RNA interference is a powerful tool for gene silencing, which is mediated by introducing siRNA. In the present study, statistical analyses of published siRNA selection criteria, the interpretation of some criteria and systematic searching for new criteria have been carried out for CGB siRNA and siRecords databases. The results of the analyses are as follows: (i) Our study supports the two-state model of the RNA-induced silencing complex (RISC). (ii) Stable 5'-S ends of a siRNA sequence, higher stability of the whole siRNA, and low breaking energy of siRNA duplex occurs in effective siRNA sequences. Also low internal stability of the 5'-AS terminus is preferred. (iii) Secondary structure can be successfully used as an RNAi selection criterion. (iv) Several published sequence criteria have been confirmed and also new criteria have been developed. (v) Also a Target Patterns criterion, which is comparable or better than the best known criteria, has been created.

• MeSH
• interpretace statistických dat MeSH
• malá interferující RNA genetika   MeSH
• modely genetické * MeSH
• molekulární sekvence - údaje MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza RNA metody   MeSH
• statistické modely MeSH
• umlčování genů * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• malá interferující RNA MeSH

Multivariate statistical comparisons of two-dimensional protein (2-D) gel patterns were used for the first time to define stages of a biological developmental system. The differentiating procaryote, Streptomyces coelicolor, was radiolabeled in liquid cultures at 16 intervals during development, and radioactive proteins were separated and quantified on 2-D gels. Cluster, principal component, and correlation analyses classified these gel patterns into four distinct groups, each reflecting a pattern of gene expression specific for a stage of development. These studies focused our attention on a phase of arrested growth as a key regulatory transition leading to secondary metabolism and a phase of renewed growth. Proteins whose synthesis was switched on or off during the "transitional" phase (some 21 and 18, respectively) were identified and will be the focus of future studies designed to identify their physiological or regulatory function.

• MeSH
• 2D gelová elektroforéza statistika a číselné údaje   MeSH
• algoritmy MeSH
• bakteriální proteiny genetika   izolace a purifikace   MeSH
• databáze faktografické MeSH
• genom bakteriální MeSH
• interpretace statistických dat MeSH
• multivariační analýza MeSH
• peptidové mapování statistika a číselné údaje   MeSH
• prokaryotické buňky MeSH
• shluková analýza MeSH
• Streptomyces chemie   genetika   růst a vývoj   MeSH
• vývojová regulace genové exprese MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH

Results of meta-analyses are regarded as the highest level of evidence. A statistically non-significant effect size from a meta-analysis is typically considered true negative even in the presence of a statistically significant signal in individual studies, presumed to be false positive. Here we provide examples from neuroimaging, genetics and psychopharmacology of why meta-analyses may frequently yield false negative results from true positive findings. This may happen in situations when individual studies report findings in opposing directions, the sum of which yields a non-significant overall effect size. Such non-significant meta-analyses, which show statistical heterogeneity and include studies with opposing effect sizes do not provide an accurate estimate of the overall effect and may have lower heuristic value than individual studies. Over reliance on such meta-analyses may falsely identify certain potentially fruitful research avenues as blind alleys.

• Klíčová slova
• False negative, Meta-analyses, Statistical heterogeneity,
• MeSH
• biomedicínský výzkum metody   MeSH
• genetické asociační studie MeSH
• lidé MeSH
• medicína založená na důkazech * MeSH
• metaanalýza jako téma * MeSH
• neurozobrazování MeSH
• psychofarmakologie metody   MeSH
• reprodukovatelnost výsledků MeSH
• statistické modely * MeSH
• velikost vzorku MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Enhancing plant productivity and mitigating the impact of environmental stressors require a thorough understanding of phytomonitoring and physiological features indicative of plant health. This study delves into the response of cucumber plants to phosphorus deficiency employing diverse tools to identify key indicators and unravel the underlying mechanisms. Under phosphorus deficiency, a rapid response in older leaves was observed through the analysis of chlorophyll and carotenoid content. Molecular-level changes in photosynthetic performance were found to be age-dependent, as revealed by multidimensional statistical methods, highlighting the interconnectedness of examined features with the experimental setup timing. This can assist in understanding the long-term fluctuations in traits linked to phosphorus deficiency, facilitating early detection of stress.

• Klíčová slova
• chlorophyll fluorescence, confocal microscopy, greenhouse cucumber, leaf area index, multivariate statistical analyses, photosynthetic pigment,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Infection with feline immunodeficiency virus (FIV) causes an immunosuppressive disease whose consequences are less severe if cats are co-infected with an attenuated FIV strain (PLV). We use virus diversity measurements, which reflect replication ability and the virus response to various conditions, to test whether diversity of virulent FIV in lymphoid tissues is altered in the presence of PLV. Our data consisted of the 3' half of the FIV genome from three tissues of animals infected with FIV alone, or with FIV and PLV, sequenced by 454 technology. RESULTS: Since rare variants dominate virus populations, we had to carefully distinguish sequence variation from errors due to experimental protocols and sequencing. We considered an exponential-normal convolution model used for background correction of microarray data, and modified it to formulate an error correction approach for minor allele frequencies derived from high-throughput sequencing. Similar to accounting for over-dispersion in counts, this accounts for error-inflated variability in frequencies - and quite effectively reproduces empirically observed distributions. After obtaining error-corrected minor allele frequencies, we applied ANalysis Of VAriance (ANOVA) based on a linear mixed model and found that conserved sites and transition frequencies in FIV genes differ among tissues of dual and single infected cats. Furthermore, analysis of minor allele frequencies at individual FIV genome sites revealed 242 sites significantly affected by infection status (dual vs. single) or infection status by tissue interaction. All together, our results demonstrated a decrease in FIV diversity in bone marrow in the presence of PLV. Importantly, these effects were weakened or undetectable when error correction was performed with other approaches (thresholding of minor allele frequencies; probabilistic clustering of reads). We also queried the data for cytidine deaminase activity on the viral genome, which causes an asymmetric increase in G to A substitutions, but found no evidence for this host defense strategy. CONCLUSIONS: Our error correction approach for minor allele frequencies (more sensitive and computationally efficient than other algorithms) and our statistical treatment of variation (ANOVA) were critical for effective use of high-throughput sequencing data in understanding viral diversity. We found that co-infection with PLV shifts FIV diversity from bone marrow to lymph node and spleen.

• MeSH
• algoritmy MeSH
• DNA virů genetika   MeSH
• interpretace statistických dat * MeSH
• kočičí AIDS genetika   imunologie   virologie   MeSH
• kočky MeSH
• nemoci koček genetika   imunologie   přenos   virologie   MeSH
• statistické modely * MeSH
• virus kočičí imunodeficience klasifikace   genetika   patogenita   MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• zvířata MeSH
• Check Tag
• kočky MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• DNA virů MeSH

Structured and complex data can be found in many applications in research and development, and also in industrial practice. We developed a methodology for describing the structured data complexity and applied it in development and industrial practice. The methodology uses fractal dimension together with statistical tools and with software modification is able to analyse data in a form of sequence (signals, surface roughness), 2D images, and dividing lines. The methodology had not been tested for a relatively large collection of data. For this reason, samples with structured surfaces produced with different technologies and properties were measured and evaluated with many types of parameters. The paper intends to analyse data measured by a surface roughness tester. The methodology shown compares standard and nonstandard parameters, searches the optimal parameters for a complete analysis, and specifies the sensitivity to directionality of samples for these types of surfaces. The text presents application of fractal geometry (fractal dimension) for complex surface analysis in combination with standard roughness parameters (statistical tool).

• MeSH
• fraktály * MeSH
• interpretace statistických dat MeSH
• povrchové vlastnosti MeSH
• software trendy   MeSH
• testování materiálů normy   statistika a číselné údaje   MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH

This paper presents a statistical model for estimating probability, which states that a quality of radon measurements using the electret ion chamber system RM-1 will be accurate. The quality of the electret measurement was modelled as a ratio between the reference radon concentration and values measured under real conditions with varied levels of indoor radon concentration and microclimate indoor conditions. It was stated that the accuracy tolerance of measured values is 20 % of the given reference value. To estimate the uncertainty of the statistical model, the exact confidence limits for the estimated probabilities are computed. The statistical model was confirmed by an independent set of measurements. Moreover, the effect of absolute humidity on the quality estimation of electret detectors are also statistically analysed and discussed. The results of the statistical model confirm that the electret system is robust and suitable for estimation of radon concentration.

• MeSH
• design vybavení MeSH
• elektřina * MeSH
• lidé MeSH
• monitorování radiace přístrojové vybavení   MeSH
• radioaktivní látky znečišťující vzduch analýza   MeSH
• radon analýza   MeSH
• statistické modely * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• radioaktivní látky znečišťující vzduch MeSH
• radon MeSH

Temperature drives development in insects and other ectotherms because their metabolic rate and growth depends directly on thermal conditions. However, relative durations of successive ontogenetic stages often remain nearly constant across a substantial range of temperatures. This pattern, termed 'developmental rate isomorphy' (DRI) in insects, appears to be widespread and reported departures from DRI are generally very small. We show that these conclusions may be due to the caveats hidden in the statistical methods currently used to study DRI. Because the DRI concept is inherently based on proportional data, we propose that Dirichlet regression applied to individual-level data is an appropriate statistical method to critically assess DRI. As a case study we analyze data on five aquatic and four terrestrial insect species. We find that results obtained by Dirichlet regression are consistent with DRI violation in at least eight of the studied species, although standard analysis detects significant departure from DRI in only four of them. Moreover, the departures from DRI detected by Dirichlet regression are consistently much larger than previously reported. The proposed framework can also be used to infer whether observed departures from DRI reflect life history adaptations to size- or stage-dependent effects of varying temperature. Our results indicate that the concept of DRI in insects and other ectotherms should be critically re-evaluated and put in a wider context, including the concept of 'equiproportional development' developed for copepods.

• MeSH
• biologické modely * MeSH
• hmyz růst a vývoj   MeSH
• stadia vývoje * MeSH
• statistické modely * MeSH
• teplota * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

To contribute to the understanding of noncovalent binding of halogenated molecules with biological activity, electrostatic potential (ESP) maps of more than 2500 compounds were thoroughly analysed. A peculiar region of positive ESP, called the σ-hole, is a concept of central importance for halogen bonding. We aim to simplify the view on σ-holes and to provide general trends in organic drug-like molecules. The results are in fair agreement with crystallographic surveys of small molecules as well as biomolecular complexes and may help to improve the intuition of chemists when dealing with halogenated compounds.

• MeSH
• halogeny chemie   MeSH
• interpretace statistických dat * MeSH
• statická elektřina MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• halogeny MeSH

The thermo-physiological and tactile properties of socks were analysed by using hybrid yarns which were made by Polyethylene (PE) fibre with different fibres in variable ratios, using full-factorial experimental design. Socks samples were designed using hybrid yarns made with three blend ratios of polyethylene filament with cotton (Co), polyester (PET), polypropylene (PP), modal (Mo) and viscose (Vis) spun yarns. Statistical analysis was carried out according to response surface regression analysis (RSM). Among various analytical tools, RSM is adopted for prediction of multiple responses and response optimizer (RO) was used to optimize the thermo-physiological and tactile comfort i.e. softness and smoothness properties of socks by using the desirability function approach. It was inferred that the combination of cotton with polyethylene was most influencing for thermal conductivity and softness properties. Experimental validation confirmed that predicted variables can be used to design knitted socks fabric with desired thermo-physiological and tactile comfort properties.

• Klíčová slova
• Comfort, Hybrid yarn, Polyethylene (PE), Socks, Summer, Thermal conductivity,
• MeSH
• hmat * MeSH
• lidé MeSH
• odívání * MeSH
• polyethylen chemie   MeSH
• polypropyleny chemie   MeSH
• sporty * MeSH
• statistické modely * MeSH
• tepelná vodivost MeSH
• textilie * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• polyethylen MeSH
• polypropyleny MeSH