Taking account of asymptomatic infections: A modeling study of the COVID-19 outbreak on the Diamond Princess cruise ship

The COVID-19 outbreak on the Diamond Princess (DP) cruise ship has provided empirical data to study the transmission potential of COVID-19 with the presence of pre/asymptomatic cases. We studied the changes in R0 on DP from January 21 to February 19, 2020 based on chain binomial models under two scenarios: no quarantine assuming a random mixing condition, and quarantine of passengers in cabins-passengers may get infected either by an infectious case in a shared cabin or by pre/asymptomatic crew who continued to work. Estimates of R0 at the beginning of the epidemic were 3.27 (95% CI, 3.02-3.54) and 3.78 (95% CI, 3.49-4.09) respectively for serial intervals of 5 and 6 days; and when quarantine started, with the reported asymptomatic ratio 0.505, R0 rose to 4.18 (95%CI, 3.86-4.52) and 4.73 (95%CI, 4.37-5.12) respectively for passengers who might be exposed to the virus due to pre/asymptomatic crew. Results confirm that the higher the asymptomatic ratio is, the more infectious contacts would happen. We find evidence to support a US CDC report that a high proportion of asymptomatic infections could partially explain the high attack rate among cruise ship passengers and crew. Our study suggests that if the asymptomatic ratio is high, the conventional quarantine procedure may not be effective to stop the spread of virus

Biomass distribution of different-aged needles in young and old Pinus cembra trees at highland and lowland sites

Conifer needles of different ages perform differently in ecophysiology. However, no study has investigated the biomass distribution of different-aged needles in a tree crown or/and a stand canopy. We carried out a study on young (∼50 years old) and old (∼200 years) Pinus cembra L. trees at highland (2100-2300ma.s.l.) and lowland (570m) sites in Switzerland. We found that both the young and the old trees living in the highlands had more needle biomass per tree than the same-aged trees of the same species living in the lowlands. This is mainly due to the greater longevity of needles in highland trees. It reflects the strategic responses of trees to low resource availability or high abiotic stress level. Having older needles increases the time that nutrients are resident in trees in less favorable environments, and compensates for shorter growing period in cold temperature

Soil fungal community characteristics vary with bamboo varieties and soil compartments

Soil fungi play an important role in nutrient cycling, mycorrhizal symbiosis, antagonism against pathogens, and organic matter decomposition. However, our knowledge about the community characteristics of soil fungi in relation to bamboo varieties is still limited. Here, we compared the fungal communities in different soil compartments (rhizosphere vs. bulk soil) of moso bamboo (Phyllostachys edulis) and its four varieties using ITS high-throughput sequencing technology. The fungal α diversity (Shannon index) in bulk soil was significantly higher than that in rhizosphere soil, but it was not affected by bamboo variety or interactions between the soil compartment and bamboo variety. Soil compartment and bamboo variety together explained 31.74% of the variation in fungal community diversity. Soil compartment and bamboo variety were the key factors affecting the relative abundance of the major fungal taxa at the phylum and genus levels. Soil compartment mainly affected the relative abundance of the dominant fungal phylum, while bamboo variety primarily influenced the dominant fungal genus. Network analysis showed that the fungal network in rhizosphere soil was more complex, stable, and connected than that in bulk soil. A FUNGuild database analysis indicated that both soil compartment and bamboo variety affect fungal functions. Our findings provide new insights into the roles of both soil compartments and plant species (including variety) in shaping soil fungal communities

Effect of elevation on composition and diversity of fungi in the rhizosphere of a population of Deyeuxia angustifolia on Changbai Mountain, northeastern China

Soil fungi are a key component of terrestrial ecosystems and play a major role in soil biogeochemical cycling. Although the diversity and composition of fungal communities are regulated by many abiotic and biotic factors, the effect of elevation on soil fungal community diversity and composition remains largely unknown. In this study, the soil fungal composition and diversity in Deyeuxia angustifolia populations along an elevational gradient (1,690 m to 2020 m a.s.l.) were assessed, using Illumina MiSeq sequencing, on the north-facing slope of the Changbai Mountain, northeastern China. Our results showed that soil physicochemical parameters changed significantly along with the elevational gradients. The Ascomycota and Basidiomycota were the most dominant phyla along with the gradient. Alpha diversity of soil fungi decreased significantly with elevation. Soil nitrate nitrogen (NO3−-N) was positively correlated with fungal richness and phylogenetic diversity (PD), indicating that soil nitrate nitrogen (NO3−-N) is a key soil property determining fungal community diversity. In addition to soil nitrate content, soil pH and soil moisture were the most important environmental properties determining the soil fungal diversity. Our results suggest that the elevational changes in soil physicochemical properties play a key role in shaping the community composition and diversity of soil fungi. This study will allow us to better understand the biodiversity distribution patterns of soil microorganisms in mountain ecosystems

Spatial Heterogeneity in Light Supply Affects Intraspecific Competition of a Stoloniferous Clonal Plant

Spatial heterogeneity in light supply is common in nature. Many studies have examined the effects of heterogeneous light supply on growth, morphology, physiology and biomass allocation of clonal plants, but few have tested those effects on intraspecific competition. In a greenhouse experiment, we grew one (no competition) or nine ramets (with intraspecific competition) of a stoloniferous clonal plant, Duchesnea indica, in three homogeneous light conditions (high, medium and low light intensity) and two heterogeneous ones differing in patch size (large and small patch treatments). The total light in the two heterogeneous treatments was the same as that in the homogeneous medium light treatment. Both decreasing light intensity and intraspecific competition significantly decreased the growth (biomass, number of ramets and total stolon length) of D. indica. As compared with the homogeneous medium light treatment, the large patch treatment significantly increased the growth of D. indica without intraspecific competition. However, the growth of D. indica with competition did not differ among the homogeneous medium light, the large and the small patch treatments. Consequently, light heterogeneity significantly increased intraspecific competition intensity, as measured by the decreased log response ratio. These results suggest that spatial heterogeneity in light supply can alter intraspecific interactions of clonal plants

Effects of environmental factors on vertical distribution of the eukaryotic plankton community in early summer in Danjiangkou Reservoir, China

IntroductionEukaryotic plankton plays crucial roles in ecosystem processes, impacting aquatic ecosystem stability. This study focuses on Danjiangkou Reservoir, a canyon lake in central China, that acts as the water source of the Mid-route of the South-to-North Water Diversion Project.MethodsIn this study, high-throughput 18S rDNA gene sequencing was employed to investigate eukaryotic plankton community at four water depths (0.5 m, 5 m, 10 m, and 20 m). The environmental factors including pH, water temperature (WT), nitrate nitrogen (NO3−-N), ammonia nitrogen (NH4+-N), total nitrogen (TN), conductivity (Cond), and dissolved oxygen (DO) in reservoir areas were measured, and their correlations with abundance and diversity of eukaryotic plankton were analyzed.ResultsThe results showed the presence of 122 genera of eukaryotic plankton from 38 phyla. Eukaryotic plankton communities were mainly composed of Eurytemora, Thermocyclops, Sinocalanus, Mesocyclops, and Cryptomonas. In particular, significant differences in the diversity of eukaryotic plankton communities were found in vertical distribution. The diversity and abundance of eukaryotic plankton communities in 7 sampling sites decreased with the increase of depth from 0.5 to 10 m, while the diversity and abundance of plankton communities increased at 20 m. RDA analysis indicated that pH, depth, WT, NH4+-N, DO, Cond, and NO3−-N could influence the vertical distribution of the eukaryotic plankton community in the Danjiangkou Reservoir. Among these eukaryotic plankton, Eurytemora, Thermocyclops, and Volvox were negatively correlated with pH and WT and positively correlated with depth.DiscussionThis study revealed a novel perspective on the distribution of the eukaryotic plankton community in Danjiangkou Reservoir, particularly in terms of vertical variation, which will be helpful to comprehensively understand ecological processes and to further ensure the water quality safety in this canyon-style reservoir

TransGCN:Coupling Transformation Assumptions with Graph Convolutional Networks for Link Prediction

Link prediction is an important and frequently studied task that contributes to an understanding of the structure of knowledge graphs (KGs) in statistical relational learning. Inspired by the success of graph convolutional networks (GCN) in modeling graph data, we propose a unified GCN framework, named TransGCN, to address this task, in which relation and entity embeddings are learned simultaneously. To handle heterogeneous relations in KGs, we introduce a novel way of representing heterogeneous neighborhood by introducing transformation assumptions on the relationship between the subject, the relation, and the object of a triple. Specifically, a relation is treated as a transformation operator transforming a head entity to a tail entity. Both translation assumption in TransE and rotation assumption in RotatE are explored in our framework. Additionally, instead of only learning entity embeddings in the convolution-based encoder while learning relation embeddings in the decoder as done by the state-of-art models, e.g., R-GCN, the TransGCN framework trains relation embeddings and entity embeddings simultaneously during the graph convolution operation, thus having fewer parameters compared with R-GCN. Experiments show that our models outperform the-state-of-arts methods on both FB15K-237 and WN18RR

Needle δ13C and mobile carbohydrates in Pinus koraiensis in relation to decreased temperature and increased moisture along an elevational gradient in NE China

A tree's crown interacts with atmospheric variables such as CO2, temperature, and humidity. Physioecology of leaves/needles (e.g. δ13C, mobile carbohydrates, and nitrogen) is, therefore, strongly affected by microclimate in and surrounding a tree crown. To understand the physiological responses of leaves to changes in air temperature and moisture, we measured δ13C, soluble sugars, starch, and total nitrogen (N) concentrations in current year and 1-yr-old needles of Pinus koraiensis trees, and compared the growing season air temperature and relative humidity within and outside P. koraiensis crowns along an elevational gradient from 760 to 1,420ma.s.l. on Changbai Mountain, NE China. Our results indicated that needle N and mobile carbohydrates concentrations, as well as needle δ13C values changed continuously with increasing elevation, corresponding to a continuous decrease in air temperature and an increase in relative humidity. Needle carbon and nitrogen status is highly significantly negatively correlated with temperature, but positively correlated with relative humidity. These results indicate that increases in air temperature in combination with decreases in relative humidity may result in lower levels of N and mobile carbohydrates in P. koraiensis trees, suggesting that future climate changes such as global warming and changes in precipitation patterns will directly influence the N and carbon physiology at P. koraiensis individual level, and indirectly affect the competitive ability, species composition, productivity and functioning at the stand and ecosystem level in NE China. Due to the relatively limited range of the transect (760-1,420m) studied, further research is needed to explain whether the present results are applicable to scales across large elevational gradient