2016.bib

@article{Chen2016,
  abstract = {OBJECTIVE: The existence of void regions and the complexity of structural heterogeneity and optical specificity are two challenges encountered in three-dimensional (3-D) optical imaging of in situ gastric cancer. An adaptively alternative light-transport-model-based 3-D optical imaging method was developed for addressing these challenges. METHODS: In this newly developed imaging method, both the anatomical structure and optical properties are considered as a priori information, which makes the full use of the specificity of the biological tissues and improves both the quality and efficiency of the reconstructed images. The soul of the adaptively alternative technique is technique is configured to first classify the tissues based on the anatomical structure and optical properties and then select various equations to specifically characterize the light transport in different categories of tissues. RESULTS: A series of rigorous simulations were conducted to demonstrate the performance of the hybrid light transport model, and the quality of the reconstructed images was then evaluated using a digital-mouse-based gastric cancer mimicing simulation, which showed that the localization error was less than 1 mm and the quantification error was approximately 10{\%}. Finally, the applicability of the proposed method for in vivo imaging of gastric cancer was illustrated using groups of gastric cancer-bearing mice, which demonstrated the ability of the proposed method for longitudinal and quantitative monitoring of gastric cancer. CONCLUSION: The developed method offers improved probability and great potential in the applications of earlier detecting in situ gastric cancer and longitudinal and quantitative observation of its development.},
  author = {Chen, Xueli and Yang, Defu and Sun, Fangfang and Cao, Xu and Liang, Jimin},
  doi = {10.1109/TBME.2015.2510369},
  file = {:E$\backslash$:/Mendeley Papers/2016/Unknown/2016 - Unknown - Adaptively Alternative Light-Transport-Model-Based Three-Dimensional Optical Imaging for Longitudinal and Quantitative.pdf:pdf},
  issn = {15582531},
  journal = {IEEE Transactions on Biomedical Engineering},
  keywords = {Adaptively alternative strategy,Gastric cancer,Hybrid light transport model,Quantitative and longitudinal imaging},
  number = {10},
  pages = {2095--2107},
  pmid = {26700857},
  title = {{Adaptively alternative light-transport-model-based three-dimensional optical imaging for longitudinal and quantitative monitoring of gastric cancer in live animal}},
  volume = {63},
  year = {2016}
}

@article{Dai2016,
  abstract = {We quantified molecular specificity of Cy5.5-GX1 in vivo with dynamic fluorescence imaging to better understand its kinetic properties. According to whether or not free GX1 was injected and when it was injected, twelve of BGC-823 xenografted mice were randomly divided into three groups and underwent a 60 minute dynamic fluorescence scanning. Combined with a principal-component analysis, the binding potential (Bp) of the probe was determined by both Logan graphical analysis with reference tissue model (GARTM) and Lammertsma simplified reference tissue model (SRTM). The sum of the pharmacokinetic rate constants (SKRC) was quantified by the Gurfinkel exponential model (GEXPM). Cy5.5-GX1 specifically targeted tumor both in vitro and in vivo. We obtained similar quantification results of Bp (GARTM Bp = 0.582 +/- 0.2655, SRTM Bp = 0.618 +/- 0.2923), and obtained a good linear relation between the Bp value and the SKRC value. Our results indicate that the SKRC value is more suitable for an early-stage kinetic data analysis, and the Bp value depicts kinetic characteristics under the equilibrium state. Dynamic fluorescence imaging in conjunction with various kinetic models are optimal tools to quantify molecular specificity of the Cy5.5-GX1 probe in vivo.},
  author = {Dai, Yunpeng and Yin, Jipeng and Huang, Yu and Chen, Xueli and Wang, Guodong and Liu, Yajun and Zhang, Xianghan and Nie, Yongzhan and Wu, Kaichun and Liang, Jimin},
  doi = {10.1364/BOE.7.001149},
  file = {:E$\backslash$:/Mendeley Papers/2016/Unknown/2016 - Unknown - In vivo quantifying molecular specificity of Cy5 . 5-labeled cyclic 9-mer peptide probe with dynamic fluorescence imagi.pdf:pdf},
  issn = {2156-7085},
  journal = {Biomedical Optics Express},
  number = {4},
  pages = {1149},
  pmid = {27446643},
  title = {{In vivo quantifying molecular specificity of Cy55-labeled cyclic 9-mer peptide probe with dynamic fluorescence imaging}},
  url = {https://www.osapublishing.org/abstract.cfm?URI=boe-7-4-1149},
  volume = {7},
  year = {2016}
}

@article{Dai2016a,
  abstract = {The aim of this article is to investigate the influence of a tracer injection dose (ID) and camera integration time (IT) on quantifying pharmacokinetics of Cy5.5-GX1 in gastric cancer BGC-823 cell xenografted mice. Based on three factors, including whether or not to inject free GX1, the ID of Cy5.5-GX1, and the camera IT, 32 mice were randomly divided into eight groups and received 60-min dynamic fluorescence imaging. Gurfinkel exponential model (GEXPM) and Lammertsma simplified reference tissue model (SRTM) combined with a singular value decomposition analysis were used to quantitatively analyze the acquired dynamic fluorescent images. The binding potential (Bp) and the sum of the pharmacokinetic rate constants (SKRC) of Cy5.5-GX1 were determined by the SRTM and EXPM, respectively. In the tumor region, the SKRC value exhibited an obvious trend with change in the tracer ID, but the Bp value was not sensitive to it. Both the Bp and SKRC values were independent of the camera IT. In addition, the ratio of the tumor-To-muscle region was correlated with the camera IT but was independent of the tracer ID. Dynamic fluorescence imaging in conjunction with a kinetic analysis may provide more quantitative information than static fluorescence imaging, especially for a priori information on the optimal ID of targeted probes for individual therapy.},
  author = {Dai, Yunpeng and Chen, Xueli and Yin, Jipeng and Kang, Xiaoyu and Wang, Guodong and Zhang, Xianghan and Nie, Yongzhan and Wu, Kaichun and Liang, Jimin},
  doi = {10.1117/1.JBO.21.8.086001},
  file = {:E$\backslash$:/Mendeley Papers/2016/Journal of Biomedical Optics/2016 - Journal of Biomedical Optics - Investigation of injection dose and camera integration time on quantifying pharmacokinetics of a C.pdf:pdf},
  issn = {15602281},
  journal = {Journal of Biomedical Optics},
  keywords = {Cy5.5-GX1,dose dependency,dynamic fluorescence imaging,pharmacokinetic quantification},
  number = {8},
  title = {{Investigation of injection dose and camera integration time on quantifying pharmacokinetics of a Cy5.5-GX1 probe with dynamic fluorescence imaging in vivo}},
  volume = {21},
  year = {2016}
}

@article{Ren2016,
  abstract = {Bioluminescence tomography (BLT) has been a valuable optical molecular imaging technique to non-invasively depict the cellular and molecular processes in living animals with high sensitivity and specificity. Due to the inherent ill-posedness of BLT, a priori information of anatomical structure is usually incorporated into the reconstruction. The structural information is usually provided by computed tomography (CT) or magnetic resonance imaging (MRI). In order to obtain better quantitative results, BLT reconstruction with heterogeneous tissues needs to segment the internal organs and discretize them into meshes with the finite element method (FEM). It is time-consuming and difficult to handle the segmentation and discretization problems. In this paper, we present a fast reconstruction method for BLT based on multi-atlas registration and adaptive voxel discretization to relieve the complicated data processing procedure involved in the hybrid BLT/CT system. A multi-atlas registration method is first adopted to estimate the internal organ distribution of the imaged animal. Then, the animal volume is adaptively discretized into hexahedral voxels, which are fed into FEM for the following BLT reconstruction. The proposed method is validated in both numerical simulation and an in vivo study. The results demonstrate that the proposed method can reconstruct the bioluminescence source efficiently with satisfactory accuracy.},
  author = {Ren, Shenghan and Hu, Haihong and Li, Gen and Cao, Xu and Zhu, Shouping and Chen, Xueli and Liang, Jimin},
  doi = {10.1364/BOE.7.001549},
  file = {:E$\backslash$:/Mendeley Papers/2016/Unknown/2016 - Unknown - Multi-atlas registration and adaptive hexahedral voxel discretization for fast bioluminescence tomography.pdf:pdf},
  issn = {2156-7085},
  journal = {Biomedical Optics Express},
  number = {4},
  pages = {1549},
  pmid = {27446674},
  title = {{Multi-atlas registration and adaptive hexahedral voxel discretization for fast bioluminescence tomography}},
  url = {https://www.osapublishing.org/abstract.cfm?URI=boe-7-4-1549},
  volume = {7},
  year = {2016}
}

@article{Ren2016a,
  abstract = {Simplified spherical harmonics approximation (SPN) equations are widely used in modeling light propagation in biological tissues. However, with the increase of order N, its computational burden will severely aggravate. We propose a graphics processing unit (GPU) accelerated framework for SPN equations. Compared with the conventional central processing unit implementation, an increased performance of the GPU framework is obtained with an increase in mesh size, with the best speed-up ratio of 25 among the studied cases. The influence of thread distribution on the performance of the GPU framework is also investigated.},
  author = {Ren, Shenghan and Chen, Xueli and Cao, Xu and Zhu, Shouping and Liang, Jimin},
  doi = {10.3788/COL201614.071701},
  file = {:E$\backslash$:/Mendeley Papers/2016/Unknown/2016 - Unknown - GPU accelerated simplified harmonic spherical approximation equations for three-dimensional optical imaging.pdf:pdf},
  issn = {16717694},
  journal = {Chinese Optics Letters},
  keywords = {Light propagation in tissues,Parallel processing,Turbid media},
  number = {7},
  pages = {071701},
  title = {{GPU accelerated simplified harmonic spherical approximation equations for three-dimensional optical imaging}},
  url = {http://www.osapublishing.org/abstract.cfm?uri=col-14-7-071701},
  volume = {14},
  year = {2016}
}

@article{Zhao2016,
  author = {Zhao, Fengjun and Liang, Jimin and Chen, Xueli and Liu, Junting and Chen, Dongmei and Yang, Xiang and Tian, Jie},
  doi = {10.1007/s11517-015-1337-0},
  file = {:E$\backslash$:/Mendeley Papers/2016/Medical {\&} Biological Engineering {\&} Computing/2016 - Medical {\&} Biological Engineering {\&} Computing - Quantitative analysis of vascular parameters for micro ‑ CT imaging of vascular ne.pdf:pdf},
  isbn = {1151701513},
  issn = {17410444},
  journal = {Medical and Biological Engineering and Computing},
  keywords = {Micro-computed tomography,Multi-resolution,Quantitative analysis,Vascular networks},
  number = {2-3},
  pages = {511--524},
  publisher = {Springer Berlin Heidelberg},
  title = {{Quantitative analysis of vascular parameters for micro-CT imaging of vascular networks with multi-resolution}},
  volume = {54},
  year = {2016}
}

@article{Qu2016,
  abstract = {The widespread use of whole-body small animal in vivo imaging in preclinical research has proposed the new demands on imaging processing and analysis. Micro-CT provides detailed anatomical structural information for continuous detection and different individual comparison, but the body deformation happened during different data acquisition needs sophisticated registration. In this paper, we propose a hybrid method for registering micro-CT mice images, which combines the strengths of point-based and intensity-based registration methods. Point-based non-rigid method using thin-plate spline robust point matching algorithm is utilized to acquire a coarse registration. And then intensity-based non-rigid method using normalized mutual information, Halton sampling and adaptive stochastic gradient descent optimization is used to acquire precise registration. Two accuracy metrics, Dice coefficient and average surface distance are used to do the quantitative evaluation. With the intra- and intersubject micro-CT mice images registration assessment, the hybrid method has been proven capable of excellent performance on micro-CT mice images registration.},
  author = {Qu, Xiaochao and Gao, Xueyuan and Xu, Xianhui and Zhu, Shouping and Liang, Jimin},
  doi = {10.1007/s11517-015-1386-4},
  file = {:E$\backslash$:/Mendeley Papers/2016/Medical {\&} Biological Engineering {\&} Computing/2016 - Medical {\&} Biological Engineering {\&} Computing - A hybrid registration ‑ based method for whole ‑ body micro ‑ CT mice images.pdf:pdf},
  isbn = {1151701513},
  issn = {17410444},
  journal = {Medical and Biological Engineering and Computing},
  keywords = {Hybrid registration,Micro-CT mice images,Non-rigid registration},
  number = {7},
  pages = {1037--1048},
  publisher = {Springer Berlin Heidelberg},
  title = {{A hybrid registration-based method for whole-body micro-CT mice images}},
  volume = {54},
  year = {2016}
}

@article{Qu2016a,
  author = {Qu, Xiaochao and Li, Xiaoxiao and Liang, Jingning and Wang, Yanran and Liu, Muhan and Liang, Jimin},
  doi = {10.1155/2016/8368154},
  file = {:E$\backslash$:/Mendeley Papers/2016/Journal of Nanomaterials/2016 - Journal of Nanomaterials - Micro-CT Imaging of RGD-Conjugated Gold Nanorods Targeting Tumor In Vivo.pdf:pdf},
  issn = {16874129},
  journal = {Journal of Nanomaterials},
  number = {Article ID 8368154},
  title = {{Micro-CT Imaging of RGD-Conjugated Gold Nanorods Targeting Tumor In Vivo}},
  volume = {2016},
  year = {2016}
}

@article{Zhan2016,
  author = {Zhan, Yonghua and Ai, Fanrong and Chen, Feng and Valdovinos, Hector F. and Orbay, Hakan and Sun, Haiyan and Liang, Jimin and Barnhart, Todd E. and Tian, Jie and Cai, Weibo},
  doi = {10.1002/smll.201600594},
  file = {:E$\backslash$:/Mendeley Papers/2016/Unknown/2016 - Unknown - Intrinsically Zirconium-89 Labeled Gd 2 O 2 S Eu Nanoprobes for In Vivo Positron Emission Tomography and Gamma-Ray-Ind.pdf:pdf},
  issn = {16136829},
  journal = {Small},
  keywords = {intrinsic radiolabeling,nanoparticles,positron emission tomography,radioluminescence imaging},
  number = {21},
  pages = {2872--2876},
  title = {{Intrinsically Zirconium-89 Labeled Gd2O2S:Eu Nanoprobes for in Vivo Positron Emission Tomography and Gamma-Ray-Induced Radioluminescence Imaging}},
  volume = {12},
  year = {2016}
}

@article{Qin2016,
  abstract = {Cancer is a common cause of death worldwide. Despite significant advances in cancer treatments, the morbidity and mortality are still enormous. Tumor heterogeneity, especially intratumoral heterogeneity, is a significant reason underlying difficulties in tumor treatment and failure of a number of current therapeutic modalities, even of molecularly targeted therapies. The development of a virtually noninvasive "liquid biopsy" from the blood has been attempted to characterize tumor heterogeneity. This review focuses on cell-free circulating tumor DNA (ctDNA) in the bloodstream as a versatile biomarker. ctDNA analysis is an evolving field with many new methods being developed and optimized to be able to successfully extract and analyze ctDNA, which has vast clinical applications. ctDNA has the potential to accurately genotype the tumor and identify personalized genetic and epigenetic alterations of the entire tumor. In addition, ctDNA has the potential to accurately monitor tumor burden and treatment response, while also being able to monitor minimal residual disease, reducing the need for harmful adjuvant chemotherapy and allowing more rapid detection of relapse. There are still many challenges that need to be overcome prior to this biomarker getting wide adoption in the clinical world, including optimization, standardization, and large multicenter trials.},
  author = {Qin, Zhen and Ljubimov, Vladimir A. and Zhou, Cuiqi and Tong, Yunguang and Liang, Jimin},
  doi = {10.1186/s40880-016-0092-4},
  file = {:E$\backslash$:/Mendeley Papers/2016/Chinese Journal of Cancer/2016 - Chinese Journal of Cancer - Cell ‑ free circulating tumor DNA in cancer.pdf:pdf},
  isbn = {1000-467X 1944-446X},
  issn = {1944446X},
  journal = {Chinese Journal of Cancer},
  keywords = {Cancer,Circulating tumor DNA,Liquid biopsy},
  number = {5},
  pages = {1--9},
  pmid = {27056366},
  publisher = {BioMed Central},
  title = {{Cell-free circulating tumor DNA in cancer}},
  volume = {35},
  year = {2016}
}

@article{Cao2016,
  abstract = {Cerenkov luminescence imaging (CLI) can provide information of medical radionuclides used in nuclear imaging based on Cerenkov radiation, which makes it possible for optical means to image clinical radionuclide labeled probes. However, the exceptionally weak Cerenkov luminescence (CL) from Cerenkov radiation is susceptible to lots of impulse noises introduced by high energy gamma rays generating from the decays of radionuclides. In this work, a temporal median filter is proposed to remove this kind of impulse noises. Unlike traditional CLI collecting a single CL image with long exposure time and smoothing it using median filter, the proposed method captures a temporal sequence of CL images with shorter exposure time and employs a temporal median filter to smooth a temporal sequence of pixels. Results of in vivo experiments demonstrated that the proposed temporal median method can effectively remove random pulse noises induced by gamma radiation and achieve a robust CLI image.},
  author = {Cao, Xu and Li, Yang and Zhan, Yonghua and Chen, Xueli and Kang, Fei and Wang, Jing and Liang, Jimin},
  doi = {10.1155/2016/7948432},
  file = {:E$\backslash$:/Mendeley Papers/2016/BioMed Research International/2016 - BioMed Research International - Removing Noises Induced by Gamma Radiation in Cerenkov Luminescence Imaging Using a Temporal Medi.pdf:pdf},
  issn = {23146141},
  journal = {BioMed Research International},
  number = {Article ID 7948432},
  title = {{Removing Noises Induced by Gamma Radiation in Cerenkov Luminescence Imaging Using a Temporal Median Filter}},
  volume = {2016},
  year = {2016}
}

@article{Chen2016a,
  author = {Chen, Duofan and Liang, Jimin and Li, Yao and Qiu, Guanghui},
  doi = {10.1155/2016/4504161},
  file = {:E$\backslash$:/Mendeley Papers/2016/BioMed Research International/2016 - BioMed Research International - A sparsity-constrained preconditioned Kaczmarz reconstruction method for fluorescence molecular t.pdf:pdf},
  journal = {BioMed Research International},
  number = {Article ID 4504161},
  pages = {1--15},
  title = {{A sparsity-constrained preconditioned Kaczmarz reconstruction method for fluorescence molecular tomography}},
  volume = {2016},
  year = {2016}
}