Biomedical subjects

Ming Li

Publications and source records attributed to Ming Li.

At least 181 records · Page 10Linked to original sources

PubMed2005

Spatial motion constraints for robot assisted suturing using virtual fixtures.

We address the problem of the stitching task in endoscopic surgery using a circular needle under robotic assistance. Our main focus is to present an algorithm for suturing using guidance virtual fixtures (VF) that assist the surgeon to move towards a desired goal. A weighted multi-objective, constraint optimization framework is used to compute the joint motions required for the tasks. We show that with the help of VF, suturing can be performed at awkward angles without multiple trials, thus avoiding damage to tissue. In this preliminary study we show the feasibility of our approach and demonstrate the promise of cooperative assistance in complex tasks such as suturing.

Feasibility Studies↗

PubMed2005

Antiapoptotic mechanism of insulin in reoxygenation-induced injury in cultured cardiomyocytes of neonatal rats.

To examine the protective effect of insulin on reoxygenation-induced injury and explore the underlying mechanisms, the model of anoxia/reoxygenation (A/R) injury was established by inducing anoxia for 2 h and reoxygenation for 4 h in cultured cardiomyocytes of neonatal rats. The rats were randomized to four groups receiving vehicle, insulin, LY294002, insulin plus LY294002 at the onset of reoxygenation after 2 h of anoxia. At the end of reoxygenation of 4 h, activity of lactate dehydrogenase (LDH) and content of malondialdehyde (MDA) were spectrophotometrically determined, apoptosis of cardiomyocytes were detected by using TUNEL and DNA Ladder, and Western blotting was employed to examine the expression of phosphorylated Akt in all groups. Our results showed that compared with vehicle-treated group, activities of LDH, contents of MDA, apoptosis index (AI) were significantly decreased, and expression of phosphorylated Akt was increased significantly in insulin-treated group. However, changes in LDH, MDA, AI and phosphorylated Akt resulting from insulin were attenuated or abolished by LY294002 (PI3K inhibitor). These data strongly suggest that early administration of insulin at reoxygenation protects cardiomyocytes from reoxygenation-induced apoptosis through PI3K/Akt signaling pathway.

Animals↗

PubMed2005

Inhibition of neuropathy target esterase expressing by antisense RNA does not affect neural differentiation in human neuroblastoma (SK-N-SH) cell line.

Neuropathy target esterase (NTE) is phosphorylated and aged by oraganophosphorus compounds (OP) that induce delayed neuropathy in human and some animals. NTE has been proposed to play a role in neurite outgrowth and process elongation during neural differentiation. However, to date, there is no direct evidence of the relevance of NTE in neural differentiation under physiological conditions. In this study we have investigated a possible role for NTE in the all-trans retinoic acid (ATRA)-induced differentiation of neuroblastoma cells by antisense RNA. A NTE antisense RNA construct was generated and then transfected into human neuroblastoma SK-N-SH cells. A positive cell clone that can stably express NTE antisense RNA was obtained by G418 selection and then identified by western blotting. NTE activity was depressed in the transfected cells with only about 50% activity of the enzyme in the control cells. ATRA-induced differentiation of the neuroblastoma cells with lowered NTE activity revealed that inhibition of NTE expression does not affect neural differentiation in SK-N-SH cells. The result suggested that organophosphates may inhibit neural differentiation by initially acting on other targets other than NTE.

Carboxylic Ester Hydrolases↗

PubMed2005

Transforming growth factor beta (TGF-beta) and autoimmunity.

TGF-beta1 deficient mice develop multifocal inflammatory autoimmune disease and serve as a valuable animal model of autoimmunity. Transgenic expression of a dominant negative form of TGF-beta receptor type II in T cells have enabled the study of cell lineage specific effects of TGF-beta providing clues to the potential etiology of autoimmunity. These studies suggest that TGF-beta deficiency may induce autoimmune disease by influencing a number of immunological phenomena including lymphocyte activation and differentiation, cell adhesion molecule expression, regulatory T cell function, the expression of MHC molecules and cytokines, and cell apoptosis. The spectrum of effects appears to be significant in mucosal immunity and may contribute to the pathogenesis of inflammatory bowel disease.

Animals↗

PubMed2005

A functional single nucleotide polymorphism site detected in nasopharyngeal carcinoma-associated transforming gene Tx.

Tx is a transforming gene cloned from a nasopharyngeal carcinoma (NPC) cell line CNE2. Sequence analysis revealed that Tx encoded an aberrant immunoglobulin kappa light chain, which is abnormally expressed in epithelial tumor cells and plays an important role in nasopharyngeal carcinogenesis. Bioinformatic analysis confirmed the presence of a single nucleotide polymorphism (SNP) site in the Tx gene as matched to the Cancer Genome Anatomy Project SNP clusters database, which predicted 8 candidate SNP sites. Distribution of the confirmed SNP site in the genomes of healthy individuals and NPC patients was analyzed by denaturing high performance liquid chromatography. Heteroduplex genotype (GC/CG) occurred in NPC patients with a frequency significantly higher (52.44%) than that detected in healthy individuals (33.75%). In contrast, homoduplex genotype (GG) was less frequent in NPC patients (31.70%) than in normal individuals (56.25%), suggesting that heteroduplex genotype of Tx gene might be a risk factor for NPC.

Adolescent↗

PubMed2005

Regulatory mutations of mir-48, a C. elegans let-7 family MicroRNA, cause developmental timing defects.

The C. elegans heterochronic genes program stage-specific temporal identities in multiple tissues during larval development. These genes include the first two miRNA-encoding genes discovered, lin-4 and let-7. We show that lin-58 alleles, identified as lin-4 suppressors, define another miRNA that controls developmental time. These alleles are unique in that they contain point mutations in a gene regulatory element of mir-48, a let-7 family member. mir-48 is expressed prematurely in lin-58 mutants, whereas expression of mir-241, another let-7 family member residing immediately upstream of mir-48, appears to be unaffected. A mir-48 transgene bearing a lin-58 point mutation causes strong precocious phenotypes in the hypodermis and vulva when expressed from multicopy arrays. mir-48::gfp fusions reveal expression in these tissues, and inclusion of a lin-58 mutation causes precocious and enhanced gfp expression. These results suggest that lin-58 alleles disrupt a repressor binding site that restricts the time of miR-48 action in wild-type animals.

Animals↗

PubMed2005

Scale-invariant registration of monocular endoscopic images to CT-scans for sinus surgery.

In this paper, we present a novel method for intra-operative registration directly from monocular endoscopic images. This technique has the potential to provide a more accurate surface registration at the surgical site than existing methods. It can operate autonomously from as few as two images and can be particularly useful in revision cases where surgical landmarks may be absent. A by-product of video registration is an estimate of the local surface structure of the anatomy, thus providing the opportunity to dynamically update anatomical models as the surgery progresses. Our approach is based on a previously presented method [Burschka, D., Hager, G.D., 2004. V-GPS (SLAM):--Vision-based inertial system for mobile robots. In: Proceedings of ICRA, 409-415] for reconstruction of a scaled 3D model of the environment from unknown camera motion. We use this scaled reconstruction as input to a PCA-based algorithm that registers the reconstructed data to the CT data and recovers the scale and pose parameters of the camera in the coordinate frame of the CT scan. The result is used in an ICP registration step to refine the registration estimates. The details of our approach and the experimental results with a phantom of a human skull and a head of a pig cadaver are presented in this paper.

Algorithms↗

PubMed2005

Preparation and evaluation of new brominated paclitaxel analogues.

Two diastereomers of 2'',3''-dibromo-7-epi-10-deacetylcephalomannine, 4 and 5, have been synthesized, purified and identified for evaluation as antitumour drugs. The cytotoxicity of the two diastereomers, assessed in cell culture against MCF-7 breast cancer, A549 lung cancer and A2780 ovarian cancer, was slightly stronger than that of paclitaxel. The cytotoxicity of 5 outweighs that of 4. In the light of the difference in cytotoxicity between the two diastereomers, we can assume that the differing configurations of C-2'' and C-3'' of the two diastereomers may result in different bioactive conformations in solution and, consequently, different biologically relevant conformations for binding to tubulin/microtubules -- a matter we are studying further.

Antineoplastic Agents↗

PubMed2005

The central nervous system is a viral reservoir in simian immunodeficiency virus--infected macaques on combined antiretroviral therapy: a model for human immunodeficiency virus patients on highly active antiretroviral therapy.

This study used a simian immunodeficiency virus (SIV)-macaque model to determine whether virus persists in the central nervous system (CNS) of human immunodeficiency virus (HIV)-infected individuals in which plasma viral load has been suppressed by highly active antiretroviral therapy. SIV-infected macaques were treated with two reverse transcriptase inhibitors: PMPA (q- R-(2-phosphonomethoxypropyl)adenine)which does not cross the blood-brain barrier, and FTC (beta-2('),3(')-dideoxy-3 thia-5-fluorocytidine), which does. Viral DNA and RNA were quantitated in the brain after 6 months of suppression of virus replication in blood and cerebrospinal fluid (CSF). Viral DNA was detected in brain from all macaques, including those in which peripheral viral replication had been suppressed either by antiretroviral therapy or host immune responses. Significant neurological lesions were observed only in one untreated macaque that had active virus replication in the CNS. Expression of the inflammatory markers, major histocmopatibility complex (MHC) II and CD68 was significantly lower in macaques treated with PMPA/FTC. Thus, although antiretroviral treatment may suppress virus replication in the periphery and the brain and reduce CNS inflammation, viral DNA persists in the brain despite treatment. This suggests that the brain may serve as a long-term viral reservoir in HIV-infected individuals treated with antiretroviral drugs that suppress virus replication.

Adenine↗

PubMed2005

Association of CCR5 human haplogroup E with rapid HIV type 1 disease progression.

The combination of unique single nucleotide polymorphisms in the CCR5 regulatory and in the CCR2 and CCR5 coding regions, defined nine CCR5 human haplogroups (HH): HHA-HHE, HHF*1, HHF*2, HHG*1, and HHG*2. Here we examined the distribution of CCR5 HH and their association with HIV infection and disease progression in 36 HIV-seronegative and 76 HIV-seropositive whites from North America and Spain [28 rapid progressors (RP) and 48 slow progressors (SP)]. Although analyses revealed that HHE frequencies were similar between HIV-seronegative and HIV-seropositive groups (25.0% vs. 32.2%, p > 0.05), HHE frequency in RP was significantly higher than that in SP (48.2% vs. 22.9%, p = 0.002). Survival analysis also showed that HHE heterozygous and homozygous were associated with an accelerated CD4 cell count decline to less than 200 cells/microL (adjusted RH 2.44, p = 0.045; adjusted RH = 3.12, p = 0.037, respectively). These data provide further evidence that CCR5 human haplogroups influence HIV-1 disease progression in HIV-infected persons.

Acquired Immunodeficiency Syndrome↗

PubMed2005

Genetic diversification and recombination of HIV type 1 group M in Kinshasa, Democratic Republic of Congo.

As the HIV-1 pandemic becomes increasingly complex, the genetic characterization of HIV strains bears important implications for vaccine research. To better understand the molecular evolution of HIV-1 viral diversity, we performed a comparative molecular analysis of HIV strains collected from high-risk persons in Kinshasa, Democratic Republic of Congo (DRC). Analysis of the gag-p24, env-C2V3 and -gp41 regions from 83 specimens collected in 1999-2000 revealed that 44 (53%) had concordant subtypes in the three regions (14 subsubtype A1, 10 subtype G, 8 subtype D, 5 subtype C, 2 each subsubtype F1 and CRF01_AE, and one each of subtypes H and J, and subsubtype A2, while the remaining 39 (47%) had mosaic genomes comprising multiple subtype combinations. Similar multisubtype patterns were also observed in 24 specimens collected in 1985. Sequence analysis of the gag-pol region (2.1 kb) from 21 discordant specimens in the gag-p24, env-C2V3 and -gp41 regions in 1985 and 1999-2000 further confirmed the complex recombinant patterns. Despite the remarkable similarity in overall subtype distribution, the intra- and intersubtype distances of major subtypes A1 and G increased significantly from 1985 to 1999-2000 (p=0.018 and p=0.0016, respectively). Given the complexity of HIV-1 viruses circulating in DRC, efforts should focus on the development of vaccines that result in cross-clade immunity.

Democratic Republic of the Congo↗

PubMed2005

Finding cancer biomarkers from mass spectrometry data by decision lists.

Finding accurate biomarkers is key to early diagnosis and successful treatment of many otherwise incurable diseases. In this work, we study the problem of finding biomarkers through mass spectrometry (SELDI-TOF) spectra from cancerous and normal tissues. In contrast to the common practice of using vague methods such as genetic algorithms, or uninterpretable methods such as Support Vector Machines, we look for a method that is simple, intuitive, interpretable, usable, and more accurate. We introduce decision lists to this domain. Our experiments on clinical cancer datasets demonstrate that decision lists can achieve more accurate results than other methods. More interestingly, the resulting decision lists are more interpretable for possible causal relationship between cancer and differentially expressed proteins, and directly usable in clinical biomarker design. In particular, our approach is capable of finding multiple biomarkers with high sensitivity and specificity. Such a feature will provide clues for medical experts to thoroughly investigate the roles of protein in cancer development and progression.

Animals↗

PubMed2005

ExonHunter: a comprehensive approach to gene finding.

MOTIVATION: We present ExonHunter, a new and comprehensive gene finding system that outperforms existing systems and features several new ideas and approaches. Our system combines numerous sources of information (genomic sequences, expressed sequence tags and protein databases of related species) into a gene finder based on a hidden Markov model in a novel and systematic way. In our framework, various sources of information are expressed as partial probabilistic statements about positions in the sequence and their annotation. We then combine these into the final prediction via a quadratic programming method, which we show to be an extension of existing methods. Allowing only partial statements is key to our transparent handling of missing information and coping with the heterogeneous character of individual sources of information. In addition, we give a new method for modeling the length distribution of intergenic regions in hidden Markov models. RESULTS: On a commonly used test set, ExonHunter performs significantly better than the existing gene finders ROSETTA, SLAM and TWINSCAN, with more than two-thirds of genes predicted completely correctly. AVAILABILITY: Supplementary material available at http://www.bioinformatics.uwaterloo.ca/supplements/05eh/

Animals↗

PubMed2005

Regenerative and therapeutic effects of heparin-binding epidermal growth factor-like growth factor on diabetes by gene transduction through retrograde pancreatic duct injection of adenovirus vector.

OBJECTIVES: In the adult pancreas, pre-existing beta cells, stem cells, and endocrine progenitor cells residing in the duct lining are considered important sources for beta-cell regeneration. A member of the epidermal growth factor (EGF) family, heparin binding (HB)-EGF, may promote this process. We examined whether HB-EGF gene transduction into duct cells could promote beta-cell regeneration. METHODS: We administered an HB-EGF adenovirus vector construct to male Institute of Cancer Research mice by retrograde injection through the pancreatic duct. We also performed HB-EGF gene transduction into cultured duct cells. RESULTS: On immunohistochemical and histomorphometric analysis of the experimental group, insulin-positive cells differentiated from duct cells, and the 5-bromo-2-deoxyuridine labeling index of beta cells was significantly increased. beta-cell mass was also increased, and the glucose tolerance of diabetic mice was improved at 12 weeks after injection. Using cultured pancreatic duct cells, we confirmed that HB-EGF gene transduction induced both insulin gene expression and insulin production by these cells. CONCLUSIONS: These results indicate that HB-EGF gene transduction into adult pancreatic duct cells not only promotes the proliferation of pre-existing beta cells but also leads to beta-cell differentiation from duct cells, and the resulting increase in beta-cell mass improves glucose tolerance.

Adenoviridae↗

PubMed2005

Experimental autoimmune Goodpasture's disease: a pathogenetic role for both effector cells and antibody in injury.

BACKGROUND: Goodpasture's disease [antiglomerular basement membrane (GBM) glomerulonephritis] is a classic autoimmune disease and the only organ-specific autoimmune renal disease in which the antigen is well described. The importance of antibodies against the non-collagenous domain of the alpha3 chain of type IV collagen [alpha3(IV)NC1] is well established. However, observational human studies and studies in experimental systems also imply a role for cell-mediated effector injury. METHODS: Active experimental autoimmune glomerulonephritis (EAG) was induced by immunization with alpha3-alpha5(IV)NC1 heterodimers in B cell intact C57BL/6 mice and B cell (mu chain-deficient) mice. Passive disease was induced by transferring sera from B cell intact and B cell deficient mice with EAG to RAG-1-/- mice (that lack adaptive immunity). Histologic and functional injury was studied. RESULTS: Despite the absence of B cells and immunoglobulin in B-cell-deficient mice, histologic and functional injury developed in mice immunized with alpha3-alpha5(IV)NC1, with T cells and macrophages in glomeruli. Injury occurred to a similar degree to that found in B-cell-intact mice. Transfer of sera from B-cell-intact mice with EAG containing antibodies (but not from B-cell-deficient mice with EAG) to RAG-1-/- mice induced linear immunoglobulin deposits on the glomerular basement membrane (GBM) and pathologic proteinuria. CONCLUSION: Both cell-mediated and humoral effectors are capable of inducing renal injury in EAG. Given the similarity of the disease-initiating antigen in this model to the antigen in human anti-GBM glomerulonephritis, similar overlapping mechanisms are likely to operate in human disease.

Animals↗

PubMed2005

Towards selective antagonists of T-type calcium channels: design, characterization and potential applications of NNC 55-0396.

NNC 55-0396 is a structural analog of mibefradil (Ro 40-5967) that inhibits both T-type and high-voltage-activated (HVA) Ca2+ channels with a higher selectivity for T-type Ca2+ channels. The inhibitory effect of mibefradil on HVA Ca2+ channels can be attributed to a hydrolyzed metabolite of the drug: the methoxy acetate side chain of mibefradil is removed by intracellular enzymes, thus it forms (1S,2S)-2-(2-(N-[(3-benzoimidazol-2-yl)propyl]-N-methylamino)ethyl)-6-fluoro-1,2,3,4-tetrahydro-1-isopropyl-2-naphtyl hydroxy dihydrochloride (dm-mibefradil), which causes potent inhibition of HVA Ca2+ currents. By replacing the methoxy acetate chain of mibefradil with cyclopropanecarboxylate, a more stable analog was developed (NNC 55-0396). The acute IC50 of NNC 55-0396 to block recombinant Cav3.1 T-type channels expressed in HEK293 cells is approximately 7 muM, whereas 100 microM NNC 55-0396 has no detectable effect on high voltage-activated currents in INS-1 cells. Block of T-type Ca2+ current was partially reduced by membrane hyperpolarization and was enhanced at high stimulus frequency. Washing NNC 55-0396 out of the recording chamber did not reverse the T-type Ca2+ current activity, suggesting that the compound dissolves in or passes through the plasma membrane to exert its effect; however, intracellular perfusion of the compound did not block T-type Ca2+ currents, arguing against a cytoplasmic route of action. We conclude that NNC 55-0396, by virtue of its modified structure, does not produce the metabolite that causes inhibition of L-type Ca2+ channel channels, thus rendering it more selective to T-type Ca2+ channels.

Animals↗

PubMed2005

Integrating software into PRA: a test-based approach.

Probabilistic risk assessment (PRA) is a methodology to assess the probability of failure or success of a system's operation. PRA has been proved to be a systematic, logical, and comprehensive technique for risk assessment. Software plays an increasing role in modern safety critical systems. A significant number of failures can be attributed to software failures. Unfortunately, current probabilistic risk assessment concentrates on representing the behavior of hardware systems, humans, and their contributions (to a limited extent) to risk but neglects the contributions of software due to a lack of understanding of software failure phenomena. It is thus imperative to consider and model the impact of software to reflect the risk in current and future systems. The objective of our research is to develop a methodology to account for the impact of software on system failure that can be used in the classical PRA analysis process. A test-based approach for integrating software into PRA is discussed in this article. This approach includes identification of software functions to be modeled in the PRA, modeling of the software contributions in the ESD, and fault tree. The approach also introduces the concepts of input tree and output tree and proposes a quantification strategy that uses a software safety testing technique. The method is applied to an example system, PACS.

Journal Article↗

PubMed2005

Matrix metalloproteinases expression correlates with survival in patients with esophageal squamous cell carcinoma.

OBJECTIVES: The matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases capable of degrading the extracellular matrix and play important roles in malignancies. We evaluated the expression of four MMPs in esophageal squamous cell carcinoma (ESCC), and assessed the association between MMP expression and clinicopathologic characteristics and disease-free survival time. METHODS: We evaluated MMP1, MMP7, MMP9, and MMP13 expression in tissues from 208 patients with ESCC using immunohistochemistry (IHC), and correlated MMP expression to clinicopathologic characteristics and disease-free survival time. To confirm MMP9 expression at different levels, we simultaneously performed RT-PCR, Western blotting, and IHC on tissues from a separate cohort of 23 patients with ESCC. RESULTS: IHC analysis showed that 63.0%, 41.8%, 49.0%, and 32.2% of 208 ESCC samples were positive for MMP1, MMP7, MMP9, and MMP13, respectively. MMPs were strongly expressed in the cytoplasm of cancer cells, especially in the invasive margin, and weakly expressed in stromal cells. No immunostaining was detected in non-cancerous esophageal mucosa. MMP9 expression was positively associated with poor tumor cell differentiation (p= 0.001), vessel permeation (p= 0.027), and lymph node metastasis (p= 0.027). MMP9 expression was a negative, independent predictor of disease-free survival time (Hazard ratio, 1.470; 95% CI, 1.105 approximately 1.955; p= 0.008). The expression of MMP7 (median survival time: 23 months for MMP7 positive patients, >77 months for MMP7 negative patients; p= 0.001) and MMP13 (median survival time: 18 months for MMP13 positive patients, 39 months for MMP13 negative patients; p= 0.014) correlated negatively with disease-free survival in relatively early stage ESCC patients. Co-expression of MMP7, MMP9, and MMP13 in relatively early stage ESCC samples identified patients with a poor prognosis (13 months median survival time) compared to those lacking MMP7, MMP9, and MMP13 expression (58 months median survival time, p < 0.001). CONCLUSIONS: MMP9 expression is a negative, independent prognostic factor in ESCC and correlates with tumor cell differentiation, vessel permeation, and lymph node metastasis. MMP7, MMP9, and MMP13 may function in early stage ESCC, and their co-expression predicts poor outcome for relatively early stage ESCC patients.

Adult↗