ShinyGPAS: interactive genomic prediction accuracy simulator based on deterministic formulas

Background: Deterministic formulas for the accuracy of genomic predictions highlight the relationships among prediction accuracy and potential factors influencing prediction accuracy prior to performing computationally intensive cross-validation. Visualizing such deterministic formulas in an interactive manner may lead to a better understanding of how genetic factors control prediction accuracy. Results: The software to simulate deterministic formulas for genomic prediction accuracy was implemented in R and encapsulated as a web-based Shiny application. Shiny genomic prediction accuracy simulator (ShinyGPAS) simulates various deterministic formulas and delivers dynamic scatter plots of prediction accuracy versus genetic factors impacting prediction accuracy, while requiring only mouse navigation in a web browser. ShinyGPAS is available at: https://chikudaisei.shinyapps.io/shinygpas/ Conclusion: ShinyGPAS is a shiny-based interactive genomic prediction accuracy simulator using deterministic formulas. It can be used for interactively exploring potential factors that influence prediction accuracy in genomeenabled prediction, simulating achievable prediction accuracy prior to genotyping individuals, or supporting in-class teaching. ShinyGPAS is open source software and it is hosted online as a freely available web-based resource with an intuitive graphical user interfac

Properties of GaP(001) surfaces treated in aqueous HF solutions

Chemically cleaned GaP(001) surfaces in aqueous HF solutions have been studied using spectroscopic ellipsometry (SE), ex situ atomic force microscopy (AFM), x-ray photoelectron spectroscopy (XPS), wettability, and photoluminescence (PL) measurements. The SE data clearly indicate that the solutions cause removal of the native oxide film immediately upon immersing the sample (?1 min). The SE data, however, suggest that the native oxide film cannot be completely etch-removed. This is due to the fact that as soon as the etched sample is exposed to air, the oxide starts to regrow. The SE estimated roughness is ～1 nm, while the AFM roughness value is ～0.3 nm. The XPS spectra confirm the removal of the native oxide and also the presence of regrown oxide on the HF-etched GaP surface. The wettability measurements indicate that the HF-cleaned surface is hydrophobic, which is in direct contrast to those obtained from alkaline-cleaned surfaces (hydrophilic). A slight increase in the PL intensity is also observed after etching in aqueous HF solutions

Properties of GaP(001) surfaces chemically treated in NH4OH solution

Chemically cleaned GaP(001) surfaces in 25% NH4OH solution have been studied using spectroscopic ellipsometry (SE), ex situ atomic force microscopy (AFM), x-ray photoelectron spectroscopy (XPS), and wettability measurement techniques. The SE data clearly indicate that the solution causes removal of the native oxide film immediately upon immersing the sample. The SE data also indicate that when the native oxide film is completely etch removed, the resulting surface is still roughened. The estimated roughness thickness is ～1.2 nm, in excellent agreement with the AFM rms value (～1.2 nm). The XPS spectra confirm the removal of the native oxide from the GaP surface. The XPS data also suggest a thin oxide overlayer, ～0.3 nm thick, on the etch-cleaned GaP surface. The wettability measurements indicate that the as-degreased surface is hydrophobic, while the NH4OH-cleaned surface is hydrophilic. This result is in direct contrast to those obtained from acid cleaned surfaces, which are usually hydrophobic. The origin of hydrophilicity may be singular and associated hydroxyl groups bonded on the GaP surface

Respiratory uncoupling by increased H+ or K+ flux is beneficial for heart mitochondrial turnover of reactive oxygen species but not for permeability transition

Background: Ischemic preconditioning has been proposed to involve changes in mitochondrial H+ and K+ fluxes, in particular through activation of uncoupling proteins and ATP-sensitive K+ channels (MitoK(ATP)). The objectives of the present study were to explore how increased H+ and K+ fluxes influence heart mitochondrial physiology with regard to production and scavenging of reactive oxygen species (ROS), volume changes and resistance to calcium-induced mitochondrial permeability transition (mPT). Results: Isolated rat heart mitochondria were exposed to a wide concentration range of the protonophore CCCP or the potassium ionophore valinomycin to induce increased H+ and K+ conductance, respectively. Simultaneous monitoring of mitochondrial respiration and calcium retention capacity (CRC) demonstrated that the relative increase in respiration caused by valinomycin or CCCP correlated with a decrease in CRC, and that no level of respiratory uncoupling was associated with enhanced resistance to mPT. Mitochondria suspended in hyperosmolar buffer demonstrated a dose-dependent reduction in CRC with increasing osmolarity. However, mitochondria in hypoosmolar buffer to increase matrix volume did not display increased CRC. ROS generation was reduced by both K+- and H+-mediated respiratory uncoupling. The ability of heart mitochondria to detoxify H2O2 was substantially greater than the production rate. The H2O2 detoxification was dependent on respiratory substrates and was dramatically decreased following calcium-induced mPT, but was unaffected by uncoupling via increased K+ and H+ conductance. Conclusion: It is concluded that respiratory uncoupling is not directly beneficial to rat heart mitochondrial resistance to calcium overload irrespective of whether H+ or K+ conductance is increased. The negative effects of respiratory uncoupling thus probably outweigh the reduction in ROS generation and a potential positive effect by increased matrix volume, resulting in a net sensitization of heart mitochondria to mPT activation

Indication of intrinsic spin Hall effect in 4d and 5d transition metals

We have investigated spin Hall effects in 4$d$ and 5$d$ transition metals, Nb, Ta, Mo, Pd and Pt, by incorporating the spin absorption method in the lateral spin valve structure; where large spin current preferably relaxes into the transition metals, exhibiting strong spin-orbit interactions. Thereby nonlocal spin valve measurements enable us to evaluate their spin Hall conductivities. The sign of the spin Hall conductivity changes systematically depending on the number of $d$ electrons. This tendency is in good agreement with the recent theoretical calculation based on the intrinsic spin Hall effect.Comment: 5 pages, 4 figure

Synthesis and cationic polymerization of halogen bonding vinyl ether monomers

Halogen bonding is rapidly becoming recognized as a viable and useful intermolecular interaction in supramolecular chemistry. While various monomers amenable to radical polymerization methods containing halogen bonding donors have been developed, this study aims to expand the type of monomers that incorporate this intermolecular interaction to facilitate use of cationic polymerization by developing three novel vinyl ether monomers containing halogen bonding donor moieties: 2, 3, 5, 6-tetrafluoro-4-iodophenoxyethyl vinyl ether (C2I), 2, 3, 5, 6-tetrafluoro-4-iodophenoxybutyl vinyl ether (C4I), and 2-(2, 3, 5, 6-tetrafluoro-4-iodophenoxyethoxy)ethyl vinyl ether (O3I). Well controlled cationic polymerization is achievable through the use of a proton trap, 2, 6-di-tert-butylpyridine. The use of SnCl4 as a co-Lewis acid was found to accelerate the reaction. Between the three monomers, the difference in the chain length is shown to influence the reaction rate, with the longest chain demonstrating the fastest polymerization. Initial studies of the halogen bonding ability shows that halogen bonding exists for all three monomers but is most pronounced in C4I. The polymerized vinyl ethers also exhibit halogen bonding. Due to the ease of synthesis and polymerization, these are promising new monomers to increase functionality available for polymers synthesized using cationic polymerization

Extrinsic Spin Hall Effect Induced by Iridium Impurities in Copper

We study the extrinsic spin Hall effect induced by Ir impurities in Cu by injecting a pure spin current into a CuIr wire from a lateral spin valve structure. While no spin Hall effect is observed without Ir impurity, the spin Hall resistivity of CuIr increases linearly with the impurity concentration. The spin Hall angle of CuIr, $(2.1 \pm 0.6)$% throughout the concentration range between 1% and 12%, is practically independent of temperature. These results represent a clear example of predominant skew scattering extrinsic contribution to the spin Hall effect in a nonmagnetic alloy.Comment: 5 pages, 4 figure