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1. CrossMP: Enabling Cross-Modality Translation between Single-Cell RNA-Seq and Single-Cell ATAC-Seq through Web-Based Portal

   https://doi.org/10.3390/genes15070882  

   Lyu, Zhen; Dahal, Sabin; Zeng, Shuai; Wang, Juexin; Xu, Dong; Joshi, Trupti (July 2024, Genes)

   In recent years, there has been a growing interest in profiling multiomic modalities within individual cells simultaneously. One such example is integrating combined single-cell RNA sequencing (scRNA-seq) data and single-cell transposase-accessible chromatin sequencing (scATAC-seq) data. Integrated analysis of diverse modalities has helped researchers make more accurate predictions and gain a more comprehensive understanding than with single-modality analysis. However, generating such multimodal data is technically challenging and expensive, leading to limited availability of single-cell co-assay data. Here, we propose a model for cross-modal prediction between the transcriptome and chromatin profiles in single cells. Our model is based on a deep neural network architecture that learns the latent representations from the source modality and then predicts the target modality. It demonstrates reliable performance in accurately translating between these modalities across multiple paired human scATAC-seq and scRNA-seq datasets. Additionally, we developed CrossMP, a web-based portal allowing researchers to upload their single-cell modality data through an interactive web interface and predict the other type of modality data, using high-performance computing resources plugged at the backend. 

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2. Meteoroid Mass Estimation Based on Single‐Frequency Radar Cross Section Measurements

   https://doi.org/10.1029/2021JA029525  

   Tarnecki, L. K.; Marshall, R. A.; Stober, G.; Kero, J. (September 2021, Journal of Geophysical Research: Space Physics)

   Abstract Both high‐power large aperture radars and smaller meteor radars readily observe the dense head plasma produced as a meteoroid ablates. However, determining the mass of such meteors based on the information returned by the radar is challenging. We present a new method for deriving meteor masses from single‐frequency radar measurements, using a physics‐based plasma model and finite‐difference time‐domain (FDTD) simulations. The head plasma model derived in Dimant and Oppenheim (2017),https://doi.org/10.1002/2017ja023963depends on the meteoroids altitude, speed, and size. We use FDTD simulations of a radar pulse interacting with such head plasmas to determine the radar cross section (RCS) that a radar system would observe for a meteor with a given set of physical properties. By performing simulations over the observed parameter space, we construct tables relating meteor size, velocity, and altitude to RCS. We then use these tables to map a set of observations from the MAARSY radar (53.5 MHz) to fully defined plasma distributions, from which masses are calculated. To validate these results, we repeat the analysis using observations of the same meteors by the EISCAT radar (929 MHz). The resulting masses are strongly linearly correlated; however, the masses derived from EISCAT measurements are on average 1.33 times larger than those derived from MAARSY measurements. Since this method does not require dual‐frequency measurements for mass determination, only validation, it can be applied in the future to observations made by many single‐frequency radar systems. 

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3. Cross-correlation image analysis for real-time single particle tracking

   https://doi.org/10.1063/5.0206405  

   Werneck, L R; Jessup, C; Brandenberger, A; Knowles, T; Lewandowski, C W; Nolan, M; Sible, K; Etienne, Z B; D’Urso, B (July 2024, Review of Scientific Instruments)

   Accurately measuring the translations of objects between images is essential in many fields, including biology, medicine, chemistry, and physics. One important application is tracking one or more particles by measuring their apparent displacements in a series of images. Popular methods, such as the center of mass, often require idealized scenarios to reach the shot noise limit of particle tracking and, therefore, are not generally applicable to multiple image types. More general methods, such as maximum likelihood estimation, reliably approach the shot noise limit, but are too computationally intense for use in real-time applications. These limitations are significant, as real-time, shot-noise-limited particle tracking is of paramount importance for feedback control systems. To fill this gap, we introduce a new cross-correlation-based algorithm that approaches shot-noise-limited displacement detection and a graphics processing unit-based implementation for real-time image analysis of a single particle. 

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4. Single-molecule spectroelectrochemical cross-correlation during redox cycling in recessed dual ring electrode zero-mode waveguides

   https://doi.org/10.1039/C7SC02250F  

   Han, Donghoon; Crouch, Garrison M.; Fu, Kaiyu; Zaino III, Lawrence P.; Bohn, Paul W (January 2017, Chemical Science)

   null (Ed.)

   The ability of zero-mode waveguides (ZMW) to guide light into subwavelength-diameter nanoapertures has been exploited for studying electron transfer dynamics in zeptoliter-volume nanopores under single-molecule occupancy conditions. In this work, we report the spectroelectrochemical detection of individual molecules of the redox-active, fluorogenic molecule flavin mononucleotide (FMN) freely diffusing in solution. Our approach is based on an array of nanopore-confined recessed dual ring electrodes, wherein repeated reduction and oxidation of a single molecule at two closely spaced annular working electrodes yields amplified electrochemical signals. We have articulated these structures with an optically transparent bottom, so that the nanopores are bifunctional, exhibiting both nanophotonic and nanoelectrochemical behaviors allowing the coupling between electron transfer and fluorescence dynamics to be studied under redox cycling conditions. We also investigated the electric field intensity in electrochemical ZMWs (E-ZMW) through finite-element simulations, and the amplification of fluorescence by redox cycling agrees well with predictions based on optical confinement effects inside the E-ZMW. Proof-of-principle experiments are conducted showing that electrochemical and fluorescence signals may be correlated to reveal single molecule fluctuations in the array population. Cross-correlation of single molecule fluctuations in amperometric response and single photon emission provides unequivocal evidence of single molecule sensitivity. 

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5. Coexpression enhances cross-species integration of single-cell RNA sequencing across diverse plant species

   https://doi.org/10.1038/s41477-024-01738-4  

   Passalacqua, Michael_John; Gillis, Jesse (June 2024, Nature Plants)

   Abstract Single-cell RNA sequencing is increasingly used to investigate cross-species differences driven by gene expression and cell-type composition in plants. However, the frequent expansion of plant gene families due to whole-genome duplications makes identification of one-to-one orthologues difficult, complicating integration. Here we demonstrate that coexpression can be used to trim many-to-many orthology families down to identify one-to-one gene pairs with proxy expression profiles, improving the performance of traditional integration methods and reducing barriers to integration across a diverse array of plant species. 

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