Covidscope: An atlas-scale COVID-19 resource for single-cell meta analysis at sample and cell levels (preprint)

Recent advancements in the use of single-cell technologies in large cohort studies enable the investigation of cellular response and mechanisms associated with disease outcome, including COVID-19. Several efforts have been made using single-cell RNA-sequencing to better understand the immune response to COVID-19 virus infection. Nonetheless, it is often difficult to compare or integrate data from multiple data sets due to challenges in data normalisation, metadata harmonisation, and having a common interface to quickly query and access this vast amount of data. Here we present Covidscope (http://covidsc.d24h.hk/), a well-curated open web resource that currently contains single-cell gene expression data and associated metadata of almost 5 million blood and immune cells extracted from almost 1,000 COVID-19 patients across 20 studies around the world. Our collection contains the integrated data with harmonised metadata and multi-level cell type annotations. By combining NoSQL and optimised index, our Covidscope achieves rapid subsetting of high-dimensional gene expression data based on both data set level, donor-level (e.g., age and sex of patients) and cell-level (e.g., expression of specific gene markers) metadata, enabling multiple efficient downstream single-cell meta-analysis.

A hesitation-feedback recommendation approach and its application in large-scale group emergency decision making

Group Decision Making (GDM) has been well studied in the last two decades. Yet, two challenges exist: (a) how to resolve large-scale groups in GDM and achieve the consensus of preferences and (b) how to conduct GDM under risk and emergency conditions. In this paper, we develop a complete problem-solving approach for GDM that orients twofold settings of the complex large-scale group and the time-sensitive emergency decision scenarios. The crux of the matter is to design a feasible mechanism of group consensus strategies in the environment of time pressure and natural language preferences. To solve this problem, we propose a closed-loop mechanism of feedback recommendation strategies accompanied with a new subgroup identification method. This mechanism is underlain by a fourfold decomposition of complex large-scale groups, which entails multiple thresholds of group consensus, group hesitation, and time-related iteration of loops. Our mechanism and the whole GDM approach thoroughly orient the most intuitive representation of preferences - human natural language, which can be elicited and quantitatively formulated in probability linguistic preference systems. We illustrate the proposed approach through a real case study of China's fight against the COVID-19 epidemic. We verify that our mechanism can perfectly tradeoff between the effectiveness and the efficiency of complex large-scale GDM under risk and emergency. The results of this research provide proposals for mechanisms on large-scale GDM and are expected to contribute to emergency management such as epidemic controls, anti-terrorism, and other man-made or natural hazards.