BACKGROUND: RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy - producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). RESULTS: A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. CONCLUSIONS: Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds.

• Klíčová slova
• Aethionema arabicum, Dimorphic seeds, RNA-seq, Reference and reference-free, Transcriptome,
• MeSH
• anotace sekvence MeSH
• Brassicaceae genetika   růst a vývoj   MeSH
• genom rostlinný MeSH
• genová ontologie MeSH
• klíčení MeSH
• regulace genové exprese u rostlin * MeSH
• rostlinné proteiny genetika   MeSH
• semena rostlinná genetika   růst a vývoj   MeSH
• stanovení celkové genové exprese MeSH
• transkriptom * MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• rostlinné proteiny MeSH

BACKGROUND: Free light chains, type kappa (FLC-K), in cerebrospinal fluid (CSF) were compared to oligoclonal IgG in many studies for sensitive detection of immune reactions in brain. The missing consensus about CSF data interpretation prevents reliable conclusions. This can be overcome by a theory-based hyperbolic reference range in CSF/serum quotient diagrams. METHODS: Mean Quotients for FLC-K, QKappa, and albumin, QAlb, of grouped, biochemically defined controls (N = 433) are fitted with the hyperbolic function QKappa(mean) = a/b (QAlb2 + b2)0.5 - c by a generally applicable procedure excluding outliers. RESULTS: With QKappa(mean), the coefficient of variation CV (22.5%) and the reference range (QKappa(mean) ± 3 CV) we got the discrimination line QKappa(lim) = (3.27(QAlb2 + 33)0.5-8.2) ×10-3 in a FLC-K Reibergram. Intrathecal FLC-K was found in 8% of another control group without OCB (N = 388) but was missed in 7% of patients with definite Multiple sclerosis (N = 95). In MS the mean intrathecal fraction was threefold larger for FLC-K (95%) compared to total IgG (36%). Similar mean quantities of intrathecal FLC-K contradict an immunological conversion between a Clinically isolated syndrome and MS. DISCUSSION: The hyperbolic reference range is superior to linear FLC-K Index (10 to 15% false negatives) and exponential curves (30% false positive interpretations for controls) in the analytical range of MS data, with excellent data fit for up to ten-fold larger QAlb values. Dynamics of the small molecule FLC-K contribute to the understanding of molecular size dependent barrier functions.

• Klíčová slova
• CIS, Cerebrospinal fluid, Clinically isolated syndrome, Free light chain kappa, Grouped data statistics, Hyperbolic function, Multiple sclerosis, Reference range,
• MeSH
• albuminy analýza   normy   MeSH
• imunoglobuliny - kappa-řetězce analýza   MeSH
• lidé MeSH
• mozkomíšní mok chemie   MeSH
• referenční hodnoty MeSH
• retrospektivní studie MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• albuminy MeSH
• imunoglobuliny - kappa-řetězce MeSH

MOTIVATION: Clustering of genetic sequences is one of the key parts of bioinformatics analyses. Resulting phylogenetic trees are beneficial for solving many research questions, including tracing the history of species, studying migration in the past, or tracing a source of a virus outbreak. At the same time, biologists provide more data in the raw form of reads or only on contig-level assembly. Therefore, tools that are able to process those data without supervision need to be developed. RESULTS: In this paper, we present a tool for reference-free phylogeny capable of handling data where no mature-level assembly is available. The tool allows distance calculation for raw reads, contigs, and the combination of the latter. The tool provides an estimation of the Levenshtein distance between the sequences, which in turn estimates the number of mutations between the organisms. Compared to the previous research, the novelty of the method lies in a newly proposed combination of the read and contig measures, a new method for read-contig mapping, and an efficient embedding of contigs.

• Klíčová slova
• Contigs, Levenshtein distance, Phylogeny, Reads, Sequence similarity,
• Publikační typ
• časopisecké články MeSH

Fat mass and fat-free mass have become useful clinical indices in determining healthy growth and physical development during critical periods of childhood and adolescence; however, despite a wide range of nutritional surveillance its study is limited by a lack of reference data. The purpose of this study was to establish sex-specific and age-specific standards for fat mass and fat-free mass in a large sample of Croatian children and adolescents. In this cross-sectional study, we collected data from 12,678 participants aged 11 to 18 years old (mean age ± standard deviation (SD): 14.17 ± 2.25 years; height 164.56 ± 11.31 cm; weight: 57.45 ± 13.73 kg; body mass index: 21.24 ± 3.67 kg/m2; 53% girls). Fat mass and fat-free mass were measured three times by bioelectrical impedance. The Lambda, Mu and Sigma methods were used to create percentile charts for fat mass index (FMI) and fat-free mass index (FFMI; fat mass and fat-free mass divided by height2). Sex and age differences were calculated using an analysis of variance (ANOVA) with post hoc comparisons. Boys had lower FMI (from 2.66 to 3.89) and higher FFMI values (from 16.90 to 17.80) in all age groups, compared to girls (for FMI from 2.79 to 5.17 and for FFMI from 14.50 to 14.90, p < 0.001). In boys, FMI slightly declined until the age of 14, after which an increase from the age of 15 to 18 was observed. In girls, FMI gradually increased from the age of 11 to 18 (p < 0.001). In general, FFMI increased by age in boys [F(7,5440) = 52.674, p < 0.001], while girls had more stable FFMI across all age groups [F(7,7222) = 2.728, p = 0.057]. The newly established sex-specific and age-specific reference data could be used for national surveillance and to screen for children and adolescents with high FMI and low FFMI.

• Klíčová slova
• adolescents, body composition, children, normative,
• MeSH
• dítě MeSH
• elektrická impedance MeSH
• index tělesné hmotnosti MeSH
• lidé MeSH
• mladiství MeSH
• průřezové studie MeSH
• referenční standardy MeSH
• složení těla * MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• mladiství MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

We develop an algorithm for calculating the normal modes of vibration of mechanical systems with constraints, particularly of molecules with rigid bonds and models of rigid molecules, and use it to obtain the harmonic free energy of a crystal. The anharmonic correction is then calculated by the conventional thermodynamic integration over temperature in the NVT ensemble. Attention is paid to finite-size errors, tail corrections, thermostat choice, ergodicity, and other sources of inaccuracies. The calculated free energy of ice XIV modeled by the TIP4P/2005 potential agrees with the previously reported value and is by one order more accurate.

• Publikační typ
• časopisecké články MeSH

BACKGROUND: Negative lifestyle trends are reflected in overweight and obese children, in which their lack of physical activity results in decreased muscle mass. This study aimed to define age- and sex-specific reference curves for body fat mass (BFM), skeletal muscle mass (SMM), fat-free mass (FFM), and percent body fat (%BF) in Czech children. METHODS: Body composition was measured by segmental bioelectrical impedance (BIA, InBody 720). The research sample included 2093 children aged 6-11 years (1008 boys and 1085 girls). Only children whose parents provided informed consent were included. Statistical analysis was performed using SPSS v. 22. The statistical analysis was performed separately by age and sex. Anthropometric data were summarized as means and standard deviation. The percentile curves (P3, P10, P25, P50, P75, P90, and P97) of BFM, FFM, %BF, and SMM were calculated using the gamlss package in R 3.4.2 (R Foundation for Statistical Computing, Vienna, Austria). RESULTS: This study developed age- and gender-specific percentile curves of SMM, FFM, BFM, and %BF for Czech children aged 6-11 years. During childhood, BFM and %BF increased in boys, peaking at approximately 11 years of age. Girls displayed a different pattern of age-related changes in BFM and %BF compared to that in boys. These parameters gradually increased during childhood. This pattern was also observed for SMM and FFM in both sexes. CONCLUSIONS: The purpose of this study was to serve as a reference to improve methods to evaluate body composition in Czech children and for comparison with studies worldwide.

• Klíčová slova
• bioelectrical impedance, body composition, centiles, children,
• Publikační typ
• časopisecké články MeSH

A new large-volume metal reference standard has been developed. The intended use is for calibration of free-release radioactivity measurement systems and is made up of cast iron tubes placed inside a box of the size of a Euro-pallet (80 × 120 cm). The tubes contain certified activity concentrations of (60)Co (0.290 ± 0.006 Bq g(-1)) and (110m)Ag (3.05 ± 0.09 Bq g(-1)) (reference date: 30 September 2013). They were produced using centrifugal casting from a smelt into which (60)Co was first added and then one piece of neutron irradiated silver wire was progressively diluted. The iron castings were machined to the desirable dimensions. The final material consists of 12 iron tubes of 20 cm outer diameter, 17.6 cm inner diameter, 40 cm length/height and 245.9 kg total mass. This paper describes the reference standard and the process of determining the reference activity values.

• MeSH
• lidé MeSH
• monitorování radiace metody   MeSH
• nakládání s odpady normy   MeSH
• radioaktivní odpad analýza   MeSH
• radioizotopy kobaltu analýza   MeSH
• referenční standardy MeSH
• stříbro analýza   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• radioaktivní odpad MeSH
• radioizotopy kobaltu MeSH
• stříbro MeSH

Ethylene glycol monobutyl ether (EGBE), an industrial solvent, is absorbed by the body not only by inhalation but also by dermal absorption (liquid or vapour). EGBE is metabolized to butoxyacetic acid (BAA). Pooled freeze-dried urine candidate reference material (RM) was prepared from urine obtained from persons occupationally exposed to EGBE. This material has the advantage of containing butoxyacetic acid in both the free and conjugated (glutamine and glycine) forms, as found in native urine. In all GC method modifications used, acid hydrolysis was used to release BAA from its conjugated form. The amount of butoxyacetic acid in homogeneity and stability testing was measured by GC after derivatisation with N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide. Detection was by MS in EI mode, in the authors' laboratory. For interlaboratory comparison of the reference material GC methods with MS, FID, and ECD were used. Different extraction solvents (dichloromethane-isopropanol 2:1, ethyl acetate, or dichloromethane) and derivatisation reagents (trimethylsilyldiazomethane, N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide) were used. Using ANOVA (at the statistical level alpha = 0.05) no changes were found in the concentration of butoxyacetic acid during fifteen month isochronous stability testing, or in homogeneity testing. The uncertainty contributions were u (h) = 8.8 mg L(-1) and u (s) = 6.5 mg L(-1). The concentration of butoxyacetic acid in freeze-dried urine RM was evaluated from the results of eight laboratory data sets within an interlaboratory comparison by use of the interactive statistical software IPECA. The contribution to total uncertainty derived from interlaboratory comparison was u (i) = 12.7 mg L(-1). The reference value (c = 273 +/- 33 mg L(-1)) is an unweighted arithmetic average of accepted results. The value is traceable to the pure butoxyacetic acid (98% w/w; Acros Organic #257760010) used as calibrant. The uncertainty given is combined expanded uncertainty derived from the results from interlaboratory comparison, and from homogeneity and stability tests (k = 2). The reference material will be used to verify method performance in the biological monitoring of occupational exposure to EGBE.

• MeSH
• ethylenglykoly metabolismus   MeSH
• glykoláty normy   moč   MeSH
• lidé MeSH
• plynová chromatografie s hmotnostně spektrometrickou detekcí metody   MeSH
• pracovní expozice MeSH
• referenční standardy MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ethylenglykoly MeSH
• glykoláty MeSH
• n-butoxyacetic acid MeSH Prohlížeč
• n-butoxyethanol MeSH Prohlížeč

OBJECTIVES: Cardio-ankle vascular index (CAVI), a parameter of arterial stiffness, has been increasingly used for cardiovascular risk estimation. Currently used CAVI reference values are derived from the Japanese population. It is not clear whether the same reference values can be used in the white population. The aim of the present study was to describe cardiovascular risk factors influencing CAVI and to establish CAVI reference values. METHODS: A total of 2160 individuals randomly selected from the Brno city population aged 25-65 years were examined. Of these, 1347 patients were free from cardiovascular disease, nondiabetic and untreated by antihypertensive or lipid-lowering drugs, forming the reference value population. CAVI was measured using the VaSera VS-1000 device (Fukuda Denshi, Tokyo, Japan). RESULTS: At each blood pressure (BP) level, there was a quadratic association between CAVI and age, except for a linear association in the optimal BP group. Although there was no association between BP and CAVI in younger patients, there was a linear association between CAVI and BP after 40 years of age. Reference values by age and sex were established. In each age group, except for the male 60-65-year group, reference values in our population were lower than in the Japanese one with the difference ranging from -0.29 to 0.21 for men, and from -0.38 to -0.03 for women. CONCLUSION: This is the first study providing CAVI reference values in a random sample of the white population. Our results suggest that the currently used values slightly overestimate CAVI in younger white, possibly underestimating cardiovascular risk.

• MeSH
• běloši MeSH
• dospělí MeSH
• kardiovaskulární nemoci patofyziologie   MeSH
• kotník krevní zásobení   MeSH
• krevní tlak fyziologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• měření krevního tlaku MeSH
• referenční hodnoty MeSH
• rizikové faktory MeSH
• rychlost toku krve MeSH
• senioři MeSH
• tlakový index kotník-paže * MeSH
• věkové faktory MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH

Retinal microcirculation reflects retinal perfusion abnormalities and retinal arterial structural changes at relatively early stages of various cardiovascular diseases. Our objective has been to establish reference values for major functional and structural parameters of retinal microcirculation in a randomly selected urban population sample. A total of 398 randomly selected individuals from an urban population aged 25 to 65 years, resident in Pilsen, Czech Republic, were screened for major cardiovascular risk factors. Retinal microcirculation was assessed using scanning laser Doppler flowmetry (SLDF), with data evaluable in 343 patients. Of this number, complete data were available for 256 individuals free from manifest cardiovascular disease, diabetes and drug treatment for hypertension and/or dyslipidemia, constituting the reference value population. Juxtapapillary retinal capillary blood flow has increased significantly with age whereas vessel and luminal diameters have decreased. No sex differences in retinal microcirculation parameters have been found. Therefore, reference values for retinal microcirculation parameters have been established by age groups. Unattended automated office systolic BP, after adjusting for age, correlated significantly with wall-to-lumen ratio (WLR) and wall thickness (WT). Moreover, after adjusting for age and mean BP, a positive relationship has been found between carotid femoral pulse wave velocity and WT, WLR and wall cross-sectional area, indicating the interaction between micro- and macro-vasculature. In conclusion, our study is the first to provide reference values of retinal microcirculation parameters in a random Caucasian population sample. Our results have shown that, at the population level, the first structural changes in retinal microcirculation are those in lumen diameters. Of note, a close relationship between BP and vascular remodeling of retinal arterioles and between aortic stiffness and WLR of retinal arterioles suggests an interaction between micro- and macro-vasculature.

• Klíčová slova
• Czech post-MONICA study, Juxtapapillary retinal capillary blood flow, Luminal diameter, Retinal vascular resistance, Scanning laser Doppler flowmetry, Vessel diameter, Wall cross-sectional area, Wall thickness, Wall-to-lumen ratio,
• MeSH
• běloši MeSH
• dospělí MeSH
• krevní tlak MeSH
• laser doppler flowmetrie * MeSH
• lidé středního věku MeSH
• lidé MeSH
• mikrocirkulace * MeSH
• prediktivní hodnota testů MeSH
• průřezové studie MeSH
• rasové faktory MeSH
• referenční hodnoty MeSH
• regionální krevní průtok MeSH
• remodelace cév MeSH
• retinální cévy patofyziologie   MeSH
• rychlost toku krve MeSH
• senioři MeSH
• tuhost cévní stěny MeSH
• věkové faktory MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH