433 research outputs found
A Non Exercise Based Estimation of the Critical Velocity and Anaerobic Distance Capacity in Collegiate Swimmers
This study determined if the parameters of the critical velocity (CV) model could be obtained from estimated performance times at various swimming distances. Fourteen collegiate swimmers provided their actual fastest long-course times (ATcom) at standard distances and inquired completion times (ITcom) at non-standard distances. The total distance (TD) versus ATcom and ITcom relationships were used to estimate the parameters of the CV model. . . . To read the remainder of this abstract, please download this thesis
Using Strategy Improvement to Stay Alive
We design a novel algorithm for solving Mean-Payoff Games (MPGs). Besides
solving an MPG in the usual sense, our algorithm computes more information
about the game, information that is important with respect to applications. The
weights of the edges of an MPG can be thought of as a gained/consumed energy --
depending on the sign. For each vertex, our algorithm computes the minimum
amount of initial energy that is sufficient for player Max to ensure that in a
play starting from the vertex, the energy level never goes below zero. Our
algorithm is not the first algorithm that computes the minimum sufficient
initial energies, but according to our experimental study it is the fastest
algorithm that computes them. The reason is that it utilizes the strategy
improvement technique which is very efficient in practice
The tropical shadow-vertex algorithm solves mean payoff games in polynomial time on average
We introduce an algorithm which solves mean payoff games in polynomial time
on average, assuming the distribution of the games satisfies a flip invariance
property on the set of actions associated with every state. The algorithm is a
tropical analogue of the shadow-vertex simplex algorithm, which solves mean
payoff games via linear feasibility problems over the tropical semiring
. The key ingredient in our approach is
that the shadow-vertex pivoting rule can be transferred to tropical polyhedra,
and that its computation reduces to optimal assignment problems through
Pl\"ucker relations.Comment: 17 pages, 7 figures, appears in 41st International Colloquium, ICALP
2014, Copenhagen, Denmark, July 8-11, 2014, Proceedings, Part
Saffron and its major ingredients’ effect on colon cancer cells with mismatch repair deficiency and microsatellite instability
Background: Colorectal cancer (CRC) is one of the most common cancers worldwide. One of its subtypes is associated with defective mismatch repair (dMMR) genes. Saffron has many potentially protective roles against colon malignancy. However, these roles in the context of dMMR tumors have not been explored. In this study, we aimed to investigate the effects of saffron and its constituents in CRC cell lines with dMMR. Methods: Saffron crude extracts and specific compounds (safranal and crocin) were used in the human colorectal cancer cell lines HCT116, HCT116+3 (inserted MLH1), HCT116+5 (inserted MSH3), and HCT116+3+5 (inserted MLH1 and MSH3). CDC25b, p-H2AX, TPDP1, and GAPDH were analyzed by Western blot. Proliferation and cytotoxicity were analyzed by MTT. The scratch wound assay was also performed. Results: Saffron crude extracts restricted (up to 70%) the proliferation in colon cells with deficient MMR (HCT116) compared to proficient MMR. The wound healing assay indicates that deficient MMR cells are doing better (up to 90%) than proficient MMR cells when treated with saffron. CDC25b and TDP1 downregulated (up to 20-fold) in proficient MMR cells compared to deficient MMR cells, while p.H2AX was significantly upregulated in both cell types, particularly at >10 mg/mL saffron in a concentration-dependent manner. The reduction in cellular proliferation was accompanied with upregulation of caspase 3 and 7. The major active saffron compounds, safranal and crocin reproduced most of the saffron crude extracts' effects. Conclusions: Saffron's anti-proliferative effect is significant in cells with deficient MMR. This novel effect may have therapeutic implications and benefits for MSI CRC patients who are generally not recommended for the 5-fluorouracil-based treatment
BioDiVinE: A Framework for Parallel Analysis of Biological Models
In this paper a novel tool BioDiVinEfor parallel analysis of biological
models is presented. The tool allows analysis of biological models specified in
terms of a set of chemical reactions. Chemical reactions are transformed into a
system of multi-affine differential equations. BioDiVinE employs techniques for
finite discrete abstraction of the continuous state space. At that level,
parallel analysis algorithms based on model checking are provided. In the
paper, the key tool features are described and their application is
demonstrated by means of a case study
Efficient Parallel Statistical Model Checking of Biochemical Networks
We consider the problem of verifying stochastic models of biochemical
networks against behavioral properties expressed in temporal logic terms. Exact
probabilistic verification approaches such as, for example, CSL/PCTL model
checking, are undermined by a huge computational demand which rule them out for
most real case studies. Less demanding approaches, such as statistical model
checking, estimate the likelihood that a property is satisfied by sampling
executions out of the stochastic model. We propose a methodology for
efficiently estimating the likelihood that a LTL property P holds of a
stochastic model of a biochemical network. As with other statistical
verification techniques, the methodology we propose uses a stochastic
simulation algorithm for generating execution samples, however there are three
key aspects that improve the efficiency: first, the sample generation is driven
by on-the-fly verification of P which results in optimal overall simulation
time. Second, the confidence interval estimation for the probability of P to
hold is based on an efficient variant of the Wilson method which ensures a
faster convergence. Third, the whole methodology is designed according to a
parallel fashion and a prototype software tool has been implemented that
performs the sampling/verification process in parallel over an HPC
architecture
Platform Dependent Verification: On Engineering Verification Tools for 21st Century
The paper overviews recent developments in platform-dependent explicit-state
LTL model checking.Comment: In Proceedings PDMC 2011, arXiv:1111.006
Microbiome Analysis of Stool Samples from African Americans with Colon Polyps
Background: Colonic polyps are common tumors occurring in similar to 50% of Western populations with similar to 10% risk of malignant progression. Dietary agents have been considered the primary environmental exposure to promote colorectal cancer (CRC) development. However, the colonic mucosa is permanently in contact with the microbiota and its metabolic products including toxins that also have the potential to trigger oncogenic transformation. Aim: To analyze fecal DNA for microbiota composition and functional potential in African Americans with pre-neoplastic lesions. Materials & Methods: We analyzed the bacterial composition of stool samples from 6 healthy individuals and 6 patients with colon polyps using 16S ribosomal RNA-based phylogenetic microarray; the Human intestinal Tract Chip (HITChip) and 16S rRNA gene barcoded 454 pyrosequencing. The functional potential was determined by sequence-based metagenomics using 454 pyrosequencing. Results: Fecal microbiota profiling of samples from the healthy and polyp patients using both a phylogenetic microarraying (HITChip) and barcoded 454 pyrosequencing generated similar results. A distinction between both sets of samples was only obtained when the analysis was performed at the sub-genus level. Most of the species leading to the dissociation were from the Bacteroides group. The metagenomic analysis did not reveal major differences in bacterial gene prevalence/abundances between the two groups even when the analysis and comparisons were restricted to available Bacteroides genomes. Conclusion: This study reveals that at the pre-neoplastic stages, there is a trend showing microbiota changes between healthy and colon polyp patients at the sub-genus level. These differences were not reflected at the genome/functions levels. Bacteria and associated functions within the Bacteroides group need to be further analyzed and dissected to pinpoint potential actors in the early colon oncogenic transformation in a large sample size
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract)
In this paper, a novel computational technique for finite discrete
approximation of continuous dynamical systems suitable for a significant class
of biochemical dynamical systems is introduced. The method is parameterized in
order to affect the imposed level of approximation provided that with
increasing parameter value the approximation converges to the original
continuous system. By employing this approximation technique, we present
algorithms solving the reachability problem for biochemical dynamical systems.
The presented method and algorithms are evaluated on several exemplary
biological models and on a real case study.Comment: In Proceedings CompMod 2011, arXiv:1109.104
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