Browsing by Subject "X-Ray Microtomography"
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Item Open Access A Deep Learning Approach for Rapid and Generalizable Denoising of Photon-Counting Micro-CT Images.(Tomography (Ann Arbor, Mich.), 2023-07) Nadkarni, Rohan; Clark, Darin P; Allphin, Alex J; Badea, Cristian TPhoton-counting CT (PCCT) is powerful for spectral imaging and material decomposition but produces noisy weighted filtered backprojection (wFBP) reconstructions. Although iterative reconstruction effectively denoises these images, it requires extensive computation time. To overcome this limitation, we propose a deep learning (DL) model, UnetU, which quickly estimates iterative reconstruction from wFBP. Utilizing a 2D U-net convolutional neural network (CNN) with a custom loss function and transformation of wFBP, UnetU promotes accurate material decomposition across various photon-counting detector (PCD) energy threshold settings. UnetU outperformed multi-energy non-local means (ME NLM) and a conventional denoising CNN called UnetwFBP in terms of root mean square error (RMSE) in test set reconstructions and their respective matrix inversion material decompositions. Qualitative results in reconstruction and material decomposition domains revealed that UnetU is the best approximation of iterative reconstruction. In reconstructions with varying undersampling factors from a high dose ex vivo scan, UnetU consistently gave higher structural similarity (SSIM) and peak signal-to-noise ratio (PSNR) to the fully sampled iterative reconstruction than ME NLM and UnetwFBP. This research demonstrates UnetU's potential as a fast (i.e., 15 times faster than iterative reconstruction) and generalizable approach for PCCT denoising, holding promise for advancing preclinical PCCT research.Item Open Access A digital collection of rare and endangered lemurs and other primates from the Duke Lemur Center.(PloS one, 2019-01) Yapuncich, Gabriel S; Kemp, Addison D; Griffith, Darbi M; Gladman, Justin T; Ehmke, Erin; Boyer, Doug MScientific study of lemurs, a group of primates found only on Madagascar, is crucial for understanding primate evolution. Unfortunately, lemurs are among the most endangered animals in the world, so there is a strong impetus to maximize as much scientific data as possible from available physical specimens. MicroCT scanning efforts at Duke University have resulted in scans of more than 100 strepsirrhine cadavers representing 18 species from the Duke Lemur Center. An error study of the microCT scanner recovered less than 0.3% error at multiple resolution levels. Scans include specimen overviews and focused, high-resolution selections of complex anatomical regions (e.g., cranium, hands, feet). Scans have been uploaded to MorphoSource, an online digital repository for 3D data. As captive (but free ranging) individuals, these specimens have a wealth of associated information that is largely unavailable for wild populations, including detailed life history data. This digital collection maximizes the information obtained from rare and endangered animals with minimal degradation of the original specimens.Item Open Access A Novel Method for Assessing Enamel Thickness Distribution in the Anterior Dentition as a Signal for Gouging and Other Extractive Foraging Behaviors in Gummivorous Mammals.(Folia primatologica; international journal of primatology, 2020-01) Selig, Keegan R; López-Torres, Sergi; Hartstone-Rose, Adam; Nash, Leanne T; Burrows, Anne M; Silcox, Mary TGummivory poses unique challenges to the dentition as gum acquisition may often require that the anterior teeth be adapted to retain a sharp edge and to resist loading because they sometimes must penetrate a highly obdurate substrate during gum extraction by means of gouging or scraping. It has been observed previously that the enamel on the labial surface of the teeth used for extraction is thicker relative to that on the lingual surface in taxa that extract gums, while enamel is more evenly distributed in the anterior teeth of taxa that do not regularly engage in extractive behaviors. This study presents a quantitative methodology for measuring the distribution of labial versus lingual enamel thickness among primate and marsupial taxa in the context of gummivory. Computed microtomography scans of 15 specimens representing 14 taxa were analyzed. Ten measurements were taken at 20% intervals starting from the base of the crown of the extractive tooth to the tip of the cutting edge across the lingual and labial enamel. A method for including worn or broken teeth is also presented. Mann-Whitney U tests, canonical variates analysis, and between-group principal components analysis were used to examine variation in enamel thickness across taxa. Our results suggest that the differential distribution of enamel thickness in the anterior dentition can serve as a signal for gouging behavior; this methodology distinguishes between gougers, scrapers, and nonextractive gummivores. Gouging taxa are characterized by significantly thicker labial enamel relative to the lingual enamel, particularly towards the crown tip. Examination of enamel thickness patterning in these taxa permits a better understanding of the adaptations for the extraction of gums in extant taxa and offers the potential to test hypotheses concerning the dietary adaptations of fossil taxa.Item Open Access Advances in micro-CT imaging of small animals.(Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB), 2021-08) Clark, DP; Badea, CTPurpose
Micron-scale computed tomography (micro-CT) imaging is a ubiquitous, cost-effective, and non-invasive three-dimensional imaging modality. We review recent developments and applications of micro-CT for preclinical research.Methods
Based on a comprehensive review of recent micro-CT literature, we summarize features of state-of-the-art hardware and ongoing challenges and promising research directions in the field.Results
Representative features of commercially available micro-CT scanners and some new applications for both in vivo and ex vivo imaging are described. New advancements include spectral scanning using dual-energy micro-CT based on energy-integrating detectors or a new generation of photon-counting x-ray detectors (PCDs). Beyond two-material discrimination, PCDs enable quantitative differentiation of intrinsic tissues from one or more extrinsic contrast agents. When these extrinsic contrast agents are incorporated into a nanoparticle platform (e.g. liposomes), novel micro-CT imaging applications are possible such as combined therapy and diagnostic imaging in the field of cancer theranostics. Another major area of research in micro-CT is in x-ray phase contrast (XPC) imaging. XPC imaging opens CT to many new imaging applications because phase changes are more sensitive to density variations in soft tissues than standard absorption imaging. We further review the impact of deep learning on micro-CT. We feature several recent works which have successfully applied deep learning to micro-CT data, and we outline several challenges specific to micro-CT.Conclusions
All of these advancements establish micro-CT imaging at the forefront of preclinical research, able to provide anatomical, functional, and even molecular information while serving as a testbench for translational research.Item Open Access Altered trabecular bone structure and delayed cartilage degeneration in the knees of collagen VI null mice.(PLoS One, 2012) Christensen, Susan E; Coles, Jeffrey M; Zelenski, Nicole A; Furman, Bridgette D; Leddy, Holly A; Zauscher, Stefan; Bonaldo, Paolo; Guilak, FarshidMutation or loss of collagen VI has been linked to a variety of musculoskeletal abnormalities, particularly muscular dystrophies, tissue ossification and/or fibrosis, and hip osteoarthritis. However, the role of collagen VI in bone and cartilage structure and function in the knee is unknown. In this study, we examined the role of collagen VI in the morphology and physical properties of bone and cartilage in the knee joint of Col6a1(-/-) mice by micro-computed tomography (microCT), histology, atomic force microscopy (AFM), and scanning microphotolysis (SCAMP). Col6a1(-/-) mice showed significant differences in trabecular bone structure, with lower bone volume, connectivity density, trabecular number, and trabecular thickness but higher structure model index and trabecular separation compared to Col6a1(+/+) mice. Subchondral bone thickness and mineral content increased significantly with age in Col6a1(+/+) mice, but not in Col6a1(-/-) mice. Col6a1(-/-) mice had lower cartilage degradation scores, but developed early, severe osteophytes compared to Col6a1(+/+) mice. In both groups, cartilage roughness increased with age, but neither the frictional coefficient nor compressive modulus of the cartilage changed with age or genotype, as measured by AFM. Cartilage diffusivity, measured via SCAMP, varied minimally with age or genotype. The absence of type VI collagen has profound effects on knee joint structure and morphometry, yet minimal influences on the physical properties of the cartilage. Together with previous studies showing accelerated hip osteoarthritis in Col6a1(-/-) mice, these findings suggest different roles for collagen VI at different sites in the body, consistent with clinical data.Item Open Access Assessing cardiac injury in mice with dual energy-microCT, 4D-microCT, and microSPECT imaging after partial heart irradiation.(Int J Radiat Oncol Biol Phys, 2014-03-01) Lee, Chang-Lung; Min, Hooney; Befera, Nicholas; Clark, Darin; Qi, Yi; Das, Shiva; Johnson, G Allan; Badea, Cristian T; Kirsch, David GPURPOSE: To develop a mouse model of cardiac injury after partial heart irradiation (PHI) and to test whether dual energy (DE)-microCT and 4-dimensional (4D)-microCT can be used to assess cardiac injury after PHI to complement myocardial perfusion imaging using micro-single photon emission computed tomography (SPECT). METHODS AND MATERIALS: To study cardiac injury from tangent field irradiation in mice, we used a small-field biological irradiator to deliver a single dose of 12 Gy x-rays to approximately one-third of the left ventricle (LV) of Tie2Cre; p53(FL/+) and Tie2Cre; p53(FL/-) mice, where 1 or both alleles of p53 are deleted in endothelial cells. Four and 8 weeks after irradiation, mice were injected with gold and iodinated nanoparticle-based contrast agents, and imaged with DE-microCT and 4D-microCT to evaluate myocardial vascular permeability and cardiac function, respectively. Additionally, the same mice were imaged with microSPECT to assess myocardial perfusion. RESULTS: After PHI with tangent fields, DE-microCT scans showed a time-dependent increase in accumulation of gold nanoparticles (AuNp) in the myocardium of Tie2Cre; p53(FL/-) mice. In Tie2Cre; p53(FL/-) mice, extravasation of AuNp was observed within the irradiated LV, whereas in the myocardium of Tie2Cre; p53(FL/+) mice, AuNp were restricted to blood vessels. In addition, data from DE-microCT and microSPECT showed a linear correlation (R(2) = 0.97) between the fraction of the LV that accumulated AuNp and the fraction of LV with a perfusion defect. Furthermore, 4D-microCT scans demonstrated that PHI caused a markedly decreased ejection fraction, and higher end-diastolic and end-systolic volumes, to develop in Tie2Cre; p53(FL/-) mice, which were associated with compensatory cardiac hypertrophy of the heart that was not irradiated. CONCLUSIONS: Our results show that DE-microCT and 4D-microCT with nanoparticle-based contrast agents are novel imaging approaches complementary to microSPECT for noninvasive assessment of the change in myocardial vascular permeability and cardiac function of mice in whom myocardial injury develops after PHI.Item Open Access Characterization of porous, dexamethasone-releasing polyurethane coatings for glucose sensors.(Acta Biomaterialia, 2014-11) Vallejo-Heligon, Suzana G; Klitzman, Bruce; Reichert, William MCommercially available implantable needle-type glucose sensors for diabetes management are robust analytically but can be unreliable clinically primarily due to tissue-sensor interactions. Here, we present the physical, drug release and bioactivity characterization of tubular, porous dexamethasone (Dex)-releasing polyurethane coatings designed to attenuate local inflammation at the tissue-sensor interface. Porous polyurethane coatings were produced by the salt-leaching/gas-foaming method. Scanning electron microscopy and micro-computed tomography (micro-CT) showed controlled porosity and coating thickness. In vitro drug release from coatings monitored over 2 weeks presented an initial fast release followed by a slower release. Total release from coatings was highly dependent on initial drug loading amount. Functional in vitro testing of glucose sensors deployed with porous coatings against glucose standards demonstrated that highly porous coatings minimally affected signal strength and response rate. Bioactivity of the released drug was determined by monitoring Dex-mediated, dose-dependent apoptosis of human peripheral blood derived monocytes in culture. Acute animal studies were used to determine the appropriate Dex payload for the implanted porous coatings. Pilot short-term animal studies showed that Dex released from porous coatings implanted in rat subcutis attenuated the initial inflammatory response to sensor implantation. These results suggest that deploying sensors with the porous, Dex-releasing coatings is a promising strategy to improve glucose sensor performance.Item Open Access Dental sculpting and compensatory shearing crests demonstrated in a WEAR series of Presbytis rubicunda (Cercopithecoidea, Colobidae) with dental topography analysis.(American journal of biological anthropology, 2024-09) Pampush, James D; Morse, Paul E; Kay, Richard FObjectives
Maintaining effective and efficient occlusal morphology presents adaptive challenges for mammals, particularly because mastication produces interactions with foods and other materials that alters the geometry of occlusal surfaces through macrowear and/or catastrophic failure (i.e. "chipping"). Altered occlusal morphologies are often less effective for masticating materials of given diet-but not always-some species exhibit dental sculpting, meaning their dentitions are set up to harness macrowear to hone their occlusal surfaces into more effective morphologies (i.e. secondary morphologies). Here we show that dental sculpting is present in the folivorous Presbytis rubicunda of Borneo.Methods
Thirty-one undamaged lower second molars of P. rubicunda exhibiting various stages of macroscopic wear were micro-CT scanned and processed into digital surfaces. The surfaces were measured for convex Dirichlet normal energy (vDNE, a measure of surface sharpness), and degree of surface wear. Regression analyses compared surface sharpness with several measures of wear to test for the presence and magnitude of dental sculpting.Results
Positive correlations between the wear proxies and vDNE reveal that P. rubicunda wear in such a way as to become sharper, and therefore more effective chewing surfaces by exposing enamel-dentine junctions on their occlusal surfaces and then honing these junctions into sharpened edges. Compared to another primate folivore in which increasing surface sharpness with macrowear has been demonstrated (i.e., Alouatta palliata), the worn surfaces are similarly sharp, but the dental sculpting process appears to be different.Discussion
The results presented here suggest that not only do some primates exhibit dental sculpting and the attendant secondary morphology, but that there appear to be multiple different morphological configurations that can achieve this result. P. rubicunda has thicker enamel and a more stereotyped wear pattern than A. palliata, although both show positive correlations of occlusal surface sharpness (vDNE) with various wear proxies. These findings shed light on the varied approaches for the maintenance of effective and efficient occlusal surfaces in primates.Item Open Access Dual source hybrid spectral micro-CT using an energy-integrating and a photon-counting detector.(Physics in medicine and biology, 2020-10-21) Holbrook, MD; Clark, DP; Badea, CTPreclinical micro-CT provides a hotbed in which to develop new imaging technologies, including spectral CT using photon counting detector (PCD) technology. Spectral imaging using PCDs promises to expand x-ray CT as a functional imaging modality, capable of molecular imaging, while maintaining CT's role as a powerful anatomical imaging modality. However, the utility of PCDs suffers due to distorted spectral measurements, affecting the accuracy of material decomposition. We attempt to improve material decomposition accuracy using our novel hybrid dual-source micro-CT system which combines a PCD and an energy integrating detector. Comparisons are made between PCD-only and hybrid CT results, both reconstructed with our iterative, multi-channel algorithm based on the split Bregman method and regularized with rank-sparse kernel regression. Multi-material decomposition is performed post-reconstruction for separation of iodine (I), gold (Au), gadolinium (Gd), and calcium (Ca). System performance is evaluated first in simulations, then in micro-CT phantoms, and finally in an in vivo experiment with a genetically modified p53fl/fl mouse cancer model with Au, Gd, and I nanoparticle (NP)-based contrasts agents. Our results show that the PCD-only and hybrid CT reconstructions offered very similar spatial resolution at 10% MTF (PCD: 3.50 lp mm-1; hybrid: 3.47 lp mm-1) and noise characteristics given by the noise power spectrum. For material decomposition we note successful separation of the four basis materials. We found that hybrid reconstruction reduces RMSE by an average of 37% across all material maps when compared to PCD-only of similar dose but does not provide much difference in terms of concentration accuracy. The in vivo results show separation of targeted Au and accumulated Gd NPs in the tumor from intravascular iodine NPs and bone. Hybrid spectral micro-CT can benefit nanotechnology and cancer research by providing quantitative imaging to test and optimize various NPs for diagnostic and therapeutic applications.Item Open Access Dual-energy micro-CT functional imaging of primary lung cancer in mice using gold and iodine nanoparticle contrast agents: a validation study.(PLoS One, 2014) Ashton, Jeffrey R; Clark, Darin P; Moding, Everett J; Ghaghada, Ketan; Kirsch, David G; West, Jennifer L; Badea, Cristian TPURPOSE: To provide additional functional information for tumor characterization, we investigated the use of dual-energy computed tomography for imaging murine lung tumors. Tumor blood volume and vascular permeability were quantified using gold and iodine nanoparticles. This approach was compared with a single contrast agent/single-energy CT method. Ex vivo validation studies were performed to demonstrate the accuracy of in vivo contrast agent quantification by CT. METHODS: Primary lung tumors were generated in LSL-Kras(G12D); p53(FL/FL) mice. Gold nanoparticles were injected, followed by iodine nanoparticles two days later. The gold accumulated in tumors, while the iodine provided intravascular contrast. Three dual-energy CT scans were performed-two for the single contrast agent method and one for the dual contrast agent method. Gold and iodine concentrations in each scan were calculated using a dual-energy decomposition. For each method, the tumor fractional blood volume was calculated based on iodine concentration, and tumor vascular permeability was estimated based on accumulated gold concentration. For validation, the CT-derived measurements were compared with histology and inductively-coupled plasma optical emission spectroscopy measurements of gold concentrations in tissues. RESULTS: Dual-energy CT enabled in vivo separation of gold and iodine contrast agents and showed uptake of gold nanoparticles in the spleen, liver, and tumors. The tumor fractional blood volume measurements determined from the two imaging methods were in agreement, and a high correlation (R(2) = 0.81) was found between measured fractional blood volume and histology-derived microvascular density. Vascular permeability measurements obtained from the two imaging methods agreed well with ex vivo measurements. CONCLUSIONS: Dual-energy CT using two types of nanoparticles is equivalent to the single nanoparticle method, but allows for measurement of fractional blood volume and permeability with a single scan. As confirmed by ex vivo methods, CT-derived nanoparticle concentrations are accurate. This method could play an important role in lung tumor characterization by CT.Item Open Access G protein-coupled receptor kinase 3 modulates mesenchymal stem cell proliferation and differentiation through sphingosine-1-phosphate receptor regulation.(Stem cell research & therapy, 2022-01-29) Brozowski, Jaime M; Timoshchenko, Roman G; Serafin, D Stephen; Allyn, Brittney; Koontz, Jessica; Rabjohns, Emily M; Rampersad, Rishi R; Ren, Yinshi; Eudy, Amanda M; Harris, Taylor F; Abraham, David; Mattox, Daniel; Rubin, Clinton T; Hilton, Matthew J; Rubin, Janet; Allbritton, Nancy L; Billard, Matthew J; Tarrant, Teresa KBackground
The bone marrow niche supports hematopoietic cell development through intimate contact with multipotent stromal mesenchymal stem cells; however, the intracellular signaling, function, and regulation of such supportive niche cells are still being defined. Our study was designed to understand how G protein receptor kinase 3 (GRK3) affects bone marrow mesenchymal stem cell function by examining primary cells from GRK3-deficient mice, which we have previously published to have a hypercellular bone marrow and leukocytosis through negative regulation of CXCL12/CXCR4 signaling.Methods
Murine GRK3-deficient bone marrow mesenchymal stromal cells were harvested and cultured to differentiate into three lineages (adipocyte, chondrocyte, and osteoblast) to confirm multipotency and compared to wild type cells. Immunoblotting, modified-TANGO experiments, and flow cytometry were used to further examine the effects of GRK3 deficiency on bone marrow mesenchymal stromal cell receptor signaling. Microcomputed tomography was used to determine trabecular and cortical bone composition of GRK3-deficient mice and standard ELISA to quantitate CXCL12 production from cellular cultures.Results
GRK3-deficient, bone marrow-derived mesenchymal stem cells exhibit enhanced and earlier osteogenic differentiation in vitro. The addition of a sphingosine kinase inhibitor abrogated the osteogenic proliferation and differentiation, suggesting that sphingosine-1-phosphate receptor signaling was a putative G protein-coupled receptor regulated by GRK3. Immunoblotting showed prolonged ERK1/2 signaling after stimulation with sphingosine-1-phosphate in GRK3-deficient cells, and modified-TANGO assays suggested the involvement of β-arrestin-2 in sphingosine-1-phosphate receptor internalization.Conclusions
Our work suggests that GRK3 regulates sphingosine-1-phosphate receptor signaling on bone marrow mesenchymal stem cells by recruiting β-arrestin to the occupied GPCR to promote internalization, and lack of such regulation affects mesenchymal stem cell functionality.Item Open Access High-resolution hybrid micro-CT imaging pipeline for mouse brain region segmentation and volumetric morphometry.(PloS one, 2024-01) Nadkarni, Rohan; Han, Zay Yar; Anderson, Robert J; Allphin, Alex J; Clark, Darin P; Badea, Alexandra; Badea, Cristian TBackground
Brain region segmentation and morphometry in humanized apolipoprotein E (APOE) mouse models with a human NOS2 background (HN) contribute to Alzheimer's disease (AD) research by demonstrating how various risk factors affect the brain. Photon-counting detector (PCD) micro-CT provides faster scan times than MRI, with superior contrast and spatial resolution to energy-integrating detector (EID) micro-CT. This paper presents a pipeline for mouse brain imaging, segmentation, and morphometry from PCD micro-CT.Methods
We used brains of 26 mice from 3 genotypes (APOE22HN, APOE33HN, APOE44HN). The pipeline included PCD and EID micro-CT scanning, hybrid (PCD and EID) iterative reconstruction, and brain region segmentation using the Small Animal Multivariate Brain Analysis (SAMBA) tool. We applied SAMBA to transfer brain region labels from our new PCD CT atlas to individual PCD brains via diffeomorphic registration. Region-based and voxel-based analyses were used for comparisons by genotype and sex.Results
Together, PCD and EID scanning take ~5 hours to produce images with a voxel size of 22 μm, which is faster than MRI protocols for mouse brain morphometry with voxel size above 40 μm. Hybrid iterative reconstruction generates PCD images with minimal artifacts and higher spatial resolution and contrast than EID images. Our PCD atlas is qualitatively and quantitatively similar to the prior MRI atlas and successfully transfers labels to PCD brains in SAMBA. Male and female mice had significant volume differences in 26 regions, including parts of the entorhinal cortex and cingulate cortex. APOE22HN brains were larger than APOE44HN brains in clusters from the hippocampus, a region where atrophy is associated with AD.Conclusions
This work establishes a pipeline for mouse brain analysis using PCD CT, from staining to imaging and labeling brain images. Our results validate the effectiveness of the approach, setting a foundation for research on AD mouse models while reducing scanning durations.Item Open Access Micro-CT imaging of multiple K-edge elements using GaAs and CdTe photon counting detectors.(Physics in medicine and biology, 2023-04) Allphin, AJ; Clark, DP; Thuering, T; Bhandari, P; Ghaghada, KB; Badea, CTObjective.To evaluate the performance of two photon-counting (PC) detectors based on different detector materials, gallium arsenide (GaAs) and cadmium telluride (CdTe), for PC micro-CT imaging of phantoms with multiple contrast materials. Another objective is to determine if combining these two detectors in the same micro-CT system can offer higher spectral performance and significant artifact reduction compared to a single detector system.Approach. We have constructed a dual-detector, micro-CT system equipped with two PCDs based on different detector materials: gallium arsenide (GaAs) and cadmium telluride (CdTe). We demonstrate the performance of these detectors for PC micro-CT imaging of phantoms with up to 5 contrast materials with K-edges spread across the x-ray spectrum ranging from iodine with a K-edge at 33.2 keV to bismuth with a K-edge at 90.5 keV. We also demonstrate the use of our system to image a mouse prepared with both iodine and bismuth contrast agents to target different biological systems.Main results.When using the same dose and scan parameters, GaAs shows increased low energy (<50 keV) spectral sensitivity and specificity compared to CdTe. However, GaAs performance at high energies suffers from spectral artifacts and has comparatively low photon counts indicating wasted radiation dose. We demonstrate that combining a GaAs-based and a CdTe-based PC detector in the same micro-CT system offers higher spectral performance and significant artifact reduction compared to a single detector system.Significance.More accurate PC micro-CT using a GaAs PCD alone or in combination with a CdTe PCD could serve for developing new contrast agents such as nanoparticles that show promise in the developing field of theranostics (therapy and diagnostics).Item Open Access Micro-CT of rodents: state-of-the-art and future perspectives.(Phys Med, 2014-09) Clark, DP; Badea, CTMicron-scale computed tomography (micro-CT) is an essential tool for phenotyping and for elucidating diseases and their therapies. This work is focused on preclinical micro-CT imaging, reviewing relevant principles, technologies, and applications. Commonly, micro-CT provides high-resolution anatomic information, either on its own or in conjunction with lower-resolution functional imaging modalities such as positron emission tomography (PET) and single-photon emission computed tomography (SPECT). More recently, however, advanced applications of micro-CT produce functional information by translating clinical applications to model systems (e.g., measuring cardiac functional metrics) and by pioneering new ones (e.g. measuring tumor vascular permeability with nanoparticle contrast agents). The primary limitations of micro-CT imaging are the associated radiation dose and relatively poor soft tissue contrast. We review several image reconstruction strategies based on iterative, statistical, and gradient sparsity regularization, demonstrating that high image quality is achievable with low radiation dose given ever more powerful computational resources. We also review two contrast mechanisms under intense development. The first is spectral contrast for quantitative material discrimination in combination with passive or actively targeted nanoparticle contrast agents. The second is phase contrast which measures refraction in biological tissues for improved contrast and potentially reduced radiation dose relative to standard absorption imaging. These technological advancements promise to develop micro-CT into a commonplace, functional and even molecular imaging modality.Item Open Access Oldest known cranium of a juvenile New World monkey (Early Miocene, Patagonia, Argentina): implications for the taxonomy and the molar eruption pattern of early platyrrhines.(J Hum Evol, 2014-09) Perry, Jonathan MG; Kay, Richard F; Vizcaíno, Sergio F; Bargo, M SusanaA juvenile cranium of Homunculus patagonicus Ameghino, 1891a from the late Early Miocene of Santa Cruz Province (Argentina) provides the first evidence of developing cranial anatomy for any fossil platyrrhine. The specimen preserves the rostral part of the cranium with deciduous and permanent alveoli and teeth. The dental eruption sequence in the new specimen and a reassessment of eruption patterns in living and fossil platyrrhines suggest that the ancestral platyrrhine pattern of tooth replacement was for the permanent incisors to erupt before M(1), not an accelerated molar eruption (before the incisors) as recently proposed. Two genera and species of Santacrucian monkeys are now generally recognized: H. patagonicus Ameghino, 1891a and Killikaike blakei Tejedor et al., 2006. Taxonomic allocation of Santacrucian monkeys to these species encounters two obstacles: 1) the (now lost) holotype and a recently proposed neotype of H. patagonicus are mandibles from different localities and different geologic members of the Santa Cruz Formation, separated by approximately 0.7 million years, whereas the holotype of K. blakei is a rostral part of a cranium without a mandible; 2) no Santacrucian monkey with associated cranium and mandible has ever been found. Bearing in mind these uncertainties, our examination of the new specimen as well as other cranial specimens of Santacrucian monkeys establishes the overall dental and cranial similarity between the holotype of Killikaike blakei, adult cranial material previously referred to H. patagonicus, and the new juvenile specimen. This leads us to conclude that Killikaike blakei is a junior subjective synonym of H. patagonicus.Item Open Access Photon-counting cine-cardiac CT in the mouse.(PloS one, 2019-01) Clark, Darin P; Holbrook, Matthew; Lee, Chang-Lung; Badea, Cristian TThe maturation of photon-counting detector (PCD) technology promises to enhance routine CT imaging applications with high-fidelity spectral information. In this paper, we demonstrate the power of this synergy and our complementary reconstruction techniques, performing 4D, cardiac PCD-CT data acquisition and reconstruction in a mouse model of atherosclerosis, including calcified plaque. Specifically, in vivo cardiac micro-CT scans were performed in four ApoE knockout mice, following their development of calcified plaques. The scans were performed with a prototype PCD (DECTRIS, Ltd.) with 4 energy thresholds. Projections were sampled every 10 ms with a 10 ms exposure, allowing the reconstruction of 10 cardiac phases at each of 4 energies (40 total 3D volumes per mouse scan). Reconstruction was performed iteratively using the split Bregman method with constraints on spectral rank and spatio-temporal gradient sparsity. The reconstructed images represent the first in vivo, 4D PCD-CT data in a mouse model of atherosclerosis. Robust regularization during iterative reconstruction yields high-fidelity results: an 8-fold reduction in noise standard deviation for the highest energy threshold (relative to unregularized algebraic reconstruction), while absolute spectral bias measurements remain below 13 Hounsfield units across all energy thresholds and scans. Qualitatively, image domain material decomposition results show clear separation of iodinated contrast and soft tissue from calcified plaque in the in vivo data. Quantitatively, spatial, spectral, and temporal fidelity are verified through a water phantom scan and a realistic MOBY phantom simulation experiment: spatial resolution is robustly preserved by iterative reconstruction (10% MTF: 2.8-3.0 lp/mm), left-ventricle, cardiac functional metrics can be measured from iodine map segmentations with ~1% error, and small calcifications (615 μm) can be detected during slow moving phases of the cardiac cycle. Given these preliminary results, we believe that PCD technology will enhance dynamic CT imaging applications with high-fidelity spectral and material information.Item Open Access Targeting pro-inflammatory cytokines following joint injury: acute intra-articular inhibition of interleukin-1 following knee injury prevents post-traumatic arthritis.(Arthritis Res Ther, 2014-06-25) Furman, Bridgette D; Mangiapani, Daniel S; Zeitler, Evan; Bailey, Karsyn N; Horne, Phillip H; Huebner, Janet L; Kraus, Virginia B; Guilak, Farshid; Olson, Steven AINTRODUCTION: Post-traumatic arthritis (PTA) is a progressive, degenerative response to joint injury, such as articular fracture. The pro-inflammatory cytokines, interleukin 1(IL-1) and tumor necrosis factor alpha (TNF-α), are acutely elevated following joint injury and remain elevated for prolonged periods post-injury. To investigate the role of local and systemic inflammation in the development of post-traumatic arthritis, we targeted both the initial acute local inflammatory response and a prolonged 4 week systemic inflammatory response by inhibiting IL-1 or TNF-α following articular fracture in the mouse knee. METHODS: Anti-cytokine agents, IL-1 receptor antagonist (IL-1Ra) or soluble TNF receptor II (sTNFRII), were administered either locally via an acute intra-articular injection or systemically for a prolonged 4 week period following articular fracture of the knee in C57BL/6 mice. The severity of arthritis was then assessed at 8 weeks post-injury in joint tissues via histology and micro computed tomography, and systemic and local biomarkers were assessed in serum and synovial fluid. RESULTS: Intra-articular inhibition of IL-1 significantly reduced cartilage degeneration, synovial inflammation, and did not alter bone morphology following articular fracture. However, systemic inhibition of IL-1, and local or systemic inhibition of TNF provided no benefit or conversely led to increased arthritic changes in the joint tissues. CONCLUSION: These results show that intra-articular IL-1, rather than TNF-α, plays a critical role in the acute inflammatory phase of joint injury and can be inhibited locally to reduce post-traumatic arthritis following a closed articular fracture. Targeted local inhibition of IL-1 following joint injury may represent a novel treatment option for PTA.Item Open Access The impact of respiratory gating on improving volume measurement of murine lung tumors in micro-CT imaging.(PloS one, 2020-01) Blocker, SJ; Holbrook, MD; Mowery, YM; Sullivan, DC; Badea, CTSmall animal imaging has become essential in evaluating new cancer therapies as they are translated from the preclinical to clinical domain. However, preclinical imaging faces unique challenges that emphasize the gap between mouse and man. One example is the difference in breathing patterns and breath-holding ability, which can dramatically affect tumor burden assessment in lung tissue. As part of a co-clinical trial studying immunotherapy and radiotherapy in sarcomas, we are using micro-CT of the lungs to detect and measure metastases as a metric of disease progression. To effectively utilize metastatic disease detection as a metric of progression, we have addressed the impact of respiratory gating during micro-CT acquisition on improving lung tumor detection and volume quantitation. Accuracy and precision of lung tumor measurements with and without respiratory gating were studied by performing experiments with in vivo images, simulations, and a pocket phantom. When performing test-retest studies in vivo, the variance in volume calculations was 5.9% in gated images and 15.8% in non-gated images, compared to 2.9% in post-mortem images. Sensitivity of detection was examined in images with simulated tumors, demonstrating that reliable sensitivity (true positive rate (TPR) ≥ 90%) was achievable down to 1.0 mm3 lesions with respiratory gating, but was limited to ≥ 8.0 mm3 in non-gated images. Finally, a clinically-inspired "pocket phantom" was used during in vivo mouse scanning to aid in refining and assessing the gating protocols. Application of respiratory gating techniques reduced variance of repeated volume measurements and significantly improved the accuracy of tumor volume quantitation in vivo.Item Open Access Three-Dimensional Geometric Morphometric Analysis of Treeshrew (Scandentia) Lower Molars: Insight into Dental Variation and Systematics.(Anatomical record (Hoboken, N.J. : 2007), 2019-07) Selig, Keegan R; Sargis, Eric J; Silcox, Mary TScandentia (treeshrews) is an order of small-bodied Indomalayan mammals generally agreed to be a member of Euarchonta with Primates and Dermoptera (colugos). However, intraordinal relationships among treeshrews are less well understood. Although recent studies have begun to clarify treeshrew taxonomy using morphological and molecular datasets, previous analysis of treeshrew dentition has yielded little clarity in terms of species-level relationships within the order. However, these studies made use of character-based methods, scoring traits across the dental arcade, which depend on there being clear differences among taxa that can be encapsulated in coding schemes. Geometric morphometrics has the potential to capture subtler shape variation, so it may be better for examining similarities among closely related taxa whose teeth have a similar bauplan. We used three-dimensional geometric morphometrics on a sample of treeshrew lower second molars and compared the patterns of variation to the results of previous studies. We captured 19 landmarks on a sample of 43 specimens representing 15 species. Using specimen-based principal components analysis and between-group principal component analysis, the two treeshrew families (Tupaiidae and Ptilocercidae) were well separated in morphospace. Moreover, several treeshrew species plot in morphospace according to the clades established in previous molecular work, with closely related species plotting closer to one another than to more distantly related species, suggesting that dental morphology can be useful when studying relationships among treeshrews. As most extinct treeshrews are known only from teeth, understanding morphological patterns in treeshrew molars is important for future work on the evolutionary history of Scandentia. Anat Rec, 302:1154-1168, 2019. © 2019 Wiley Periodicals, Inc.