Numerical Simulation for Solute Transport in Fractal Porous Media

A modified Fokker-Planck equation with continuous source for solute transport in fractal porous media is considered. The dispersion term of the governing equation uses a fractional-order derivative and the diffusion coefficient can be time and scale dependent. In this paper, numerical solution of the modified Fokker-Planck equation is proposed. The effects of different fractional orders and fractional power functions of time and distance are numerically investigated. The results show that motions with a heavy tailed marginal distribution can be modelled by equations that use fractional-order derivatives and/or time and scale dependent dispersivity

Quality Assurance of Software Applications Using the In Vivo Testing Approach

Software products released into the field typically have some number of residual defects that either were not detected or could not have been detected during testing. This may be the result of flaws in the test cases themselves, incorrect assumptions made during the creation of test cases, or the infeasibility of testing the sheer number of possible configurations for a complex system; these defects may also be due to application states that were not considered during lab testing, or corrupted states that could arise due to a security violation. One approach to this problem is to continue to test these applications even after deployment, in hopes of finding any remaining flaws. In this paper, we present a testing methodology we call in vivo testing, in which tests are continuously executed in the deployment environment. We also describe a type of test we call in vivo tests that are specifically designed for use with such an approach: these tests execute within the current state of the program (rather than by creating a clean slate) without affecting or altering that state from the perspective of the end-user. We discuss the approach and the prototype testing framework for Java applications called Invite. We also provide the results of case studies that demonstrate Invite's effectiveness and efficiency

How Trustworthy are the Existing Performance Evaluations for Basic Vision Tasks?

This paper examines performance evaluation criteria for basic vision tasks involving sets of objects namely, object detection, instance-level segmentation and multi-object tracking. The rankings of algorithms by current criteria fluctuate with different choices of parameters, e.g. Intersection over Union (IoU) threshold, making their evaluations unreliable. More importantly, there is no means to even verify whether we can trust the evaluations of a criterion. This work advocates a notion of trustworthiness for criteria, which requires (i) robustness to parameters for reliability, (ii) contextual meaningfulness in sanity tests, and (iii) consistency with mathematical requirements such as the metric properties. We show that such requirements were overlooked by many widely-used criteria. We also explore alternative criteria using metrics for sets of shapes, and assess them against these requirements to find trustworthy criteria

Review of economy and environment program for southeast Asia (EEPSEA) for the period 2013 to 2016

The report evaluates the accomplishments of Economy and Environment Program for Southeast Asia (EEPSEA) in the 2013-2016 funding phase. It also considers the future, as EEPSEA transitions away from its historic structure and funding base towards a decentralized network of country-based groups. In view of past successes, the evaluation makes recommendations to donors suggesting a focused two to four-year funding mechanism for achieving specific national and cross-national goals during the transition to this new structure

A numerical method for the fractional Fitzhugh–Nagumo monodomain model

A fractional FitzHugh–Nagumo monodomain model with zero Dirichlet boundary conditions is presented, generalising the standard monodomain model that describes the propagation of the electrical potential in heterogeneous cardiac tissue. The model consists of a coupled fractional Riesz space nonlinear reaction-diffusion model and a system of ordinary differential equations, describing the ionic fluxes as a function of the membrane potential. We solve this model by decoupling the space-fractional partial differential equation and the system of ordinary differential equations at each time step. Thus, this means treating the fractional Riesz space nonlinear reaction-diffusion model as if the nonlinear source term is only locally Lipschitz. The fractional Riesz space nonlinear reaction-diffusion model is solved using an implicit numerical method with the shifted Grunwald–Letnikov approximation, and the stability and convergence are discussed in detail in the context of the local Lipschitz property. Some numerical examples are given to show the consistency of our computational approach. References B. Baeumer, M. Kovaly, and M. M. Meerschaert, Fractional reproduction-dispersal equations and heavy tail dispersal kernels, Bulletin of Mathematical Biology 69:2281–2297, 2007. doi:10.1007/s11538-007-9220-2 B. Baeumer, M. Kovaly, and M. M. Meerschaert, Numerical solutions for fractional reaction-diffusion equations, Computers and Mathematics with Applications 55:2212–2226, 2008. doi:10.1016/j.camwa.2007.11.012 N. Badie and N. Bursac, Novel micropatterned cardiac cell cultures with realistic ventricular microstructure, Biophys J 96:3873–3885, 2009. doi:10.1016/j.bpj.2009.02.019 A. Bueno-Orovio, D. Kay, K. Burrage, Fourier spectral methods for fractional-in-space reaction-diffusion equations, Technical report, University of Oxford, 2013. A. Bueno-Orovioy, D. Kay, V. Grau, B. Rodriguez and K. Burrage, Fractional dffusion models of electrical propagation in cardiac tissue: electrotonic effects and the modulated dispersion of repolarization, Technical report, University of Oxford, 2013. K. F. Decker, J. Heijman, J. R. Silva, T. J. Hund and Y. Rudy, Properties and ionic mechanisms of action potential adaptation, restitution, and accommodation in canine epicardium, Am. J. Physiol Heart Circ. Physiol. 296:H1017–H1026, 2009. doi:10.1152/ajpheart.01216.2008 J. S. Frank and G. A. Langer, The myocardial interstitium: its structure and its role in ionic exchange, J Cell Biol 60:586–601, 1974. doi:10.1083/jcb.60.3.586 A. L. Hodgkin and A. F. Huxley, A quantitative description of membrane current and its application to conduction and excitation in nerve, J. Physiol. 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Henriquez, Effect of nonuniform interstitial space properties on impulse propagation: a discrete multidomain model, Biophys J 95:3724–3737, 2008. doi:10.1529/biophysj.108.137349 J. Sundnes, G. T. Lines, X. Cai, B. F. Nielsen, K. A. Mardal and A. Tveitio, Computing the electrical activity in the heart, Springer-Verlag, 2006. G. D. Smith, Numerical Solution of Partial Differential Equations: Finite Difference Methods, Clarendon Press, Oxford, 1985. F. J. Valdes-Parada, J. A. Ochoa-Tapia and J. Alvarez-Ramirez, Effective medium equations for fractional Fick law in porous media, Physica A, 373:339–353, 2007. doi:10.1016/j.physa.2006.06.007 Q. Yang, F. Liu and I. Turner, Stability and convergence of an effective numerical method for the time-space fractional Fokker-Planck equation with a nonlinear source term, International Journal of Differential Equations, 2010:464321, 2010, doi:10.1155/2010/464321 W. Ying, A multilevel adaptive approach for computational cardiology, PhD thesis, Duke University, 2005. Q. Yu, F. Liu, I. Turner and K. Burrage, A computationally effective alternating direction method for the space and time fractional Bloch-Torrey equation in 3-D, Appl. Math. Comp., 219:4082–4095, 2012. doi:10.1016/j.amc.2012.10.056 Q. Yu, F. Liu, I. Turner and K. Burrage, Stability and convergence of an implicit numerical method for the space and time fractional Bloch-Torrey equation, the special issue of Fractional Calculus and Its Applications in-Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 371:20120150, 2013. doi:10.1098/rsta.2012.0150 Q. Yu, F. Liu, I. Turner and K. Burrage, Numerical simulation of the fractional Bloch equations, J. Comp. Appl. Math., 255:635–651, 2014. doi:10.1016/j.cam.2013.06.027 P. Zhuang, F. Liu, V. Anh and I. Turner, Numerical methods for the variable-order fractional advection-diffusion equation with a nonlinear source term, SIAM J. Num. Anal., 47:1760–1781, 2009. doi:10.1137/08073059

Exploring the Socioeconomic Importance of Antimicrobial Use in the Small-Scale Pig Sector in Vietnam

Antimicrobial resistance (AMR) is influenced by antimicrobial use in human and animal health. This use exerts selection pressure on pathogen populations with the development of resistance and the exchange of resistance genes. While the exact scale of AMR in Vietnam remains uncertain, recent studies suggest that it is a major issue in both human and animal health. This study explored antimicrobial use behaviors in 36 pig farms in the Nam Dinh Province (North) and the Dong Nai Province (South) of Vietnam (with a median of 5.5 breeding sows and 41 fattening pigs). It also estimated the economic costs and benefits of use for the producer. Data were collected through a structured face-to-face interview with additional productivity data collected by farmers during a six-week period following the initial interview. Overall, antimicrobial use was high across the farms; however, in-feed antimicrobial use is likely to be under-reported due to misleading and imprecise labelling on premixed commercial feeds. An economic analysis found that the cost of antimicrobials was low relative to other farm inputs (~2% of total costs), and that farm profitability was precariously balanced, with high disease and poor prices leading to negative and low profits. Future policies for smallholder farms need to consider farm-level economics and livestock food supply issues when developing further antimicrobial use interventions in the region

Probing cluster structures through sub-barrier transfer reactions

Multinucleon transfer probabilities and excitation energy distributions have been measured in 16,18O, 19F + 208Pb at energies between 90% - 100% of the Coulomb barrier. A strong 2p2n enhancement is observed for all reactions, though most spectacularly in the 18O induced reaction. Results are interpreted in terms of the Semiclassical model, which seems to suggest α-cluster transfer in all studied systems. The relation to cluster-states in the projectile is discussed, with the experimental results consistent with previous structure studies. Dissipation of energy in the collisions of 18O is compared between different reaction modes, with cluster transfer associated with dissipation over a large number of internal states. Cluster transfer is shown to be a long range dissipation mechanism, which will inform the development of future models to treat these dynamic processes in reactions

Nuclear structure effects in quasifission - Understanding the formation of the heaviest elements

Quasifission is an important process suppressing the fusion of two heavy nuclei in reactions used to create superheavy elements. Quasifission results in rapid separation of the dinuclear system initially formed at contact. Achieving reliable a priori prediction of quasifission probabilities is a very difficult problem. Through measurements with projectiles from C to Ni, the Australian National University's Heavy Ion Accelerator Facility and CUBE spectrometer have been used to map out mass-angle distributions (MAD) - the fission mass-ratio as a function of centre-of-mass angle. These provide information on quasifission dynamics in the least modeldependent way. Average quasifission time-scales have been extracted, and compared with TDHF calculations of the collisions, with good agreement being found. With the baseline information from the survey of experimental MAD, strong influences of the nuclear structure of the projectile and target nuclei can be clearly determinedWe acknowledge NCRIS operations support for the ANU Heavy Ion Accelerator Facility, and ARC grants DP130101569, DP140101337, FL110100098, FT120100760 and DE140100784. Thanks to N. Lobanov, T. Kibedi and the accelerator staff for supporting use of the superconducting Linac accelerator

Structure/Function Analysis of Recurrent Mutations in SETD2 Protein Reveals a Critical and Conserved Role for a SET Domain Residue in Maintaining Protein Stability and Histone H3 Lys-36 Trimethylation

The yeast Set2 histone methyltransferase is a critical enzyme that plays a number of key roles in gene transcription and DNA repair. Recently, the human homologue, SETD2, was found to be recurrently mutated in a significant percentage of renal cell carcinomas, raising the possibility that the activity of SETD2 is tumor-suppressive. Using budding yeast and human cell line model systems, we examined the functional significance of two evolutionarily conserved residues in SETD2 that are recurrently mutated in human cancers. Whereas one of these mutations (R2510H), located in the Set2 Rpb1 interaction domain, did not result in an observable defect in SETD2 enzymatic function, a second mutation in the catalytic domain of this enzyme (R1625C) resulted in a complete loss of histone H3 Lys-36 trimethylation (H3K36me3). This mutant showed unchanged thermal stability as compared with the wild type protein but diminished binding to the histone H3 tail. Surprisingly, mutation of the conserved residue in Set2 (R195C) similarly resulted in a complete loss of H3K36me3 but did not affect dimethylated histone H3 Lys-36 (H3K36me2) or functions associated with H3K36me2 in yeast. Collectively, these data imply a critical role for Arg-1625 in maintaining the protein interaction with H3 and specific H3K36me3 function of this enzyme, which is conserved from yeast to humans. They also may provide a refined biochemical explanation for how H3K36me3 loss leads to genomic instability and cancer

The First Provenance Challenge

The first Provenance Challenge was set up in order to provide a forum for the community to help understand the capabilities of different provenance systems and the expressiveness of their provenance representations. To this end, a Functional Magnetic Resonance Imaging workflow was defined, which participants had to either simulate or run in order to produce some provenance representation, from which a set of identified queries had to be implemented and executed. Sixteen teams responded to the challenge, and submitted their inputs. In this paper, we present the challenge workflow and queries, and summarise the participants contributions