Biomedical subjects

Xiaochuan Pan

Publications and source records attributed to Xiaochuan Pan.

At least 19 recordsLinked to original sources

PubMed2026

A regulatory network underlying idiopathic pulmonary fibrosis.

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease in which genetic susceptibility interacts with epithelial, immune, and mesenchymal remodeling. Although the chromosome 11p15.5 locus contains established IPF susceptibility signals near MUC5B and TOLLIP, the broader regulatory architecture of this region remains incompletely resolved. METHODS: We integrated IPF genome-wide association study summary statistics with methylation, expression, and protein quantitative trait loci using summary-data-based Mendelian randomization (SMR). SMR-prioritized candidates were evaluated in independent transcriptomic and methylation cohorts and further contextualized using microRNA, transcription-factor, protein-interaction, machine-learning, single-cell, and spatial transcriptomic analyses. Fibrosis-associated expression patterns were assessed in a bleomycin-induced pulmonary fibrosis rat model. RESULTS: The analyses recovered the established MUC5B and TOLLIP signals and prioritized BRSK2 as a comparatively underexplored candidate supported by eQTL-based SMR and independent molecular evidence. The BRSK2 pQTL association did not pass the HEIDI test and was therefore not interpreted as convergent protein-level genetic evidence. Network analyses linked BRSK2 to cell-cycle, metabolic-stress, and senescence-related programs, while cross-cohort machine learning prioritized FOXA2, CDC25B, and NFE2 as informative network features. Single-cell and spatial analyses localized BRSK2 preferentially to fibroblast and myofibroblast compartments and to regions with greater histological fibrosis severity. In fibrotic rat lungs, BRSK2 expression increased, whereas FOXA2 and CDC25B decreased at the transcript and protein levels. CONCLUSIONS: These findings refine the molecular landscape of the chromosome 11p15.5 IPF susceptibility locus and prioritize BRSK2 as a candidate component of an IPF-associated profibrotic fibroblast state. Its causal contribution, direct regulatory relationships, and therapeutic tractability require targeted mechanistic validation.

Idiopathic Pulmonary Fibrosis↗

PubMed2006

Behavioral inhibition and prefrontal cortex in decision-making.

Every day we make innumerable decisions; some require no effort at all whereas others require considerable deliberation and weighing of various options. Despite the importance of decision-making in our lives and increased research interest, the specific neural mechanisms underlying decision-making remain unclear. We propose that the brain has at least two cortical pathways that independently generate a decision about appropriate behavior in given circumstances. These two pathways are extensions of the dorsal and ventral streams of the visual processing pathways. The parieto-premotor (extended dorsal) pathway makes decisions about motor actions in a largely autonomous and automatic fashion whereas the temporo-ventrolateral prefrontal (extended ventral) pathway is involved primarily in deliberate decisions and inhibitory control over behavior through the inhibitory function of the ventrolateral prefrontal cortex.

Animals↗

PubMed2006

A model of the hippocampal-cortical memory system.

Based on physiological evidence, we propose a theoretical model of the hippocampal-cortical memory system. The model consists of the following components: the sensory system, the hippocampus (short-term memory), and the association cortex (long-term memory). A series of key codes (local information) is supplied from the sensory system, while context (global information) is inputted from the hippocampus. The two inputs interact dynamically in the association cortex. The interactive neurons work as a detector of coincidence. The cortical network learns the memory information through the coincidence window and, finally, stores it in the form of attractors. This local-global information works as an addressor to designate the stored location of the memory in the association cortex and accelerates the process of storing and retrieving memory information.

Action Potentials↗

PubMed2006

Region of interest reconstruction from truncated data in circular cone-beam CT.

The circular scanning trajectory is one of the most widely adopted data-acquisition configurations in computed tomography (CT). The Feldkamp, Davis, Kress (FDK) algorithm and its various modifications have been developed for reconstructing approximately three-dimensional images from circular cone-beam data. When data contain transverse truncations, however, these algorithms may reconstruct images with significant truncation artifacts. It is of practical significance to develop algorithms that can reconstruct region-of-interest (ROI) images from truncated circular cone-beam data that are free of truncation artifacts and that have an accuracy comparable to that obtained from nontruncated cone-beam data. In this work, we have investigated and developed a backprojection-filtration (BPF)-based algorithm for ROI-image reconstruction from circular cone-beam data containing transverse truncations. Furthermore, we have developed a weighted BPF algorithm to exploit "redundant" information in data for improving image quality. In an effort to validate and evaluate the proposed BPF algorithms for circular cone-beam CT, we have performed numerical studies by using both computer-simulation data and experimental data acquired with a radiotherapy cone-beam CT system. Quantitative results in these studies demonstrate that the proposed BPF algorithms for circular cone-beam CT can reconstruct ROI images free of truncation artifacts.

Algorithms↗

PubMed2006

Region-of-interest reconstruction of motion-contaminated data using a weighted backprojection filtration algorithm.

The recently developed weighted backprojection filtration (WBPF) algorithm using data redundancy has capabilities that make this algorithm an attractive candidate for reconstructing images from motion-contaminated projection data. First, the WBPF algorithm is capable of reconstructing region-of-interest (ROI) images from reduced-scan fan-beam data, which have less data than the short-scan data required to reconstruct the entire field of view (FOV). Second, this algorithm can reconstruct ROI images from truncated data. Using phantom simulation studies, we demonstrate how these unique capabilities can be exploited to reduce the amount of motion-contaminated data used for reconstruction. In particular, we use examples from cardiac imaging to illustrate how off-center phantom positioning combined with phase-interval ROI reconstruction can result in the suppression of motion artifacts. In terms of temporal resolution, reduced-scan reconstruction with 45% of a full-scan dataset can be used to improve the temporal resolution of a short-scan reconstruction by 25.8% if ungated data are used. For data gated at 66 beats per minute, reduced-scan reconstruction with 45% of a full-scan dataset can be used to improve the temporal resolution of a short-scan reconstruction by 7.9%. As a result of our studies, we believe that the WBPF algorithm demonstrates the potential for reconstructing quality ROI images from motion-contaminated fan-beam data.

Algorithms↗

PubMed2005

Minimum data image reconstruction algorithms with shift-invariant filtering for helical, cone-beam CT.

We derive accurate and efficient reconstruction algorithms for helical, cone-beam CT that employ shift-invariant filtering. Specifically, a new backprojection-filtration algorithm is developed, and a minimum data filtered-backprojection algorithm is derived. These reconstruction algorithms with shift-invariant filtering can accept data with transverse truncation, and hence allow for minimum data image reconstruction.

Algorithms↗

PubMed2005

Image reconstruction in regions-of-interest from truncated projections in a reduced fan-beam scan.

In a reduced fan-beam scan, the scanned angular range is smaller than that in a short scan (i.e., a half-scan). In this work, we have developed a new algorithm, which is referred to as the backprojection-filtration (BPF) algorithm, for exact image reconstruction within ROIs from reduced-scan data containing truncations. Explicit conditions on data acquisition have also been derived for exact image reconstruction within an ROI. We have performed a preliminary quantitative study whose results demonstrated and verified the proposed fan-beam BPF algorithm and the derived conditions on data acquisition. The proposed BPF algorithm can have significant implications for clinical and animal CT imaging, therapy imaging, electron paramagnetic resonance imaging and other tomographic imaging because it allows for reconstruction from truncated data and for a potentially drastic reduction of radiation dose and/or of imaging time.

Algorithms↗

PubMed2005

A hybrid approach to reducing computed tomography metal artifacts in intracavitary brachytherapy.

PURPOSE: To develop a hybrid approach to reduce computed tomography (CT) metal artifacts caused by the Fletcher-Suit applicator. METHODS AND MATERIALS: Using the acquired raw projection data, the hybrid algorithm determines the separate contributions from the metal and non-metal objects. Next, reconstructions of metal and non-metal images are separately obtained from their estimated projections. A final image is formed by appropriately combining the individual images. Phantom and patient data are used to evaluate the performance of this method. RESULTS: CT images reconstructed by use of the standard filtered-backprojection (FBP) algorithm contain significant artifacts even for small metal objects. However, images reconstructed using the hybrid algorithm contain virtually no artifacts. For metal objects with complex structures, the hybrid algorithm can also yield images containing fewer severe streak artifacts than those reconstructed using the FBP algorithm alone. CONCLUSIONS: These studies demonstrate that the hybrid approach can effectively reduce CT metal artifacts caused by the Fletcher-Suit applicator.

Algorithms↗

PubMed2005

EPR imaging: the relationship between CW spectra acquired from an extended sample subjected to fixed stepped gradients and the Radon transform of the resonance density.

EPR spectroscopy can be extended to a spectroscopic imaging modality by applying magnetic field gradients across the sample to encode spatial information in the measured spectra. In this work, we present a mathematical model of the EPR imaging process in terms of the Radon transform. We describe a model for electron paramagnetic resonance imaging, derive its explicit relationship to the Radon transform, and discuss several options for reconstructing the sample absorption and dispersion densities. An important extension to previous descriptions is the incorporation of large amplitude magnetic field modulation, which can be used to improve the signal-to-noise ratio for continuous wave signal acquisition. Magnetic field modulation is shown to cause well understood changes in the shapes of spectra in the reconstructed images, but does not affect the spatial resolution achieved in these images. Since many of the novel image reconstruction strategies and noise filtering algorithms that have been developed for other modalities start from this formalism, this work allows for their direct application to EPR imaging. This promises to lead to further improvements in EPR imaging techniques.

Algorithms↗

PubMed2005

Half-time image reconstruction in thermoacoustic tomography.

Thermoacoustic tomography (TAT) is an emerging imaging technique with great potential for a wide range of biomedical imaging applications. In this paper, we propose and investigate reconstruction approaches for TAT that are based on the half-time reflectivity tomography paradigm. We reveal that half-time reconstruction approaches permit for the explicit control of statistically complementary information that can result in the optimal reduction of image variances. We also show that half-time reconstruction approaches can mitigate image artifacts due to heterogeneous acoustic properties of an object. Reconstructed images and numerical results produced from simulated and experimental TAT measurement data are employed to demonstrate these effects.

Acoustics↗

PubMed2005

Spatial-resolution enhancement in computed tomography.

We propose an approach that combines an asymmetric fan-beam configuration and a new reconstruction algorithm to enhancing spatial resolution in computed tomography (CT). The asymmetric configuration can be achieved by changing the center of rotation (COR) from the conventional symmetric configuration. It does not, however, require new detectors and X-ray source nor alter the relative geometry between the detector and the X-ray source. By effectively reducing the distance of the COR to the X-ray source, the asymmetric configuration can increase the effective sampling density in projection data without reducing the size of the field of view (FOV). The proposed algorithm, on the other hand, can reconstruct images directly from data acquired with this asymmetric configuration. We performed numerical studies to demonstrate and validate the proposed acquisition/reconstruction approach. Results in these studies confirm that the proposed approach can lead to enhanced spatial resolution in reconstructed images. The proposed acquisition/reconstruction approach may find applications in micro-CT and industrial CT in which the CORs may be changed.

Algorithms↗

PubMed2005

Weighted expectation maximization reconstruction algorithms for thermoacoustic tomography.

Thermoacoustic tomography (TAT) is an emerging imaging technique with potential for a wide range of biomedical imaging applications. In this correspondence, we propose an infinite family of weighted expectation maximization (EM) algorithms for reconstruction of images from temporally truncated TAT measurement data. The weighted EM algorithms are equivalent mathematically to the conventional EM algorithm, but are shown to propagate data inconsistencies in different ways. Using simulated and experimental TAT measurement data, we demonstrate that suitable choices of weighted EM algorithms can effectively mitigate image artifacts that are attributable to temporal truncation of the TAT data function.

Acoustics↗

PubMed2005

Feasibility of half-data image reconstruction in 3-D reflectivity tomography with a spherical aperture.

Reflectivity tomography is an imaging technique that seeks to reconstruct certain acoustic properties of a weakly scattering object. Besides being applicable to pure ultrasound imaging techniques, the reconstruction theory of reflectivity tomography is also pertinent to hybrid imaging techniques such as thermoacoustic tomography. In this work, assuming spherical scanning apertures, redundancies in the three-dimensional (3-D) reflectivity tomography data function are identified and formulated mathematically. These data redundancies are used to demonstrate that knowledge of the measured data function over half of its domain uniquely specifies the 3-D object function. This indicates that, in principle, exact image reconstruction can be performed using a "half-scan" data function, which corresponds to temporally untruncated measurements acquired on a hemi-spherical aperture, or using a "half-time" data function, which corresponds to temporally truncated measurements acquired on the entire spherical aperture. Both of these minimal scanning configurations have important biological imaging applications. An iterative reconstruction method is utilized for reconstruction of a simulated 3-D object from noiseless and noisy half-scan and half-time data functions.

Algorithms↗

PubMed2005

Image reconstruction in peripheral and central regions-of-interest and data redundancy.

Algorithms have been developed for image reconstruction within a region-of-interest (ROI) from fan-beam data less than that required for reconstructing the entire image. However, these algorithms do not admit truncated data. In this work, we investigate exact ROI-image reconstruction from fan-beam data containing truncations by use of the so-called fan-beam backprojection-filtration (BPF) algorithm. We also generalize the fan-beam BPF algorithm to exploit redundant information inherent in the truncated fan-beam data. Because the parallel-beam scan can be interpreted as a special case of the fan-beam scan, based upon the fan-beam BPF algorithm, we derive a parallel-beam BPF algorithm for exactly reconstructing ROI images from truncated parallel-beam data. Furthermore, we investigate image reconstruction within two types of distinctive ROIs, which are referred to as the peripheral and central ROIs, respectively, from fan-beam data containing truncations and discuss their potential clinical applications. The results can readily be generalized to reconstructing 3D ROI images from data acquired in circular and helical cone-beam scan. They can also be extended to address ROI-image-reconstruction problems in parallel-, fan-, and cone-beam scans with general trajectories. The work not only has significant implications for clinical and animal-imaging applications of CT, but also may find applications in other imaging modalities.

Algorithms↗

PubMed2005

PI-line-based image reconstruction in helical cone-beam computed tomography with a variable pitch.

Current applications of helical cone-beam computed tomography (CT) involve primarily a constant pitch where the translating speed of the table and the rotation speed of the source-detector remain constant. However, situations do exist where it may be more desirable to use a helical scan with a variable translating speed of the table, leading a variable pitch. One of such applications could arise in helical cone-beam CT fluoroscopy for the determination of vascular structures through real-time imaging of contrast bolus arrival. Most of the existing reconstruction algorithms have been developed only for helical cone-beam CT with constant pitch, including the backprojection-filtration (BPF) and filtered-backprojection (FBP) algorithms that we proposed previously. It is possible to generalize some of these algorithms to reconstruct images exactly for helical cone-beam CT with a variable pitch. In this work, we generalize our BPF and FBP algorithms to reconstruct images directly from data acquired in helical cone-beam CT with a variable pitch. We have also performed a preliminary numerical study to demonstrate and verify the generalization of the two algorithms. The results of the study confirm that our generalized BPF and FBP algorithms can yield exact reconstruction in helical cone-beam CT with a variable pitch. It should be pointed out that our generalized BPF algorithm is the only algorithm that is capable of reconstructing exactly region-of-interest image from data containing transverse truncations.

Algorithms↗

PubMed2005

Reconstruction of 3D regions-of-interest from data in reduced helical cone-beam scans.

The sufficiency conditions are derived for exact image reconstruction of a 3D ROI from projections acquired with a reduced helical scan over an angular range considerably smaller than that required by image reconstruction in, e.g., the conventional long object problem, for which the scanned angular range is often more than 2pi. ROI reconstruction is investigated by a recently developed filtered-backprojection algorithm that can make use of data acquired with a reduced helical scan. Preliminary numerical studies demonstrate and validate the ROI reconstruction. This work may have significant practical implications because a reduced scan in CT often translates to reduced motion artifacts and reduced radiation dose delivered to the subject.

Algorithms↗

PubMed2005

Theory and algorithms for image reconstruction on chords and within regions of interest.

We introduce a formula for image reconstruction on a chord of a general source trajectory. We subsequently develop three algorithms for exact image reconstruction on a chord from data acquired with the general trajectory. Interestingly, two of the developed algorithms can accommodate data containing transverse truncations. The widely used helical trajectory and other trajectories discussed in literature can be interpreted as special cases of the general trajectory, and the developed theory and algorithms are thus directly applicable to reconstructing images exactly from data acquired with these trajectories. For instance, chords on a helical trajectory are equivalent to the n-PI-line segments. In this situation, the proposed algorithms become the algorithms that we proposed previously for image reconstruction on PI-line segments. We have performed preliminary numerical studies, which include the study on image reconstruction on chords of two-circle trajectory, which is nonsmooth, and on n-PI lines of a helical trajectory, which is smooth. Quantitative results of these studies verify and demonstrate the proposed theory and algorithms.

Algorithms↗

PubMed2004

An extended data function and its generalized backprojection for image reconstruction in helical cone-beam CT.

We have recently proposed a general formula (i.e., equations (9) to (11) in Zou and Pan (2004a Phys. Med. Biol. 49 941-59)) for image reconstruction from helical cone-beam data. On the basis of the formula, we have also developed two reconstruction algorithms, which are referred to as the backprojection filtration (BPF) algorithm (Zou and Pan 2004a) and the filtered backprojection (FBP) algorithm (Zou and Pan 2004b Phys. Med. Biol. 49 2717-31), respectively. The two algorithms have been implemented and evaluated in numerical studies. In this note, however, we point out that the data function previously used for proving the general formula in Zou and Pan (2004a) is incomplete and that, instead, an extended data function and its generalized backprojection, which are described in this note, should be used to complete the proof of the general formula. On the other hand, we also demonstrate in this note that the additional term in the extended data function has no effect on the previously developed BPF and FBP algorithms. The results can also be extended to general, smooth trajectories.

Algorithms↗