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 .