A Unifying Model of Genome Evolution Under Parsimony

We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph $G$, a finite set of AVGs describe all parsimonious interpretations of $G$, and this set can be explored with a few sampling moves.Comment: 52 pages, 24 figure

Approximation algorithms for general cluster routing problem

Graph routing problems have been investigated extensively in operations research, computer science and engineering due to their ubiquity and vast applications. In this paper, we study constant approximation algorithms for some variations of the general cluster routing problem. In this problem, we are given an edge-weighted complete undirected graph $G=(V,E,c),$ whose vertex set is partitioned into clusters $C_{1},\dots ,C_{k}.$ We are also given a subset $V'$ of $V$ and a subset $E'$ of $E.$ The weight function $c$ satisfies the triangle inequality. The goal is to find a minimum cost walk $T$ that visits each vertex in $V'$ only once, traverses every edge in $E'$ at least once and for every $i\in [k]$ all vertices of $C_i$ are traversed consecutively.Comment: In COCOON 202

Induced Disjoint Paths in Circular-Arc Graphs in Linear Time

The Induced Disjoint Paths problem is to test whether a graph G with k distinct pairs of vertices (si,ti) contains paths P1,…,Pk such that Pi connects si and ti for i=1,…,k, and Pi and Pj have neither common vertices nor adjacent vertices (except perhaps their ends) for 1≤

The history of degenerate (bipartite) extremal graph problems

This paper is a survey on Extremal Graph Theory, primarily focusing on the case when one of the excluded graphs is bipartite. On one hand we give an introduction to this field and also describe many important results, methods, problems, and constructions.Comment: 97 pages, 11 figures, many problems. This is the preliminary version of our survey presented in Erdos 100. In this version 2 only a citation was complete

Business Models and E-Services: an Ontological Approach in a Cross-border Environment

Monograph's chapter

Search for CP Violation in Neutrino and Antineutrino Oscillations by the T2K Experiment with 2.2×1021 Protons on Target

The T2K experiment measures muon neutrino disappearance and electron neutrino appearance in accelerator-produced neutrino and antineutrino beams. With an exposure of 14.7(7.6)×1020 protons on target in the neutrino (antineutrino) mode, 89 νe candidates and seven anti-νe candidates are observed, while 67.5 and 9.0 are expected for δCP=0 and normal mass ordering. The obtained 2σ confidence interval for the CP-violating phase, δCP, does not include the CP-conserving cases (δCP=0, π). The best-fit values of other parameters are sin2θ23=0.526-0.036+0.032 and Δm322=2.463-0.070+0.071×10-3 eV2/c4

Measurement of the muon neutrino charged-current single π+ production on hydrocarbon using the T2K off-axis near detector ND280

We report the measurements of the single and double differential cross section of muon neutrino charged-current interactions on carbon with a single positively charged pion in the final state at the T2K off-axis near detector using 5.56×1020 protons on target. The analysis uses data control samples for the background subtraction and the cross section signal, defined as a single negatively charged muon and a single positively charged pion exiting from the target nucleus, is extracted using an unfolding method. The model-dependent cross section, integrated over the T2K off-axis neutrino beam spectrum peaking at 0.6 GeV, is measured to be σ=(11.76±0.44(stat)±2.39(syst))×10-40 cm2 nucleon-1. Various differential cross sections are measured, including the first measurement of the Adler angles for single charged pion production in neutrino interactions with heavy nuclei target

Measurement of inclusive double-differential νμ charged-current cross section with improved acceptance in the T2K off-axis near detector

We report a measurement of the flux-integrated cross section for inclusive muon neutrino charged-current interactions on carbon. The double-differential measurements are given as a function of the muon momentum and angle. Relative to our previous publication on this topic, these results have an increased angular acceptance and higher statistics. The data sample presented here corresponds to 5.7×1020 protons on target. The total flux-integrated cross section is measured to be (6.950±0.662)×10-39 cm2 nucleon-1 and is consistent with our simulation

Characterization of nuclear effects in muon-neutrino scattering on hydrocarbon with a measurement of final-state kinematics and correlations in charged-current pionless interactions at T2K

This paper reports measurements of final-state proton multiplicity, muon and proton kinematics, and their correlations in charged-current pionless neutrino interactions, measured by the T2K ND280 near detector in its plastic scintillator (C8H8) target. The data were taken between years 2010 and 2013, corresponding to approximately 6×1020 protons on target. Thanks to their exploration of the proton kinematics and of imbalances between the proton and muon kinematics, the results offer a novel probe of the nuclear-medium effects most pertinent to the (sub-)GeV neutrino-nucleus interactions that are used in accelerator-based long-baseline neutrino oscillation measurements. These results are compared to many neutrino-nucleus interaction models which all fail to describe at least part of the observed phase space. In case of events without a proton above a detection threshold in the final state, a fully consistent implementation of the local Fermi gas model with multinucleon interactions gives the best description of the data. In the case of at least one proton in the final state, the spectral function model agrees well with the data, most notably when measuring the kinematic imbalance between the muon and the proton in the plane transverse to the incoming neutrino. Within the models considered, only the existence of multinucleon interactions are able to describe the extracted cross section within regions of high transverse kinematic imbalance. The effect of final-state interactions is also discussed