The Computational Complexity of Symbolic Dynamics at the Onset of Chaos

In a variety of studies of dynamical systems, the edge of order and chaos has been singled out as a region of complexity. It was suggested by Wolfram, on the basis of qualitative behaviour of cellular automata, that the computational basis for modelling this region is the Universal Turing Machine. In this paper, following a suggestion of Crutchfield, we try to show that the Turing machine model may often be too powerful as a computational model to describe the boundary of order and chaos. In particular we study the region of the first accumulation of period doubling in unimodal and bimodal maps of the interval, from the point of view of language theory. We show that in relation to the ``extended'' Chomsky hierarchy, the relevant computational model in the unimodal case is the nested stack automaton or the related indexed languages, while the bimodal case is modeled by the linear bounded automaton or the related context-sensitive languages.Comment: 1 reference corrected, 1 reference added, minor changes in body of manuscrip

DNA metabarcoding of trawling bycatch reveals diversity and distribution patterns of sharks and rays in the central Tyrrhenian Sea

Conservation and management of chondrichthyans are becoming increasingly important, as many species are particularly vulnerable to fishing activities, primarily as bycatch, which leads to incomplete catch reporting, potentially hiding the impact on these organisms. Here, we aimed at implementing an eDNA metabarcoding approach to reconstruct shark and ray bycatch composition from 24 hauls of a bottom trawl fishing vessel in the central Mediterranean. eDNA samples were collected through the passive filtration of seawater by simple gauze rolls encapsulated in a probe (the "metaprobe"), which already showed great efficiency in detecting marine species from trace DNA in the environment. To improve molecular taxonomic detection, we enhanced the 12S target marker reference library by generating sequences for 14 Mediterranean chondrichthyans previously unrepresented in public repositories. DNA metabarcoding data correctly identifies almost all bycaught species and detected five additional species not present in the net, highlighting the potential of this method to detect rare species. Chondrichthyan diversity showed significant association with some key environmental variables (depth and distance from the coast) and the fishing effort, which are known to influence demersal communities. As DNA metabarcoding progressively positions itself as a staple tool for biodiversity monitoring, we expect that its melding with opportunistic, fishery-dependent surveys could reveal additional distribution features of threatened and elusive megafauna

Self-repair ability of evolved self-assembling systems in cellular automata

Self-repairing systems are those that are able to reconfigure themselves following disruptions to bring them back into a defined normal state. In this paper we explore the self-repair ability of some cellular automata-like systems, which differ from classical cellular automata by the introduction of a local diffusion process inspired by chemical signalling processes in biological development. The update rules in these systems are evolved using genetic programming to self-assemble towards a target pattern. In particular, we demonstrate that once the update rules have been evolved for self-assembly, many of those update rules also provide a self-repair ability without any additional evolutionary process aimed specifically at self-repair

Molecular characterization of Mycobacterium abscessus subspecies isolated from patients attending an Italian Cystic Fibrosis Centre

Mycobacterium abscessus (MABS) infection represents significant management challenge in cystic fibrosis (CF) patients. This retrospective study (2005-2016) aims to determine the prevalence of the subspecies of MABS isolated from CF patients, to evaluate the persistence over the years of a single subspecies of MABS and to correlate mutations responsible for macrolides and amikacin resistance with MIC values. We investigated 314 strains (1 isolate/patient/year) isolated from the lower respiratory tract of 51 chronically infected CF patients. Sequencing of rpoB gene was performed to identify the MABS subspecies. The erm(41) gene was sequenced to differentiate the strains with and without inducible macrolide resistance. Regions of 23S and 16S rRNA were sequenced to investigate mutations responsible for constitutive resistance to macrolides and aminoglycosides, respectively. Antibiotic susceptibility, using commercial microdilution plates, was evaluated according to CLSI. M. abscessus subsp. abscessus accounted for 64% of the isolates, bolletii subspecies for 16% and massiliense subspecies for 20%. All the massiliense strains presented truncated erm(41) gene while 12 abscessus strains presented the mutation T28->C in the erm(41) gene, which makes it inactive. The 23S rRNA analysis did not show constitutive resistance to macrolides in any strain. Mutation of the 16S rRNA gene was highlighted in 2 strains out of 314, in agreement with high MIC values. The correct identification at the subspecies level and the molecular analysis of 23S rRNA, 16S rRNA and erm gene is useful to guide the treatment strategy in patients with M. abscessus lung infection

Combined COI barcode-based methods to avoid mislabelling of threatened species of deep-sea skates

Skates are characterised by conservative body morphology which hampers identification and leads to frequent taxonomic confusion and market mislabelling. Accurate specimen classification is crucial for reliable stock assessments and effective conservation plans, otherwise the risk of extinction could be unnoticed. The misclassification issue is evident for the genus Dipturus, distributed worldwide, from the continental shelf and slope to the deep sea. In this study, barcode cytochrome oxidase I gene (COI) sequences were used along with species delimitation and specimen assignment methods to improve taxonomy and zoogeography of species of conservation interest inhabiting the Atlantic Ocean and Mediterranean Sea. In this study, we provided new evidence of the occurence of D. nidarosiensis in the Central-Western Mediterranean Sea and the lack of Atlantic-Mediterranean genetic divergence. The Atlantic endangered species D. laevis and D. batis clustered together under the same molecular operational taxonomic unit (MOTU) with any delimitation methods used, while the assignment approach correctly discriminated specimens into the two species. These results provided evidence that the presence of the barcode gap is not an essential predictor of identification success, but the use of different approaches is crucially needed for specimen classification, especially when threshold- or tree-based methods result less powerful. The analyses also showed how different putative, vulnerable, species dwelling across South-Western Atlantic and South-Eastern Pacific are frequently misidentified in public sequence repositories. Our study emphasised the limits associated to public databases, highlighting the urgency to verify and implement the information deposited therein in order to guarantee accurate species identification and thus effective conservation measures for deep-sea skates

In Vitro Synergism of Colistin and N-acetylcysteine against Stenotrophomonas maltophilia

Stenotrophomonas maltophilia is an emerging global opportunistic pathogen, responsible for a wide range of human infections, including respiratory tract infections. Intrinsic multidrug resistance and propensity to form biofilms make S. maltophilia infections recalcitrant to treatment. Colistin is among the second-line options in case of difficult-to-treat S. maltophilia infections, with the advantage of being also administrable by nebulization. We investigated the potential synergism of colistin in combination with N-acetylcysteine (NAC) (a mucolytic agent with antioxidant and anti-inflammatory properties) against S. maltophilia grown in planktonic phase and biofilm. Eighteen S. maltophilia clinical isolates (comprising three isolates from cystic fibrosis (CF) and two trimethoprim-sulfamethoxazole (SXT)-resistant strains) were included. Checkerboard assays showed a synergism of colistin/NAC combinations against the strains with colistin Minimum Inhibitory Concentration (MIC) >2 \ub5g/mL (n = 13), suggesting that NAC could antagonize the mechanisms involved in colistin resistance. Nonetheless, time-kill assays revealed that NAC might potentiate colistin activity also in case of lower colistin MICs. A dose-dependent potentiation of colistin activity by NAC was also clearly observed against S. maltophilia biofilms, also at sub-MIC concentrations. Colistin/NAC combinations, at concentrations likely achievable by topical administration, might represent a valid option for the treatment of S. maltophilia respiratory infections and should be examined further

Molecular epidemiology of meticillin-resistant Staphylococcus aureus in Italian cystic fibrosis patients: A national overview

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Genetic structure of the long-snouted seahorse, Hippocampus guttulatus, in the Central-Western Mediterranean Sea

The seahorse Hippocampus guttulatus reaches its highest abundance in confined environments, where it has unique biological and ecological traits that suggest significant genetic differentiation among populations. In the present study, we aimed to reveal the genetic structure of this species by analysing eight microsatellite loci and a mitochondrial DNA region (cytochrome b) of eight populations from the Central-Western Mediterranean Sea, including lagoon sites. Levels of genetic diversity, as measured by the total number of alleles, number of private alleles, allelic richness and heterozygosity, ranged from low to moderate. The overall value of inbreeding was high, indicating a deficiency in heterozygotes. The haplotype network had a star-like construction, with the most common haplotype present in all populations. Data from the two molecular markers congruently displayed a similar pattern and revealed low genetic differentiation, notwithstanding predictions based on species traits. The observed genetic structure is probably the result of both historical population demographic events and current gene flow. The investigated lagoons, however, revealed a unique genetic profile, which is especially highlighted by the Taranto population. At this site, the results also showed altered values of observed/expected heterozygosity and allelic richness, a characteristic of marginal populations. Our study suggests that lagoon populations should be managed as distinct genetic units

Правда коммунизма. 1982. № 121

This paper concerns the semantic difference between strong and weak neces-sity modals. First we identify a number of explananda: their well-known in-tuitive difference in strength between ‘must’ and ‘ought’ as well as differ-ences in connections to probabilistic considerations and acts of requiring and recommending. Here we argue that important extant analyses of the se-mantic differences, though tailored to account for some of these aspects, fail to account for all. We proceed to suggest that the difference between ’ought’ and ’must’ lies in how they relate to scalar and binary standards. Briefly put, must(φ) says that among the relevant alternatives, φ is selected by the relevant binary standard, whereas ought(φ) says that among the relevant al-ternatives, φ is selected by the relevant scale. Given independently plausi-ble assumptions about how standards are provided by context, this ex-plains the relevant differences discussed