aPC/PAR1 confers endothelial anti-apoptotic activity via a discrete, ß-arrestin-2-mediated SphK1-S1PR1-Akt signaling axis.

Endothelial dysfunction is associated with vascular disease and results in disruption of endothelial barrier function and increased sensitivity to apoptosis. Currently, there are limited treatments for improving endothelial dysfunction. Activated protein C (aPC), a promising therapeutic, signals via protease-activated receptor-1 (PAR1) and mediates several cytoprotective responses, including endothelial barrier stabilization and anti-apoptotic responses. We showed that aPC-activated PAR1 signals preferentially via ß-arrestin-2 (ß-arr2) and dishevelled-2 (Dvl2) scaffolds rather than G proteins to promote Rac1 activation and barrier protection. However, the signaling pathways utilized by aPC/PAR1 to mediate anti-apoptotic activities are not known. aPC/PAR1 cytoprotective responses also require coreceptors; however, it is not clear how coreceptors impact different aPC/PAR1 signaling pathways to drive distinct cytoprotective responses. Here, we define a ß-arr2-mediated sphingosine kinase-1 (SphK1)-sphingosine-1-phosphate receptor-1 (S1PR1)-Akt signaling axis that confers aPC/PAR1-mediated protection against cell death. Using human cultured endothelial cells, we found that endogenous PAR1 and S1PR1 coexist in caveolin-1 (Cav1)-rich microdomains and that S1PR1 coassociation with Cav1 is increased by aPC activation of PAR1. Our study further shows that aPC stimulates ß-arr2-dependent SphK1 activation independent of Dvl2 and is required for transactivation of S1PR1-Akt signaling and protection against cell death. While aPC/PAR1-induced, extracellular signal-regulated kinase 1/2 (ERK1/2) activation is also dependent on ß-arr2, neither SphK1 nor S1PR1 are integrated into the ERK1/2 pathway. Finally, aPC activation of PAR1-ß-arr2-mediated protection against apoptosis is dependent on Cav1, the principal structural protein of endothelial caveolae. These studies reveal that different aPC/PAR1 cytoprotective responses are mediated by discrete, ß-arr2-driven signaling pathways in caveolae.

High-Resolution Full-3D Specimen Imaging for Lumpectomy Margin Assessment in Breast Cancer.

BACKGROUND: Two-dimensional (2D) specimen radiography (SR) and tomosynthesis (DBT) for breast cancer yield data that lack high-depth resolution. A volumetric specimen imager (VSI) was developed to provide full-3D and thin-slice cross-sectional visualization at a 360° view angle. The purpose of this prospective trial was to compare VSI, 2D SR, and DBT interpretation of lumpectomy margin status with the final pathologic margin status of breast lumpectomy specimens. METHODS: The study enrolled 200 cases from two institutions. After standard imaging and interpretation was performed, the main lumpectomy specimen was imaged with the VSI device. Image interpretation was performed by three radiologists after surgery based on VSI, 2D SR, and DBT. A receiver operating characteristic (ROC) curve was created for each method. The area under the curve (AUC) was computed to characterize the performance of the imaging method interpreted by each user. RESULTS: From 200 lesions, 1200 margins were interpreted. The AUC values of VSI for the three radiologists were respectively 0.91, 0.90, and 0.94, showing relative improvement over the AUCs of 2D SR by 54%, 13%, and 40% and DBT by 32% and 11%, respectively. The VSI has sensitivity ranging from 91 to 94%, specificity ranging from 81 to 85%, a positive predictive value ranging from 25 to 30%, and a negative predicative value of 99%. CONCLUSIONS: The ROC curves of the VSI were higher than those of the other specimen imaging methods. Full-3D specimen imaging can improve the correlation between the main lumpectomy specimen margin status and surgical pathology. The findings from this study suggest that using the VSI device for intraoperative margin assessment could further reduce the re-excision rates for women with malignant disease.

Dual-energy CT imaging over non-overlapping, orthogonal arcs of limited-angular ranges.

BACKGROUND: Interest exists in dual-energy computed tomography (DECT) imaging with scanning arcs of limited-angular ranges (LARs) for reducing scan time and radiation dose, and for enabling scan configurations of C-arm CT that can avoid possible collision between the rotating X-ray tube/detector and the imaged subject. OBJECTIVE: In this work, we investigate image reconstruction for a type of configurations of practical DECT interest, referred to as the two-orthogonal-arc configuration, in which low- and high-kVp data are collected over two non-overlapping arcs of equal LAR α, ranging from 30° to 90°, separated by 90°. The configuration can readily be implemented, e.g., on CT with dual sources separated by 90° or with the slow-kVp-switching technique. METHODS: The directional-total-variation (DTV) algorithm developed previously for image reconstruction in conventional, single-energy CT is tailored to enable image reconstruction in DECT with two-orthogonal-arc configurations. RESULTS: Performing visual inspection and quantitative analysis of monochromatic images obtained and effective atomic numbers estimated, we observe that the monochromatic images of the DTV algorithm from LAR data are with substantially reduced LAR artifacts, which are observed otherwise in those of existing algorithms, and thus visually correlate reasonably well, in terms of metrics PCC and nMI, with their reference images obtained from full-angular-range data. In addition, effective atomic numbers estimated from LAR data of DECT with two-orthogonal-arc configurations are in reasonable agreement, with relative errors up to ∼ 10%, with those estimated from full-angular-range data in DECT. CONCLUSIONS: The results acquired in the work may yield insights into the design of LAR configurations of practical dual-energy application relevance in diagnostic CT or C-arm CT imaging.

The antiviral mechanism of viperin and its splice variant in spring viremia of carp virus infected fathead minnow cells.

Viperin is known to play an important role in innate immune and its antiviral mechanisms are well demonstrated in mammals. Fish Viperin mediates antiviral activity against several viruses. However, little has been done to the underlying mechanism. Here, we discovered a novel Viperin splice variant named Viperin_sv1 from viral-infected FHM cells. Spring varimia of carp virus (SVCV) was able to increase the mRNA levels of both Viperin and Viperin_sv1, while poly(I:C) only has effect on Viperin. Viperin functions as an antiviral protein at 24 h post-SVCV infection, but the antiviral activity dramatically declined at late infection stages. However, Viperin_sv1 inhibited SVCV replication significantly at all the tested time. Viperin_sv1, but not Viperin can facilitate the production of type I IFN and IFN stimulate genes (ISGs) through activation of RIG-1, IRF3 and IRF7 signaling cascades. On the other hand, SVCV down-regulated Viperin_sv1 at the protein level through the proteasome pathway to keep itself away from the immune system monitoring. Taken together, these findings provide new insights into the regulation of Viperin from the posttranscriptional modification perspective and the role of splicing variant Viperin_sv1 in virus-host interaction.

14-3-3ß/α-A interacts with glycoprotein of spring viremia of carp virus and positively affects viral entry.

Spring viremia of carp virus (SVCV) is a fierce pathogen causing high mortality in the common carp. The glycoprotein (G protein) of SVCV is a pivotal component of the viral structure, located in the surface of the virion, and plays a key role in viral endocytosis. In this study, tandem affinity purification (TAP) followed by mass spectrometry analysis (LC-MS/MS) was carried out to search for novel host molecules that interact with SVCV G protein and a 14-3-3ß/α-A protein was identified. The level of 14-3-3ß/α-A mRNA expression was dramatically down regulated by SVCV infection. Furthermore, over expression of 14-3-3ß/α-A results in a significantly increased SVCV attachment and entry in FHM cells. This study reveals an important role of 14-3-3 protein in regulating the early stage of SVCV infection, which offers a potential target for development of anti-SVCV therapies.

N-linked glycosylation of protease-activated receptor-1 at extracellular loop 2 regulates G-protein signaling bias.

Protease-activated receptor-1 (PAR1) is a G-protein-coupled receptor (GPCR) for the coagulant protease thrombin. Similar to other GPCRs, PAR1 is promiscuous and couples to multiple heterotrimeric G-protein subtypes in the same cell and promotes diverse cellular responses. The molecular mechanism by which activation of a given GPCR with the same ligand permits coupling to multiple G-protein subtypes is unclear. Here, we report that N-linked glycosylation of PAR1 at extracellular loop 2 (ECL2) controls G12/13 versus Gq coupling specificity in response to thrombin stimulation. A PAR1 mutant deficient in glycosylation at ECL2 was more effective at stimulating Gq-mediated phosphoinositide signaling compared with glycosylated wildtype receptor. In contrast, wildtype PAR1 displayed a greater efficacy at G12/13-dependent RhoA activation compared with mutant receptor lacking glycosylation at ECL2. Endogenous PAR1 rendered deficient in glycosylation using tunicamycin, a glycoprotein synthesis inhibitor, also exhibited increased PI signaling and diminished RhoA activation opposite to native receptor. Remarkably, PAR1 wildtype and glycosylation-deficient mutant were equally effective at coupling to Gi and ß-arrestin-1. Consistent with preferential G12/13 coupling, thrombin-stimulated PAR1 wildtype strongly induced RhoA-mediated stress fiber formation compared with mutant receptor. In striking contrast, glycosylation-deficient PAR1 was more effective at increasing cellular proliferation, associated with Gq signaling, than wildtype receptor. These studies suggest that N-linked glycosylation at ECL2 contributes to the stabilization of an active PAR1 state that preferentially couples to G12/13 versus Gq and defines a previously unidentified function for N-linked glycosylation of GPCRs in regulating G-protein signaling bias.

Contributions of the Prion Protein Sequence, Strain, and Environment to the Species Barrier.

Amyloid propagation requires high levels of sequence specificity so that only molecules with very high sequence identity can form cross-ß-sheet structures of sufficient stringency for incorporation into the amyloid fibril. This sequence specificity presents a barrier to the transmission of prions between two species with divergent sequences, termed a species barrier. Here we study the relative effects of protein sequence, seed conformation, and environment on the species barrier strength and specificity for the yeast prion protein Sup35p from three closely related species of the Saccharomyces sensu stricto group; namely, Saccharomyces cerevisiae, Saccharomyces bayanus, and Saccharomyces paradoxus. Through in vivo plasmid shuffle experiments, we show that the major characteristics of the transmission barrier and conformational fidelity are determined by the protein sequence rather than by the cellular environment. In vitro data confirm that the kinetics and structural preferences of aggregation of the S. paradoxus and S. bayanus proteins are influenced by anions in accordance with their positions in the Hofmeister series, as observed previously for S. cerevisiae. However, the specificity of the species barrier is primarily affected by the sequence and the type of anion present during the formation of the initial seed, whereas anions present during the seeded aggregation process typically influence kinetics rather than the specificity of prion conversion. Therefore, our work shows that the protein sequence and the conformation variant (strain) of the prion seed are the primary determinants of cross-species prion specificity both in vivo and in vitro.

Characterization of thrombin-bound dabigatran effects on protease-activated receptor-1 expression and signaling in vitro.

Thrombin, the key effector protease of the coagulation cascade, drives fibrin deposition and activates human platelets through protease-activated receptor-1 (PAR1). These processes are critical to the progression of thrombotic diseases. Thrombin is the main target of anticoagulant therapy, and major efforts have led to the discovery of new oral direct inhibitors of thrombin. Dabigatran is the first oral anticoagulant licensed for the prevention of thromboembolisms associated with orthopedic surgery and stroke prevention in atrial fibrillation. Dabigatran is a direct thrombin inhibitor that effectively blocks thrombin's catalytic activity but does not preclude thrombin's exosites and binding to fibrinogen. Thus, we hypothesized that catalytically inactive thrombin retains the capacity to bind to PAR1 through exosite-I and may modulate its function independent of receptor cleavage and activation. Here, we report that dabigatran at clinically relevant concentrations is an effective and acute inhibitor of thrombin-induced PAR1 cleavage, activation, internalization, and ß-arrestin recruitment in vitro. Interestingly, prolonged exposure to catalytic inactive thrombin incubated with dabigatran at 20-fold higher therapeutic concentration resulted in increased PAR1 cell-surface expression, which correlated with higher detectable levels of ubiquitinated receptor. These findings are consistent with ubiquitin function as a negative regulator of PAR1 constitutive internalization. Increased PAR1 expression also enhanced agonist-induced phosphoinositide hydrolysis and endothelial barrier permeability. Thus, catalytically inactive thrombin appears to modulate PAR1 function in vitro by stabilizing receptor cell-surface expression; but given the high clearance rate of thrombin, the high concentration of dabigatran required to achieve this effect the in vivo physiologic relevance is unknown.

Regulation of protease-activated receptor 1 signaling by the adaptor protein complex 2 and R4 subfamily of regulator of G protein signaling proteins.

The G protein-coupled protease-activated receptor 1 (PAR1) is irreversibly proteolytically activated by thrombin. Hence, the precise regulation of PAR1 signaling is important for proper cellular responses. In addition to desensitization, internalization and lysosomal sorting of activated PAR1 are critical for the termination of signaling. Unlike most G protein-coupled receptors, PAR1 internalization is mediated by the clathrin adaptor protein complex 2 (AP-2) and epsin-1, rather than ß-arrestins. However, the function of AP-2 and epsin-1 in the regulation of PAR1 signaling is not known. Here, we report that AP-2, and not epsin-1, regulates activated PAR1-stimulated phosphoinositide hydrolysis via two different mechanisms that involve, in part, a subset of R4 subfamily of "regulator of G protein signaling" (RGS) proteins. A significantly greater increase in activated PAR1 signaling was observed in cells depleted of AP-2 using siRNA or in cells expressing a PAR1 (420)AKKAA(424) mutant with defective AP-2 binding. This effect was attributed to AP-2 modulation of PAR1 surface expression and efficiency of G protein coupling. We further found that ectopic expression of R4 subfamily members RGS2, RGS3, RGS4, and RGS5 reduced activated PAR1 wild-type signaling, whereas signaling by the PAR1 AKKAA mutant was minimally affected. Intriguingly, siRNA-mediated depletion analysis revealed a function for RGS5 in the regulation of signaling by the PAR1 wild type but not the AKKAA mutant. Moreover, activation of the PAR1 wild type, and not the AKKAA mutant, induced Gαq association with RGS3 via an AP-2-dependent mechanism. Thus, AP-2 regulates activated PAR1 signaling by altering receptor surface expression and through recruitment of RGS proteins.

Accurate Reconstruction of Multiple Basis Images Directly From Dual Energy CT Data.

OBJECTIVE: We develop optimization-based algorithms to accurately reconstruct multiple ( 2) basis images directly from dual-energy (DE) data in CT. METHODS: In medical and industrial CT imaging, some basis materials such as bone, metals, and contrast agents of interest are confined often spatially within regions in the image. Exploiting this observation, we develop an optimization-based algorithm to reconstruct, directly from DE data, basis-region images from which multiple ( 2) basis images and virtual monochromatic images (VMIs) can be obtained over the entire image array. RESULTS: We conduct experimental studies using simulated and real DE data in CT, and evaluate basis images and VMIs obtained in terms of visual inspection and quantitative metrics. The study results reveal that the algorithm developed can accurately and robustly reconstruct multiple ( 2) basis images directly from DE data. CONCLUSIONS: The developed algorithm can yield accurate multiple ( 2) basis images, VMIs, and physical quantities of interest from DE data in CT. SIGNIFICANCE: The work may provide insights into the development of practical procedures for reconstructing multiple basis images, VMIs, and physical quantities from DE data in applications. The work can be extended to reconstruct multiple basis images in multi-spectral or photon-counting CT.

Prototyping optimization-based image reconstructions from limited-angular-range data in dual-energy CT.

Image reconstruction from data collected over full-angular range (FAR) in dual-energy CT (DECT) is well-studied. There exists interest in DECT with advanced scan configurations in which data are collected only over limited-angular ranges (LARs) for meeting unique workflow needs in certain practical imaging applications, and thus in the algorithm development for image reconstruction from such LAR data. The objective of the work is to investigate and prototype image reconstructions in DECT with LAR scans. We investigate and prototype optimization programs with various designs of constraints on the directional-total-variations (DTVs) of virtual monochromatic images and/or basis images, and derive the DTV algorithms to numerically solve the optimization programs for achieving accurate image reconstruction from data collected in a slew of different LAR scans. Using simulated and real data acquired with low- and high-kV spectra over LARs, we conduct quantitative studies to demonstrate and evaluate the optimization programs and their DTV algorithms developed. As the results of the numerical studies reveal, while the DTV algorithms yield images of visual quality and quantitative accuracy comparable to that of the existing algorithms from FAR data, the former reconstruct images with improved visualization, reduced artifacts, and also enhanced quantitative accuracy when applied to LAR data in DECT. Optimization-based, one-step algorithms, including the DTV algorithms demonstrated, can be developed for quantitative image reconstruction from spectral data collected over LARs of extents that are considerably smaller than the FAR in DECT. The theoretical and numerical results obtained can be exploited for prototyping designs of optimization-based reconstructions and LAR scans in DECT, and they may also yield insights into the development of reconstruction procedures in practical DECT applications. The approach and algorithms developed can naturally be applied to investigating image reconstruction from LAR data in multi-spectral and photon-counting CT.

Accurate reconstruction of 4D spectral-spatial images from sparse-view data in continuous-wave EPRI.

In continuous-wave electron paramagnetic resonance imaging (CW EPRI), data are collected generally at densely sampled views sufficient for achieving accurate reconstruction of a four dimensional spectral-spatial (4DSS) image by use of the conventional filtered-backprojection (FBP) algorithm. It is desirable to minimize the scan time by collection of data only at sparsely sampled views, referred to as sparse-view data. Interest thus remains in investigation of algorithms for accurate reconstruction of 4DSS images from sparse-view data collected for potentially enabling fast data acquisition in CW EPRI. In this study, we investigate and demonstrate optimization-based algorithms for accurate reconstruction of 4DSS images from sparse-view data. Numerical studies using simulated and real sparse-view data acquired in CW EPRI are conducted that reveal, in terms of image visualization and physical-parameter estimation, the potential of the algorithms developed for yielding accurate 4DSS images from sparse-view data in CW EPRI. The algorithms developed may be exploited for enabling sparse-view scans with minimized scan time in CW EPRI for yielding 4DSS images of quality comparable to, or better than, that of the FBP reconstruction from data collected at densely sampled views.

A directional total variation minimization algorithm for isotropic resolution in digital breast tomosynthesis.

An optimization-based image reconstruction algorithm is developed for contrast enhanced digital breast tomosynthesis (DBT) using dual-energy scanning. The algorithm minimizes directional total variation (TV) with a data discrepancy and non-negativity constraints. Iodinated contrast agent (ICA) imaging is performed by reconstructing images from dual-energy DBT data followed by weighted subtraction. Physical DBT data is acquired with a Siemens Mammomat scanner of a structured breast phantom with ICA inserts. Results are shown for both directional TV minimization and filtered back-projection for reference. It is seen that directional TV is able to substantially reduce depth blur for the ICA objects.

4D-image reconstruction directly from limited-angular-range data in continuous-wave electron paramagnetic resonance imaging.

OBJECTIVE: We investigate and develop optimization-based algorithms for accurate reconstruction of four-dimensional (4D)-spectral-spatial (SS) images directly from data collected over limited angular ranges (LARs) in continuous-wave (CW) electron paramagnetic resonance imaging (EPRI). METHODS: Basing on a discrete-to-discrete data model devised in CW EPRI employing the Zeeman-modulation (ZM) scheme for data acquisition, we first formulate the image reconstruction problem as a convex, constrained optimization program that includes a data fidelity term and also constraints on the individual directional total variations (DTVs) of the 4D-SS image. Subsequently, we develop a primal-dual-based DTV algorithm, simply referred to as the DTV algorithm, to solve the constrained optimization program for achieving image reconstruction from data collected in LAR scans in CW-ZM EPRI. RESULTS: We evaluate the DTV algorithm in simulated- and real-data studies for a variety of LAR scans of interest in CW-ZM EPRI, and visual and quantitative results of the studies reveal that 4D-SS images can be reconstructed directly from LAR data, which are visually and quantitatively comparable to those obtained from data acquired in the standard, full-angular-range (FAR) scan in CW-ZM EPRI. CONCLUSION: An optimization-based DTV algorithm is developed for accurately reconstructing 4D-SS images directly from LAR data in CW-ZM EPRI. Future work includes the development and application of the optimization-based DTV algorithm for reconstructions of 4D-SS images from FAR and LAR data acquired in CW EPRI employing schemes other than the ZM scheme. SIGNIFICANCE: The DTV algorithm developed may be exploited potentially for enabling and optimizing CW EPRI with minimized imaging time and artifacts by acquiring data in LAR scans.

Adaptor protein complex-2 (AP-2) and epsin-1 mediate protease-activated receptor-1 internalization via phosphorylation- and ubiquitination-dependent sorting signals.

Signaling by protease-activated receptor-1 (PAR1), a G protein-coupled receptor (GPCR) for thrombin, is regulated by desensitization and internalization. PAR1 desensitization is mediated by ß-arrestins, like most classic GPCRs. In contrast, internalization of PAR1 occurs through a clathrin- and dynamin-dependent pathway independent of ß-arrestins. PAR1 displays two modes of internalization. Constitutive internalization of unactivated PAR1 is mediated by the clathrin adaptor protein complex-2 (AP-2), where the µ2-adaptin subunit binds directly to a tyrosine-based motif localized within the receptor C-tail domain. However, AP-2 depletion only partially inhibits agonist-induced internalization of PAR1, suggesting a function for other clathrin adaptors in this process. Here, we now report that AP-2 and epsin-1 are both critical mediators of agonist-stimulated PAR1 internalization. We show that ubiquitination of PAR1 and the ubiquitin-interacting motifs of epsin-1 are required for epsin-1-dependent internalization of activated PAR1. In addition, activation of PAR1 promotes epsin-1 de-ubiquitination, which may increase its endocytic adaptor activity to facilitate receptor internalization. AP-2 also regulates activated PAR1 internalization via recognition of distal C-tail phosphorylation sites rather than the canonical tyrosine-based motif. Thus, AP-2 and epsin-1 are both required to promote efficient internalization of activated PAR1 and recognize discrete receptor sorting signals. This study defines a new pathway for internalization of mammalian GPCRs.

Image reconstruction from data over two orthogonal arcs of limited-angular ranges.

PURPOSE: Computed tomography (CT) scanning over limited-angular ranges (LARs) is of practical interest in possible reduction of imaging dose and time and in design of nonstandard scans. This work aims to investigate image reconstruction for two nonoverlapping arcs of LARs, and to demonstrate that they may allow more accurate image reconstruction than may a single arc of LAR. METHODS: We consider a configuration with two nonoverlapping arcs of LARs α 1 $\alpha _1$ and α 2 $\alpha _2$ , whose centers are separated by 90 ∘ $90^\circ$ , and refer to it as a two-orthogonal-arc configuration. Data are generated from a chest phantom with two-orthogonal-arc configurations over total angular coverage α τ = α 1 + α 2 $\alpha _\tau =\alpha _1+\alpha _2$ ranging from 18 ∘ $18^\circ$ to 180 ∘ $180^\circ$ , and images are reconstructed subsequently by use of the directional-total-variation (DTV) algorithm. For comparison, we also consider image reconstruction for a single-arc configuration of angular range α τ $\alpha _\tau$ . Quantitative metrics such as the normalized root-mean-square-error (nRMSE) are used for evaluation of image reconstruction accuracy. RESULTS: Visual inspection and quantitative analysis of images reconstructed reveal that a two-orthogonal-arc configuration generally yields more accurate image reconstruction than does its single-arc counterpart. As total angular range α τ $\alpha _\tau$ increases, the DTV algorithm yields image reconstruction with enhanced accuracy, as expected. Also, if α τ $\alpha _\tau$ remains constant, the two-orthogonal-arc configuration with α 1 = α 2 $\alpha _1 = \alpha _2$ generally leads to image reconstruction more accurate than those of two-orthogonal-arc configurations with α 1 ≠ α 2 $\alpha _1 \ne \alpha _2$ , as the nRMSE of the former can be lower than that of the latter for up to more than one order of magnitude. CONCLUSIONS: Appropriately designed two-orthogonal-arc configurations may be exploited for improving image-reconstruction accuracy in CT imaging with reduced angular coverage. This study may yield insights into the design of innovative CT scans for lowering scan time and radiation dose, and/or for avoiding scan collision in, for example, C-arm CT.

Accurate Image Reconstruction in Dual-Energy CT with Limited-Angular-Range Data Using a Two-Step Method.

Dual-energy CT (DECT) with scans over limited-angular ranges (LARs) may allow reductions in scan time and radiation dose and avoidance of possible collision between the moving parts of a scanner and the imaged object. The beam-hardening (BH) and LAR effects are two sources of image artifacts in DECT with LAR data. In this work, we investigate a two-step method to correct for both BH and LAR artifacts in order to yield accurate image reconstruction in DECT with LAR data. From low- and high-kVp LAR data in DECT, we first use a data-domain decomposition (DDD) algorithm to obtain LAR basis data with the non-linear BH effect corrected for. We then develop and tailor a directional-total-variation (DTV) algorithm to reconstruct from the LAR basis data obtained basis images with the LAR effect compensated for. Finally, using the basis images reconstructed, we create virtual monochromatic images (VMIs), and estimate physical quantities such as iodine concentrations and effective atomic numbers within the object imaged. We conduct numerical studies using two digital phantoms of different complexity levels and types of structures. LAR data of low- and high-kVp are generated from the phantoms over both single-arc (SA) and two-orthogonal-arc (TOA) LARs ranging from 14∘ to 180∘. Visual inspection and quantitative assessment of VMIs obtained reveal that the two-step method proposed can yield VMIs in which both BH and LAR artifacts are reduced, and estimation accuracy of physical quantities is improved. In addition, concerning SA and TOA scans with the same total LAR, the latter is shown to yield more accurate images and physical quantity estimations than the former. We investigate a two-step method that combines the DDD and DTV algorithms to correct for both BH and LAR artifacts in image reconstruction, yielding accurate VMIs and estimations of physical quantities, from low- and high-kVp LAR data in DECT. The results and knowledge acquired in the work on accurate image reconstruction in LAR DECT may give rise to further understanding and insights into the practical design of LAR scan configurations and reconstruction procedures for DECT applications.

Genetic and epigenetic control of the efficiency and fidelity of cross-species prion transmission.

Self-perpetuating amyloid-based protein isoforms (prions) transmit neurodegenerative diseases in mammals and phenotypic traits in yeast. Although mechanisms that control species specificity of prion transmission are poorly understood, studies of closely related orthologues of yeast prion protein Sup35 demonstrate that cross-species prion transmission is modulated by both genetic (specific sequence elements) and epigenetic (prion variants, or 'strains') factors. Depending on the prion variant, the species barrier could be controlled at the level of either heterologous co-aggregation or conversion of the aggregate-associated heterologous protein into a prion polymer. Sequence divergence influences cross-species transmission of different prion variants in opposing ways. The ability of a heterologous prion domain to either faithfully reproduce or irreversibly switch the variant-specific prion patterns depends on both sequence divergence and the prion variant. Sequence variations within different modules of prion domains contribute to transmission barriers in different cross-species combinations. Individual amino acid substitutions within short amyloidogenic stretches drastically alter patterns of cross-species prion conversion, implicating these stretches as major determinants of species specificity.

Non-convex primal-dual algorithm for image reconstruction in spectral CT.

The work seeks to develop an algorithm for image reconstruction by directly inverting the non-linear data model in spectral CT. Using the non-linear data model, we formulate the image-reconstruction problem as a non-convex optimization program, and develop a non-convex primal-dual (NCPD) algorithm to solve the program. We devise multiple convergence conditions and perform verification studies numerically to demonstrate that the NCPD algorithm can solve the non-convex optimization program and under appropriate data condition, can invert the non-linear data model. Using the NCPD algorithm, we then reconstruct monochromatic images from simulated and real data of numerical and physical phantoms acquired with a standard, full-scan dual-energy configuration. The result of the reconstruction studies shows that the NCPD algorithm can correct accurately for the non-linear beam-hardening effect. Furthermore, we apply the NCPD algorithm to simulated and real data of the numerical and physical phantoms collected with non-standard, short-scan dual-energy configurations, and obtain monochromatic images comparable to those of the standard, full-scan study, thus revealing the potential of the NCPD algorithm for enabling non-standard scanning configurations in spectral CT, where the existing indirect methods are limited.

Directional-TV algorithm for image reconstruction from limited-angular-range data.

Investigation of image reconstruction from data collected over a limited-angular range in X-ray CT remains a topic of active research because it may yield insight into the development of imaging workflow of practical significance. This reconstruction problem is well-known to be challenging, however, because it is highly ill-conditioned. In the work, we investigate optimization-based image reconstruction from data acquired over a limited-angular range that is considerably smaller than the angular range in short-scan CT. We first formulate the reconstruction problem as a convex optimization program with directional total-variation (TV) constraints applied to the image, and then develop an iterative algorithm, referred to as the directional-TV (DTV) algorithm for image reconstruction through solving the optimization program. We use the DTV algorithm to reconstruct images from data collected over a variety of limited-angular ranges for breast and bar phantoms of clinical- and industrial-application relevance. The study demonstrates that the DTV algorithm accurately recovers the phantoms from data generated over a significantly reduced angular range, and that it considerably diminishes artifacts observed otherwise in reconstructions of existing algorithms. We have also obtained empirical conditions on minimal-angular ranges sufficient for numerically accurate image reconstruction with the DTV algorithm.