164 Works

Data from: Historical introgression and the persistence of ghost alleles in the intermediate horseshoe bat (Rhinolophus affinis)

Xiuguang Mao, Guimei He, Panyu Hua, Gareth Jones, Shuyi Zhang & Stephen J. Rossiter
Phylogenetic conflicts between genetic markers can help to disentangle complex histories of phylogeography and introgression among taxa. We previously proposed that the Chinese mainland subspecies of the intermediate horseshoe bat Rhinolophus affinis himalayanus colonized Hainan Island to form the subspecies R. a. hainanus. Subsequent recolonization of the mainland formed a third taxon, R. a macrurus, and a secondary contact zone with the ancestral himalayanus. To test for historical and recurrent genetic exchange between these mainland...

Data from: Asymmetric sensitivity of ecosystem carbon and water processes in response to precipitation change in a semi-arid steppe

Bingwei Zhang, Xingru Tan, Shanshan Wang, Minling Chen, Shiping Chen, Tingting Ren, Jianyang Xia, Yongfei Bai, Jianhui Huang & Xingguo Han
Semi-arid ecosystems play an important role in regulating the dynamics of the global terrestrial CO2 sink. These dynamics are mainly driven by increasing inter-annual precipitation variability. However, how ecosystem carbon processes respond to changes in precipitation is not well understood, due to a lack of substantial experimental evidence that combines increased and decreased precipitation treatments. This study, a 3-year field manipulation experiment with five precipitation levels conducted in a semi-arid steppe, examined the impacts of...

Data from: Carrying capacity in a heterogeneous environment with habitat connectivity

Bo Zhang, Alex Kula, Keenan M.L. Mack, Lu Zhai, Arrix L. Ryce, Wei-Ming Ni, Donald L. DeAngelis & J. David Van Dyken
A large body of theory predicts that populations diffusing in heterogeneous environments reach higher total size than if non-diffusing, and, paradoxically, higher size than in a corresponding homogeneous environment. However, this theory and its assumptions have not been rigorously tested. Here, we extended previous theory to include exploitable resources, proving qualitatively novel results, which we tested experimentally using spatially diffusing laboratory populations of yeast. Consistent with previous theory, we predicted and experimentally observed that spatial...

Grazing intensity significantly changes the C:N:P stoichiometry in grassland ecosystems

Guiyao Zhou, Miao He, Tengfei Yuan, Kees Jan Van Groenigen, Junjiong Shao & Xuhui Zhou
Aim: Livestock grazing can alter carbon (C), nitrogen (N) and phosphorus (P) cycles, thereby affecting the C:N:P stoichiometry in grasslands. In this study, we aimed to examine the underlying mechanisms for the impacts of grazing intensity on grassland C:N:P stoichiometry, especially for the belowground processes and their linkages with aboveground vegetation properties. Location: Global. Time period: 1900-2018. Major taxa studied: Grassland ecosystems. Methods: Here, we conducted a meta-analysis based on 129 published studies to synthesize...

The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity

Shanshan Dong, Chaoxian Zhao, Shouzhou Zhang, Hong Wu, Weixue Mu, Tong Wei, Na Li, Tao Wan, Huan Liu, Jie Cui, Ruiliang Zhu, Bernard Goffinet & Yang Liu
RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded PPR proteins in the transcriptome assemblies of these taxa. We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059...

Data from: Nighttime warming enhances ecosystem carbon-use efficiency in a temperate steppe

Jing Wang, Qian Zhang, Jian Song, Jingyi Ru, Zhenxing Zhou, Jianyang Xia, Jeffrey Dukes & Shiqiang Wan
1. Reductions in the diurnal temperature range (DTR), e.g., greater increases in daily minimum than maximum temperatures, have occurred for several decades and are projected to continue over this century, which could affect terrestrial carbon (C) cycling. Carbon-use efficiency of plants (CUEp) and ecosystems (CUEe) represents the capacity of plants to capture C and ecosystems to store C fixed from the atmosphere, respectively. Few studies have examined how grassland CUE responds to asymmetric warming. 2....

Data from: Loss of top-down biotic interactions changes the relative benefits for obligate mutualists

Rong Wang, Xiao-Yong Chen, Yan Chen, Gang Wang, Derek Dunn, Rupert Quinnell & Steve Compton
The collapse of mutualisms due to anthropogenic changes is contributing to losses of biodiversity. Top predators can regulate biotic interactions between species at lower trophic levels and may contribute to the stability of such mutualisms, but they are particularly likely to be lost after disturbance of communities. We focused on the mutualism between the fig tree Ficus microcarpa and its host-specific pollinator fig wasp and compared the benefits accrued by the mutualists in natural and...

Diversity and identity of economics traits determine the extent of tree mixture effects on ecosystem productivity

Liting Zheng, Han Chen, Shekhar Biswas, Difeng Bao, Xiaochen Fang, Muhammad Abdullah & Enrong Yan
1. Although both observational and experimental studies have shown that positive tree species diversity-productivity relationships are predominant in global forests, weak or the lack of tree species diversity and productivity relationships also exist. Growing evidence has revealed that ecosystem productivity depends more on the functional characteristics of species than on their number. However, exactly to what extent tree diversity effects on ecosystem productivity are influenced by the variability and composition of functional traits have been...

Source–sink dynamics assists the maintenance of a pollinating wasp

Xin Tong, Yuan-Yuan Ding, Jun-Yin Deng, Rong Wang & Xiao-Yong Chen
Dispersal that unites spatially subdivided populations into a metapopulation with source–sink dynamics is crucial for species persistence in fragmented landscapes. Understanding such dynamics for pollinators is particularly urgent owing to the ongoing global pollination crisis. Here, we investigated the population structure and source–sink dynamics of a pollinating wasp (Wiebesia sp. 3) of Ficus pumila in the Zhoushan Archipelago of China. We found significant asymmetry in the pairwise migrant numbers for 22 of 28 cases on...

Additional file 2 of Comprehensive characterization of ubiquitinome of human colorectal cancer and identification of potential survival-related ubiquitination

Wei Zhang, Yan Yang, Liewen Lin, Jingquan He, Jingjing Dong, Bin Yan, Wanxia Cai, Yumei Chen, Lianghong Yin, Donge Tang, Fanna Liu & Yong Dai
Additional file 2. Table S1. Ubiquitination annotation. Table S2. Protein annotation. Table S3. 42 proteins having ten or more than ten ubiquitination modifications. Table S4. 20 ubiquitin-binding motifs. Table S5. 2242 proteins with an upregulated ubiquitination and 1204 proteins with a down-regulated ubiquitination. Table S6. 1172 up-regulated proteins and 1700 down-regulated proteins. Table S7. 646 Secretory proteins. Table S8. 53 proteins having an upregulated expression simultaneously with a down-regulated ubiquitination and 116 proteins having down-regulated...

A dose-finding design for phase I clinical trials based on Bayesian stochastic approximation

Jin Xu, Dapeng Zhang & Rongji Mu
Abstract Background Current dose-finding designs for phase I clinical trials can correctly select the MTD in a range of 30–80% depending on various conditions based on a sample of 30 subjects. However, there is still an unmet need for efficiency and cost saving. Methods We propose a novel dose-finding design based on Bayesian stochastic approximation. The design features utilization of dose level information through local adaptive modelling and free assumption of toxicity probabilities and hyper-parameters....

Additional file 1 of A dose-finding design for phase I clinical trials based on Bayesian stochastic approximation

Jin Xu, Dapeng Zhang & Rongji Mu
Additional file 1: Supplementary Materials.

Additional file 10 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 10: Table S6. Allele frequencies of Q9311B and WSSM in 1946 accessions from 3 K-RG.

Additional file 11 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 11: Fig. S5. Speculation of the subpopulation source of the parental allele at all 14,397 segregating genes by comparing the allele frequencies of Q9311B and WSSM in 772 Geng and 1,174 Xian accessions from 3 K-RG.

Additional file 7 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 7: Table S4. Epistasis QTLs for 12 traits in the three environments.

Additional file 9 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 9: Fig. S4. Whole-genome variation of two parental lines of QYSM. a, Density and chromosome distribution of polymorphic SNPs between Q9311B and WSSM. b, The principal component analysis. c, Phylogenetic positions of two parental lines (Q9311B and WSSM) in the neighbor-joining tree of 1,946 rice accessions from 3 K-RG, in which the known information on the clades of 3 K-RG is indicated.

Additional file 13 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 13: Table S8. The genotypic and phenotypic matrix of the population in ICIMapping format.

Additional file 1 of Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Additional file 1: Table S1. Phenotypic performance and heterosis of traits in Q9311B/WSSM RILs and backcross F1s (Q9311A × RIL).

Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations

Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen & Jianlong Xu
Abstract Background Since its development and wide adoption in China, hybrid rice has reached the yield plateau for more than three decades. To understand the genetic basis of heterosis in rice and accelerate hybrid rice breeding, the yield performances of the elite rice hybrid, Quan-you-si-miao (QYSM) were genetically dissected by whole-genome sequencing, large-scale phenotyping of 1061 recombined inbred lines (RILs) and 1061 backcross F1 (BCF1) hybrids derived from QYSM’s parents across three environments and gene-based...

Additional file 3 of Microbiota and metabolites alterations in proximal and distal gastric cancer patients

Yan Yang, Daofeng Dai, Wen Jin, Yingying Huang, Yingzi Zhang, Yiran Chen, Wankun Wang, Wu Lin, Xiangliu Chen, Jing Zhang, Haohao Wang, Haibin Zhang & Lisong Teng
Additional file 3: Figure S2. The microbial relative abundance of proximal, distal tumor tissues and matched non-tumor tissues at the genus level. Proximal T,proximal GC tumor tissues; Proximal N,proximal GC non-tumor tissues; Distal T, distal GC tumor tissues; Distal N, distal GC non-tumor tissues.

Additional file 4 of Microbiota and metabolites alterations in proximal and distal gastric cancer patients

Yan Yang, Daofeng Dai, Wen Jin, Yingying Huang, Yingzi Zhang, Yiran Chen, Wankun Wang, Wu Lin, Xiangliu Chen, Jing Zhang, Haohao Wang, Haibin Zhang & Lisong Teng
Additional file 4: Figure S3. Differential microbiota of gastric cancer tissues and non-tumor tissues. A Differential taxa from phylum to genus of Distal T and Distal N. B Differential taxa from phylum to genus of Proximal T and Proximal N.

Additional file 5 of Microbiota and metabolites alterations in proximal and distal gastric cancer patients

Yan Yang, Daofeng Dai, Wen Jin, Yingying Huang, Yingzi Zhang, Yiran Chen, Wankun Wang, Wu Lin, Xiangliu Chen, Jing Zhang, Haohao Wang, Haibin Zhang & Lisong Teng
Additional file 5: Figure S4. Metabolite composition and difference between Proximal N and Distal N. A, B OPLS-DA showed that Proximal N and Distal N were not separated into two clusters. Test for OPLS-DA model showed that the OPLS-DA model for this study was valid.

Additional file 1 of The bidirectional association of C-peptide with cardiovascular risk in nondiabetic adults and patients with newly diagnosed type 2 diabetes mellitus: a retrospective cohort study

Shuang-Tong Yan, Jing Sun, Zhao-Yan Gu, Xin-Yu Miao, Li-Chao Ma, Ban-Ruo Sun, Xiao-Min Fu, Hong-Zhou Liu, Guang Yang, Fu-Sheng Fang & Hong Li
Additional file 1: Table S1. Baseline characteristics and cardiovascular events in the participants who visited the hospital at least twice. Table S2. Differences in demographic characteristics among the groups stratified by levels of fasting C-peptide for the participants without previous T2DM. Table S3. Sensitivity analyses of the associations stratified by glucose metabolism status and tertiles of HOMA-IR for the participants without previous T2DM. Table S4. Prevalence of cardiovascular events in the participants stratified by quantiles...

Effects of intensive blood pressure control on mortality and cardiorenal function in chronic kidney disease patients

Yong Zhang, Jing-Jing Li, An-Jun Wang, Bo Wang, Shou-Liang Hu, Heng Zhang, Tian Li & Yan-Hong Tuo
Blood pressure (BP) variability is highly correlated with cardiovascular and kidney outcomes in patients with chronic kidney disease (CKD). However, appropriate BP targets in patients with CKD remain uncertain. We searched PubMed, Embase, and the Cochrane Library for randomized controlled trials (RCTs) of CKD patients who underwent intensive BP management. Kappa score was used to assess inter-rater agreement. A good agreement between the authors was observed to inter-rater reliability of RCTs selection (kappa = 0.77;...

Acute kidney injury in idiopathic membranous nephropathy with nephrotic syndrome

Tianxin Chen, Ying Zhou, Xinxin Chen, Bo Chen & Jingye Pan
The impact of acute kidney injury (AKI) on the progression of renal function in idiopathic membranous nephropathy (iMN) with nephrotic syndrome (NS) patients have not yet been reported, we sought to investigate the incidence, clinical features and prognosis of AKI in iMN with NS patients and determine clinical predictors for progression from AKI to advanced chronic kidney disease (CKD) stage. We analyzed clinical and pathological data of iMN with NS patients retrospectively collected from Jan...

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