Recognizable Graph Languages for Checking Invariants

We generalize the order-theoretic variant of the Myhill-Nerode theorem to graph languages, and characterize the recognizable graph languages as the class of languages for which the Myhill-Nerode quasi order is a well quasi order. In the second part of the paper we restrict our attention to graphs of bounded interface size, and use Myhill-Nerode quasi orders to verify that, for such bounded graphs, a recognizable graph property is an invariant of a graph transformation system. A recognizable graph property is a recognizable graph language, given as an automaton functor. Finally, we present an algorithm to approximate the Myhill-Nerode ordering

Concatenation and other Closure Properties of Recognizable Languages in Adhesive Categories

We consider recognizable languages of cospans in adhesive categories, ofwhich recognizable graph languages are a special case. We show that such languages are closed under concatenation, i.e. under cospan composition, by providing a con-crete construction that creates a concatenation automaton from two given automata.The construction is considerably more complex than the corresponding construction for finite automata. We conclude by showing negative closure properties for Kleene star and substitution

Towards Alternating Automata for Graph Languages

In this paper we introduce alternating automata for languages of arrows of an arbitrary category, and as an instantiation thereof alternating automata for graph languages. We study some of their closure properties and compare them, with respect to expressiveness, to other methods for describing graph languages. We show, by providing several examples, that many graph properties (of graphs of bounded path width) can be naturally expressed as alternating automata

Treewidth, Pathwidth and Cospan Decompositions

We will revisit the categorical notion of cospan decompositions of graphs and compare it to the well-known notions of path decomposition and tree decomposition from graph theory. More specifically, we will define several types of cospan decompositions with appropriate width measures and show that these width measures coincide with pathwidth and treewidth. Such graph decompositions of small width are used to efficiently decide graph properties, for instance via graph automata

Vessel-specific reintroduction of CINNAMOYL-COA REDUCTASE1 (CCR1) in dwarfed ccr1 mutants restores vessel and xylary fiber integrity and increases biomass

Lignocellulosic biomass is recalcitrant toward deconstruction into simple sugars due to the presence of lignin. To render lignocellulosic biomass a suitable feedstock for the bio-based economy, plants can be engineered to have decreased amounts of lignin. However, engineered plants with the lowest amounts of lignin exhibit collapsed vessels and yield penalties. Previous efforts were not able to fully overcome this phenotype without settling in sugar yield upon saccharification. Here, we reintroduced CINNAMOYL-COENZYME A REDUCTASE1 (CCR1) expression specifically in the protoxylem and metaxylem vessel cells of Arabidopsis (Arabidopsis thaliana) ccr1 mutants. The resulting ccr1 ProSNBE: CCR1 lines had overcome the vascular collapse and had a total stem biomass yield that was increased up to 59% as compared with the wild type. Raman analysis showed that monolignols synthesized in the vessels also contribute to the lignification of neighboring xylary fibers. The cell wall composition and metabolome of ccr1 ProSNBE: CCR1 still exhibited many similarities to those of ccr1 mutants, regardless of their yield increase. In contrast to a recent report, the yield penalty of ccr1 mutants was not caused by ferulic acid accumulation but was (largely) the consequence of collapsed vessels. Finally, ccr1 ProSNBE: CCR1 plants had a 4-fold increase in total sugar yield when compared with wild-type plants

Neutrophil extracellular trap formation is elicited in response to cold physical plasma

Cold physical plasma is an ionized gas with a multitude of components, including hydrogen peroxide and other reactive oxygen and nitrogen species. Recent studies suggest that exposure of wounds to cold plasma may accelerate healing. Upon wounding, neutrophils are the first line of defense against invading microorganisms but have also been identified to play a role in delayed healing. In this study, we examined how plasma treatment affects the functions of peripheral blood neutrophils. Plasma treatment induced oxidative stress, as assessed by the oxidation of intracellular fluorescent redox probes; reduced metabolic activity; but did not induce early apoptosis. Neutrophil oxidative burst was only modestly affected after plasma treatment, and the killing of Pseudomonas aeruginosa and Staphylococcus aureus was not significantly affected. Intriguingly, we found that plasma induced profound extracellular trap formation. This was inhibited by the presence of catalase during plasma treatment but was not replicated by adding an equivalent concentration of hydrogen peroxide. Plasma-induced neutrophil extracellular trap formation was not dependent on the activity of myeloperoxidase or NADPH oxidase 2 but seemed to involve short-lived molecules. The amount of DNA release and the time course after plasma treatment were similar to that with the common neutrophil extracellular trap inducer PMA. After neutrophil extracellular traps had formed, concentrations of IL-8 were also significantly increased in supernatants of plasma-treated neutrophils. Both neutrophil extracellular traps and IL-8 release may aid antimicrobial activity and spur inflammation at the wound site. Whether this aids or exacerbates wound healing needs to be tested

Longitudinal increase in the detection rate of Mycobacterium chimaera in heater-cooler device-derived water samples

Colonization with Mycobacterium chimaera and other nontuberculous mycobacteria (NTM) has been reported for heater-cooler devices (HCD) produced by several manufacturers. Up to now, exclusively LivaNova (London, UK) HCDs have been associated with M. chimaera infections after cardiac surgery. The vast majority of studies on HCD colonization were cross-sectional. We were interested in longitudinal dynamics of mycobacterial growth in HCD water samples and analyzed data of a prospective mycobacterial surveillance of five LivaNova 3T HCDs. Nontuberculous mycobacteria were isolated in 319 (48.0%, 21 water samples grew more than one mycobacterial species) of a total of 665 water samples. The most frequently detected species were M. chimaera (N= 247/319, 77.4%), Mycobacterium gordonae (46/319, 14.4%) and Mycobacterium paragordonae (34/319, 10.7%). Detection rates increased longitudinally for any NTM (odds ratio (OR) per year in use: 1.60, 95% CI 1.17-2.24, P<0.001) and for M. chimaera (OR per year in use: 1.67, 95% CI 1.11-2.57, P<0.01)