Product structure of graph classes with strongly sublinear separators

We investigate the product structure of hereditary graph classes admitting strongly sublinear separators. We characterise such classes as subgraphs of the strong product of a star and a complete graph of strongly sublinear size. In a more precise result, we show that if any hereditary graph class $\mathcal{G}$ admits $O(n^{1-\epsilon})$ separators, then for any fixed $\delta\in(0,\epsilon)$ every $n$-vertex graph in $\mathcal{G}$ is a subgraph of the strong product of a graph $H$ with bounded tree-depth and a complete graph of size $O(n^{1-\epsilon+\delta})$. This result holds with $\delta=0$ if we allow $H$ to have tree-depth $O(\log\log n)$. Moreover, using extensions of classical isoperimetric inequalties for grids graphs, we show the dependence on $\delta$ in our results and the above $\text{td}(H)\in O(\log\log n)$ bound are both best possible. We prove that $n$-vertex graphs of bounded treewidth are subgraphs of the product of a graph with tree-depth $t$ and a complete graph of size $O(n^{1/t})$, which is best possible. Finally, we investigate the conjecture that for any hereditary graph class $\mathcal{G}$ that admits $O(n^{1-\epsilon})$ separators, every $n$-vertex graph in $\mathcal{G}$ is a subgraph of the strong product of a graph $H$ with bounded tree-width and a complete graph of size $O(n^{1-\epsilon})$. We prove this for various classes $\mathcal{G}$ of interest.Comment: v2: added bad news subsection; v3: removed section "Polynomial Expansion Classes" which had an error, added section "Lower Bounds", and added a new author; v4: minor revisions and corrections

Notes on Graph Product Structure Theory

It was recently proved that every planar graph is a subgraph of the strong product of a path and a graph with bounded treewidth. This paper surveys generalisations of this result for graphs on surfaces, minor-closed classes, various non-minor-closed classes, and graph classes with polynomial growth. We then explore how graph product structure might be applicable to more broadly defined graph classes. In particular, we characterise when a graph class defined by a cartesian or strong product has bounded or polynomial expansion. We then explore graph product structure theorems for various geometrically defined graph classes, and present several open problems.Comment: 19 pages, 0 figure

SmSP2: A serine protease secreted by the blood fluke pathogen Schistosoma mansoni with anti-hemostatic properties.

BackgroundSerine proteases are important virulence factors for many pathogens. Recently, we discovered a group of trypsin-like serine proteases with domain organization unique to flatworm parasites and containing a thrombospondin type 1 repeat (TSR-1). These proteases are recognized as antigens during host infection and may prove useful as anthelminthic vaccines, however their molecular characteristics are under-studied. Here, we characterize the structural and proteolytic attributes of serine protease 2 (SmSP2) from Schistosoma mansoni, one of the major species responsible for the tropical infectious disease, schistosomiasis.Methodology/principal findingsSmSP2 comprises three domains: a histidine stretch, TSR-1 and a serine protease domain. The cleavage specificity of recombinant SmSP2 was determined using positional scanning and multiplex combinatorial libraries and the determinants of specificity were identified with 3D homology models, demonstrating a trypsin-like endopeptidase mode of action. SmSP2 displayed restricted proteolysis on protein substrates. It activated tissue plasminogen activator and plasminogen as key components of the fibrinolytic system, and released the vasoregulatory peptide, kinin, from kininogen. SmSP2 was detected in the surface tegument, esophageal glands and reproductive organs of the adult parasite by immunofluorescence microscopy, and in the excretory/secretory products by immunoblotting.Conclusions/significanceThe data suggest that SmSP2 is secreted, functions at the host-parasite interface and contributes to the survival of the parasite by manipulating host vasodilatation and fibrinolysis. SmSP2 may be, therefore, a potential target for anti-schistosomal therapy

A revision of the genus Geitlerinema and a description of the genus Anagnostidinema gen. nov. (Oscillatoriophycidae, Cyanobacteria)

The simple filamentous cyanobacterial genus Geitlerinema is heterogeneous. At least two distinct phylogenetic clades can be derived from the set of most common freshwater Geitlerinema species. Our revision is based on the original description of the type species G. splendidum aka Oscillatoria spendida and on molecular sequencing of morphologically relevant strains. The revised Geitlerinema contains only one species according to morphological similarity with its original description. Consequently, the majority of other freshwater species inferred from molecular sequencing of 16S rRNA gene and 16S–23S ITS analysis (related both genetically and morphologically to G. pseudacutissimum) must be classified as a special taxon on the generic level. The name Anagnostidinema is proposed for this genus, which was selected in memory of the prominent late cyanobacterial specialist Konstantinos Anagnostidis. The genetic position, short review and characteristics of the newly defined genus Anagnostidinema is presented in this paper. The taxonomy of the rest of species (including the marine taxa), which are currently unable to be classified taxonomically with certainty, remain to be resolved in future studies

The Complexity of Repairing, Adjusting, and Aggregating of Extensions in Abstract Argumentation

We study the computational complexity of problems that arise in abstract argumentation in the context of dynamic argumentation, minimal change, and aggregation. In particular, we consider the following problems where always an argumentation framework F and a small positive integer k are given. - The Repair problem asks whether a given set of arguments can be modified into an extension by at most k elementary changes (i.e., the extension is of distance k from the given set). - The Adjust problem asks whether a given extension can be modified by at most k elementary changes into an extension that contains a specified argument. - The Center problem asks whether, given two extensions of distance k, whether there is a "center" extension that is a distance at most (k-1) from both given extensions. We study these problems in the framework of parameterized complexity, and take the distance k as the parameter. Our results covers several different semantics, including admissible, complete, preferred, semi-stable and stable semantics

Protective immune responses against Schistosoma mansoni infection by immunization with functionally active gut-derived cysteine peptidases alone and in combination with glyceraldehyde 3-phosphate dehydrogenase

© 2017 Tallima et al. Background: Schistosomiasis, a severe disease caused by parasites of the genus Schistosoma, is prevalent in 74 countries, affecting more than 250 million people, particularly children. We have previously shown that the Schistosoma mansoni gut-derived cysteine peptidase, cathepsin B1 (SmCB1), administered without adjuvant, elicits protection (>60%) against challenge infection of S. mansoni or S. haematobium in outbred, CD-1 mice. Here we compare the immunogenicity and protective potential of another gut-derived cysteine peptidase, S. mansoni cathepsin L3 (SmCL3), alone, and in combination with SmCB1. We also examined whether protective responses could be boosted by including a third non-peptidase schistosome secreted molecule, glyceraldehyde 3-phosphate dehydrogenase (SG3PDH), with the two peptidases. Methodology/Principal findings: While adjuvant-free SmCB1 and SmCL3 induced type 2 polarized responses in CD-1 outbred mice those elicited by SmCL3 were far weaker than those induced by SmCB1. Nevertheless, both cysteine peptidases evoked highly significant (P < 0.005) reduction in challenge worm burden (54–65%) as well as worm egg counts and viability. A combination of SmCL3 and SmCB1 did not induce significantly stronger immune responses or higher protection than that achieved using each peptidase alone. However, when the two peptidases were combined with SG3PDH the levels of protection against challenge S. mansoni infection reached 70–76% and were accompanied by highly significant (P < 0.005) decreases in worm egg counts and viability. Similarly, high levels of protection were achieved in hamsters immunized with the cysteine peptidase/SG3PDH-based vaccine. Conclusions/Significance: Gut-derived cysteine peptidases are highly protective against schistosome challenge infection when administered subcutaneously without adjuvant to outbred CD-1 mice and hamsters, and can also act to enhance the efficacy of other schistosome antigens, such as SG3PDH. This cysteine peptidase-based vaccine should now be advanced to experiments in non-human primates and, if shown promise, progressed to Phase 1 safety trials in humans

Fluorescence (TALIF) measurement of atomic hydrogen concentration in a coplanar surface dielectric barrier discharge

Spatially and temporally resolved measurements of atomic hydrogen concentration above the dielectric of coplanar barrier discharge are presented for atmospheric pressure in 2.2% H2/Ar. The measurements were carried out in the afterglow phase by means of two-photon absorption laser-induced fluorescence (TALIF). The difficulties of employing the TALIF technique in close proximity to the dielectric surface wall were successfully addressed by taking measurements on a suitable convexly curved dielectric barrier, and by proper mathematical treatment of parasitic signals from laser–surface interactions. It was found that the maximum atomic hydrogen concentration is situated closest to the dielectric wall from which it gradually decays. The maximum absolute concentration was more than 10^22 m-3. In the afterglow phase, the concentration of atomic hydrogen above the dielectric surface stays constant for a considerable time (10 us - 1 ms), with longer times for areas situated farther from the dielectric surface. The existence of such a temporal plateau was explained by the presented 1D model: the recombination losses of atomic hydrogen farther from the dielectric surface are compensated by the diffusion of atomic hydrogen from regions close to the dielectric surface. The fact that a temporal plateau exists even closest to the dielectric surface suggests that the dielectric surface acts as a source of atomic hydrogen in the afterglow phase

The complexity landscape of decompositional parameters for ILP : programs with few global variables and constraints

Integer Linear Programming (ILP) has a broad range of applications in various areas of artificial intelligence. Yet in spite of recent advances, we still lack a thorough understanding of which structural restrictions make ILP tractable. Here we study ILP instances consisting of a small number of “global” variables and/or constraints such that the remaining part of the instance consists of small and otherwise independent components; this is captured in terms of a structural measure we call fracture backdoors which generalizes, for instance, the well-studied class of N-fold ILP instances. Our main contributions can be divided into three parts. First, we formally develop fracture backdoors and obtain exact and approximation algorithms for computing these. Second, we exploit these backdoors to develop several new parameterized algorithms for ILP; the performance of these algorithms will naturally scale based on the number of global variables or constraints in the instance. Finally, we complement the developed algorithms with matching lower bounds. Altogether, our results paint a near-complete complexity landscape of ILP with respect to fracture backdoors

Lattice models and Landau theory for type II incommensurate crystals

Ground state properties and phonon dispersion curves of a classical linear chain model describing a crystal with an incommensurate phase are studied. This model is the DIFFOUR (discrete frustrated phi4) model with an extra fourth-order term added to it. The incommensurability in these models may arise if there is frustration between nearest-neighbor and next-nearest-neighbor interactions. We discuss the effect of the additional term on the phonon branches and phase diagram of the DIFFOUR model. We find some features not present in the DIFFOUR model such as the renormalization of the nearest-neighbor coupling. Furthermore the ratio between the slopes of the soft phonon mode in the ferroelectric and paraelectric phase can take on values different from -2. Temperature dependences of the parameters in the model are different above and below the paraelectric transition, in contrast with the assumptions made in Landau theory. In the continuum limit this model reduces to the Landau free energy expansion for type II incommensurate crystals and it can be seen as the lowest-order generalization of the simplest Lifshitz-point model. Part of the numerical calculations have been done by an adaption of the Effective Potential Method, orginally used for models with nearest-neighbor interaction, to models with also next-nearest-neighbor interactions.Comment: 33 pages, 7 figures, RevTex, submitted to Phys. Rev.