OmicsON : integration of omics data with molecular networks and statistical procedures

A huge amount of atomized biological data collected in various databases and the need for a description of their relation by theoretical methods causes the development of data integration methods. The omics data analysis by integration of biological knowledge with mathematical procedures implemented in the OmicsON R library is presented in the paper. OmicsON is a tool for the integration of two sets of data: transcriptomics and metabolomics. In the workflow of the library, the functional grouping and statistical analysis are applied. Subgroups among the transcriptomic and metabolomics sets are created based on the biological knowledge stored in Reactome and String databases. It gives the possibility to analyze such sets of data by multivariate statistical procedures like Canonical Correlation Analysis (CCA) or Partial Least Squares (PLS). The integration of metabolomic and transcriptomic data based on the methodology contained in OmicsON helps to easily obtain information on the connection of data from two different sets. This information can significantly help in assessing the relationship between gene expression and metabolite concentrations, which in turn facilitates the biological interpretation of the analyzed process

Automatic method of analysis of OCT images in the assessment of the tooth enamel surface after orthodontic treatment with fixed braces

Introduction: Fixed orthodontic appliances, despite years of research and development, still raise a lot of controversy because of its potentially destructive influence on enamel. Therefore, it is necessary to quantitatively assess the condition and therein the thickness of tooth enamel in order to select the appropriate orthodontic bonding and debonding methodology as well as to assess the quality of enamel after treatment and clean-up procedure in order to choose the most advantageous course of treatment. One of the assessment methods is computed tomography where the measurement of enamel thickness and the 3D reconstruction of image sequences can be performed fully automatically. Material and method: OCT images of 180 teeth were obtained from the Topcon 3D OCT-2000 camera. The images were obtained in vitro by performing sequentially 7 stages of treatment on all the teeth: before any interference into enamel, polishing with orthodontic paste, etching and application of a bonding system, orthodontic bracket bonding, orthodontic bracket removal, cleaning off adhesive residue. A dedicated method for the analysis and processing of images involving median filtering, mathematical morphology, binarization, polynomial approximation and the active contour method has been proposed. Results: The obtained results enable automatic measurement of tooth enamel thickness in 5 seconds using the Core i5 CPU M460 @ 2.5GHz 4GB RAM. For one patient, the proposed method of analysis confirms enamel thickness loss of 80 μm (from 730 ± 165 μm to 650 ± 129 μm) after polishing with paste, enamel thickness loss of 435 μm (from 730 ± 165 μm to 295±55 μm) after etching and bonding resin application, growth of a layer having a thickness of 265 μm (from 295 ± 55 μm to 560 ± 98 μm after etching) which is the adhesive system. After removing an orthodontic bracket, the adhesive residue was 105 μm and after cleaning it off, the enamel thickness was 605 μm. The enamel thickness before and after the whole treatment decreased by about 125 μm. Conclusions: This paper presents an automatic quantitative method for the assessment of tooth enamel thickness. This method has proven to be an effective diagnostic tool that allows evaluation of the surface and cross section of tooth enamel after orthodontic treatment with fixed thin-arched braces and proper selection of the methodology and course of treatment

Ferroelectric liquid crystal for use in a new generation of LCDs

The key to improvements in liquid crystalline displays lies in the continuous synthesis and studies of new kinds of liquid crystalline substances. Among them, ferroelectric compounds are the subject of much attention, due to the potential progresses in switching time, colour depth, and other qualities of liquid crystal displays. In this paper we describe the research of the physical properties of 4-(2-methylbutoxy)phenyl 4-(octyloxy)-benzoate for purposes of its potential application in liquid crystal displays

Low virus to prokaryote ratios in the cold: benthic viruses and prokaryotes in a subpolar marine ecosystem (Hornsund, Svalbard)

The density and spatial distribution of benthic viruses and prokaryotes in relation to biotic and abioticfactors were investigated in sediment cores collected in Hornsund, a permanently cold fjord on the West coast of Svalbard,Norway. The cores were obtained from the mouth of the fjord to the central basin, along a longitudinal transect. Theresults of our analyses showed lower densities of viruses (0.2 × 108 to 5.4 × 108 virus-like particles/g) and lower virus-toprokaryoteratios (0.2-0.6, with the exception of the uppermost layer in the central basin, where the ratio was about 1.2)at the study site than generally found in the temperate areas, despite the relatively high organic matter content in subpolarsediments. Variations in benthic viral and prokaryote abundances along gradients of particle sedimentation rates, phytopigmentconcentrations, and macrobenthic species composition together suggested the influence of particle sedimentationand macrobenthic bioturbation on the abundance and spatial distribution of prokaryotes and viruses in cold habitats. [IntMicrobiol 2013; 16(1):45-52

The HPLC/DAD Fingerprints and Chemometric Analysis of Flavonoid Extracts from the Selected Sage (Salvia) Species

The results of spectrophotometric and HPLC/DAD analysis are discussed, and a comparison is made of selectively extracted flavonoid fractions derived from twenty six sage species belonging to the Salvia genus. The sage samples were harvested in the vegetation seasons 2007, 2008, and 2009. It was a goal of this study to find out which species contain the highest yields of flavonoids (recognized for their free-radical-scavenging activity), as those with the highest yields could be applied in official medicine. It was spectrophotometrically established that the four sage species can be recognized for their highest flavonoid levels, while the HPLC/DAD analysis pointed out to the four other species. The source of the discrepancy between the two evaluation approaches was discussed.Moreover, the HPLC/DAD fingerprints of the flavonoid fraction underwent a chemometric pre-treatment, and then the purified fingerprints were analyzed by means of Principal Component Analysis (PCA) for the differences in the harvesting period. A difference was revealed between the herbs harvested in the 2007 season, and those harvested in 2008 and 2009. The main source of this difference could be the seasonal weather variation and the relatively longest storage period with the plants harvested in 2007

Studies of new antiferroelectric liquid crystal based on quantum-chemical model

Physical properties of new thermotropic antiferroelectric liquid crystal have been studied. Experiments were done by use of complementary methods such as differential scanning calorimetry, polarizing optical microscopy and X-ray powder diffractometry. Acquired data from X-ray powder diffractometry was examined under application of quantum chemical approach. It has been found that compound studied exhibits stable enantiotropic antiferroelectric SmC_{A}^{*} phase in the wide temperature range while ferroelectric phase SmC^{*} is very narrow