deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns

Motivation: High-throughput sequencing methods allow whole transcriptomes to be sequenced fast and cost-effectively. Short RNA sequencing provides not only quantitative expression data but also an opportunity to identify novel coding and non-coding RNAs. Many long transcripts undergo post-transcriptional processing that generates short RNA sequence fragments. Mapped back to a reference genome, they form distinctive patterns that convey information on both the structure of the parent transcript and the modalities of its processing. The miR-miR* pattern from microRNA precursors is the best-known, but by no means singular, example

RIsearch:fast RNA-RNA interaction search using a simplified nearest-neighbor energy model

Motivation: Regulatory, non-coding RNAs often function by forming a duplex with other RNAs. It is therefore of interest to predict putative RNA–RNA duplexes in silico on a genome-wide scale. Current computational methods for predicting these interactions range from fast complementary-based searches to those that take intramolecular binding into account. Together these methods constitute a trade-off between speed and accuracy, while leaving room for improvement within the context of genome-wide screens. A fast pre-filtering of putative duplexes would therefore be desirable. Results: We present RIsearch, an implementation of a simplified Turner energy model for fast computation of hybridization, which significantly reduces runtime while maintaining accuracy. Its time complexity for sequences of lengths m and n is [Image: see text] with a much smaller pre-factor than other tools. We show that this energy model is an accurate approximation of the full energy model for near-complementary RNA–RNA duplexes. RIsearch uses a Smith–Waterman-like algorithm using a dinucleotide scoring matrix which approximates the Turner nearest-neighbor energies. We show in benchmarks that we achieve a speed improvement of at least 2.4× compared with RNAplex, the currently fastest method for searching near-complementary regions. RIsearch shows a prediction accuracy similar to RNAplex on two datasets of known bacterial short RNA (sRNA)–messenger RNA (mRNA) and eukaryotic microRNA (miRNA)–mRNA interactions. Using RIsearch as a pre-filter in genome-wide screens reduces the number of binding site candidates reported by miRNA target prediction programs, such as TargetScanS and miRanda, by up to 70%. Likewise, substantial filtering was performed on bacterial RNA–RNA interaction data. Availability: The source code for RIsearch is available at: http://rth.dk/resources/risearch. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Relationship Between Prospective Teachers' Deontic Justice Attitudes And Academic Dishonesty Tendencies

The aim of the study was to determine the relationsip between deontic justice attitudes among prospective teachers and their tendencies towards academic dishonesty. Participants in the study were 403 university students attending different departments of the Education Faculty of the Hacettepe University, a state university in the Central Anatolia Region of Turkey. The sample was determined by means of a stratified sampling technique, and students were chosen randomly from different departments. Attitudes towards deontic justice and tendencies towards academic dishonesty among the participants were stratified in terms of gender and students' affiliation to a specific department of education. The findings suggested that female students and participants from the English Language Education Department had the highest deontic justice attitudes; male students and participants from the Physical Education and Sports Department had the highest tendencies towards academic dishonesty. A low, negative and statistically significant relationship between deontic justice attitudes and academic dishonesty tendencies exists.WoSScopu

School Engagement As A Predictor Of Burnout In University Students

The aim of this study is to examine the relationship between school engagement and burnout of university students. The research employs relational survey model and the participants are 472 students studying at a public university in Ankara in Turkey. The data collection tools were “The Maslach Burnout Inventory-Student Survey” and “University Student Engagement Inventory”. The findings of the research show that the relationship between university students' school engagement and emotional exhaustion, cynicism and efficacy subscales of burnout levels was moderate whereas students' school engagement is found to be a significant predictor of all subscales burnout. The findings of the research showed that the level of the relationship between university students' school engagement and subscales of burnout (exhaustion, cynicism, academic efficacy) was moderate and students' school engagement is found to be a significant predictor of all subscales of burnout.Wo

A Tribute to the Hazelnut Plant (Corylus spp.) - the Multiple Uses of Nature's Magnificent Gifts

8th International Congress on Hazelnut -- MAR 19-22, 2012 -- Temuco, CHILEOzman-Sullivan, Sebahat/0000-0001-5240-8110WOS: 000357660300051The hazelnuts (Corylus spp.) are some of the most useful plants known to humanity. Corylus avellana, the most common species, is naturally distributed from Britain to Russia, from Scandinavia to the Mediterranean, and across to Iran in the east. It is now cultivated in Europe, Asia, North America, South America, Africa and Australia. Hazelnuts are supremely adapted to a wide range of soil types and environments. Their nuts and wood have been used for at least 9,000 years and mythologies have developed around these revered plants. Wild species have been selectively bred to produce edible nuts but almost every part of the plant, including bark, husks, leaves, nuts, roots, shells and wood, is utilized. Uses include aesthetics, alcoholic beverages, animal husbandry, biofuels, carbon sequestration, craftwork, farm implements, fertilizer, food, food production, health products, industrial chemicals and products, oils, pharmaceuticals and wildlife habitat.Int Soc Horticultural Sc