• MeSH
• statistika jako téma MeSH

• Konspekt
• Statistika
• NLK Obory
• statistika, zdravotnická statistika

• MeSH
• kauzalita MeSH
• pravděpodobnost MeSH

• Konspekt
• Přírodní vědy. Matematické vědy
• NLK Obory
• přírodní vědy
• statistika, zdravotnická statistika

Permutation methods are commonly used to test the significance of regressors of interest in general linear models (GLMs) for functional (image) data sets, in particular for neuroimaging applications as they rely on mild assumptions. Permutation inference for GLMs typically consists of three parts: choosing a relevant test statistic, computing pointwise permutation tests, and applying a multiple testing correction. We propose new multiple testing methods as an alternative to the commonly used maximum value of test statistics across the image. The new methods improve power and robustness against inhomogeneity of the test statistic across its domain. The methods rely on sorting the permuted functional test statistics based on pointwise rank measures; still, they can be implemented even for large data. The performance of the methods is demonstrated through a designed simulation experiment and an example of brain imaging data. We developed the R package GET, which can be used for the computation of the proposed procedures.

• MeSH
• lidé MeSH
• lineární modely MeSH
• mozek * diagnostické zobrazování   MeSH
• neurozobrazování * MeSH
• počítačová simulace MeSH
• výzkumný projekt MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Resource specialization is a key concept in ecology, but it is unexpectedly difficult to parameterize. Differences in resource availability, sampling effort and abundances preclude comparisons of incompletely sampled biotic interaction webs. Here, we extend the distance-based specialization index (DSI) that measures trophic specialization by taking resource phylogenetic relatedness and availability into account into a rescaled version, DSI*. It is a versatile metric of specialization that expands considerably the scope and applicability, hence the usefulness, of DSI. The new metric also accounts for differences in abundance and sampling effort of consumers, which enables robust comparisons among distinct guilds of consumers. It also provides an abundance threshold for the reliability of the metric for rare species, a very desirable property given the difficulty of assessing any aspect of rare species accurately. We apply DSI* to an extensive dataset on interactions between insect herbivores from four folivorous guilds and their host plants in Papua New Guinean rainforests. We demonstrate that DSI*, contrary to the original DSI, is largely independent of sample size and weakly and non-linearly related with several host specificity measures that do not adjust for plant phylogeny. Thus, DSI* provides further insights into host specificity patterns; moreover, it is robust to the number and phylogenetic diversity of plant species selected to be sampled for herbivores. DSI* can be used for a broad range of comparisons of distinct feeding guilds, geographical locations and ecological conditions. This is a key advance in elucidating the interaction structure and evolution of highly diversified systems.

• MeSH
• býložravci * MeSH
• fylogeneze * MeSH
• hmyz klasifikace   genetika   MeSH
• nutriční stav MeSH
• potravní řetězec MeSH
• reprodukovatelnost výsledků MeSH
• rostliny klasifikace   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Discussions of the survival determinism concept have previously focused on its primary role in the evolution of early unicellular organisms in the light of findings which have been reported on a number of diseases. The rationale for such parallel was in the view according to which multicellular organisms could be regarded as sophisticated colonies of semi-autonomous, single-celled entities, whereby various diseases were described as conditions arising upon the activation of the respective survival mechanisms in a milieu unsuitable for such robust stress response. The cellular mechanisms that were discussed in these contexts have been known to play various roles in other biological processes. The proposed notion could thereby be further extended to discussion on mechanisms for the implementation of the respective survival pathways in the development of metazoa, considering that they would have been propagated in their evolution for so long. This manuscript first presents a concise overview of the model previously discussed, followed by the discussion on the role of respective mechanism(s) in origins and development of metazoa. Finally, a reflection on the concept in relation to the prominent evolutionary models is put forward to illustrate a broader context of what is being discussed.

• MeSH
• biologická evoluce * MeSH
• buněčný rodokmen MeSH
• Caenorhabditis elegans MeSH
• Drosophila melanogaster MeSH
• fylogeneze * MeSH
• genetická variace MeSH
• genetický drift MeSH
• genomika MeSH
• modely genetické MeSH
• mutace MeSH
• mutageneze MeSH
• populační genetika MeSH
• Saccharomyces cerevisiae MeSH
• selekce (genetika) * MeSH
• stochastické procesy MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Analysis of population genetic structure has become a standard approach in population genetics. In polyploid complexes, clustering analyses can elucidate the origin of polyploid populations and patterns of admixture between different cytotypes. However, combining diploid and polyploid data can theoretically lead to biased inference with (artefactual) clustering by ploidy. We used simulated mixed-ploidy (diploid-autotetraploid) data to systematically compare the performance of k-means clustering and the model-based clustering methods implemented in STRUCTURE, ADMIXTURE, FASTSTRUCTURE and INSTRUCT under different scenarios of differentiation and with different marker types. Under scenarios of strong population differentiation, the tested applications performed equally well. However, when population differentiation was weak, STRUCTURE was the only method that allowed unbiased inference with markers with limited genotypic information (co-dominant markers with unknown dosage or dominant markers). Still, since STRUCTURE was comparatively slow, the much faster but less powerful FASTSTRUCTURE provides a reasonable alternative for large datasets. Finally, although bias makes k-means clustering unsuitable for markers with incomplete genotype information, for large numbers of loci (>1000) with known dosage k-means clustering was superior to FASTSTRUCTURE in terms of power and speed. We conclude that STRUCTURE is the most robust method for the analysis of genetic structure in mixed-ploidy populations, although alternative methods should be considered under some specific conditions.

• MeSH
• diploidie MeSH
• genetická variace genetika   MeSH
• genetické markery genetika   MeSH
• genotyp MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• mikrosatelitní repetice genetika   MeSH
• ploidie * MeSH
• populační genetika statistika a číselné údaje   MeSH
• shluková analýza MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi.muni.cz/predictsnp.

• MeSH
• algoritmy MeSH
• databáze proteinů MeSH
• fylogeneze MeSH
• genetická variace MeSH
• genetické nemoci vrozené genetika   MeSH
• genom lidský MeSH
• internet MeSH
• jednonukleotidový polymorfismus * MeSH
• lidé MeSH
• mutace * MeSH
• počítačová simulace MeSH
• software MeSH
• výpočetní biologie metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The analysis of functional magnetic resonance imaging (fMRI) data involves multiple stages of data pre-processing before the activation can be statistically detected. Spatial smoothing is a very common pre-processing step in the analysis of functional brain imaging data. This study presents a broad perspective on the influence of spatial smoothing on fMRI group activation results. The data obtained from 20 volunteers during a visual oddball task were used for this study. Spatial smoothing using an isotropic gaussian filter kernel with full width at half maximum (FWHM) sizes 2 to 30 mm with a step of 2 mm was applied in two levels - smoothing of fMRI data and/or smoothing of single-subject contrast files prior to general linear model random-effects group analysis generating statistical parametric maps. Five regions of interest were defined, and several parameters (coordinates of nearest local maxima, t value, corrected threshold, effect size, residual values, etc.) were evaluated to examine the effects of spatial smoothing. The optimal filter size for group analysis is discussed according to various criteria. For our experiment, the optimal FWHM is about 8 mm. We can conclude that for robust experiments and an adequate number of subjects in the study, the optimal FWHM for single-subject inference is similar to that for group inference (about 8 mm, according to spatial resolution). For less robust experiments and fewer subjects in the study, a higher FWHM would be optimal for group inference than for single-subject inferences.

• MeSH
• algoritmy MeSH
• artefakty MeSH
• design vybavení MeSH
• dospělí MeSH
• financování organizované MeSH
• kontrastní látky MeSH
• lidé MeSH
• magnetická rezonanční tomografie metody   MeSH
• mapování mozku metody   přístrojové vybavení   MeSH
• mozek patologie   MeSH
• normální rozdělení MeSH
• počítačové zpracování obrazu MeSH
• reprodukovatelnost výsledků MeSH
• statistické modely MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH

Anaerobic fungi occupy the rumen and digestive tract of herbivores, where they play an important role in enzymatic digestion of lignocellulosic and cellulosic substrates, i.e. organic material that their hosts are unable to decompose on their own. In this study we isolated anaerobic fungi from a typical alpine herbivore, the Alpine ibex (C. ibex). Three fungal strains, either as pure culture (ST2) or syntrophic co-culture with methanogens (ST3, ST4) were successfully obtained and morphologically characterised by different microscopy- and staining-techniques and by rDNA ITS gene sequencing. The isolated fungi were identified as Neocallimastix frontalis (ST2) and Caecomyces communis (ST3 and ST4). We introduce a novel field of application for lactofuchsin-staining, combined with confocal laser scanning microscopy. This approach proved as an effective method to visualize fungal structures, especially in the presence of plant biomass, generally exhibiting high autofluorescence. Moreover, we could demonstrate that fungal morphology is subject to changes depending on the carbon source used for cultivation. Oxygen tolerance was confirmed for both, C. communis-cultures for up to three, and for the N. frontalis-isolate for up to 12 h, respectively. With PCR, FISH and an oligonucleotide microarray we found associated methanogens (mainly Methanobacteriales) for C. communis, but not for N. frontalis.

• MeSH
• anaerobióza MeSH
• bachor mikrobiologie   MeSH
• DNA archebakterií genetika   MeSH
• DNA fungální genetika   MeSH
• feces mikrobiologie   MeSH
• fermentace MeSH
• fylogeneze MeSH
• konfokální mikroskopie MeSH
• kozy mikrobiologie   MeSH
• methan biosyntéza   MeSH
• Methanobacteriales klasifikace   genetika   izolace a purifikace   metabolismus   MeSH
• mezerníky ribozomální DNA genetika   MeSH
• Neocallimastigomycota klasifikace   genetika   izolace a purifikace   metabolismus   MeSH
• polymerázová řetězová reakce MeSH
• sekvenční analýza DNA MeSH
• symbióza fyziologie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA "superbarcodes" for testing hypotheses regarding global patterns of diversity.

• MeSH
• brouci genetika   MeSH
• deštný prales MeSH
• frekvence genu MeSH
• fylogeneze MeSH
• genetická variace MeSH
• genom mitochondriální MeSH
• hmyzí geny MeSH
• kontigové mapování MeSH
• metagenom MeSH
• mitochondrie genetika   MeSH
• sekvenční analýza DNA MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Borneo MeSH