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Biomedical subjects

Y Chen

Publications and source records attributed to Y Chen.

At least 217 records · Page 12Linked to original sources
PubMed2003

A quality assurance phantom for IMRT dose verification.

This paper investigates a quality assurance (QA) phantom specially designed to verify the accuracy of dose distributions and monitor units (MU) calculated by clinical treatment planning optimization systems and by the Monte Carlo method for intensity-modulated radiotherapy (IMRT). The QA phantom is a PMMA cylinder of 30 cm diameter and 40 cm length with various bone and lung inserts. A procedure (and formalism) has been developed to measure the absolute dose to water in the PMMA phantom. Another cylindrical phantom of the same dimensions, but made of water, was used to confirm the results obtained with the PMMA phantom. The PMMA phantom was irradiated by 4, 6 and 15 MV photon beams and the dose was measured using an ionization chamber and compared to the results calculated by a commercial inverse planning system (CORVUS, NOMOS, Sewickley, PA) and by the Monte Carlo method. The results show that the dose distributions calculated by both CORVUS and Monte Carlo agreed to within 2% of dose maximum with measured results in the uniform PMMA phantom for both open and intensity-modulated fields. Similar agreement was obtained between Monte Carlo calculations and measured results with the bone and lung heterogeneity inside the PMMA phantom while the CORVUS results were 4% different. The QA phantom has been integrated as a routine QA procedure for the patient's IMRT dose verification at Stanford since 1999.

Equipment Design↗
PubMed2003

Disappearance of back-to-back high-pT hadron correlations in central Au+Au collisions at sqrt[s NN ] =200 GeV.

Azimuthal correlations for large transverse momentum charged hadrons have been measured over a wide pseudorapidity range and full azimuth in Au+Au and p+p collisions at sqrt[s(NN)]=200 GeV. The small-angle correlations observed in p+p collisions and at all centralities of Au+Au collisions are characteristic of hard-scattering processes previously observed in high-energy collisions. A strong back-to-back correlation exists for p+p and peripheral Au+Au. In contrast, the back-to-back correlations are reduced considerably in the most central Au+Au collisions, indicating substantial interaction as the hard-scattered partons or their fragmentation products traverse the medium.

Journal Article↗
PubMed2003

Azimuthal anisotropy and correlations in the hard scattering regime at RHIC.

Azimuthal anisotropy (v(2)) and two-particle angular correlations of high p(T) charged hadrons have been measured in Au+Au collisions at sqrt[s(NN)]=130 GeV for transverse momenta up to 6 GeV/c, where hard processes are expected to contribute significantly. The two-particle angular correlations exhibit elliptic flow and a structure suggestive of fragmentation of high p(T) partons. The monotonic rise of v(2)(p(T)) for p(T)<2 GeV/c is consistent with collective hydrodynamical flow calculations. At p(T)>3 GeV/c, a saturation of v(2) is observed which persists up to p(T)=6 GeV/c.

Journal Article↗
PubMed2003

Ensembl 2002: accommodating comparative genomics.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

Animals↗
PubMed2003

Towards understanding language organisation in the brain using fMRI.

Functional magnetic resonance imaging (fMRI), which allows non-invasive mapping of human cognitive functions, has become an important tool for understanding language function. An understanding of component processes and sources of noise in the images is contributing to increased confidence in the reproductability of studies. This allows clinical applications, e.g., for pre-surgical lateralisation of language functions in patients with temporal lobe epilepsy. fMRI is a sensitive method for mapping regions involved in language functions. We recently have applied it to study the effect of word surface form on reading with a comparison of responses to Chinese characters or alphabetical Pinyin. Interpretation of fMRI activations must be made with caution; fMRI suggests task-associated activation, but does not independently confirm that such activity is necessary. However, complementary studies can be performed using transcranial magnetic stimulation (TMS), which can be used to interfere with brain activity in a specific region transiently for characterisation of the behavioural effects. We describe how TMS combined with fMRI has confirmed a role for the left inferior frontal cortex in semantic processing.

Asian People↗
PubMed2003

A new & robust information theoretic measure and its application to image alignment.

In this paper we develop a novel measure of information in a random variable based on its cumulative distribution that we dub cumulative residual entropy (CRE). This measure parallels the well known Shannon entropy but has the following advantages: (1) it is more general than the Shannon Entropy as its definition is valid in the discrete and continuous domains, (2) it possess more general mathematical properties and (3) it can be easily computed from sample data and these computations asymptotically converge to the true values. Based on CRE, we define the cross-CRE (CCRE) between two random variables, and apply it to solve the image alignment problem for parameterized (3D rigid and affine) transformations. The key strengths of the CCRE over using the mutual information (based on Shannon's entropy) are that the former has significantly larger tolerance to noise and a much larger convergence range over the field of parameterized transformations. We demonstrate these strengths via experiments on synthesized and real image data.

Algorithms↗
PubMed2003

A constrained variational principle for direct estimation and smoothing of the diffusion tensor field from DWI.

In this paper, we present a novel constrained variational principle for simultaneous smoothing and estimation of the diffusion tensor field from diffusion weighted imaging (DWI). The constrained variational principle involves the minimization of a regularization term in an LP norm, subject to a nonlinear inequality constraint on the data. The data term we employ is the original Stejskal-Tanner equation instead of the linearized version usually employed in literature. The original nonlinear form leads to a more accurate (when compared to the linearized form) estimated tensor field. The inequality constraint requires that the nonlinear least squares data term be bounded from above by a possibly known tolerance factor. Finally, in order to accommodate the positive definite constraint on the diffusion tensor, it is expressed in terms of cholesky factors and estimated. variational principle is solved using the augmented Lagrangian technique in conjunction with the limited memory quasi-Newton method. Both synthetic and real data experiments are shown to depict the performance of the tensor field estimation algorithm. Fiber tracts in a rat brain are then mapped using a particle system based visualization technique.

Algorithms↗
PubMed2003

Antioxidant properties of the vasoactive endocannabinoid, 2-arachidonoyl glycerol (2-AG).

Reactive oxygen species (ROS) were shown to play a role in altering blood-brain barrier (BBB) permeability and formation of brain edema induced by trauma and/or ischemia. 2-arachidonoyl glycerol (2-AG), a novel, potent vasodilatory and cytoprotective endocannabinoid has been implicated to act as an antioxidative agent. This study examines: 1) the possible 2-AG modulation of BBB injury and edema formation induced by closed head injury (CHI); and 2) comparable effects between 2-AG and 4-hydroxy-2,2,6,6-tetramethylpiperidine-N-oxyl (TPL), a known antioxidant nitroxide on endothelial Ca2+ and cytoskeletal responses to H2O2 (ROS). 2-AG treatment reduced the CHI-induced increase in BBB permeability and brain edema. The endothelial H2O2-stimulated Ca2+ mobilization and cytoskeleton (vimentin) rearrangement was modified by either 2-AG or TPL. These findings provide evidence of 2-AG antioxidant activity and are consistent with the involvement of ROS in the pathomechanism of CHI-induced BBB injury and brain edema.

Animals↗
PubMed2003

Multiple deep-seated cavernomas in the third ventricle, hypothalamus and thalamus.

BACKGROUND: Cavernomas are rarely located in the third ventricle, hypothalamus, or thalamus. In this report, we present our experience managing a patient with three cavernomas, one each in the floor of the third ventricle, hypothalamus, and left thalamus. CASE PRESENTATION: This 62-year-old woman had had an unsteady gait and weakness of both legs for six months. Magnetic resonance imaging (MRI) revealed multiple intracranial tumours in the third ventricle, hypothalamus, and left thalamus. The third ventricle tumour was found to be a cavernoma by intra-operative endoscopic examination and then was excised via a transcortical, transventricular approach. Pathology revealed a cavernoma. The other two tumours were assumed to be cavernomas because of their MRI features. Three days after surgery, the patient developed right hemiparesis and disturbance of consciousness. Computed tomography revealed a left thalamic haemorrhage. After conservative treatment, her conscious level gradually recovered and she could walk with support seven months after surgery. INTERPRETATION: Our experience with this rare case of multiple, deep-seated cavernomas suggests that management of such patients requires specific consideration of the clinical manifestations, location, size, and previous bleeding history.

Brain Neoplasms↗
PubMed2003

Protective effect of ginsenoside Rg1 on MPP+-induced apoptosis in SHSY5Y cells.

The neuroprotective mechanism of Rg1 was studied in this paper by means of its obvious anti-apoptotic effect on human SHSY5Y cells. SHSY5Y cells were treated with MPP+ (1-methyl-4-phenyl-pyridinium) for 72 hours to induce apoptosis. During the apoptosis, production of reactive oxygen species (ROS), activation of c-Jun N-terminal kinase (JNK) and activation of caspase-3 were observed. The results showed that the signal transduction pathway of MPP+-induced apoptosis might be ROS to JNK, then to caspase-3. MPP+-induced apoptosis in SHSY5Y cells was obviously inhibited in both NAC (N-acetylcysteine) pretreated groups and Rg1 pretreated groups. Meanwhile, compared to that of the controls, our results showed decreased level of ROS, less JNK activity and lower expression of cleaved caspase-3 in pretreated NAC groups and in Rg1 pretreated groups. The protection by Rg1 might be mediated by removing of ROS. The removal of ROS might inhibit the activity of JNK and the expression of cleaved caspase-3. These results suggest that ginsenoside Rg1 may take effect through its anti-apoptotic activity in neurodegenerative diseases.

1-Methyl-4-phenylpyridinium↗
PubMed2003

Gene expression profiles in human non-small and small-cell lung cancers.

Suppression subtractive hybridisation (SSH) was performed comparing normal bronchial epithelial cells with a lung squamous cell carcinoma (SCC) and a metastatic small-cell lung carcinoma (SCLC). The sequence analysis of four cDNA libraries revealed 869 individual sequences. Of these, 342 were tested using northern blots of lung cancer cell lines representing the three major subtypes (SCC, adenocarcinoma, SCLC) which confirmed the differential expression of 236 cDNAs. The extended analysis of 31 randomly chosen fragments confirmed the validity of the approach to identify genes associated with lung cancer development. Additionally, five novel full-length cDNA were isolated encoding the microtubule-associated proteins 1A/1B light chain 3, the epithelial V-like antigen 1 (EVA1), the GTP-binding protein SAR1, a new member of the S100-type calcium binding protein family and a new homeobox-containing gene.

Blotting, Northern↗
PubMed2003

Image registration via level-set motion: applications to atlas-based segmentation.

Image registration is an often encountered problem in various fields including medical imaging, computer vision and image processing. Numerous algorithms for registering image data have been reported in these areas. In this paper, we present a novel curve evolution approach expressed in a level-set framework to achieve image intensity morphing and a simple non-linear PDE for the corresponding coordinate registration. The key features of the intensity morphing model are that (a) it is very fast and (b) existence and uniqueness of the solution for the evolution model are established in a Sobolev space as opposed to using viscosity methods. The salient features of the coordinate registration model are its simplicity and computational efficiency. The intensity morph is easily achieved via evolving level-sets of one image into the level-sets of the other. To explicitly estimate the coordinate transformation between the images, we derive a non-linear PDE-based motion model which can be solved very efficiently. We demonstrate the performance of our algorithm on a variety of images including synthetic and real data. As an application of the PDE-based motion model, atlas based segmentation of hippocampal shape from several MR brain scans is depicted. In each of these experiments, automated hippocampal shape recovery results are validated via manual "expert" segmentations.

Adult↗
PubMed2003

Dural metastasis in patients with malignant neoplasm and chronic subdural hematoma.

OBJECTIVES: Dural metastasis associated with chronic subdural hematoma (CSH) is rare in patients with malignant neoplasm. In this study, biopsy of the dura and cytological examination of the subdural hematoma was performed for patients with malignant neoplasm and chronic subdural hematoma to investigate the association of dural metastasis and CSH. MATERIALS AND METHODS: Four patients with malignant neoplasm (one breast, one lung, and one colon cancers, and one lymphoma) were diagnosed with CSH. Biopsy of the dura and cytological examination of the subdural fluid were performed for each of these patients. RESULTS: Pathological examination of the dura revealed metastasis for two patients (one lymphoma and one breast cancer), with no specific change except neomembrane formation revealed for the dura of the other two patients. The cytology study was negative for all four patients. All these four patients died within 10 days of the operation; one from recurrent subdural hematoma, and three from infection. CONCLUSION: The results suggest that dural metastasis should be considered in patients with malignant neoplasm and CSH. Further, the prognosis for patients with malignant neoplasm and CSH may be poor because of systemic metastasis and the side-effects of chemotherapy.

Brain Neoplasms↗
PubMed2003

Gene therapy for new bone formation using adeno-associated viral bone morphogenetic protein-2 vectors.

Previous reports have suggested that bone morphogenetic protein (BMP) gene therapy could be applied for in vivo bone regeneration. However, these studies were conducted either using immunodeficient animals because of immunogenicity of adenovirus vectors, or using ex vivo gene transfer technique, which is much more difficult to handle. Adeno-associated virus (AAV) is a replication-defective virus without any association with immunogenicity and human disease. This study was conducted to investigate whether orthotopic new bone formation could be induced by in vivo gene therapy using AAV-based BMP2 vectors. To test the feasibility of this approach, we constructed an AAV vector carrying human BMP2 gene. Mouse myoblast cells (C2C12) transduced with this vector could produce and secrete biologically active BMP2 protein and induce osteogenic activity, which was confirmed by ELISA and alkaline phosphatase activity assay. For in vivo study, AAV-BMP2 vectors were directly injected into the hindlimb muscle of immunocompetent Sprague-Dawley rats. Significant new bone under X-ray films could be detected as early as 3 weeks postinjection. The ossification tissue was further examined by histological and immunohistochemical analysis. This study is, to our knowledge, the first to establish the feasibility of AAV-based BMP2 gene therapy for endochondral ossification in immunocompetent animals.

Animals↗