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Studying placental functions is crucial for understanding pregnancy complications. However, imaging placenta is challenging due to its depth, volume, and motion distortions. In this study, we have developed an implantable placenta window in mice that enables high-resolution photoacoustic and fluorescence imaging of placental development throughout the pregnancy. The placenta window exhibits excellent transparency for light and sound. By combining the placenta window with ultrafast functional photoacoustic microscopy, we were able to investigate the placental development during the entire mouse pregnancy, providing unprecedented spatiotemporal details. Consequently, we examined the acute responses of the placenta to alcohol consumption and cardiac arrest, as well as chronic abnormalities in an inflammation model. We have also observed viral gene delivery at the single-cell level and chemical diffusion through the placenta by using fluorescence imaging. Our results demonstrate that intravital imaging through the placenta window can be a powerful tool for studying placenta functions and understanding the placental origins of adverse pregnancy outcomes.

Single-cell RNA sequencing (scRNA-seq) is a widely used technique for characterizing individual cells and studying gene expression at the single-cell level. Clustering plays a vital role in grouping similar cells together for various downstream analyses. However, the high sparsity and dimensionality of large scRNA-seq data pose challenges to clustering performance. Although several deep learning-based clustering algorithms have been proposed, most existing clustering methods have limitations in capturing the precise distribution types of the data or fully utilizing the relationships between cells, leaving a considerable scope for improving the clustering performance, particularly in detecting rare cell populations from large scRNA-seq data. We introduce DeepScena, a novel single-cell hierarchical clustering tool that fully incorporates nonlinear dimension reduction, negative binomial-based convolutional autoencoder for data fitting, and a self-supervision model for cell similarity enhancement. In comprehensive evaluation using multiple large-scale scRNA-seq datasets, DeepScena consistently outperformed seven popular clustering tools in terms of accuracy. Notably, DeepScena exhibits high proficiency in identifying rare cell populations within large datasets that contain large numbers of clusters. When applied to scRNA-seq data of multiple myeloma cells, DeepScena successfully identified not only previously labeled large cell types but also subpopulations in CD14 monocytes, T cells and natural killer cells, respectively.

Inferring gene regulatory networks (GRNs) from single-cell RNA-seq (scRNA-seq) data is an important computational question to find regulatory mechanisms involved in fundamental cellular processes. Although many computational methods have been designed to predict GRNs from scRNA-seq data, they usually have high false positive rates and none infer GRNs by directly using the paired datasets of case-versus-control experiments. Here we present a novel deep-learning-based method, named scTIGER, for GRN detection by using the co-differential relationships of gene expression profiles in paired scRNA-seq datasets. scTIGER employs cell-type-based pseudotiming, an attention-based convolutional neural network method and permutation-based significance testing for inferring GRNs among gene modules. As state-of-the-art applications, we first applied scTIGER to scRNA-seq datasets of prostate cancer cells, and successfully identified the dynamic regulatory networks of AR, ERG, PTEN and ATF3 for same-cell type between prostatic cancerous and normal conditions, and two-cell types within the prostatic cancerous environment. We then applied scTIGER to scRNA-seq data from neurons with and without fear memory and detected specific regulatory networks for BDNF, CREB1 and MAPK4. Additionally, scTIGER demonstrates robustness against high levels of dropout noise in scRNA-seq data.

We conduct a systematic search for quasars with periodic variations from the archival photometric data of the Zwicky Transient Facility by cross-matching with the quasar catalogues of the Sloan Digital Sky Survey and Véron-Cetty and Véron. We first select out 184 primitive periodic candidates using the generalized Lomb–Scargle periodogram and autocorrelation function and then estimate their statistical significance of periodicity based on two red-noise models, i.e. damped random walk (DRW) and single power-law (SPL) models. As such, we finally identify 106 (DRW) and 86 (SPL) candidates with the most significant periodic variations out of 143 700 quasars. We further compare DRW and SPL models using Bayes factors, which indicate a relative preference of the SPL model for our primitive sample. We thus adopt the candidates identified with SPL as the final sample and summarize its basic properties. We extend the light curves of the selected candidates by supplying other archival survey data to verify their periodicity. However, only three candidates (with 6–8 cycles of periods) meet the selection criteria. This result clearly implies that, instead of being strictly periodic, the variability must be quasi-periodic or caused by stochastic red-noise. This exerts a challenge to the existing search approaches and calls for developing new effective methods.

We performed a rigorous reverberation-mapping analysis of the broad-line region (BLR) in a highly accreting (L/L_Edd= 0.74–3.4) active galactic nucleus, Markarian 142 (Mrk 142), for the first time using concurrent observations of the inner accretion disk and the BLR to determine a time lag for the Hβλ4861 emission relative to the ultraviolet (UV) continuum variations. We used continuum data taken with the Niel Gehrels Swift Observatory in theUVW2 band, and the Las Cumbres Observatory, Dan Zowada Memorial Observatory, and Liverpool Telescope in thegband, as part of the broader Mrk 142 multiwavelength monitoring campaign in 2019. We obtained new spectroscopic observations covering the Hβbroad emission line in the optical from the Gemini North Telescope and the Lijiang 2.4 m Telescope for a total of 102 epochs (over a period of 8 months) contemporaneous to the continuum data. Our primary result states a UV-to-Hβtime lag of${8.68}_{-0.72}^{+0.75}$days in Mrk 142 obtained from light-curve analysis with a Python-based running optimal average algorithm. We placed our new measurements for Mrk 142 on the optical and UV radius–luminosity relations for NGC 5548 to understand the nature of the continuum driver. The positions of Mrk 142 on the scaling relations suggest that UV is closer to the “true” driving continuum than the optical. Furthermore, we obtain$\log (M_{•}/M_{\odot })$= 6.32 ± 0.29 assuming UV as the primary driving continuum.