129 research outputs found
Relation Embedding with Dihedral Group in Knowledge Graph
Link prediction is critical for the application of incomplete knowledge graph
(KG) in the downstream tasks. As a family of effective approaches for link
predictions, embedding methods try to learn low-rank representations for both
entities and relations such that the bilinear form defined therein is a
well-behaved scoring function. Despite of their successful performances,
existing bilinear forms overlook the modeling of relation compositions,
resulting in lacks of interpretability for reasoning on KG. To fulfill this
gap, we propose a new model called DihEdral, named after dihedral symmetry
group. This new model learns knowledge graph embeddings that can capture
relation compositions by nature. Furthermore, our approach models the relation
embeddings parametrized by discrete values, thereby decrease the solution space
drastically. Our experiments show that DihEdral is able to capture all desired
properties such as (skew-) symmetry, inversion and (non-) Abelian composition,
and outperforms existing bilinear form based approach and is comparable to or
better than deep learning models such as ConvE.Comment: ACL 201
3D tumor localization through real-time volumetric x-ray imaging for lung cancer radiotherapy
Recently we have developed an algorithm for reconstructing volumetric images
and extracting 3D tumor motion information from a single x-ray projection. We
have demonstrated its feasibility using a digital respiratory phantom with
regular breathing patterns. In this work, we present a detailed description and
a comprehensive evaluation of the improved algorithm. The algorithm was
improved by incorporating respiratory motion prediction. The accuracy and
efficiency were then evaluated on 1) a digital respiratory phantom, 2) a
physical respiratory phantom, and 3) five lung cancer patients. These
evaluation cases include both regular and irregular breathing patterns that are
different from the training dataset. For the digital respiratory phantom with
regular and irregular breathing, the average 3D tumor localization error is
less than 1 mm. On an NVIDIA Tesla C1060 GPU card, the average computation time
for 3D tumor localization from each projection ranges between 0.19 and 0.26
seconds, for both regular and irregular breathing, which is about a 10%
improvement over previously reported results. For the physical respiratory
phantom, an average tumor localization error below 1 mm was achieved with an
average computation time of 0.13 and 0.16 seconds on the same GPU card, for
regular and irregular breathing, respectively. For the five lung cancer
patients, the average tumor localization error is below 2 mm in both the axial
and tangential directions. The average computation time on the same GPU card
ranges between 0.26 and 0.34 seconds
Poly(delta-gluconolactone) and Poly(delta-gluconolactone- ε
Poly(delta-gluconolactone) (PGL) and poly(delta-gluconolactone-ε-caprolactone) (P(GL-CL)) were synthesized through ring-opening polymerization (ROP) and characterized by FT-IR, NMR, XRD, intrinsic viscosity, GPC, DSC, and TGA. The crystallinity of P(GL-CL) with various d-GL/CL ratios (d-GL/CL = 5 : 5, 4 : 6, 3 : 7, 2 : 8, and 1 : 9) was 12.09 to 59.78% while PGL was amorphous. Melting temperature (Tm) of these polymers was 49.8 to 62.0°C and decomposition temperature was 282 to 489°C depending on the d-GL/CL ratios. In addition, all these polymers were degradable and the degradation rates could be controlled by adjusting d-GL/CL ratios. These results indicated that PGL and P(GL-CL) might be promising novel absorbable materials
GPU-based Fast Low-dose Cone Beam CT Reconstruction via Total Variation
Cone-beam CT (CBCT) has been widely used in image guided radiation therapy
(IGRT) to acquire updated volumetric anatomical information before treatment
fractions for accurate patient alignment purpose. However, the excessive x-ray
imaging dose from serial CBCT scans raises a clinical concern in most IGRT
procedures. The excessive imaging dose can be effectively reduced by reducing
the number of x-ray projections and/or lowering mAs levels in a CBCT scan. The
goal of this work is to develop a fast GPU-based algorithm to reconstruct high
quality CBCT images from undersampled and noisy projection data so as to lower
the imaging dose. The CBCT is reconstructed by minimizing an energy functional
consisting of a data fidelity term and a total variation regularization term.
We developed a GPU-friendly version of the forward-backward splitting algorithm
to solve this model. A multi-grid technique is also employed. We test our CBCT
reconstruction algorithm on a digital NCAT phantom and a head-and-neck patient
case. The performance under low mAs is also validated using a physical Catphan
phantom and a head-and-neck Rando phantom. It is found that 40 x-ray
projections are sufficient to reconstruct CBCT images with satisfactory quality
for IGRT patient alignment purpose. Phantom experiments indicated that CBCT
images can be successfully reconstructed with our algorithm under as low as 0.1
mAs/projection level. Comparing with currently widely used full-fan
head-and-neck scanning protocol of about 360 projections with 0.4
mAs/projection, it is estimated that an overall 36 times dose reduction has
been achieved with our algorithm. Moreover, the reconstruction time is about
130 sec on an NVIDIA Tesla C1060 GPU card, which is estimated ~100 times faster
than similar iterative reconstruction approaches.Comment: 20 pages, 10 figures, Paper was revised and more testing cases were
added
Real-time volumetric image reconstruction and 3D tumor localization based on a single x-ray projection image for lung cancer radiotherapy
Purpose: To develop an algorithm for real-time volumetric image
reconstruction and 3D tumor localization based on a single x-ray projection
image for lung cancer radiotherapy. Methods: Given a set of volumetric images
of a patient at N breathing phases as the training data, we perform deformable
image registration between a reference phase and the other N-1 phases,
resulting in N-1 deformation vector fields (DVFs). These DVFs can be
represented efficiently by a few eigenvectors and coefficients obtained from
principal component analysis (PCA). By varying the PCA coefficients, we can
generate new DVFs, which, when applied on the reference image, lead to new
volumetric images. We then can reconstruct a volumetric image from a single
projection image by optimizing the PCA coefficients such that its computed
projection matches the measured one. The 3D location of the tumor can be
derived by applying the inverted DVF on its position in the reference image.
Our algorithm was implemented on graphics processing units (GPUs) to achieve
real-time efficiency. We generated the training data using a realistic and
dynamic mathematical phantom with 10 breathing phases. The testing data were
360 cone beam projections corresponding to one gantry rotation, simulated using
the same phantom with a 50% increase in breathing amplitude. Results: The
average relative image intensity error of the reconstructed volumetric images
is 6.9% +/- 2.4%. The average 3D tumor localization error is 0.8 mm +/- 0.5 mm.
On an NVIDIA Tesla C1060 GPU card, the average computation time for
reconstructing a volumetric image from each projection is 0.24 seconds (range:
0.17 and 0.35 seconds). Conclusions: We have shown the feasibility of
reconstructing volumetric images and localizing tumor positions in 3D in near
real-time from a single x-ray image.Comment: 8 pages, 3 figures, submitted to Medical Physics Lette
Pathogenic infection of Macaca nemestrina with a CCR5-tropic subtype-C simian-human immunodeficiency virus
Background: Although pig-tailed macaques (Macaca nemestrina) have been used in AIDS research for years, less is known about the early immunopathogenic events in this species, as compared to rhesus macaques (Macaca mulatta). Similarly, the events in early infection are well-characterized for simian immunodeficiency viruses (SIV), but less so for chimeric simian-human immunodeficiency viruses (SHIV), although the latter have been widely used in HIV vaccine studies. Here, we report the consequences of intrarectal infection with a CCR5-tropic clade C SHIV-1157ipd3N4 in pig-tailed macaques. Results: Plasma and cell-associated virus was detectable in peripheral blood and intestinal tissues of all four pig-tailed macaques following intrarectal inoculation with SHIV-1157ipd3N4. We also observed a rapid and irreversible loss of CD4+ T cells at multiple mucosal sites, resulting in a marked decrease of CD4:CD8 T cell ratios 0.5–4 weeks after inoculation. This depletion targeted subsets of CD4+ T cells expressing the CCR5 coreceptor and having a CD28-CD95+ effector memory phenotype, consistent with the R5-tropism of SHIV-1157ipd3N4. All three animals that were studied beyond the acute phase seroconverted as early as week 4, with two developing cross-clade neutralizing antibody responses by week 24. These two animals also demonstrated persistent plasma viremia for >48 weeks. One of these animals developed AIDS, as shown by peripheral blood CD4+ T-cell depletion starting at 20 weeks post inoculation. Conclusion: These findings indicate that SHIV-1157ipd3N4-induced pathogenesis in pig-tailed macaques followed a similar course as SIV-infected rhesus macaques. Thus, R5 SHIV-C-infection of pig-tailed macaques could provide a useful and relevant model for AIDS vaccine and pathogenesis research
Luminescent Solar Concentrators Fabricated by Dispersing Rare Earth Particles in PMMA Waveguide
Luminescent solar concentrators (LSCs) were fabricated by dispersing CaAlSiN3 : Eu2+ particles in a PMMA waveguide. A series of LSCs (dimension 5.0 cm × 5.0 cm × 0.5 cm) with different CaAlSiN3 : Eu2+ particle concentration were obtained and their performance was evaluated. The maximum optical concentration ratio is 1.23 with a power conversion efficiency of 1.44% for the LSC containing 0.5 wt% CaAlSiN3 : Eu2+ particles concentration. This strategy of dispersing rare earth particles in PMMA waveguide represents an alternative approach to producing highly durable LSCs
CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks
Transcription factors (TFs) and microRNAs (miRNAs) are well-characterized trans-acting essential players in gene expression regulation. Growing evidence indicates that TFs and miRNAs can work cooperatively, and their dysregulation has been associated with many diseases including cancer. A unified picture of regulatory interactions of these regulators and their joint target genes would shed light on cancer studies. Although online resources developed to support probing of TF-gene and miRNA-gene interactions are available, online applications for miRNA-TF co-regulatory analysis, especially with a focus on cancers, are lacking. In light of this, we developed a web tool, namely CMTCN (freely available at http://www.cbportal.org/CMTCN), which constructs miRNA-TF co-regulatory networks and conducts comprehensive analyses within the context of particular cancer types. With its user-friendly provision of topological and functional analyses, CMTCN promises to be a reliable and indispensable web tool for biomedical studies
PCA-based lung motion model
Organ motion induced by respiration may cause clinically significant
targeting errors and greatly degrade the effectiveness of conformal
radiotherapy. It is therefore crucial to be able to model respiratory motion
accurately. A recently proposed lung motion model based on principal component
analysis (PCA) has been shown to be promising on a few patients. However, there
is still a need to understand the underlying reason why it works. In this
paper, we present a much deeper and detailed analysis of the PCA-based lung
motion model. We provide the theoretical justification of the effectiveness of
PCA in modeling lung motion. We also prove that under certain conditions, the
PCA motion model is equivalent to 5D motion model, which is based on physiology
and anatomy of the lung. The modeling power of PCA model was tested on clinical
data and the average 3D error was found to be below 1 mm.Comment: 4 pages, 1 figure. submitted to International Conference on the use
of Computers in Radiation Therapy 201
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