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Abstract Clustered regularly interspaced short palindromic repeats (CRISPR) screening coupled with single-cell RNA sequencing has emerged as a powerful tool to characterize the effects of genetic perturbations on the whole transcriptome at a single-cell level. However, due to its sparsity and complex structure, analysis of single-cell CRISPR screening data is challenging. In particular, standard differential expression analysis methods are often underpowered to detect genes affected by CRISPR perturbations. We developed a statistical method for such data, called guided sparse factor analysis (GSFA). GSFA infers latent factors that represent coregulated genes or gene modules; by borrowing information from these factors, it infers the effects of genetic perturbations on individual genes. We demonstrated through extensive simulation studies that GSFA detects perturbation effects with much higher power than state-of-the-art methods. Using single-cell CRISPR data from human CD8⁺T cells and neural progenitor cells, we showed that GSFA identified biologically relevant gene modules and specific genes affected by CRISPR perturbations, many of which were missed by existing methods, providing new insights into the functions of genes involved in T cell activation and neurodevelopment. 

Abstract Many existing pipelines for scRNA-seq data apply pre-processing steps such as normalization or imputation to account for excessive zeros or “drop-outs. Here, we extensively analyze diverse UMI data sets to show that clustering should be the foremost step of the workflow. We observe that most drop-outs disappear once cell-type heterogeneity is resolved, while imputing or normalizing heterogeneous data can introduce unwanted noise. We propose a novel framework HIPPO (Heterogeneity-Inspired Pre-Processing tOol) that leverages zero proportions to explain cellular heterogeneity and integrates feature selection with iterative clustering. HIPPO leads to downstream analysis with greater flexibility and interpretability compared to alternatives. 

Low-temperature direct ammonia fuel cells (DAFCs) use carbon-neutral ammonia as a fuel, which has attracted increasing attention recently due to ammonia's low source-to-tank energy cost, easy transport and storage, and wide availability. However, current DAFC technologies are greatly limited by the kinetically sluggish ammonia oxidation reaction (AOR) at the anode. Herein, we report an AOR catalyst, in which ternary PtIrZn nanoparticles with an average size of 2.3 ± 0.2 nm were highly dispersed on a binary composite support comprising cerium oxide (CeO 2 ) and zeolitic imidazolate framework-8 (ZIF-8)-derived carbon (PtIrZn/CeO 2 -ZIF-8) through a sonochemical-assisted synthesis method. The PtIrZn alloy, with the aid of abundant OH ad provided by CeO 2 and uniform particle dispersibility contributed by porous ZIF-8 carbon (surface area: ∼600 m 2 g −1 ), has shown highly efficient catalytic activity for the AOR in alkaline media, superior to that of commercial PtIr/C. The rotating disk electrode (RDE) results indicate a lower onset potential (0.35 vs. 0.43 V), relative to the reversible hydrogen electrode at room temperature, and a decreased activation energy (∼36.7 vs. 50.8 kJ mol −1 ) relative to the PtIr/C catalyst. Notably, the PtIrZn/CeO 2 -ZIF-8 catalyst was assembled with a high-performance hydroxide anion-exchange membrane to fabricate an alkaline DAFC, reaching a peak power density of 91 mW cm −2 . Unlike in aqueous electrolytes, supports play a critical role in improving uniform ionomer distribution and mass transport in the anode. PtIrZn nanoparticles on silicon dioxide (SiO 2 ) integrated with carboxyl-functionalized carbon nanotubes (CNT–COOH) were further studied as the anode in a DAFC. A significantly enhanced peak power density of 314 mW cm −2 was achieved. Density functional theory calculations elucidated that Zn atoms in the PtIr alloy can reduce the theoretical limiting potential of *NH 2 dehydrogenation to *NH by ∼0.1 V, which can be attributed to a Zn-modulated upshift of the Pt–Ir d-band that facilitates the N–H bond breakage.