Pressure-energy correlations and thermodynamic scaling in viscous Lennard-Jones liquids

We use molecular dynamics simulation results on viscous binary Lennard-Jones mixtures to examine the correlation between the potential energy and the virial. In accord with a recent proposal [U. R. Pedersen et. al. Phys. Rev. Lett. 100, 015701 (2008)], the fluctuations in the two quantities are found to be strongly correlated, exhibiting a proportionality constant, Gamma, numerically equal to one-third the slope of an inverse power law approximation to the intermolecular potential function. The correlation is stronger at higher densities, where interatomic separations are in the range where the inverse power law approximation is more accurate. These same liquids conform to thermodynamic scaling of their dynamics, with the scaling exponent equal to Gamma. Thus, the properties of strong correlation between energy and pressure and thermodynamic scaling both reflect the ability of an inverse power law representation of the potential to capture interesting features of the dynamics of dense, highly viscous liquids.Comment: 5 pages, 4 figures; published version, one figure remove

Use of Iverson's language APL for statistical computing

APL computer language for statistical computatio

Seriously misleading results using inverse of Freeman-Tukey double arcsine transformation in meta-analysis of single proportions.

Standard generic inverse variance methods for the combination of single proportions are based on transformed proportions using the logit, arcsine, and Freeman-Tukey double arcsine transformations. Generalized linear mixed models are another more elaborate approach. Irrespective of the approach, meta-analysis results are typically back-transformed to the original scale in order to ease interpretation. Whereas the back-transformation of meta-analysis results is straightforward for most transformations, this is not the case for the Freeman-Tukey double arcsine transformation, albeit possible. In this case study with five studies, we demonstrate how seriously misleading the back-transformation of the Freeman-Tukey double arcsine transformation can be. We conclude that this transformation should only be used with special caution for the meta-analysis of single proportions due to potential problems with the back-transformation. Generalized linear mixed models seem to be a promising alternative

Proprietary Reasons and Joint Action

Some of the reasons one acts on in joint action are shared with fellow participants. But others are proprietary: reasons of one’s own that have no direct practical significance for other participants. The compatibility of joint action with proprietary reasons serves to distinguish the former from other forms of collective agency; moreover, it is arguably a desirable feature of joint action. Advocates of “team reasoning” link the special collective intention individual participants have when acting together with a distinctive form of practical reasoning that purports to put individuals in touch with group or collective reasons. Such views entail the surprising conclusion that one cannot engage in joint action for proprietary reasons. Suppose we understand the contrast between minimal and robust forms of joint action in terms of the extent to which participants act on proprietary reasons as opposed to shared reasons. Then, if the team reasoning view of joint intention and action is correct, it makes no sense to talk of minimal joint action. As soon as the reason for which one participates is proprietary, then one is not, on this view, genuinely engaged in joint action

A non-uniform semantic analysis of the Italian temporal connectives Prima and Dopo

In this paper, I argue that the temporal connective prima ('before') is a comparative adverb. The argument is based on a number of grammatical facts from Italian, showing that there is an asymmetry between prima and dopo ('after'). On the ground of their divergent behaviour, I suggest that dopo has a different grammatical status from prima. I propose a semantic treatment for prima that is based on an independently motivated analysis of comparatives which can be traced back to Seuren (1973). Dopo is analyzed instead as an atomic two-place predicate which contributes a binary relation over events to the sentence meaning. The different semantic treatments of the two connectives provide an explanation for the grammatical asymmetries considered at the outset; interestingly, it also sheds some light on other asymmetries between prima and dopo which are known to hold for the English temporal connectives before and after as well: these asymmetries are related to the veridicality properties, the distribution of NPIs, and the logical properties of these connectives first described in Anscombe (1964)

Seasonal changes in patterns of gene expression in avian song control brain regions.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Photoperiod and hormonal cues drive dramatic seasonal changes in structure and function of the avian song control system. Little is known, however, about the patterns of gene expression associated with seasonal changes. Here we address this issue by altering the hormonal and photoperiodic conditions in seasonally-breeding Gambel's white-crowned sparrows and extracting RNA from the telencephalic song control nuclei HVC and RA across multiple time points that capture different stages of growth and regression. We chose HVC and RA because while both nuclei change in volume across seasons, the cellular mechanisms underlying these changes differ. We thus hypothesized that different genes would be expressed between HVC and RA. We tested this by using the extracted RNA to perform a cDNA microarray hybridization developed by the SoNG initiative. We then validated these results using qRT-PCR. We found that 363 genes varied by more than 1.5 fold (>log(2) 0.585) in expression in HVC and/or RA. Supporting our hypothesis, only 59 of these 363 genes were found to vary in both nuclei, while 132 gene expression changes were HVC specific and 172 were RA specific. We then assigned many of these genes to functional categories relevant to the different mechanisms underlying seasonal change in HVC and RA, including neurogenesis, apoptosis, cell growth, dendrite arborization and axonal growth, angiogenesis, endocrinology, growth factors, and electrophysiology. This revealed categorical differences in the kinds of genes regulated in HVC and RA. These results show that different molecular programs underlie seasonal changes in HVC and RA, and that gene expression is time specific across different reproductive conditions. Our results provide insights into the complex molecular pathways that underlie adult neural plasticity

Three phylogenetic groups have driven the recent population expansion of Cryptococcus neoformans.

Cryptococcus neoformans (C. neoformans var. grubii) is an environmentally acquired pathogen causing 181,000 HIV-associated deaths each year. We sequenced 699 isolates, primarily C. neoformans from HIV-infected patients, from 5 countries in Asia and Africa. The phylogeny of C. neoformans reveals a recent exponential population expansion, consistent with the increase in the number of susceptible hosts. In our study population, this expansion has been driven by three sub-clades of the C. neoformans VNIa lineage; VNIa-4, VNIa-5 and VNIa-93. These three sub-clades account for 91% of clinical isolates sequenced in our study. Combining the genome data with clinical information, we find that the VNIa-93 sub-clade, the most common sub-clade in Uganda and Malawi, was associated with better outcomes than VNIa-4 and VNIa-5, which predominate in Southeast Asia. This study lays the foundation for further work investigating the dominance of VNIa-4, VNIa-5 and VNIa-93 and the association between lineage and clinical phenotype

The practical other : teleology and its development

We argue for teleology as a description of the way in which we ordinarily understand others’ intentional actions. Teleology starts from the close resemblance between the reasoning involved in understanding others’ actions and one’s own practical reasoning involved in deciding what to do. We carve out teleology’s distinctive features more sharply by comparing it to its three main competitors: theory theory, simulation theory, and rationality theory. The plausibility of teleology as our way of understanding others is underlined by developmental data in its favour

Heteroskedasticity testing through a comparison of Wald statistics

This paper shows that a test for heteroskedasticity within the context of classical linear regression can be based on the difference between Wald statistics in heteroskedasticity-robust and nonrobust forms. The test is asymptotically distributed under the null hypothesis of homoskedasticity as chi-squared with one degree of freedom. The power of the test is sensitive to the choice of parametric restriction used by the Wald statistics, so the supremum of a range of individual test statistics is proposed. Two versions of a supremum-based test are considered: the first version does not have a known asymptotic null distribution, so the bootstrap is employed to approximate its empirical distribution. The second version has a known asymptotic distribution and, in some cases, is asymptotically pivotal under the null. A simulation study illustrates the use and finite-sample performance of both versions of the test. In this study, the bootstrap is found to provide better size control than asymptotic critical values, namely with heavy-tailed, asymmetric distributions of the covariates. In addition, the use of well-known modifications of the heteroskedasticity consistent covariance matrix estimator of OLS coefficients is also found to benefit the tests’ overall behaviour.info:eu-repo/semantics/publishedVersio