MobilityGraphs: Visual Analysis of Mass Mobility Dynamics via Spatio-Temporal Graphs and Clustering

Learning more about people mobility is an important task for official decision makers and urban planners. Mobility data sets characterize the variation of the presence of people in different places over time as well as movements (or flows) of people between the places. The analysis of mobility data is challenging due to the need to analyze and compare spatial situations (i.e., presence and flows of people at certain time moments) and to gain an understanding of the spatio-temporal changes (variations of situations over time). Traditional flow visualizations usually fail due to massive clutter. Modern approaches offer limited support for investigating the complex variation of the movements over longer time periods

Bioirrigation by Chironomus plumosus: advective flow investigated by particle image velocimetry

Bioirrigation by tube-dwelling macrozoobenthos species causes an advective flow of overlying water through the burrow lumen. Particle image velocimetry (PIV) and color tracer measurements were used to measure flow velocities. The volumetric flow rate was calculated based on measured velocities and visual observation of larval body movements. Investigations were done with Chironomus plumosus (Diptera:Chironomidae) larvae and pupae. During pumping periods, flow velocity was 15.0 ± 10.7 (with color tracers: 13.6 ± 1.7) mm/s and volumetric flow rate was 40 ± 24 (with color tracers: 30.9 ± 3.9) µL/s for larvae. For pupae, these values were only 5.1 ± 0.7 mm/s and 11 ± 1 µL/s, respectively. Pupae conduct no filter feeding, so our results indicate that high volumetric flow rates occur because of filter-feeding. Furthermore, PIV measurements revealed the filtering effect of C. plumosus bioirrigation activity. A projection of the measured volumetric flow rate to Lake Müggelsee in Berlin, Germany (745 4th-instar larvae/m2), resulted in a flow of 1.3 m3 m−2 d−1. A volume equivalent to the water body of the lake is being pumped through the sediment every 4.8 d. This emphasizes the importance of burrow ventilation and filter-feeding for ecosystems

Quantification of pumping rate of Chironomus plumosus larvae in natural burrows

This paper investigates and compares experimentally determined water velocity field above natural macrozoobenthos burrows generated by Chironomus Plumosus larva during their bio-irrigation activity. All experiments were carried out using particle image velocimetry and performed in mesocosms filled with sediment burrowed by larvae, and the water velocity fields near the inlets and outlets of the U-shaped burrows were measured. From water velocity data the average volumetric flow rates between 54.6 and 61.1 mm3/s were calculated. Assuming an average burrow diameter of 2.25 mm, the volumetric flow rates suggest the average flow velocities through burrows during the pumping period between 13.7 and 15.4 mm/s. Two additional interesting phenomena could also be shown by analyzing the flow field generated by the larva. The analysis of the amount of tracers used for visualizations revealed that some of the tracer particles added to the water must have been consumed along their path from the inlet toward the outlet, hinting clearly to the so-called filter-feeding action of C. plumosus. The second phenomenon is due to the form of motion C. plumosus generates. By careful flow visualizations it was found that unlike other organisms such as Urechis caupo that use peristaltic body contractions, C. plumosus worms its body sinusoidally catapulting the fluid far into the overlying water body. This action is of ecological advantage for it avoids generating short oxygen circuits for their respiration and filter feeding

Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus

Background: ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data. Results: Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control. Furthermore, we developed bespoke methods to estimate the width of the protected region resulting from protein-DNA binding and to infer binding positions from ChIP-nexus data. Finally, we applied our peak calling method as well as the two other methods MACE and MACS2 to the available ChIP-nexus data. Conclusions: The Q-nexus software is efficient and easy to use. Novel statistics about duplication rates in consideration of random barcodes are calculated. Our method for the estimation of the width of the protected region yields unbiased signatures that are highly reproducible for biological replicates and at the same time very specific for the respective factors analyzed. As judged by the irreproducible discovery rate (IDR), our peak calling algorithm shows a substantially better reproducibility. An implementation of Q-nexus is available at http://charite.github.io/Q/.This project was supported by the Bundesministerium für Bildung und Forschung (BMBF; project no. 0313911 and 13GW0099) and the European Community’s Seventh Framework Programme (grant agreement no. 602300; SYBIL). Furthermore, we acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’