GLM permutation - nonparametric inference for arbitrary general linear models

Introduction: Permutation methods are finding growing use in neuroimag- ing data analyses (e.g. randomise in FSL, SnPM in SPM, XBAMM/BAMM/CAMBA, etc). These methods provide ex- act control of false positives, make only weak assumptions, and allow nonstandard types of statistics (e.g. smoothed variance t- test). With fast and inexpensive computing, there would seem few reasons not to use nonparametric methods. A significant limitation of these methods, however, is the lack of flexibility with respect to the experimental design and nuisance variables. Each specific design dictates the type of exchange- ability of null data, and hence how to permute. Nuisance effects (e.g. age) render data non-exchangeable even when the effect of interest is null. Hence, even something as simple as ANCOVA has no exact permutation test. Recently there has been an active literature on approximate– but accurate–permutation tests for 2-variable regression, one effect of interest, one nuisance (see review by Anderson & Robinson [1]). Here we extend and evaluate these methods for use with an arbitrary General Linear Model (GLM)

Establishing microbial baselines to identify indicators of coral reef health

Microorganisms make a significant contribution to reef ecosystem health and resilience via their critical role in mediating nutrient transformations, their interactions with macro-organisms and their provision of chemical cues that underpin the recruitment of diverse reef taxa. However, environmental changes often cause compositional and functional shifts in microbial communities that can have flow-on consequences for microbial-mediated processes. These microbial alterations may impact the health of specific host organisms and can have repercussions for the functioning of entire coral ecosystems. Assessing changes in reef microbial communities should therefore provide an early indicator of ecosystem impacts and would underpin the development of diagnostic tools that could help forecast shifts in coral reef health under different environmental states. Monitoring, management and active restoration efforts have recently intensified and diversified in response to global declines in coral reef health. Here we propose that regular monitoring of coral reef microorganisms could provide a rapid and sensitive platform for identifying declining ecosystem health that can complement existing management frameworks. By summarising the most common threats to coral reefs, with a particular focus on the Great Barrier Reef, and elaborating on the role of microbes in coral reef health and ecosystem stability, we highlight the diagnostic applicability of microbes in reef management programs. Fundamental to this objective is the establishment of microbial baselines for Australia's coral reefs.AIMS@JCU PhD Scholarship; GBRMPA Science Management Research Award; Advance Queensland PhD Scholarship; Portuguese Science and Technology Foundation (FCT) [SFRH/BPD/110285/2015

Polarization-controlled single photons

Vacuum-stimulated Raman transitions are driven between two magnetic substates of a rubidium-87 atom strongly coupled to an optical cavity. A magnetic field lifts the degeneracy of these states, and the atom is alternately exposed to laser pulses of two different frequencies. This produces a stream of single photons with alternating circular polarization in a predetermined spatio-temporal mode. MHz repetition rates are possible as no recycling of the atom between photon generations is required. Photon indistinguishability is tested by time-resolved two-photon interference.Comment: 4 pages, 3 figure

von Neuman algebras of strongly connected higher-rank graphs

We investigate the factor types of the extremal KMS states for the preferred dynamics on the Toeplitz algebra and the Cuntz--Krieger algebra of a strongly connected finite $k$-graph. For inverse temperatures above 1, all of the extremal KMS states are of type I$_\infty$. At inverse temperature 1, there is a dichotomy: if the $k$-graph is a simple $k$-dimensional cycle, we obtain a finite type I factor; otherwise we obtain a type III factor, whose Connes invariant we compute in terms of the spectral radii of the coordinate matrices and the degrees of cycles in the graph.Comment: 16 pages; 1 picture prepared using TikZ. Version 2: this version to appear in Math. An

Simple manipulation of a microwave dressed-state ion qubit

Many schemes for implementing quantum information processing require that the atomic states used have a non-zero magnetic moment, however such magnetically sensitive states of an atom are vulnerable to decoherence due to fluctuating magnetic fields. Dressing an atom with an external field is a powerful method of reducing such decoherence [N. Timoney et al., Nature 476, 185], even if the states being dressed are strongly coupled to the environment. We introduce an experimentally simpler method of manipulating such a dressed-state qubit, which allows the implementation of general rotations of the qubit, and demonstrate this method using a trapped ytterbium ion

Isolation and characterisation of 17 microsatellite loci for the red-billed chough (Pyrrhocorax pyrrhocorax)

Peer reviewedPostprin