Xianghui Xiao

TomoPy: a framework for the analysis of synchrotron tomographic data

A collaborative framework for the analysis of synchrotron tomographic data which has the potential to unify the effort of different facilities and beamlines performing similar tasks is described. The proposed Python-based framework is open-source, platform- and data-format-independent, has multiprocessing capability and supports functional programming that many researchers prefer.

The systemic delivery of an oncolytic adenovirus expressing decorin inhibits bone metastasis in a mouse model of human prostate cancer.

In an effort to develop a new therapy for prostate cancer (PCa) bone metastases, we have created Ad.dcn, a recombinant oncolytic adenovirus carrying the human decorin gene. Infection of PC-3 and DU-145, the human prostate tumor cells, with Ad.dcn or a non-replicating adenovirus Ad(E1-).dcn resulted in decorin expression; Ad.dcn produced high viral titers and cytotoxicity in human prostate tumor cells. Adenoviral-mediated decorin expression inhibited Met, the Wnt/β-catenin signaling axis, vascular endothelial growth factor A, reduced mitochondrial DNA levels and inhibited tumor cell migration. To examine the antitumor response of Ad.dcn, PC-3-luc cells were inoculated in the left heart ventricle to establish bone metastases in nude mice. Ad.dcn, in conjunction with control replicating and non-replicating vectors were injected via tail vein. The real-time monitoring of mice, once a week, by bioluminescence imaging and X-ray radiography showed that Ad.dcn produced significant inhibition of skeletal metastases. Analyses of the mice at the terminal time point indicated a significant reduction in the tumor burden, osteoclast number, serum tartrate-resistant acid phosphatase 5b levels, osteocalcin levels, hypercalcemia, inhibition of cancer cachexia and an increase in the animal survival. Based on these studies, we believe that Ad.dcn can be developed as a potential new therapy for PCa bone metastasis.

Anomalous high-pressure behavior of amorphous selenium from synchrotron x-ray diffraction and microtomography

The high-pressure behavior of amorphous selenium has been investigated with time-resolved diamond anvil cell synchrotron x-ray diffraction and computed microtomography techniques. A two-step dynamic crystallization process is observed in which the monoclinic phase crystallized from the amorphous selenium and gradually converted to the trigonal phase, thereby explaining previously observed anomalous changes in electrical conductivity of the material under pressure. The crystallization of this elemental system involves local topological fluctuations and results in an unusual pressure-induced volume expansion. The metastability of the phases involved in the transition accounts for this phenomenon. The results demonstrate the use of pressure to control and directly monitor the relative densities and energetics of phases to create new phases from highly metastable states. The microtomographic technique developed here represents a method for determination of the equations of state of amorphous materials at extreme pressures and temperatures.

TIMBIR: A Method for Time-Space Reconstruction From Interlaced Views

Synchrotron X-ray computed tomography (SXCT) is increasingly being used for 3-D imaging of material samples at micron and finer scales. The success of these techniques has increased interest in 4-D reconstruction methods that can image a sample in both space and time. However, the temporal resolution of widely used 4-D reconstruction methods is severely limited by the need to acquire a very large number of views for each reconstructed 3-D volume. Consequently, the temporal resolution of current methods is insufficient to observe important physical phenomena. Furthermore, measurement nonidealities also tend to introduce ring and streak artifacts into the 4-D reconstructions. In this paper, we present a time-interlaced model-based iterative reconstruction (TIMBIR) method, which is a synergistic combination of two innovations. The first innovation, interlaced view sampling, is a novel method of data acquisition, which distributes the view angles more evenly in time. The second innovation is a 4-D model-based iterative reconstruction algorithm (MBIR), which can produce time-resolved volumetric reconstruction of the sample from the interlaced views. In addition to modeling both the sensor noise statistics and the 4-D object, the MBIR algorithm also reduces ring and streak artifacts by more accurately modeling the measurement nonidealities. We present reconstructions of both simulated and real X-ray synchrotron data, which indicate that TIMBIR can improve temporal resolution by an order of magnitude relative to existing approaches.

Systemic Delivery of Oncolytic Adenoviruses Targeting Transforming Growth Factor-β Inhibits Established Bone Metastasis in a Prostate Cancer Mouse Model

We have examined whether Ad.sTβRFc and TAd.sTβRFc, two oncolytic viruses expressing soluble transforming growth factor-β receptor II fused with human Fc (sTGFβRIIFc), can be developed to treat bone metastasis of prostate cancer. Incubation of PC-3 and DU-145 prostate tumor cells with Ad.sTβRFc and TAd.sTβRFc produced sTGFβRIIFc and viral replication; sTGFβRIIFc caused inhibition of TGF-β-mediated SMAD2 and SMAD3 phosphorylation. Ad(E1-).sTβRFc, an E1(-) adenovirus, produced sTGFβRIIFc but failed to replicate in tumor cells. To examine the antitumor response of adenoviral vectors, PC-3-luc cells were injected into the left heart ventricle of nude mice. On day 9, mice were subjected to whole-body bioluminescence imaging (BLI). Mice bearing hind-limb tumors were administered viral vectors via the tail vein on days 10, 13, and 17 (2.5×10(10) viral particles per injection per mouse, each injection in a 0.1-ml volume), and subjected to BLI and X-ray radiography weekly until day 53. Ad.sTβRFc, TAd.sTβRFc, and Ad(E1-).sTβRFc caused significant inhibition of tumor growth; however, Ad.sTβRFc was the most effective among all the vectors. Only Ad.sTβRFc and TAd.sTβRFc inhibited tumor-induced hypercalcemia. Histomorphometric and synchrotron micro-computed tomographic analysis of isolated bones indicated that Ad.sTβRFc induced significant reduction in tumor burden, osteoclast number, and trabecular and cortical bone destruction. These studies suggest that Ad.sTβRFc and TAd.sTβRFc can be developed as potential new therapies for prostate cancer bone metastasis.

Heterogeneous silicon mesostructures for lipid-supported bioelectric interfaces

Silicon-based materials have widespread application as biophysical tools and biomedical devices. Here we introduce a biocompatible and degradable mesostructured form of silicon with multiscale structural and chemical heterogeneities. The material was synthesized using mesoporous silica as a template through a chemical-vapor-deposition process. It has an amorphous atomic structure, an ordered nanowire-based framework, and random submicrometre voids, and shows an average Young’s modulus that is 2–3 orders of magnitude smaller than that of single crystalline silicon. In addition, we used the heterogeneous silicon mesostructures to design a lipid-bilayer-supported bioelectric interface that is remotely controlled and temporally transient, and that permits non-genetic and subcellular optical modulation of the electrophysiology dynamics in single dorsal root ganglia neurons. Our findings suggest that the biomimetic expansion of silicon into heterogeneous and deformable forms can open up opportunities in extracellular biomaterial or bioelectric systems.

The Three-Dimensional Morphology of Growing Dendrites

The processes controlling the morphology of dendrites have been of great interest to a wide range of communities, since they are examples of an out-of-equilibrium pattern forming system, there is a clear connection with battery failure processes, and their morphology sets the properties of many metallic alloys. We determine the three-dimensional morphology of free growing metallic dendrites using a novel X-ray tomographic technique that improves the temporal resolution by more than an order of magnitude compared to conventional techniques. These measurements show that the growth morphology of metallic dendrites is surprisingly different from that seen in model systems, the morphology is not self-similar with distance back from the tip, and that this morphology can have an unexpectedly strong influence on solute segregation in castings. These experiments also provide benchmark data that can be used to validate simulations of free dendritic growth.

Improved tomographic reconstructions using adaptive time dependent intensity normalization

The first processing step in synchrotron-based micro-tomography is the normalization of the projection images against the background, also referred to as a white field. Owing to time-dependent variations in illumination and defects in detection sensitivity, the white field is different from the projection background. In this case standard normalization methods introduce ring and wave artefacts into the resulting three-dimensional reconstruction. In this paper the authors propose a new adaptive technique accounting for these variations and allowing one to obtain cleaner normalized data and to suppress ring and wave artefacts. The background is modelled by the product of two time-dependent terms representing the illumination and detection stages. These terms are written as unknown functions, one scaled and shifted along a fixed direction (describing the illumination term) and one translated by an unknown two-dimensional vector (describing the detection term). The proposed method is applied to two sets (a stem Salix variegata and a zebrafish Danio rerio) acquired at the parallel beam of the micro-tomography station 2-BM at the Advanced Photon Source showing significant reductions in both ring and wave artefacts. In principle the method could be used to correct for time-dependent phenomena that affect other tomographic imaging geometries such as cone beam laboratory X-ray computed tomography.

Systemic delivery of an oncolytic adenovirus expressing decorin for the treatment of breast cancer bone metastases

The development of novel therapies for breast cancer bone metastasis is a major unmet medical need. Toward that end, we have constructed an oncolytic adenovirus, Ad.dcn, and a nonreplicating adenovirus, Ad(E1-).dcn, both containing the human decorin gene. Our in vitro studies showed that Ad.dcn produced high levels of viral replication and the decorin protein in the breast tumor cells. Ad(E1-).dcn-mediated decorin expression in MDA-MB-231 cells downregulated the expression of Met, β-catenin, and vascular endothelial growth factor A, all of which are recognized decorin targets and play pivotal roles in the progression of breast tumor growth and metastasis. Adenoviral-mediated decorin expression inhibited cell migration and induced mitochondrial autophagy in MDA-MB-231 cells. Mice bearing MDA-MB-231-luc skeletal metastases were systemically administered with the viral vectors, and skeletal tumor growth was monitored over time. The results of bioluminescence imaging and X-ray radiography indicated that Ad.dcn and Ad(E1-).dcn significantly inhibited the progression of bone metastases. At the terminal time point, histomorphometric analysis, micro-computed tomography, and bone destruction biomarkers showed that Ad.dcn and Ad(E1-).dcn reduced tumor burden and inhibited bone destruction. A nonreplicating adenovirus Ad(E1-).luc expressing the luciferase 2 gene had no significant effect on inhibiting bone metastases, and in several assays, Ad.dcn and Ad(E1-).dcn were better than Ad.luc, a replicating virus expressing the luciferase 2 gene. Our data suggest that adenoviral replication coupled with decorin expression could produce effective antitumor responses in a MDA-MB-231 bone metastasis model of breast cancer. Thus, Ad.dcn could potentially be developed as a candidate gene therapy vector for treating breast cancer bone metastases.

In situ experimental techniques to study the mechanical behavior of materials using X-ray synchrotron tomography

In situ X-ray synchrotron tomography is an excellent technique for understanding deformation behavior of materials in 4D (the fourth dimension here is time). However, performing in situ experiments in synchrotron is challenging, particularly in regard to the design of the mechanical testing stage. Here, we report on several in situ testing methods developed by our group in collaboration with Advanced Photon source at Argonne National Laboratory used to study the mechanical behavior of materials. The issues associated with alignment during mechanical testing along with the improvements made to the in situ mechanical testing devices, over time, are described. In situ experiments involving corrosion-fatigue and stress corrosion cracking in various environments are presented and discussed. These include fatigue loading of metal matrix composites (MMCs), corrosion-fatigue, and stress corrosion cracking of Al 7075 alloys.