Axiomatic opportunities and obstacles for inferring a species tree from gene trees

The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all taxa are present in every gene tree. Here, we list four apparently desirable properties that a method for estimating a species tree from gene trees could have (the strongest property states that building a species tree from input gene trees and then pruning leaves gives a tree that is the same as, or more resolved than, the tree obtained by first removing the taxa from the input trees and then building the species tree). We show that while it is technically possible to simultaneously satisfy these properties when taxon coverage is complete, they cannot all be satisfied in the more general supertree setting. In part two, we discuss a concordance-based consensus method based on Baum's `plurality clusters', and an extension to concordance supertrees.Comment: 19 pages, 2 figure

Manual measurement of retinal bifurcation features

This paper introduces a new computerized tool for accurate manual measurement of features of retinal bifurcation geometry, designed for use in investigating correlations between measurement features and clinical conditions. The tool uses user-placed rectangles to measure the vessel width, and lines placed along vessel center lines to measure the angles. An analysis is presented of measurements taken from 435 bifurcations. These are compared with theoretical predictions based on optimality principles presented in the literature. The new tool shows better agreement with the theoretical predictions than a simpler manual method published in the literature, but there remains a significant discrepancy between current theory and measured geometry

Marine tethysuchian crocodyliform from the ?Aptian-Albian (Lower Cretaceous) of the Isle of Wight, UK

A marine tethysuchian crocodyliform from the Isle of Wight, most likely from the Upper Greensand Formation (upper Albian, Lower Cretaceous), is described. However, we cannot preclude it being from the Ferruginous Sands Formation (upper Aptian), or more remotely, the Sandrock Formation (upper Aptian-upper Albian). The specimen consists of the anterior region of the right dentary, from the tip of the dentary to the incomplete fourth alveolus. This specimen increases the known geological range of marine tethysuchians back into the late Lower Cretaceous. Although we refer it to Tethysuchia incertae sedis, there are seven anterior dentary characteristics that suggest a possible relationship with the Maastrichtian-Eocene clade Dyrosauridae. We also review ‘middle’ Cretaceous marine tethysuchians, including putative Cenomanian dyrosaurids. We conclude that there is insufficient evidence to be certain that any known Cenomanian specimen can be safely referred to Dyrosauridae, as there are some cranial similarities between basal dyrosaurids and Cenomanian–Turonian marine ‘pholidosaurids’. Future study of middle Cretaceous tethysuchians could help unlock the origins of Dyrosauridae and improve our understanding of tethysuchian macroevolutionary trends

Adiabatic optical entanglement between electron spins in separate quantum dots

We present an adiabatic approach to the design of entangling quantum operations with two electron spins localized in separate InAs/GaAs quantum dots via the Coulomb interaction between optically-excited localized states. Slowly-varying optical pulses minimize the pulse noise and the relaxation of the excited states. An analytic "dressed state" solution gives a clear physical picture of the entangling process, and a numerical solution is used to investigate the error dynamics. For two vertically-stacked quantum dots we show that, for a broad range of dot parameters, a two-spin state with concurrence $C>0.85$ can be obtained by four optical pulses with durations $\sim 0.1 - 1$ ns.Comment: 7 pages, 5 figure

Fast initialization of the spin state of an electron in a quantum dot in the Voigt configuration

We consider the initialization of the spin-state of a single electron trapped in a self-assembled quantum dot via optical pumping of a trion level. We show that with a magnetic field applied perpendicular to the growth direction of the dot, a near-unity fidelity can be obtained in a time equal to a few times the inverse of the spin-conserving trion relaxation rate. This method is several orders-of-magnitude faster than with the field aligned parallel, since this configuration must rely on a slow hole spin-flip mechanism. This increase in speed does result in a limit on the maximum obtainable fidelity, but we show that for InAs dots, the error is very small.Comment: 4 pages, 4 figure

Measurement of retinal vessel widths from fundus images based on 2-D modeling

Changes in retinal vessel diameter are an important sign of diseases such as hypertension, arteriosclerosis and diabetes mellitus. Obtaining precise measurements of vascular widths is a critical and demanding process in automated retinal image analysis as the typical vessel is only a few pixels wide. This paper presents an algorithm to measure the vessel diameter to subpixel accuracy. The diameter measurement is based on a two-dimensional difference of Gaussian model, which is optimized to fit a two-dimensional intensity vessel segment. The performance of the method is evaluated against Brinchmann-Hansen's half height, Gregson's rectangular profile and Zhou's Gaussian model. Results from 100 sample profiles show that the presented algorithm is over 30% more precise than the compared techniques and is accurate to a third of a pixel