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Biomedical subjects

H Hong

Publications and source records attributed to H Hong.

At least 19 recordsLinked to original sources
PubMed2006

Scutellarin protects PC12 cells from oxidative stress-induced apoptosis.

The present study investigated the effects of scutellarin on oxidative stress-induced cell apoptosis in PC12 cells. Exposure of cells to hydrogen peroxide (H2O2) triggered a typical apoptosis, as evidenced by DNA fragmentation, DNA loss and externalization of phosphatidylserine (PS). This treatment also caused significant elevation of oxidative stress characterized by intracellular accumulations of reactive oxygen species (ROS) and malondialdehyde (MDA), a product of lipid peroxidation. Preincubation of cells with scutellarin significantly inhibited the fragmentation and loss of DNA, the externalization of PS, and decreased the percentage of cell apoptosis. Also, intracellular accumulations of ROS and MDA resulting from H2O2 exposure were significantly reduced by scutellarin. These findings suggest that scutellarin exerts significant protection against oxidative stress-induced apoptosis, which might be beneficial for the prevention and treatment of oxidative stress-mediated disorders.

Animals↗
PubMed2006

Gene-activated matrices for cartilage defect reparation.

A cartilage defect has a very limited ability to repair itself spontaneously due to the shortage of blood. Many attempts have been made to restore the integrity of cartilage in clinical and experimental studies. Recently, tissue engineering has emerged as a new protocol for lost tissue regeneration. Meanwhile, the defect-repairing environment can be improved by gene therapy methods. Gene-activated matrices (GAM) fabricated with biomaterials and plasmids fill the cartilage defects to restore the integrity of joint surface, facilitating repair cell adhesion and proliferation as well as the synthesis of extracelluar matrix. And they also serve as a local gene delivery system, inducing therapeutic agent expression at the repair site. In the present study, we fabricated two- and three-dimensional matrices from chitosan and gelatin, then added a plasmid DNA encoding transforming growth factors-ss1 (TGF-ss1) for cartilage defect regeneration. First, we demonstrated primary chondrocytes could maintain their biological characteristics and secrete therapeutic proteins when they were cultured onto GAM in vitro. Subsequently we inserted three-dimensional GAM into cartilage defects of rabbit knee joints. With the results of the new cartilage tissue formation, we came to the conclusion that GAM was helpful for new tissue production and this therapeutic protocol provided a cheap, simple, and effective method for cartilage defect reparation.

Animals↗
PubMed2005

Modular synchronization in complex networks.

We study the synchronization transition (ST) of a modified Kuramoto model on two different types of modular complex networks. It is found that the ST depends on the type of intermodular connections. For the network with decentralized (centralized) intermodular connections, the ST occurs at finite coupling constant (behaves abnormally). Such distinct features are found in the yeast protein interaction network and the Internet, respectively. Moreover, by applying the finite-size scaling analysis to an artificial network with decentralized intermodular connections, we obtain the exponent associated with the order parameter of the ST to be beta approximately 1 different from beta(MF) approximately 1/2 obtained from the scale-free network with the same degree distribution but the absence of modular structure, corresponding to the mean field value.

Journal Article↗
PubMed2005

Collective synchronization in spatially extended systems of coupled oscillators with random frequencies.

We study collective behavior of locally coupled limit-cycle oscillators with random intrinsic frequencies, spatially extended over d -dimensional hypercubic lattices. Phase synchronization as well as frequency entrainment are explored analytically in the linear (strong-coupling) regime and numerically in the nonlinear (weak-coupling) regime. Our analysis shows that the oscillator phases are always desynchronized up to d=4 , which implies the lower critical dimension dP(l) =4 for phase synchronization. On the other hand, the oscillators behave collectively in frequency (phase velocity) even in three dimensions (d=3) , indicating that the lower critical dimension for frequency entrainment is dF(l)=2 . Nonlinear effects due to the periodic nature of limit-cycle oscillators are found to become significant in the weak-coupling regime: So-called runaway oscillators destroy the synchronized (ordered) phase and there emerges a fully random (disordered) phase. Critical behavior near the synchronization transition into the fully random phase is unveiled via numerical investigation. Collective behavior of globally coupled oscillators is also examined and compared with that of locally coupled oscillators.

Action Potentials↗
PubMed2005

Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling.

BACKGROUND: The completion of the sequencing of human, mouse and rat genomes and knowledge of cross-species gene homologies enables studies of differential gene expression in animal models. These types of studies have the potential to greatly enhance our understanding of diseases such as liver cancer in humans. Genes co-expressed across multiple species are most likely to have conserved functions. We have used various bioinformatics approaches to examine microarray expression profiles from liver neoplasms that arise in albumin-SV40 transgenic rats to elucidate genes, chromosome aberrations and pathways that might be associated with human liver cancer. RESULTS: In this study, we first identified 2223 differentially expressed genes by comparing gene expression profiles for two control, two adenoma and two carcinoma samples using an F-test. These genes were subsequently mapped to the rat chromosomes using a novel visualization tool, the Chromosome Plot. Using the same plot, we further mapped the significant genes to orthologous chromosomal locations in human and mouse. Many genes expressed in rat 1q that are amplified in rat liver cancer map to the human chromosomes 10, 11 and 19 and to the mouse chromosomes 7, 17 and 19, which have been implicated in studies of human and mouse liver cancer. Using Comparative Genomics Microarray Analysis (CGMA), we identified regions of potential aberrations in human. Lastly, a pathway analysis was conducted to predict altered human pathways based on statistical analysis and extrapolation from the rat data. All of the identified pathways have been known to be important in the etiology of human liver cancer, including cell cycle control, cell growth and differentiation, apoptosis, transcriptional regulation, and protein metabolism. CONCLUSION: The study demonstrates that the hepatic gene expression profiles from the albumin-SV40 transgenic rat model revealed genes, pathways and chromosome alterations consistent with experimental and clinical research in human liver cancer. The bioinformatics tools presented in this paper are essential for cross species extrapolation and mapping of microarray data, its analysis and interpretation.

Animals↗
PubMed2005

Enhancement of coherent response by quenched disorder.

We investigate the effects of quenched disorder on the coherent response in a driven system of coupled oscillators. In particular, the interplay between quenched noise and periodic driving is explored, with particular attention to the possibility of resonance. The phase velocity is examined as the response of the system; revealed is the enhancement of the fraction of oscillators locked to the periodic driving, displaying resonance behavior. It is thus concluded that resonance behavior may also be induced by quenched disorder that does not have time-dependent correlations.

Journal Article↗
PubMed2005

An in silico ensemble method for lead discovery: decision forest.

Recent progress in combinatorial chemistry and parallel synthesis has radically changed the approach to drug discovery in the pharmaceutical industry. At present, thousands of compounds can be made in a short period, creating a need for fast and effective in silico methods to select the most promising lead candidates. Decision forest is a novel pattern recognition method, which combines the results of multiple distinct but comparable decision tree models to reach a consensus prediction. In this article, a decision forest model was developed using a structurally diverse training data set containing 232 compounds whose estrogen receptor binding activity was tested at the U.S. Food and Drug Administration (FDA)'s National Center for Toxicological Research (NCTR). The model was subsequently validated using a test data set of 463 compounds selected from the literature, and then applied to a large data set with 57,145 compounds as a screening example. The results show that the decision forest method is a fast, reliable and effective in silico approach, which could be useful in drug discovery.

Decision Trees↗
PubMed2004

Organochlorine micropollutants in the Jiulong River Estuary and Western Xiamen Sea, China.

Organochlorine contaminants including 12 polychlorinated biphenyl (PCB) congeners and 18 insecticides were determined in water, pore water and sediments of the Jiulong River Estuary and Western Xiamen Sea, China. The results showed that the levels of the total PCBs ranged from non-detectable to 1500 ng l(-1) in water, from 209 to 3870 ng l(-1) in pore water, and from 2.78 to 14.8 ng g(-1) dry weight in sediments. Total organochlorine insecticide concentrations were from below the limit of detection to 2480 ng l(-1) in water, from 267 to 33400 ng l(-1) in pore water, and from 4.22 to 46.3 ng g(-1) dry weight in sediments. Concentrations of PCBs and insecticides in pore water were significantly higher than those in surface water, due to the high affinity of these hydrophobic compounds for sediment phase. The PCB congeners with the highest concentrations were CB153, CB180 and CB194, which together accounted for 68-87% of total PCBs in water, pore water and sediment. Among the hexachlorocyclohexane (HCH) compounds, beta-HCH was found to be a major isomer. Analysis of 1,1,1-trichloro-2,2-bis-chlorophenyl-ethane (DDT) and its metabolites showed that 1,1-dichloro-2[o-chlorophenyl]-2[p-chlorophenyl]-ethylene (DDE) was dominant in the group. In comparison to a 1998 study in the Western Xiamen Sea, levels of organochlorines were enhanced due probably to recent inputs and changes in sediments.

China↗
PubMed2004

Collective phase synchronization in locally coupled limit-cycle oscillators.

We study collective behavior of locally coupled limit-cycle oscillators with scattered intrinsic frequencies on d -dimensional lattices. A linear analysis shows that the system should always be desynchronized up to d=4 . On the other hand, numerical investigation for d=5 and d=6 reveals the emergence of the synchronized (ordered) phase via a continuous transition from the fully random desynchronized phase. This demonstrates that the lower critical dimension for the phase synchronization in this system is d(l) =4 .

Journal Article↗
PubMed2004

Factors that predict better synchronizability on complex networks.

While shorter characteristic path length has in general been believed to enhance synchronizability of a coupled oscillator system on a complex network, the suppressing tendency of the heterogeneity of the degree distribution, even for shorter characteristic path length, has also been reported. To see this, we investigate the effects of various factors such as the degree, characteristic path length, heterogeneity, and betweenness centrality on synchronization, and find a consistent trend between the synchronization and the betweenness centrality. The betweenness centrality is thus proposed as a good indicator for synchronizability.

Computer Simulation↗
PubMed2003

Phase transition in the Ising model on a small-world network with distance-dependent interactions.

We study the collective behavior of an Ising system on a small-world network with the interaction J(r) proportional to r(-alpha), where r represents the Euclidean distance between two nodes. In the case of alpha=0 corresponding to the uniform interaction, the system is known to possess a phase transition of the mean-field nature, while the system with the short-range interaction (alpha-->infinity) does not exhibit long-range order at any finite temperature. The Monte Carlo simulations are performed at various values of alpha, and the critical value alpha(c) beyond which the long-range order does not emerge is estimated to be 0. Thus, concluded is the absence of a phase transition in the system with the algebraically decaying interaction r(-alpha) for any nonzero positive value of alpha.

Journal Article↗
PubMed2003

Optimal size of a complex network.

We investigate the response behavior of an Ising system, driven by an oscillating field, on a small-world network, with particular attention to the effects of the system size. The responses of the magnetization to the driving field are probed by means of Monte Carlo dynamic simulations with the varied rewiring probability. It is found that at low and high temperatures the occupancy ratio, measuring how many spins follow the driving field, behaves monotonically with the system size. At intermediate temperatures, on the other hand, the occupancy ratio first grows and then reduces as the size is increased, displaying a resonancelike peak at a finite value of the system size. In all cases, further increase of the size eventually leads to saturation to finite values; the size at which saturation emerges is observed to depend on the temperature, similarly to the correlation length of the system.

Journal Article↗
PubMed2002

Comment on "Ising model on a small world network".

In the recent study of the Ising model on a small world network by Pekalski [Phys. Rev. E 64, 057104 (2001)], a surprisingly small value of the critical exponent beta approximately 0.0001 has been obtained for the temperature dependence of the magnetization. We perform extensive Monte Carlo simulations of the same model and conclude, via the standard finite-size scaling of various quantities, that the phase transition in the model is of the mean-field nature, in contrast to the work by Pekalski, but in accordance with other existing studies.

Comment↗
PubMed2002

Stochastic resonance in the driven Ising model on small-world networks.

We investigate the stochastic resonance phenomena in the field-driven Ising model on small-world networks. The response of the magnetization to an oscillating magnetic field is examined by means of Monte Carlo dynamic simulations, with the rewiring probability varied. At any finite value of the rewiring probability, the system is found to undergo a dynamic phase transition at a finite temperature, giving rise to double resonance peaks. While the peak in the ferromagnetic phase grows with the rewiring probability, which in the paramagnetic phase tends to reduce, indicating opposite effects of the long-range interactions on the resonance in the two phases.

Journal Article↗
PubMed2002

Phase ordering on small-world networks with nearest-neighbor edges.

We investigate global phase coherence in a system of coupled oscillators on small-world networks constructed from a ring with nearest-neighbor edges. The effects of both thermal noise and quenched randomness on phase ordering are examined and compared with the global coherence in the corresponding XY model without quenched randomness. It is found that in the appropriate regime phase ordering emerges at finite temperatures, even for a tiny fraction of shortcuts. The nature of the phase transition is also discussed.

Journal Article↗
PubMed2002

Noise-enhanced temporal association in neural networks.

We consider a network of globally coupled neuronal oscillators subject to random force, and investigate numerically dynamic responses to external periodic driving. The order parameter, which measures the overlap between the configuration of the system and embedded patterns, is found to exhibit stochastic resonance behavior, as manifested by the signal-to-noise ratio (SNR). The optimal noise level at which the SNR reaches its maximum is found to depend on the driving frequency. On the other hand, as the randomness in the driving amplitude is increased, the system undergoes a transition from the memory-retrieval state to the mixed-memory one. The noise effects on the temporal-association state in the absence of external periodic driving are also investigated, revealing similar noise-enhanced resonance.

Journal Article↗
PubMed2002

Synchronization on small-world networks.

We investigate collective synchronization in a system of coupled oscillators on small-world networks. The order parameters that measure synchronization of phases and frequencies are introduced and analyzed by means of dynamic simulations and finite-size scaling. Phase synchronization is observed to emerge in the presence of even a tiny fraction P of shortcuts and to display saturated behavior for P > or similar to 0.5. This indicates that the same synchronizability as the random network (P=1) can be achieved with relatively small number of shortcuts. The transient behavior of the synchronization, obtained from the measurement of the relaxation time, is also discussed.

Journal Article↗