Cell Taxonomy: a curated repository of cell types with multifaceted characterization.

Single-cell studies have delineated cellular diversity and uncovered increasing numbers of previously uncharacterized cell types in complex tissues. Thus, synthesizing growing knowledge of cellular characteristics is critical for dissecting cellular heterogeneity, developmental processes and tumorigenesis at single-cell resolution. Here, we present Cell Taxonomy (https://ngdc.cncb.ac.cn/celltaxonomy), a comprehensive and curated repository of cell types and associated cell markers encompassing a wide range of species, tissues and conditions. Combined with literature curation and data integration, the current version of Cell Taxonomy establishes a well-structured taxonomy for 3,143 cell types and houses a comprehensive collection of 26,613 associated cell markers in 257 conditions and 387 tissues across 34 species. Based on 4,299 publications and single-cell transcriptomic profiles of ∼3.5 million cells, Cell Taxonomy features multifaceted characterization for cell types and cell markers, involving quality assessment of cell markers and cell clusters, cross-species comparison, cell composition of tissues and cellular similarity based on markers. Taken together, Cell Taxonomy represents a fundamentally useful reference to systematically and accurately characterize cell types and thus lays an important foundation for deeply understanding and exploring cellular biology in diverse species.

LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system.

LncRNAWiki, a knowledgebase of human long non-coding RNAs (lncRNAs), has been rapidly expanded by incorporating more experimentally validated lncRNAs. Since it was built based on MediaWiki as its database system, it fails to manage data in a structured way and is ineffective to support systematic exploration of lncRNAs. Here we present LncRNAWiki 2.0 (https://ngdc.cncb.ac.cn/lncrnawiki), which is significantly improved with enhanced database system and curation model. In LncRNAWiki 2.0, all contents are organized in a structured manner powered by MySQL/Java and curators are able to submit/edit annotations based on the curation model that includes a wider range of annotation items. Moreover, it is equipped with popular online tools to help users identify lncRNAs with potentially important functions, and provides more user-friendly web interfaces to facilitate data curation, retrieval and visualization. Consequently, LncRNAWiki 2.0 incorporates a total of 2512 lncRNAs and 106 242 associations for disease, function, drug, interacting partner, molecular signature, experimental sample, CRISPR design, etc., thus providing a comprehensive and up-to-date resource of functionally annotated lncRNAs in human.

Identify Non-mutational p53 Functional Deficiency in Human Cancers.

An accurate assessment of p53's functional status is critical for cancer genomic medicine. However, there is a significant challenge in identifying tumors with non-mutational p53 inactivations that are not detectable through DNA sequencing. These undetected cases are often misclassified as p53-normal, leading to inaccurate prognosis and downstream association analyses. To address this issue, we built the support vector machine (SVM) models to systematically reassess p53's functional status in TP53 wild-type (TP53  WT) tumors from multiple The Cancer Genome Atlas (TCGA) cohorts. Cross-validation demonstrated the good performance of the SVM models with a mean area under curve (AUC) of 0.9822, precision of 0.9747, and recall of 0.9784. Our study revealed that a significant proportion (87%-99%) of TP53  WT tumors actually have compromised p53 function. Additional analyses uncovered that these genetically intact but functionally impaired (termed as predictively reduced function of p53 or TP53  WT-pRF) tumors exhibited genomic and pathophysiologic features akin to TP53 mutant tumors: heightened genomic instability and elevated levels of hypoxia. Clinically, patients with TP53  WT-pRF tumors experienced significantly shortened overall survival or progression-free survival compared to those with predictively normal function of p53 (TP53  WT-pN) tumors, and these patients also displayed increased sensitivity to platinum-based chemotherapy and radiation therapy.

Mesoporous Pt@Pt-skin Pt3Ni core-shell framework nanowire electrocatalyst for efficient oxygen reduction.

The design of Pt-based nanoarchitectures with controllable compositions and morphologies is necessary to enhance their electrocatalytic activity. Herein, we report a rational design and synthesis of anisotropic mesoporous Pt@Pt-skin Pt3Ni core-shell framework nanowires for high-efficient electrocatalysis. The catalyst has a uniform core-shell structure with an ultrathin atomic-jagged Pt nanowire core and a mesoporous Pt-skin Pt3Ni framework shell, possessing high electrocatalytic activity, stability and Pt utilisation efficiency. For the oxygen reduction reaction, the anisotropic mesoporous Pt@Pt-skin Pt3Ni core-shell framework nanowires demonstrated exceptional mass and specific activities of 6.69 A/mgpt and 8.42 mA/cm2 (at 0.9 V versus reversible hydrogen electrode), and the catalyst exhibited high stability with negligible activity decay after 50,000 cycles. The mesoporous Pt@Pt-skin Pt3Ni core-shell framework nanowire configuration combines the advantages of three-dimensional open mesopore molecular accessibility and compressive Pt-skin surface strains, which results in more catalytically active sites and weakened chemisorption of oxygenated species, thus boosting its catalytic activity and stability towards electrocatalysis.