High-throughput sequencing technologies, such as the Illumina Hi-seq, are powerful new tools for investigating a wide range of biological and medical problems. Massive and complex data sets produced by the sequencers create a need for development of statistical and computational methods that can tackle the analysis and management of data. The data normalization is one of the most crucial steps of data processing and this process must be carefully considered as it has a profound effect on the results of the analysis. In this work, we focus on a comprehensive comparison of five normalization methods related to sequencing depth, widely used for transcriptome sequencing (RNA-seq) data, and their impact on the results of gene expression analysis. Based on this study, we suggest a universal workflow that can be applied for the selection of the optimal normalization procedure for any particular data set. The described workflow includes calculation of the bias and variance values for the control genes, sensitivity and specificity of the methods, and classification errors as well as generation of the diagnostic plots. Combining the above information facilitates the selection of the most appropriate normalization method for the studied data sets and determines which methods can be used interchangeably.

BackgroundDifferentiated thyroid carcinoma (DTC) originates from thyroid follicular epithelial cells and belongs to a group of slowly progressing tumors with a relatively good prognosis. However, recurrences and metastases are a serious problem in advanced stages. Furthermore, progression from a well differentiated thyroid carcinoma to an aggressive anaplastic one is possible.The majority of differentiated thyroid carcinomas are sporadic but a few alleles increasing the cancer risk are known. One of them is the c.470 T > C (p.I157T, rs17879961) missense substitution in the CHEK2 gene.Aim of the studyThe aim of this study was to investigate whether this specific CHEK2 alteration, c.470 T > C, predisposes the Great Poland (Wielkopolska) population to thyroid cancer.Methods602 differentiated thyroid carcinoma patients and 829 controls randomly selected from population were genotyped for the presence of the c.470C allele using pyrosequencing. Hardy-Weinberg Equilibrium (HWE) was tested for both groups by chi-square distribution and Fisher’s exact test. The odds ratios (ORs), 95% confidence intervals (CIs), and p-values were calculated using the R software.ResultsThe results of genotyping showed the presence of the c.470C allele in 51 patients with a frequency of 4.49%, while in a controls in 42 patients with a frequency of 2.53%. We demonstrated that in the Great Poland population the c.470C CHEK2 variant increases the risk of developing differentiated thyroid cancer almost twice (OR = 1.81, p = 0.004). The risk of papillary thyroid carcinoma in female patients homozygous for the c.470C allele was shown to increase almost 13-fold (OR = 12.81, p = 0.019).ConclusionsIdentification of c.470C CHEK2 gene variant ought to be taken into account by healthcare policymakers. Future well-designed and larger population studies are of great value in confirming these findings. Moreover, a combination of genetic factors together with environmental exposures should also be considered.Electronic supplementary materialThe online version of this article (doi:10.1186/s13053-015-0030-5) contains supplementary material, which is available to authorized users.

The cream with the aqueous extract from leaf of five-leaf serratula proved to be an effective and safe preparation for lightening skin discolorations (66.67 % of the female patients in the study group).

SummaryThe main estimation and hypothesis testing procedures are presented for experiments conducted in row-column designs of a certain desirable type. It is shown that, under appropriate randomization, these experiments have the convenient orthogonal block structure. Due to this property, the analysis of experimental data can be performed in a comparatively simple way. Relevant simplifying procedures are indicated. The main advantage of the presented methodology concerns the analysis of variance and related hypothesis testing procedures. Under the adopted approach one can perform these analytical methods directly, not by combining results from analyses based on some stratum submodels. Practical application of the presented theory is illustrated by four examples of real experiments in the relevant row-column designs. The present paper is the third in the projected series of publications concerning the analysis of experiments with orthogonal block structure.

Temperature strongly influences the growth of maize, particularly in the early growth stages. The exogenous application of some amino acids has been proven to have a positive effect on plant growth and development under stressful conditions. The objective of the study was to evaluate the response of maize that was grown under an optimal and stress (fluctuating) temperature to L-Arginine (L-Arg) and Glycine (Gly) application. In the study, it was assumed that the exogenously applied amino acids would alleviate the adverse effects of temperature stress on the maize height, as well as on the biomass of shoots and roots. Ten concentrations of each amino acid from 0.006 mM to 9.0 mM were tested under constant temperature conditions 20–22 °C/23–25 °C (night/day) an fluctuating stress of rising and dropping temperatures between 12–15 °C (night) and 30–38 °C (day). The amino acids were applied to the crop at growth stages V3–V4. In plants that were obtained from seeds pre-treated with L-Arg and Gly, the amino acids increased both the length of radicles and the number of lateral roots. A large discrepancy between the effects of the two amino acids was observed after foliar application. Under optimal thermal conditions, L-Arg increased the mass of shoots and roots by 55–59%. Under stress conditions, root mass was increased even by 100% when compared to the control plants. The best results were recorded at concentrations of 6 mM and 3 mM. Plants that were treated with Gly concentrations generally reached the height of untreated plants or less. It was shown that Gly applied at concentrations of 0.2 mM to 3 mM has a negative effect on the fresh mass of the crop.

Textbooks have played the leading role in academic education for centuries and their form has evolved, adapting to the needs of students, teachers and technological possibilities. Advances in technology have caused educators to look for new sources of knowledge development, which students could use inside and outside the classroom. Today’s sophisticated learning tools range from virtual environments to interactive multimedia resources, which can be called e-textbooks. Different types of new educational materials that go beyond printed books are now used to support the academic curriculum, with the most interesting ones exemplified in this article to show their value in medical and life sciences education. Certain interesting attempts by Polish publishers at applying technology to support both self-paced and tutor-paced student learning in the medical profession and related areas are presented. The data was collected through a review of literature, discussions with e-learning specialists and medical students, as well as an analysis of examples of good practices. The article also discusses the results of a countrywide survey on the use of e-textbooks to enhance medical education. The research investigates the targeted academic staff’s attitudes towards the use of e-textbooks, the limitations of their implementation, and the character of e-resources currently used by Polish higher education medical institutions.

No abstract

Peanut stunt virus (PSV) is a widespread pathogen infecting legumes. The PSV strains are classified into four subgroups and some are defined by the association of satellite RNAs (satRNAs). In the case of PSV, the presence of satRNAs alters the symptoms of disease in infected plants. In this study, we elucidated the plant response to PSV-G strain, which occurs in natural conditions without satRNA. However, it was found that it might easily acquire satRNA, which exacerbated pathogenesis in Nicotiana benthamiana. To explain the mechanisms underlying PSV infection and symptoms exacerbation caused by satRNA, we carried out transcriptome profiling of N. benthamiana challenged by PSV-G and satRNA using species-specific microarrays. Co-infection of plants with PSV-G + satRNA increased the number of identified differentially expressed genes (DEGs) compared with the number identified in PSV-G-infected plants. In both treatments, the majority of up-regulated DEGs were engaged in translation, ribosome biogenesis, RNA metabolism, and response to stimuli, while the down-regulated DEGs were required for photosynthesis. The presence of satRNA in PSV-G-infected plants caused different trends in expression of DEGs associated with phosphorylation, ATP binding, and plasma membrane.