Search for: All records

Heterogenous deformation enables exceptional plasticity in a strong and ductile gradient nanostructured steel. 

Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as biological signals representing no or low gene expression, while others regard zeros as missing data to be corrected. To help address the controversy, here we discuss the sources of biological and non-biological zeros; introduce five mechanisms of adding non-biological zeros in computational benchmarking; evaluate the impacts of non-biological zeros on data analysis; benchmark three input data types: observed counts, imputed counts, and binarized counts; discuss the open questions regarding non-biological zeros; and advocate the importance of transparent analysis.

 

Abstract A pressing challenge in single-cell transcriptomics is to benchmark experimental protocols and computational methods. A solution is to use computational simulators, but existing simulators cannot simultaneously achieve three goals: preserving genes, capturing gene correlations, and generating any number of cells with varying sequencing depths. To fill this gap, we propose scDesign2, a transparent simulator that achieves all three goals and generates high-fidelity synthetic data for multiple single-cell gene expression count-based technologies. In particular, scDesign2 is advantageous in its transparent use of probabilistic models and its ability to capture gene correlations via copulas. 

Observational and modeling studies show that the relative frequency of El Niño and La Niña varies in association with El Niño–Southern Oscillation (ENSO)‐like tropical Pacific decadal variability (TPDV), but the causality of the linkage remains unclear. This study presents evidence that ENSO‐like TPDV affects the frequency of ENSO events, particularly of El Niño, through a set of climate model experiments. During the positive phase of TPDV, tropical Pacific warming relative to the Indian and Atlantic Oceans increases the occurrence of anomalous westerly winds over the western equatorial Pacific in late boreal winter‐spring, triggering more El Niño and fewer La Niña events. The opposite happens for the negative TPDV phase. The La Niña frequency is also influenced by oceanic adjustments following El Niño, which tends to counteract the effect of wind changes. The mean state control of ENSO offers a potential opportunity for decadal predictions of climate extremes.

 

Stochastic variability of internal atmospheric modes, known as teleconnection patterns, drives large-scale patterns of low-frequency SST variability in the extratropics . To investigate how the decadal component of this stochastically driven variability in the South and North Pacific affects the tropical Pacific and contributes to the observed basinwide pattern of decadal variability, a suite of climate model experiments was conducted . In these experiments, the models are forced with constant surface heat flux anomalies associated with the decadal component of the dominant atmospheric modes, particularly the Pacific–South American (PSA) and North Pacific Oscillation (NPO) patterns . Both the PSA and NPO modes induce basinwide SST anomalies in the tropical Pacific and beyond that resemble the observed interdecadal Pacific oscillation . The subtropical SST anomalies forced by the PSA and NPO modes propagate to the equatorial Pacific mainly through the wind–evaporation–SST feedback . This atmospheric bridge is stronger from the South Pacific than the North Pacific due to the northward displacement of the intertropical convergence zone and the associated northward advection of momentum anomalies. The equatorial ocean dynamics is also more strongly influenced by atmospheric circulation changes induced by the PSA mode than the NPO mode. In the PSA experiment, persistent and zonally coherent wind stress curl anomalies over the South Pacific affect the zonal mean depth of the equatorial thermocline and weaken the equatorial SST anomalies resulting from the atmospheric bridge. This oceanic adjustment serves as a delayed negative feedback and may be important for setting the time scales of tropical Pacific decadal variability.