parallel processes
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119 s. ; 22 cm
BACKGROUND: Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. RESULTS: We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. CONCLUSIONS: The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.
- MeSH
- genetická variace MeSH
- genomika metody MeSH
- internet * MeSH
- lidé MeSH
- mikrobiota genetika MeSH
- software * MeSH
- viry genetika MeSH
- vysoce účinné nukleotidové sekvenování * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Audio-visual integration has been shown to be present in a wide range of different conditions, some of which are processed through the dorsal, and others through the ventral visual pathway. Whereas neuroimaging studies have revealed integration-related activity in the brain, there has been no imaging study of the possible role of segregated visual streams in audio-visual integration. We set out to determine how the different visual pathways participate in this communication. We investigated how audio-visual integration can be supported through the dorsal and ventral visual pathways during the double flash illusion. Low-contrast and chromatic isoluminant stimuli were used to drive preferably the dorsal and ventral pathways, respectively. In order to identify the anatomical substrates of the audio-visual interaction in the two conditions, the psychophysical results were correlated with the white matter integrity as measured by diffusion tensor imaging.The psychophysiological data revealed a robust double flash illusion in both conditions. A correlation between the psychophysical results and local fractional anisotropy was found in the occipito-parietal white matter in the low-contrast condition, while a similar correlation was found in the infero-temporal white matter in the chromatic isoluminant condition. Our results indicate that both of the parallel visual pathways may play a role in the audio-visual interaction.
- MeSH
- akustická stimulace MeSH
- anizotropie MeSH
- bílá hmota fyziologie MeSH
- dospělí MeSH
- lidé MeSH
- mapování mozku MeSH
- sluchová percepce fyziologie MeSH
- světelná stimulace MeSH
- teorie detekce signálu fyziologie MeSH
- zobrazování difuzních tenzorů MeSH
- zobrazování trojrozměrné MeSH
- zraková percepce fyziologie MeSH
- zrakové dráhy fyziologie MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The paper describes a novel control strategy for simultaneous manipulation of several microscale particles over a planar microelectrode array using dielectrophoresis. The approach is based on a combination of numerical nonlinear optimization, which gives a systematic computational procedure for finding the voltages applied to the individual electrodes, and exploitation of the intrinsic noise, which compensates for the loss of controllability when two identical particles are exposed to identical forces. Although interesting on its own, the proposed functionality can also be seen as a preliminary achievement in a quest for a technique for separation of two particles. The approach is tested experimentally with polystyrene beads (50 microns in diameter) immersed in deionized water on a flat microelectrode array with parallel electrodes. A digital camera and computer vision algorithm are used to measure the positions. Two distinguishing features of the proposed control strategy are that the range of motion is not limited to interelectrode gaps and that independent manipulation of several particles simultaneously is feasible even on a simple microelectrode array.
- MeSH
- algoritmy MeSH
- design vybavení MeSH
- elektrody MeSH
- elektroforéza metody MeSH
- hluk MeSH
- mikromanipulace přístrojové vybavení metody MeSH
- mikrosféry MeSH
- počítačové zpracování signálu přístrojové vybavení MeSH
- teoretické modely MeSH
- zpětná vazba * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Guanine quadruplexes (G4s) are non-canonical nucleic acids structures common in important genomic regions. Parallel-stranded G4 folds are the most abundant, but their folding mechanism is not fully understood. Recent research highlighted that G4 DNA molecules fold via kinetic partitioning mechanism dominated by competition amongst diverse long-living G4 folds. The role of other intermediate species such as parallel G-triplexes and G-hairpins in the folding process has been a matter of debate. Here, we use standard and enhanced-sampling molecular dynamics simulations (total length of ∼0.9 ms) to study these potential folding intermediates. We suggest that parallel G-triplex per se is rather an unstable species that is in local equilibrium with a broad ensemble of triplex-like structures. The equilibrium is shifted to well-structured G-triplex by stacked aromatic ligand and to a lesser extent by flanking duplexes or nucleotides. Next, we study propeller loop formation in GGGAGGGAGGG, GGGAGGG and GGGTTAGGG sequences. We identify multiple folding pathways from different unfolded and misfolded structures leading towards an ensemble of intermediates called cross-like structures (cross-hairpins), thus providing atomistic level of description of the single-molecule folding events. In summary, the parallel G-triplex is a possible, but not mandatory short-living (transitory) intermediate in the folding of parallel-stranded G4.
- MeSH
- DNA chemie genetika metabolismus MeSH
- G-kvadruplexy * MeSH
- guanin chemie metabolismus MeSH
- jednovláknová DNA chemie genetika metabolismus MeSH
- kinetika MeSH
- konformace nukleové kyseliny * MeSH
- lidé MeSH
- sekvence nukleotidů MeSH
- simulace molekulární dynamiky * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- MeSH
- kinezika MeSH
- králíci MeSH
- patologický nystagmus etiologie MeSH
- vestibulární aparát patofyziologie patologie MeSH
- vývojová biologie MeSH
- Check Tag
- králíci MeSH
- Publikační typ
- srovnávací studie MeSH
Dědičná onemocnění ledvin jsou příčinou renálního selhání u 10–15 % pacientů. K vývojovým anomáliím ledvin přispívají i genetické faktory, které se mohou vyskytovat v rodinách opakovaně. V článku jsou prezentovány dvě kazuistiky molekulárněgenetického vyšetření genů asociovaných s onemocněním ledvin. Na těchto případech je popisován proces klinické a genetické indikace lékařem, následné zpracování vzorku metodou masivního paralelního sekvenování (MPS, NGS – next generation sequencing), Sangerova sekvenování a bioinformatické zpracování hrubých dat. Ta jsou dále hodnocena a interpretována pomocí predikčních programů a odborných databází. V první případové studii byla v rodině nalezena genetická etiologie onemocnění a potvrzena diagnóza. V druhé případové studii nemohla být genetická etiologie onemocnění potvrzena z důvodu nejasné patogenity nalezených variant. Nicméně přesto bude docházet k dispenzarizaci jedinců, u kterých budou tyto varianty nalezeny.
Hereditary kidney diseases are the cause of renal failure in 10-15 % of patients. What also contributes to the development of renal abnormalities are genetic factors that can appear in families repeatedly. The article presents two case studies of molecular genetic testing of genes associated with kidney diseases. The clinical and genetic indication process carried out by the physician is described in these cases, together with the following processing of samples by massive parallel sequencing (MPS, NGS – next-generation sequencing), Sanger sequencing, and bioinformatic processing of raw data. These are further evaluated and interpreted using prediction programs and professional databases. In the first case study, a genetic etiology for the disease was discovered in the family and a diagnosis was confirmed. In the second case study, the genetic etiology of the disease could not have been confirmed due to the unclear pathogenicity of the variants found. Nevertheless, there will be dispensarization of individuals in whom these variants will be found.
- MeSH
- diagnostické techniky molekulární MeSH
- dítě MeSH
- genetické nemoci vrozené * MeSH
- indukovaný porod MeSH
- lidé MeSH
- nemoci ledvin * vrozené MeSH
- plod abnormality MeSH
- polycystická choroba ledvin diagnóza genetika MeSH
- polycystické ledviny autozomálně recesivní diagnóza genetika MeSH
- sekvenční analýza DNA MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mužské pohlaví MeSH
- Publikační typ
- kazuistiky MeSH
