An EBE finite element method for simulating nonlinear flows in rotating spheroidal cavities

Many planetary and astrophysical bodies are rotating rapidly, fluidic and, as a consequence of rapid rotation, in the shape of an ablate spheroid. We present an efficient element-by-element (EBE) finite element method for the numerical simulation of nonlinear flows in rotating incompressible fluids that are confined in an ablate spheroidal cavity with arbitrary eccentricity. Our focus is placed on temporal and spatial tetrahedral discretization of the EBE finite element method in spheroidal geometry, the EBE parallelization scheme and the validation of the nonlinear spheroidal code via both the constructed exact nonlinear solution and the special resonant forcing in the inviscid limit. Copyright © 2009 John Wiley & Sons, Ltd.postprin

On nonlinear multiarmed spiral waves in slowly rotating systems

Stable nonlinear equilibria of convection in the form of quasistationary, multiarmed spiral waves, up to a maximum of six spiral arms, are found in a slowly rotating fluid confined within a thin spherical shell governed by the three-dimensional Navier–Stokes equation, driven by a radial unstable temperature gradient and affected by a weak Coriolis force. It is shown that three essential ingredients are generally required for the formation of the multiarmed spirals: the influence of slow rotation, large-aspect-ratio geometry and the effect of weak nonlinearity.published_or_final_versio

The non-resonant response of fluid in a rapidly rotating sphere undergoing longitudinal libration

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A molecular dynamics simulation on the oxidation of core-shell aluminum nanoparticles in oxygen and water environments

The oxidation mechanisms of core-shell aluminum nanoparticles (ANPs) in high-temperature steam and oxygen are investigated by ReaxFF molecular dynamics (MD) simulation. The details concerning reaction heat release, heat transfer, atomic diffusion process, and ANP structure evolution are studied by examining the temporal variations of temperature, energy, atoms concentration distributions and particle structure, respectively. The atomic-level heat and mass transfer processes reveal that for both ANP/H2O and ANP/O2 systems, at the initial stage of oxidation, the heat transfer between ANP and environmental oxidizer is dominant. Thereafter, the reaction plays an increasingly significant role. The heat transfer efficiency of ANP/H2O is higher than that of ANP/O2, while the reaction exotherm of ANP/H2O is lower than ANP/O2. The final particle temperature for ANP/O2 system is much higher than that of ANP/H2O. The diameter of the former is also larger. During the oxidation of ANP, the core Al atoms diffuse outward into the oxide shell, which pushes the shell Al atoms outward and results in the expansion of ANP. The shell O atoms diffuse inward and left a vacant lattice site, through which the ambient H and O atoms diffuse into the oxide shell

Size-derived reaction mechanism of core-shell aluminum nanoparticle

To prompt the application of aluminum nanoparticles (ANPs) in combustion as the fuel additive and in chemical synthesis as the catalyst, this study examines the reaction dynamics of core-shell ANPs under an oxygen atmosphere via Transient Non-Equilibrium Reactive Molecular Dynamics simulations. Two distinct oxidation modes determined by the competition between the oxide shell melting and core reaction have been identified. One is the fast oxidation mode with a high reaction heat release rate, where core Al and ambient O atoms diffuse into each other to form a homogeneous alumina particle. The other is the moderate oxidation with lower heat release, where only core Al atoms diffuse into the oxide shell to form a hollow spherical structure. By modeling the shell melting and Al core reaction, a size-derived oxidation model has been proposed to conveniently but accurately predict the ANP reaction dynamics. This work also provides fundamental insight into the synthesis of ANPs that serve as a high energy density fuel and high-performance catalyst

Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53

Background: The availability of various "omics" datasets creates a prospect of performing the study of genome-wide genetic regulatory networks. However, one of the major challenges of using mathematical models to infer genetic regulation from microarray datasets is the lack of information for protein concentrations and activities. Most of the previous researches were based on an assumption that the mRNA levels of a gene are consistent with its protein activities, though it is not always the case. Therefore, a more sophisticated modelling framework together with the corresponding inference methods is needed to accurately estimate genetic regulation from "omics" datasets. Results: This work developed a novel approach, which is based on a nonlinear mathematical model, to infer genetic regulation from microarray gene expression data. By using the p53 network as a test system, we used the nonlinear model to estimate the activities of transcription factor (TF) p53 from the expression levels of its target genes, and to identify the activation/inhibition status of p53 to its target genes. The predicted top 317 putative p53 target genes were supported by DNA sequence analysis. A comparison between our prediction and the other published predictions of p53 targets suggests that most of putative p53 targets may share a common depleted or enriched sequence signal on their upstream non-coding region. Conclusions: The proposed quantitative model can not only be used to infer the regulatory relationship between TF and its down-stream genes, but also be applied to estimate the protein activities of TF from the expression levels of its target genes

Water dispersible microbicidal cellulose acetate phthalate film

BACKGROUND: Cellulose acetate phthalate (CAP) has been used for several decades in the pharmaceutical industry for enteric film coating of oral tablets and capsules. Micronized CAP, available commercially as "Aquateric" and containing additional ingredients required for micronization, used for tablet coating from water dispersions, was shown to adsorb and inactivate the human immunodeficiency virus (HIV-1), herpesviruses (HSV) and other sexually transmitted disease (STD) pathogens. Earlier studies indicate that a gel formulation of micronized CAP has a potential as a topical microbicide for prevention of STDs including the acquired immunodeficiency syndrome (AIDS). The objective of endeavors described here was to develop a water dispersible CAP film amenable to inexpensive industrial mass production. METHODS: CAP and hydroxypropyl cellulose (HPC) were dissolved in different organic solvent mixtures, poured into dishes, and the solvents evaporated. Graded quantities of a resulting selected film were mixed for 5 min at 37°C with HIV-1, HSV and other STD pathogens, respectively. Residual infectivity of the treated viruses and bacteria was determined. RESULTS: The prerequisites for producing CAP films which are soft, flexible and dispersible in water, resulting in smooth gels, are combining CAP with HPC (other cellulose derivatives are unsuitable), and casting from organic solvent mixtures containing ≈50 to ≈65% ethanol (EtOH). The films are ≈100 µ thick and have a textured surface with alternating protrusions and depressions revealed by scanning electron microscopy. The films, before complete conversion into a gel, rapidly inactivated HIV-1 and HSV and reduced the infectivity of non-viral STD pathogens >1,000-fold. CONCLUSIONS: Soft pliable CAP-HPC composite films can be generated by casting from organic solvent mixtures containing EtOH. The films rapidly reduce the infectivity of several STD pathogens, including HIV-1. They are converted into gels and thus do not have to be removed following application and use. In addition to their potential as topical microbicides, the films have promise for mucosal delivery of pharmaceuticals other than CAP

A four-gene LincRNA expression signature predicts risk in multiple cohorts of acute myeloid leukemia patients.

Prognostic gene expression signatures have been proposed as clinical tools to clarify therapeutic options in acute myeloid leukemia (AML). However, these signatures rely on measuring large numbers of genes and often perform poorly when applied to independent cohorts or those with older patients. Long intergenic non-coding RNAs (lincRNAs) are emerging as important regulators of cell identity and oncogenesis, but knowledge of their utility as prognostic markers in AML is limited. Here we analyze transcriptomic data from multiple cohorts of clinically annotated AML patients and report that (i) microarrays designed for coding gene expression can be repurposed to yield robust lincRNA expression data, (ii) some lincRNA genes are located in close proximity to hematopoietic coding genes and show strong expression correlations in AML, (iii) lincRNA gene expression patterns distinguish cytogenetic and molecular subtypes of AML, (iv) lincRNA signatures composed of three or four genes are independent predictors of clinical outcome and further dichotomize survival in European Leukemia Net (ELN) risk groups and (v) an analytical tool based on logistic regression analysis of quantitative PCR measurement of four lincRNA genes (LINC4) can be used to determine risk in AML

Prognostic value of hedgehog signal component expressions in hepatoblastoma patients

<p>Abstract</p> <p>Objective</p> <p>Activation of hedgehog (Hh) pathway has been implicated in the development of human malignancies. Hh as well as related downstream target genes has been extensively studied in many kinds of malignant tumours for clinical diagnostic or prognostic utilities. This study aimed at investigating whether Hh molecules provides a molecular marker of hepatoblastoma malignancy.</p> <p>Methods</p> <p>We obtained tissue sections from 32 patients with hepatoblastoma as well as cholestasis and normal control. Immunohistochemical analysis were performed to determine Hh signal components in human hepatoblastoma. The prognostic significance of single expression of Hh signal components were evaluated using Cox proportional hazards regression models and Kaplan-Meier survival analysis for statistical analysis.</p> <p>Results</p> <p>Expression of Hh signal components showed an increase in hepatoblastoma compared with chole stasis and normal tissues. There was a positive correlation between Smo or Gli1 expression and tumor clinicopathological features, such as histological type, tumor grade, tumor size and clinical stage. Both Smo or Gli1 protein high expression was significantly associated with poor prognosis by univariate analyses and multivariate analyses.</p> <p>Conclusions</p> <p>Abnormal Hh signaling activation plays important roles in the malignant potential of hepatoblastoma. Gli1 expression is an independent prognostic marker.</p

Disparities and risks of sexually transmissible infections among men who have sex with men in China: a meta-analysis and data synthesis.

BACKGROUND: Sexually transmitted infections (STIs), including Hepatitis B and C virus, are emerging public health risks in China, especially among men who have sex with men (MSM). This study aims to assess the magnitude and risks of STIs among Chinese MSM. METHODS: Chinese and English peer-reviewed articles were searched in five electronic databases from January 2000 to February 2013. Pooled prevalence estimates for each STI infection were calculated using meta-analysis. Infection risks of STIs in MSM, HIV-positive MSM and male sex workers (MSW) were obtained. This review followed the PRISMA guidelines and was registered in PROSPERO. RESULTS: Eighty-eight articles (11 in English and 77 in Chinese) investigating 35,203 MSM in 28 provinces were included in this review. The prevalence levels of STIs among MSM were 6.3% (95% CI: 3.5-11.0%) for chlamydia, 1.5% (0.7-2.9%) for genital wart, 1.9% (1.3-2.7%) for gonorrhoea, 8.9% (7.8-10.2%) for hepatitis B (HBV), 1.2% (1.0-1.6%) for hepatitis C (HCV), 66.3% (57.4-74.1%) for human papillomavirus (HPV), 10.6% (6.2-17.6%) for herpes simplex virus (HSV-2) and 4.3% (3.2-5.8%) for Ureaplasma urealyticum. HIV-positive MSM have consistently higher odds of all these infections than the broader MSM population. As a subgroup of MSM, MSW were 2.5 (1.4-4.7), 5.7 (2.7-12.3), and 2.2 (1.4-3.7) times more likely to be infected with chlamydia, gonorrhoea and HCV than the broader MSM population, respectively. CONCLUSION: Prevalence levels of STIs among MSW were significantly higher than the broader MSM population. Co-infection of HIV and STIs were prevalent among Chinese MSM. Integration of HIV and STIs healthcare and surveillance systems is essential in providing effective HIV/STIs preventive measures and treatments. TRIAL REGISTRATION: PROSPERO NO: CRD42013003721