Comparison of Image Registration Based Measures of Regional Lung Ventilation from Dynamic Spiral CT with Xe-CT

Purpose: Regional lung volume change as a function of lung inflation serves as an index of parenchymal and airway status as well as an index of regional ventilation and can be used to detect pathologic changes over time. In this article, we propose a new regional measure of lung mechanics --- the specific air volume change by corrected Jacobian. Methods: 4DCT and Xe-CT data sets from four adult sheep are used in this study. Nonlinear, 3D image registration is applied to register an image acquired near end inspiration to an image acquired near end expiration. Approximately 200 annotated anatomical points are used as landmarks to evaluate registration accuracy. Three different registration-based measures of regional lung mechanics are derived and compared: the specific air volume change calculated from the Jacobian (SAJ); the specific air volume change calculated by the corrected Jacobian (SACJ); and the specific air volume change by intensity change (SAI). Results: After registration, the mean registration error is on the order of 1 mm. For cubical ROIs in cubes with size 20 mm $\times$ 20 mm $\times$ 20 mm, the SAJ and SACJ measures show significantly higher correlation (linear regression, average $r^2=0.75$ and $r^2=0.82$) with the Xe-CT based measure of specific ventilation (sV) than the SAI measure. For ROIs in slabs along the ventral-dorsal vertical direction with size of 150 mm $\times$ 8 mm $\times$ 40 mm, the SAJ, SACJ, and SAI all show high correlation (linear regression, average $r^2=0.88$, $r^2=0.92$ and $r^2=0.87$) with the Xe-CT based sV without significant differences when comparing between the three methods. Conclusion: Given a deformation field by an image registration algorithm, significant differences between the SAJ, SACJ, and SAI measures were found at a regional level compared to the Xe-CT sV in four sheep that were studied

Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland

Bovine tuberculosis (bTB) is a costly, epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole-genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra-species host transmission for disease persistence. We sequenced an exceptional data set of 619 Mycobacterium bovis isolates from badgers and cattle in a 100 km2 bTB 'hotspot' in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area. Birth death models and TransPhylo analyses indicated that cattle were likely driving the local epidemic, with transmission from cattle to badgers being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution of M. bovis genetic diversity, suggesting that badger-to-badger transmission is not playing a major role in transmission dynamics. Our data were consistent with badgers playing a smaller role in transmission of M. bovis infection in this study site, compared to cattle. We hypothesize, however, that this minor role may still be important for persistence. Comparison to other areas suggests that M. bovis transmission dynamics are likely to be context dependent, with the role of wildlife being difficult to generalize.ISSN:2057-585

Squeezed by a Habitat Split: Warm Ocean Conditions and Old‐forest Loss Interact to Reduce Long‐term Occupancy of a Threatened Seabird

Theory predicts that species requiring multiple habitat types simultaneously should have heightened sensitivity to anthropogenic pressures, yet tests of this prediction are especially rare. We tested whether breeding site occupancy of the threatened marbled murrelet (Brachyramphus marmoratus) was driven by the synergistic effects of nesting habitat loss in forests, and changing ocean condi- tions. We paired 70,700 murrelet surveys at 19,837 sites across 20 years from the Oregon Coast Range with annual data on the extent of old forest and biophysical ocean conditions. Dynamic occupancy models indicated that local murrelet col- onization rates were strongly reduced during warm ocean conditions with low prey availability. Landscapes that contained more old forest and were closer to the ocean showed reduced rates of local extinction. Given predictions of accel- erated ocean warming and increased global timber demand, our results suggest murrelets may continue to be imperiled by deterioration of the two habitats upon which they depend

Toward a Coordinated Understanding of Hydro-Biogeochemical Root Functions in Tropical Forests for Application in Vegetation Models

Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest–climate feedbacks for these carbon-rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics that represent important functional processes in tropical forests. We focus on: (1) fine-root strategies for soil resource exploration, (2) coupling and trade-offs in fine-root water vs nutrient acquisition, and (3) aboveground–belowground linkages in plant resource acquisition and use. We suggest avenues for representing these extremely diverse plant communities in computationally manageable and ecologically meaningful groups in models for linked aboveground–belowground hydro-nutrient functions. Tropical forests are undergoing warming, shifting rainfall regimes, and exacerbation of soil nutrient scarcity caused by elevated atmospheric CO2. The accurate model representation of tropical forest functions is crucial for understanding the interactions of this biome with the climate

Treatment of Periodontitis by Local Administration of Minocycline Microspheres: A Controlled Trial

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141491/1/jper1535.pd

Vetting of 384 TESS Objects of Interest with TRICERATOPS and Statistical Validation of 12 Planet Candidates

We present TRICERATOPS, a new Bayesian tool that can be used to vet and validate TESS Objects of Interest (TOIs). We test the tool on 68 TOIs that have been previously confirmed as planets or rejected as astrophysical false positives. By looking in the false positive probability (FPP) -- nearby false positive probability (NFPP) plane, we define criteria that TOIs must meet to be classified as validated planets (FPP < 0.015 and NFPP < 10^-3), likely planets (FPP 10^-1). We apply this procedure on 384 unclassified TOIs and statistically validate 12, classify 125 as likely planets, and classify 52 as likely nearby false positives. Of the 12 statistically validated planets, 9 are newly validated. TRICERATOPS is currently the only TESS vetting and validation tool that models transits from nearby contaminant stars in addition to the target star. We therefore encourage use of this tool to prioritize follow-up observations that confirm bona fide planets and identify false positives originating from nearby stars.Comment: Accepted to A