Previous resting-state functional magnetic resonance imaging (rs-fMRI) studies frequently applied the spatial normalization on fMRI time series before the calculation of temporal features (here referred to as "Prenorm"). We hypothesized that calculating the rs-fMRI features, for example, functional connectivity (FC), regional homogeneity (ReHo), or amplitude of low-frequency fluctuation (ALFF) in individual space, before the spatial normalization (referred to as "Postnorm") can be an improvement to avoid artifacts and increase the results' reliability. We utilized two datasets: (1) simulated images where temporal signal-to-noise ratio (tSNR) is kept a constant and (2) an empirical fMRI dataset with 50 healthy young subjects. For simulated images, the tSNR is constant as generated in individual space but increased after Prenorm and intersubject variability of tSNR was induced. In contrast, tSNR was kept constant after Postnorm. Consistently, for empirical images, higher tSNR, ReHo, and FC (default mode network, seed in precuneus) and lower ALFF were found after Prenorm compared to those of Postnorm. Coefficient of variability of tSNR and ALFF was higher after Prenorm compared to those of Postnorm. Moreover, the significant correlation was found between simulated tSNR after Prenorm and empirical tSNR, ALFF, and ReHo after Prenorm, indicating algorithmic variation in empirical rs-fMRI features. Furthermore, comparing to Prenorm, ALFF and ReHo showed higher intraclass correlation coefficients between two serial scans after Postnorm. Our results indicated that Prenorm may induce algorithmic intersubject variability on tSNR and reduce its reliability, which also significantly affected ALFF and ReHo. We suggest using Postnorm instead of Prenorm for future rs-fMRI studies using ALFF/ReHo.

• Klíčová slova
• fMRI methods, fMRI preprocessing, reliability, resting-state fMRI, spatial normalization,
• Publikační typ
• časopisecké články MeSH

Histologically verified pairs (n=10) of pancreatic tumors and non-neoplastic tissues were used for quantitative real-time PCR and the stability of 24 reference genes was analyzed with geNorm and NormFinder software. Raw C{q} values correlated with the degree of RNA degradation. This correlation was abolished by normalization to C{q} of 18S endogenous control gene. Both geNorm and NormFinder programs suggested EIF2B1, ELF1, MRPL19, and POP4 as the same most stable genes. We have thus identified suitable reference genes for future expression studies in pancreatic carcinoma. Normalization method reducing the effects of RNA degradation on the quality of results was also developed.

• MeSH
• eukaryotický iniciační faktor 2B genetika   MeSH
• exprese genu MeSH
• jaderné proteiny genetika   MeSH
• karcinom diagnóza   genetika   patologie   MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• lidé středního věku MeSH
• lidé MeSH
• mitochondriální proteiny genetika   MeSH
• nádorové biomarkery genetika   MeSH
• nádory slinivky břišní diagnóza   genetika   patologie   MeSH
• pankreas metabolismus   patologie   MeSH
• ribonukleasy genetika   MeSH
• ribonukleoproteiny genetika   MeSH
• ribozomální proteiny genetika   MeSH
• senioři MeSH
• software MeSH
• stabilita RNA MeSH
• stanovení celkové genové exprese MeSH
• transkripční faktory genetika   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ELF1 protein, human MeSH Prohlížeč
• eukaryotický iniciační faktor 2B MeSH
• jaderné proteiny MeSH
• mitochondriální proteiny MeSH
• MRPL19 protein, human MeSH Prohlížeč
• nádorové biomarkery MeSH
• POP4 protein, human MeSH Prohlížeč
• ribonukleasy MeSH
• ribonukleoproteiny MeSH
• ribozomální proteiny MeSH
• transkripční faktory MeSH

We performed a gene expression study using RT-qPCR in Staphylococcus aureus. The influence of normalization method was investigated. We confirmed that a recent standard, using more reference genes, was the best normalization strategy. The application of the most commonly used reference genes in 2011 (gyrB and 16S rRNA gene) failed.

• MeSH
• bakteriální geny * MeSH
• bakteriální RNA genetika   MeSH
• DNA gyráza genetika   MeSH
• exprese genu MeSH
• kvantitativní polymerázová řetězová reakce normy   MeSH
• polymerázová řetězová reakce s reverzní transkripcí normy   MeSH
• referenční standardy MeSH
• RNA ribozomální 16S genetika   MeSH
• Staphylococcus aureus genetika   MeSH
• transkriptom MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální RNA MeSH
• DNA gyráza MeSH
• RNA ribozomální 16S MeSH

This article deals with Gaussian process surrogate models for the Covariance Matrix Adaptation Evolutionary Strategy (CMA-ES)-several already existing and two by the authors recently proposed models are presented. The work discusses different variants of surrogate model exploitation and focuses on the benefits of employing the Gaussian process uncertainty prediction, especially during the selection of points for the evaluation with a surrogate model. The experimental part of the article thoroughly compares and evaluates the five presented Gaussian process surrogate and six other state-of-the-art optimizers on the COCO benchmarks. The algorithm presented in most detail, DTS-CMA-ES, which combines cheap surrogate-model predictions with the objective function evaluations in every iteration, is shown to approach the function optimum at least comparably fast and often faster than the state-of-the-art black-box optimizers for budgets of roughly 25-100 function evaluations per dimension, in 10- and less-dimensional spaces even for 25-250 evaluations per dimension.

• Klíčová slova
• Black-box optimization, CMA-ES., Gaussian processes, evolution strategies, surrogate modeling,
• MeSH
• algoritmy * MeSH
• biologická evoluce * MeSH
• normální rozdělení MeSH
• počítačová simulace MeSH
• Publikační typ
• časopisecké články MeSH

INTRODUCTION: Cervical cancer causes approximately 350,000 deaths each year. The availability of sensitive and specific diagnostic tests to detect cervical cancer in its early stages is essential to improve survival rates. METHODS: In this study, we compared two strategies for selecting endogenous controls: miRNA profiling by small-RNA sequencing and a commercially available microfluidic card with 30 recommended endogenous controls preloaded by the manufacturer. We used the RefFinder algorithm and coefficient of variation to select endogenous controls. We selected the combination of miR-181a-5p and miR-423-3p as the most optimal normalizer. In the second part of this study, we determined the differential expression (between tumor/non-tumor groups) of microRNA in cervical cancer FFPE tissue samples. We determined the comprehensive miRNA expression profile using small-RNA sequencing technology and verified the results by real-time PCR. We determined the relative expression of selected miRNAs using the 2-ΔΔCt method. RESULTS: We detected statistically significant upregulation of miR-320a-3p, miR-7704, and downregulation of miR-26a-5p in the tumor group compared to the control group. The combination of these miRNAs may have the potential to be utilized as a diagnostic panel for cervical cancer. Using ROC curve analysis, the proposed panel showed 93.33% specificity and 96.97% sensitivity with AUC = 0.985. CONCLUSIONS: We proposed a combination of miR-181a-5p and miR-423-3p as optimal endogenous control and detected potentially significant miRNAs (miR-320a-3p, miR-7704, miR-26a-5p). After further validation of our results, these miRNAs could be used in a diagnostic panel for cervical cancer.

• Klíčová slova
• NGS, cervical cancer, diagnostic biomarkers, endogenous control, microRNA, normalization strategy,
• Publikační typ
• časopisecké články MeSH

There is a growing corpus of evidence indicating that anti-VEGF therapy may normalize the abnormal tumor vasculature with the potential to re-program the tumor immune microenvironment to a more immunosupportive profile. Tumor vessel normalization increases tumor perfusion, and, consequently, oxygen and nutrient supply, and thus can be assumed to improve the general response to anticancer immunotherapy. The increased antitumor immunity responses seen following anti-VEGF therapy may also be associated with the inhibition of the immunosuppressive action deployed by VEGF on effector T cells. Bearing in mind the recent advances of combination immunotherapy, combinations of anti-VEGF therapy with immune checkpoint inhibitors now appear to represent an attractive strategy. Key to the successful implementation of a combination strategy for treating cancer is understanding the interaction of these two therapeutic interventions, particularly in regards to appropriate reprogramming of the tumor immune microenvironment to improve antitumor immunity.

• Klíčová slova
• antitumor immunity, colorectal cancer, vascular endothelial growth factor inhibition,
• MeSH
• imunoterapie * metody   MeSH
• kolorektální nádory imunologie   terapie   MeSH
• lidé MeSH
• nádorové mikroprostředí imunologie   MeSH
• vaskulární endoteliální růstové faktory antagonisté a inhibitory   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• vaskulární endoteliální růstové faktory MeSH

The growth rate is a fundamental characteristic of bacterial species, determining its contributions to the microbial community and carbon flow. High-throughput sequencing can reveal bacterial diversity, but its quantitative inaccuracy precludes estimation of abundances and growth rates from the read numbers. Here, we overcame this limitation by normalizing Illumina-derived amplicon reads using an internal standard: a constant amount of Escherichia coli cells added to samples just before biomass collection. This approach made it possible to reconstruct growth curves for 319 individual OTUs during the grazer-removal experiment conducted in a freshwater reservoir Římov. The high resolution data signalize significant functional heterogeneity inside the commonly investigated bacterial groups. For instance, many Actinobacterial phylotypes, a group considered to harbor slow-growing defense specialists, grew rapidly upon grazers' removal, demonstrating their considerable importance in carbon flow through food webs, while most Verrucomicrobial phylotypes were particle associated. Such differences indicate distinct life strategies and roles in food webs of specific bacterial phylotypes and groups. The impact of grazers on the specific growth rate distributions supports the hypothesis that bacterivory reduces competition and allows existence of diverse bacterial communities. It suggests that the community changes were driven mainly by abundant, fast, or moderately growing, and not by rare fast growing, phylotypes. We believe amplicon read normalization using internal standard (ARNIS) can shed new light on in situ growth dynamics of both abundant and rare bacteria.

• MeSH
• Bacteria genetika   růst a vývoj   MeSH
• mikrobiota MeSH
• potravní řetězec MeSH
• referenční standardy MeSH
• sekvenční analýza DNA normy   MeSH
• sladká voda mikrobiologie   MeSH
• vysoce účinné nukleotidové sekvenování normy   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The mouse model of monosodium glutamate induced obesity was used to examine and consequently optimize the strategy for analysis of urine samples by NMR spectroscopy. A set of nineteen easily detectable metabolites typical in obesity-related studies was selected. The impact of urine collection protocol, choice of (1)H NMR pulse sequence, and finally the impact of the normalization method on the detected concentration of selected metabolites were investigated. We demonstrated the crucial effect of food intake and diurnal rhythms resulting in the choice of a 24-hour fasting collection protocol as the most convenient for tracking obesity-induced increased sensitivity to fasting. It was shown that the Carr-Purcell-Meiboom-Gill (CPMG) experiment is a better alternative to one-dimensional nuclear Overhauser enhancement spectroscopy (1D-NOESY) for NMR analysis of mouse urine due to its ability to filter undesirable signals of proteins naturally present in rodent urine. Normalization to total spectral area provided comparable outcomes as did normalization to creatinine or probabilistic quotient normalization in the CPMG-based model. The optimized approach was found to be beneficial mainly for low abundant metabolites rarely monitored due to their overlap by strong protein signals.

• Klíčová slova
• Mouse, NMR metabolomics, Obesity, Urine,
• MeSH
• analýza hlavních komponent MeSH
• biologické markery moč   MeSH
• inbrední kmeny myší MeSH
• interpretace statistických dat MeSH
• metabolom * MeSH
• metabolomika metody   MeSH
• modely nemocí na zvířatech MeSH
• novorozená zvířata MeSH
• nukleární magnetická rezonance biomolekulární metody   MeSH
• obezita metabolismus   MeSH
• odběr biologického vzorku MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• biologické markery MeSH

In response to shading, plant leaves acclimate through a range of morphological, physiological and biochemical changes. Plants produce a myriad of structurally and functionally diverse metabolites that play many important roles in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. To develop a clearer understanding of the effects of shade on soybeans at different growth stages, a comprehensive, three-year, stage-wise study was conducted. Leaf area, leaf thickness, stem diameter, chlorophyll contents, photosynthetic characteristics and other morphological and physiological features were measured along with biochemical assays for antioxidants such as superoxide dismutase, peroxidase and caralase and yield attributes of different soybean genotypes (Guixia 2, Nandou12, Nandong Kang-22, E61 and C103) under shading nets with 50% light transmittance. It was observed that early shading (VER1 and VER2) significantly decreased main stem length and main stem length/stem diameter. Later shading (R1R8 and R2R8) had significant effects on morphological characters such as branch number and pod height. In Nandou 12, the protein contents in plants shaded at R1R8, R2R8 and R5R8 were 9.20, 8.98 and 6.23% higher than in plants grown under normal light levels (CK), respectively, and the crude fat content was 9.31, 10.74 and 4.28% lower. The influence of shading in the later period on anatomy was greater than that in the earlier period. Shading reduced the light saturation point (LSP), the light compensation point (LCP) and the maximum photosynthetic rate (Pnmax), and increased the apparent quantum yield (AQ). Shading also increased the antioxidant enzyme activity in the plants, and this increase was greater with early shading than late. The variability in the chlorophyll (a + b) content and the chlorophyll a/b ratio in R2 stage plants was less than in R5 stage (VER5) plants. Similarly, the activity of antioxidant enzymes in R2 after returning the plants to normal light levels (VER2) was lower than in R5 after relighting (VER5). Compared with later shading, the early shading had a greater effect on the photosynthetic and related characteristics. The longer the shading time, the greater the adverse effects and the less able the plants' were to recover. The data collected in this study contribute to an understanding of the physiological mechanisms underlying the early and late growth stage acclimation strategies in different soybean genotypes subjected to shade stress.

• MeSH
• aklimatizace MeSH
• chlorofyl a MeSH
• genotyp MeSH
• Glycine max * genetika   MeSH
• světlo * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chlorofyl a MeSH

Migratory birds often move significantly within their non-breeding range before returning to breed. It remains unresolved under which circumstances individuals relocate, whether movement patterns are consistent between populations and to what degree the individuals benefit from the intra-tropical movement (ITM). We tracked adult great reed warblers Acrocephalus arundinaceus from a central and a southeastern European breeding population, which either stay at a single non-breeding site, or show ITM, i.e. move to a second site. We related ITM to the normalized difference vegetation index (NDVI) describing vegetation conditions and probably reflecting food abundance for these insectivorous birds. Three-quarters of birds showed ITM across the non-breeding range. We found no difference in range values and mean values of NDVI between the single non-breeding sites of stationary birds and the two sites of moving birds. The vegetation conditions were better at the second sites compared to the first sites during the period which moving birds spent at the first sites. Vegetation conditions further deteriorated at the first sites during the period the moving birds resided at their second sites. Our study provides evidence that birds probably benefit from improved conditions after ITM compared to the conditions at the sites from where they departed.

• Klíčová slova
• NDVI, geolocator, habitat deterioration, passerines, sub-Saharan Africa, vegetation conditions,
• Publikační typ
• časopisecké články MeSH