Relative Localization
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Študovali sme kritickú micelárnu koncentráciu (c.m.c.) homológov lokálneho anestetika heptakaínuv roztoku 0,1 mol/l NaCl pomocou spektrofotometrie v ultrafialovej oblasti pri teplote T=21 °C a pH= 4,5-5,0. Na základe získaných experimentálnych výsledkov predpokladá sa, že v homologickýchradoch amfifilných zlúčenín za kváziparabolické závislosti biologických účinností na dľžke ichhydrofóbneho substituenta (—cut-offit efekt) je zodpovedná c.m.c.
We have studied the critical micellar concentration (c.m.c.) of the homologs of the local anestheticheptacaine in the medium 0.1 mol/l NaCl, employing spectrophotometry in the UV region of thespectrum at T=21 °C and pH = 4.5Œ5.0. On the basis of our experimental results, it is assumed thatin the homologous series of amphiphilic compounds the quasi-parabolic dependence of biologicalpotencies on the length of their hydrophobic substituent (—cut-offit effect) could be caused by c.m.c.
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.
- 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
OBJECTIVE: High-frequency oscillations are considered among the most promising interictal biomarkers of the epileptogenic zone in patients suffering from pharmacoresistant focal epilepsy. However, there is no clear definition of pathological high-frequency oscillations, and the existing detectors vary in methodology, performance, and computational costs. This study proposes relative entropy as an easy-to-use novel interictal biomarker of the epileptic tissue. METHODS: We evaluated relative entropy and high-frequency oscillation biomarkers on intracranial electroencephalographic data from 39 patients with seizure-free postoperative outcome (Engel Ia) from three institutions. We tested their capability to localize the epileptogenic zone, defined as resected contacts located in the seizure onset zone. The performance was compared using areas under the receiver operating curves (AUROCs) and precision-recall curves. Then we tested whether a universal threshold can be used to delineate the epileptogenic zone across patients from different institutions. RESULTS: Relative entropy in the ripple band (80-250 Hz) achieved an average AUROC of .85. The normalized high-frequency oscillation rate in the ripple band showed an identical AUROC of .85. In contrast to high-frequency oscillations, relative entropy did not require any patient-level normalization and was easy and fast to calculate due to its clear and straightforward definition. One threshold could be set across different patients and institutions, because relative entropy is independent of signal amplitude and sampling frequency. SIGNIFICANCE: Although both relative entropy and high-frequency oscillations have a similar performance, relative entropy has significant advantages such as straightforward definition, computational speed, and universal interpatient threshold, making it an easy-to-use promising biomarker of the epileptogenic zone.
Navrhuje sa teoretický model, podľa ktorého kváziparabolický priebeh biologickej účinnosti lokálnych anestetík typu terciárnych amínov v závislosti na dĺžke hydrofóbneho substituenta („cut-off" efekt) je podmienený kombináciou rozdělovačích a ionizačných rovnováh a geometrických parametrov týchto látok interagujúcich s dvojvrstvou fosfolipidovej membrány. Študuje sa vplyv povrchového elektrického náboja, ktorý pozorujeme pri interkalácii nabitých molekúl lokálneho anestetika do dvoj vrstvy.
A theoretical model is proposed according to which the quasi-parabolic course of the biological activity of local anaesthetics of tertiary amines in dependence on the length of the hydrophobic substituents (the „cut-off' effect) is conditioned by a combination of partition and ionizing balances and geometrical parameters of these substances interacting with the bilayer of the phospholipid membrane. The influence of the surface electric charge, which is observed in the intercalation of the charged molecules of the local anaesthetic into the bilayer is studied.
In fragmented landscapes, plant species richness may depend not only on local habitat conditions but also on landscape structure. In addition, both present and past landscape structure may be important for species richness. There are, however, only a few studies that have investigated the relative importance of all of these factors. The aim of this study was to examine the effect of current and past landscape structures and habitat conditions on species richness at dry grassland-like forest openings in a forested landscape and to assess their relative importance for species richness. We analyzed information on past and present landscape structures using aerial photographs from 1938, 1973, 1988, 2000 and 2007. We calculated the area of each locality and its isolation in the present and in the past and the continuity of localities in GIS. At each locality, we recorded all vascular plant species (296 species in 110 forest openings) and information on abiotic conditions of the localities. We found that the current species richness of the forest openings was significantly determined by local habitat conditions as well as by landscape structure in the present and in the past. The highest species richness was observed on larger and more heterogeneous localities with rocks and shallow soils, which were already large and well connected to other localities in 1938. The changes in the landscape structure in the past can thus have strong effects on current species richness. Future studies attempting to understand determinants of species diversity in fragmented landscapes should also include data on past landscape structure, as it may in fact be more important than the present structure.
- MeSH
- biodiverzita * MeSH
- lesy * MeSH
- pastviny * MeSH
- rostliny * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Barley (Hordeum vulgare) accumulates phenolic compounds (PhCs), which play a key role in plant defense against environmental stressors as antioxidants or UV screening compounds. The influence of light and atmospheric CO2 concentration ([CO2]) on the accumulation and localization of PhCs in barley leaves was examined for two varieties with different tolerances to oxidative stress. PhC localization was visualized in vivo using fluorescence microscopy. Close relationships were found between fluorescence-determined localization of PhCs in barley leaves and PhC content estimated using liquid chromatography coupled with mass spectroscopy detection. Light intensity had the strongest effect on the accumulation of PhCs, but the total PhC content was similar at elevated [CO2], minimizing the differences between high and low light. PhCs localized preferentially near the surfaces of leaves, but under low light, an increasing allocation of PhCs in deeper mesophyll layers was observed. The PhC profile was significantly different between barley varieties. The relatively tolerant variety accumulated significantly more hydroxycinnamic acids, indicating that these PhCs may play a more prominent role in oxidative stress prevention. Our research presents novel evidence that [CO2] modulates the accumulation of PhCs in barley leaves. Mesophyll cells, rather than epidermal cells, were most responsive to environmental stimuli in terms of PhC accumulation.
- Publikační typ
- časopisecké články MeSH
We analysed the size, relative age and chromosomal localization of nuclear sequences of plastid and mitochondrial origin (NUPTs-nuclear plastid DNA and NUMTs-nuclear mitochondrial DNA) in six completely sequenced plant species. We found that the largest insertions showed lower divergence from organelle DNA than shorter insertions in all species, indicating their recent origin. The largest NUPT and NUMT insertions were localized in the vicinity of the centromeres in the small genomes of Arabidopsis and rice. They were also present in other chromosomal regions in the large genomes of soybean and maize. Localization of NUPTs and NUMTs correlated positively with distribution of transposable elements (TEs) in Arabidopsis and sorghum, negatively in grapevine and soybean, and did not correlate in rice or maize. We propose a model where new plastid and mitochondrial DNA sequences are inserted close to centromeres and are later fragmented by TE insertions and reshuffled away from the centromere or removed by ectopic recombination. The mode and tempo of TE dynamism determines the turnover of NUPTs and NUMTs resulting in their species-specific chromosomal distributions.
- MeSH
- buněčné jádro MeSH
- chromozomy rostlin genetika MeSH
- druhová specificita MeSH
- genom rostlinný MeSH
- mitochondriální DNA genetika MeSH
- mitochondrie genetika MeSH
- mutace INDEL genetika MeSH
- plastidy genetika MeSH
- rostliny genetika MeSH
- sekvenční analýza DNA MeSH
- transpozibilní elementy DNA genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
DNA double stranded breaks (DSBs) are the most serious type of lesions introduced into chromatin by ionizing radiation. During DSB repair, cells recruit different proteins to the damaged sites in a manner dependent on local chromatin structure, DSB location in the nucleus, and the repair pathway entered. 53BP1 is one of the important players participating in repair pathway decision of the cell. Although many molecular biology details have been investigated, the architecture of 53BP1 repair foci and its development during the post-irradiation time, especially the period of protein recruitment, remains to be elucidated. Super-resolution light microscopy is a powerful new tool to approach such studies in 3D-conserved cell nuclei. Recently, we demonstrated the applicability of single molecule localization microscopy (SMLM) as one of these highly resolving methods for analyses of dynamic repair protein distribution and repair focus internal nano-architecture in intact cell nuclei. In the present study, we focused our investigation on 53BP1 foci in differently radio-resistant cell types, moderately radio-resistant neonatal human dermal fibroblasts (NHDF) and highly radio-resistant U87 glioblastoma cells, exposed to high-LET 15N-ion radiation. At given time points up to 24 h post irradiation with doses of 1.3 Gy and 4.0 Gy, the coordinates and spatial distribution of fluorescently tagged 53BP1 molecules was quantitatively evaluated at the resolution of 10⁻20 nm. Clusters of these tags were determined as sub-units of repair foci according to SMLM parameters. The formation and relaxation of such clusters was studied. The higher dose generated sufficient numbers of DNA breaks to compare the post-irradiation dynamics of 53BP1 during DSB processing for the cell types studied. A perpendicular (90°) irradiation scheme was used with the 4.0 Gy dose to achieve better separation of a relatively high number of particle tracks typically crossing each nucleus. For analyses along ion-tracks, the dose was reduced to 1.3 Gy and applied in combination with a sharp angle irradiation (10° relative to the cell plane). The results reveal a higher ratio of 53BP1 proteins recruited into SMLM defined clusters in fibroblasts as compared to U87 cells. Moreover, the speed of foci and thus cluster formation and relaxation also differed for the cell types. In both NHDF and U87 cells, a certain number of the detected and functionally relevant clusters remained persistent even 24 h post irradiation; however, the number of these clusters again varied for the cell types. Altogether, our findings indicate that repair cluster formation as determined by SMLM and the relaxation (i.e., the remaining 53BP1 tags no longer fulfill the cluster definition) is cell type dependent and may be functionally explained and correlated to cell specific radio-sensitivity. The present study demonstrates that SMLM is a highly appropriate method for investigations of spatiotemporal protein organization in cell nuclei and how it influences the cell decision for a particular repair pathway at a given DSB site.
Mutations of the gene for nucleophosmin (NPM1) are the most frequent genetic aberration in patients with acute myeloid leukemia (AML). The mechanism of leukemic transformation in this leukemia subtype is not fully understood, but aberrant cytoplasmic localization of mutated NPM (NPMmut) is widely considered as an important factor for leukemia manifestation. We analyzed the subcellular localization of three types of NPM with a C-terminal mutation (A, B and E). Genes for the individual NPM forms were fused with a gene for one of fluorescent protein variants in plasmids, which were transfected into three cell lines with different endogenous NPM expression. Subcellular localization of the fluorescent protein-labeled NPM was further correlated with the relative expression of all NPM forms. We confirmed a high cytoplasmic expression of NPMmutA and NPMmutB whereas a substantial fraction of NPMmutE was found to be localized in nucleoli. Moreover, we revealed that the localization of fluorescently labeled NPM is affected by the interaction between various forms of the protein.
- MeSH
- akutní myeloidní leukemie metabolismus MeSH
- buňky NIH 3T3 MeSH
- jaderné proteiny genetika metabolismus MeSH
- lidé MeSH
- mutace * MeSH
- myši MeSH
- nádorové buněčné linie MeSH
- subcelulární frakce metabolismus MeSH
- vazba proteinů MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
