Will blockchain technology revolutionise excipient supply chain management?

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Automating biomedical data science through tree-based pipeline optimization

Over the past decade, data science and machine learning has grown from a mysterious art form to a staple tool across a variety of fields in academia, business, and government. In this paper, we introduce the concept of tree-based pipeline optimization for automating one of the most tedious parts of machine learning---pipeline design. We implement a Tree-based Pipeline Optimization Tool (TPOT) and demonstrate its effectiveness on a series of simulated and real-world genetic data sets. In particular, we show that TPOT can build machine learning pipelines that achieve competitive classification accuracy and discover novel pipeline operators---such as synthetic feature constructors---that significantly improve classification accuracy on these data sets. We also highlight the current challenges to pipeline optimization, such as the tendency to produce pipelines that overfit the data, and suggest future research paths to overcome these challenges. As such, this work represents an early step toward fully automating machine learning pipeline design.Comment: 16 pages, 5 figures, to appear in EvoBIO 2016 proceeding

Substance Use and Mild Traumatic Brain Injury Risk Reduction and Prevention: A Novel Model for Treatment

Traumatic brain injury (TBI) and substance use disorders (SUDs) frequently co-occur. Individuals with histories of alcohol or other drug use are at greater risk for sustaining TBI, and individuals with TBI frequently misuse substances before and after injury. Further, a growing body of literature supports the relationship between comorbid histories of mild TBI (mTBI) and SUDs and negative outcomes. Alcohol and other drug use are strongly associated with risk taking. Disinhibition, impaired executive function, and/or impulsivity as a result of mTBI also contribute to an individual's proclivity towards risk-taking. Risk-taking behavior may therefore, be a direct result of SUD and/or history of mTBI, and risky behaviors may predispose individuals for subsequent injury or continued use of substances. Based on these findings, evaluation of risk-taking behavior associated with the co-occurrence of SUD and mTBI should be a standard clinical practice. Interventions aimed at reducing risky behavior among members of this population may assist in decreasing negative outcomes. A novel intervention (Substance Use and Traumatic Brain Injury Risk Reduction and Prevention (STRRP)) for reducing and preventing risky behaviors among individuals with co-occurring mTBI and SUD is presented. Areas for further research are discussed

Asymmetrical crossing barriers in angiosperms

Patterns of reproductive isolation between species may provide insight into the mechanisms and evolution of barriers to interspeci¢c gene exchange. We used data from published interspeci¢c hybridization experiments from 14 genera of angiosperms in order to test for the presence of asymmetrical barriers to gene exchange. Reproductive isolation was examined at three life-history stages: the ability of interspeci¢c crosses to produce seeds, the viability of F 1 hybrids, and the fertility of F 1 hybrids. Statistically signi¢cant asymmetries in the strength of reproductive isolation between species were detected in all genera and at each of the three life-history stages. Asymmetries in seed production may be caused by a variety of mechanisms including di¡erences in stigma/style lengths, self compatibility and di¡erential fruit abortion. Asymmetries in post-zygotic isolation are probably caused by nuclear^cytoplasmic interactions. Asymmetrical reproductive isolation between plant taxa may have important implications for the dynamics of hybrid zones, the direction of genetic introgression and the probability of reinforcement

Two-dimensional hydrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic fluid flow through porous media

The behaviour of two dimensional binary and ternary amphiphilic fluids under flow conditions is investigated using a hydrodynamic lattice gas model. After the validation of the model in simple cases (Poiseuille flow, Darcy's law for single component fluids), attention is focussed on the properties of binary immiscible fluids in porous media. An extension of Darcy's law which explicitly admits a viscous coupling between the fluids is verified, and evidence of capillary effects are described. The influence of a third component, namely surfactant, is studied in the same context. Invasion simulations have also been performed. The effect of the applied force on the invasion process is reported. As the forcing level increases, the invasion process becomes faster and the residual oil saturation decreases. The introduction of surfactant in the invading phase during imbibition produces new phenomena, including emulsification and micellisation. At very low fluid forcing levels, this leads to the production of a low-resistance gel, which then slows down the progress of the invading fluid. At long times (beyond the water percolation threshold), the concentration of remaining oil within the porous medium is lowered by the action of surfactant, thus enhancing oil recovery. On the other hand, the introduction of surfactant in the invading phase during drainage simulations slows down the invasion process -- the invading fluid takes a more tortuous path to invade the porous medium -- and reduces the oil recovery (the residual oil saturation increases).Comment: 48 pages, 26 figures. Phys. Rev. E (in press

Bethe--Salpeter equation in QCD

We extend to regular QCD the derivation of a confining $q \bar{q}$ Bethe--Salpeter equation previously given for the simplest model of scalar QCD in which quarks are treated as spinless particles. We start from the same assumptions on the Wilson loop integral already adopted in the derivation of a semirelativistic heavy quark potential. We show that, by standard approximations, an effective meson squared mass operator can be obtained from our BS kernel and that, from this, by ${1\over m^2}$ expansion the corresponding Wilson loop potential can be reobtained, spin--dependent and velocity--dependent terms included. We also show that, on the contrary, neglecting spin--dependent terms, relativistic flux tube model is reproduced.Comment: 23 pages, revte

Charged multifluids in general relativity

The exact 1+3 covariant dynamical fluid equations for a multi-component plasma, together with Maxwell's equations are presented in such a way as to make them suitable for a gauge-invariant analysis of linear density and velocity perturbations of the Friedmann-Robertson-Walker model. In the case where the matter is described by a two component plasma where thermal effects are neglected, a mode representing high-frequency plasma oscillations is found in addition to the standard growing and decaying gravitational instability picture. Further applications of these equations are also discussed.Comment: 14 pages (example added), to appear in Class. Quantum Gra

Three dimensional hysdrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic flow through porous media

We report the results of a study of multiphase flow in porous media. A Darcy's law for steady multiphase flow was investigated for both binary and ternary amphiphilic flow. Linear flux-forcing relationships satisfying Onsager reciprocity were shown to be a good approximation of the simulation data. The dependence of the relative permeability coefficients on water saturation was investigated and showed good qualitative agreement with experimental data. Non-steady state invasion flows were investigated, with particular interest in the asymptotic residual oil saturation. The addition of surfactant to the invasive fluid was shown to significantly reduce the residual oil saturation.Comment: To appear in Phys. Rev.

Three-dimensional adaptive evolution of gravitational waves in numerical relativity

Adaptive techniques are crucial for successful numerical modeling of gravitational waves from astrophysical sources such as coalescing compact binaries, since the radiation typically has wavelengths much larger than the scale of the sources. We have carried out an important step toward this goal, the evolution of weak gravitational waves using adaptive mesh refinement in the Einstein equations. The 2-level adaptive simulation is compared with unigrid runs at coarse and fine resolution, and is shown to track closely the features of the fine grid run.Comment: REVTeX, 7 pages, including three figures; submitted to Physical Review