Which phylogenetic networks are merely trees with additional arcs?

A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines whether or not any given network can be realized in this way. Moreover, the proof provides a polynomial-time algorithm for finding one or more trees (when they exist) on which the network can be based. A number of interesting consequences are presented as corollaries; these lead to some further relevant questions and observations, which we outline in the conclusion.Comment: The final version of this article will appear in Systematic Biology. 20 pages, 7 figure

Comparison of fine structural mice via coarse iteration

Let M be a fine structural mouse. Let D be a fully backgrounded L[E]-construction computed inside an iterable coarse premouse S. We describe a process comparing M with D, through forming iteration trees on M and on S. We then prove that this process succeeds

Proposal for an Integrated Raman-free Correlated Photon Source

We propose a dual-pump third-order nonlinear scheme for producing pairs of correlated photons that is less susceptible to Raman noise than typical spontaneous four wave mixing methods (SFWM). Beginning with the full multimode Hamiltonian we derive a general expression for the joint spectral amplitude, from which the probability of producing a pair of photons can be calculated. As an example, we demonstrate that a probability of 0.028 pairs per pulse can be achieved in an appropriately designed fused silica microfiber. As compared with single pump SFWM in standard fiber, we calculate that our process shows significant suppression of the spontaneous Raman scattering and an improvement in the signal to noise ratio.Comment: 7 pages, 3 figures (two containing 2 subfigures

The perception of self-produced sensory stimuli in patients with auditory hallucinations and passivity experiences: evidence for a breakdown in self-monitoring

BACKGROUND: To test the hypothesis that certain psychotic symptomatology is due to a defect in self-monitoring, we investigated the ability of groups of psychiatric patients to differentiate perceptually between self-produced and externally produced tactile stimuli. METHODS: Responses to tactile stimulation were assessed in three groups of subjects: schizophrenic patients; patients with bipolar affective disorder or depression; and normal control subjects. Within the psychiatric groups subjects were divided on the basis of the presence or absence of auditory hallucinations and/or passivity experiences. The subjects were asked to rate the perception of a tactile sensation on the palm of their left hand. The tactile stimulation was either self-produced by movement of the subject's right hand or externally produced by the experimenter. RESULTS: Normal control subjects and those psychiatric patients with neither auditory hallucinations nor passivity phenomena experienced self-produced stimuli as less intense, tickly and pleasant than identical, externally produced tactile stimuli. In contrast, psychiatric patients with these symptoms did not show a decrease in their perceptual ratings for tactile stimuli produced by themselves as compared with those produced by the experimenter. This failure to show a difference in perception between self-produced and externally produced stimuli appears to relate to the presence of auditory hallucinations and/or passivity experiences rather than to the diagnosis of schizophrenia. CONCLUSIONS: We propose that auditory hallucinations and passivity experiences are associated with an abnormality in the self-monitoring mechanism that normally allows us to distinguish self-produced from externally produced sensations

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