Comparison of depth-averaged concentration and bed load flux sediment transport models of dam-break flow

This paper presents numerical simulations of dam-break flow over a movable bed. Two different mathematical models were compared: a fully coupled formulation of shallow water equations with erosion and deposition terms (a depth-averaged concentration flux model), and shallow water equations with a fully coupled Exner equation (a bed load flux model). Both models were discretized using the cell-centered finite volume method, and a second-order Godunov-type scheme was used to solve the equations. The numerical flux was calculated using a Harten, Lax, and van Leer approximate Riemann solver with the contact wave restored (HLLC). A novel slope source term treatment that considers the density change was introduced to the depth-averaged concentration flux model to obtain higher-order accuracy. A source term that accounts for the sediment flux was added to the bed load flux model to reflect the influence of sediment movement on the momentum of the water. In a one-dimensional test case, a sensitivity study on different model parameters was carried out. For the depth-averaged concentration flux model, Manning's coefficient and sediment porosity values showed an almost linear relationship with the bottom change, and for the bed load flux model, the sediment porosity was identified as the most sensitive parameter. The capabilities and limitations of both model concepts are demonstrated in a benchmark experimental test case dealing with dam-break flow over variable bed topography

Wave propagation speeds and source term influences in single and integral porosity shallow water equations

In urban flood modeling, so-called porosity shallow water equations (PSWEs), which conceptually account for unresolved structures, e.g., buildings, are a promising approach to addressing high CPU times associated with state-of-the-art explicit numerical methods. The PSWE can be formulated with a single porosity term, referred to as the single porosity shallow water model (SP model), which accounts for both the reduced storage in the cell and the reduced conveyance, or with two porosity terms: one accounting for the reduced storage in the cell and another accounting for the reduced conveyance. The latter form is referred to as an integral or anisotropic porosity shallow water model (AP model). The aim of this study was to analyze the differences in wave propagation speeds of the SP model and the AP model and the implications of numerical model results. First, augmented Roe-type solutions were used to assess the influence of the source terms appearing in both models. It is shown that different source terms have different influences on the stability of the models. Second, four computational test cases were presented and the numerical models were compared. It is observed in the eigenvalue-based analysis as well as in the computational test cases that the models converge if the conveyance porosity in the AP model is close to the storage porosity. If the porosity values differ significantly, the AP model yields different wave propagation speeds and numerical fluxes from those of the BP model. In this study, the ratio between the conveyance and storage porosities was determined to be the most significant parameter

A Bayesian method for evaluating and discovering disease loci associations

Background: A genome-wide association study (GWAS) typically involves examining representative SNPs in individuals from some population. A GWAS data set can concern a million SNPs and may soon concern billions. Researchers investigate the association of each SNP individually with a disease, and it is becoming increasingly commonplace to also analyze multi-SNP associations. Techniques for handling so many hypotheses include the Bonferroni correction and recently developed Bayesian methods. These methods can encounter problems. Most importantly, they are not applicable to a complex multi-locus hypothesis which has several competing hypotheses rather than only a null hypothesis. A method that computes the posterior probability of complex hypotheses is a pressing need. Methodology/Findings: We introduce the Bayesian network posterior probability (BNPP) method which addresses the difficulties. The method represents the relationship between a disease and SNPs using a directed acyclic graph (DAG) model, and computes the likelihood of such models using a Bayesian network scoring criterion. The posterior probability of a hypothesis is computed based on the likelihoods of all competing hypotheses. The BNPP can not only be used to evaluate a hypothesis that has previously been discovered or suspected, but also to discover new disease loci associations. The results of experiments using simulated and real data sets are presented. Our results concerning simulated data sets indicate that the BNPP exhibits both better evaluation and discovery performance than does a p-value based method. For the real data sets, previous findings in the literature are confirmed and additional findings are found. Conclusions/Significance: We conclude that the BNPP resolves a pressing problem by providing a way to compute the posterior probability of complex multi-locus hypotheses. A researcher can use the BNPP to determine the expected utility of investigating a hypothesis further. Furthermore, we conclude that the BNPP is a promising method for discovering disease loci associations. © 2011 Jiang et al

Proteomics: in pursuit of effective traumatic brain injury therapeutics

Effective traumatic brain injury (TBI) therapeutics remain stubbornly elusive. Efforts in the field have been challenged by the heterogeneity of clinical TBI, with greater complexity among underlying molecular phenotypes than initially conceived. Future research must confront the multitude of factors comprising this heterogeneity, representing a big data challenge befitting the coming informatics age. Proteomics is poised to serve a central role in prescriptive therapeutic development, as it offers an efficient endpoint within which to assess post-TBI biochemistry. We examine rationale for multifactor TBI proteomic studies and the particular importance of temporal profiling in defining biochemical sequences and guiding therapeutic development. Lastly, we offer perspective on repurposing biofluid proteomics to develop theragnostic assays with which to prescribe, monitor and assess pharmaceutics for improved translation and outcome for TBI patients

Homozygous microdeletion of exon 5 in ZNF277 in a girl with specific language impairment

Peer reviewedPublisher PD

Anti-epileptic effect of Ganoderma lucidum polysaccharides by inhibition of intracellular calcium accumulation and stimulation of expression of CaMKII a in epileptic hippocampal neurons

Purpose: To investigate the mechanism of the anti-epileptic effect of Ganoderma lucidum polysaccharides (GLP), the changes of intracellular calcium and CaMK II a expression in a model of epileptic neurons were investigated. Method: Primary hippocampal neurons were divided into: 1) Control group, neurons were cultured with Neurobasal medium, for 3 hours; 2) Model group I: neurons were incubated with Mg2+ free medium for 3 hours; 3) Model group II: neurons were incubated with Mg2+ free medium for 3 hours then cultured with the normal medium for a further 3 hours; 4) GLP group I: neurons were incubated with Mg2+ free medium containing GLP (0.375 mg/ml) for 3 hours; 5) GLP group II: neurons were incubated with Mg2+ free medium for 3 hours then cultured with a normal culture medium containing GLP for a further 3 hours. The CaMK II a protein expression was assessed by Western-blot. Ca2+ turnover in neurons was assessed using Fluo-3/AM which was added into the replacement medium and Ca2+ turnover was observed under a laser scanning confocal microscope. Results: The CaMK II a expression in the model groups was less than in the control groups, however, in the GLP groups, it was higher than that observed in the model group. Ca2+ fluorescence intensity in GLP group I was significantly lower than that in model group I after 30 seconds, while in GLP group II, it was reduced significantly compared to model group II after 5 minutes. Conclusion: GLP may inhibit calcium overload and promote CaMK II a expression to protect epileptic neuron

Atomically dispersed Pt-N-4 sites as efficient and selective electrocatalysts for the chlorine evolution reaction

Chlorine evolution reaction (CER) is a critical anode reaction in chlor-alkali electrolysis. Although precious metal-based mixed metal oxides (MMOs) have been widely used as CER catalysts, they suffer from the concomitant generation of oxygen during the CER. Herein, we demonstrate that atomically dispersed Pt-N-4 sites doped on a carbon nanotube (Pt-1/CNT) can catalyse the CER with excellent activity and selectivity. The Pt-1/CNT catalyst shows superior CER activity to a Pt nanoparticle-based catalyst and a commercial Ru/Ir-based MMO catalyst. Notably, Pt-1/CNT exhibits near 100% CER selectivity even in acidic media, with low Cl- concentrations (0.1M), as well as in neutral media, whereas the MMO catalyst shows substantially lower CER selectivity. In situ electrochemical X-ray absorption spectroscopy reveals the direct adsorption of Cl- on Pt-N-4 sites during the CER. Density functional theory calculations suggest the PtN4C12 site as the most plausible active site structure for the CER

Evidence-based obstetrics in four hospitals in China: An observational study to explore clinical practice, women's preferences and provider's views

BACKGROUND: Evidence-based obstetric care is widely promoted in developing countries, but the success of implementation is not known. Using selected childbirth care procedures in four hospitals in Shanghai, we compared practice against evidence-based information, and explored user and provider views about each procedure. METHODS: Observational study. Using the Cochrane Library, we identified six procedures that should be avoided as routine and two that should be encouraged. Procedure rate determined by exit interviews with women, verified using hospital notes. Views of women and providers explored with in depth interviews. The study sites were three hospitals in Shanghai and one in neighbouring province of Jiangsu. 150 women at each centre for procedure rate, and 48 in-depth interviews with women and providers. RESULTS: Vaginal births were 50% (303/599) of the total. Of the six practices where evidence suggests they should be avoided as routine, three were performed with rates above 70%: pubic shaving (3 hospitals), rectal examination (3 hospitals), and episiotomy (3 hospitals). Most women delivered lying down, pain relief was rarely given, and only in the urban district hospital did women routinely have a companion. Most women wanted support or companionship during labour and to be given pain relief; but current practice is insufficient to meet women's needs. CONCLUSION: Obstetric practice is not following best available evidence in the hospitals studied. There is a need to adjust hospital policy to support the use of interventions proven to be of benefit to women during childbirth, and develop approaches that ensure clinical practice changes