Background: An outbreak of pneumonia associated with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan city and then to other city. It is very urgent to delineate the epidemiological and clinical characteristics of these affected patients. Methods: To investigate the epidemiological characteristics of the COVID-19, we describe a case series of 459 patients with con rmed COVID-19 in WZ of China from January 27 to February 12, 2020. Results: The median age of all patients was 48.0 years, and 46.8% were females. 37.5% of patients had a history of residence in Wuhan. Fever (72.1%) and cough (43.6%) were the most frequent symptoms. In addition, three kinds of unconventional cases were observed, in which included 4.4% con rmed virus carrier who were asymptomatic, 7.8% con rmed patients who had no link to Wuhan city but contact with individuals from Wuhan without any symptoms at the time of contact, and 10.7% con rmed patients who had no link to Wuhan city nor a history of intimate contact with patients or individuals from Wuhan without any symptoms, respectively. Conclusion: Our ndings presented the possibility of asymptomatic carriers affected with SARS-CoV-2, and this phenomenon suggested that chances of uncontrollable transmission in the larger population might be higher than formerly estimated, and transmission by these three kinds of unconventional patients in WZ may be one of the characteristics of infection in other Chinese cities outside the Wuhan epidemic area.

Porcine reproductive and respiratory syndrome (PRRS) is a severe viral disease in pigs, causing great economic losses worldwide each year. The causative agent of the disease, PRRS virus (PRRSV), is a member of the family Arteriviridae. Here we report our investigation of the unparalleled large-scale outbreaks of an originally unknown, but so-called “high fever” disease in China in 2006 with the essence of PRRS, which spread to more than 10 provinces (autonomous cities or regions) and affected over 2,000,000 pigs with about 400,000 fatal cases. Different from the typical PRRS, numerous adult sows were also infected by the “high fever” disease. This atypical PRRS pandemic was initially identified as a hog cholera-like disease manifesting neurological symptoms (e.g., shivering), high fever (40–42°C), erythematous blanching rash, etc. Autopsies combined with immunological analyses clearly showed that multiple organs were infected by highly pathogenic PRRSVs with severe pathological changes observed. Whole-genome analysis of the isolated viruses revealed that these PRRSV isolates are grouped into Type II and are highly homologous to HB-1, a Chinese strain of PRRSV (96.5% nucleotide identity). More importantly, we observed a unique molecular hallmark in these viral isolates, namely a discontinuous deletion of 30 amino acids in nonstructural protein 2 (NSP2). Taken together, this is the first comprehensive report documenting the 2006 epidemic of atypical PRRS outbreak in China and identifying the 30 amino-acid deletion in NSP2, a novel determining factor for virulence which may be implicated in the high pathogenicity of PRRSV, and will stimulate further study by using the infectious cDNA clone technique.

Water-soluble carbon nanocrystals (CNCs) with electrochemiluminescence (ECL) activity were released into aqueous solution from a graphite rod by applying a scanning potential. ECL emission of CNCs observed during their preparation probably provides a useful method for monitoring and screening nanocrystal preparation. The ECL behavior and its mechanism in CNCs have been studied in detail for the first time. The results suggest promising applications of CNCs in the development of new types of biosensors and display devices in the future on the basis of their strong and stable ECL emission, good stability, low cytotoxicity, excellent water solubility, easy labeling, and environmental friendliness.

Cancer immunotherapy targeting co-inhibitory pathways by checkpoint blockade shows remarkable efficacy in a variety of cancer types. However, only a minority of patients respond to treatment due to the stochastic heterogeneity of tumor microenvironment (TME). Recent advances in single-cell RNA-seq technologies enabled comprehensive characterization of the immune system heterogeneity in tumors but posed computational challenges on integrating and utilizing the massive published datasets to inform immunotherapy. Here, we present Tumor Immune Single Cell Hub (TISCH, http://tisch.comp-genomics.org), a large-scale curated database that integrates single-cell transcriptomic profiles of nearly 2 million cells from 76 high-quality tumor datasets across 27 cancer types. All the data were uniformly processed with a standardized workflow, including quality control, batch effect removal, clustering, cell-type annotation, malignant cell classification, differential expression analysis and functional enrichment analysis. TISCH provides interactive gene expression visualization across multiple datasets at the single-cell level or cluster level, allowing systematic comparison between different cell-types, patients, tissue origins, treatment and response groups, and even different cancer-types. In summary, TISCH provides a user-friendly interface for systematically visualizing, searching and downloading gene expression atlas in the TME from multiple cancer types, enabling fast, flexible and comprehensive exploration of the TME.

Genome-wide screening using CRISPR coupled with nuclease Cas9 (CRISPR/Cas9) is a powerful technology for the systematic evaluation of gene function. Statistically principled analysis is needed for the accurate identification of gene hits and associated pathways. Here, we describe how to perform computational analysis of CRISPR screens using the MAGeCKFlute pipeline. MAGeCKFlute combines the MAGeCK and MAGeCK-VISPR algorithms and incorporates additional downstream analysis functionalities. MAGeCKFlute is distinguished from other currently available tools by being a comprehensive pipeline that contains a series of functions for analyzing CRISPR screen data. This protocol explains how to use MAGeCKFlute to perform quality control, normalization, batch effect removal, copy number bias correction, gene hit identification, and downstream functional enrichment analysis for CRISPR screens. We also describe gene identification and data analysis in CRISPR screens involving drug treatment. Completing the entire MAGeCKFlute pipeline requires approximately two hours on a desktop computer running Linux or Mac OS and with R support. The MAGeCKFlute package is available at http://www.bioconductor.org/packages/release/bioc/html/MAGeCKFlute.html.

In water treatment processes that involve contaminant reduction by zerovalent iron (ZVI), reduction of water to dihydrogen is a competing reaction that must be minimized to maximize the efficiency of electron utilization from the ZVI. Sulfidation has recently been shown to decrease H formation significantly, such that the overall electron efficiency of (or selectivity for) contaminant reduction can be greatly increased. To date, this work has focused on nanoscale ZVI (nZVI) and solution-phase sulfidation agents (e.g., bisulfide, dithionite or thiosulfate), both of which pose challenges for up-scaling the production of sulfidated ZVI for field applications. To overcome these challenges, we developed a process for sulfidation of microscale ZVI by ball milling ZVI with elemental sulfur. The resulting material (S-mZVI) exhibits reduced aggregation, relatively homogeneous distribution of Fe and S throughout the particle (not core-shell structure), enhanced reactivity with trichloroethylene (TCE), less H formation, and therefore greatly improved electron efficiency of TCE dechlorination (ε). Under ZVI-limited conditions (initial Fe/TCE = 1.6 mol/mol), S-mZVI gave surface-area normalized reduction rate constants (k') and ε that were ∼2- and 10-fold greater than the unsulfidated ball-milled control (mZVI). Under TCE-limited conditions (initial Fe/TCE = 2000 mol/mol), sulfidation increased k and ε ≈ 5- and 50-fold, respectively. The major products from TCE degradation by S-mZVI were acetylene, ethene, and ethane, which is consistent with dechlorination by β-elimination, as is typical of ZVI, iron oxides, and/or sulfides. However, electrochemical characterization shows that the sulfidated material has redox properties intermediate between ZVI and FeO, mostly likely significant coverage of the surface with FeS.

We developed a computational method to infer the complementarity determining region 3 (CDR3) sequences of tumor infiltrating T-cells in 9,142 RNA-seq samples across 29 cancer types. We identified over 600 thousand CDR3 sequences, including 15% with full-length. CDR3 sequence length distribution and amino acid conservation, as well as variable gene usage of infiltrating T-cells in many tumors, except brain and kidney cancers, resembled those in the peripheral blood of healthy donors. We observed a strong association between T-cell diversity and tumor mutation load, and predicted SPAG5 and TSSK6 as putative immunogenic cancer/testis antigens in multiple cancers. Finally, we identified 3 potential immunogenic somatic mutations based on their co-occurrence with CDR3 sequences. One of them, PRAMEF4 F300V, was predicted to bind strongly to both MHC-I and MHC-II, with matched HLA types in its carriers. Our analyses have the potential to simultaneously identify immunogenic neoantigens and the tumor-reactive T-cell clonotypes.

Representing a basal branch of arachnids, scorpions are known as ‘living fossils’ that maintain an ancient anatomy and are adapted to have survived extreme climate changes. Here we report the genome sequence of Mesobuthus martensii, containing 32,016 protein-coding genes, the most among sequenced arthropods. Although M. martensii appears to evolve conservatively, it has a greater gene family turnover than the insects that have undergone diverse morphological and physiological changes, suggesting the decoupling of the molecular and morphological evolution in scorpions. Underlying the long-term adaptation of scorpions is the expansion of the gene families enriched in basic metabolic pathways, signalling pathways, neurotoxins and cytochrome P450, and the different dynamics of expansion between the shared and the scorpion lineage-specific gene families. Genomic and transcriptomic analyses further illustrate the important genetic features associated with prey, nocturnal behaviour, feeding and detoxification. The M. martensii genome reveals a unique adaptation model of arthropods, offering new insights into the genetic bases of the living fossils.