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Search Results: 1 - 10 of 59105 matches for " Jinzhong Yang "
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A Hybrid Algorithm to Address Ambiguities in Deformable Image Registration for Radiation Therapy  [PDF]
Song Gao, Yongbin Zhang, Jinzhong Yang, Catherine H. Wang, Lifei Zhang, Laurence E. Court, Lei Dong
International Journal of Medical Physics,Clinical Engineering and Radiation Oncology (IJMPCERO) , 2012, DOI: 10.4236/ijmpcero.2012.12007
Abstract: We proposed the use of a hybrid deformable image registration approach that combines compact-support radial basis functions (CSRBF) spline registration with intensity-based image registration. The proposed method first uses the pre-viously developed image intensity-based method to achieve voxel-by-voxel correspondences over the entire image re-gion. Next, for those areas of inaccurate registration, a sparse set of landmark correspondences was defined for local deformable image registration using a multi-step CSRBF approach. This hybrid registration takes advantage of both intensity-based method for automatic processing of entire images and the CSRBF spline method for fine adjustment over specific regions. The goal of using this hybrid registration is to locally control the quality of registration results in specific regions of interest with minimal human intervention. The major applications of this approach in radiation ther-apy are for the corrections of registration failures caused by various imaging artifacts resulting in, low image contrast, and non-correspondence situations where an object may not be imaged in both target and source images. Both synthetic and real patient data have been used to evaluate this hybrid method. We used contours mapping to validate the accuracy of this method on real patient image. Our studies demonstrated that this hybrid method could improve overall registra-tion accuracy with moderate overhead. In addition, we have also shown that the multi-step CSRBF registration proved to be more effective in handling large deformations while maintaining the smoothness of the transformation than origi-nal CSRBF.
Passivity analysis of neutral fuzzy system with linear fractional uncertainty
Jun Yang,Wenpin Luo,Jinzhong Cui
International Journal of Intelligent Systems and Applications , 2011,
Abstract: In this paper, the passivity analysis of Takagi-Sugeno (T-S) fuzzy neutral system with interval time-varying delay and linear fractional parametric uncertainty is investigated. Based on the Lyapunov-Krasovskii functional and the free weighting matrix method, delay-dependent sufficient conditions for solvability of the passive problem are obtained in terms of Linear matrix inequalities (LMIs). Finally, a simulation example is provided to demonstrate effectiveness and applicability of the theoretical results.
Remote Sensing Monitoring of Changes in Soil Salinity: A Case Study in Inner Mongolia, China
Jingwei Wu,Bernard Vincent,Jinzhong Yang,Sami Bouarfa,Alain Vidal
Sensors , 2008, DOI: 10.3390/s8117035
Abstract: This study used archived remote sensing images to depict the history of changes in soil salinity in the Hetao Irrigation District in Inner Mongolia, China, with the purpose of linking these changes with land and water management practices and to draw lessons for salinity control. Most data came from LANDSAT satellite images taken in 1973, 1977, 1988, 1991, 1996, 2001, and 2006. In these years salt-affected areas were detected using a normal supervised classification method. Corresponding cropped areas were detected from NVDI (Normalized Difference Vegetation Index) values using an unsupervised method. Field samples and agricultural statistics were used to estimate the accuracy of the classification. Historical data concerning irrigation/drainage and the groundwater table were used to analyze the relation between changes in soil salinity and land and water management practices. Results showed that: (1) the overall accuracy of remote sensing in detecting soil salinity was 90.2%, and in detecting cropped area, 98%; (2) the installation/innovation of the drainage system did help to control salinity; and (3) a low ratio of cropped land helped control salinity in the Hetao Irrigation District. These findings suggest that remote sensing is a useful tool to detect soil salinity and has potential in evaluating and improving land and water management practices.
Schmeissneria: A missing link to angiosperms?
Xin Wang, Shuying Duan, Baoyin Geng, Jinzhong Cui, Yong Yang
BMC Evolutionary Biology , 2007, DOI: 10.1186/1471-2148-7-14
Abstract: In this paper, after careful SEM and light microscopic work, we report fossils with angiospermous traits of the Jurassic age. The fossils were collected from the Haifanggou Formation (middle Jurassic) in western Liaoning, northeast China. They include two female structures and an associated leaf on the same slab. One of the female structures is physically connected to the apex of a short shoot. The female organs are borne in pairs on short peduncles that are arranged along the axis of the female structure. Each of the female organs has a central unit that is surrounded by an envelope with characteristic longitudinal ribs. Each central unit has two locules completely separated by a vertical septum. The apex of the central unit is completely closed. The general morphology places these fossils into the scope of Schmeissneria, an early Jurassic genus that was previously attributed to Ginkgoales.Because the closed carpel is a character only found in angiosperms, the closed apex of the central unit suggests the presence of angiospermy in Schmeissneria. This angiospermous trait implies either a Jurassic angiosperm or a new seed plant group parallel to angiosperms and other known seed plants. As an angiosperm, the Liassic age (earliest Jurassic) of Schmeissneria microstachys would suggest an origin of angiosperms during the Triassic. Although still uncertain, this could have a great impact on our perspective of the history, diversity and systematics of seed plants and angiosperms.Angiosperms are the dominating plant group in current vegetation. They account for the majority of terrestrial primary production, demonstrate the highest diversity in the plant kingdom, and dominate highly diversified habitats [1-4]. The rapid radiation and diversification of angiosperms during the Cretaceous led to major ecological changes on the earth, the latter were a prerequisite for many critical evolutionary events [3] including the later evolution of human beings. However, the origin of th
Noise Removal of Spaceborne SAR Image Based on the FIR Digital Filter
Wei Zhang,Jinzhong Yang,Conghui Fang,Dongli Fan
Computer and Information Science , 2010, DOI: 10.5539/cis.v3n1p12
Abstract: The speckle effect inevitably exists in the image of the Synthetic Aperture Radar (SAR). The removal of the speckle noise is the necessary approach before automatic partition, classification, target detection and abstraction of other quantitative special information in the SAR image, so it is very meaningful to eliminate or furthest restrain the speckle noises when the spatial resolution of the image is not be reduced. In this paper, the FIR filter is used to remove the noise in the SAR image, and optimal filtering coefficient is selected through experiment and analysis in the filtering process. The results show that the FIR filter used to remove noises in the SAR image is better than other traditional filtering methods in keeping the radiolocation feature and restraining the speckle noises, and the filtering speed is quicker. At the same time, the selection of the filtering coefficient will largely influence the de-noising effect of the FIR filter.
Toward understanding the genetic basis of adaptation to high-elevation life in poikilothermic species: A comparative transcriptomic analysis of two ranid frogs, Rana chensinensis and R. kukunoris
Yang Weizhao,Qi Yin,Bi Ke,Fu Jinzhong
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-588
Abstract: Background Understanding how organisms adapt to high-elevation environments at a genome scale provides novel insights into the process of adaptive evolution. Previous studies have mainly focused on endothermic organisms, while poikilothermic species may have evolved different mechanisms to cope with high-elevation environments. In this context, we sequenced transcriptomes of a pair of closely related anuran species, Rana chensinensis and R. kukunoris, which inhabit respective low- and high-elevation habitats. By comparing the two transcriptomes, we identified candidate genes that may be involved in high-elevation adaption in poikilothermic species. Results Over 66 million sequence reads from each transcriptome were generated. A total of 41,858 and 39,293 transcripts for each species were obtained by de novo assembly. By comparing the orthologous transcripts, we identified 125 protein-coding genes that have likely experienced strong positive selection (Ka/Ks>1). In addition, 335 genes that may bear a signature of positive selection (1≥Ka/Ks>0.5) were also recognized. By considering their functions, fourteen candidate genes were determined to be likely involved in high-elevation adaptation, including two CYP genes, USP-1, and several others. Conclusions We identified a set of candidate genes that may have promoted adaptation of R. kukunoris to its high-elevation environment. These include several genes that have previously been associated with oxygen binding, response to UV radiation, and repair of free radical injury. Detailed molecular, physiological, and phenotypic studies are required to better understand the roles of these genes in improving the performance of R. kukunoris in a high-elevation environment. We have evidence for both convergent and divergent evolution between endothermic and poikilothemic species, but additional research across a wide range of organisms will be necessary to comprehend the complexity of high-elevation adaptation.
Transcriptome Profile of the Green Odorous Frog (Odorrana margaretae)
Liang Qiao, Weizhao Yang, Jinzhong Fu, Zhaobin Song
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0075211
Abstract: Transcriptome profiles provide a practical and inexpensive alternative to explore genomic data in non-model organisms, particularly in amphibians where the genomes are very large and complex. The odorous frog Odorrana margaretae (Anura: Ranidae) is a dominant species in the mountain stream ecosystem of western China. Limited knowledge of its genetic background has hindered research on this species, despite its importance in the ecosystem and as biological resources. Here we report the transcriptome of O. margaretae in order to establish the foundation for genetic research. Using an Illumina sequencing platform, 62,321,166 raw reads were acquired. After a de novo assembly, 37,906 transcripts were obtained, and 18,933 transcripts were annotated to 14,628 genes. We functionally classified these transcripts by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). A total of 11,457 unique transcripts were assigned to 52 GO terms, and 1,438 transcripts were assigned to 128 KEGG pathways. Furthermore, we identified 27 potential antimicrobial peptides (AMPs), 50,351 single nucleotide polymorphism (SNP) sites, and 2,574 microsatellite DNA loci. The transcriptome profile of this species will shed more light on its genetic background and provide useful tools for future studies of this species, as well as other species in the genus Odorrana. It will also contribute to the accumulation of amphibian genomic data.
Using Genes as Characters and a Parsimony Analysis to Explore the Phylogenetic Position of Turtles
Bin Lu, Weizhao Yang, Qiang Dai, Jinzhong Fu
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0079348
Abstract: The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a “genes as characters” approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog) and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara) but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis), similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as characters provides a convenient method for examining gene and genome evolution.
Motion of the Esophagus Due to Cardiac Motion
Jacob Palmer, Jinzhong Yang, Tinsu Pan, Laurence E. Court
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0089126
Abstract: When imaging studies (e.g. CT) are used to quantify morphological changes in an anatomical structure, it is necessary to understand the extent and source of motion which can give imaging artifacts (e.g. blurring or local distortion). The objective of this study was to assess the magnitude of esophageal motion due to cardiac motion. We used retrospective electrocardiogram-gated contrast-enhanced computed tomography angiography images for this study. The anatomic region from the carina to the bottom of the heart was taken at deep-inspiration breath hold with the patients' arms raised above their shoulders, in a position similar to that used for radiation therapy. The esophagus was delineated on the diastolic phase of cardiac motion, and deformable registration was used to sequentially deform the images in nearest-neighbor phases among the 10 cardiac phases, starting from the diastolic phase. Using the 10 deformation fields generated from the deformable registration, the magnitude of the extreme displacements was then calculated for each voxel, and the mean and maximum displacement was calculated for each computed tomography slice for each patient. The average maximum esophageal displacement due to cardiac motion for all patients was 5.8 mm (standard deviation: 1.6 mm, maximum: 10.0 mm) in the transverse direction. For 21 of 26 patients, the largest esophageal motion was found in the inferior region of the heart; for the other patients, esophageal motion was approximately independent of superior-inferior position. The esophagus motion was larger at cardiac phases where the electrocardiogram R-wave occurs. In conclusion, the magnitude of esophageal motion near the heart due to cardiac motion is similar to that due to other sources of motion, including respiratory motion and intra-fraction motion. A larger cardiac motion will result into larger esophagus motion in a cardiac cycle.
Enhancing $t\bar{t}hh$ production through CP-violating top-Higgs interaction at the LHC, ILC and a 100 TeV collider
Ning Liu,Yanming Zhang,Jinzhong Han,Bingfang Yang
Physics , 2015,
Abstract: The measurement of Higgs self-coupling is one of the most crucial physics goals at the future colliders. At the LHC, the di-Higgs production is a main way to measure the Higgs trilinear coupling. As a complementary to the di-Higgs production, $t \bar{t} hh$ process may open a new avenue to measure di-Higgs physics at the LHC and a future 100 TeV $pp$ collider or a high energy $e^+e^-$ collider since the extra $t\bar t$ in the final states may efficiently suppress the backgrounds. However, such a kind of process is also controlled by the top-Higgs coupling. In this work, we investigate the impact of CP-violating top-Higgs coupling on $t\bar{t}hh$ production at the LHC, ILC and a 100 TeV hadron collider under the current Higgs data. Within 2$\sigma$ Higgs data allowed parameter region, we find that the cross section of $t\bar{t}hh$ at the LHC-14 TeV, ILC-1 TeV and VHE-LHC/SPPC-100 TeV can be enhanced up to 2.1 times the SM predictions. The future precise measurement of Higgs coupling will reveal the nature of top-Higgs interaction and improve the sensitivity of the determination of Higgs self-coupling through $t\bar{t}hh$ production.
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