Segmenting Medical MRI via Recurrent Decoding Cell

The encoder-decoder networks are commonly used in medical image segmentation due to their remarkable performance in hierarchical feature fusion. However, the expanding path for feature decoding and spatial recovery does not consider the long-term dependency when fusing feature maps from different layers, and the universal encoder-decoder network does not make full use of the multi-modality information to improve the network robustness especially for segmenting medical MRI. In this paper, we propose a novel feature fusion unit called Recurrent Decoding Cell (RDC) which leverages convolutional RNNs to memorize the long-term context information from the previous layers in the decoding phase. An encoder-decoder network, named Convolutional Recurrent Decoding Network (CRDN), is also proposed based on RDC for segmenting multi-modality medical MRI. CRDN adopts CNN backbone to encode image features and decode them hierarchically through a chain of RDCs to obtain the final high-resolution score map. The evaluation experiments on BrainWeb, MRBrainS and HVSMR datasets demonstrate that the introduction of RDC effectively improves the segmentation accuracy as well as reduces the model size, and the proposed CRDN owns its robustness to image noise and intensity non-uniformity in medical MRI.Comment: 8 pages, 7 figures, AAAI-2

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

Secondary Succession in the Tropical Lowland Rainforest Reduced the Stochasticity of Soil Bacterial Communities through the Stability of Plant Communities

The effects of natural succession on plant and soil bacterial communities were previously established, but changes in plant and soil bacterial communities and their response to soil properties are not well characterized in different stages of secondary forest succession, especially in tropical regions with endemic plant species. We investigated the dynamics of plant communities, soil properties and the structure of soil bacterial communities at sites representing 33 (early successional stage), 60 (early-mid successional stage) and 73 (mid successional stage) years of secondary succession in the tropical lowland rainforest of Hainan, China, by using16S rRNA high-throughput sequencing. From the perspective of plant composition, the number of families, genera and species were increasing along with the progress of succession. Additionally, the changes in the ranking of important values along with the progress of the forest succession were consistent with the niche width calculated by the previous stage of the plant community. The results of niche overlap, Pearson’s correlation and Spearman’s rank correlation coefficients and significance indicated that in the early stage of succession, tree species did not fully utilize environmental resources. Then, as time went by, the number of negative correlations of plants in the early-mid stage was more than that in the mid stage of succession. Significant differences were found in the species richness of soil microorganisms among the three successional stages. Nutrient contents in early successional stage rainforests were less abundant than in early-mid and mid forest soils. The influence of soil nutrient concentration, particularly N and P content, on soil bacterial composition at the phylum level was larger in the early-mid stage than in the mid stage. The stochasticity of the soil bacterial community at the early successional stage of the rainforest was significantly higher than that at mid stage. Overall, as the diversity of plant communities increased, the competition decreased, the soil nutrient content changed and the stochasticity of soil bacterial communities decreased as a result of forest succession

Secondary Succession Altered the Diversity and Co-Occurrence Networks of the Soil Bacterial Communities in Tropical Lowland Rainforests

The characteristics of plant and soil bacterial communities in forest ecosystems have been reported, but our understanding of the relationship between plant communities and soil bacteria in different stages of secondary tropical rainforest succession is still poor. In June 2018, three different natural successional stages of tropical lowland rainforests, early (33 years), early-mid (60 years), and mid successional stage (73 years), in Hainan Island, China, were selected for this study. By conducting field investigation and 16S rRNA gene high-throughput sequencing, the composition and diversity of tree communities, the niche overlap of tree species with legumes among tree species, and the diversity and composition of soil bacterial communities and co-occurrence networks within communities across the successional stages were investigated. The results showed that plant richness and species diversity increased significantly during the secondary succession of tropical lowland rainforests. The order of positive correlations between nitrogen-fixing legumes and other species in plant communities was early-mid > mid > early successional stage. Soil nutrient content and soil bacterial richness were highest in the early-mid stages of succession, followed by mid and early stages of succession. Organic matter (OM), total nitrogen (TN), alkali nitrogen (AN), and available phosphorus (AP) had a stronger positive impact on soil bacterial communities. Co-occurrence network analysis showed that with the advancement of rainforests succession, the negative correlation between soil bacterial species decreased, and the community stability increased. Overall, as a result of tropical lowland rainforest secondary natural succession, the richness and diversity of plant communities increased, which altered the living conditions of nitrogen-fixing legumes and the soil properties, and the network complexity of soil bacterial communities increased with the rising of rainforest soil nutrient content

Soil physicochemical properties determine leaf traits but not size traits of moso bamboo (Phyllostachys edulis)

Understanding the relationships among leaf and size traits and environment factors is essential for understanding and predicting the dynamics and ecophysiological processes of moso bamboo ( Phyllostachys edulis ) forests across their distribution range. Here, we evaluated these relationships at six sites within the moso bamboo distribution area in China. Specifically, we collected climate (mean annual temperature and precipitation) and soil physicochemical data from the sites, and we measured 14 leaf traits and 2 size traits (height and diameter) of both new and old moso bamboos and evaluated the relationship among environment factors, size traits and leaf traits. Climate factors had significant effects on the leaf traits of new bamboos but on those of old bamboos. For instance, mean annual precipitation (MAP) was the main driver of leaf-trait variation in new bamboos but not in old bamboos. Specifically, MAP was significantly negatively correlated with leaf mass (LM), leaf dry matter content, single leaf area (LA), and leaf width, but positively correlated with specific leaf area and the leaf length to width ratio. Moreover, potential evapotranspiration and solar radiation (SR) significantly affected the leaf nutrient traits of new bamboos. Mean annual temperature and actual evapotranspiration were significantly positively correlated with bamboo height. Bamboo diameter at breast height (DBH) had more explanatory power with respect to leaf traits than plant height, and LA, leaf length and width, and LM all decreased with increasing DBH in new bamboos. A structural equation model showed that soil physicochemical traits significantly affected leaf traits, but not size traits, of new bamboos. Overall, our study indicated an age-dependent response of bamboo leaf traits to environmental factors, although bamboos do not have secondary growth. These results suggest that future environmental changes, including climate change, will lead to age-related responses of bamboo leaf traits, which may further result in changes in stand structure and productivity of moso bamboo forests

Leaf stomatal traits rather than anatomical traits regulate gross primary productivity of moso bamboo (Phyllostachys edulis) stands

Leaf stomatal and anatomical traits strongly influence plant productivity. Understanding the environmental adaptation mechanisms of leaf stomatal and anatomical traits and their relationship with ecosystem productivity is essential to better understand and predict the long-term adaptation strategies to climate change of moso bamboo forests. Here, we selected 6 sites within the moso bamboo distribution area, measured 3 leaf stomatal traits and 10 leaf anatomical traits of unmanaged moso bamboo stands. We explored the spatial variation characteristics of these traits and their response to environmental changes, assessed the relationships among these traits at regional scales through network analysis, and tested the direct and indirect effects of environmental, leaf stomatal and anatomical traits on gross primary productivity (GPP) of bamboo stands using structural equation modeling (SEM). The results showed that both climate and soil factors significantly affected leaf stomatal and anatomical traits of moso bamboo. Solar radiation (SR) and mean annual precipitation (MAP) out of the climatic factors were the key drivers of variation in leaf stomatal and anatomical traits, respectively. Soil moisture and nutrients out of the soil properties significantly affected both leaf stomatal and anatomical traits of moso bamboo. Network analysis further indicated that there was a significant correlation between leaf stomata and anatomical traits. Stomatal size (SS) showed the highest centrality value at the regional scale, indicating that it plays a key role in adjusting the adaptation of plants to external environmental conditions. SEM analysis showed that environment did not directly but indirectly affect GPP via stomatal performance. The environment explained 53.3% and 39.2% of the variation in leaf stomatal and anatomical traits, respectively, and leaf stomatal traits explained 20.8% of the regional variation in GPP. Our results demonstrate a direct effect of leaf stomatal traits rather than leaf anatomical traits on bamboo ecosystem productivity, which provides new insights into model predictions of bamboo forests under global climate change