Revisiting bisimilarity and its modal logic for nondeterministic and probabilistic processes

The logic PML is a probabilistic version of Hennessy–Milner logic introduced by Larsen and Skou to characterize bisimilarity over probabilistic processes without internal nondeterminism. In this paper, two alternative interpretations of PML over nondeterministic and probabilistic processes as models are considered, and two new bisimulation-based equivalences that are in full agreement with those interpretations are provided. The new equivalences include as coarsest congruences the two bisimilarities for nondeterministic and probabilistic processes proposed by Segala and Lynch. The latter equivalences are instead known to agree with two versions of Hennessy–Milner logic extended with an additional probabilistic operator interpreted over state distributions in place of individual states. The new interpretations of PML and the corresponding new bisimilarities are thus the first ones to offer a uniform framework for reasoning on processes that are purely nondeterministic or reactive probabilistic or that mix nondeterminism and probability in an alternating/nonalternating way

Ecological Diversification of Vibrio fischeri Serially Passaged for 500 Generations in Novel Squid Host Euprymna tasmanica

Vibrio fischeri isolated from Euprymna scolopes (Cephalopoda: Sepiolidae) was used to create 24 lines that were serially passaged through the non-native host Euprymna tasmanica for 500 generations. These derived lines were characterized for biofilm formation, swarming motility, carbon source utilization, and in vitro bioluminescence. Phenotypic assays were compared between "ES" (E. scolopes) and "ET" (E. tasmanica) V. fischeri wild isolates to determine if convergent evolution was apparent between E. tasmanica evolved lines and ET V. fischeri. Ecological diversification was observed in utilization of most carbon sources examined. Convergent evolution was evident in motility, biofilm formation, and select carbon sources displaying hyperpolymorphic usage in V. fischeri. Convergence in bioluminescence (a 2.5-fold increase in brightness) was collectively evident in the derived lines relative to the ancestor. However, dramatic changes in other properties--time points and cell densities of first light emission and maximal light output and emergence of a lag phase in growth curves of derived lines--suggest that increased light intensity per se was not the only important factor. Convergent evolution implies that gnotobiotic squid light organs subject colonizing V. fischeri to similar selection pressures. Adaptation to novel hosts appears to involve flexible microbial metabolism, establishment of biofilm and swarmer V. fischeri ecotypes, and complex changes in bioluminescence. Our data demonstrate that numerous alternate fitness optima or peaks are available to V. fischeri in host adaptive landscapes, where novel host squids serve as habitat islands. Thus, V. fischeri founder flushes occur during the initiation of light organ colonization that ultimately trigger founder effect diversification.

IncP-1 and PromA Group Plasmids Are Major Providers of Horizontal Gene Transfer Capacities Across Bacteria in the Mycosphere of Different Soil Fungi

Plasmids of the IncP-1β group have been found to be important carriers of accessory genes that enhance the ecological fitness of bacteria, whereas plasmids of the PromA group are key agents of horizontal gene transfer in particular soil settings. However, there is still a paucity of knowledge with respect to the diversity, abundance, and involvement in horizontal gene transfer of plasmids of both groups in the mycosphere. Using triparental exogenous isolation based on the IncQ tracer plasmid pSUP104 as well as direct molecular detection, we analyzed the pool of mobilizer and self-transferable plasmids in mycosphere soil. Replicate mushroom types that were related to Russula, Inocybe, Ampulloclitocybe, and Galerina spp. were sampled from a forest soil area, and bulk soil was used as the control. The data showed that the levels of IncP-1β plasmids are significantly raised across several of the mycospheres analyzed, whereas those of PromA group plasmids were similar across the mycospheres and corresponding bulk soil. Moreover, the frequencies of triparental exogenous isolation of mobilizer plasmids into a Pseudomonas fluorescens recipient strain were significantly elevated in communities from several mycospheres as compared with those from bulk soil. Molecular analysis of selected transconjugants, as well as from directly isolated strains, revealed the presence of plasmids of three size groups, i.e., (1) 40-45, (2) 50-60, and (3) ≥60 kb, across all isolations. Replicon typing using IncN, IncW and IncA/C proxies revealed no positive signals. In contrast, a suite of plasmids produced signals with IncP-1β as well as PromA type replicon typing systems. Moreover, a selected subset of plasmids, obtained from the Inocybe and Galerina isolates, was transferred out further, revealing their capacities to transfer and mobilize across a broad host range.

IncP-1β Plasmids Are Important Carriers of Fitness Traits for Variovorax Species in the Mycosphere—Two Novel Plasmids, pHB44 and pBS64, with Differential Effects Unveiled

The Laccaria proxima mycosphere strongly selects Variovorax paradoxus cells. Fifteen independent V. paradoxus strains, isolated from mycospheres sampled at two occasions, were investigated with respect to the occurrence of plasmids of sizes <60-100 kb. Two V. paradoxus strains, HB44 and BS64, were found to contain such plasmids, which were coined pHB44 and pBS64. Replicon typing using a suite of plasmid-specific PCR systems indicated that both plasmids belong to the IncP-1β group. Also, both were able to mobilize selectable IncQ group plasmids into Escherichia coli as well as Pseudomonas fluorescens. Moreover, they showed stable replication in these organisms, confirming their broad host range. Strain BS64 was cured of pBS64 and plasmid pHB44 was subsequently moved into this cured strain by making use of the IncQ group tracer plasmid pSUP104, which was then removed at elevated temperature. Thus, both plasmids could be screened for their ability to confer a phenotype upon strain BS64. No evidence for the presence of genes for xenobiotic degradation and/or antibiotic or heavy metal resistances was found for either of the two plasmids. Remarkably, both could stimulate the production of biofilm material by strain BS64. Also, the population densities of pBS64-containing strain BS64 were temporarily raised in liquid as well as soil systems (versus the plasmid-cured strain), both in the presence of the fungal host Lyophyllum sp. strain Karsten. Strikingly, plasmid pHB44 significantly enhanced the fitness of strain BS64 in soil containing Lyophyllum sp. strain Karsten, but decreased its fitness in soil supplemented with extra FeCl3. The effect was noted both in separate (no inter-strain competition) and joint (competition) inoculations.

The impact of 5-formyltetrahydrofolate on the anti-tumor activity of pralatrexate, as compared to methotrexate, in HeLa cells in vitro

To investigate the impact of 5-formyltetrahydrofolate on the activities of pralatrexate, as compared to methotrexate (MTX), in vitro.

Testicular microlithiasis imaging and follow-up: guidelines of the ESUR scrotal imaging subcommittee

The subcommittee on scrotal imaging, appointed by the board of the European Society of Urogenital Radiology (ESUR), have produced guidelines on imaging and follow-up in testicular microlithiasis (TML).

Erratum to: Clinical and pathological outcomes of renal cell carcinoma (RCC) in native kidneys of patients with end-stage renal disease: a long-term comparative retrospective study with RCC diagnosed in the general population

Development and external validation of nomograms predicting disease-free and cancer-specific survival after radical cystectomy

To develop two nomograms predicting disease-free survival (DFS) and cancer-specific survival (CSS) and to externally validate them in multiple series.

Do we value mobility?

Is there a trade-off between people’s preference for income equality and income mobility? Testing for the existence of such a trade-off is difficult because mobility is a multifaceted concept. We analyse results from a questionnaire experiment based on simple precise concepts of income inequality and income mobility. We find no direct trade-off in preference between mobility and equality, but an indirect trade-off, applying when more income mobility can only be obtained at the expense of some income inequality. Mobility preference—but not equality preference—appears to be driven by personal experience of mobility

Erratum to: Design of pharmaceutical products to meet future patient needs requires modification of current development paradigms and business models