and control groups with statistical significance (p = 0.034), D2 was better able to differentiate the groups (p<0.001) and did so without any overlap between the control and smoke-exposed individual animal data. In addition, the fully automated implementation of D2 represented a time savings of at least 24x over semi-automated Lm measurements. Although D2 does not provide 3D stereological metrics of airspace dimensions as Lm does, results show that it has higher sensitivity and specificity for detecting the subtle airspace enlargement one would expect to find in mild or early stage emphysema. Therefore, D2 may serve as a more accurate screening measure for detecting early lung disease than Lm.

Morphometric Comparison of Clavicle Outlines from 3D Bone Scans and 2D Chest Radiographs: A Shortlisting Tool to Assist Radiographic Identification of Human Skeletons†

This paper describes a computerized clavicle identification system primarily designed to resolve the identities of unaccounted‐for U.S. soldiers who fought in the Korean War. Elliptical Fourier analysis is used to quantify the clavicle outline shape from skeletons and postero‐anterior antemortem chest radiographs to rank individuals in terms of metric distance. Similar to leading fingerprint identification systems, shortlists of the top matching candidates are extracted for subsequent human visual assessment. Two independent tests of the computerized system using 17 field‐recovered skeletons and 409 chest radiographs demonstrate that true‐positive matches are captured within the top 5% of the sample 75% of the time. These results are outstanding given the eroded state of some field‐recovered skeletons and the faintness of the 1950s photofluorographs. These methods enhance the capability to resolve several hundred cold cases for which little circumstantial information exists and current DNA and dental record technologies cannot be applied.

False-Negative Rate and Recovery Efficiency Performance of a Validated Sponge Wipe Sampling Method

ABSTRACT Recovery of spores from environmental surfaces varies due to sampling and analysis methods, spore size and characteristics, surface materials, and environmental conditions. Tests were performed to evaluate a new, validated sponge wipe method using Bacillus atrophaeus spores. Testing evaluated the effects of spore concentration and surface material on recovery efficiency (RE), false-negative rate (FNR), limit of detection (LOD), and their uncertainties. Ceramic tile and stainless steel had the highest mean RE values (48.9 and 48.1%, respectively). Faux leather, vinyl tile, and painted wood had mean RE values of 30.3, 25.6, and 25.5, respectively, while plastic had the lowest mean RE (9.8%). Results show roughly linear dependences of RE and FNR on surface roughness, with smoother surfaces resulting in higher mean REs and lower FNRs. REs were not influenced by the low spore concentrations tested (3.10 × 10−3 to 1.86 CFU/cm2). Stainless steel had the lowest mean FNR (0.123), and plastic had the highest mean FNR (0.479). The LOD90 (≥1 CFU detected 90% of the time) varied with surface material, from 0.015 CFU/cm2 on stainless steel up to 0.039 on plastic. It may be possible to improve sampling results by considering surface roughness in selecting sampling locations and interpreting spore recovery data. Further, FNR values (calculated as a function of concentration and surface material) can be used presampling to calculate the numbers of samples for statistical sampling plans with desired performance and postsampling to calculate the confidence in characterization and clearance decisions.

Simulated Passage Through A Modified Kaplan Turbine Pressure Regime: A Supplement to "Laboratory Studies of the Effects of Pressure and Dissolved Gas Supersaturation on Turbine-Passed Fish"

A previous test series (Abernethy et al. 2001) evaluated the effects of passage through a Kaplan turbine under the “worst case” pressure conditions. For this series of tests, pressure changes were modified to simulate passage through a Kaplan turbine under a more “fish-friendly” mode of operation. The results were compared to results from Abernethy et al. (2001). These data indicate that altered operating conditions that raise the nadir (low point) of the turbine passage pressure regime could reduce the injury and mortality rates of fish during turbine passage. Fall Chinook salmon were not injured or killed when subjected to the modified pressure scenario. Bluegills were more sensitive to pressure effects than fall Chinook salmon, but injury and mortality rates were lower under the modified Kaplan pressure regime. This improvement was particularly significant among fish that were acclimated to greater water pressures (traveling at greater depth).

Laboratory studies on surface sampling of Bacillus anthracis contamination: summary, gaps and recommendations

This article summarizes previous laboratory studies to characterize the performance of methods for collecting, storing/transporting, processing and analysing samples from surfaces contaminated by Bacillus anthracis or related surrogates. The focus is on plate culture and count estimates of surface contamination for swab, wipe and vacuum samples of porous and nonporous surfaces. Summaries of the previous studies and their results were assessed to identify gaps in information needed as inputs to calculate key parameters critical to risk management in biothreat incidents. One key parameter is the number of samples needed to make characterization or clearance decisions with specified statistical confidence. Other key parameters include the ability to calculate, following contamination incidents, the (i) estimates of B. anthracis contamination, as well as the bias and uncertainties in the estimates and (ii) confidence in characterization and clearance decisions for contaminated or decontaminated buildings. Gaps in knowledge and understanding identified during the summary of the studies are discussed. Additional work is needed to quantify (i) the false‐negative rates of surface‐sampling methods with lower concentrations on various surfaces and (ii) the effects on performance characteristics of: aerosol vs liquid deposition of spores, using surrogates instead of B. anthracis, real‐world vs laboratory conditions and storage and transportation conditions. Recommendations are given for future evaluations of data from existing studies and possible new studies.

Signatures for mass spectrometry data quality.

Ensuring data quality and proper instrument functionality is a prerequisite for scientific investigation. Manual quality assurance is time-consuming and subjective. Metrics for describing liquid chromatography mass spectrometry (LC–MS) data have been developed; however, the wide variety of LC–MS instruments and configurations precludes applying a simple cutoff. Using 1150 manually classified quality control (QC) data sets, we trained logistic regression classification models to predict whether a data set is in or out of control. Model parameters were optimized by minimizing a loss function that accounts for the trade-off between false positive and false negative errors. The classifier models detected bad data sets with high sensitivity while maintaining high specificity. Moreover, the composite classifier was dramatically more specific than single metrics. Finally, we evaluated the performance of the classifier on a separate validation set where it performed comparably to the results for the testing/training data sets. By presenting the methods and software used to create the classifier, other groups can create a classifier for their specific QC regimen, which is highly variable lab-to-lab. In total, this manuscript presents 3400 LC–MS data sets for the same QC sample (whole cell lysate of Shewanella oneidensis), deposited to the ProteomeXchange with identifiers PXD000320–PXD000324.

False negative rate and other performance measures of a sponge-wipe surface sampling method for low contaminant concentrations.

Recovery of spores from environmental surfaces is known to vary due to sampling methodology, techniques, spore size and characteristics, surface materials, and environmental conditions. A series of tests were performed to evaluate a new, validated sponge-wipe method. Specific factors evaluated were the effects of contaminant concentrations and surface materials on recovery efficiency (RE), false negative rate (FNR), limit of detection (LOD) - and the uncertainties of these quantities. Ceramic tile and stainless steel had the highest mean RE values (48.9 and 48.1%, respectively). Faux leather, vinyl tile, and painted wood had mean RE values of 30.3, 25.6, and 25.5, respectively, while plastic had the lowest mean RE (9.8%). Results show a roughly linear dependence of surface roughness on RE, where the smoothest surfaces have the highest mean RE values. REs were not influenced by the low spore concentrations tested (3 x 10{sup -3} to 1.86 CFU/cm{sup 2}). The FNR data were consistent with RE data, showing a trend of smoother surfaces resulting in higher REs and lower FNRs. Stainless steel generally had the lowest mean FNR (0.123) and plastic had the highest mean FNR (0.479). The LOD{sub 90} varied with surface material, from 0.015 CFU/cm{sup 2} on stainless steel up to 0.039 on plastic. Selecting sampling locations on the basis of surface roughness and using roughness to interpret spore recovery data can improve sampling. Further, FNR values, calculated as a function of concentration and surface material, can be used pre-sampling to calculate the numbers of samples for statistical sampling plans with desired performance, and post-sampling to calculate the confidence in characterization and clearance decisions.