On the upstream mobility scheme for two-phase flow in porous media

When neglecting capillarity, two-phase incompressible flow in porous media is modelled as a scalar nonlinear hyperbolic conservation law. A change in the rock type results in a change of the flux function. Discretizing in one-dimensional with a finite volume method, we investigate two numerical fluxes, an extension of the Godunov flux and the upstream mobility flux, the latter being widely used in hydrogeology and petroleum engineering. Then, in the case of a changing rock type, one can give examples when the upstream mobility flux does not give the right answer.Comment: A preprint to be published in Computational Geoscience

Delayed nephrectomy has comparable long-term overall survival to immediate nephrectomy for cT1a renal cell carcinoma: A population-based analysis

Objectives: Early surgical resection remains the recommended treatment option for most small renal mass (≤4 cm). We examined the long-term overall survival (OS) of patients managed with delayed and immediate nephrectomy of cT1a renal cancer. / Patient and methods: We utilized the National Cancer Database (2005–2010) to identify 14,677 patients (immediate nephrectomy: 14,050 patients vs. late nephrectomy: 627 patients) aged 180 days from diagnosis, respectively. Inverse probability of treatment weighting–adjusted Kaplan-Meier curves and Cox proportional hazards regression analyses were used to compare OS of patients in the 2 treatment arms. Influence of patient age and Charlson Comorbidity Index on treatment effect was tested by interactions. Sensitivity analysis was performed to explore the outcome of delaying nephrectomy for >12 months. / Results: Median patient age was 55 years with a median follow-up of 82.5 months. Inverse probability of treatment weighting-adjusted Kaplan-Meier curves suggest no significant difference between treatment arms (immediate nephrectomy [180 days]) (Hazard ratio 0.96; 95% confidence interval 0.73–1.26; P = 0.77). This outcome was consistent between all patients regardless of age (P = 0.48). Sensitivity analysis reports no difference in OS even if nephrectomy was delayed by >12 months (P = 0.60). / Conclusions: We report that delayed and immediate nephrectomy for cT1a renal cell carcinoma confers comparable long-term OS. These findings suggest that a period of observation of between 6 and 12 months is safe to allow identification of renal masses, which will benefit from surgical resection

CheS-Mapper - Chemical Space Mapping and Visualization in 3D

Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. To that respect, visualization tools can help to better comprehend the underlying correlations. Our recently developed 3D molecular viewer CheS-Mapper (Chemical Space Mapper) divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kind of features, like structural fragments as well as quantitative chemical descriptors. These features can be highlighted within CheS-Mapper, which aids the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. As a final function, the tool can also be used to select and export specific subsets of a given dataset for further analysis

A general modeling and visualization tool for comparing different members of a group: application to studying tau-mediated regulation of microtubule dynamics

<p>Abstract</p> <p>Background</p> <p>Innumerable biological investigations require comparing collections of molecules, cells or organisms to one another with respect to one or more of their properties. Almost all of these comparisons are performed manually, which can be susceptible to inadvertent bias as well as miss subtle effects. The development and application of computer-assisted analytical and interpretive tools could help address these issues and thereby dramatically improve these investigations.</p> <p>Results</p> <p>We have developed novel computer-assisted analytical and interpretive tools and applied them to recent studies examining the ability of 3-repeat and 4-repeat tau to regulate the dynamic behavior of microtubules in vitro. More specifically, we have developed an automated and objective method to define growth, shortening and attenuation events from real time videos of dynamic microtubules, and demonstrated its validity by comparing it to manually assessed data. Additionally, we have used the same data to develop a general strategy of building different models of interest, computing appropriate dissimilarity functions to compare them, and embedding them on a two-dimensional plot for visualization and easy comparison. Application of these methods to assess microtubule growth rates and growth rate distributions established the validity of the embedding procedure and revealed non-linearity in the relationship between the tau:tubulin molar ratio and growth rate distribution.</p> <p>Conclusion</p> <p>This work addresses the need of the biological community for rigorously quantitative and generally applicable computational tools for comparative studies. The two-dimensional embedding method retains the inherent structure of the data, and yet markedly simplifies comparison between models and parameters of different samples. Most notably, even in cases where numerous parameters exist by which to compare the different samples, our embedding procedure provides a generally applicable computational strategy to detect subtle relationships between different molecules or conditions that might otherwise escape manual analyses.</p

Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality.

Biofilm formation in drinking water distribution systems (DWDS) is influenced by the source water, the supply infrastructure and the operation of the system. A holistic approach was used to advance knowledge on the development of mixed species biofilms in situ, by using biofilm sampling devices installed in chlorinated networks. Key physico-chemical parameters and conventional microbial indicators for drinking water quality were analysed. Biofilm coverage on pipes was evaluated by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). The microbial community structure, bacteria and fungi, of water and biofilms was assessed using pyrosequencing. Conventional wisdom leads to an expectation for less microbial diversity in groundwater supplied systems. However, the analysis of bulk water showed higher microbial diversity in groundwater site samples compared with the surface water site. Conversely, higher diversity and richness were detected in biofilms from the surface water site. The average biofilm coverage was similar among sites. Disinfection residual and other key variables were similar between the two sites, other than nitrates, alkalinity and the hydraulic conditions which were extremely low at the groundwater site. Thus, the unexpected result of an exceptionally low diversity with few dominant genera (Pseudomonas and Basidiobolus) in groundwater biofilm samples, despite the more diverse community in the bulk water, is attributed to the low-flow hydraulic conditions. This finding evidences that the local environmental conditions are shaping biofilm formation, composition and amount, and hence managing these is critical for the best operation of DWDS to safeguard water quality

Predicting Life Expectancy in Men Diagnosed with Prostate Cancer

Context: The widespread use of prostate-specific antigen (PSA) screening has led to the detection of more indolent prostate cancer (PCa) in healthy men. PCa treatment and screening must therefore balance the potential for life gained against the potential for harm. Fundamental to this balance is physician awareness of a patient's estimated life expectancy (LE). Objective: To review the evidence on LE differences between men diagnosed with PCa and the general population. To examine clinician-and model-predicted LE and publicly available LE calculators. Evidence acquisition: A comprehensive search of the PubMed database between 1990 and September 2014 was performed according to Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) guidelines. Free text protocols of the following search terms were used "life expectancy prostate cancer", "life expectancy non-cancer", "non-cancer mortality prostate", and "comorbidity-adjusted life expectancy". Two internet search engines were queried daily for 1 mo for the search term "life expectancy calculator", and the top 20 results were examined. Evidence synthesis: Of 992 articles and 32 websites screened, 17 articles and nine websites were selected for inclusion. Men with non-screening-detected PCa and distant disease at diagnosis were found to have shorter LE than age-matched peers, whereas men with localized PCa had prolonged LE. In general, clinician-predicted 10-yr LE was pessimistic and of limited accuracy; however, model-predicted LE provided only modest improvements in accuracy (c-index of models 0.65-0.84). Online LE calculators provide consistent LE estimates, but government life tables provide LE estimates near the mean for all calculators examined. Conclusions: The accuracy of clinician-predicted survival is limited, and while available statistical models offer improvement in discrimination, it is unclear whether they provide advantages over freely available government life tables. Patient summary: We examined differences in life expectancy between men diagnosed with prostate cancer and the general population, and ways of predicting life expectancy to help guide treatment decisions. We found that current models for predicting life expectancy specific to prostate cancer might not be any better than government life tables or simple rules of thumb. (C) 2015 European Association of Urology. Published by Elsevier B.V. All rights reserved