Biomedical subjects

Chunlei Liu

Publications and source records attributed to Chunlei Liu.

16 recordsLinked to original sources

PubMed2007

Augmented generalized SENSE reconstruction to correct for rigid body motion.

The correction of motion artifacts continues to be a significant problem in MRI. In the case of uncooperative patients, such as children, or patients who are unable to remain stationary, the accurate determination and correction of motion artifacts becomes a very important prerequisite for achieving good image quality. The application of conventional motion-correction strategies often produces inconsistencies in k-space data. As a result, significant residual artifacts can persist. In this work a formalism is introduced for parallel imaging in the presence of motion. The proposed method can improve overall image quality because it diminishes k-space inconsistencies by exploiting the complementary image encoding capacity of individual receiver coils. Specifically, an augmented version of an iterative SENSE reconstruction is used as a means of synthesizing the missing data in k-space. Motion is determined from low-resolution navigator images that are coregistered by an automatic registration routine. Navigator data can be derived from self-navigating k-space trajectories or in combination with other navigation schemes that estimate patient motion. This correction method is demonstrated by interleaved spiral images collected from volunteers. Conventional spiral scans and scans corrected with proposed techniques are shown, and the results illustrate the capacity of this new correction approach.

Algorithms↗

PubMed2006

CDD: a conserved domain database for interactive domain family analysis.

The conserved domain database (CDD) is part of NCBI's Entrez database system and serves as a primary resource for the annotation of conserved domain footprints on protein sequences in Entrez. Entrez's global query interface can be accessed at http://www.ncbi.nlm.nih.gov/Entrez and will search CDD and many other databases. Domain annotation for proteins in Entrez has been pre-computed and is readily available in the form of 'Conserved Domain' links. Novel protein sequences can be scanned against CDD using the CD-Search service; this service searches databases of CDD-derived profile models with protein sequence queries using BLAST heuristics, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. Protein query sequences submitted to NCBI's protein BLAST search service are scanned for conserved domain signatures by default. The CDD collection contains models imported from Pfam, SMART and COG, as well as domain models curated at NCBI. NCBI curated models are organized into hierarchies of domains related by common descent. Here we report on the status of the curation effort and present a novel helper application, CDTree, which enables users of the CDD resource to examine curated hierarchies. More importantly, CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies.

Amino Acid Sequence↗

PubMed2006

Enhanced immunogenicity of heat shock protein 70 peptide complexes from dendritic cell-tumor fusion cells.

We have developed a molecular chaperone-based tumor vaccine that reverses the immune tolerance of cancer cells. Heat shock protein (HSP) 70 extracted from fusions of dendritic (DC) and tumor cells (HSP70.PC-F) possess superior properties such as stimulation of DC maturation and T cell proliferation over its counterpart from tumor cells. More importantly, immunization of mice with HSP70.PC-F resulted in a T cell-mediated immune response including significant increase of CD8 T cells and induction of the effector and memory T cells that was able to break T cell unresponsiveness to a nonmutated tumor Ag and provide protection of mice against challenge with tumor cells. By contrast, the immune response to vaccination with HSP70-PC derived from tumor cells is muted against such nonmutated tumor Ag. HSP70.PC-F complexes differed from those derived from tumor cells in a number of key manners, most notably, enhanced association with immunologic peptides. In addition, the molecular chaperone HSP90 was found to be associated with HSP70.PC-F as indicated by coimmunoprecipitation, suggesting ability to carry an increased repertoire of antigenic peptides by the two chaperones. Significantly, activation of DC by HSP70.PC-F was dependent on the presence of an intact MyD88 gene, suggesting a role for TLR signaling in DC activation and T cell stimulation. These experiments indicate that HSP70-peptide complexes (PC) derived from DC-tumor fusion cells have increased their immunogenicity and therefore constitute an improved formulation of chaperone protein-based tumor vaccine.

Animals↗

PubMed2005

Assessment of fusion cells from patient-derived ovarian carcinoma cells and dendritic cells as a vaccine for clinical use.

PURPOSE: To evaluate a protocol that allowed the successful generation of DC and OVCA cells, fusion of these two cell types and assessment of stimulatory ability of the fusion cells for clinical use. PATIENTS AND METHODS: Ovarian cancer (OVCA) cells and dendritic cells (DC) were isolated or generated from 22 patients with OVCA and subsequently fused with PEG. The stimulatory ability of fusion cells including T cell proliferation and induction of cytotocic T lymphocytes (CTL) was assessed. In addition, the impact of radiation, freezing and thawing of the fusion cells was evaluated. RESULTS: OVCA cells derived from 22 patients were successfully fused with autologous DC. The created heterokaryons expressed tumor-associated antigens, such as MUC1 and CA-125, and DC-derived MHC class II and costimulatory molecules. The fusion cells were functional in stimulating the proliferation of autologous T cells. In addition, CD4 and CD8 T cells derived from patients with ovarian cancer were stimulated by fusion cells and produced IFN-gamma as demonstrated with intracellular staining. Significantly, T cells primed by fusion cells produced MHC class I-dependent lysis of autologous ovarian tumor cells. One cycle of fusion-cell stimulation can maintain the CTL activity up to 25 days. CONCLUSIONS: The fusion of human OVCA cells and DC created immunogenic cells capable of stimulating CD4 and CD8 T cells. The effects of the processes required for preparing a vaccine for clinical use, including freezing and thawing and irradiation, do not interfere with the immunogenic properties of the fusion cells.

CD4-Positive T-Lymphocytes↗

PubMed2005

Induction of impaired antitumor immunity by fusion of MHC class II-deficient dendritic cells with tumor cells.

To dissect the role of Ag presentation through MHC class I and/or II pathways by dendritic cell (DC)-tumor fusion cells, we have created various types of DC-tumor fusion cells by alternating fusion cell partners. Fusions of MC38/MUC1 carcinoma cells with DC from wild-type (WT-DC), MHC class I knockout (IKO-DC), class II knockout (IIKO-DC), or class I and II knockout (I/IIKO-DC) mice created WTDC-fusion cells (FC), IKO-FC, IIKO-FC, and I/IIKO-FC, respectively. MHC class II- and MUC1-positive fusion cells were constructed by fusion of B16/MUC1 melanoma cells with IKO-DC (IKO/B16-FC). Immunization of MUC1 transgenic mice with 5 x 10(5) WTDC-FC, IKO-FC, IIKO-FC, or I/IIKO-FC provided 100, 91.7, 61.5, and 15.4% protection, respectively, against tumor challenge with MC38/MUC1 cells. In contrast, all mice immunized with irradiated MC38/MUC1 tumor cells or WT-DC developed tumors. One group of mice was immunized with 5 x 10(5) IKO/B16-FC and then challenged with B16/Ia(+)/MUC1 on one flank and MC38/MUC1 on the other flank. Immunization of these mice with IKO/B16-FC resulted in 100 and 78.6% protection against B16/Ia(+)/MUC1 and MC38/MUC1 tumor challenge, respectively. The antitumor immunity induced by immunization with IKO/B16-FC was able to inhibit the growth of MHC class II-negative tumor. In addition, in vivo results correlated with the induction of Ag-specific CTL. Collectively, the data indicate that MHC class II Ag presentation targeting activation of CD4 T cells is indispensable for antitumor immunity.

Animals↗

PubMed2005

CDD: a Conserved Domain Database for protein classification.

The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein-protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.

Amino Acid Sequence↗

PubMed2005

Limitations of apparent diffusion coefficient-based models in characterizing non-gaussian diffusion.

Diffusion in complex heterogeneous structures, for example, the neural fiber system, is non-gaussian. Recently, several methods have been introduced to address the issue of non-gaussian diffusion in multifiber systems. Some are based on apparent diffusion coefficient (ADC) analysis; and some are based on q-space analysis. Here, using a simple mathematic derivation, ADC-based models are shown to be mathematically self-inconsistent in the presence of non-gaussian diffusion. Monte Carlo simulation on restricted diffusion is applied to demonstrate the poor data fitting that can result from ADC-based models. Specific comparisons are performed between two generalized diffusion tensor imaging methods: one of them is based on ADC analysis, and the other is shown to be consistent with q-space formalism. The issue of imaging asymmetric microstructures is also investigated. Signal phase and spin exchange are necessary to resolve multiple orientations of an asymmetric structure.

Anisotropy↗

PubMed2005

Simultaneous phase correction and SENSE reconstruction for navigated multi-shot DWI with non-cartesian k-space sampling.

Phase-navigated multi-shot acquisition and parallel imaging are two techniques that have been applied to diffusion-weighted imaging (DWI) to diminish distortions and to enhance spatial resolution. Specifically, sensitivity encoding (SENSE) has been combined with single-shot echo planar imaging (EPI). Thus far, it has been difficult to apply parallel imaging methods, like SENSE, to multi-shot DWI because motion-induced phase error varies from shot to shot and interferes with sensitivity encoding. Although direct phase subtraction methods have been introduced to correct this phase error, they generally are not suitable for SENSE reconstruction, and they cannot remove all the motion artifacts even if the phase error is fully known. Here, an effective algorithm is proposed to correct the motion-induced phase error using an iterative reconstruction. In this proposed conjugate-gradient (CG) algorithm, the phase error is treated as an image encoding function. Given the complex perturbation terms, diffusion-weighted images can be reconstructed using an augmented sensitivity map. The mathematical formulation and image reconstruction procedures of this algorithm are similar to the SENSE reconstruction. By defining a dynamic composite sensitivity, the CG phase correction method can be conveniently incorporated with SENSE reconstruction for the application of multi-shot SENSE DWI. Effective phase correction and multi-shot SENSE DWI (R = 1 to 3) are demonstrated on both simulated and in vivo data acquired with PROPELLER and SNAILS.

Algorithms↗

PubMed2005

Foundations of advanced magnetic resonance imaging.

During the past decade, major breakthroughs in magnetic resonance imaging (MRI) quality were made by means of quantum leaps in scanner hardware and pulse sequences. Some advanced MRI techniques have truly revolutionized the detection of disease states and MRI can now-within a few minutes-acquire important quantitative information noninvasively from an individual in any plane or volume at comparatively high resolution. This article provides an overview of the most common advanced MRI methods including diffusion MRI, perfusion MRI, functional MRI, and the strengths and weaknesses of MRI at high magnetic field strengths.

Animals↗

PubMed2004

Development of antigen-specific CD8+ CTL in MHC class I-deficient mice through CD4 to CD8 conversion.

CD8+ CTL are the predominant tumoricidal effector cells. We find, however, that MHC class I-deficient mice depleted of CD8+ T cells are able to mount an effective antitumor immunity after immunization with fused dendritic/tumor cells. Such immunity appears to be mediated by the generation of phenotypic and functional CD8+ CTL through CD4+ to CD8+ conversion, which we have demonstrated at the single cell level. CD4+ to CD8+ conversion depends on effective in vivo activation and is promoted by CD4+ T cell proliferation. The effectiveness of this process is shown by the generation of antitumor immunity through adoptive transfer of primed CD4 T cells to provide protection against tumor cell challenge and to eliminate established pulmonary metastases.

Adoptive Transfer↗

PubMed2004

Characterizing non-Gaussian diffusion by using generalized diffusion tensors.

Diffusion tensor imaging (DTI) is known to have a limited capability of resolving multiple fiber orientations within one voxel. This is mainly because the probability density function (PDF) for random spin displacement is non-Gaussian in the confining environment of biological tissues and, thus, the modeling of self-diffusion by a second-order tensor breaks down. The statistical property of a non-Gaussian diffusion process is characterized via the higher-order tensor (HOT) coefficients by reconstructing the PDF of the random spin displacement. Those HOT coefficients can be determined by combining a series of complex diffusion-weighted measurements. The signal equation for an MR diffusion experiment was investigated theoretically by generalizing Fick's law to a higher-order partial differential equation (PDE) obtained via Kramers-Moyal expansion. A relationship has been derived between the HOT coefficients of the PDE and the higher-order cumulants of the random spin displacement. Monte-Carlo simulations of diffusion in a restricted environment with different geometrical shapes were performed, and the strengths and weaknesses of both HOT and established diffusion analysis techniques were investigated. The generalized diffusion tensor formalism is capable of accurately resolving the underlying spin displacement for complex geometrical structures, of which neither conventional DTI nor diffusion-weighted imaging at high angular resolution (HARD) is capable. The HOT method helps illuminate some of the restrictions that are characteristic of these other methods. Furthermore, a direct relationship between HOT and q-space is also established.

Anisotropy↗

PubMed2004

Self-navigated interleaved spiral (SNAILS): application to high-resolution diffusion tensor imaging.

A fat-saturated twice-refocused spin echo sequence was implemented on a GE Signa 1.5-T whole-body system for diffusion-weighted imaging. Data were acquired using an analytically designed interleaved variable-density (VD) spiral readout trajectory. This flexible design algorithm allowed real-time prescription on the scanner. Each interleaf of the VD spiral oversampled the center of k-space. The oversampling provided an inherent motion compensation capability. The resultant diffusion-weighted images showed good quality without any retrospective motion correction. An iterated motion correction algorithm was developed to further reduce the signal cancellation artifact caused by motion-induced phase error. In this algorithm, a low-resolution phase map was estimated using the oversampled data in the center of k-space in order to correct for phase error in image space. In vivo diffusion tensor imaging (DTI) studies were performed on the brains of healthy volunteers. High-quality isotropic diffusion-weighted images, trace maps, and FA maps from axial, sagittal, and coronal slices were obtained using a VD spiral readout trajectory with matrix size 256 x 256. To our knowledge, this was also the first time in vivo 512 x 512 DTI results were reported.

Algorithms↗

PubMed2004

Dendritic cells fused with human cancer cells: morphology, antigen expression, and T cell stimulation.

Fusion of human dendritic cells (DC) with tumor cells is an effective approach for delivering tumor antigens to DC, and DC/tumor fusion cells are potent stimulators of autologous T cells. However, the integration and morphology of DC/tumor fusion cells has not been examined. In the present study, we fused patient-derived DC to autologous breast or ovarian carcinoma cells. The fusion cells possessed the properties of both parent cells. After fusion, the cytoplasm of the two cells was integrated, whereas their nuclei remained separate entities. Colocalization of MUC1 peptide and HLA-DR molecules was observed on fusion cells under the immunoelectron microscope. Coculture of patient-derived peripheral blood mononuclear cells (PBMC) with DC/tumor fusion cells resulted in activation of CD4 and CD8 T cells as assessed by IFN-gamma secretion, HLA-A*0201-MUC1 tetramer, and standard cytotoxic T lymphocyte (CTL) assays. The present study provides first evidence of integration of human DC and tumor cells and links their properties to T cell activation.

Antigens↗

PubMed2003

Prevention of spontaneous breast carcinoma by prophylactic vaccination with dendritic/tumor fusion cells.

Genetically modified mice with spontaneous development of mammary carcinoma provide a powerful tool to study the efficacy of tumor vaccines, since they mimic breast cancer development in humans. We used a transgenic murine model expressing polyomavirus middle T oncogene and mucin 1 tumor-associated Ag to determine the preventive effect of a dendritic/tumor fusion cell vaccine. The MMT (a transgenic murine model) mice developed mammary carcinoma between the ages of 65-108 days with 100% penetrance. No spontaneous CTL were detected. However, prophylactic vaccination of MMT mice with dendritic/tumor fusion cells induced polyclonal CTL activity against spontaneous mammary carcinoma cells and rendered 57-61% of the mice free of the disease at the end of experiment (180 days). Furthermore, the level of CTL activity was maintained with multiple vaccinations. The antitumor immunity induced by vaccination with dendritic/tumor fusion cells reacted differently to injected tumor cells and autochthonous tumor. Whereas the injected tumor cells were rejected, the autochthonous tumor evaded the attack and was allowed to grow. Collectively these results indicate that prophylactic vaccination with dendritic/tumor fusion cells confers sufficient antitumor immunity to counter the tumorigenesis of potent oncogenic products. The findings in the present study are highly relevant to cancers in humans.

Animals↗

PubMed2003

MMDB: Entrez's 3D-structure database.

Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. To this end, Entrez's search engine provides several powerful features: (i) links between databases, for example between a protein's sequence and structure; (ii) pre-computed sequence and structure neighbors; and (iii) structure and sequence/structure alignment visualization. Here, we focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative analysis. MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/structure.html.

Animals↗

PubMed2003

CDD: a curated Entrez database of conserved domain alignments.

The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE(R). This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez's sequence database. CDD can be accessed on the WorldWideWeb at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. Users may also employ the CD-Search service to identify conserved domains in new sequences, at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. CD-Search results, and pre-computed links from Entrez's protein database, are calculated using the RPS-BLAST algorithm and Position Specific Score Matrices (PSSMs) derived from CDD alignments. CD-Searches are also run by default for protein-protein queries submitted to BLAST(R) at http://www.ncbi.nlm.nih.gov/BLAST. CDD mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI. Structure information is used to identify the core substructure likely to be present in all family members, and to produce sequence alignments consistent with structure conservation. This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members.

Amino Acid Sequence↗