On using longer RNA-seq reads to improve transcript prediction accuracy

Over the past decade, sequencing read length has increased from tens to hundreds and then to thousands of bases. Current cDNA synthesis methods prevent RNA-seq reads from being long enough to entirely capture all the RNA transcripts, but long reads can still provide connectivity information on chains of multiple exons that are included in transcripts. We demonstrate that exploiting full connectivity information leads to significantly higher prediction accuracy, as measured by the F-score. For this purpose we implemented the solution to the Minimum Path Cover with Subpath Constraints problem introduced in (Rizzi et al., 2014), which is an extension of the classical Minimum Path Cover problem and was shown solvable by min-cost flows. We show that, under hypothetical conditions of perfect sequencing, our approach is able to use long reads more effectively than two state-of-the-art tools, StringTie and FlipFlop. Even in this setting the problem is not trivial, and errors in the underlying flow graph introduced by sequencing and alignment errors complicate the problem further. As such our work also demonstrates the need for a development of a good spliced read aligner for long reads. Our proof-of-concept implementation is available at http://www.cs.helsinki.fi/en/gsa/traphlor. Copyright \ua9 2016 by SCITEPRESS - Science and Technology Publications, Lda. All rights reserved

The impact of electronic gaming on upper limb neuropathies among esports athletes

Background The authors aimed to explore carpal tunnel syndrome (CTS) among electronic sports (esports) athletes, to compare hand symptoms and their severity between esports athletes and the control group and within the esports athletes, and to study the relationship between esports athletes’ variables. Material and Methods A cross-sectional survey study via telephone with systematic randomized approach was used for esport athletes sampling. Control group were non-esports athletes who do not use computer for prolonged duration. The survey consisted of sports athletes’ characteristics, hand symptoms and functions, and the Boston Carpal Tunnel Questionnaire (BCTQ). The unpaired student’s t-test, Mann-Whitney U test, and χ2 test were utilised for statistical comparison, with p < 0.05. Pearson’s and Spearman’s correlation coefficient tests were used for relationship analyses. Results Eligible participants were 198 out of 229. Compared to control group, esport athletes reported more CTS (p = 0.01), and radiated pain and numbness in their hands (p = 0.05). Males complained of hand symptoms (p < 0.01) and its radiation (p < 0.01) more than females among esports athletes. Higher BCTQ Symptom Severity Scale (BCTQ-SSS) scores were reported for esports athletes who had been playing esports for prolonged periods compared to those who had playing recently (p = 0.003), with a moderate positive correlation (+0.59, p = 0.004). A significant moderate positive correlation was reported for BCTQ Functional Severity Symptoms (BCTQ-FSS) scores in terms of hours of playing (+0.44, p = 0.04). Esports athletes who used armrests and a PC with a controller for gaming reported less hand symptoms and had milder BCTQ scores than those who used a PC with a keyboard/mouse. Generally, esports athletes spend 5–10 h/day on gaming. Conclusions Esports athletes might be at risk of developing upper-extremity nerve compression and CTS. Prolonged playing, hours of playing, type of esports device, and using armrests are possible risk factors