Parallel processing
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- MeSH
- elektrofyziologie MeSH
- epilepsie parciální patofyziologie MeSH
- lidé MeSH
- mozek patofyziologie MeSH
- Check Tag
- lidé MeSH
119 s. ; 22 cm
A new reconstruction method for parallel MRI called PROBER is proposed. The method PROBER works in an image domain similar to methods based on Sensitivity Encoding (SENSE). However, unlike SENSE, which first estimates the spatial sensitivity maps, PROBER approximates the reconstruction coefficients directly by B-splines. Also, B-spline coefficients are estimated at once in order to minimize the reconstruction error instead of estimating the reconstruction in each pixel independently (as in SENSE). This makes the method robust to noise in reference images. No presmoothing of reference images is necessary. The number of estimated parameters is reduced, which speeds up the estimation process. PROBER was tested on simulated, phantom, and in vivo data. The results are compared with commercial implementations of the algorithms SENSE and GRAPPA (Generalized Autocalibrating Partially Parallel Acquisitions) in terms of elapsed time and reconstruction quality. The experiments showed that PROBER is faster than GRAPPA and SENSE for images wider than 150x150 pixels for comparable reconstruction quality. With more basis functions, PROBER outperforms both SENSE and GRAPPA in reconstruction quality at the cost of slightly increased computational time. Copyright (c) 2007 Wiley-Liss, Inc.
- MeSH
- algoritmy MeSH
- artefakty MeSH
- časové faktory MeSH
- diethylentriaminpentaacetát gadolinia diagnostické užití MeSH
- dospělí MeSH
- fantomy radiodiagnostické MeSH
- financování organizované MeSH
- hlava anatomie a histologie MeSH
- hrudník anatomie a histologie MeSH
- kalibrace MeSH
- kontrastní látky MeSH
- lidé MeSH
- magnetická rezonanční tomografie metody MeSH
- počítačová simulace MeSH
- počítačové zpracování obrazu metody statistika a číselné údaje MeSH
- vylepšení obrazu metody MeSH
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- dospělí MeSH
- lidé MeSH
- Publikační typ
- srovnávací studie MeSH
The automated detection of arrhythmia in a Holter ECG signal is a challenging task due to its complex clinical content and data quantity. It is also challenging due to the fact that Holter ECG is usually affected by noise. Such noise may be the result of the regular activity of patients using the Holter ECG-partially unplugged electrodes, short-time disconnections due to movement, or disturbances caused by electric devices or infrastructure. Furthermore, regular patient activities such as movement also affect the ECG signals and, in connection with artificial noise, may render the ECG non-readable or may lead to misinterpretation of the ECG. OBJECTIVE: In accordance with the PhysioNet/CinC Challenge 2017, we propose a method for automated classification of 1-lead Holter ECG recordings. APPROACH: The proposed method classifies a tested record into one of four classes-'normal', 'atrial fibrillation', 'other arrhythmia' or 'too noisy to classify'. It uses two machine learning methods in parallel. The first-a bagged tree ensemble (BTE)-processes a set of 43 features based on QRS detection and PQRS morphology. The second-a convolutional neural network connected to a shallow neural network (CNN/NN)-uses ECG filtered by nine different filters (8× envelograms, 1× band-pass). If the output of CNN/NN reaches a specific level of certainty, its output is used. Otherwise, the BTE output is preferred. MAIN RESULTS: The proposed method was trained using a reduced version of the public PhysioNet/CinC Challenge 2017 dataset (8183 records) and remotely tested on the hidden dataset on PhysioNet servers (3658 records). The method achieved F1 test scores of 0.92, 0.82 and 0.74 for normal recordings, atrial fibrillation and recordings containing other arrhythmias, respectively. The overall F1 score measured on the hidden test-set was 0.83. SIGNIFICANCE: This F1 score led to shared rank #2 in the follow-up PhysioNet/CinC Challenge 2017 ranking.
- MeSH
- kinezika MeSH
- králíci MeSH
- patologický nystagmus etiologie MeSH
- vestibulární aparát patofyziologie patologie MeSH
- vývojová biologie MeSH
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- králíci MeSH
- Publikační typ
- srovnávací studie MeSH
Germline DNA testing using the next-gene-ration sequencing (NGS) technology has become the analytical standard for the diagnostics of hereditary diseases, including cancer. Its increasing use places high demands on correct sample identification, independent confirmation of prioritized variants, and their functional and clinical interpretation. To streamline these processes, we introduced parallel DNA and RNA capture-based NGS using identical capture panel CZECANCA, which is routinely used for DNA analysis of hereditary cancer predisposition. Here, we present the analytical workflow for RNA sample processing and its analytical and diagnostic performance. Parallel DNA/RNA analysis allowed credible sample identification by calculating the kinship coefficient. The RNA capture-based approach enriched transcriptional targets for the majority of clinically relevant cancer predisposition genes to a degree that allowed analysis of the effect of identified DNA variants on mRNA processing. By comparing the panel and whole-exome RNA enrichment, we demonstrated that the tissue-specific gene expression pattern is independent of the capture panel. Moreover, technical replicates confirmed high reproducibility of the tested RNA analysis. We concluded that parallel DNA/RNA NGS using the identical gene panel is a robust and cost-effective diagnostic strategy. In our setting, it allows routine analysis of 48 DNA/RNA pairs using NextSeq 500/550 Mid Output Kit v2.5 (150 cycles) in a single run with sufficient coverage to analyse 226 cancer predisposition and candidate ge-nes. This approach can replace laborious Sanger confirmatory sequencing, increase testing turnaround, reduce analysis costs, and improve interpretation of the impact of variants by analysing their effect on mRNA processing.
- MeSH
- DNA genetika MeSH
- genetická predispozice k nemoci * MeSH
- lidé MeSH
- nádory genetika diagnóza MeSH
- reprodukovatelnost výsledků MeSH
- RNA genetika MeSH
- sekvenční analýza DNA metody MeSH
- sekvenční analýza RNA metody MeSH
- vysoce účinné nukleotidové sekvenování * metody MeSH
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- lidé MeSH
- Publikační typ
- časopisecké články MeSH
PURPOSE: To investigate the fundamental connectivity architecture of neural structures involved in the goal-directed processing of target events. METHODS: Twenty healthy volunteers underwent event-related functional magnetic resonance imaging (fMRI) while performing a standard oddball task. In the task, two types of visual stimuli - rare (target) and frequent - were randomly presented, and subjects were instructed to mentally count the target stimuli. Dynamic causal modeling (DCM), in combination with Bayes factors was used to compare competing neurophysiological models with different intrinsic connectivity structures and input regions within the network of brain regions underlying target stimulus processing. RESULTS: Conventional analysis of fMRI data revealed significantly greater activation in response to the target stimuli (in comparison to the frequent stimuli) in several brain regions, including the intraparietal sulci and supramarginal gyri, the anterior and posterior cingulate gyri, the inferior and middle frontal gyri, the superior temporal sulcus, the precuneus/cuneus, and the subcortical grey matter (caudate and thalamus). The most extensive cortical activations were found in the right intraparietal sulcus (IPS), the anterior cingulate cortex (ACC), and the right lateral prefrontal cortex (PFC). These three regions were entered into the DCM. A comparison on a group level revealed that the dynamic causal models in which the ACC and alternatively the IPS served as input regions were superior to a model in which the PFC was assumed to receive external inputs. No significant difference was observed between the fully connected models with ACC and IPS as input regions. Subsequent analysis of the intrinsic connectivity within two investigated models (IPS and ACC) disclosed significant parallel forward connections from the IPS to the frontal areas and from the ACC to the PFC and the IPS. CONCLUSION: Our findings indicate that during target stimulus processing there is a bidirectional frontoparietal information flow, very likely reflecting parallel activation of two distinct but partially overlapping attentional or attentional/event-encoding neural systems. Additionally, a simple hierarchy within the right frontal lobe is suggested with the ACC exerting influence over the PFC.
- MeSH
- dospělí MeSH
- duševní procesy fyziologie MeSH
- financování organizované MeSH
- lidé MeSH
- magnetická rezonanční tomografie MeSH
- mladiství MeSH
- mozek fyziologie MeSH
- světelná stimulace MeSH
- zraková percepce genetika MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mladiství MeSH
- mužské pohlaví MeSH
- ženské pohlaví 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
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
