Jabba: hybrid error correction for long sequencing reads using maximal exact matches

Third generation sequencing platforms produce longer reads with higher error rates than second generation sequencing technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. Error correction methods in which accurate short reads are used to correct noisy long reads appear to be attractive to generate high-quality long reads. Methods that align short reads to long reads do not optimally use the information contained in the second generation data, and suffer from large runtimes. Recently, a new hybrid error correcting method has been proposed, where the second generation data is first assembled into a de Bruijn graph, on which the long reads are then aligned. In this context we present Jabba, a hybrid method to correct long third generation reads by mapping them on a corrected de Bruijn graph that was constructed from second generation data. Unique to our method is that this mapping is constructed with a seed and extend methodology, using maximal exact matches as seeds. In addition to benchmark results, certain theoretical results concerning the possibilities and limitations of the use of maximal exact matches in the context of third generation reads are presented

Examining the potential of floating car data for dynamic traffic management

Traditional traffic monitoring systems are mostly based on road side equipment (RSE) measuring traffic conditions throughout the day. With more and more GPS-enabled connected devices, floating car data (FCD) has become an interesting source of traffic information, requiring only a fraction of the RSE infrastructure investment. While FCD is commonly used to derive historic travel times on individual roads and to evaluate other traffic data and algorithms, it could also be used in traffic management systems directly. However, as live systems only capture a small percentage of all traffic, its use in live operating systems needs to be examined. Here, the authors investigate the potential of FCD to be used as input data for live automated traffic management systems. The FCD in this study is collected by a live country-wide FCD system in the Netherlands covering 6-8% of all vehicles. The (anonymised) data is first compared to available road side measurements to show the current quality of FCD. It is then used in a dynamic speed management system and compared to the installed system on the studied highway. Results indicate the FCD set-up can approximate the installed system, showing the feasibility of a live system

Modeling real-world vehicle routing problems with dependencies

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Alzheimer's disease and glaucoma: Is there a causal relationship?

Evidence of a link between Alzheimer's disease (AD) and glaucoma has emerged from studies showing that patients with AD may have a significantly increased rate of glaucoma occurrence. In addition, it has been reported that patients with AD exhibit optic nerve degeneration and loss of retinal ganglion cells. In spite of intensive research, the clinical and genetic relationships between AD and glaucoma remain obscure. It is unclear whether the clinical correlation between the two diseases might be due to shared risk factors or the influence of one disorder on the other. Interestingly, certain observations may provide a clue towards a better understanding of the high rate of comorbidity reported between AD and glaucoma. In this article, we hypothesise that there may be a causal relationship between AD and glaucoma that may be explained by decreased cerebrospinal fluid pressure (CSFP) in patients with AD. A very recent study reported the intriguing new observation that mean CSFP was 33% lower in subjects with primary open-angle glaucoma than that of non-glaucomatous controls. It was noted that this observation supports the concept that an abnormal high trans-lamina cribrosa pressure difference, whether the result of elevated intraocular pressure, reduced CSFP, or both, plays an important role in glaucomatous optic nerve damage. Interestingly, it was also reported that a substantial proportion of AD patients have very low CSFP. Therefore, we hypothesise that an abnormal high trans-lamina cribrosa pressure difference may explain why patients with AD have a greater risk for developing glaucoma