Quantitative Analysis of the Effectiveness of Antigen-and Polymerase Chain Reaction-Based Combination Strategies for Containing COVID-19 Transmission in a Simulated Community

The number of coronavirus disease 2019(COVID-19)cases continues to surge,overwhelming healthcare systems and causing excess mortality in many countries.Testing of infectious populations remains a key strategy to contain the COVID-19 outbreak,delay the exponential spread of the disease,and flatten the epidemic curve.Using the Omicron variant outbreak as a background,this study aimed to evaluate the effectiveness of testing strategies with different test combinations and frequencies,analyze the factors associated with testing effectiveness,and optimize testing strategies based on these influencing factors.We developed a stochastic,agent-based,discrete-time susceptible–latent–infectious–recovered model simulating a community to estimate the association between three levels of testing strategies and COVID-19 transmission.Antigen testing and its combination strategies were more efficient than polymerase chain reaction(PCR)-related strategies.Antigen testing also showed better performance in reducing the demand for hospital beds and intensive care unit beds.The delay in the turnaround time of test results had a more significant impact on the efficiency of the testing strategy compared to the detection limit of viral load and detection-related contacts.The main advantage of antigen testing strategies is the short turnaround time,which is also a critical factor to be optimized to improve PCR strategies.After modifying the turnaround time,the strategies with less frequent testing were comparable to daily testing.The choice of testing strategy requires consideration of containment goals,test efficacy,community prevalence,and economic factors.This study provides evidence for the selection and optimization of testing strategies in the post-pandemic era and provides guidance for optimizing healthcare resources.

Genome assembly of the snow lotus species Saussurea involucrata provides insights into acacetin and rutin biosynthesis and tolerance to an alpine environment

Dear Editor,Understanding the evolution and survival mechanisms of endangered wild medicinal herbs is crucial for their cultivation,utilization,and conservation.The snow lotus species Saussurea involucrata(Kar.&Kir.)Sch.Bip.(2n=32)(i.e.the well-known Tianshan snow lotus)which belongs to the eudicot family Asteraceae,is a famous traditional Chinese medicinal herb having anti-inflammatory.

Evaluation of Pre-Harvest Sprouting(PHS)Resistance and Screening of High-Quality Varieties from Thirty-Seven Quinoa(Chenopodium quinoa Willd.)Resources in Chengdu Plain

Pre-harvest sprouting(PHS)will have a serious effect both on the yield and quality of quinoa(Chenopodium quinoaWilld.).It is crucial to select and breed quinoa varieties with PHS resistance and excellent agronomic traits for guidance production and utilization of quinoa.A comprehensive evaluation of the PHS resistance and agronomic traits of 37 species of quinoa resources was conducted in Chengdu Plain.The evaluation used various methods,including grain germination rate(GR),grain germination index(GI),total spike germination rate(SR),total grain germination index(SI),grey correlation analysis(GCA),cluster analysis and correlation analysis.Results showed significant differences in PHS resistance and agronomic traits amongst the 37 quinoa resources.CDU-23 was most resistant to PHS within 24 h,with a germination rate of 2.67%and 0%according to the GR and SR results,respectively.However,in the same time,CDU-31 showed the maximum susceptibility to PHS based on the SR of 31.07%,while CDU-34 was the most sensitive to PHS according to the GR of 100%.The comprehensive evaluation identified one and nine kinds of high resistance species for grain and whole spike germination,respectively.In both cases,the coefficients of variation(CV)for these parameters were 34.78%and 82.13%,respectively.GCA results showed that the magnitude of the association between each trait and yield in the thirty-seven quinoa resources was in the following order:thousand grain weight>seed length>seed area>seed width.Although the seed weight of CDU-18 reached 3.7010 g,the seed weight of CDU-5 was only 1.6030 g.However,the size of the seeds,their width and area did not correlate with their 1000-grain weight.There was a complex correlation between PHS resistance index and agronomic traits.Based on clustering analysis,thirty-seven quinoa resources were classified into three taxa.It was found that various taxa differed in PHS resistance and agronomic traits.Several comparisons of the aggregated data led to the selection of five varieties of quinoa,of which CDU-2 presented excellent agronomic qualities and strong PHS resistance.This study has provided a reference for breeding excellent quinoa varieties with PHS resistance.

Discussion on Construction and Mechanism of Practice Bases for Professional Degree Postgraduates Based on the Integration of Production and Education in Local Universities

Under the background of emerging agricultural education,practice bases are an important place to train profession talented person that match social needs,so it is very important to build stable and long-term practice bases.At present,the main problems in the construction of practice bases for postgraduates in local colleges and universities are mainly focusing on construction and neglecting management,imperfect cooperation mechanism and lack of teaching management effectively.It is of great significance to build a long-term management mechanism to ensure the education quality of practice bases.Therefore,constructing the mode of"double integration and double promotion of production and education"with practice bases as the carrier and realizing the organic combination of industrial needs and postgraduate projects is an important idea for local colleges and universities to train professional degree postgraduates to"know agriculture,love agriculture,strengthen agriculture and promote agriculture",and it also provides a reference for the mechanism construction of postgraduate bases.

Evaluation of oasis stability in the lower reaches of the Tarim River

Oasis stability in the lower reaches of the Tarim River was assessed at the landscape scale（including changes in landscape pattern and land use in the oasis） and at the regional scale（including the cold-island effect and NDVI of the oasis） based on the methods of landscape ecology,GIS and Remote Sensing（RS）.Thematic Mapping（TM） remote sensing images from 1990,2000 and 2009 were employed along with the related meteorological and hydrological data pertaining to the reclamation area of the oasis in the lower reaches of the Tarim River.The results indicated that landscape heterogeneity and oasis complexity increased between 1990 and 2000.The comprehensive index of the degree of land use,the average index of the cold-island effect,NDVI value and oasis stability all decreased.However,the change trends in the indices referred to above were opposite between 2000 and 2009,and oasis stability was enhanced to some extent.

Molecular phylogeny of tribe Atraphaxideae(Polygonaceae)evidenced from five cpDNA genes

Traditionally, Atraphaxis, Calligonum, Pteropyrum and Parapteropyrum are included in the tribe Atraphxideae. Recently, sequence data has revealed that this tribe is not monophyletic. The structure of the tribe was examined by adding more taxa and sequences to clarify the congruence between morphology and molecular phylogeny, the systematic placements of four genera in Polygonaceae, as well as the infra-generic relationships of Atraphaxis and Calligonum within Atraphaxideae. Five chloroplast genes, atpB-rbcL, psbA-trnH, trnL-tmF, psbK-psbl, and rbcL of Atraphaxis, Calligonum, Pteropyrum, and Parapteropyrum were sequenced. The non-monophyly of Atraphaxideae was confirmed. Atraphaxis and Calligonum, respectively, formed a monophyletic group that was well supported. Calligonum is closely related to Pteropyrum; Atraphaxis is sister to Polygonum s. str. and Parapteropyrum is allied with Fagopyrum. Although the morphology suggested the four genera should form a tribe, the molecular data indicated Atraphaxideae was not one monophyletic group. The clades identified within Atraphaxis corresponded well with the current sectional classification based on morphological features. As for Cal- ligonum, Medusa was identified as a non-monophyletic section.

Cellulose derived biochar:Preparation,characterization and Benzo[α]pyrene adsorption capacity

Edible oil is prone to be contaminated by Benzo[a]pyrene(BaP)during production and processing.Adsorption is an important technology for the removal of BaP from edible oil,and biochar as a new type of adsorbent for the treatment BaP has received extensive attention.In this study,we prepared unmodified biochar and ZnCl_(2)-modified biochar from sesame straw cellulose(SSB and SSZ)and sesame capsule cellulose(SCB and SCZ),carried out structure characterization by Fourier Transform Infrared(FT-IR),Brunauer-Emmett-Teller(BET)and Scanning Electron Microscope(SEM),and finally evaluated their potential effectiveness in BaP removal from sesame oil.FT-IR results revealed that SSZ and SCZ showed higher peak intensities,indicating that they could provide more active sites for adsorption.The results of XRD presented that SSZ and SCZ had a higher graphitization degree than the unmodified biochar.SEM results showed that the SSZ and SCZ had more complex pore structure,which is beneficial to adsorption.BET analysis results showed that SSZ and SCZ had a higher specific surface area of 1622.83-1797.39 m^(2)/g and a better developed porous structure(the total pore volume Vtotal was 0.9434-1.0023 cm^(3)/g)than the SSB and SCB(specific surface area was 350.55-352.59 m^(2)/g,and Vtotal was 0.1907-0.1918 cm^(3)/g),indicating that modification promoted the formation of porous structure and thus improved the adsorption capacity of biochar.Adsorption experiments confirmed once again that the BaP removal rates of SSZ and SCZ(92.67%-96.13%)were much higher than that of unmodified biochar(3.34%-4.28%),and the BaP content in the sesame oil treated by SSZ and SCZ were far below the current EU maximum levels(2μg/kg).Therefore,the modified biochar from cellulose is a promising adsorbent for BaP removal.In future studies,the influences of bichar on the nutritional quality of edible oil should be taken into consideration so as to find an ideal active carbon substitute for BaP removal in edible oil.

Plastome sequencing of Myripnois dioica and comparison within Asteraceae

Myripnois is a monotypic shrub genus in the daisy family constricted to northern China.Although wild populations of Myripnois dioica are relatively rare,this plant may potentially be cultured as a fine ornamental.In the present study,we sequenced the complete plastome of M.dioica,generating the first plastome sequences of the subfamily Pertyoideae.The plastome of M.dioica has a typical quadripartite circular structure.A large^20-kb and a small^3-kb inversion were detected in the large single copy(LSC)region and shared by other Asteraceae species.Plastome phylogenomic analyses based on 78 Asteraceae species and three outgroups revealed four groups,corresponding to four Asteraceae subfamilies:Asteroideae,Cichorioideae,Pertyoideae and Carduoideae.Among these four subfamilies,Pertyoideae is sister to Asteroideae+Cichorioideae;Carduoideae is the most basal clade.In addition,we characterized 13 simple sequence repeats(SSRs)that may be useful in future studies on population genetics.

Genomic convergence underlying high-altitude adaptation in alpine plants

Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection.However, genomic evidence for convergent adaptation to extreme environments remains scarce.Here, we assembled reference genomes of two alpine plants, Saussurea obvallata(Asteraceae)and Rheum alexandrae(Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes,we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of diseaseresistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present.We identified signatures of positive selection on a set of genes involved in reproduction and respiration(e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification,DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive “greenhouse” morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level,aiding in a deep understanding of genetic adaptation to complex environments.

CCGD-ESCC： A Comprehensive Database for Genetic Variants Associated with Esophageal Squamous Cell Carcinoma in Chinese Population

Esophageal squamous-cell carcinoma （ESCC） is one of the most lethal malignancies in the world and occurs at particularly higher frequency in China. While several genome-wide association studies （GWAS） of germline variants and whole-genome or whole-exome sequencing studies of somatic mutations in ESCC have been published, there is no comprehensive database publically available for this cancer. Here, we developed the Chinese Cancer Genomic Database-Esophageal Squamous Cell Carcinoma （CCGD-ESCC） database, which contains the associations of 69,593 single nucleotide polymorphisms （SNPs） with ESCC risk in 2022 cases and 2039 controls, survival time of 1006 ESCC patients （survival GWAS） and gene expression （expression quantitative trait loci,eQTL） in 94 ESCC patients. Moreover, this database also provides the associations between8833 somatic mutations and survival time in 675 ESCC patients. Our user-friendly database is a resource useful for biologists and oncologists not only in identifying the associations of genetic variants or somatic mutations with the development and progression of ESCC but also in studying the underlying mechanisms for tumorigenesis of the cancer. CCGD-ESCC is freely accessible at http：//db.cbi.pku.edu.cn/ccgd/ESCCdb.

Multi-omic characterization of genome-wide abnormal DNA methylation reveals diagnostic and prognostic markers for esophageal squamous-cell carcinoma

This study investigates aberrant DNA methylations as potential diagnosis and prognosis markers for esophageal squamous-cell carcinoma(ESCC),which if diagnosed at advanced stages has<30%five-year survival rate.Comparing genome-wide methylation sites of 91 ESCC and matched adjacent normal tissues,we identified 35,577 differentially methylated CpG sites(DMCs)and characterized their distribution patterns.

A Large-Scale Online Survey on Clinical Severity and Associated Risk Factors for SARS-CoV-2 Omicron Infection — China, April–May 2023

What is already known about this topic?Individuals who initially contract severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)lack significant mixed immunity.Therefore,it is crucial to monitor the clinical characteristics and associated factors of these individuals in order to inform policymaking.What is added by this report?The common symptoms reported were fever,cough,and sore throat.Reinfections and receiving four vaccination doses within a 6-month period were found to be associated with a shorter duration of virus shedding,decreased hospitalization rate,and reduced risk of pneumonia.Individuals aged 60 years and older,as well as those with underlying medical conditions,had a higher risk of developing pneumonia.What are the implication for public health practices?Online surveys conducted through social media platforms have the potential to complement disease surveillance and data collection efforts.In terms of vaccination prioritization,it is recommended to prioritize older individuals and those with underlying diseases.