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

Het roer moet om: een nieuwe organisatie met een nieuwe doelstelling

De 'werkgroep doelstellingen'van de Stuurgroep Bedrijfsraad 2000 bracht advies uit over de doelstellingen van een nieuwe bijenteeltorganisatie. Vanuit een beschrijving van de historische ontwikkeling van de georganiseerde imkerij en het afnemende belang als economische (landbouw)sector wordt een nieuw perspectief geschetst: van belangenorganisatie naar een natuurorganisatie, die niet alleen het bedrijfsmatige en imkertechnische aspect onder haar hoede heeft maar ook de natuurwaarde die met bijen verbonden is naar voren brengt voor een breder publie

Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets

Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set T of binary binets or trinets over a taxon set X, and constructing such a network whenever it exists. We show that this is NP-hard for trinets but polynomial-time solvable for binets. Moreover, we show that the problem is still polynomial-time solvable for inputs consisting of binets and trinets as long as the cycles in the trinets have size three. Finally, we present an O(3^{|X|} poly(|X|)) time algorithm for general sets of binets and trinets. The latter two algorithms generalise to instances containing level-1 networks with arbitrarily many leaves, and thus provide some of the first supernetwork algorithms for computing networks from a set of rooted 1 phylogenetic networks

Long-term mesh erosion rate following abdominal robotic reconstructive pelvic floor surgery:a prospective study and overview of the literature

Introduction and hypothesis: The use of synthetic mesh in transvaginal pelvic floor surgery has been subject to debate internationally. Although mesh erosion appears to be less associated with an abdominal approach, the long-term outcome has not been studied intensively. This study was set up to determine the long-term mesh erosion rate following abdominal pelvic reconstructive surgery. Methods: A prospective, observational cohort study was conducted in a tertiary care setting. All consecutive female patients who underwent robot-assisted laparoscopic sacrocolpopexy and sacrocolporectopexy in 2011 and 2012 were included. Primary outcome was mesh erosion. Preoperative and postoperative evaluation (6 weeks, 1 year, 5 years) with a clinical examination and questionnaire regarding pelvic floor symptoms was performed. Mesh-related complications were assessed using a transparent vaginal speculum, proctoscopy, and digital vaginal and rectal examination. Kaplan–Meier estimates were calculated for mesh erosion. A review of the literature on mesh exposure after minimally invasive sacrocolpopexy was performed (≥12 months’ follow-up). Results: Ninety-six of the 130 patients included (73.8%) were clinically examined. Median follow-up time was 48.1 months (range 36.0–62.1). Three mesh erosions were diagnosed (3.1%; Kaplan–Meier 4.9%, 95% confidence interval 0–11.0): one bladder erosion for which mesh resection and an omental patch interposition were performed, and two asymptomatic vaginal erosions (at 42.7 and 42.3 months) treated with estrogen cream in one. Additionally, 22 patients responded solely by questionnaire and/or telephone; none reported mesh-related complaints. The literature, mostly based on retrospective studies, described a median mesh erosion rate of 1.9% (range 0–13.3%). Conclusions: The long-term rate of mesh erosion following an abdominally placed synthetic graft is low

A Note on Encodings of Phylogenetic Networks of Bounded Level

Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i.e. uniquely describe) the network that induces it? In this note, we present a complete answer to this question for the special case of a level-1 (phylogenetic) network by characterizing those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. Given that this type of network forms the first layer of the rich hierarchy of level-k networks, k a non-negative integer, it is natural to wonder whether our arguments could be extended to members of that hierarchy for higher values for k. By giving examples, we show that this is not the case

hiPathDB: a human-integrated pathway database with facile visualization

One of the biggest challenges in the study of biological regulatory networks is the systematic organization and integration of complex interactions taking place within various biological pathways. Currently, the information of the biological pathways is dispersed in multiple databases in various formats. hiPathDB is an integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. In total, it includes 1661 pathways consisting of 8976 distinct physical entities. hiPathDB provides two different types of integration. The pathway-level integration, conceptually a simple collection of individual pathways, was achieved by devising an elaborate model that takes distinct features of four databases into account and subsequently reformatting all pathways in accordance with our model. The entity-level integration creates a single unified pathway that encompasses all pathways by merging common components. Even though the detailed molecular-level information such as complex formation or post-translational modifications tends to be lost, such integration makes it possible to investigate signaling network over the entire pathways and allows identification of pathway cross-talks. Another strong merit of hiPathDB is the built-in pathway visualization module that supports explorative studies of complex networks in an interactive fashion. The layout algorithm is optimized for virtually automatic visualization of the pathways. hiPathDB is available at http://hiPathDB.kobic.re.kr