Non-canonical Helitrons in <em>Fusarium oxysporum</em>

BACKGROUND: Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occur widely in plants and animals, and have thus far been relatively little investigated in fungi. RESULTS: Here, we comprehensively survey Helitrons in several completely sequenced genomes representing the F. oxysporum species complex (FOSC). We thoroughly characterize 5 different Helitron subgroups and determine their impact on genome evolution and assembly in this species complex. FOSC Helitrons resemble members of the Helitron2 variant that includes Helentrons and DINEs. The fact that some Helitrons appeared to be still active in FOSC provided the opportunity to determine whether Helitrons occur as a circular intermediate in FOSC. We present experimental evidence suggesting that at least one Helitron subgroup occurs with joined ends, suggesting a circular intermediate. We extend our analyses to other Pezizomycotina and find that most fungal Helitrons we identified group phylogenetically with Helitron2 and probably have similar characteristics. CONCLUSIONS: FOSC genomes harbour non-canonical Helitrons that are characterized by asymmetric terminal inverted repeats, show hallmarks of recent activity and likely transpose via a circular intermediate. Bioinformatic analyses indicate that they are representative of a large reservoir of fungal Helitrons that thus far has not been characterized

Challenging Distributional Models with a Conceptual Network of Philosophical Terms

Computational linguistic research on language change through distributional semantic (DS) models has inspired researchers from fields such as philosophy and literary studies, who use these methods for the exploration and comparison of comparatively small datasets traditionally analyzed by close reading. Research on methods for small data is still in early stages and it is not clear which methods achieve the best results. We investigate the possibilities and limitations of using distributional semantic models for analyzing philosophical data by means of a realistic use-case. We provide a ground truth for evaluation created by philosophy experts and a blueprint for using DS models in a sound methodological setup. We compare three methods for creating specialized models from small datasets. Though the models do not perform well enough to directly support philosophers yet, we find that models designed for small data yield promising directions for future work

The introduction of Corded Ware Culture at a local level: an exploratory study of cultural change during the Late Neolithic of the Dutch West Coast through ceramic technology

The introduction of the Corded Ware Culture (3000–2500 BCE) is considered a formative event in Europe's past. Ancient DNA analyses demonstrate that migrations played a crucial role in this event. However, these analyses approach the issue at a supra-regional scale, leaving questions about the regional and local impact of this event unresolved. This study pilots an approach to ceramics that brings this small-scale impact into focus by using the transmission of ceramic technology as a proxy for social change. It draws on ethno-archaeological studies of the effects of social changes on the transmission of ceramic production techniques to hypothesise the impact of three idealised scenarios that archaeologists have proposed for the introduction of Corded Ware Culture: migration, diffusion, and network interactions. Subsequently, it verifies these hypotheses by integrating geochemical (WDXRF), mineralogical (petrography), and macromorphological analysis of ceramics with network analysis. This method is applied to 30 Late Neolithic ceramic vessels from three sites in the western coastal area of the Netherlands (Hazerswoude-Rijndijk N11, Zandwerven, and Voorschoten-De Donk). This study concludes that the introduction of Corded Ware material culture is a process that varies from site to site in the western coastal area of the Netherlands. Moreover, the introduction of the Corded Ware Culture is characterised by continuity in technological traditions throughout the study area, indicating a degree of social continuity despite typological changes in ceramics

Effector profiles distinguish <em>formae speciales</em> of <em>Fusarium oxysporum</em>

Formae speciales (ff.spp.) of the fungus Fusarium oxysporum are often polyphyletic within the species complex, making it impossible to identify them on the basis of conserved genes. However, sequences that determine host-specific pathogenicity may be expected to be similar between strains within the same forma specialis. Whole genome sequencing was performed on strains from five different ff.spp. (cucumerinum, niveum, melonis, radicis-cucumerinum and lycopersici). In each genome, genes for putative effectors were identified based on small size, secretion signal, and vicinity to a "miniature impala" transposable element. The candidate effector genes of all genomes were collected and the presence/absence patterns in each individual genome were clustered. Members of the same forma specialis turned out to group together, with cucurbit-infecting strains forming a supercluster separate from other ff.spp. Moreover, strains from different clonal lineages within the same forma specialis harbour identical effector gene sequences, supporting horizontal transfer of genetic material. These data offer new insight into the genetic basis of host specificity in the F. oxysporum species complex and show that (putative) effectors can be used to predict host specificity in F. oxysporum

The effect of nasal steroid aqueous spray on nasal complaint scores and cellular infiltrates in the nasal mucosa of patients with nonallergic, noninfectious perennial rhinitis

Topical corticosteroids are the therapy of choice for nonallergic, noninfectious perennial rhinitis (NANIPER). However, the efficacy of steroid therapy in NANIPER is controversial, as is its mode of action. To our surprise, of 300 patients initially diagnosed as having NANIPER, only 65 reached threshold nasal symptom scores. Patients were randomized into four different treatment regimens: placebo administered twice daily (BD) for 8 weeks, fluticasone propionate aqueous nasal spray (FPANS) (200 microg) once daily (OD) and placebo OD for 8 weeks, FPANS (200 microg) OD and placebo OD for 4 weeks followed by FPANS (200 microg) BD for 4 weeks, and FPANS (200 microg) BD for 8 weeks. A small decrease in nasal symptoms was found, which only reached significance for sneezing in the FPANS 200 microg BD group. A significant dose-dependent decrease in immunocompetent cells was found in nasal biopsy specimens obtained before, after 4 weeks, and after 8 weeks of treatment. We conclude that FPANS did not significantly reduce nasal symptoms in this group of selected NANIPER patients, even though a significant effect on cells in the nasal mucosa was see