Survival and fidelity of translocated and resident burrowing owls in Arizona

Given the rapid pace of urbanization, mitigation translocations are increasingly being used to reduce human-wildlife conflicts, especially to move animals out of the path of land development. Burrowing owls (Athene cunicularia) are commonly subjected to translocations because of their association with flat, open lands that are attractive to development. But outcomes of burrowing owl translocations and the effects they have on their demographic parameters are seldom documented. From 2017–2019, we tracked the fates of 42 resident (non-translocated) burrowing owls and 43 translocated owls using very high frequency radio-telemetry across 4 release sites in southcentral Arizona, USA. Translocations were conducted by Wild At Heart (WAH), a non-profit raptor rehabilitation program, and owls were moved from areas with planned development activities to release sites that contained artificial burrows. Each year, WAH held translocated owls in groups of 6–10 owls with varying male to female ratios in aviaries prior to taking the owls to release sites where the owls stayed in soft-release tents for an acclimation period of 30 days before release. Resident owls were located at or near the 4 release sites. We used the joint live encounter and dead recovery model to evaluate differences in survival and fidelity probabilities between resident (non-translocated) and translocated burrowing owls and to assess factors that influenced these probabilities including sex, year, site, captivity duration, and the number of males in release cohorts for translocated owls. Annual survival was consistently lower for translocated owls (0.35, 95% CI = 0.10, 0.61 and 0.01, 95% CI = 0.00, 0.03 for 2017 and 2018, respectively) compared to resident owls (0.68, 95% CI = 0.45, 0.92 and 0.69, 95% CI = 0.47, 0.90 for 2017 and 2018, respectively). Annual fidelity was lower for translocated owls (0.05, 95% CI = 0.00, 0.15) compared to resident owls (0.79, 95% CI = 0.57, 1.00) in 2018, but fidelity did not differ significantly between translocated (0.54, 95% CI = 0.19, 0.89) and resident owls (0.62, 95% CI = 0.37, 0.87) in 2017. For translocated owls, the number of males in release cohorts negatively affected survival ($\hat{\mathrm{\beta }}$ = −0.74, 95% CI = −1.07, −0.40) and fidelity ($\hat{\mathrm{\beta }}$ = −0.73, 95% CI = −1.17, −0.29). Our results indicate the need for substantial changes to the current translocation methodology for burrowing owls in Arizona. Breeding season releases that included owl groups and multiple males within cohorts resulted in agonistic interactions, high mortality, and low fidelity. Translocations of this territorial species should be restricted to male-female pairs or single individuals. Earlier releases may allow owls time to become established on release sites prior to the breeding season, which could promote fidelity. We recommend these changes be implemented and evaluated along with an examination of other release methods.     

A tale of two populations: vital rates of fishers in British Columbia,Canada

Fishers (Pekania pennanti) are a forest-dependent carnivore of conservation concern in British Columbia, Canada. Ecological, spatial, and genetic evidence suggests that there are 2 distinct populations (Boreal and Columbian) that occur in forests at low to moderate elevations in the boreal and central interior regions of the province. In British Columbia, fishers occur at low densities relative to other parts of their range in North America, are trapped for their fur, and are sensitive to habitat change. Despite these factors, little demographic information exists to assist with management decisions for these populations. We collated and analyzed survival and reproductive data from 100 radio-tagged fishers from 5 independent studies conducted between 1990 and 2012 in British Columbia: 2 in the Boreal population, and 3 in the Columbian population. We also collated litter size data from 1 den box study and a translocation project of fishers from the Columbian population. Annual survival rates were not significantly different between the populations or between males and females; however, adult survival rates were higher than subadults (0.79 and 0.63, respectively). Subadult females had significantly lower survival rates than other sex or age classes. Reproductive rates were significantly different between the 2 populations (denning rate = 0.54 [Columbian], 0.82 [Boreal]; $\overline{x}$ litter size = 1.7 [Columbian], 2.6 [Boreal]). These differences resulted in net reproductive rates in the Columbian population that were less than half of those in the Boreal population (0.92 kits/reproductive season compared to 2.13, respectively). Population growth rates suggest that the Columbian population may have been declining during the studies, whereas the Boreal population may have been increasing (0.96 compared to 1.20). Consequently, we suggest that focused and intensive habitat and population management for fishers are needed in British Columbia to ensure population sustainability, particularly for the Columbian population.     

Evaluating risks associated with capture and handling of mule deer for individual-based,long-term research

Capture and handling techniques for individual-based, long-term research that tracks the life history of animals by recapturing the same individuals for several years has vastly improved study inferences and our understanding of animal ecology. Yet there are corresponding risks to study animals associated with physical trauma or capture myopathy that can occur during or following capture events. Rarely has empirical evidence existed to guide decisions associated with understanding the magnitude of capture-related risks, how to reduce these risks when possible, and implications for mortality censoring and survival estimates. We used data collected from 2,399 capture events of mule deer (Odocoileus hemionus) via helicopter net-gunning to compare daily survival probabilities within a 10-week period centered on a capture event and evaluated how animal age, nutritional condition (body fat), and various handling methods influenced survival before, during, and following a capture event. Direct mortality resulting from capture efforts was 1.59%. Mean daily survival was 0.9993 ± 0.0001 (SE) during the 5-week pre-capture window, was depressed the day of capture at 0.9841 ± 0.0004, and rebounded to 0.9990 ± 0.0008 during the 5-week post-capture window. Neither capture nor handling had a detectable effect on post-capture survival, including handling time ($\overline{x}$ = 13.30 ± 1.87 min), capture time of year (i.e., Dec or Mar), tooth extraction, and the number of times an animal had been recaptured (2–17 times). Although mortality rate was slightly elevated during capture (resulting from physical trauma associated with capture), age and nutritional condition did not influence the probability of mortality during a capture event. Following a capture event, nutritional condition influenced survival; however, that relationship was consistent with expected effects of nutritional condition on winter survival and independent of capture and handling. Overall survival rates 5 weeks before capture and 5 weeks after capture were not different. A specified window of time with depressed survival following capture and handling was not evident, which contradicts the implementation of a predetermined window often used by researchers and managers for censoring mortalities that occur after capture. Previous notions that censorship of all mortality data in the 2 weeks following capture is unwarranted and risks removal of meaningful data. With previous evidence guiding our protocols for capture (e.g., reduced chase time) and handling (e.g., temperature mitigation), low direct mortality and almost undetectable indirect mortality post capture reinforces the efficacy of helicopter net-gunning for capture and recapture of mule deer in long-term, individual-based studies.     

Social dynamics and sexual segregation of Australian humpback dolphins (Sousa sahulensis) in Moreton Bay,Queensland

Understanding the social organization of coastal dolphins, particularly those that reside adjacent to major cities and urbanized regions, is important for understanding the vulnerability of populations to human impacts. We investigated the sexual segregation and social dynamics in a population of Australian humpback dolphins (Sousa sahulensis) inhabiting the near-urban embayment of Moreton Bay, Queensland. Over 160 vessel-based surveys, 148 adults were photographically identified. This included 116 assumed females and 32 assumed males. The population was sexually segregated (SSAS = 0.52, p < .001) and individuals preferred to associate with others of the same sex occupying the same spatial area (p < .025). Association indices between paired males were almost double those of females ($\text{◂=▸}\overline{x}\mathrm{HWI}=0.09$, SD = 0.04 and $\text{◂=▸}\overline{x}\mathrm{HWI}=0.05$, SD = 0.02, respectively). However, females were more gregarious than males and maintained a larger network of associates based on preferred companionships. The social network was also modular with five clusters identified, and a limited number of individuals had a disproportionate influence on connectivity between clusters. This highly fragmented social network implies that the population may be vulnerable to social disruptions from human impacts.     

Energy compensated synthetic aperture focusing technique for photoacoustic microscopy

We report an adaptive energy-compensated synthetic aperture focusing technique (eC-SAFT) for improving the imaging performance of photoacoustic microscopy (PAM) in terms of depth of field (DOF), spatial resolution (both axial and lateral), and SNR. In addition to coherency and time-delay (in conventional SAFT), our beamforming-based reconstruction algorithm takes into account acoustic energy loss—a primary physical parameter in acoustic wave propagation—following Beer-Lambert's law. Experimental validation studies were performed in tissue-mimicking (Agar) phantoms, complex leaf veins, and chicken breast tissues. Results demonstrate that our proposed eC-SAFT+CF outperforms conventional SAFT+CF to improve axial resolution (up to $\sim 5\%$), lateral resolution (up to $\sim 5\%$), SNR (up to $\sim 6\%$) and CR (up to $\sim 8\%$).     

Power analysis for cluster randomized trials with multiple binary co-primary endpoints

Cluster randomized trials (CRTs) are widely used in different areas of medicine and public health. Recently, with increasing complexity of medical therapies and technological advances in monitoring multiple outcomes, many clinical trials attempt to evaluate multiple co-primary endpoints. In this study, we present a power analysis method for CRTs with $K\ge 2$ binary co-primary endpoints. It is developed based on the GEE (generalized estimating equation) approach, and three types of correlations are considered: inter-subject correlation within each endpoint, intra-subject correlation across endpoints, and inter-subject correlation across endpoints. A closed-form joint distribution of the K test statistics is derived, which facilitates the evaluation of power and type I error for arbitrarily constructed hypotheses. We further present a theorem that characterizes the relationship between various correlations and testing power. We assess the performance of the proposed power analysis method based on extensive simulation studies. An application example to a real clinical trial is presented.     

Optimal sampling design and the accuracy of occupancy models

We present general theoretical limits on the possible accuracy (mean squared error or MSE) of occupancy estimates for a large range of occupancy study designs with imperfect detection and confirm our theoretical results via a simulation study. In particular, we show that for a given total survey effort, the best possible MSE is driven by two design-related factors: the fraction of visits made at occupied sites (regardless of whether that occupancy status is known or not) and the number of visits made to each site with unknown occupancy status (ie, sites with no detections). The limits reveal that there is very little room for improvement over optimal implementations of the three existing occupancy design paradigms: standard design (visit S sites K times each), removal design (visit S sites up to K times each, halting visits to each site following a positive detection), and conditional design (visit S sites once, then resurvey sites with a positive detection an additional $K-1$ times). For the small portion of the occupancy-detection parameter space where improvement can be achieved, we introduce a new hybrid survey design with accuracy closer to the theoretical limit, which we illustrate by reanalyzing an existing coyote (Canis latrans) camera trap dataset. Our results provide new clarity and intuition regarding key factors of occupancy study design.     

Estimating quantitative physiological and morphological tissue parameters of murine tumor models using hyperspectral imaging and optical profilometry

Understanding tumors and their microenvironment are essential for successful and accurate disease diagnosis. Tissue physiology and morphology are altered in tumors compared to healthy tissues, and there is a need to monitor tumors and their surrounding tissues, including blood vessels, non-invasively. This preliminary study utilizes a multimodal optical imaging system combining hyperspectral imaging (HSI) and three-dimensional (3D) optical profilometry (OP) to capture hyperspectral images and surface shapes of subcutaneously grown murine tumor models. Hyperspectral images are corrected with 3D OP data and analyzed using the inverse-adding doubling (IAD) method to extract tissue properties such as melanin volume fraction and oxygenation. Blood vessels are segmented using the B-COSFIRE algorithm from oxygenation maps. From 3D OP data, tumor volumes are calculated and compared to manual measurements using a vernier caliper. Results show that tumors can be distinguished from healthy tissue based on most extracted tissue parameters (). Furthermore, blood oxygenation is 50% higher within the blood vessels than in the surrounding tissue, and tumor volumes calculated using 3D OP agree within 26% with manual measurements using a vernier caliper. Results suggest that combining HSI and OP could provide relevant quantitative information about tumors and improve the disease diagnosis.     

Biclustering via sparse clustering

In identifying subgroups of a heterogeneous disease or condition, it is often desirable to identify both the observations and the features which differ between subgroups. For instance, it may be that there is a subgroup of individuals with a certain disease who differ from the rest of the population based on the expression profile for only a subset of genes. Identifying the subgroup of patients and subset of genes could lead to better-targeted therapy. We can represent the subgroup of individuals and genes as a bicluster, a submatrix, $\mathbf{U}$, of a larger data matrix, $\mathbf{X}$, such that the features and observations in $\mathbf{U}$ differ from those not contained in $\mathbf{U}$. We present a novel two-step method, SC-Biclust, for identifying $\mathbf{U}$. In the first step, the observations in the bicluster are identified to maximize the sum of the weighted between-cluster feature differences. In the second step, features in the bicluster are identified based on their contribution to the clustering of the observations. This versatile method can be used to identify biclusters that differ on the basis of feature means, feature variances, or more general differences. The bicluster identification accuracy of SC-Biclust is illustrated through several simulated studies. Application of SC-Biclust to pain research illustrates its ability to identify biologically meaningful subgroups.     

Estimating average treatment effects with a double-index propensity score

We consider estimating average treatment effects (ATE) of a binary treatment in observational data when data-driven variable selection is needed to select relevant covariates from a moderately large number of available covariates $\mathbf{X}$. To leverage covariates among $\mathbf{X}$ predictive of the outcome for efficiency gain while using regularization to fit a parametric propensity score (PS) model, we consider a dimension reduction of $\mathbf{X}$ based on fitting both working PS and outcome models using adaptive LASSO. A novel PS estimator, the Double-index Propensity Score (DiPS), is proposed, in which the treatment status is smoothed over the linear predictors for $\mathbf{X}$ from both the initial working models. The ATE is estimated by using the DiPS in a normalized inverse probability weighting estimator, which is found to maintain double robustness and also local semiparametric efficiency with a fixed number of covariates p. Under misspecification of working models, the smoothing step leads to gains in efficiency and robustness over traditional doubly robust estimators. These results are extended to the case where p diverges with sample size and working models are sparse. Simulations show the benefits of the approach in finite samples. We illustrate the method by estimating the ATE of statins on colorectal cancer risk in an electronic medical record study and the effect of smoking on C-reactive protein in the Framingham Offspring Study.     

Use of thermal imaging and the photochemical reflectance index (PRI) to detect wheat response to elevated CO2 and drought

The spectral-based photochemical reflectance index (PRI) and leaf surface temperature (T_leaf) derived from thermal imaging are two indicative metrics of plant functioning. The relationship of PRI with radiation-use efficiency (RUE) and T_leaf with leaf transpiration could be leveraged to monitor crop photosynthesis and water use from space. Yet, it is unclear how such relationships will change under future high carbon dioxide concentrations ([CO₂]) and drought. Here we established an [CO₂] enrichment experiment in which three wheat genotypes were grown at ambient (400 ppm) and elevated (550 ppm) [CO₂] and exposed to well-watered and drought conditions in two glasshouse rooms in two replicates. Leaf transpiration (T_r) and latent heat flux (LE) were derived to assess evaporative cooling, and RUE was calculated from assimilation and radiation measurements on several dates along the season. Simultaneous hyperspectral and thermal images were taken at $~$1.5 m from the plants to derive PRI and the temperature difference between the leaf and its surrounding air ($∆$T_leaf−air). We found significant PRI and RUE and $∆$T_leaf−air and T_r correlations, with no significant differences among the genotypes. A PRI–RUE decoupling was observed under drought at ambient [CO₂] but not at elevated [CO₂], likely due to changes in photorespiration. For a LE range of 350 W m^–2, the ΔT_leaf−air range was $~$10°C at ambient [CO₂] and only $~$4°C at elevated [CO₂]. Thicker leaves in plants grown at elevated [CO₂] suggest higher leaf water content and consequently more efficient thermoregulation at high [CO₂] conditions. In general, T_leaf was maintained closer to the ambient temperature at elevated [CO₂], even under drought. PRI, RUE, ΔT_leaf−air, and T_r decreased linearly with canopy depth, displaying a single PRI-RUE and ΔT_leaf−air T_r model through the canopy layers. Our study shows the utility of these sensing metrics in detecting wheat responses to future environmental changes.     

Adjusting for time-varying confounders in survival analysis using structural nested cumulative survival time models

Accounting for time-varying confounding when assessing the causal effects of time-varying exposures on survival time is challenging. Standard survival methods that incorporate time-varying confounders as covariates generally yield biased effect estimates. Estimators using weighting by inverse probability of exposure can be unstable when confounders are highly predictive of exposure or the exposure is continuous. Structural nested accelerated failure time models (AFTMs) require artificial recensoring, which can cause estimation difficulties. Here, we introduce the structural nested cumulative survival time model (SNCSTM). This model assumes that intervening to set exposure at time $t$ to zero has an additive effect on the subsequent conditional hazard given exposure and confounder histories when all subsequent exposures have already been set to zero. We show how to fit it using standard software for generalized linear models and describe two more efficient, double robust, closed-form estimators. All three estimators avoid the artificial recensoring of AFTMs and the instability of estimators that use weighting by the inverse probability of exposure. We examine the performance of our estimators using a simulation study and illustrate their use on data from the UK Cystic Fibrosis Registry. The SNCSTM is compared with a recently proposed structural nested cumulative failure time model, and several advantages of the former are identified.     

Total free energy analysis of fully hydrated proteins

The total free energy of a hydrated biomolecule and its corresponding decomposition of energy and entropy provides detailed information about regions of thermodynamic stability or instability. The free energies of four hydrated globular proteins with different net charges are calculated from a molecular dynamics simulation, with the energy coming from the system Hamiltonian and entropy using multiscale cell correlation. Water is found to be most stable around anionic residues, intermediate around cationic and polar residues, and least stable near hydrophobic residues, especially when more buried, with stability displaying moderate entropy-enthalpy compensation. Conversely, anionic residues in the proteins are energetically destabilized relative to singly solvated amino acids, while trends for other residues are less clear-cut. Almost all residues lose intraresidue entropy when in the protein, enthalpy changes are negative on average but may be positive or negative, and the resulting overall stability is moderate for some proteins and negligible for others. The free energy of water around single amino acids is found to closely match existing hydrophobicity scales. Regarding the effect of secondary structure, water is slightly more stable around loops, of intermediate stability around $\beta$ strands and turns, and least stable around helices. An interesting asymmetry observed is that cationic residues stabilize a residue when bonded to its N-terminal side but destabilize it when on the C-terminal side, with a weaker reversed trend for anionic residues.     

Anthropogenic Disturbance and Population Viability of Woodland Caribou in Ontario

One of the most challenging tasks in wildlife conservation and management is to clarify how spatial variation in land cover due to anthropogenic disturbance influences wildlife demography and long-term viability. To evaluate this, we compared rates of survival and population growth by woodland caribou (Rangifer tarandus caribou) from 2 study sites in northern Ontario, Canada that differed in the degree of anthropogenic disturbance because of commercial logging and road development, resulting in differences in predation risk due to gray wolves (Canis lupus). We used an individual-based model for population viability analysis (PVA) that incorporated adaptive patterns of caribou movement in relation to predation risk and food availability to predict stochastic variation in rates of caribou survival. Field estimates of annual survival rates for adult female caribou in the unlogged ( 0.90) and logged ( 0.76) study sites recorded during 2010–2014 did not differ significantly (P > 0.05) from values predicted by the individual-based PVA model (unlogged: = 0.87; logged: 0.79). Outcomes from the individual-based PVA model and a simpler stage-structured matrix model suggest that substantial differences in adult survival largely due to wolf predation are likely to lead to long-term decline of woodland caribou in the commercially logged landscape, whereas the unlogged landscape should be considerably more capable of sustaining caribou. Estimates of population growth rates (λ) for the 2010–2014 period differed little between the matrix model and the individual-based PVA model for the unlogged (matrix model = 1.01; individual-based model = 0.98) and logged landscape (matrix model = 0.88; individual-based model = 0.89). We applied the spatially explicit PVA model to assess the viability of woodland caribou across 14 woodland caribou ranges in Ontario. Outcomes of these simulations suggest that woodland caribou ranges that have experienced significant levels of commercial forestry activities in the past had annual growth rates <0.89, whereas caribou ranges that had not experienced commercial forestry operations had population growth rates >0.96. These differences were strongly related to regional variation in wolf densities. Our results suggest that increased wolf predation risk due to anthropogenic disturbance is of sufficient magnitude to cause appreciable risk of population decline in woodland caribou in Ontario. © 2020 The Authors. The Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.