The organic waste gold rush: optimising resource recovery in the UK bioeconomy

The use of organic waste in the bioeconomy has the potential to contribute towards the UK’s strategic goals of clean growth, resource security and reducing use of fossil fuels. While the reduction of avoidable organic waste remains a priority, a number of waste streams are likely to persist and could provide a significant feedstock for the UK bioeconomy. The greatest environmental, social and economic benefits of resource recovery from organic wastes are associated with the displacement of fossil fuel derived chemicals and materials, and the combined products of nutrients and energy from anaerobic digestion. Organic wastes offer multiple resources that can be exploited most efficiently by technologies working in synergy with each other. Investments into different options for using organic wastes are driven by government policy and resource demand, in addition to technology readiness. Policy and regulations should encourage industrial synergies and an increase in the diversity of resources recovered from organic waste in order to be able to respond to future resource demands

Editorial: Resource Recovery From Waste

This is the final version. Available from Frontiers Media via the DOI in this record. NERCESRCDEFR

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

Quarnet Inference Rules for Level-1 Networks

An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set X of species from a collection of trees, each having leaf-set some subset of X. In the 1980s, Colonius and Schulze gave certain inference rules for deciding when a collection of 4-leaved trees, one for each 4-element subset of X, can be simultaneously displayed by a single supertree with leaf-set X. Recently, it has become of interest to extend this and related results to phylogenetic networks. These are a generalization of phylogenetic trees which can be used to represent reticulate evolution (where species can come together to form a new species). It has recently been shown that a certain type of phylogenetic network, called a (unrooted) level-1 network, can essentially be constructed from 4-leaved trees. However, the problem of providing appropriate inference rules for such networks remains unresolved. Here, we show that by considering 4-leaved networks, called quarnets, as opposed to 4-leaved trees, it is possible to provide such rules. In particular, we show that these rules can be used to characterize when a collection of quarnets, one for each 4-element subset of X, can all be simultaneously displayed by a level-1 network with leaf-set X. The rules are an intriguing mixture of tree inference rules, and an inference rule for building up a cyclic ordering of X from orderings on subsets of X of size 4. This opens up several new directions of research for inferring phylogenetic networks from smaller ones, which could yield new algorithms for solving the supernetwork problem in phylogenetics

Tree-Based Unrooted Phylogenetic Networks

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms. Correction available at dx.doi.org/10.1007/s11538-018-0530-

Beyond representing orthology relations by trees

Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple relations on a set of sequences called orthology relations may be employed. In addition to being interesting from a practical point of view they are also attractive from a theoretical perspective in that e.\,g.\,a characterization is known for when such a relation is representable by a certain type of phylogenetic tree. For an orthology relation inferred from real biological data it is however generally too much to hope for that it satisfies that characterization. Rather than trying to correct the data in some way or another which has its own drawbacks, as an alternative, we propose to represent an orthology relation $\delta$ in terms of a structure more general than a phylogenetic tree called a phylogenetic network. To compute such a network in the form of a level-1 representation for $\delta$, we formalize an orthology relation in terms of the novel concept of a symbolic 3- dissimilarity which is motivated by the biological concept of a ``cluster of orthologous groups'', or COG for short. For such maps which assign symbols rather that real values to elements, we introduce the novel {\sc Network-Popping} algorithm which has several attractive properties. In addition, we characterize an orthology relation $\delta$ on some set $X$ that has a level-1 representation in terms of eight natural properties for $\delta$ as well as in terms of level-1 representations of orthology relations on certain subsets of $X$

Correlates of Obsessive–Compulsive Disorder in a Sample of HIV-Positive, Methamphetamine-using Men Who have Sex with Men

Substance use has been identified as a risk factor for elevated levels of obsessive–compulsive disorder (OCD). This study examined methamphetamine use and sexual risk behaviors as correlates of OCD in a sample of 245 HIV-positive men having sex with men (MSM) in San Diego, CA. In a logistic regression analysis, OCD was associated with greater frequency of methamphetamine use, more depressive symptoms, seeking out risky venues and risky sexual partners when “high” on methamphetamine, and reporting fewer sex acts in the past 2 months. These data suggest the need for increased awareness and understanding of the role that OCD may play in the drug use behaviors and risky sexual practices of methamphetamine users

Learning to live with Parkinson’s disease in the family unit:an interpretative phenomenological analysis of well-being

We investigated family members’ lived experience of Parkinson’s disease (PD) aiming to investigate opportunities for well-being. A lifeworld-led approach to healthcare was adopted. Interpretative phenomenological analysis was used to explore in-depth interviews with people living with PD and their partners. The analysis generated four themes: It’s more than just an illness revealed the existential challenge of diagnosis; Like a bird with a broken wing emphasizing the need to adapt to increasing immobility through embodied agency; Being together with PD exploring the kinship within couples and belonging experienced through support groups; and Carpe diem! illuminated the significance of time and fractured future orientation created by diagnosis. Findings were interpreted using an existential-phenomenological theory of well-being. We highlighted how partners shared the impact of PD in their own ontological challenges. Further research with different types of families and in different situations is required to identify services required to facilitate the process of learning to live with PD. Care and support for the family unit needs to provide emotional support to manage threats to identity and agency alongside problem-solving for bodily changes. Adopting a lifeworld-led healthcare approach would increase opportunities for well-being within the PD illness journey

A Cost-Effectiveness Analysis of “Test” versus “Treat” Patients Hospitalized with Suspected Influenza in Hong Kong

BACKGROUND: Seasonal and 2009 H1N1 influenza viruses may cause severe diseases and result in excess hospitalization and mortality in the older and younger adults, respectively. Early antiviral treatment may improve clinical outcomes. We examined potential outcomes and costs of test-guided versus empirical treatment in patients hospitalized for suspected influenza in Hong Kong. METHODS: We designed a decision tree to simulate potential outcomes of four management strategies in adults hospitalized for severe respiratory infection suspected of influenza: "immunofluorescence-assay" (IFA) or "polymerase-chain-reaction" (PCR)-guided oseltamivir treatment, "empirical treatment plus PCR" and "empirical treatment alone". Model inputs were derived from literature. The average prevalence (11%) of influenza in 2010-2011 (58% being 2009 H1N1) among cases of respiratory infections was used in the base-case analysis. Primary outcome simulated was cost per quality-adjusted life-year (QALY) expected (ICER) from the Hong Kong healthcare providers' perspective. RESULTS: In base-case analysis, "empirical treatment alone" was shown to be the most cost-effective strategy and dominated the other three options. Sensitivity analyses showed that "PCR-guided treatment" would dominate "empirical treatment alone" when the daily cost of oseltamivir exceeded USD18, or when influenza prevalence was <2.5% and the predominant circulating viruses were not 2009 H1N1. Using USD50,000 as the threshold of willingness-to-pay, "empirical treatment alone" and "PCR-guided treatment" were cost-effective 97% and 3% of time, respectively, in 10,000 Monte-Carlo simulations. CONCLUSIONS: During influenza epidemics, empirical antiviral treatment appears to be a cost-effective strategy in managing patients hospitalized with severe respiratory infection suspected of influenza, from the perspective of healthcare providers in Hong Kong