Between Treewidth and Clique-width

Many hard graph problems can be solved efficiently when restricted to graphs of bounded treewidth, and more generally to graphs of bounded clique-width. But there is a price to be paid for this generality, exemplified by the four problems MaxCut, Graph Coloring, Hamiltonian Cycle and Edge Dominating Set that are all FPT parameterized by treewidth but none of which can be FPT parameterized by clique-width unless FPT = W[1], as shown by Fomin et al [7, 8]. We therefore seek a structural graph parameter that shares some of the generality of clique-width without paying this price. Based on splits, branch decompositions and the work of Vatshelle [18] on Maximum Matching-width, we consider the graph parameter sm-width which lies between treewidth and clique-width. Some graph classes of unbounded treewidth, like distance-hereditary graphs, have bounded sm-width. We show that MaxCut, Graph Coloring, Hamiltonian Cycle and Edge Dominating Set are all FPT parameterized by sm-width

Mixed quantum state detection with inconclusive results

We consider the problem of designing an optimal quantum detector with a fixed rate of inconclusive results that maximizes the probability of correct detection, when distinguishing between a collection of mixed quantum states. We develop a sufficient condition for the scaled inverse measurement to maximize the probability of correct detection for the case in which the rate of inconclusive results exceeds a certain threshold. Using this condition we derive the optimal measurement for linearly independent pure-state sets, and for mixed-state sets with a broad class of symmetries. Specifically, we consider geometrically uniform (GU) state sets and compound geometrically uniform (CGU) state sets with generators that satisfy a certain constraint. We then show that the optimal measurements corresponding to GU and CGU state sets with arbitrary generators are also GU and CGU respectively, with generators that can be computed very efficiently in polynomial time within any desired accuracy by solving a semidefinite programming problem.Comment: Submitted to Phys. Rev.

Systemic immunosuppression depletes peripheral blood regulatory B cells in patients with immune thrombocytopenia

Regulatory B (Breg) cells are potentially implicated in the pathogenesis of immune thrombocytopenia (ITP). We analysed a prospective cohort of newly diagnosed steroid naïve ITP patients enrolled in the multicentre FLIGHT trial and found that the numbers of Bregs in their peripheral blood were similar to healthy controls. In contrast, Breg numbers were significantly reduced in ITP patients treated with systemic immunosuppression (glucocorticoids or mycophenolate mofetil). We also demonstrate that glucocorticoid treatment impairs Breg interleukin-10 production via an indirect T-cell-mediated mechanism

EPTAS and Subexponential Algorithm for Maximum Clique on Disk and Unit Ball Graphs

A (unit) disk graph is the intersection graph of closed (unit) disks in the plane. Almost three decades ago, an elegant polynomial-time algorithm was found for Maximum Cliqe on unit disk graphs [Clark, Colbourn, Johnson; Discrete Mathematics ’90]. Since then, it has been an intriguing open question whether or not tractability can be extended to general disk graphs. We show that the disjoint union of two odd cycles is never the complement of a disk graph nor of a unit (3-dimensional) ball graph. From that fact and existing results, we derive a simple QPTAS and a subexponential algorithm running in time 2O˜(n2/3) for Maximum Cliqe on disk and unit ball graphs. We then obtain a randomized EPTAS for computing the independence number on graphs having no disjoint union of two odd cycles as an induced subgraph, bounded VC-dimension, and linear independence number. This, in combination with our structural results, yields a randomized EPTAS for Max Cliqe on disk and unit ball graphs. Max Cliqe on unit ball graphs is equivalent to finding, given a collection of points in R3, a maximum subset of points with diameter at most some fixed value. In stark contrast, Maximum Cliqe on ball graphs and unit 4-dimensional ball graphs, as well as intersection graphs of filled ellipses (even close to unit disks) or filled triangles is unlikely to have such algorithms. Indeed, we show that, for all those problems, there is a constant ratio of approximation which cannot be attained even in time 2n1−ε, unless the Exponential Time Hypothesis fails

Last interglacial temperature evolution – a model inter-comparison

Abstract. There is a growing number of proxy-based reconstructions detailing the climatic changes during the Last Interglacial period. This period is of special interest because large parts of the globe were characterized by a warmer-than-present-day climate, making this period an interesting test bed for climate models in the light of projected global warming. However, mainly because synchronizing the different records is difficult, there is no consensus on a global picture of Last Interglacial temperature changes. Here we present the first model inter-comparison of transient simulations covering the Last Interglacial period. By comparing the different simulations we aim at investigating the robustness of the simulated surface air temperature evolution. The model inter-comparison shows a robust Northern Hemisphere July temperature evolution characterized by a maximum between 130–122 ka BP with temperatures 0.4 to 6.8 K above pre-industrial values. This temperature evolution is in line with the changes in June insolation and greenhouse-gas concentrations. For the evolution of July temperatures in the Southern Hemisphere, the picture emerging from the inter-comparison is less clear. However, it does show that including greenhouse-gas concentration changes is critical. The simulations that include this forcing show an early, 128 ka BP July temperature anomaly maximum of 0.5 to 2.6 K. The robustness of simulated January temperatures is large in the Southern Hemisphere and the mid-latitudes of the Northern Hemisphere. In these latitudes maximum January temperature anomalies of respectively −2.5 to 2 K and 0 to 2 K are simulated for the period after 118 ka BP. The inter-comparison is inconclusive on the evolution of January temperatures in the high-latitudes of the Northern Hemisphere. Further investigation of regional anomalous patterns and inter-model differences indicate that in specific regions, feedbacks within the climate system are important for the simulated temperature evolution. Firstly in the Arctic region, changes in the summer sea-ice cover control the evolution of Last Interglacial winter temperatures. Secondly, for the Atlantic region, the Southern Ocean and the North Pacific, possible changes in the characteristics of the Atlantic meridional overturning circulation are critical. The third important feedback, having an impact on the temperature evolution of the Northern Hemisphere, is shown to be the presence of remnant continental ice from the preceding glacial period. Another important feedback are changes in the monsoon regime which controls the evolution of temperatures over parts of Africa and India. Finally, the simulations reveal an important land-sea contrast, with temperature changes over the oceans lagging continental temperatures by up to several thousand years. The aforementioned feedback mechanisms tend to be highly model-dependent, indicating that specific proxy-data is needed to constrain future climate simulations and to further enhance our understanding of the evolution of the climate during the Last Interglacial period

Binets: fundamental building blocks for phylogenetic networks

Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph having a unique root in which the leaves are labelled by a given set of species. Recently, some approaches have been developed to construct phylogenetic networks from collections of networks on 2- and 3-leaved networks, which are known as binets and trinets, respectively. Here we study in more depth properties of collections of binets, one of the simplest possible types of networks into which a phylogenetic network can be decomposed. More speci_cally, we show that if a collection of level-1 binets is compatible with some binary network, then it is also compatible with a binary level-1 network. Our proofs are based on useful structural results concerning lowest stable ancestors in networks. In addition, we show that, although the binets do not determine the topology of the network, they do determine the number of reticulations in the network, which is one of its most important parameters. We also consider algorithmic questions concerning binets. We show that deciding whether an arbitrary set of binets is compatible with some network is at least as hard as the well-known Graph Isomorphism problem. However, if we restrict to level-1 binets, it is possible to decide in polynomial time whether there exists a binary network that displays all the binets. We also show that to _nd a network that displays a maximum number of the binets is NP-hard, but that there exists a simple polynomial-time 1/3-approximation algorithm for this problem. It is hoped that these results will eventually assist in the development of new methods for constructing phylogenetic networks from collections of smaller networks

Effects of deletion of the Streptococcus pneumoniae lipoprotein diacylglyceryl transferase gene lgt on ABC transporter function and on growth in vivo

Lipoproteins are an important class of surface associated proteins that have diverse roles and frequently are involved in the virulence of bacterial pathogens. As prolipoproteins are attached to the cell membrane by a single enzyme, prolipoprotein diacylglyceryl transferase (Lgt), deletion of the corresponding gene potentially allows the characterisation of the overall importance of lipoproteins for specific bacterial functions. We have used a Δlgt mutant strain of Streptococcus pneumoniae to investigate the effects of loss of lipoprotein attachment on cation acquisition, growth in media containing specific carbon sources, and virulence in different infection models. Immunoblots of triton X-114 extracts, flow cytometry and immuno-fluorescence microscopy confirmed the Δlgt mutant had markedly reduced lipoprotein expression on the cell surface. The Δlgt mutant had reduced growth in cation depleted medium, increased sensitivity to oxidative stress, reduced zinc uptake, and reduced intracellular levels of several cations. Doubling time of the Δlgt mutant was also increased slightly when grown in medium with glucose, raffinose and maltotriose as sole carbon sources. These multiple defects in cation and sugar ABC transporter function for the Δlgt mutant were associated with only slightly delayed growth in complete medium. However the Δlgt mutant had significantly reduced growth in blood or bronchoalveolar lavage fluid and a marked impairment in virulence in mouse models of nasopharyngeal colonisation, sepsis and pneumonia. These data suggest that for S. pneumoniae loss of surface localisation of lipoproteins has widespread effects on ABC transporter functions that collectively prevent the Δlgt mutant from establishing invasive infection

New Emigration and Portuguese Society: Transnationalism and Return

This chapter addresses the theme of transnationalism and return in recent Portuguese emigration, namely the flows that occurred after the turn of the century. It starts with a brief theoretical overview on those topics, which constitute two relatively neglected characteristics of Portuguese emigration. Next, based on a survey carried out in 2014–2015 to more than 6000 recent emigrants, it reveals some of the links that they maintain with their home country, as well as their plans for the future, which include settlement in the destination country, return and re-emigration. Lastly, it examines data on returning emigrants – especially those that returned between 2001 and 2011 – extracted from the 2011 Census. The evidence reveals a significant number of returns, including individuals at both working and retirement ages and at all skill levels, thus exposing the unexpected complexity of movements. The results are based on the research project “Back to the future: new emigration and links with Portuguese society” (REMIGR), which aimed to ascertain the extent and characteristics of the new emigration wave. The project included an overview of emigration and return to and from all regions of the world, as well as case studies in UK, France, Luxembourg, Angola, Mozambique and Brazil.info:eu-repo/semantics/publishedVersio

Molecular control of sucrose utilization in Escherichia coli W, an efficient sucrose-utilizing strain

Sucrose is an industrially important carbon source for microbial fermentation. Sucrose utilization in Escherichia coli, however, is poorly understood, and most industrial strains cannot utilize sucrose. The roles of the chromosomally encoded sucrose catabolism (csc) genes in E. coli W were examined by knockout and overexpression experiments. At low sucrose concentrations, the csc genes are repressed and cells cannot grow. Removal of either the repressor protein (cscR) or the fructokinase (cscK) gene facilitated derepression. Furthermore, combinatorial knockout of cscR and cscK conferred an improved growth rate on low sucrose. The invertase (cscA) and sucrose transporter (cscB) genes are essential for sucrose catabolism in E. coli W, demonstrating that no other genes can provide sucrose transport or inversion activities. However, cscK is not essential for sucrose utilization. Fructose is excreted into the medium by the cscK-knockout strain in the presence of high sucrose, whereas at low sucrose (when carbon availability is limiting), fructose is utilized by the cell. Overexpression of cscA, cscAK, or cscAB could complement the W Delta cscRKAB knockout mutant or confer growth on a K-12 strain which could not naturally utilize sucrose. However, phenotypic stability and relatively good growth rates were observed in the K-12 strain only when overexpressing cscAB, and full growth rate complementation in W Delta cscRKA Balso required cscAB. Our understanding of sucrose utilization can be used to improve E. coli Wand engineer sucrose utilization in strains which do not naturally utilize sucrose, allowing substitution of sucrose for other, less desirable carbon sources in industrial fermentations

Effects of anti-malarial drugs on the electrocardiographic QT interval modelled in the isolated perfused guinea pig heart system

<p>Abstract</p> <p>Background</p> <p>Concern over the potential cardiotoxicity of anti-malarial drugs inducing a prolonged electrocardiographic QT interval has resulted in the almost complete withdrawal from the market of one anti-malarial drug - halofantrine. The effects on the QT interval of four anti-malarial drugs were examined, using the guinea pig heart.</p> <p>Methods</p> <p>The guinea pig heart was isolated, mounted on a Langendorff apparatus, and was then perfused with pyruvate-added Klebs-Henseleit solutions containing graded concentrations of the four agents such as quinidine (0.15 - 1.2 μM), quinine (0.3 - 2.4 μM), halofantrine (0.1 - 2.0 μM) and mefloquine (0.1 - 2.0 μM). The heart rate-corrected QaTc intervals were measured to evaluate drug-induced QT prolongation effects.</p> <p>Results</p> <p>Quinidine, quinine, and halofantrine prolonged the QaTc interval in a dose-dependent manner, whereas no such effect was found with mefloquine. The EC₅₀values for the QaTc prolongation effects, the concentration that gives a half-maximum effect, were quinidine < quinine ≈ halofantrine.</p> <p>Conclusions</p> <p>In this study, an isolated, perfused guinea pig heart system was constructed to assess the cardiotoxic potential of anti-malarial drugs. This isolated perfused guinea pig heart system could be used to test newly developed anti-malarial drugs for their inherent QT lengthening potential. More information is required on the potential variation in unbound drug concentrations in humans, and their role in cardiotoxicity.</p