Uncertainty in phylogenetic tree estimates

Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly model the multivariate uncertainty of tree estimates. We consider both the cases where uncertainty information arises extrinsically (through covariate information) and intrinsically (through the tree estimates themselves). The importance of accounting for tree uncertainty in tree space is demonstrated in two case studies. In the first instance, differences between gene trees are small relative to their uncertainties, while in the second, the differences are relatively large. Our main goal is visualization of tree uncertainty, and we demonstrate advantages of our method with respect to reproducibility, speed and preservation of topological differences compared to visualization based on multidimensional scaling. The proposal highlights that phylogenetic trees are estimated in an extremely high-dimensional space, resulting in uncertainty information that cannot be discarded. Most importantly, it is a method that allows biologists to diagnose whether differences between gene trees are biologically meaningful, or due to uncertainty in estimation.Comment: Final version accepted to Journal of Computational and Graphical Statistic

Static inverters which sum a plurality of waves Patent

Describing static inverter with single or multiple phase outpu

Towards the graviton from spinfoams: higher order corrections in the 3d toy model

We consider the recent calculation gr-qc/0508124 of the graviton propagator in the spinfoam formalism. Within the 3d toy model introduced in gr-qc/0512102, we test how the spinfoam formalism can be used to construct the perturbative expansion of graviton amplitudes. Although the 3d graviton is a pure gauge, one can choose to work in a gauge where it is not zero and thus reproduce the structure of the 4d perturbative calculations. We compute explicitly the next to leading and next to next to leading orders, corresponding to one-loop and two-loop corrections. We show that while the first arises entirely from the expansion of the Regge action around the flat background, the latter receives contributions from the microscopic, non Regge-like, quantum geometry. Surprisingly, this new contribution reduces the magnitude of the next to next to leading order. It thus appears that the spinfoam formalism is likely to substantially modify the conventional perturbative expansion at higher orders. This result supports the interest in this approach. We then address a number of open issues in the rest of the paper. First, we discuss the boundary state ansatz, which is a key ingredient in the whole construction. We propose a way to enhance the ansatz in order to make the edge lengths and dihedral angles conjugate variables in a mathematically well-defined way. Second, we show that the leading order is stable against different choices of the face weights of the spinfoam model; the next to leading order, on the other hand, is changed in a simple way, and we show that the topological face weight minimizes it. Finally, we extend the leading order result to the case of a regular, but not equilateral, tetrahedron.Comment: 24 pages, many figure

Good Pond Fishing is No Accident

There are approximately 100,000 ponds (also called stock dams) in South Dakota; 48,000 contain fish. Most ponds are privately owned and are on ranches in western and central South Dakota. Ponds must be managed if they are to provide quality angling. And if properly managed, they can provide memorable fishing year after year. A common misconception is that a pond can have it all, that it can be stocked with any and all fish species and that the fishing will be good for all species. It is more likely that fishing may not be good for any species. In reality, you must decide what you want and choose that management option that best fits your needs. We present the following key and discussion to help you decide the best pond management strategy for you. Start with Number 1 in the key and follow the directions after the answer that best fits you and your pond

Identification of possible intense historical geomagnetic storms using combined sunspot and auroral observations from East Asia

Comprehensive catalogues of ancient sunspot and auroral observations from East Asia are used to identify possible intense historical geomagnetic storms in the interval 210 BC-AD 1918. There are about 270 entries in the sunspot catalogue and about 1150 entries in the auroral catalogue. Special databases have been constructed in which the scientific information in these two catalogues is placed in specified fields. For the purposes of this study, an historical geomagnetic storm is defined in terms of an auroral observation that is apparently associated with a particular sunspot observation, in the sense that the auroral observation occurred within several days of the sunspot observation. More precisely, a selection criterion is formulated for the automatic identification of such geomagnetic storms, using the oriental records stored in the sunspot and auroral databases. The selection criterion is based on specific assumptions about the duration of sunspot visibility with the unaided eye, the likely range of heliographic longitudes of an energetic solar feature, and the likely range of transit times for ejected solar plasma to travel from the Sun to the Earth. This selection criterion results in the identification of nineteen putative historical geomagnetic storms, although two of these storms are spurious in the sense that there are two examples of a single sunspot observation being associated with two different auroral observations separated by more than half a (synodic) solar rotation period. The literary and scientific reliabilities of the East Asian sunspot and auroral records that define the nineteen historical geomagnetic storms are discussed in detail in a set of appendices. A possible time sequence of events is presented for each geomagnetic storm, including possible dates for both the central meridian passage of the sunspot and the occurrence of the energetic solar feature, as well as likely transit times for the ejected solar plasma. European telescopic sunspot drawings from the seventeenth century are also used to assess the credibility of some of the later historical geomagnetic storms defined solely by the East Asian sunspot and auroral records. These drawings cast doubt on a few of the associations between sunspot and auroral observations based entirely on the oriental records, at least to the extent that the occidental drawings provide a more realistic date for central meridian passage of the sunspot actually associated with a particular auroral observation. Nevertheless, on those occasions for which European sunspot drawings are available, the dates of all the pertinent East Asian sunspot and auroral observations are corroborated, apart from just one Chinese sunspot observation. The ancient historical observations of sunspots and aurorae are discussed briefly in terms of modern observations of great geomagnetic storms

Developing enterprise culture in a northern educational authority in the UK: involving trainee teachers in learning-orientated evaluation

In this paper we discuss our use of innovative methods - at least in the context of regeneration evaluation - to help evaluate an enterprise project in northern England, paying particular attention to the involvement of trainee teachers. We discuss the methods used and critically appraise the methods and methodology, present some emerging findings from the trainee teachers strand and conclude by discussing the place of what might be termed 'learning-orientated evaluation' in relation to the currently dominant output-focussed evaluation paradigm.</p

Possible configurations of the magnetic field in the outer magnetosphere during geomagnetic polarity reversals

International audiencePossible configurations of the magnetic field in the outer magnetosphere during geomagnetic polarity reversals are investigated by considering the idealized problem of a magnetic multipole of order m and degree n located at the centre of a spherical cavity surrounded by a boundless perfect diamagnetic medium. In this illustrative idealization, the fixed spherical (magnetopause) boundary layer behaves as a perfectly conducting surface that shields the external diamagnetic medium from the compressed multipole magnetic field, which is therefore confined within the spherical cavity. For a general magnetic multipole of degree n, the non-radial components of magnetic induction just inside the magnetopause are increased by the factor {1 + [(n + 1)/n]} relative to their corresponding values in the absence of the perfectly conducting spherical magnetopause. An exact equation is derived for the magnetic field lines of an individual zonal (m = 0), or axisymmetric, magnetic multipole of arbitrary degree n located at the centre of the magnetospheric cavity. For such a zonal magnetic multipole, there are always two neutral points and n-1 neutral rings on the spherical magnetopause surface. The two neutral points are located at the poles of the spherical magnetopause. If n is even, one of the neutral rings is coincident with the equator; otherwise, the neutral rings are located symmetrically with respect to the equator. The actual existence of idealized higher-degree (n>1) axisymmetric magnetospheres would necessarily imply multiple (n + 1) magnetospheric cusps and multiple (n) ring currents. Exact equations are also derived for the magnetic field lines of an individual non-axisymmetric magnetic multipole, confined by a perfectly conducting spherical magnetopause, in two special cases; namely, a symmetric sectorial multipole (m = n) and an antisymmetric sectorial multipole (m = n-1). For both these non-axisymmetric magnetic multipoles, there exists on the spherical magnetopause surface a set of neutral points linked by a network of magnetic field lines. Novel magnetospheric processes are likely to arise from the existence of magnetic neutral lines that extend from the magnetopause to the surface of the Earth. Finally, magnetic field lines that are confined to, or perpendicular to, either special meridional planes or the equatorial plane, when the multipole is in free space, continue to be confined to, or perpendicular to, these same planes when the perfectly conducting magnetopause is present

Applications of ethylene vinyl acetate as an encapsulation material for terrestrial photovoltaic modules

Terrestrial photovoltaic modules must undergo substantial reductions in cost in order to become economically attractive as practical devices for large scale production of electricity. Part of the cost reductions must be realized by the encapsulation materials that are used to package, protect, and support the solar cells, electrical interconnects, and other ancillary components. As many of the encapsulation materials are polymeric, cost reductions necessitate the use of low cost polymers. The performance and status of ethylene vinyl acetate, a low cost polymer that is being investigated as an encapsulation material for terrestrial photovoltaic modules, are described