In epidemiological investigations, pathogen genomics can provide insights and test epidemiological hypotheses that would not have been possible through traditional epidemiology. Tools to synthesize genomic analysis with other types of data are a key requirement of genomic epidemiology. We propose a new ‘phylepic’ visualization that combines a phylogenomic tree with an epidemic curve. The combination visually links the molecular time represented in the tree to the calendar time in the epidemic curve, a correspondence that is not easily represented by existing tools. Using an example derived from a foodborne bacterial outbreak, we demonstrated that the phylepic chart communicates that what appeared to be a point-source outbreak was in fact composed of cases associated with two genetically distinct clades of bacteria. We provide an R package implementing the chart. We expect that visualizations that place genomic analyses within the epidemiological context will become increasingly important for outbreak investigations and public health surveillance of infectious diseases.

This paper retrospectively analysed the prevalence of macrolide-resistant Mycoplasma pneumoniae (MRMP) in some parts of China. Between January 2013 and December 2019, we collected 4,145 respiratory samples, including pharyngeal swabs and alveolar lavage fluid. The highest PCR-positive rate of M. pneumoniae was 74.5% in Beijing, the highest resistance rate was 100% in Shanghai, and Gansu was the lowest with 20%. The highest PCR-positive rate of M. pneumoniae was 74.5% in 2013, and the highest MRMP was 97.4% in 2019; the PCR-positive rate of M. pneumoniae for adults in Beijing was 17.9% and the MRMP was 10.48%. Among the children diagnosed with community-acquired pneumonia (CAP), the PCR-positive and macrolide-resistant rates of M. pneumoniae were both higher in the severe ones. A2063G in domain V of 23S rRNA was the major macrolide-resistant mutation, accounting for more than 90%. The MIC values of all MRMP to erythromycin and azithromycin were ≥ 64 μg/ml, and the MICs of tetracycline and levofloxacin were ≤ 0.5 μg/ml and ≤ 1 μg/ml, respectively. The macrolide resistance varied in different regions and years. Among inpatients, the macrolide-resistant rate was higher in severe pneumonia. A2063G was the common mutation, and we found no resistance to tetracycline and levofloxacin.

The zosterophyllopsids had a widespread distribution and constituted a dominant component in many plant assemblages during the Early Devonian. Although a large number of zosterophyllopsids have been documented, knowledge about the paleogeographic distribution of different genera/species remains to be expanded by further fossil evidence. In this article, new material assigned to the genus Gosslingia Heard, 1927 and designated as Gosslingia cf. G. breconensis Heard, 1927 is described from a new locality of the Lower Devonian of Guizhou Province, China. The Guizhou material shows main axes that are pseudomonopodially branched, pseudomonopodial lateral branching systems, subaxillary tubercle branches, circinate apices, elliptical xylem strand, exarch maturation of xylem, and G-type tracheids, and exhibits considerable similarities with the type and only species of Gosslingia, Gosslingia breconensis. Our finding represents the first report of Gosslingia in the South China Block and the most convincing occurrence of this genus outside of Wales, UK. Gosslingia adds to the diversity of genera shared among the Early Devonian floras of South China, western Europe, and North America, along with Distichophytum Mägdefrau, Estinnophyton Fairon-Demaret, Zosterophyllum Penhallow, and others, and indicates that the dispersal of early vascular plants among different paleocontinents was more common than previously appreciated.

Examination of plant microfossils (phytoliths and starch granules) preserved in dental calculus allows for the direct identification of some components of prehistoric diets. In this article, the authors present the results of microfossil analysis of dental calculus from wild and domestic animals at the Late Neolithic site of Kangjia in the Central Plains, an area critical in the emergence of early Chinese states. Consumption of cooked plant foods by domestic pigs and dogs, and of domestic crops by wild animals, at this site hints, the authors argue, at an interdependent relationship between animal management, agricultural production and ritual practices that contributed to the political transformations of Late Neolithic China.

Considering straw resource utilization and air pollution prevention, straw return has been commonly practiced in China. However, the practicability of plenty straw return in an emerging maize–rice rotation and their effects on soil C and N pools have not been extensively investigated. This study has been conducted to examine the effects of straw return on soil nutrients, soil functional C and N fractions, and then to figure out their relationships with yield and N use efficiency. Two treatments of straw return (S2Nck) and without straw return (S0Nck) were compared in 3-year field experiment, and subplots without N application were added in their respective plots in the third year. The results showed that, relative to the control (S0Nck), straw return significantly increased soil mineralized nitrogen (Nmin), available P, and exchange K content by 11.7%, 41.1%, and 17.4% averaged across 3-year experiments, respectively. Straw return substantially increased soil dissolved organic C, microbial biomass C, and microbial biomass N content by 73.0%, 25.2%, and 36.8%, respectively. Furthermore, straw return markedly increased C and N retention in particulate organic matter in microaggregates (iPOM) and mineral associated organic matter within microaggregates (intra-SC), but significantly reduced in free mineral associated organic matter (free-SC) fraction. The structural equation modeling analysis showed that yield and the partial factor productivity of N were positively correlated with labile and slow soil C and N fractions. Consequently, straw incorporation significantly increased grain yields of maize by 14.7% and rice by 15.1%. The annual potential reduction proportion in fertilizer-N induced by straw return was estimated to be 25.7% in the third year. This study suggests that the incorporation of straws is an effective way to enhance soil nutrients and regulate soil C and N pools to improve crop production and has the potential to reduce N fertilizer application under maize–rice rotation in subtropical regions.

Objective. The current study aimed to compare the characteristics of chromosome abnormalities detected by conventional G-banding karyotyping, chromosome microarray analysis (CMA), or fluorescence in situ hybridization (FISH)/CNVplex analysis and further explore the application value of combined karyotype analysis and CMA in prenatal diagnosis with a larger sample size. Methods. From March 2019 to March 2021, 3710 amniocentesis samples were retrospectively collected from women who accepted prenatal diagnosis at 16 to 22 + 6 weeks of pregnancy. The pregnant women underwent karyotype analysis and CMA. In the case of fetal chromosomal mosaicism, FISH or CNVplex analysis was utilized for validation. Results. In total, 3710 G-banding karyotype results and CMA results from invasive prenatal diagnosis were collected. Of these, 201 (5.41%) fetuses with an abnormal karyotype were observed. The CMA analysis showed that the abnormality rate was 9.14% (340/3710). The detection rate of CMA combined with karyotype analysis was 0.35% higher than that of CMA alone and 4.08% higher than that of karyotyping alone. Additionally, 12 cases had abnormal karyotype analysis, despite normal CMA results. To further detect the chromosome mosaicism, we used FISH analysis to correct the karyotype results of case 1. Correspondingly, a total of 157 cases showed abnormal CMA results but normal karyotype analysis. We also found chromosomal mosaicism in 4 cases using CMA. Moreover, CNVplex and CMA demonstrated that representative case 15 was mosaicism for trisomy 2. Conclusions. Conventional G-banding karyotyping and CMA have their own advantages and limitations. A combination of karyotype analysis and CMA can increase the detection rate of chromosome abnormalities and make up for the limitation of signal detection.

As a common mineral phase on Earth and Martian regolith, natural rutile was reported as a potential candidate for use as a Fenton catalyst in this study. The influences of Fe and V in various chemical states on the generation of reactive oxygen species (ROSs) and the catalytic activity of rutile were examined. A series of rutile samples with various surface and bulk states of Fe and V were obtained initially by hydrogen annealing of natural rutile at ~773–1173 K. X-ray diffraction, electron paramagnetic resonance spectra, and X-ray photoelectron spectroscopy demonstrated that the atomic fractions of Fe(III) and V(V) decreased sharply with increasing temperature, along with the accumulation of surface Fe(II) and bulk V(III). All as-prepared materials showed enhanced Fenton degradation efficiency on methylene blue (MB) compared with P25-TiO2, and the treated samples exhibited up to 3.5-fold improvement in efficiency at pH 3 compared to the untreated sample. The improved efficiency was attributed mainly to Fenton catalysis involving Fe(II) and V(III). The dissolved Fe2+ played a crucial role in the homogeneous Fenton reaction, while the bound V(III) favored adsorption primarily and may have facilitated heterogeneous Fenton reaction and the regeneration of Fe2+. The pH regulated the reaction mechanism among homogeneous (pH = 3) and heterogeneous (pH = 3.7) Fenton catalysis and physical adsorption (pH = 5, 6). The aim of the present study was to improve the understanding of the potential role of natural rutile with advanced oxidation functions in Earth systems and even on Mars, which also provide an inspiration for screening natural rutile and any other similar, Earth-abundant, low-cost minerals for environmental application.

The clinical significance and potential targets of miR-150-5p have not been elucidated in nasopharyngeal carcinoma (NPC). The pooled analysis based on 539 NPC samples and 75 non-NPC nasopharyngeal samples demonstrated that the expression of miR-150-5p was down-regulated in NPC, with the area under the curve being 0.89 and the standardized mean difference being −0.66. Subsequently, we further screened the differentially expressed genes (DEGs) of 14 datasets, including 312 NPC samples and 70 non-NPC nasopharyngeal samples. After the DEGs were narrowed down with the predicted targets from the miRWalk database, 1316 prospective target genes of miR-150-5p were identified. The enrichment analysis suggested that “pathways in cancer” was the most significant pathway. Finally, six hub genes of “pathways in cancer”, including EGFR, TP53, HRAS, CCND1, CDH1, and FGF2, were screened out through the STRING database. In conclusion, the down-regulation of miR-150-5p modulates the tumorigenesis and progression of NPC.

In this paper, we propose a numerical model to simulate gas–liquid–solid interaction problems, coupling the lattice Boltzmann method and discrete element method (LBM–DEM). A cascaded LBM is used to simulate the liquid–gas flow field using a pseudopotential interaction model for describing the liquid–gas multiphase behaviour. A classical DEM resorting to fictitious overlaps between the particles is used to simulate the multiple-solid-particle system. A multiphase fluid–solid two-way coupling algorithm between LBM and DEM is constructed. The model is validated by four benchmarks: (i) single disc sedimentation, (ii) single floating particle on a liquid–gas interface, (iii) sinking of a horizontal cylinder and (iv) self-assembly of three particles on a liquid–gas interface. Our simulations agree well with the numerical results reported in the literature. Our proposed model is further applied to simulate droplet impact on deformable granular porous media at pore scale. The dynamic droplet spreading process, the deformation of the porous media (composed of up to 1277 solid particles) as well as the invasion of the liquid into the pores are well captured, within a wide range of impact Weber number. The droplet spreading dynamics on particles is analysed based on the energy budget, which reveals mechanisms at play, showing the evolution of particle energy, surface energy and viscous dissipation energy. A scaling relation based on the impact Weber number is proposed to describe the maximum spreading ratio.

Dietary antioxidant indices (DAI) may be potentially associated with relative telomere length (RTL) of leucocytes. This study aimed to investigate the relationship between DAI and RTL. A cross-sectional study involving 1656 participants was conducted. A generalised linear regression model and a restricted cubic spline model were used to assess the correlation of DAI and its components with RTL. Generalised linear regression analysis revealed that DAI (β = 0·005, P = 0·002) and the intake of its constituents vitamin C (β = 0·043, P = 0·027), vitamin E (β = 0·088, P < 0·001), Se (β = 0·075, P = 0·003), and Zn (β = 0·075, P = 0·023) were significantly and positively correlated with RTL. Sex-stratified analysis showed that DAI (β = 0·006, P = 0·005) and its constituents vitamin E (β = 0·083, P = 0·012), Se (β = 0·093, P = 0·006), and Zn (β = 0·092, P = 0·034) were significantly and positively correlated with RTL among females. Meanwhile, among males, only vitamin E intake (β = 0·089, P = 0·013) was significantly and positively associated with RTL. Restricted cubic spline analysis revealed linear positive associations between DAI and its constituents’ (vitamin E, Se and Zn) intake and RTL in the total population. Sex-stratified analysis revealed a linear positive correlation between DAI and its constituents’ (vitamin E, Se and Zn) intake and RTL in females. Our study found a significant positive correlation between DAI and RTL, with sex differences.

In spring 2020, U.S. schools universally transitioned to online learning due to the COVID-19 pandemic’s onset, thus creating a natural experiment for examining adolescents’ risk and resilience during an ongoing school crisis response. This longitudinal study used a daily-diary approach to investigate the role of social support in the link between remote learning and psychological well-being across 64 days among a national sample of adolescents (n = 744; 42% Black, 36% White, 22% Other ethnicity/race; 41% boys; 72% eligible for free/reduced-priced lunch; Mage=14.60, SDage=1.71, age-range = 12–17 years). On days when youth attended remote learning, they reported lower daily positive affect, more daily stress, and higher parent social support. There were no significant differences in the effect of remote learning on affect or stress by race or economic status. On days when youth experienced more parent support, they reported lower daily stress and negative affect and higher daily positive affect. On days when youth experienced more peer support, they reported higher daily positive affect. Overall, the study highlights the impact of pandemic-onset remote learning on adolescents’ psychological well-being and emphasizes the need for future research on school crisis contingency planning to address these challenges.