Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples

The discordance in results of independent genome-wide association studies (GWAS) indicates the potential for Type I and Type II errors. We assessed the repeatibility of current Affymetrix technologies that support GWAS. Reasonable reproducibility was observed for both raw intensity and the genotypes/copy number variants. We also assessed consistencies between different SNP arrays and between genotype calling algorithms. We observed that the inconsistency in genotypes was generally small at the specimen level. To further examine whether the differences from genotyping and genotype calling are possible sources of variation in GWAS results, an association analysis was applied to compare the associated SNPs. We observed that the inconsistency in genotypes not only propagated to the association analysis, but was amplified in the associated SNPs. Our studies show that inconsistencies between SNP arrays and between genotype calling algorithms are potential sources for the lack of reproducibility in GWAS results.

Depletion of CD4+CD25+ regulatory T cells enhances natural killer T cell-mediated anti-tumour immunity in a murine mammary breast cancer model

Both invariant natural killer T (NK T) cells and CD4(+)CD25(+) T regulatory cells (T(regs)) regulate the immune system to maintain homeostasis. In a tumour setting, NK T cells activated by alpha-galactosylceramide (alpha-GalCer) execute anti-tumour activity by secreting cytokines. By contrast, T(regs) intrinsically suppress antigen-specific immune responses and are often found to be elevated in tumour patients. In this study, we have shown that T(regs) regulate NK T cell function negatively in vitro, suggesting a direct interaction between these cell types. In a murine mammary tumour model, we demonstrated that administration of either alpha-GalCer or anti-CD25 antibody alone markedly suppressed tumour formation and pulmonary metastasis, and resulted in an increase in the survival rate up to 44% (from a baseline of 0%). When treatments were combined, depletion of T(regs) boosted the anti-tumour effect of alpha-GalCer, and the survival rate jumped to 85%. Our results imply a potential application of combining T(reg) cell depletion with alpha-GalCer to stimulate NK T cells for cancer therapy.

Percutaneous thermal ablation in the head and neck: current role and future applications

Patients with recurrent head and neck cancer have poor quality of life and suffer dismally from debilitating symptoms. Ablative techniques offer patients an alternative, minimally invasive treatment option. As a palliative treatment, they improve quality of life with decreased pain, improved function and appearance. In addition, there is a reduction in tumor bulk and analgesia requirements. Advantages include a reduction in procedural cost, avoidance of complex repetitive surgeries, and an ability to visualize the treated area at the time of the procedure. Ablation therapies are an evolving and exciting treatment option in the head and neck, but a consensus on appropriate indications is currently unclear.

Effectiveness of peer education in HIV/STD prevention at different types of senior high schools in Shanghai, People's Republic of China

The epidemic of HIV/AIDS greatly threatens Chinese youth. Our study was intended to examine the effectiveness of the peer education method in HIV/AIDS prevention in different types of senior high schools in Shanghai. A peer education intervention was conducted in 10 different types of senior high schools, including three key senior schools, four ordinary senior schools and three vocational schools in Shanghai for three months. A cohort of 1910 students was surveyed (n=976 intervention group, n=934 control group) through anonymous questionnaires, both pre- and postintervention. There were significant differences in the results among these different types of senior schools. Peer education is an efficient method of increasing the knowledge of AIDS/sexually transmitted diseases in senior school students. However, the contents and the schedule should be different between different types of schools, and students in vocational schools require more health education.

Long-term follow-up study on peer-led school-based HIV/AIDS prevention among youths in Shanghai

SUMMARY

The HIV/AIDS epidemic is a major problem around the world and an increasing percentage of new HIV cases is reported to be by sexual transmission. Many studies have been carried out in the field of peer education on HIV/AIDS among young people, however, few studies focused on the long-term effect of this education. To evaluate both the short- and long-term effects of the peer education programme, we conducted a follow-up study to evaluate the related knowledge, attitudes and behaviour intention to HIV/AIDS among senior high-school students in Shanghai, China. We selected 1950 students from 10 senior high schools in Shanghai, from whom 968 students were selected at random for the intervention group and 982 students for the control group. The same questionnaires were carried out before intervention, one month and one year later in both the groups. In the intervention group, the knowledge score of reproductive health, HIV/AIDS and sexually transmitted disease rose from 21.66 to 31.72 one month later (P < 0.001). After one year it was still 30.97, and there was no significant difference between one month and one year (P > 0.05). The behaviour intention to HIV/AIDS prevention, such as condom use during sexual intercourse also changed before and after the intervention. After both the one month and one-year follow-up intervention, we found that more students declared that they would use condoms during sexual intercourse when compared with the control group (P < 0.001). No change was seen in either knowledge or behaviour intention in the control group. These results showed that peer education on HIV/AIDS prevention among high-school students is both effective in promoting knowledge and in changing behaviour intention long term.

Direct evidence for mesoscopic relaxations in cobalt nanoislands on Cu(001)

Surface x-ray diffraction in combination with scanning tunneling microscopy and molecular dynamics calculations provide first quantitative evidence for unusually large relaxations in nanometer-sized Co islands deposited on Cu(001) at 170 K. These lead to sharply reduced interatomic Co distances as low as 2.36 A as compared to bulk Co (2.51 A) involving low symmetry Co adsorption sites. Our results prove the validity of the concept of mesoscopic mismatch which governs the strain relaxation of nanosized islands in general.

Quantum oscillations and beats in X-ray diffraction during film growth

X-ray diffraction from a growing film at an anti-Bragg point should exhibit bilayer oscillations caused by interference. In an experiment of TiN film growth by laser ablation onto sapphire, an unexpected beating envelope function is found to modulate the oscillations. The successive nodes and antinodes are identified with the development of new growth domains separated by one atomic layer in thickness. This effect allows atomic layer counting of the film thickness distribution. The results imply that the growth is not characterized by a continuum stochastic process, as usually assumed.

Dynamic fluctuations and static speckle in critical X-ray scattering from SrTiO3

We report a study of critical x-ray scattering from SrTiO3 near the antiferrodistortive structural phase transition at T(C) approximately 105 K. A line shape analysis of the thermal diffuse scattering results in the most precise experimental determination to date of the critical exponent gamma. The microscopic mechanism behind the anomalous "central peak" critical scattering component is clarified here by the first-ever observation of a static coherent diffraction pattern (speckle pattern) within the anomalous critical scattering of SrTiO3. This observation allows us to directly attribute the origins of the central peak to Bragg diffraction from remnant static disorder above T(C).

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.

Simulation of Depressurization for Gas Production From Gas Hydrate Reservoirs

Abstract

Gas hydrates as a significant resource of natural gas have attracted considerable attention in recent years. However, the severe environmental conditions of gas hydrate reservoirs and the solid form of hydrates require extensive technological development before commercial gas production becomes possible. Numerical studies often give useful information for predicting the potential and technical viability of a recovery process.

This paper presents a 2D cylindrical simulator for gas production from hydrate reservoirs. The model includes the equations for gas-water two-phase flow, conductive and convective heat transfer, and intrinsic kinetics of hydrate decomposition. The simulator is used to model a hydrate reservoir where the hydrate- bearing layer overlies a free gas zone, such as those discovered in the arctic. A well is drilled and completed in the free gas zone. Pressure reduction in the free gas zone leads to the decomposition of the overlying hydrate and subsequent production of the generated gas.

In this paper, we study the impact of the overlying hydrate in improving the production performance of the underlying gas reservoir and investigate the effect of various parameters on gas production behaviour. The rate of gas generated and produced, pressure, temperature, and saturation distributions are studied to investigate the sensitivity of results on individual input parameters. The results suggest that the development of gas reservoirs with overlying hydrates can lead to significant production rates and that the top hydrates have a large impact on increasing the reserve and improving the productivity of the underlying gas reservoir.

Introduction

Today, increasingly more stringent environmental considerations require that clean sources of energy be found. It is therefore anticipated that the demand for natural gas will continue to increase significantly. Some studies indicate that the amount of methane trapped in gas hydrates in natural settings is 100 times that of conventional gas reserves(1, 2). Therefore, gas hydrates are being considered as a potential source for natural gas production. However, it is not clear what percentage of this huge resource is recoverable, and the technologies for recovering natural gas from hydrates are still under development. Sloan(3) has presented an extensive review of some suggested methods, including depressurization, thermal stimulation, and inhibitor injection. The least energy intensive process is thought to be the depressurization method, since in this method the heat of decomposition is provided by the surrounding formation.

Modelling of gas production from hydrate reservoirs involves solving the coupled equations of mass and energy balances. A review of analytical and numerical models given by Hong et al.(4) suggests that two approaches with respect to conditions at the decomposition zone have been taken: equilibrium and non-equilibrium. In models using the equilibrium approach, the three-phase hydrate-gas-water interface is at a thermodynamic equilibrium. The underlying assumption in these models is that the intrinsic rate of hydrate dissociation is fast enough so that the overall rate of hydrate dissociation is controlled by other mechanisms, i.e., fluid flow or heat transfer. In non-equilibrium models however, the condition at the hydrate-gas-water interface is kinetically approaching equilibrium.

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.

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.

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.

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.

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.

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.

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 .

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.

Analytical Modelling of Gas Production From Hydrates in Porous Media

Abstract

Gas hydrates are being considered as an alternative energy resource of thefuture since they exist in enormous quantities in permafrost and offshoreenvironments. However, gas production potential from hydrate reservoirs throughdifferent production schemes has not been fully investigated yet. This workintroduces a simple analytical model for simulating gas production from hydratedecomposition in porous media by a depressurization method.

We consider the heat transfer to the decomposing zone, intrinsic kinetics ofhydrate decomposition, and gas-water two-phase flow as the three primarymechanisms involved in hydrate decomposition in porous media. In this study, the relative importance of these mechanisms is compared over a realistic rangeof the physical properties. It is shown that for the cases studied, the effectof two-phase flow is significantly smaller than the heat transfer and theintrinsic kinetics of hydrate decomposition. Considering the rate-controllingmechanisms, an analytical model is developed to predict the performance ofdecomposition of gas hydrates in porous media. The model is used to performsensitivity studies to investigate the feasibility of commercial gas productionfrom hydrate reservoirs. The results suggest that significant quantities of gascan be produced from gas hydrate reservoirs where the hydrate overlies the gaszone. Such reservoirs have been found in the permafrost regions of Siberia, Alaska, and Canada.

Introduction

The enormous natural gas reserves associated with the in situ gas hydratesin permafrost regions and offshore environments of the earth is expected to bean energy resource of the future. The gas could be produced from the hydratedissociation by depressurization, thermal stimulation, solvent injection, or acombination of these methods. The potential for gas production from hydratereservoirs through different production techniques is still uncertain and underinvestigation. One method of investigation is with the help of mathematicalmodels. For a mathematical model to be representative, it should include theimportant mechanisms. In a depressurization scheme considered in this study, three important mechanisms are involved: intrinsic decomposition of the hydratethat results in reduced temperature; heat flow towards the cooled zone thatprovides the necessary energy for further decomposition; and, flow of thedecomposed gas and water through the porous rock.

[Experimental study on the pathogenesis of Entamoeba gingivalis]

OBJECTIVE

To study the pathogenesis of Entamoeba gingivalis (E. g.) and its relation to periodontal diseases.

METHODS

Rats were treated with immuno-inhibitor for one week and the neck of incisor teeth of the rats was bound with steel wire. They were randomly divided into three groups: the first group was infected by E. g. in the periodontal tissue, the second group was infected by symbiotic bacteria (s. b.), and the third group was given physiological saline as control. Observation on the periodontal inflammation was made for each group of rats, and the purulent secretion from periodontal abscess was examined for living pathogens.

RESULTS

The incidence of periodontal diseases in rats infected by E. g. was higher than that of symbiotic bacteria group and that of control (P < 0.05), the incidence of periodontal diseases in rats infected by s. b. was higher than that of control group (P < 0.05). Living pathogens were found in the abscess liquid.

CONCLUSION

E. g. is an opportunistic pathogen, which, together with synergistic symbiotic bacteria, can cause periodontal diseases in hosts with low immunity.

Comparative molecular field analysis (CoMFA) model using a large diverse set of natural, synthetic and environmental chemicals for binding to the androgen receptor

A large number of natural, synthetic and environmental chemicals are capable of disrupting the endocrine systems of experimental animals, wildlife and humans. These so-called endocrine disrupting chemicals (EDCs), some mimic the functions of the endogenous androgens, have become a concern to the public health. Androgens play an important role in many physiological processes, including the development and maintenance of male sexual characteristics. A common mechanism for androgen to produce both normal and adverse effects is binding to the androgen receptor (AR). In this study, we used Comparative Molecular Field Analysis (CoMFA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) technique, to examine AR-ligand binding affinities. A CoMFA model with r2 = 0.902 and q2 = 0.571 was developed using a large training data set containing 146 structurally diverse natural, synthetic, and environmental chemicals with a 10(6)-fold range of relative binding affinity (RBA). By comparing the binding characteristics derived from the CoMFA contour map with these observed in a human AR crystal structure, we found that the steric and electrostatic properties encoded in this training data set are necessary and sufficient to describe the RBA of AR ligands. Finally, the CoMFA model was challenged with an external test data set; the predicted results were close to the actual values with average difference of 0.637 logRBA. This study demonstrates the utility of this CoMFA model for real-world use in predicting the AR binding affinities of structurally diverse chemicals over a wide RBA range.

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.

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.

Regulatory application of SAR/QSAR for priority setting of endocrine disruptors: A perspective

Some seven years have passed since the U.S. legislature mandated the EPA to develop and implement a screening and testing program for chemicals that may disrupt the delicate endocrine system. The envisioned EPA program has evolved to incorporate a tiered scheme of in vitro and in vivo assays, and considered QSAR as a viable method to set testing priorities. At the U.S. FDA's National Center for Toxicological Research (NCTR), the Endocrine Disruptor Knowledge Base Project has developed models to predict estrogen and androgen receptor binding. Our approach rationally integrates various QSAR models into a sequential "Four-Phase" scheme according to the strength of each type of model. In four hierarchical phases, models predict the inactive chemicals that are then eliminated from the pool of chemicals to which increasingly precise but more time-consuming models are subsequently applied. Each phase employs different models selected to work complementarily in representing key activity-determining structure features in order to absolutely minimize the rate of false negatives, an outcome we view as paramount for regulatory use. In this paper, the QSAR models developed at NCTR, and particularly how we integrated these models into the "Four-Phase" system will be discussed for a number of datasets, including 58 000 chemicals identified by the U.S. EPA.

Dissolved insecticides and polychlorinated biphenyls in the Pearl River Estuary and South China Sea

Persistent organic pollutants (POPs) such as organochlorine (OCl) insecticides and polychlorinated biphenyls (PCB), together with the new generation of organophosphorus (OP) insecticides, are of global concern, due to their widespread occurrence, persistence, bioaccumulation and hormone disruption potential. This paper represents an attempt to study the source and transportation of such pollutants in estuarine and coastal environments as an integrated ecosystem, by determining the levels of 18 OCl insecticides, 21 PCB congeners, and 17 OP insecticides in the Pearl River Estuary and South China Sea. The total concentrations varied from 126-1198 ng l(-1) for OCl insecticides, 33.38-1064 ng l(-1) for PCB congeners, and 4.44-6356 ng l(-1) for OP insecticides in the Pearl River Estuary. In comparison, their levels in the South China Sea were significantly lower, varying from 57.09-202 ng l(-1) for OCl insecticides, 21.72-144 ng l(-1) for PCBs, and 1.27-122 ng l(-1) for OP insecticides, respectively. The predominance of beta-HCH in HCHs, and DDE in DDTs in all water samples was clearly observed, suggesting beta-HCH and DDE's resistance to further degradation. The PCBs were dominated by those with 3-6 chlorines. The distribution characteristic of OP insecticides shows that five compounds (methamidophos, dimethoate, malathion, dichlorvos and omethoate) accounted for 56% and 72% of the total OP insecticide concentration. The relationship between pollutant concentrations and salinity in the estuary showed that they were all removed during the mixing process, therefore behaving non-conservatively.

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.

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.

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.

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.

An integrated "4-phase" approach for setting endocrine disruption screening priorities--phase I and II predictions of estrogen receptor binding affinity

Recent legislation mandates the US Environmental Protection Agency (EPA) to develop a screening and testing program for potential endocrine disrupting chemicals (EDCs), of which xenoestrogens figure prominently. Under the legislation, a large number of chemicals will undergo various in vitro and in vivo assays for their potential estrogenicity, as well as other hormonal activities. There is a crucial need for priority setting before this strategy can be effectively implemented. Here we report an integrated computational approach to priority setting using estrogen receptor (ER) binding as an example. This approach rationally integrates different predictive computational models into a "Four-Phase" scheme so that it can effectively identify potential estrogenic EDCs based on their predicted ER relative binding affinity (RBA). The system has been validated using an in-house ER binding assay dataset for 232 chemicals that was designed to have both broad structural diversity and a wide range of binding affinities. When applied to 58,000 chemicals identified by Walker et al. as candidates for endocrine disruption screening, some 9100 chemicals were predicted to bind to ER. Of these, only 3600 were expected to bind to ER at RBA values up to 100,000-fold less than that of 17beta-estradiol. The method ruled out 83% of the chemicals as non-binders with a very low rate of false negatives. We believe that the same integrated scheme will be equally applicable to endpoints of other endocrine disrupting mechanisms, e.g. androgen receptor binding.

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.

Spontaneous phase oscillation induced by inertia and time delay

We consider a system of coupled oscillators with finite inertia and time-delayed interaction, and investigate the interplay between inertia and delay both analytically and numerically. The phase velocity of the system is examined; revealed in numerical simulations is the emergence of spontaneous phase oscillation without external driving, which turns out to be in good agreement with analytical results derived in the strong-coupling limit. Such self-oscillation is found to suppress synchronization, and its frequency is observed to decrease with inertia and delay. We obtain the phase diagram, which displays oscillatory and stationary phases in the appropriate regions of the parameters.

XY model in small-world networks

The phase transition in the XY model on one-dimensional small-world networks is investigated by means of Monte Carlo simulations. It is found that long-range order is present at finite temperatures, even for very small values of the rewiring probability, suggesting a finite-temperature transition for any nonzero rewiring probability. Nature of the phase transition is discussed in comparison with the globally coupled XY model.

Ventricular shape visualization using selective volume rendering of cardiac datasets

In this paper, we present a novel technique of improving volume rendering quality and speed by integrating original volume data and global model information attained by segmentation. The segmentation information prevents object occlusions that may appear when volume rendering is based on local image features only. Thus the presented visualization technique provides meaningful visual results that enable a clear understanding of complex anatomical structures. In the first part, we describe a segmentation technique for extracting the region of interest based on an active contour model. In the second part, we propose a volume rendering method for visualizing the selected portions of fuzzy surfaces extracted by local image processing methods. We show the results of selective volume rendering of left and right ventricle based on cardiac datasets from clinical routines. Our method offers an accelerated technique to accurately visualize the surfaces of segmented objects.

Biosynthesis of the vancomycin group of antibiotics: characterisation of a type III polyketide synthase in the pathway to (S)-3,5-dihydroxyphenylglycine

3,5-dihydroxyphenylacetate, a precursor for the non-proteinogenic amino acid 3,5-dihydroxyphenylglycine occurring in glycopeptide antibiotics, is determined to be catalysed by a type III polyketide synthase using malonyl-CoA as a starter unit.

Identification of a Delta 4 fatty acid desaturase from Thraustochytrium sp. involved in the biosynthesis of docosahexanoic acid by heterologous expression in Saccharomyces cerevisiae and Brassica juncea

The existence of Delta 4 fatty acid desaturation in the biosynthesis of docosahexanoic acid (DHA) has been questioned over the years. In this report we describe the identification from Thraustochytrium sp. of two cDNAs, Fad4 and Fad5, coding for Delta 4 and Delta 5 fatty acid desaturases, respectively. The Delta 4 desaturase, when expressed in Saccharomyces cerevisiae, introduced a double bond at position 4 of 22:5(n-3) and 22:4(n-6) resulting in the production of DHA and docosapentanoic acid. The enzyme, when expressed in Brassica juncea under the control of a constitutive promoter, desaturated the exogenously supplied substrate 22:5(n-3), resulting in the production of DHA in vegetative tissues. These results support the notion that DHA can be synthesized via Delta 4 desaturation and suggest the possibility that DHA can be produced in oilseed crops on a large scale.