Ruth Joy

Dietary analysis from fecal samples : How many scats are enough?

Abstract Diets of mammals are increasingly being inferred from identification of hard parts from prey eaten and recovered in fecal remains (scats). Frequencies with which particular prey species occur among collections of scats are easily compiled to describe the average diet, and can be used to compare diets between and within geographic regions, and across years and seasons. Important to these analyses is the question of statistical power. In other words, how many scats should be collected to compare the diet among and between species? We addressed this problem by using Monte Carlo simulations and frequency of occurrence methods to analytically determine the consequence of sample size on the dietary analysis of scats. We considered 2 questions. First, how is the statistical power affected by sample size? Second, what is the likelihood of not identifying a prey species? We randomly sampled predetermined numbers of scats (n = 10–200) from computer-generated populations of scats containing prey of known species and frequencies of occurrences. We also randomly sampled a large database of field-collected scats from Steller sea lions (Eumetopias jubatus). We then used standard contingency table tests such as chi-square and Fishers exact test to determine whether differences between our samples and populations were statistically significant. We found that a minimum size of 59 scats is necessary to identify principal prey remains occurring in >5% of scats. However, 94 samples are required when comparing diets to distinguish moderate effect sizes over time or between areas. These findings have significant implications for the interpretation of published dietary data, as well as for the design of future scat-based dietary studies for pinnipeds and other species.

Impact of neighborhood-level socioeconomic status on HIV disease progression in a universal health care setting.

Objectives:The objectives of this study were to examine neighborhood measures of socioeconomic status and their effect on the risk of mortality among HIV-positive persons accessing and not accessing treatment, the effects of late access to treatment by CD4 cell count, and survival among those who accessed treatment. Methods:We limited our analysis to the era of highly active antiretroviral therapy (HAART). We used individual-level patient and clinical characteristics and neighborhood-level socioeconomic data to address our objectives. The Pearson χ2 and Wilcoxon sign rank tests were used to compare mortality among HIV-positive persons accessing and not accessing treatment, logistic regression models were used to compare persons who accessed treatment with low CD4 cell counts (<50 cells/mm3) with those who accessed treatment earlier (CD4 count ≥50 cells/mm3), and Weibull survival models were used to compare mortality among those who accessed treatment. Results:Forty percent of people who died from HIV/AIDS-related causes never accessed treatment. Among those who accessed treatment, 16% did so when their CD4 counts were <50 cells/mm3. Unemployment was associated with delayed access to treatment (odds ratio = 1.41, 95% confidence interval [CI]: 1.14 to 1.74). Postsecondary education (hazard ratio [HR] = 0.80, 95% CI: 0.71 to 0.91) and percent of residents below the poverty line (HR = 1.07, 95% CI: 1.01 to 1.13) were associated with mortality. Conclusions:In a setting where treatment for HIV is free of charge, a significant number of HIV-positive persons did not access HAART. Low socioeconomic status was associated with this delay and with increased mortality among persons receiving HAART. Social and health policy initiatives, beyond free and universal health care, are required to optimize access to HAART.

Enfuvirtide plasma levels and injection site reactions using a needle-free gas-powered injection system (Biojector).

Objectives:To assess the use of the Biojector B2000 needle-free gas-powered injection system for subcutaneous administration of enfuvirtide in HIV-infected patients and to compare this system with standard needles and syringes with respect to ease of use, severity of injection site reactions (ISR), and enfuvirtide plasma levels. Design:An observational study among 32 treatment-experienced HIV clinic patients receiving enfuvirtide. Methods:Adult patients were assessed before and after switching from standard needles to the Biojector for enfuvirtide administration. Patients used the Biojector for up to 24 weeks and rated ease of use from 0 (easy) to 3 (difficult). ISR were graded from 0 to 31 for signs and symptoms (erythema, induration, pruritus, nodules/cysts, ecchymosis), duration of individual lesions, and number of lesions. Plasma was collected pre-dose and 1 h post-dose for enfuvirtide measurement. The high-pressure liquid chromatography with tandem mass spectrometry method used was specific for enfuvirtide over its known plasma metabolite. Wilcoxon rank sum tests were used to compare needle-based and Biojector outcomes. Results:The Biojector was rated as being significantly easier to use (P < 0.001) and reduced the occurrence of ISR compared with standard needles (P < 0.001). Enfuvirtide plasma levels were not statistically different between the two administration methods at either pre-dose trough (P = 0.41) or 1 h post-dose (P = 0.74). Conclusions:The Biojector needle-free injection system was easy to use for enfuvirtide administration and was associated with a decreased severity of ISR. Plasma enfuvirtide levels pre-dose and 1 h post-dose were comparable when injecting with standard needles or the Biojector.

Static inflation and deflation pressure-volume curves from excised lungs of marine mammals.

SUMMARY Excised lungs from eight marine mammal species [harp seal (Pagophilus groenlandicus), harbor seal (Phoca vitulina), gray seal (Halichoerus grypush), Atlantic white-sided dolphin (Lagenorhynchus acutus), common dolphin (Delphinus delphis), Rissos dolphin (Grampus griseus), long-finned pilot whale (Globicephala melas) and harbor porpoise (Phocoena phocoena)] were used to determine the minimum air volume of the relaxed lung (MAV, N=15), the elastic properties (pressure–volume curves, N=24) of the respiratory system and the total lung capacity (TLC). Our data indicate that mass-specific TLC (sTLC, l kg–1) does not differ between species or groups (odontocete vs phocid) and agree with that estimated (TLCest) from body mass (Mb) by applying the equation: TLCest=0.135 Mb0.92. Measured MAV was on average 7% of TLC, with a range from 0 to 16%. The pressure–volume curves were similar among species on inflation but diverged during deflation in phocids in comparison with odontocetes. These differences provide a structural basis for observed species differences in the depth at which lungs collapse and gas exchange ceases.

Estimating behavioral parameters in animal movement models using a state‐augmented particle filter

Data on fine-scale animal movement are being collected worldwide, with the number of species being tagged and the resolution of data rapidly increasing. In this study, a general methodology is proposed to understand the patterns in these high-resolution movement time series that relate to marine animal behavior. The approach is illustrated with dive data from a northern fur seal (Callorhinus ursinus) tagged on the Pribilof Islands, Alaska, USA. We apply a state-space model composed of a movement model and corresponding high-resolution vertical movement data. The central goal is to estimate parameters of this movement model, particularly their variation on appropriate time scales, thereby providing a direct link to behavior. A particle filter with state augmentation is used to jointly estimate the movement parameters and the state. A multiple iterated filter using overlapping data segments is implemented to match the parameter time scale with the behavioral inference. The time variation in the auto-covariance function facilitates identification of a movement model, allows separation of observation and process noise, and provides for validation of results. The analysis yields fitted parameters that show distinct time-evolving changes in fur seal behavior over time, matching well what is observed in the original data set.