Trinets encode tree-child and level-2 phylogenetic networks

Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from triplets, that is rooted trees on three species. However, although triplets determine or encode rooted phylogenetic trees, they do not in general encode rooted phylogenetic networks, which is a potential issue for any such method. Motivated by this fact, Huber and Moulton recently introduced trinets as a natural extension of rooted triplets to networks. In particular, they showed that level-1 level-1 phylogenetic networks are encoded by their trinets, and also conjectured that all “recoverable” rooted phylogenetic networks are encoded by their trinets. Here we prove that recoverable binary level-2 networks and binary tree-child networks are also encoded by their trinets. To do this we prove two decomposition theorems based on trinets which hold for all recoverable binary rooted phylogenetic networks. Our results provide some additional evidence in support of the conjecture that trinets encode all recoverable rooted phylogenetic networks, and could also lead to new approaches to construct phylogenetic networks from trinets

Electron--Electron Scattering in Quantum Wires and it's Possible Suppression due to Spin Effects

A microscopic picture of electron-electron pair scattering in single mode quantum wires is introduced which includes electron spin. A new source of `excess' noise for hot carriers is presented. We show that zero magnetic field `spin' splitting in quantum wires can lead to a dramatic `spin'-subband dependence of electron--electron scattering, including the possibility of strong suppression. As a consequence extremely long electron coherence lengths and new spin-related phenomena are predicted. Since electron bands in III-V semiconductor quantum wires are in general spin-split in zero applied magnetic field, these new transport effects are of general importance.Comment: 11 pages, LaTeX and APS-RevteX 2, Rep.No. GF66,Figures from author, Physical Review Letters, scheduled for 7 June 199

Folding and unfolding phylogenetic trees and networks

Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network $N$ can be "unfolded" to obtain a MUL-tree $U(N)$ and, conversely, a MUL-tree $T$ can in certain circumstances be "folded" to obtain a phylogenetic network $F(T)$ that exhibits $T$. In this paper, we study properties of the operations $U$ and $F$ in more detail. In particular, we introduce the class of stable networks, phylogenetic networks $N$ for which $F(U(N))$ is isomorphic to $N$, characterise such networks, and show that they are related to the well-known class of tree-sibling networks.We also explore how the concept of displaying a tree in a network $N$ can be related to displaying the tree in the MUL-tree $U(N)$. To do this, we develop a phylogenetic analogue of graph fibrations. This allows us to view $U(N)$ as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in $U(N)$ and reconcilingphylogenetic trees with networks

Electronic and phononic Raman scattering in detwinned YBa2_2Cu3_3O6.95_{6.95} and Y0.85_{0.85}Ca0.15_{0.15}Ba2_2Cu3_3O6.95_{6.95}: s-wave admixture to the dx2−y2d_{x^2-y^2}-wave order parameter

Inelastic light (Raman) scattering has been used to study electronic excitations and phonon anomalies in detwinned, slightly overdoped YBa$_2$Cu$_3$O$_{6.95}$ and moderately overdoped Y$_{0.85}$Ca$_{0.15}$Ba$_2$Cu$_3$O$_{6.95}$ single crystals. In both samples modifications of the electronic pair-breaking peaks when interchanging the a- and b-axis were observed. The lineshapes of several phonon modes involving plane and apical oxygen vibrations exhibit pronounced anisotropies with respect to the incident and scattered light field configurations. Based on a theoretical model that takes both electronic and phononic contributions to the Raman spectra into account, we attribute the anisotropy of the superconductivity-induced changes in the phonon lineshapes to a small s-wave admixture to the $d_{x^2-y^2}$ pair wave-function. Our theory allows us to disentangle the electronic Raman signal from the phononic part and to identify corresponding interference terms. We argue that the Raman spectra are consistent with an s-wave admixture with an upper limit of 20 percent.Comment: accepted in Phys. Rev. B, 11 page

Heat Capacity of PbS: Isotope Effects

In recent years, the availability of highly pure stable isotopes has made possible the investigation of the dependence of the physical properties of crystals, in particular semiconductors, on their isotopic composition. Following the investigation of the specific heat ($C_p$, $C_v$) of monatomic crystals such as diamond, silicon, and germanium, similar investigations have been undertaken for the tetrahedral diatomic systems ZnO and GaN (wurtzite structure), for which the effect of the mass of the cation differs from that of the anion. In this article we present measurements for a semiconductor with rock salt structure, namely lead sulfide. Because of the large difference in the atomic mass of both constituents ($M_{\rm Pb}$= 207.21 and ($M_{\rm S}$=32.06 a.m.u., for the natural isotopic abundance) the effects of varying the cation and that of the anion mass are very different for this canonical semiconductor. We compare the measured temperature dependence of $C_p \approx C_v$, and the corresponding derivatives with respect to ($M_{\rm Pb}$ and $M_{\rm S}$), with \textit{\textit{ab initio}} calculations based on the lattice dynamics obtained from the local density approximation (LDA) electronic band structure. Quantitative deviations between theory and experiment are attributed to the absence of spin-orbit interaction in the ABINIT program used for the electronic band structure calculations.Comment: 17 pages including 10 Fig

Electronic Raman scattering in YBCO and other superconducting cuprates

Superconductivity induced structures in the electronic Raman spectra of high-Tc superconductors are computed using the results of ab initio LDA-LMTO three-dimensional band structure calculations via numerical integrations of the mass fluctuations, either in the whole 3D Brillouin zone or limiting the integrations to the Fermi surface. The results of both calculations are rather similar, the Brillouin zone integration yielding additional weak structures related to the extended van Hove singularities. Similar calculations have been performed for the normal state of these high-Tc cuprates. Polarization configurations have been investigated and the results have been compared to experimental spectra. The assumption of a simple d_(x^2-y^2)-like gap function allows us to explain a number of experimental features but is hard to reconcile with the relative positions of the A1g and B1g peaks.Comment: 14 pages, LaTeX (RevTeX), 5 PostScript figures, uses multicol.sty, submitted to PR

The role of adipose derived stem cells in the treatment of rotator cuff tears: From basic science to clinical application

Over the last decade, regenerative medicine has become increasingly popular throughout the scientific community. The poor healing capacity at the tendon-bone interface makes the rotator cuff an appealing target for biologic agents. Adipose derived stem cells are mesenchymalcells with the capacity for self-renewal and mul-tipotential differentiation. They have been recently proposed, both in isolation and as adjuvants to existing surgical therapies, for the treatment of rotator cuff tears. Several studies have been carried out in this research field, starting from the biological characteristics of adipose derived stem cells, their preparation and culture, up to the application in the experimental field on animal models and on humans. The purpose of this study was to provide a state of the art about the current basic science and clinical literature for the effectiveness of adipose derived stem cells in the treatment of rotator cuff tears