KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost.

Long reads that cover more variants per read raise opportunities for accurate haplotype construction, whereas the genotype errors of single nucleotide polymorphisms pose great computational challenges for haplotyping tools. Here we introduce KSNP, an efficient haplotype construction tool based on the de Bruijn graph (DBG). KSNP leverages the ability of DBG in handling high-throughput erroneous reads to tackle the challenges. Compared to other notable tools in this field, KSNP achieves at least 5-fold speedup while producing comparable haplotype results. The time required for assembling human haplotypes is reduced to nearly the data-in time.

Greedy Batch-Based Minimum-Cost Flows for Tracking Multiple Objects.

Minimum-cost flow algorithms have recently achieved state-of-the-art results in multi-object tracking. However, they rely on the whole image sequence as input. When deployed in real-time applications or in distributed settings, these algorithms first operate on short batches of frames and then stitch the results into full trajectories. This decoupled strategy is prone to errors because the batch-based tracking errors may propagate to the final trajectories and cannot be corrected by other batches. In this paper, we propose a greedy batch-based minimum-cost flow approach for tracking multiple objects. Unlike existing approaches that conduct batch-based tracking and stitching sequentially, we optimize consecutive batches jointly so that the tracking results on one batch may benefit the results on the other. Specifically, we apply a generalized minimum-cost flows (MCF) algorithm on each batch and generate a set of conflicting trajectories. These trajectories comprise the ones with high probabilities, but also those with low probabilities potentially missed by detectors and trackers. We then apply the generalized MCF again to obtain the optimal matching between trajectories from consecutive batches. Our proposed approach is simple, effective, and does not require training. We demonstrate the power of our approach on data sets of different scenarios.

Marine phytoplankton motility sensor integrated into a microfluidic chip for high-throughput pollutant toxicity assessment.

A microfluidic chip was designed to assess the toxicity of pollutants in a high-throughput way by using marine phytoplankton motility as a sensor signal. In this chip, multiple gradient generators (CGGs) with diffusible chambers enable large scale of dose-response bioassays to be performed in a simple way. Two mobile marine phytoplankton cells were confined on-chip and stimulated by 8 concentrations (generated by CGG) of Hg, Pb, Cu and phenol singly, as well as Cu and phenol jointly. CASA system was used to characterize motility by motile percentage (%MOT), curvilinear velocity (VCL), average path velocity (VAP) and straight line velocity (VSL). In all cases, dose-dependent inhibitions of motility were observed. In the present system, only 2h was needed to predict EC50. Thus, the developed microfluidic chip device was proved to be useful as a rapid/simple and high-throughput test method in marine pollution toxicity assessment.

Fabrication of high quality and low cost microlenses on a glass substrate by direct printing technique.

The fabrication of high quality and low cost microlenses on a glass substrate using a simple, rapid, and precise direct microplotting technique is shown in this paper. The fabrication method is based on the use of a microplotter system, which is significantly different from the existing inkjet, roll-to-roll printing, and reactive ion etching technology and could work with higher viscosity materials. By optimizing the parameters of voltage, dispense time, and concentration of the polymer solution, high quality microlenses with a diameter of 20 µm could be obtained. The geometrical and optical characteristics of the microlenses are analyzed by measurement of the surface profile and the imaging properties in the near-field and far-field zones as well as the diffraction pattern. We think that the fabricated microlenses could be attractive for enhancing the light extraction efficiency of light emitting diodes.

A rapid, straightforward, and print house compatible mass fabrication method for integrating 3D paper-based microfluidics.

Three-dimensional (3D) paper-based microfluidics, which is featured with high performance and speedy determination, promise to carry out multistep sample pretreatment and orderly chemical reaction, which have been used for medical diagnosis, cell culture, environment determination, and so on with broad market prospect. However, there are some drawbacks in the existing fabrication methods for 3D paper-based microfluidics, such as, cumbersome and time-consuming device assembly; expensive and difficult process for manufacture; contamination caused by organic reagents from their fabrication process. Here, we present a simple printing-bookbinding method for mass fabricating 3D paper-based microfluidics. This approach involves two main steps: (i) wax-printing, (ii) bookbinding. We tested the delivery capability, diffusion rate, homogeneity and demonstrated the applicability of the device to chemical analysis by nitrite colorimetric assays. The described method is rapid (<30 s), cheap, easy to manipulate, and compatible with the flat stitching method that is common in a print house, making itself an ideal scheme for large-scale production of 3D paper-based microfluidics.