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- Creator:
- Zongyu Li, Yuni K. Dewaraja, and Jeffrey A. Fessler
- Description:
- Current methods for patient-specific voxel-level dosimetry in radionuclide therapy suffer from a trade-off between accuracy and computational efficiency. Monte Carlo (MC) radiation transport algorithms are considered the gold standard for voxel-level dosimetry but can be computationally expensive, whereas faster dose voxel kernel (DVK) convolution can be sub-optimal in the presence of tissue heterogeneities. Furthermore, the accuracies of both these methods are limited by the spatial resolution of the reconstructed emission image. To overcome these limitations, this paper considers a single deep convolutional neural network (CNN) with residual learning (named DblurDoseNet) that learns to produce dose-rate maps while compensating for the limited resolution of SPECT images. We took the novel approach of constructing a convolutional neural network with residual learning to handle the accuracy-efficiency tradeoff while compensating for the limited resolution of SPECT images. We then test our CNN on clinically relevant phantoms and patients undergoing Lu-177 DOTATATE therapy in our clinic. Our network demonstrated superior results than Monte Carlo, the current gold standard for voxel dosimetry, but only takes a fraction of time. Thus, the DblurDoseNet has the potential for real-time patient-specific dosimetry in clinical treatment planning due to its demonstrated improvement in accuracy, resolution, noise and speed over the DVK/MC approaches. Matlab is needed to access the phantoms and Python (with Numpy package installed) is needed to access the DVKs.
- Keyword:
- Deep learning, Voxel-level dosimetry, Lu-177 therapy, SPECT resolution effects
- Citation to related publication:
- "DblurDoseNet: A Deep Residual Learning Network for Voxel Radionuclide Dosimetry Compensating for SPECT Imaging Resolution" by Zongyu Li, Jeffrey A. Fessler, Justin K. Mikell, Scott J. Wilderman and Yuni K. Dewaraja. Accepted by Medical Physics, 2021. DOI: 10.1002/mp.15397
- Discipline:
- Health Sciences
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- Creator:
- Bhaumik, Deesha
- Description:
- This cross-sectional analysis included 584 participants in the Center for Oral Health Research in Appalachia cohort 1 (COHRA1). We sequenced the V4 region of the 16S rRNA of supragingival plaque from 185 caries-active and 565 caries-free teeth using the Illumina MiSeq platform. Sequences were filtered using the R DADA2 package and assigned taxonomy using the Human Oral Microbiome Database ( http://www.homd.org/).
- Keyword:
- Amplicon Sequence Variant
- Citation to related publication:
- In press
- Discipline:
- Health Sciences
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- Creator:
- Modey, Christine A., Cheatle, Joseph, and Giaimo, Genie N.
- Description:
- Data includes information regarding session notes from sixty-three institutions, including blank session note forms, data sets of completed session notes, and survey data about how sessions notes are conceived of, and used, in writing centers.
- Keyword:
- session note, client report form, tutor notes, writing center, writing, and tutor
- Citation to related publication:
- Christine Modey, Genie Giaimo, and Joseph Cheatle. “Session Notes: Preliminary Results from a Cross-Institutional Survey.” Praxis: A Writing Center Journal 18.3 (2021): 52-75. https://issuu.com/titospanks/docs/18.3_summer_2021_full_issue_2._pdf
- Discipline:
- Humanities
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- Creator:
- Bougher, S. W. (University of Michigan) and Brecht, A. S. (NASA Ames Research Center)
- Description:
- This work examines the planetary wave-induced variability within the upper mesosphere/lower thermosphere of Venus by utilizing the Venus Thermospheric General Circulation Model (VTGCM). Rossby and Kelvin wave perturbations are driven by variations in the geopotential height of the VTGCM lower boundary (~70 km). A suite of simulations was conducted to examine the impact of the individual and combined waves propagating from two different lower boundary conditions (uniform and varying). The Kelvin wave is the more dominant wave which produces the most variability, as was shown in Hoshino et al., 2012. The combination of the Kelvin and Rossby waves provides a maximum temperature amplitude of 13 K at 92 km and maximum zonal wind amplitude of 23 m/s at 102 km. The combined waves overall are able to propagate up to 125 km. Most of the variation within the temperature, winds, and composition occurs between 70 km and 110 km. The varying lower boundary increases the magnitude of the wave deposition but weakly changes the propagation altitude. The thermal variation due to the planetary waves does not reproduce most observed variations. The simulated O2 IR nightglow emission is sensitive to the waves with respect to intensity and local time, but lacks latitudinal variation. The integrated intensity ranges from 1.2 MR to 1.65 MR and the local time ranges from 0.33 local time to 23.6 local time. Overall, planetary waves do affect the atmospheric structure, but there are still observed large variations that planetary waves alone cannot explain (i.e. thermal structure).
- Keyword:
- Venus, planetary waves, upper mesophere, lower thermosphere, and O2 nightglow
- Citation to related publication:
- Brecht, A. S., Bougher, S. W., Shields, D., & Liu, H.-L. (2021). Planetary-scale wave impacts on the Venusian upper mesosphere and lower thermosphere. Journal of Geophysical Research: Planets, 126, e2020JE006587. https://doi.org/10.1029/2020JE006587
- Discipline:
- Science
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- Creator:
- Curlis, JD, Renney, TJ, Davis Rabosky, AR, and Moore, TY
- Description:
- Efficient comparisons of biological color patterns are critical for understanding the mechanisms by which organisms evolve in ecosystems, including sexual selection, predator-prey interactions, and thermoregulation. However, elongate or spiral-shaped organisms do not conform to the standard orientation and photographic techniques required for automated analysis. Currently, large-scale color analysis of elongate animals requires time-consuming manual landmarking, which reduces their representation in coloration research despite their ecological importance. We present Batch-Mask: an automated and customizable workflow to facilitate the analysis of large photographic data sets of non-standard biological subjects. First, we present a user guide to run an open-source region-based convolutional neural network with fine-tuned weights for identifying and isolating a biological subject from a background (masking). Then, we demonstrate how to combine masking with existing manual visual analysis tools into a single streamlined, automated workflow for comparing color patterns across images. Batch-Mask was 60x faster than manual landmarking, produced masks that correctly identified 96% of all snake pixels, and produced pattern energy results that were not significantly different from the manually landmarked data set. The fine-tuned weights for the masking neural network, user guide, and automated workflow substantially decrease the amount of time and attention required to quantitatively analyze non-standard biological subjects. By using these tools, biologists will be able to compare color, pattern, and shape differences in large data sets that include significant morphological variation in elongate body forms. This advance will be especially valuable for comparative analyses of natural history collections, and through automation can greatly expand the scale of space, time, or taxonomic breadth across which color variation can be quantitatively examined.
- Keyword:
- convolutional neural network, photography, sensory ecology, color evolution, vision, and image segmentation
- Citation to related publication:
- Curlis, Renney, Davis Rabosky, Moore (submitted) Batch-Mask: An automated Mask R-CNN workflow to isolate non-standard biological specimens for color pattern analysis.
- Discipline:
- Engineering and Science
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Profiles of near-surface rock mass strength across gradients in erosion, burial, and time [Data set]
- Creator:
- Townsend, Kirk F, Clark, Marin K, and Zekkos, Dimitrios
- Description:
- These datasets support the findings of Townsend et al. (2020). In this article, we project profiles of rock mass shear strength into the shallow subsurface (~30 m depth) using the Hoek and Brown criterion with Geological Strength Index (GSI) observations of outcrop structure and surface conditions, and Schmidt hammer rebound values of intact (unfractured) rock hardness. We compare these projected rock mass shear strength profiles to shear-wave velocity profiles collected using shallow geophysical arrays. We evaluate our methods in the Western Transverse Ranges of southern California, which exhibit strong gradients in the depth of latest-Mesozoic through Cenozoic sedimentary rocks exposed at the surface today, and in erosion rates quantified from catchment-average cosmogenic radionuclide concentrations and low-temperature apatite and zircon (U-Th)/He thermochronometry. We find that stratigraphic age and burial depth exerts the strongest apparent control on rock strength and S-wave velocities, likely due to diagenetic changes associated with burial. For rocks of the same age and inferred burial history, we observe that shear strength and S-wave velocities are positively correlated with erosion rate. We suggest that increasing erosion rates cause decreased residence time of rock masses within the critical zone, resulting in less weathered rocks.
- Keyword:
- rock strength, seismic, and erosion rate
- Citation to related publication:
- Townsend, K. F., Clark, M. K., & Zekkos, D. (2021). Profiles of Near-Surface Rock Mass Strength Across Gradients in Burial, Erosion, and Time. Journal of Geophysical Research: Earth Surface, 126(4), e2020JF005694. https://doi.org/10.1029/2020JF005694
- Discipline:
- Science
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- Creator:
- Lee, Dahee, Panicker, Veena, and Landis-Lewis, Zach
- Description:
- We use the term “performance summary display” (PSD) to mean a kind of visualization that relates performance levels to other types of information. In the context of healthcare organizations, PSDs are intended to be communicated to a healthcare professional, team, or organization. and Displays were identified, classified, and elements counted and coded. The performance summary display ontology provides a set of descriptions of components of displays that have been used to annotate performance feedback visualizations.
- Keyword:
- Performance
- Citation to related publication:
- Lee, D., Panicker, V., Gross, C., Zhang, J., & Landis-Lewis, Z. (2020). What was visualized? A method for describing content of performance summary displays in feedback interventions. BMC medical research methodology, 20(1), 90. https://doi.org/10.1186/s12874-020-00951-x
- Discipline:
- Health Sciences and Science
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- Creator:
- Umaña, María Natalia and Arellano, Gabriel
- Description:
- The objective of this study was to examine the existence of congruent tree growth responses to different extreme climatic events –hurricanes and drought–affecting tropical wet forests.
- Keyword:
- Dendrometers , El Niño Southern Oscillation (ENSO), Hurricane Maria, Puerto Rico, and Tropical Forests
- Citation to related publication:
- Umaña, M.N.and Arellano G. In press. Legacy effects of drought on tree growth responses to hurricanes. Ecography. https://doi.org/10.1111/ecog.05803
- Discipline:
- Science
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- Creator:
- Tye, Alexander R, Niemi, Nathan A, Safarov, Rafig T, Kadirov, Fakhraddin A, Babayev, Gulam R
- Description:
- Apatite fission track thermochronometry data were collected from the Eastern Greater Caucasus orogen, Azerbaijan. Thermochronometry data constrain the history of exhumation and deformation of rocks within the orogen, which is an active accretionary prism. Thermochronometry data record the timing of cooling of a rock sample beneath a given closure temperature. Given an assumed or inferred geothermal gradient, thermochronometric ages can be used to infer exhumation rates and make interpretations about rates of deformation in orogens. The apatite fission track data presented here are analyzed in concert with apatite (U-Th)/He and zircon (U-Th)/He ages reported in Tye et al., in prep., to characterize the exhumation history of the Eastern Greater Caucasus.
- Keyword:
- thermochronometry, apatite fission track, Caucasus
- Citation to related publication:
- Tye, A. R., Niemi, N. A., Safarov, R. T., Kadirov, F. A., & Babayev, G. R. (2021). Sedimentary response to a collision orogeny recorded in detrital zircon provenance of Greater Caucasus foreland basin sediments. Basin Research, 33(2), 933–967. https://doi.org/10.1111/bre.12499
- Discipline:
- Science
-
- Creator:
- Moore, Talia Y, Villacis Nunez, C Nathaly, Ray, Andrew P, and Cooper, Kimberly L
- Description:
- Hind limbs can undergo dramatic changes in loading conditions during the transition from quadrupedal to bipedal locomotion. For example, the most early diverging bipedal jerboas (Rodentia: Dipodidae) are some of the smallest mammals in the world, with body masses that range 2-4 grams. The larger jerboa species exhibit developmental and evolutionary fusion of the central three metatarsals into a single cannon bone. We hypothesize that body size reduction and metatarsal fusion are mechanisms to maintain the safety factor of the hind limb bones despite the higher ground reaction forces associated with bipedal locomotion. Using finite element analysis to model collisions between the substrate and the metatarsals, we found that body size reduction was insufficient to reduce bone stress on unfused metatarsals, based on the scaled dynamics of larger jerboas, and that fused bones developed lower stresses than unfused bones when all metatarsals are scaled to the same size and loading conditions. Based on these results, we conclude that fusion reinforces larger jerboa metatarsals against high ground reaction forces. Because smaller jerboas with unfused metatarsals develop higher peak stresses in response to loading conditions scaled from larger jerboas, we hypothesize that smaller jerboas use alternative dynamics of bipedal locomotion that reduces the impact of collisions between the foot and substrate.
- Keyword:
- finite element, functional morphology, bipedal, jerboa, metatarsus, and bone fusion
- Citation to related publication:
- Villacis Nunez, Ray, Cooper, Moore (submitted). Body size reduction and metatarsal fusion were distinct mechanisms to resist bending as jerboas (Dipodidae) transitioned from quadrupedal to bipedal.
- Discipline:
- Science and Engineering