An error analysis of probabilistic fibre tracking methods: average curves optimization

Fibre tractography using diffusion tensor imaging is a promising method for estimating the pathways of white matter tracts in the human brain. The success of fibre tracking methods ultimately depends upon the accuracy of the fibre tracking algorithms and the quality of the data. Uncertainty and its representation have an important role to play in fibre tractography methods to infer useful information from real world noisy diffusion weighted data. Probabilistic fibre tracking approaches have received considerable interest recently for resolving orientational uncertainties. In this study, an average curves approach was used to investigate the impact of SNR and tensor field geometry on the accuracy of three different types of probabilistic tracking algorithms. The accuracy was assessed using simulated data and a range of tract geometries. The average curves representations were employed to represent the optimal fibre path of probabilistic tracking curves. The results are compared with streamline tracking on both simulated and in vivo data

Cubic spline prewavelets on the four-directional mesh

In this paper, we design differentiable, two dimensional, piecewise polynomial cubic prewavelets of particularly small compact support. They are given in closed form, and provide stable, orthogonal decompositions of L^2(\RR^2). In particular, the splines we use in our prewavelet constructions give rise to stable bases of spline spaces that contain all cubic polynomials, whereas the more familiar box spline constructions cannot reproduce all cubic polynomials, unless resorting to a box spline of higher polynomial degree

The oxygen isotope effect on critical temperature in superconducting copper oxides

The isotope effect provided a crucial key to the development of the BCS (Bardeen-Cooper-Schrieffer) microscopic theory of superconductivity for conventional superconductors. In superconducting cooper oxides (cuprates) showing an unconventional type of superconductivity, the oxygen isotope effect is very peculiar: the exponential coefficient strongly depends on doping level. No consensus has been reached so far on the origin of the isotope effect in the cuprates. Here we show that the oxygen isotope effect in cuprates is in agreement with the bisoliton theory of superconductivity.Comment: 3 pages including 4 figures; version 2 is with minor correction

Maintaining genetic integrity of coexisting wild and domestic populations : Genetic differentiation between wild and domestic Rangifer with long traditions of intentional interbreeding

The funding for the fieldwork and laboratory work for this study was provided by the ERC Advanced Grant 295458 Arctic Domus (PI D.G. Anderson). The writing and analysis was supported by ESRC ES-M0110548-1 JPI HUMANOR (PI D.G. Anderson). The sample set for Lake Nichatka was collected and deposited under a research programme of the Norwegian Institute for Nature Research. We thank Liv Midthjell for skilful laboratory analyses, Konstantin Klokov for help sourcing statistics on Russian reindeer populations, and Jan Heggenes for useful comments on an earlier version of this paper. A full list of project participants is in Appendix 2.Peer reviewedPublisher PD

State aggregation for fast likelihood computations in molecular evolution.

MOTIVATION: Codon models are widely used to identify the signature of selection at the molecular level and to test for changes in selective pressure during the evolution of genes encoding proteins. The large size of the state space of the Markov processes used to model codon evolution makes it difficult to use these models with large biological datasets. We propose here to use state aggregation to reduce the state space of codon models and, thus, improve the computational performance of likelihood estimation on these models. RESULTS: We show that this heuristic speeds up the computations of the M0 and branch-site models up to 6.8 times. We also show through simulations that state aggregation does not introduce a detectable bias. We analysed a real dataset and show that aggregation provides highly correlated predictions compared to the full likelihood computations. Finally, state aggregation is a very general approach and can be applied to any continuous-time Markov process-based model with large state space, such as amino acid and coevolution models. We therefore discuss different ways to apply state aggregation to Markov models used in phylogenetics. AVAILABILITY: The heuristic is implemented in the godon package (https://bitbucket.org/Davydov/godon) and in a version of FastCodeML (https://gitlab.isb-sib.ch/phylo/fastcodeml). CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Correlation of optical conductivity and ARPES spectra of strong-coupling large polarons and its display in cuprates

Common approach is used to calculate band due to strong-coupling large polaron (SCLP) photodissociation in ARPES and in optical conductivity (OC) spectra. It is based on using the coherent-states representation for the phonon field in SCLP. The calculated positions of both band maximums are universal functions of one parameter - the SCLP binding energy Ep: ARPES band maximum lies at binding energy about 3.2Ep; the OC band maximum is at the photon energy about 4.2Ep. The half-widths of the bands are mainly determined by Ep and slightly depend on Frohlich electron-phonon coupling constant: for its value 6-8 the ARPES band half-width is 1.7-1.3Ep and the OC band half-width is 2.8-2.2Ep. Using these results one can predict approximate position of ARPES band maximum and half-width from the maximum of mid-IR OC band and vice versa. Comparison of the results with experiments leads to a conclusion that underdoped cuprates contain SCLPs with Ep=0.1-0.2 eV that is in good conformity with the medium parameters in cuprates. The values of the polaron binding energy determined from experimental ARPES and OC spectra of the same material are in good conformity too: the difference between them is within 10 percent.Comment: 17 pages, 6 figure