Fast and accurate modelling of longitudinal and repeated measures neuroimaging data

Despite the growing importance of longitudinal data in neuroimaging, the standard analysis methods make restrictive or unrealistic assumptions (e.g., assumption of Compound Symmetry—the state of all equal variances and equal correlations—or spatially homogeneous longitudinal correlations). While some new methods have been proposed to more accurately account for such data, these methods are based on iterative algorithms that are slow and failure-prone. In this article, we propose the use of the Sandwich Estimator (SwE) method which first estimates the parameters of interest with a simple Ordinary Least Square model and second estimates variances/covariances with the “so-called” SwE which accounts for the within-subject correlation existing in longitudinal data. Here, we introduce the SwE method in its classic form, and we review and propose several adjustments to improve its behaviour, specifically in small samples. We use intensive Monte Carlo simulations to compare all considered adjustments and isolate the best combination for neuroimaging data. We also compare the SwE method to other popular methods and demonstrate its strengths and weaknesses. Finally, we analyse a highly unbalanced longitudinal dataset from the Alzheimer's Disease Neuroimaging Initiative and demonstrate the flexibility of the SwE method to fit within- and between-subject effects in a single model. Software implementing this SwE method has been made freely available at http://warwick.ac.uk/tenichols/SwE

Immunity Promotes Virulence Evolution in a Malaria Model

Evolutionary models predict that host immunity will shape the evolution of parasite virulence. While some assumptions of these models have been tested, the actual evolutionary outcome of immune selection on virulence has not. Using the mouse malaria model, Plasmodium chabaudi, we experimentally tested whether immune pressure promotes the evolution of more virulent pathogens by evolving parasite lines in immunized and nonimmunized (‘‘naive’’) mice using serial passage. We found that parasite lines evolved in immunized mice became more virulent to both naive and immune mice than lines evolved in naive mice. When these evolved lines were transmitted through mosquitoes, there was a general reduction in virulence across all lines. However, the immune-selected lines remained more virulent to naive mice than the naive-selected lines, though not to immunized mice. Thus, immune selection accelerated the rate of virulence evolution, rendering parasites more dangerous to naı¨ve hosts. These results argue for further consideration of the evolutionary consequences for pathogen virulence of vaccination

Empirical Support for Optimal Virulence in a Castrating Parasite

The trade-off hypothesis for the evolution of virulence predicts that parasite transmission stage production and host exploitation are balanced such that lifetime transmission success (LTS) is maximised. However, the experimental evidence for this prediction is weak, mainly because LTS, which indicates parasite fitness, has been difficult to measure. For castrating parasites, this simple model has been modified to take into account that parasites convert host reproductive resources into transmission stages. Parasites that kill the host too early will hardly benefit from these resources, while postponing the killing of the host results in diminished returns. As predicted from optimality models, a parasite inducing castration should therefore castrate early, but show intermediate levels of virulence, where virulence is measured as time to host killing. We studied virulence in an experimental system where a bacterial parasite castrates its host and produces spores that are not released until after host death. This permits estimating the LTS of the parasite, which can then be related to its virulence. We exposed replicate individual Daphnia magna (Crustacea) of one host clone to the same amount of bacterial spores and followed individuals until their death. We found that the parasite shows strong variation in the time to kill its host and that transmission stage production peaks at an intermediate level of virulence. A further experiment tested for the genetic basis of variation in virulence by comparing survival curves of daphniids infected with parasite spores obtained from early killing versus late killing infections. Hosts infected with early killer spores had a significantly higher death rate as compared to those infected with late killers, indicating that variation in time to death was at least in part caused by genetic differences among parasites. We speculate that the clear peak in lifetime reproductive success at intermediate killing times may be caused by the exceptionally strong physiological trade-off between host and parasite reproduction. This is the first experimental study to demonstrate that the production of propagules is highest at intermediate levels of virulence and that parasite genetic variability is available to drive the evolution of virulence in this system

Molecular Conductors from Neutral-Radical Charge-Transfer Salts:Preparation and Characterization of an Iodine-Doped Hexagonal Phase of 1,2,3,5-Dithiadiazolyl ([HCN2S2]∙)

Sublimation of 1,2,3,5-dithiadiazolyl in vacuo affords a triclinic phase of the dimer [HCN2S2]2. The crystals belong to the space group P¯1, a = 6.816(3), b = 13.940(2), c = 14.403(3) Å, α = 116.830(14), β = 98.64(3), γ = 99.18(3)°, FW = 212.4 (for [HCN2S2]2·[N2]0.08) Z = 6. The crystal structure consists of stacked dimers, with three dimers per asymmetric unit. Pairs of asymmetric units, related by an inversion center, generate a pinwheel motif consisting of six dimers. The columnar structure associated with these pinwheels forms close-packed sets of “molecular tubes”. Cosublimation of the radical in the presence of iodine in the mole ratio (HCN2S2:I = 5:1) yields an iodine-doped hexagonal phase of composition [HCN2S2]6[I]1.1. Crystals of this material belong to the space group P61, a = b = 14.132(16), c = 3.352(5) Å, FW = 128.20, Z = 6. The crystal structure consists of sixfold pinwheels in which the now evenly spaced HCN2S2 rings form a spiral about the 61 axis. The iodine atoms lie within the columnar cavity of the pinwheels in a disordered array wrapped tightly about the sixfold screw axis. The single-crystal conductivity of the doped material is 15 S cm-1 at room temperature. Raman spectroscopic and magnetic susceptibility measurements on the doped material are reported

On the grammar of politics—or why conservatives prefer nouns

Previous research indicates that political conservatism is associated with epistemic needs for structure and certainty (Jost et al., 2003) and that nouns elicit clearer and more definite perceptions of reality than other parts of speech (Carnaghi et al., 2008). We therefore hypothesized that conservatives would exhibit preferences for nouns (vs. verbs and adjectives), insofar as nouns are better suited to satisfy epistemic needs. In Study 1, we observed that social conservatism was associated with noun preferences in Polish and that personal need for structure accounted for the association between ideology and grammatical preferences. In Study 2, conducted in Arabic, social conservatism was associated with a preference for the use of nominal sentences (composed of nouns only) over verbal sentences (which included verbs and adjectives). In Study 3, we found that more conservative U.S. presidents used greater proportions of nouns in major speeches, and this effect was related to integrative complexity. We discuss the possibility that conservative ideology is linked to grammatical preferences that foster feelings of stability and predictability

Climate Process Team on internal wave–driven ocean mixing

Author Posting. © American Meteorological Society, 2017. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 98 (2017): 2429-2454, doi:10.1175/BAMS-D-16-0030.1.Diapycnal mixing plays a primary role in the thermodynamic balance of the ocean and, consequently, in oceanic heat and carbon uptake and storage. Though observed mixing rates are on average consistent with values required by inverse models, recent attention has focused on the dramatic spatial variability, spanning several orders of magnitude, of mixing rates in both the upper and deep ocean. Away from ocean boundaries, the spatiotemporal patterns of mixing are largely driven by the geography of generation, propagation, and dissipation of internal waves, which supply much of the power for turbulent mixing. Over the last 5 years and under the auspices of U.S. Climate Variability and Predictability Program (CLIVAR), a National Science Foundation (NSF)- and National Oceanic and Atmospheric Administration (NOAA)-supported Climate Process Team has been engaged in developing, implementing, and testing dynamics-based parameterizations for internal wave–driven turbulent mixing in global ocean models. The work has primarily focused on turbulence 1) near sites of internal tide generation, 2) in the upper ocean related to wind-generated near inertial motions, 3) due to internal lee waves generated by low-frequency mesoscale flows over topography, and 4) at ocean margins. Here, we review recent progress, describe the tools developed, and discuss future directions.We are grateful to U.S. CLIVAR for their leadership in instigating and facilitating the Climate Process Team program. We are indebted to NSF and NOAA for sponsoring the CPT series.2018-06-0

Territorialising movement: the politics of land occupation in Bangladesh

This paper considers the politics of land occupation in Bangladesh. Contentious politics have been conceptualised as 'societies in movement' by Raul Zibechi, defined through their attempts to disperse power through the reconfiguration of social relations between peasants, the state and capital. Drawing on the author's ethnographic engagement with peasant farmer movements in Bangladesh since 2002, the paper analyses the differential powers generated in, by and through the production of relations and connections involved in land occupations. This requires a consideration of both relational and structural understandings of contentious politics. Organisational structures and dynamics, as well as the 'resourcefulness' of social movements (e.g. their capacities to deploy material resources, skills and knowledges), enable land occupation since these are crucial in creating and maintaining the socio-material relations necessary for political activity to be prosecuted. Drawing together these insights, the paper conceptualises land occupation as a process of 'territorialising movement' articulated through three interwoven spatial practices: strategic occupation, reconfiguration of social relations and territorialisation of translocal solidarities

Climate Process Team on Internal-Wave Driven Ocean Mixing

Diapycnal mixing plays a primary role in the thermodynamic balance of the ocean, and consequently, in oceanic heat and carbon uptake and storage. Though observed mixing rates are on average consistent with values required by inverse models, recent attention has focused on the dramatic spatial variability, spanning several orders of magnitude, of mixing rates in both the upper and deep ocean. Climate models have been shown to be very sensitive not only to the overall level but to the detailed distribution of mixing; sub-grid-scale parameterizations based on accurate physical processes will allow model forecasts to evolve with a changing climate. Spatio-temporal patterns of mixing are largely driven by the geography of generation, propagation and destruction of internal waves, which are thought to supply much of the power for turbulent mixing. Over the last five years and under the auspices of US CLIVAR, a NSF and NOAA supported Climate Process Team has been engaged in developing, implementing and testing dynamics-base parameterizations for internal-wave driven turbulent mixing in global ocean models. The work has primarily focused on turbulence 1) near sites of internal tide generation, 2) in the upper ocean related to wind-generated near inertial motions, 3) due to internal lee waves generated by low-frequency mesoscale flows over topography, and 4) at ocean margins. Here we review recent progress, describe the tools developed, and discuss future directions

Climate Process Team On Internal Wave-Driven Ocean Mixing

The study summarizes recent advances in our understanding of internal wave–driven turbulent mixing in the ocean interior and introduces new parameterizations for global climate ocean models and their climate impacts