A genetic warning system for a hierarchically structured wildlife monitoring framework.

Genetic variation is a well-known indicator of population fitness yet is not typically included in monitoring programs for sensitive species. Additionally, most programs monitor populations at one scale, which can lead to potential mismatches with ecological processes critical to species' conservation. Recently developed methods generating hierarchically nested population units (i.e., clusters of varying scales) for greater sage-grouse (Centrocercus urophasianus) have identified population trend declines across spatiotemporal scales to help managers target areas for conservation. The same clusters used as a proxy for spatial scale can alert managers to local units (i.e., neighborhood-scale) with low genetic diversity, further facilitating identification of management targets. We developed a genetic warning system utilizing previously developed hierarchical population units to identify management-relevant areas with low genetic diversity within the greater sage-grouse range. Within this warning system we characterized conservation concern thresholds based on values of genetic diversity and developed a statistical model for microsatellite data to robustly estimate these values for hierarchically nested populations. We found that 41 of 224 neighborhood-scale clusters had low genetic diversity, 23 of which were coupled with documented local population trend decline. We also found evidence of cross-scale low genetic diversity in the small and isolated Washington population, unlikely to be reversed through typical local management actions alone. The combination of low genetic diversity and a declining population suggests relatively high conservation concern. Our findings could further facilitate conservation action prioritization in combination with population trend assessments and (or) local information, and act as a base-line of genetic diversity for future comparison. Importantly, the approach we used is broadly applicable across taxa.

Defining biologically relevant and hierarchically nested population units to inform wildlife management.

Wildlife populations are increasingly affected by natural and anthropogenic changes that negatively alter biotic and abiotic processes at multiple spatiotemporal scales and therefore require increased wildlife management and conservation efforts. However, wildlife management boundaries frequently lack biological context and mechanisms to assess demographic data across the multiple spatiotemporal scales influencing populations. To address these limitations, we developed a novel approach to define biologically relevant subpopulations of hierarchically nested population levels that could facilitate managing and conserving wildlife populations and habitats. Our approach relied on the Spatial "K"luster Analysis by Tree Edge Removal clustering algorithm, which we applied in an agglomerative manner (bottom-to-top). We modified the clustering algorithm using a workflow and population structure tiers from least-cost paths, which captured biological inferences of habitat conditions (functional connectivity), dispersal capabilities (potential connectivity), genetic information, and functional processes affecting movements. The approach uniquely included context of habitat resources (biotic and abiotic) summarized at multiple spatial scales surrounding locations with breeding site fidelity and constraint-based rules (number of sites grouped and population structure tiers). We applied our approach to greater sage-grouse (Centrocercus urophasianus), a species of conservation concern, across their range within the western United States. This case study produced 13 hierarchically nested population levels (akin to cluster levels, each representing a collection of subpopulations of an increasing number of breeding sites). These closely approximated population closure at finer ecological scales (smaller subpopulation extents with fewer breeding sites; cluster levels ≥2), where >92% of individual sage-grouse's time occurred within their home cluster. With available population monitoring data, our approaches can support the investigation of factors affecting population dynamics at multiple scales and assist managers with making informed, targeted, and cost-effective decisions within an adaptive management framework. Importantly, our approach provides the flexibility of including species-relevant context, thereby supporting other wildlife characterized by site fidelity.

Automated delineation of the clinical target volume using anatomically constrained 3D expansion of the gross tumor volume.

PURPOSE: Delineation of the clinical target volume (CTV) is arguably the weakest link in the treatment planning chain. This work aims to support clinicians in this crucial task. METHODS AND MATERIALS: While the CTV itself is ambiguous, it is much easier to identify structures that do not belong to the CTV and serve as barriers to the spread of the disease. We segment the known barrier structures using a convolutional neural network (CNN). The CTV is then obtained by starting from the manually delineated gross tumor volume (GTV) and expanding it while taking into account the barrier structures. Mathematically, we define the CTV as an iso-surface in the 3D map of shortest paths of all voxels from the GTV. The shortest paths are found with the Dijkstra algorithm. While the method is generally applicable, we test it on 206 glioma and glioblastoma cases. RESULTS: The auto-segmented barrier structures for the brain cases include the ventricles, falx cerebri, tentorium cerebelli, brain sinuses, and the outer surface of the brain. Manual and auto-segmented barrier structures agree with surface Dice Similarity Coefficients (DSC) ranging from 0.91 to 0.97 at 2 mm tolerance. Comparison of manual and automatically delineated CTVs shows a median surface DSC of 0.79. CONCLUSIONS: Barrier structures for CTV definition can be auto-delineated with outstanding precision using a CNN. An algorithm for automated calculation of the CTV by 3D expansion of the GTV while respecting anatomical barriers has been developed. It shows good agreement with manual CTV definition for brain tumors.

Automatic diaphragm segmentation for real-time lung tumor tracking on cone-beam CT projections: a convolutional neural network approach.

PURPOSE: To automatically segment the diaphragm on individual lung cone-beam CT projection images, to enable real-time tracking of lung tumors using kilovoltage imaging. METHODS: The deep neural network Mask R-CNN was trained on 3500 raw cone-beam CT projection images from 10 lung cancer patients, with the diaphragm manually segmented on each image used as a ground truth label. Ground-truth breathing traces were extracted from each patient for both diaphragm hemispheres, and apex positions were compared against the predicted output of the neural network. Ten-fold cross-validation was used to evaluate the segmentation accuracy. RESULTS: The mean diaphragm apex prediction error was 4.4 mm. The mean percentage of projection images for which a successful prediction could me made was 87.3%. Prediction accuracy at some lateral gantry angles was worse due to overlap between diaphragm hemispheres, and the increased amount of fatty tissue. CONCLUSIONS: The neural network was able to track the diaphragm apex position successfully. This allows accurate assessment of the breathing phase, which can be used to estimate the position of the lung tumor in real time.

Kilovoltage projection streaming-based tracking application (KiPSTA): First clinical implementation during spine stereotactic radiation surgery.

PURPOSE: This study aimed to develop a linac-mounted kilovoltage (kV) projection streaming-based tracking method for vertebral targets during spine stereotactic radiation surgery and evaluate the clinical feasibility of the proposed spine tracking method. METHODS AND MATERIALS: Using real-time kV projection streaming within XVI (Elekta XVI), kV-projection-based tracking was applied to the target vertebral bodies. Two-dimensional in-plane patient translation was calculated via an image registration between digitally reconstructed radiographs (DRRs) and kV projections. DRR was generated from the cone beam computed tomography (CBCT) scan, which was obtained immediately before the tracking session. During a tracking session, each kV projection was streamed for an intensity gradient-based image with similar metric-based registration to the offset DRR. The ground truth displacement for each kV beam angle was calculated at the beam isocenter using the 6 degrees-of-freedom transformation that was obtained by a CBCT-CBCT rigid registration. The resulting translation by the DRR-projection registration was compared with the ground truth displacement. The proposed tracking method was evaluated retrospectively and online, using 7 and 5 spine patients, respectively. RESULTS: The accuracy and precision of spine tracking for in-plane patient motion were 0.5 ± 0.2 and 0.2 ± 0.1 mm. The magnitude of patient motion that was estimated using the CBCT-CBCT rigid registration was (0.5 ± 0.4, 0.4 ± 0.3, 0.3 ± 0.3) mm and (0.3 ± 0.4, 0.2 ± 0.2, 0.5 ± 0.6) mm for all tracking sessions. The intrafraction motion was within 2 mm for all CBCT scans considered. CONCLUSIONS: This study demonstrated that the proposed spine tracking method can track intrafraction motion with sub-millimeter accuracy and precision, and sub-second latency.

"I Love Fruit But I Can't Afford It": Using Participatory Action Research to Develop Community-Based Initiatives to Mitigate Challenges to Chronic Disease Management in an African American Community Living in Public Housing.

As chronic conditions are on the rise in the USA, management initiatives outside of the inpatient setting should be explored to reduce associated cost and access disparities. Chronic conditions disproportionately affect African American public housing residents due to the effects of historical marginalization on the manifestation of economic and social problems exacerbating health disparities and outcomes. Informed by participatory research action tenets, this study focused on identifying the challenges to management of chronic conditions and developing community-envisioned initiatives to address these challenges in a predominantly African American public housing community. Two focus groups were conducted with former and current public housing residents and were analyzed using inductive content analysis. Physical activity, the cost associated with healthy eating, and lack of information were noted as challenges to chronic disease management. Initiatives discussed were the formation of a walking partner's program to promote physical activity, a shopper's club to exchange coupons and learn how to prepare healthy meals, and a natural remedy's book to share information intergenerationally about management tactics. Challenges identified existed predominantly on the individual and the system level, while the initiatives generated target engaging interpersonal and community relationships. These community-envisioned approaches should be explored to facilitate chronic disease management in public housing neighborhoods.

Low-cost Kinect Version 2 imaging system for breath hold monitoring and gating: Proof of concept study for breast cancer VMAT radiotherapy.

Voluntary inspiration breath hold (VIBH) for left breast cancer patients has been shown to be a safe and effective method of reducing radiation dose to the heart. Currently, VIBH protocol compliance is monitored visually. In this work, we establish whether it is possible to gate the delivery of radiation from an Elekta linac using the Microsoft Kinect version 2 (Kinect v2) depth sensor to measure a patient breathing signal. This would allow contactless monitoring during VMAT treatment, as an alternative to equipment-assisted methods such as active breathing control (ABC). Breathing traces were acquired from six left breast radiotherapy patients during VIBH. We developed a gating interface to an Elekta linac, using the depth signal from a Kinect v2 to control radiation delivery to a programmable motion platform following patient breathing patterns. Radiation dose to a moving phantom with gating was verified using point dose measurements and a Delta4 verification phantom. 60 breathing traces were obtained with an acquisition success rate of 100%. Point dose measurements for gated deliveries to a moving phantom agreed to within 0.5% of ungated delivery to a static phantom using both a conventional and VMAT treatment plan. Dose measurements with the verification phantom showed that there was a median dose difference of better than 0.5% and a mean (3% 3 mm) gamma index of 92.6% for gated deliveries when using static phantom data as a reference. It is possible to use a Kinect v2 device to monitor voluntary breath hold protocol compliance in a cohort of left breast radiotherapy patients. Furthermore, it is possible to use the signal from a Kinect v2 to gate an Elekta linac to deliver radiation only during the peak inhale VIBH phase.

Endemic chronic wasting disease causes mule deer population decline in Wyoming.

Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting white-tailed deer (Odocoileus virginianus), mule deer (Odocoileus hemionus), Rocky Mountain elk (Cervus elaphus nelsoni), and moose (Alces alces shirasi) in North America. In southeastern Wyoming average annual CWD prevalence in mule deer exceeds 20% and appears to contribute to regional population declines. We determined the effect of CWD on mule deer demography using age-specific, female-only, CWD transition matrix models to estimate the population growth rate (λ). Mule deer were captured from 2010-2014 in southern Converse County Wyoming, USA. Captured adult (≥ 1.5 years old) deer were tested ante-mortem for CWD using tonsil biopsies and monitored using radio telemetry. Mean annual survival rates of CWD-negative and CWD-positive deer were 0.76 and 0.32, respectively. Pregnancy and fawn recruitment were not observed to be influenced by CWD. We estimated λ = 0.79, indicating an annual population decline of 21% under current CWD prevalence levels. A model derived from the demography of only CWD-negative individuals yielded; λ = 1.00, indicating a stable population if CWD were absent. These findings support CWD as a significant contributor to mule deer population decline. Chronic wasting disease is difficult or impossible to eradicate with current tools, given significant environmental contamination, and at present our best recommendation for control of this disease is to minimize spread to new areas and naïve cervid populations.

The feasibility of using Microsoft Kinect v2 sensors during radiotherapy delivery.

Consumer-grade distance sensors, such as the Microsoft Kinect devices (v1 and v2), have been investigated for use as marker-free motion monitoring systems for radiotherapy. The radiotherapy delivery environment is challenging for such sen-sors because of the proximity to electromagnetic interference (EMI) from the pulse forming network which fires the magnetron and electron gun of a linear accelerator (linac) during radiation delivery, as well as the requirement to operate them from the control area. This work investigated whether using Kinect v2 sensors as motion monitors was feasible during radiation delivery. Three sensors were used each with a 12 m USB 3.0 active cable which replaced the supplied 3 m USB 3.0 cable. Distance output data from the Kinect v2 sensors was recorded under four condi-tions of linac operation: (i) powered up only, (ii) pulse forming network operating with no radiation, (iii) pulse repetition frequency varied between 6 Hz and 400 Hz, (iv) dose rate varied between 50 and 1450 monitor units (MU) per minute. A solid water block was used as an object and imaged when static, moved in a set of steps from 0.6 m to 2.0 m from the sensor and moving dynamically in two sinusoidal-like trajectories. Few additional image artifacts were observed and there was no impact on the tracking of the motion patterns (root mean squared accuracy of 1.4 and 1.1mm, respectively). The sensors' distance accuracy varied by 2.0 to 3.8 mm (1.2 to 1.4 mm post distance calibration) across the range measured; the precision was 1 mm. There was minimal effect from the EMI on the distance calibration data: 0 mm or 1 mm reported distance change (2 mm maximum change at one position). Kinect v2 sensors operated with 12 m USB 3.0 active cables appear robust to the radiotherapy treatment environment.

Chronic Wasting Disease Drives Population Decline of White-Tailed Deer.

Chronic wasting disease (CWD) is an invariably fatal transmissible spongiform encephalopathy of white-tailed deer, mule deer, elk, and moose. Despite a 100% fatality rate, areas of high prevalence, and increasingly expanding geographic endemic areas, little is known about the population-level effects of CWD in deer. To investigate these effects, we tested the null hypothesis that high prevalence CWD did not negatively impact white-tailed deer population sustainability. The specific objectives of the study were to monitor CWD-positive and CWD-negative white-tailed deer in a high-prevalence CWD area longitudinally via radio-telemetry and global positioning system (GPS) collars. For the two populations, we determined the following: a) demographic and disease indices, b) annual survival, and c) finite rate of population growth (λ). The CWD prevalence was higher in females (42%) than males (28.8%) and hunter harvest and clinical CWD were the most frequent causes of mortality, with CWD-positive deer over-represented in harvest and total mortalities. Survival was significantly lower for CWD-positive deer and separately by sex; CWD-positive deer were 4.5 times more likely to die annually than CWD-negative deer while bucks were 1.7 times more likely to die than does. Population λ was 0.896 (0.859-0.980), which indicated a 10.4% annual decline. We show that a chronic disease that becomes endemic in wildlife populations has the potential to be population-limiting and the strong population-level effects of CWD suggest affected populations are not sustainable at high disease prevalence under current harvest levels.

Decay of (p,q)-Fourier coefficients.

We show that essentially the speed of decay of the Fourier sine coefficients of a function in a Lebesgue space is comparable to that of the corresponding coefficients with respect to the basis formed by the generalized sine functions sin p,q .

Ocular plague (Yersinia pestis) in mule deer (Odocoileus hemionus) from Wyoming and Oregon.

Although plague is relatively rare in wild ungulates, this report describes ocular lesions associated with Yersinia pestis infection in three free-ranging mule deer (Odocoileus hemionus) from Wyoming and Oregon, USA. All deer were observed antemortem and seemed to be blind. Post-mortem examination revealed gross lesions of bilateral keratoconjunctivitis and/or panophthalmitis in the first two deer, but only partial retinal detachment in the third deer. Microscopically, all deer had moderate-to-severe necrotizing and fibrinopurulent endophthalmitis and varying degrees of keratoconjunctivitis with abundant intralesional coccobacilli. The lesions in the first (D1) and third deer (D3) suggested an acute course, whereas those in the second deer (D2) were subacute to chronic. Yersinia pestis was isolated from ocular tissue swabs or ocular fluids of D1 and D2, and it was demonstrated by immunohistochemistry within ocular lesions of D1 and D3. Although plague does not seem to be a major cause of morbidity or mortality in free-ranging mule deer, keratoconjunctivitis or pinkeye is relatively common in these animals and plague should be considered as a differential diagnosis in such cases, with appropriate precautions taken to protect the human and animal health.

Longitudinal study of sensitization to natural rubber latex among dental school students using powder-free gloves.

BACKGROUND: A high rate of sensitization and clinical allergy to latex proteins has been reported in health care personnel. This is thought to be due to increased occupational exposure especially to natural rubber latex (NRL) gloves with an estimated prevalence varying widely (2.8-18%). OBJECTIVE: This was a longitudinal study to monitor a cohort of first-year dental students throughout 4 study years during exposure to powder-free gloves. Their atopic status was determined by skin prick testing using a panel of common allergens, and any sensitivity to latex proteins and the cross-reacting food allergens assessed. METHODS: Skin prick testing was carried out on the volunteers using latex, avocado, kiwi, banana, grass pollens, tree pollen, house dust mite and cat dander. Each volunteer completed a questionnaire detailing allergic history and any previous latex exposure. RESULTS: Skin prick testing showed a 65% incidence of atopy in the longitudinal study group. Initial latex skin testing was positive in 3 of the 63 students followed throughout their period of study. Subsequent testing gave a negative result in one student and one declined retesting. The third continued to give a positive response on each testing; she wore only nitrile gloves and remained free of clinical NRL allergy symptoms. No student developed latex sensitivity during the 5 yr of this study. CONCLUSION: Exposure to powder-free latex gloves was not associated with subsequent sensitization over 5 yr in a population with a high atopic incidence.