A response to critiques of "The reproducibility of research and the misinterpretation of p-values"

I proposed (8, 1, 3) that p values should be supplemented by an estimate of the false positive risk (FPR). FPR was defined as the probability that, if you claim that there is a real effect on the basis of p value from a single unbiased experiment, that you will be mistaken and the result has occurred by chance. This is a Bayesian quantity and that means that there is an infinitude of ways to calculate it. My choice of a way to estimate FPR was, therefore, arbitrary. I maintain that it is a reasonable way, and has the advantage of being mathematically simpler than other proposals and easier to understand than other methods. This might make it more easily accepted by users. As always, not every statistician agrees. This paper is a response to a critique of my 2017 paper (1) by Arandjelovic (2)Comment: 10 pages 0 figures. Accepted by Royal Society Open Scienc

The protection of the unsaturated fatty acids of dried grass and sunflower seed against biohydrogenation by rumen micro-organisms : a thesis presented in partial fulfilment of the requirements for the degree of Master of Agricultural Science in Animal Science at Massey University

Ryegrass which had been dried and treated with HCHO was incubated with the rumen contents of a pasture-grazed cow. The protein in the grass was protected from degradation by the rumen microbes. The degree of protection of the protein increased with the rate of HCHO application over the range 0.5-2.0 g HCHO per 100 g of dried grass. At the highest rate of HCHO application, the digestibility of the forage dry matter (measured in vitro) was a little less than that of the untreated forage. In vitro incubations with rumen fluid also showed substantial protection of 18:3 in dried grass which had been treated with HCHO. Again, the degree of protection increased with the rate of application of HCHO. The upper level of HCHO treatment which was also the optimum was higher than the level recommended by other workers for the protection of protein in dried forage. Dried grass obtained from a commercial source was treated with HCHO (2 g HCHO/lOO g dried grass) and was fed to a cow from a monozygous twin pair. Intake was reduced and an underfeeding response was observed. The proportions of 18:2 and 18:3 in the milk fat of the cow were not elevated. This lack of response probably was due to a combination of the depressed intake by the cow and the low levels of endogenous lipid (compared with spring pasture) in the grass used. A supplement of sunflower seed and casein which had been treated with HCHO was fed to a cow. Milk fat containing about 10 moles % 18:2 was produced. When a supplement of sunflower seed and casein which had not been treated with HCHO was fed, a much smaller increase in the content of 18:2 in the milk fat was observed

Studies of NMDA receptor function and stoichiometry with truncated and tandem subunits

The subunits that compose eukaryotic glutamate ion channel receptors have three transmembrane domains (TMs) and terminate with intracellular tails that are important for controlling channel expression and localization. Truncation of NMDA receptor subunits before the final TM showed that this TM and intracellular tail region are necessary to form functional channels. However, it is shown here that these truncated subunits may be partially rescued by coexpressing the final TM and tail as a separate protein. The whole-cell currents so produced are somewhat lower than with full-length subunits, and they do not show the sag characteristic of currents from channels containing NR1 and NR2A subunits in the continued presence of an agonist. In addition, these truncated subunits were joined to full-length subunits to generate tandems. The functional expression of these tandems confirmed the tetrameric structure of NMDA receptors and also suggested that the subunits making up NMDA receptors are arranged as a dimer of dimers in the receptors with a 1-1-2-2 orientation of the subunits in the channel, and not in an alternating pattern of subunits around the pore. These results may redirect future studies into the mechanism of binding and gating in these receptors toward schemes including dimers, and may also be relevant to studies of glutamate receptor ion channels in general

Exchange reactions of poly(arylene ether ketone) dithioketals with aliphatic diols: formation and deprotection of poly(arylene ether ketal)s

The dithioketal derivatives of industrially important, semi-crystalline poly(arylene ether ketone)s undergo facile exchange with aliphatic diols in the presence of N-bromo-succinimide to give a range of novel poly(arylene ether ketal)s. These are amorphous and readily soluble in a wide range of organic solvents. Although generally stable under ambient conditions, they undergo rapid and quantitative hydrolysis in the presence of acids to regenerate the original polyketones. The poly(ether ketal)s reported here are not accessible from ketal-type monomers, nor can they be obtained by direct reaction of poly(ether ketone)s with aliphatic diols. The starting polyketones are essentially unchanged after sequential dithioketalization, dithioketal-ketal exchange, ketal hydrolysis, and re-dithioketalization. Poly(arylene ether ketal)s provide a new approach to the processing of poly(arylene ether ketone)s into carbon fiber composite materials

D meson semileptonic form factors in Nf=3 QCD with M\"obius domain-wall quarks

We present our calculation of D \to pi and D \to K semileptonic form factors in Nf = 2+1 lattice QCD. We simulate three lattice cutoffs 1/a \sim 2.5, 3.6 and 4.5 GeV with pion masses as low as 230 MeV. The M\"obius domain-wall action is employed for both light and charm quarks. We present our results for the vector and scalar form factors and discuss their dependence on the lattice spacing, light quark masses and momentum transfer.Comment: 8 pages, 5 figures, talk presented at the 35th International Symposium on Lattice Field Theory (Lattice 2017), 18-24 June 2017, Granada, Spai

Direct iminization of PEEK

Semi-crystalline poly(ether ketone)s are important high-temperature engineering thermoplastics, but are difficult to characterize at the molecular level because of their insolubility in conventional organic solvents. Here we report that polymers of this type, including PEEK, react cleanly at high temperatures with low-volatility aralkyl amines to afford stable, noncrystalline poly(ether-imine)s, which are readily soluble in solvents such as chloroform, THF and DMF and so characterizable by conventional size-exclusion chromatography

The activation mechanism of alpha 1 homomeric glycine receptors

The glycine receptor mediates fast synaptic inhibition in the spinal cord and brainstem. Its activation mechanism is not known, despite the physiological importance of this receptor and the fact that it can serve as a prototype for other homopentameric channels. We analyzed single-channel recordings from rat recombinant alpha1 glycine receptors by fitting different mechanisms simultaneously to sets of sequences of openings at four glycine concentrations (10-1000 muM). The adequacy of the mechanism and the rate constants thus fitted was judged by examining how well these described the observed dwell-time distributions, open-shut correlation, and single-channel P-open dose-response curve. We found that gating efficacy increased as more glycine molecules bind to the channel, but maximum efficacy was reached when only three (of five) potential binding sites are occupied. Successive binding steps are not identical, implying that binding sites can interact while the channel is shut. These interactions can be interpreted in the light of the topology of the binding sites within a homopentamer