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31 October 2014, Volume 19 Issue 5 Previous Issue    Next Issue

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Segmentation of Haustral Folds and Polyps on Haustral Folds in CT Colonography Using Complementary Geodesic Distance Transformation XU Yan-ran (徐嫣然), ZHAO Jun*(赵俊) 2014, 19 (5):  513-520.  doi: 10.1007/s12204-014-1534-2 Abstract ( 601 )   Computer-aided detection (CAD) for CT colonography refers to a scheme that automatically detects polyps in CT images of colon. Current CAD schemes already have a relatively high sensitivity and a low false positive rate. However, misdiagnosis and missed diagnosis are still common to happen, mainly due to the existence of haustral folds (HFs). An innovative idea of segmenting semilunar HFs from the smooth colonic wall and then using different methods to detect polyps on HFs and those on the smooth colonic wall is proposed in this paper to reduce the false positives and false negatives caused by HFs. For the polyps on HFs, a novel segmentation method is specially developed based on complementary geodesic distance transformation (CGDT). The proposed method is tested on four different models and real CT data. The property of CGDT is proved and our method turns out to be effective for HF segmentation and polyp segmentation. The encouraging experimental results primarily show the feasibility of the proposed method and its potential to improve the detection performance of CAD schemes. References | Related Articles | Metrics

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Progress of Optically Encoded Microspheres for Multiplexed Assays ZHU Ying (朱莹), XU Hong (徐宏), GU Hong-chen*(古宏晨) 2014, 19 (5):  521-530.  doi: 10.1007/s12204-014-1535-1 Abstract ( 701 )   New initiatives put forward by clinical diagnosis require the development of technologies for high throughput screening (HTS) of multiple analytes. Suspension arrays have great advantages over the planar arraybased multiplexing assays, and the encoded bead is the key for providing multiplexing capability. Among various encoding strategies, optically encoded microspheres have been widely used while the number of codes is still limited. This review discusses the progress of optical encoding strategy from mainly three aspects, namely organic dyes, quantum dots (QDs) and surface-enhanced Raman scattering (SERS) active substrates. Emphases are put up on describing how these optical encoded microbeads are manufactured and the merits and demerits of different encoding materials are compared. References | Related Articles | Metrics

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Computer-Aided Detection for CT Colonography XU Yan-ran (徐嫣然), ZHAO Jun* (赵俊) 2014, 19 (5):  531-537.  doi: 10.1007/s12204-014-1536-0 Abstract ( 526 )   CT colonography (CTC) is a non-invasive screening technique for the detection of colorectal polyps, as an alternative to optical colonoscopy in clinical practice. Computer-aided detection (CAD) for CTC refers to a scheme which automatically detects colorectal polyps and masses in CT images of the colon. It has the potential to increase radiologists’ detection performance and greatly shorten the detection time. Over the years, technical developments have advanced CAD for CTC substantially. In this paper, key techniques used in CAD for polyp detection are reviewed. Illustrations about the performance of existing CAD schemes show their relatively high sensitivity and low false positive rate. However, these CAD schemes are still suffering from technical or clinical problems. Some existing challenges faced by CAD are also pointed out at the end of this paper. References | Related Articles | Metrics

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Improvement of Immunoassay Detection Sensitivity by Using Well-Defined Raspberry-Like Magnetic Microbeads as Carriers WANG Ye-fei (王叶菲), ZHANG Xin (张欣), XU Ping (徐平), GU Hong-chen (古宏晨), XU Hong* (徐宏) 2014, 19 (5):  538-543.  doi: 10.1007/s12204-014-1537-z Abstract ( 469 )   Well-defined raspberry-like magnetic microbeads (RMMBs) as immunoassay solid carriers were prepared by chemical covalent binding between Fe3O4 magnetic microspheres and SiO2 nanoparticles. These RMMBs were not as agglomerative as nano-sized magnetie particles (< 200 nm), which was an advangtage for high efficient magnetic separation. When compared to Fe3O4@SiO2 core-shell magnetic microbeads (CMMBs) with smooth surface, RMMBs exhibited stronger capacity to bind biomolecules. Limit of blank (LoB) and limit of detection (LoD) of HBsAg detection using RMMBs as carriers via chemiluminiscence immunoassay (CLIA) were 0.472 and 1.022 μg/L, respectively, showing a notable improvement compared with CMMBs whose LoB and LoD were 1.017 and 1.988 μg/L, respectively. All these indicated a great potential of RMMBs in immunoassay application. References | Related Articles | Metrics

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Unexpected Roles of Long Non-Coding RNAs in Cancer Biology QI Yinga (戚颖), KANG Ya-nia,b (康亚妮), ZHAO Xiao-donga,b* (赵晓东) 2014, 19 (5):  544-549.  doi: 10.1007/s12204-014-1538-y Abstract ( 616 )   Recent studies show that long non-coding RNAs (lncRNAs) play important roles in the regulation of various biological processes, including chromatin remodeling, dosage-compensation, imprinting, and epigenetic regulation. Aberrant expression of lncRNAs is involved in many complex human diseases, including cancer. In this review, we summarized recent progress on lncRNAs detection methodology with emphasis on their functions and potential implication in cancer diagnosis and therapy. References | Related Articles | Metrics

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Graphic Processing Unit Based Phase Retrieval and CT Reconstruction for Differential X-Ray Phase Contrast Imaging CHEN Xiao-qinga (陈晓庆), WANG Yu-jieb (王宇杰), SUN Jian-qia*(孙建奇) 2014, 19 (5):  550-554.  doi: 10.1007/s12204-014-1539-x Abstract ( 681 )   Compared with the conventional X-ray absorption imaging, the X-ray phase-contrast imaging shows higher contrast on samples with low attenuation coefficient like blood vessels and soft tissues. Among the modalities of phase-contrast imaging, the grating-based phase contrast imaging has been widely accepted owing to the advantage of wide range of sample selections and exemption of coherent source. However, the downside is the substantially larger amount of data generated from the phase-stepping method which slows down the reconstruction process. Graphic processing unit (GPU) has the advantage of allowing parallel computing which is very useful for large quantity data processing. In this paper, a compute unified device architecture (CUDA) C program based on GPU is introduced to accelerate the phase retrieval and filtered back projection (FBP) algorithm for grating-based tomography. Depending on the size of the data, the CUDA C program shows different amount of speed-up over the standard C program on the same Visual Studio 2010 platform. Meanwhile, the speed-up ratio increases as the size of data increases. References | Related Articles | Metrics

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Discriminant Analysis in the Study of Alzheimer’s Disease Using Feature Extractions and Support Vector Machines in Positron Emission Tomography with 18F-FDG SU Sai-sai1 (苏赛赛), CHEN Ke-wei1,2 (陈克非), HUANG Qiu1* (黄秋) 2014, 19 (5):  555-560.  doi: 10.1007/s12204-014-1540-4 Abstract ( 517 )   With more successful applications of advanced medical imaging technologies in clinical diagnosis, various analytic discriminant approaches, by seeking the imaging based characteristics of a given disease to achieve automatic diagnosis, gain greater attention in the medical community. However the existing computer-aided discriminant procedures for Alzheimer’s disease (AD) are yet to be improved for better identifying patients with mild cognitive impairment (MCI) from those with AD and those who are cognitively normal. In this work we present a computer assisted diagnosis approach by first statistically extracting characteristics from whole brain 2-deoxy-2-(18F)fluoro-D-glucose positron emission tomography (18F-FDG PET) images, and then using support vector machines for classification. Evaluations of the proposed procedure with patient data exhibit satisfactory accuracies in distinguishing AD from its early stage MCI, and normal controls. References | Related Articles | Metrics

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Review on the Interlimb Neural Coupling and Its Potential Usage in Walking Rehabilitation FANG Juan (方娟), XIE Le (谢叻), YANG Guo-yuan* (杨国源) 2014, 19 (5):  561-564.  doi: 10.1007/s12204-014-1541-3 Abstract ( 478 )   Human performs bipedal gait with synchronized arm swing. Apart from the observation that arm movement during gait is the outcome of a mechanical and energetic optimization, the synergetic upper and lower limb movement during gait is a neutrally coordinated motor output, that is, the interlimb movement is neutrally coupled. Patients with injuries to the central nervous system demonstrate the interlimb neural coupling. Researches on central pattern generator and the reflex studies reveal that the interlimb neural coupling is a quadrupedal heritage. Based on the theory of the interlimb neural coupling, both the upper and lower limbs should be practiced synchronously during regular gait training to promote walking rehabilitation for patients with gait disorders. Further development of a gait robotic system with synchronized arm swing is required to test the clinical application of the neural coupling in gait restoration. References | Related Articles | Metrics

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Direct Resolution of the Pitch of DNA on Positively Charged Lipid Bilayers by Frequency-Modulation AFM ZHANG Jin-jin1 (张金金), LVJun-hong1 (吕军鸿), SUN Jie-lin2,3 (孙洁林), HU Jun1 (胡钧),CZAJKOWSKY Daniel M2*, SHEN Yi2* (沈轶) 2014, 19 (5):  565-568.  doi: 10.1007/s12204-014-1542-2 Abstract ( 610 )   High resolution structural studies of DNA and DNA binding proteins by atomic force microscopy (AFM) require well-bound samples on suitably flat substrates. Adsorbing the DNA onto a positively charged supported lipid bilayer has previously been shown to be a potentially effective strategy for structural studies with AFM. Here, using our home-built frequency-modulation AFM (FM-AFM), we show that these bilayer substrates are only maximally effective for high resolution AFM when the samples are short, linear DNA, compared with circular plasmid DNA. We find that, with the former sample, the measured width of the DNA is about 2 nm, the known DNA diameter, and there is a clear height modulation along the length of the DNA with a periodicity of about 3.4 nm, in excellent agreement with the known pitch of the double helix. This sample preparation strategy is expected to enable higher resolution studies of DNA and DNA binding proteins with FM-AFM than that can presently be achieved. References | Related Articles | Metrics

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Novel Experimental Strategy for High Resolution AFM Imaging of Membrane-Associated Bacterial Toxins LUO Meng-lina (罗梦麟), LUO Meng-lina (罗梦麟), SHAO Zhi-fenga (邵志峰), SHEN Yia (沈轶),CZAJKOWSKY Daniel Ma*, SUN Jie-linb* (孙洁林) 2014, 19 (5):  569-573.  doi: 10.1007/s12204-014-1543-1 Abstract ( 552 )   Bacterial pore-forming toxins (PFTs) are essential virulence factors of many human pathogens. Knowledge of their structure within the membrane is critical for an understanding of their function in pathogenesis and for the development of useful therapy. Atomic force microscopy (AFM) has often been employed to structurally interrogate many membrane proteins, including PFTs, owing to its ability to produce sub-nanometer resolution images of samples under aqueous solution. However, an absolute prerequisite for AFM studies is that the samples are single-layered and closely-packed, which is frequently challenging with PFTs. Here, using the prototypical member of the cholesterol-dependent cytolysin family of PFTs, perfringolysin O (PFO), as a test sample, we have developed a simple, highly robust method that routinely produces clean, closely-packed samples across the entire specimen surface. In this approach, we first use a small Teflon well to prepare the supported lipid bilayer, remove the sample from the well, and then directly apply the proteins to the bilayer. For reasons that are not clear, bilayer preparation in the Teflon well is essential. We anticipate that this simple method will prove widely useful for the preparation of similar samples, and thereby enable AFM imaging of the greatest range of bacterial PFTs to the highest possible resolution. References | Related Articles | Metrics

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Genome-Wide Profiling Identifies Saccharomyces Cerevisiae Response in PKC-SLT2 Signaling and Glycogen Metabolic Pathways to Antifungal Compound Calcofluor White ZHOU Juana(周娟), HU Chuan-shengb (胡传圣), LI Xiao-lina (李晓林),CHENG Mingb (程酩), GUO Yanb* (郭妍), SHAO Zhi-fengb (邵志峰) 2014, 19 (5):  574-579.  doi: 10.1007/s12204-014-1544-0 Abstract ( 438 )   Fungal infection remains a major problem worldwide, yet treatment options are limited owing to the lack of effective drugs, the significant toxicity of available compounds, and the emergence of drug resistance. The low toxicity of calcofluor white (CFW) is an attractive antifungal compound for its known inhibitive effects on trichophyton rubrum and candida albicans growth. However, the efficacy of CFW is limited in most cases. In order to search for effective means to improve its efficacy, using saccharomyces cerevisiae as a model, we have used microarrays to examine the cell’s response when treated with CFW on the genome scale. We found that both the PKC-SLT2 (i.e, protein kinase C-mitogen activated protein kinase) and the glycogen metabolic pathways are activated upon CFW treatment. These results suggest that the key components in these pathways could be targeted by other drugs to counter the cell’s compensative response, thus to further substantiate the inhibitive effect of CFW on fungal growth, which may lead to treatment regimens with improved efficacy of this compound in clinical applications. References | Related Articles | Metrics

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5-Cap Selection Methods and Their Application in Full-Length cDNA Library Construction and Transcription Start Site Profiling BAI Ling* (白玲), WANG Qi (王琪), LI Hong-mei (李红梅),CHENG Ming (程酩), ZHANG Ning-bo (张宁波), LI Hua* (李华) 2014, 19 (5):  580-586.  doi: 10.1007/s12204-014-1545-z Abstract ( 614 )   With the accomplishment of the genome draft sequences, identification of functional elements in genome has become an urgent task. Full-length cDNAs provide an important resource for gene identification and their precise structural feature determination. It also provides a basis for genomic element definition. As many regulatory elements are around transcription start sites (TSSs), precise localization of TSSs in the genome becomes a critical step for identifying the associated core promoters. Massive parallel snapshot of TSSs at a particular time under a specific experimental condition makes it possible to globally analyze important regulatory elements around TSSs and further construct transcriptional regulatory networks. In this paper, we first reviewed two important full-length cDNA cloning techniques: cap-trapper technique and oligo-capping technique. Then, we introduced deepCAGE, a cap-trapper and deep sequencing-based TSS profiling technique, and its applications in the research of transcriptional regulation. References | Related Articles | Metrics

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Review on Tactile Sensory Feedback of Prosthetic Hands for the Upper-Limb Amputees by Sensory Afferent Stimulation CHAI Guo-hong (柴国鸿), SUI Xiao-hong*(隋晓红), LI Peng(李鹏),LIU Xiao-xuan (刘小旋), LAN Ning (蓝宁) 2014, 19 (5):  587-591.  doi: 10.1007/s12204-014-1546-y Abstract ( 652 )   Loss of sensory function for upper-limb amputees inevitably devastates their life qualities, and lack of reliable sensory feedback is the biggest defect to sophisticated prosthetic hands, greatly hindering their usefulness and perceptual embodiment. Thus, it is extremely necessary to accomplish an intelligent prosthetic hand with effective tactile sensory feedback for an upper-limb amputee. This paper presents an overview of three kinds of existing sensory feedback approaches, including cutaneous mechanical stimulation (CMS), transcutaneous electrical nerve stimulation (TENS) and direct peripheral nerve electrical stimulation (DPNES). The emphasis concentrates on major scientific achievements, advantages and disadvantages. The TENS on the skin areas with evoked finger sensation (EFS) at upper-limb amputees’ residual limbs might be one of the most promising approaches to realize natural sensory feedback. References | Related Articles | Metrics

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Influence of GABAergic Pathway on Retinal Adaptation-Related Response Changes FENG Xin-yang (冯新阳), XIAO Lei (肖雷), GONG Hai-qing (龚海庆), ZHANG Pu-ming (张溥明), LIANG Pei-ji* (梁培基) 2014, 19 (5):  592-599.  doi: 10.1007/s12204-014-1547-x Abstract ( 568 )   Retinal ganglion cells (RGCs) exhibit adaptive changes in response to sustained light stimulation, which include decrease in firing rate, tendency to shrink in receptive field (RF) size and reduction in synchronized activities. Gamma-aminobutyric acid-ergic (GABAergic) pathway is an important inhibitory pathway in retina. In the present study, the effects of GABAergic pathway on the contrast adaptation process of bullfrog RGCs were studied using multi-electrode recording technique. It was found that the application of bicuculline (BIC), a gamma-aminobutyric acid A (GABAA) receptor antagonist, caused a number of changes in the RGCs’ response characteristics, including attenuation in adaptation-dependent firing rate decrease and the adaptation-dependent weakening in synchronized activities between adjacent neuron-pairs, whereas intensified the adaptation-dependent RF size shrinkage. These results suggest that GABAA receptors are involved in the modulation of the firing activity and synchronized activities in contrast adaptation process of the RGCs, whereas the adaptation-related RF property changes involve more complicated mechanisms. References | Related Articles | Metrics

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Target-to-Background Separation for Spectral Unmixing in In-Vivo Fluorescence Imaging ZHAO Yong (赵勇), HU Cheng (胡程), PENG Jin-liang*(彭金良), QIN Bin-jie* (秦斌杰) 2014, 19 (5):  600-611.  doi: 10.1007/s12204-014-1548-9 Abstract ( 564 )   We present a novel fluorescence spectral unmixing based on target-to-background separation preprocessing, which effectively separates the multi-target fluorescence from all background autofluorescence (BF) without any hardware-based BF acquisition and tissue specific BF estimation. Specifically, we first enhance the intrinsic accumulation contrast in target-to-background fluorescence using h-dome transformation; then separate multi-target fluorescence areas from the background in sparse multispectral data utilizing kernel maximum autocorrelation factor analysis; we further use fast marching-based image inpainting method to patch up the removed target fluorescence areas and reconstruct the multispectral BF; with the BF matrix being subtracted from the original data, the multi-target fluorophores are easily unmixed from the subtracted data using multivariate curve resolution-alternating least squares method. In two preliminary in-vivo experiments, the proposed method demonstrated excellent performance to unmix multi-target fluorescences while other state-of-art unmixing methods failed to get desired results. References | Related Articles | Metrics

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Re-evaluation of the Widely Applied Force-Frequency Relation for Frequency-Modulation AFM Under Solution HE Jian-feng1 (何健锋), HU Jun2 (胡钧), SUN Jie-lin3 (孙洁林), CZAJKOWSKY Daniel M1* 2014, 19 (5):  612-616.  doi: 10.1007/s12204-014-1549-8 Abstract ( 420 )   Frequency-modulation atomic force microscopy (FM-AFM) is a highly versatile tool for surface science. Besides imaging surfaces, FM-AFM is capable of measuring interactions between the AFM probe and the surface with high sensitivity, which can provide chemical information at sub-nanometer resolution. This is achieved by deconvoluting the frequency shift, which is directly measured in experiments, into the force between the probe and sample. At present, the widely used method to perform this deconvolution has been shown to be accurate under high quality (high-Q) factor vacuum conditions. However, under low quality (low-Q) factor conditions, such as in solution, it is not clear if this method is valid. A previous study apparently verified this relation for experiments in solution by comparing the force calculated by this equation with that obtained in separate experiments using the surface force apparatus (SFA). Here we show that, in solution, a more direct comparison of the force calculated by this relation with that directly measured by the cantilever deflection in AFM reveals significant differences, both qualitative and quantitative. However, we also find that there are complications that hinder this comparison. Namely, while contact with the surface is clear in the direct measurements (including the SFA data), it is less certain in the FM-AFM case. Hence, it is not clear if the two methods are measuring the same tip-sample distance regimes. Thus, our results suggest that a more thorough verification of this relation is required, as application of this formulation for experiments in solution may not be valid. References | Related Articles | Metrics

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Kinect-Based Automatic Spatial Registration Framework for Neurosurgical Navigation ZHANG Li-xia1 (张丽霞), ZHANG Shao-ting2 (张少霆), XIE Hong-zhi3 (谢洪智),ZHUANG Xia-hai4 (庄吓海), GU Li-xu1* (顾力栩) 2014, 19 (5):  617-623.  doi: 10.1007/s12204-014-1550-2 Abstract ( 639 )   As image-guided navigation plays an important role in neurosurgery, the spatial registration mapping the pre-operative images with the intra-operative patient position becomes crucial for a high accurate surgical output. Conventional landmark-based registration requires expensive and time-consuming logistic support. Surface-based registration is a plausible alternative due to its simplicity and efficacy. In this paper, we propose a comprehensive framework for surface-based registration in neurosurgical navigation, where Kinect is used to automatically acquire patient’s facial surface in a real time manner. Coherent point drift (CPD) algorithm is employed to register the facial surface with pre-operative images (e.g., computed tomography (CT) or magnetic resonance imaging (MRI)) using a coarse-to-fine scheme. The spatial registration results of 6 volunteers demonstrate that the proposed framework has potential for clinical use. References | Related Articles | Metrics

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Robust and Real-Time Guidewire Simulation Based on Kirchhoff Elastic Rod for Vascular Intervention Training LUO Mai-sheng1 (罗买生), XIE Hong-zhi2 (谢洪智), XIE Le3 (谢叻),CAI Ping4 (蔡萍), GU Li-xu1* (顾力栩) 2014, 19 (5):  624-629.  doi: 10.1007/s12204-014-1551-1 Abstract ( 565 )   Virtual reality (VR) based vascular intervention training is a fascinating innovation, which helps trainees develop skills in safety remote from patients. The vascular intervention training involves the use of flexible tipped guidewires to advance diagnostic or therapeutic catheters into a patient’s vascular anatomy. In this paper, a real-time physically-based modeling approach is proposed to simulate complicated behaviors of guidewires and catheters based on Kirchhoff elastic rod. The slender body of guidewire and catheter is simulated using more efficient special case of naturally straight, isotropic Kirchhoff rods, and the short flexible tip composed of straight or angled design is modeled using more complex generalized Kirchhoff rods. We derive the equations of motion for guidewire and catheter with continuous elastic energy, and then they were discretized using a linear implicit scheme that guarantees stability and robustness. In addition, we apply a fast-projection method to enforce the inextensibility of guidewire and catheter, while an adaptive sampling algorithm is implemented to improve the simulation efficiency without reducing accuracy. Experimental results reveal that our guidewire simulation method is both robust and efficient in a real-time performance. References | Related Articles | Metrics

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Lesion Segmentation and Identification of Breast Tumor on Dynamic Contrast-Enhanced Magnetic Resonance Imaging MA Wen-jun1 (马文军), HONG Rong-rong2 (洪荣荣), YE Shao-zhen2 (叶少珍), YANG Yue3 (杨月),LI Yue-hua3 (李跃华), CHEN Li4, ZHANG Su1* (张素) 2014, 19 (5):  630-635.  doi: 10.1007/s12204-014-1552-0 Abstract ( 658 )   Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) can show subtle lesion morphology, improve the display of lesion definitions, and objectively reflect the blood supply of breast tumors; it can also reflect different strengthening patterns of normal tissues and lesion areas after medical tracer injection. DCE-MRI has become an important basis for the clinical diagnosis of breast cancer. To DCE-MRI data acquired from several hospitals across multiple provinces, a series of in-silico computational methods were applied for lesion segmentation and identification of breast tumor in this paper. The image segmentation methods include Otsu segmentation of subtraction images, signal-interference-ratio segmentation method and an improved variational level set method, each has its own application scope. After that, the distribution of benign and malignant in lesion region is identified based on three-time-point theory. From the experiment, the analysis of DCE-MRI data of breast tumor can show the distribution of benign and malignant in lesion region, provide a great help for clinicians to diagnose breast cancer more expediently and lay a basis for medical diagnosis and treatment planning. References | Related Articles | Metrics

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Tribological Behavior of Polytetrafluoroethylene Coatings Based on LY12 Substrates in the Space Environment YUAN Xing-dong1* (袁兴栋), LIU Yong2 (刘勇), YANG De-zhuang2 (杨德庄), HE Shi-yu2 (何世禹) 2014, 19 (5):  636-640.  doi: 10.1007/s12204-014-1553-z Abstract ( 482 )   The spacecraft space radiation environment was simulated by 60Co source. The polytetrafluoroethylene (PTFE) coatings were fabricated on LY12 substrates. And the effect of gamma (γ) irradiation on the tribological behavior of PTFE coatings under vacuum conditions was investigated. Results indicate that the radiation dose has insignificant effect on the friction coefficient of PTFE coatings, and the wear of PTFE coatings reduces with the increase of gamma dose. As the gamma dose was 100 kGy, the friction coefficient of the PTFE coatings first increased with the increase of sliding velocity and then decreased, and the wear of the PTFE coatings decreased with the increase of sliding speed. As the gamma dose was 100 kGy, the friction coefficient of the PTFE coatings first decreased with the increase of load and then increased, and the wear rate of PTFE coatings increased with the increase of load. Scanning electron microscope was utilized. References | Related Articles | Metrics