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64 results for “Causation”

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zenodo48/100

Coding table for chapter 30 'Valency change and causation' in Bowern (ed. 2023)

This is the coding table used for chapter 30 'Valency change and causation' (pp. 344-359) in the Oxford Guide on Australian Languages (Bowern, ed. 2023).

opencc-by-4.0Dec 2023View details →

zenodo48/100

Supplemented material to "Mycobacteriosis in various pet and wild birds from Germany: pathological findings, coinfections, and characterisation of causative Mycobacteria."

This is the supplemented material to the publication "Mycobacteriosis in Various Pet and Wild Birds from Germany: Pathological Findings, Coinfections, and Characterization of Causative Mycobacteria". The causative agents and confounding factors of mycobacteriosis in a set of pet (n=45) and some wild birds (n=5) from Germany were examined in this study. Not only Mycobacterium genavense (Mg), but also M. avium subsp. avium (Maa) and M. avium subsp. hominissuis (Mah), contributed to mycobacteriosis in these birds. The isolates were characterized by a combination of different typing methods. The genetic diversity of isolates belonging to Mg, Maa and Mah differed. Various coinfections by viruses, endoparasites, fungi and other bacterial species did not affect the manifestation of mycobacteriosis. Cross pathological fidings were more often seen in mycobacteriosis caused by Ma compared to Mg suggesting a different pathogenicity of the two species. New genotypes of Mah were identified in these birds that is important for epidemiological studies and for understanding the zoonotic role of this pathogen, as the subsp. hominissuis represents an increasing public health concern. The study provides some evidence of correlation between individual Maa genotypes and virulence which will have to be confirmed by broader studies.

opencc-by-4.0Jul 2022View details →

zenodo40/100

Thematic Layers of Causative Factors of Landslide in Palungtar Municipality, Gorkha, Nepal

Eleven causative parameters responsible for instability in the area: Slope, Aspect, Land Use Land Cover, Plan Curvature, Profile Curvature, Distance from River, Distance from Road, Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI), Topographic Wetness Index (TWI), and Geology.

opencc-by-4.0Sep 2024View details →

zenodo36/100

Data required for "Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences"

In the early 1900s,mutation breeding to select varieties with desirable traits using  spontaneous mutation was actively conducted around the world, including Japan. In rice, the number of fixed mutations per generation was estimated to be 1.38-2.25. Although this low mutation rate was a major problem for breeding in those days, in the modern era with the development of NGS technology, it was conversely considered to be an advantage for efficient gene identification. In this paper, we proposed an in silico approach using next-generation sequencing (NGS) to compare the whole genome sequence of a spontaneous mutant with that of a closely related strain with a nearly identical genome, to find polymorphisms that differ between them, and to identify the causal gene by predicting the functional variation of the gene caused by the polymorphism. Using this approach, we found four causal genes for the dwarf mutation, the round shape grain mutation and the awnless mutation. Three of these genes were the same as those previously reported, but one was a novel gene involved in awn formation. The novel gene was isolated from Bozu-Aikoku, a mutant of Aikoku with the awnless trait, in which nine polymorphisms were predicted to alter gene function by their whole-genome comparison. Based on the information on gene function and tissue-specific expression patterns of these candidate genes, Os03g0115700/LOC_Os03g02460, annotated as a shortchain dehydrogenase/reductase SDR family protein, is most likely to be involved in the awnless mutation. Indeed, complementation tests by transformation showed that it is involved in awn formation. Thus, this method is an effective way to accelerate genome breeding of various crop species by enabling the identification of useful genes that can be used for crop breeding with minimal effort for NGS analysis.

opencc-by-4.0Mar 2024View details →

dryad36/100

Population genetics as a tool to elucidate pathogen reservoirs: Lessons from Pseudogymnoascus destructans, the causative agent of White-Nose disease in bats

Emerging infectious diseases pose a major threat to human, animal, and plant health. The risk of species-extinctions increases when pathogens can survive in the absence of the host. Environmental reservoirs can facilitate this. However, identifying such reservoirs and modes of infection is often highly challenging. In this study, we investigated the presence and nature of an environmental reservoir for the ascomycete fungus Pseudogymnoascus destructans, the causative agent of White-Nose disease. Using 18 microsatellite markers, we determined the genotypic differentiation between 1,497 P. destructans isolates collected from nine closely situated underground sites where bats hibernate (i.e., hibernacula) in Northeastern Germany. This approach was unique in that it ensured that every isolate and resulting multi-locus genotype was not only present, but also viable and therefore theoretically capable of infecting a bat. The distinct distribution of multi-locus genotypes across hibernacula demonstrates that each hibernaculum has an essentially unique fungal population. This would be expected if bats become infected in their hibernaculum (i.e., the site they spend winter in to hibernate) rather than in other sites visited before they start hibernating. In one hibernaculum where both the walls and the hibernating bats were sampled at regular intervals over five consecutive winter seasons (1,062 isolates), higher genotypic richness was found on walls compared to bats and multi-locus genotypes showed a stable frequency over multiple winters. This clearly implicates hibernacula walls as the main environmental reservoir of the pathogen, from which bats become re-infected annually during hibernation.

opencc-zeroNov 2021View details →

dryad36/100

Causation without correlation: Parasite-mediated frequency-dependent selection and infection prevalence

Parasite-mediated selection is thought to maintain host genetic diversity for resistance. We might thus expect to find a strong positive correlation between host genetic diversity and infection prevalence across natural populations. Here, we used computer simulations to examine host–parasite coevolution in 20 simi-isolated clonal populations across a broad range of values for both parasite virulence and parasite fecundity. We found that the correlation between host genetic diversity and infection prevalence can be significantly positive for intermediate values of parasite virulence and fecundity. But the correlation can also be weak and statistically non-significant, even when parasite-mediated frequency-dependent selection is the sole force maintaining host diversity. Hence correlational analyses of field populations, while useful, might underestimate the role of parasites in maintaining host diversity.

opencc-zeroDec 2021View details →

zenodo36/100

Transposable prophages in leptospira : an ancient, now diverse, group predominant in causative agents of Weil's disease

The virome associated to the corkscrew shaped bacterium leptospira, responsible for the Weil disease, is scarcely known and genetic tools available for these bacteria remain limited. To reduce these two issues, potential transposable prophages were searched in Leptospiraceae genomes. The 236 predicted transposable prophages are particularly abundant in the most pathogenic leptospiral clade, being potentially involved in the acquisition of virulent traits. According to genomic similarities and phylogenies, these prophages are distantly related to known transposable phages and are organized into six groups, one of them encompassing prophages with unusual TA-TA ends. Interestingly, structural and transposition proteins reconstruct different relationships between groups, suggesting ancestral recombinations. Based on the baseplate phylogeny, two large clades emerge, with specific gene-contents and high sequence divergence reflecting their ancient origin. Despite their high divergence, the size and overall genomic organization of all prophages are very conserved, a testimony of the highly constrained nature of their genomes. Finally, similarities between these prophages and the three known non-transposable phages infecting L. biflexa, suggest gene transfer between different Caudovirales inside their leptospiral host, and the possibility to use some of the transposable prophages in that model strain.

opencc-byOct 2021View details →

zenodo36/100

Supplementary materials of "Causatives in Classical Armenian"

Supplementary materials of: Petr A. Kocharov. 2023. Causatives in Classical Armenian. Folia Linguistica. The dataset contains a list of verbs for which the analytic causative construction tam 'give' plus infinitive is attested in the Armenian Bible (based on the electronic concordance available at https://bible.armeniancathedral.org/), "De Deo" by Eznik Kołbacʽi and "The History of the Armenians" by Agathangełos (based on the electronic concordance available at the Leiden Armenian Lexical Database: http://www.sd-editions.com/LALT/). The base verbs are specified with respect to the typical semantic role of the first argument, syntactic transitivity, text frequency and attestations, correspondance with the dídōmi-construction in the Greek original of the biblical contexts, and the text frequency of competing synthetic causatives when available in the biblical corpus.

opencc-by-4.0Mar 2023View details →

dryad36/100

Forecasting species distributions: Correlation does not equal causation

Aim: Identifying the mechanisms influencing species' distributions is critical for accurate climate change forecasts. However, current approaches are limited by correlative models that cannot distinguish between direct and indirect effects. Location: New Hampshire and Vermont, USA. Methods: Using causal and correlational models and new theory on range limits, we compared current (2014–2019) and future (2080s) distributions of ecologically important mammalian carnivores and competitors along range limits in the northeastern US under two global climate models (GCMs) and a high-emissions scenario (RCP8.5) of projected snow and forest biomass change. Results: Our hypothesis that causal models of climate-mediated competition would result in different distribution predictions than correlational models, both in the current and future periods, was well-supported by our results; however, these patterns were prominent only for species pairs that exhibited strong interactions. The causal model predicted the current distribution of Canada lynx (Lynx canadensis) more accurately, likely because it incorporated the influence of competitive interactions mediated by snow with the closely related bobcat (Lynx rufus). Both modeling frameworks predicted an overall decline in lynx occurrence in the central high elevation regions and increased occurrence in the northeastern region in the 2080s due to changes in land use that provided optimal habitat. However, these losses and gains were less substantial in the causal model due to the inclusion of an indirect buffering effect of snow on lynx. Main conclusions: Our comparative analysis indicates that a causal framework, steeped in ecological theory, can be used to generate spatially-explicit predictions of species distributions. This approach can be used to disentangle correlated predictors that have previously hampered understanding of range limits and species' response to climate change.

opencc-zeroJul 2023View details →

dryad36/100