The paper is a presentation of the current state of development for the Atlas of Physiology and Pathophysiology (Atlas). Our main aim is to provide a novel interactive multimedia application that can be used for biomedical education where (a) simulations are combined with tutorials and (b) the presentation layer is simplified while the underlying complexity of the model is retained. The development of the Atlas required the cooperation of many professionals including teachers, system analysts, artists, and programmers. During the design of the Atlas, tools were developed that allow for component-based creation of simulation models, creation of interactive multimedia and their final coordination into a compact unit based on the given design. The Atlas is a freely available online application, which can help to explain the function of individual physiological systems and the causes and symptoms of their disorders.

• MeSH
• atlasy jako téma * MeSH
• fyziologie * MeSH
• internet * MeSH
• počítačová simulace * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• atlasy jako téma * MeSH
• lidé MeSH
• meteorologické pojmy * MeSH
• podnebí * MeSH
• veřejné zdravotnictví * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• zprávy MeSH

• MeSH
• atlasy jako téma * MeSH
• kouření epidemiologie   mortalita   MeSH
• lidé MeSH
• mezinárodní spolupráce MeSH
• Světová zdravotnická organizace MeSH
• vytváření politiky MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

African mole-rats are subterranean rodents that spend their whole life in underground burrow systems. They show a range of morphological and physiological adaptations to their ecotope, for instance severely reduced eyes and specialized somatosensory, olfactory, and auditory systems. These adaptations are also reflected in the accessory sensory pathways in the brain that process the input coming from the sensory organs. So far, a brain atlas was available only for the naked mole-rat (Heterocephalus glaber). The Ansell's mole-rat (Fukomys anselli) has been the subject of many investigations in various disciplines (ethology, sensory physiology, and anatomy) including magnetic orientation. It is therefore surprising that an atlas of the brain of this species was not available so far. Here, we present a comprehensive atlas of the Ansell's mole-rat brain based on Nissl and Klüver-Barrera stained sections. We identify and label 375 brain regions and discuss selected differences from the brain of the closely related naked mole-rat as well as from epigeic mammals (rat), with a particular focus on the auditory brainstem. This atlas can serve as a reference for future neuroanatomical investigations of subterranean mammals.

• Klíčová slova
• Nissl, RRID:SCR_005910, RRID:SCR_014199, auditory system, magnetoreception, nervous system, neuroanatomy, rodent, subterranean mammal,
• MeSH
• anatomie pro výtvarníky * MeSH
• atlasy jako téma * MeSH
• mikroftalmičtí podzemní hlodavci anatomie a histologie   MeSH
• mozek anatomie a histologie   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Functional connectivity analysis of resting-state fMRI data has recently become one of the most common approaches to characterizing individual brain function. It has been widely suggested that the functional connectivity matrix is a useful approximate representation of the brain's connectivity, potentially providing behaviorally or clinically relevant markers. However, functional connectivity estimates are known to be detrimentally affected by various artifacts, including those due to in-scanner head motion. Moreover, as individual functional connections generally covary only very weakly with head motion estimates, motion influence is difficult to quantify robustly, and prone to be neglected in practice. Although the use of individual estimates of head motion, or group-level correlation of motion and functional connectivity has been suggested, a sufficiently sensitive measure of individual functional connectivity quality has not yet been established. We propose a new intuitive summary index, Typicality of Functional Connectivity, to capture deviations from standard brain functional connectivity patterns. In a resting-state fMRI dataset of 245 healthy subjects, this measure was significantly correlated with individual head motion metrics. The results were further robustly reproduced across atlas granularity, preprocessing options, and other datasets, including 1,081 subjects from the Human Connectome Project. In principle, Typicality of Functional Connectivity should be sensitive also to other types of artifacts, processing errors, and possibly also brain pathology, allowing extensive use in data quality screening and quantification in functional connectivity studies as well as methodological investigations.

• Klíčová slova
• atlas, functional connectivity, motion, quality, rs-fMRI,
• MeSH
• artefakty MeSH
• atlasy jako téma * MeSH
• datové soubory jako téma * MeSH
• dospělí MeSH
• hlava - pohyby MeSH
• konektom * metody   normy   MeSH
• lidé MeSH
• magnetická rezonanční tomografie * metody   normy   MeSH
• mladý dospělý MeSH
• mozek diagnostické zobrazování   fyziologie   MeSH
• počítačové zpracování obrazu * metody   normy   MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

In patients with pharmaco-resistant focal epilepsies investigated with intracranial electroencephalography (iEEG), direct electrical stimulations of a cortical region induce cortico-cortical evoked potentials (CCEP) in distant cerebral cortex, which properties can be used to infer large scale brain connectivity. In 2013, we proposed a new probabilistic functional tractography methodology to study human brain connectivity. We have now been revisiting this method in the F-TRACT project (f-tract.eu) by developing a large multicenter CCEP database of several thousand stimulation runs performed in several hundred patients, and associated processing tools to create a probabilistic atlas of human cortico-cortical connections. Here, we wish to present a snapshot of the methods and data of F-TRACT using a pool of 213 epilepsy patients, all studied by stereo-encephalography with intracerebral depth electrodes. The CCEPs were processed using an automated pipeline with the following consecutive steps: detection of each stimulation run from stimulation artifacts in raw intracranial EEG (iEEG) files, bad channels detection with a machine learning approach, model-based stimulation artifact correction, robust averaging over stimulation pulses. Effective connectivity between the stimulated and recording areas is then inferred from the properties of the first CCEP component, i.e. onset and peak latency, amplitude, duration and integral of the significant part. Finally, group statistics of CCEP features are implemented for each brain parcel explored by iEEG electrodes. The localization (coordinates, white/gray matter relative positioning) of electrode contacts were obtained from imaging data (anatomical MRI or CT scans before and after electrodes implantation). The iEEG contacts were repositioned in different brain parcellations from the segmentation of patients' anatomical MRI or from templates in the MNI coordinate system. The F-TRACT database using the first pool of 213 patients provided connectivity probability values for 95% of possible intrahemispheric and 56% of interhemispheric connections and CCEP features for 78% of intrahemisheric and 14% of interhemispheric connections. In this report, we show some examples of anatomo-functional connectivity matrices, and associated directional maps. We also indicate how CCEP features, especially latencies, are related to spatial distances, and allow estimating the velocity distribution of neuronal signals at a large scale. Finally, we describe the impact on the estimated connectivity of the stimulation charge and of the contact localization according to the white or gray matter. The most relevant maps for the scientific community are available for download on f-tract. eu (David et al., 2017) and will be regularly updated during the following months with the addition of more data in the F-TRACT database. This will provide an unprecedented knowledge on the dynamical properties of large fiber tracts in human.

• Klíčová slova
• Brain atlas, Connectivity mapping, Cortico-cortical evoked potentials, Epilepsy, Intracranial electroencephalogram,
• MeSH
• atlasy jako téma MeSH
• databáze faktografické MeSH
• dítě MeSH
• dospělí MeSH
• elektrokortikografie metody   MeSH
• epilepsie diagnostické zobrazování   patofyziologie   MeSH
• evokované potenciály fyziologie   MeSH
• konektom metody   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mozková kůra diagnostické zobrazování   patofyziologie   MeSH
• nervové dráhy diagnostické zobrazování   MeSH
• předškolní dítě MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• multicentrická studie MeSH
• práce podpořená grantem MeSH

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

• MeSH
• anotace sekvence MeSH
• atlasy jako téma MeSH
• chléb MeSH
• chov * MeSH
• fylogeneze MeSH
• genom rostlinný * MeSH
• lokus kvantitativního znaku MeSH
• multigenová rodina MeSH
• pšenice anatomie a histologie   klasifikace   genetika   růst a vývoj   MeSH
• referenční standardy MeSH
• regulace genové exprese u rostlin * MeSH
• transkriptom MeSH
• vývojová regulace genové exprese * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Parcellation-based approaches are an important part of functional magnetic resonance imaging data analysis. They are a necessary processing step for sorting data in structurally or functionally homogenous regions. Real functional magnetic resonance imaging datasets usually do not cover the atlas template completely; they are often spatially constrained due to the physical limitations of MR sequence settings, the inter-individual variability in brain shape, etc. When using a parcellation template, many regions are not completely covered by actual data. This paper addresses the issue of the area coverage required in real data in order to reliably estimate the representative signal and the influence of this kind of data loss on network analysis metrics. We demonstrate this issue on four datasets using four different widely used parcellation templates. We used two erosion approaches to simulate data loss on the whole-brain level and the ROI-specific level. Our results show that changes in ROI coverage have a systematic influence on network measures. Based on the results of our analysis, we recommend controlling the ROI coverage and retaining at least 60% of the area in order to ensure at least 80% of explained variance of the original signal.

• Klíčová slova
• Atlas, Coverage, Parcellation, Representative signal, fMRI,
• MeSH
• algoritmy MeSH
• atlasy jako téma * MeSH
• dospělí MeSH
• funkční lateralita MeSH
• individualita MeSH
• lidé MeSH
• lineární modely MeSH
• magnetická rezonanční tomografie metody   statistika a číselné údaje   MeSH
• mapování mozku metody   MeSH
• mladý dospělý MeSH
• mozek diagnostické zobrazování   MeSH
• počítačová simulace MeSH
• počítačové zpracování obrazu metody   MeSH
• reprodukovatelnost výsledků MeSH
• světelná stimulace MeSH
• zdraví dobrovolníci pro lékařské studie MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH