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  1. Free, publicly-accessible full text available January 1, 2025
  2. Abstract Motivation

    Emerging omics technologies have introduced a two-way grouping structure in multiple testing, as seen in single-cell omics data, where the features can be grouped by either genes or cell types. Traditional multiple testing methods have limited ability to exploit such two-way grouping structure, leading to potential power loss.

    Results

    We propose a new 2D Group Benjamini–Hochberg (2dGBH) procedure to harness the two-way grouping structure in omics data, extending the traditional one-way adaptive GBH procedure. Using both simulated and real datasets, we show that 2dGBH effectively controls the false discovery rate across biologically relevant settings, and it is more powerful than the BH or q-value procedure and more robust than the one-way adaptive GBH procedure.

    Availability and implementation

    2dGBH is available as an R package at: https://github.com/chloelulu/tdGBH. The analysis code and data are available at: https://github.com/chloelulu/tdGBH-paper.

     
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  3. Unmanned aerial vehicles or drones are widely used or proposed to carry out various tasks in low-altitude airspace. To safely integrate drone traffic into congested airspace, the current concept of operations for drone traffic management will reserve a static traffic volume for the whole planned trajectory, which is safe but inefficient. In this paper, we propose a dynamic traffic volume reservation method for the drone traffic management system based on a multiscale A* algorithm. The planning airspace is represented as a multiresolution grid world, where the resolution will be coarse for the area on the far side. Therefore, each drone only needs to reserve a temporary traffic volume along the finest flight path in its local area, which helps release the airspace back to others. Moreover, the multiscale A* can run nearly in real-time due to a much smaller search space, which enables dynamically rolling planning to consider updated information. To handle the infeasible corner cases of the multiscale algorithm, a hybrid strategy is further developed, which can maintain a similar optimal level to the classic A* algorithm while still running nearly in real-time. The presented numerical results support the advantages of the proposed approach. 
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    Free, publicly-accessible full text available October 1, 2024
  4. Advanced Air Mobility (AAM) using electrical vertical take-off and landing (eVTOL) aircraft is an emerging way of air transportation within metropolitan areas. A key challenge for the success of AAM is how to manage large-scale flight operations with safety guarantees in high-density, dynamic, and uncertain airspace environments in real time. To address these challenges, we introduce the concept of a data-driven probabilistic geofence, which can guarantee that the probability of potential conflicts between eVTOL aircraft is bounded under data-driven uncertainties. To evaluate the probabilistic geofences online, Kernel Density Estimation (KDE) based on Fast Fourier Transform (FFT) is customized to model data-driven uncertainties. Based on the FFT-KDE values from data-driven uncertainties, we introduce an optimization framework of Integer Linear Programming (ILP) to find a parallelogram box to approximate the data-driven probabilistic geofence. To overcome the computational burden of ILP, an efficient heuristic algorithm is further developed. Numerical results demonstrate the feasibility and efficiency of the proposed algorithms. 
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    Free, publicly-accessible full text available September 15, 2024
  5. Abstract Background

    Single-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq data analysis, cell type annotation is an essential but challenging step. In the past few years, several annotation tools have been developed. These methods require either labeled training/reference datasets, which are not always available, or a list of predefined cell subset markers, which are subject to biases. Thus, a user-friendly and precise annotation tool is still critically needed.

    Results

    We curated a comprehensive cell marker database named scMayoMapDatabase and developed a companion R package scMayoMap, an easy-to-use single-cell annotation tool, to provide fast and accurate cell type annotation. The effectiveness of scMayoMap was demonstrated in 48 independent scRNA-seq datasets across different platforms and tissues. Additionally, the scMayoMapDatabase can be integrated with other tools and further improve their performance.

    Conclusions

    scMayoMap and scMayoMapDatabase will help investigators to define the cell types in their scRNA-seq data in a streamlined and user-friendly way.

     
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  6. We consider the rate-limited quantum-to-classical optimal transport in terms of output-constrained rate-distortion coding for discrete quantum measurement systems with limited classical common randomness. The main coding theorem provides the achievable rate region of a lossy measurement source coding for an exact construction of the destination distribution (or the equivalent quantum state) while maintaining a threshold of distortion from the source state according to a generally defined distortion observable. The constraint on the output space fixes the output distribution to an i.i.d. predefined probability mass function. Therefore, this problem can also be viewed as information-constrained optimal transport which finds the optimal cost of transporting the source quantum state to the destination state via an entanglement-breaking channel with limited communication rate and common randomness. 
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  7. Free, publicly-accessible full text available June 18, 2024
  8. Free, publicly-accessible full text available July 1, 2024
  9. The self-assembly of shape-anisotropic nanocrystals into large-scale structures is a versatile and scalable approach to creating multifunctional materials. The tetrahedral geometry is ubiquitous in natural and manmade materials, yet regular tetrahedra present a formidable challenge in understanding their self-assembly behavior as they do not tile space. Here, we report diverse supracrystals from gold nanotetrahedra including the quasicrystal (QC) and the dimer packing predicted more than a decade ago and hitherto unknown phases. We solve the complex three-dimensional (3D) structure of the QC by a combination of electron microscopy, tomography, and synchrotron X-ray scattering. Nanotetrahedron vertex sharpness, surface ligands, and assembly conditions work in concert to regulate supracrystal structure. We also discover that the surface curvature of supracrystals can induce structural changes of the QC tiling and eventually, for small supracrystals with high curvature, stabilize a hexagonal approximant. Our findings bridge the gap between computational design and experimental realization of soft matter assemblies and demonstrate the importance of accurate control over nanocrystal attributes and the assembly conditions to realize increasingly complex nanopolyhedron supracrystals. 
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    Free, publicly-accessible full text available August 3, 2024