Embedded data visualizations have emerged as a powerful narrative medium for conveying complex information within video footage. However, creating such content remains labor-intensive, as existing workflows rely on manual frame-by-frame adjustments to ensure spatial and temporal consistency. To address these challenges, we present ChartBlender, an interactive authoring system designed to streamline the creation, embedding, and automatic synchronization of data visualizations within video scenes. We develop a tracking pipeline that supports both object and camera tracking, ensuring robust alignment of visualizations with dynamic video content. To maintain visual clarity and aesthetic coherence, we also explore the design space of video-suited visualizations and develop a library of customizable templates optimized for video embedding. We evaluated ChartBlender through two controlled experiments and expert interviews with five domain experts. Results show that our system enables accurate synchronization and accelerates the production of data-driven videos.

We present DIQ-MPM, a novel monolithic two-way coupling framework for simulating interactions between solids modeled with the total Lagrangian formulation and Eulerian incompressible fluids using the Material Point Method (MPM). Our approach combines an implicit TLMPM formulation with a mixed velocity-pressure scheme to robustly simulate compressible solids undergoing large deformations, while eliminating numerical fractures. To enable strong fluid-solid coupling without relying on overlapping grids, we introduce a Dual Interface Quadrature (DIQ) mechanism that maps fluid-solid interface information consistently between the current and reference configurations. This allows us to construct a unified sparse pressure-only system via Schur complement, leading to efficient and stable coupling. We also integrate a particle-based contact force model to resolve solid-solid and solid-boundary contacts within implicit TLMPM. Experimental results demonstrate that our method stably captures free-slip coupling, large deformation phenomena, and complex interactions between compressible solids and incompressible fluids.

MOTIVATION: Rapid development in sequencing technologies has dramatically improved our ability to detect genetic variants in human genome. However, current methods have variable sensitivities in detecting different types of genetic variants. One type of such genetic variants that is especially hard to detect is inversions. Analysis of public databases showed that few short inversions have been reported so far. Unlike reads that contain small insertions or deletions, which will be considered through gap alignment, reads carrying short inversions often have poor mapping quality or are unmapped, thus are often not further considered. As a result, the majority of short inversions might have been overlooked and require special algorithms for their detection. RESULTS: Here, we introduce SRinversion, a framework to analyze poorly mapped or unmapped reads by splitting and re-aligning them for the purpose of inversion detection. SRinversion is very sensitive to small inversions and can detect those less than 10 bp in size. We applied SRinversion to both simulated data and high-coverage sequencing data from the 1000 Genomes Project and compared the results with those from Pindel, BreakDancer, DELLY, Gustaf and MID. A better performance of SRinversion was achieved for both datasets for the detection of small inversions. AVAILABILITY AND IMPLEMENTATION: SRinversion is implemented in Perl and is publicly available at http://paed.hku.hk/genome/software/SRinversion/index.html CONTACT: [email protected] information: Supplementary data are available at Bioinformatics online.

BACKGROUND: Y haplogroup analyses are an important component of genealogical reconstruction, population genetic analyses, medical genetics and forensics. These fields are increasingly moving towards use of low-coverage, high throughput sequencing. While there have been methods recently proposed for assignment of Y haplogroups on the basis of high-coverage sequence data, assignment on the basis of low-coverage data remains challenging. RESULTS: We developed a new algorithm, YHap, which uses an imputation framework to jointly predict Y chromosome genotypes and assign Y haplogroups using low coverage population sequence data. We use data from the 1000 genomes project to demonstrate that YHap provides accurate Y haplogroup assignment with less than 2x coverage. CONCLUSIONS: Borrowing information across multiple samples within a population using an imputation framework enables accurate Y haplogroup assignment.