120 Works

Species packing and the latitudinal gradient in local beta-diversity

Ke Cao, Richard Condit, Xiangcheng Mi, Lei Chen, Wubing Xu, David F. R. P. Burslem, Chunrong Cai, Min Cao, Li-Wan Chang, Chengjin Chu, Hu Du, Sisira Ediriweera, C. S. V. Gunatilleke, I. U. A. N. Gunatilleke, Zhanqing Hao, Jinbo Li, Guangze Jin, Buhang Li, Yankun Liu, Yide Li, Michael J. O'Brien, Xiujuan Qiao, Hongwei Ni, Guochun Shen, Xihua Wang … & Jens-Christian Svenning
The decline in species richness at higher latitudes is among the most fundamental patterns in ecology. Whether changes in species composition across space (beta-diversity) contribute to this gradient of overall local species richness (gamma diversity) remains hotly debated. Previous studies that failed to resolve the issue suffered from a well-known tendency for small samples in areas with high gamma-diversity to have inflated measures of beta-diversity. We provide here a novel analytical test, using beta-diversity metrics...

Gapless genome assembly of East Asian finless porpoise, Neophocaena asiaeorientalis sunameri

Denghua Yin, Chunhai Chen, Danqing Lin, Jialun Zhang, Congping Ying, Yan Liu, Wang Liu, Zhichen Cao, Chenxi Zhao, Chenhe Wang, Liping Liang, Pao Xu, Jianbo Jian & Kai Liu
There are the genome sequence, gene set, coding sequence and protein sequence of Neophocaena asiaeorientalis sunameri.

Additional file 14 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 14. Functional enrichment of genes differentially expressed in the medial preoptic area (MPOA), the nucleus accumbens (NAc), or the lateral septum (LS). For each pairwise comparison, the functional enrichments in gene ontologies of the biological processes (BP), cellular components (CC), and molecular functions (MF) categories as well as in pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) were tested for the differentially expressed genes up- or down-regulated (UP, and DOWN, respectively)....

Additional file 15 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 15. Functional enrichment of overlapping and distinct sets of differentially expressed genes in the medial preoptic area (MPOA). In (A), the number of differentially expressed genes overlapping or distinct between all sets of sexually biased comparisons in the MPOA is depicted. For each set, the functional enrichments in gene ontologies of the biological processes (B), cellular components (C), and molecular functions (D) categories are displayed. ***p < 0.001, hypergeometric test for overlaps between...

Additional file 10 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 10. Differential expression analysis details. For conciseness, the labels of pairwise comparisons were coded in two letters: the first one represents the phenotype (M: mothers, F: fathers, P: paternal males, A: attackers), whereas the second one represents the structure (M: MPOA, N: NAc, L: LS). For instance, PLvAL refers to the comparison between the Paternal and Attackers phenotypes in the LS. DE: differentially expressed.

Additional file 10 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 10. Differential expression analysis details. For conciseness, the labels of pairwise comparisons were coded in two letters: the first one represents the phenotype (M: mothers, F: fathers, P: paternal males, A: attackers), whereas the second one represents the structure (M: MPOA, N: NAc, L: LS). For instance, PLvAL refers to the comparison between the Paternal and Attackers phenotypes in the LS. DE: differentially expressed.

Additional file 3 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 3. Behavioral bouts analysis. For each behavior scored, the duration of each bout was summarized by mean or median across the entire parental behavior test for each animal. Each data point represents a distinct animal, and the boxplots depict the median (thick horizontal line) and the 25th and 75th percentiles.

Additional file 5 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 5. Analysis of variance (ANOVA) results for behavioral bouts analysis.

Additional file 27 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 27. Functional enrichment of pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) in gene co-expression modules derived from the weighted gene coexpression network analysis (WGCNA).

Additional file 6 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 6. Relationships between parental behavior test behaviors. For each pair of behavior, a linear model was fit. Each individual point represents a distinct animal, and the shaded area depicts the 95% confidence interval.

Additional file 7 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 7. Detailed results from the linear regressions between all behaviors scored during the parental behaviors test, testing for an interaction of Group (Mothers/Fathers/Paternal).

Additional file 20 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 20. Analysis of variance (ANOVA) results for the estimated proportions of the “Neurons” cell type in the genes differentially expressed in the medial preoptic area (MPOA), nucleus accumbens (NAc), and lateral septum (LS).)

Additional file 21 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 21. Number of immediate early genes (IEG) in the genes differentially expressed in the medial preoptic area (MPOA), nucleus accumbens (NAc), and lateral septum (LS).

Additional file 9 of Transcriptomic analysis of paternal behaviors in prairie voles

Florian Duclot, Yan Liu, Samantha K. Saland, Zuoxin Wang & Mohamed Kabbaj
Additional file 9. Functional enrichment across structures and phenotypes. For each pairwise comparison, the functional enrichments in gene ontologies of the biological processes (BP), cellular components (CC), and molecular functions (MF) categories as well as in pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) were tested for the differentially expressed genes up- or down-regulated (UP, and DOWN, respectively). The labels of pairwise comparisons were coded in two letters: the first one represents the...

Additional file 1 of Epidemiological and etiological characteristics of mild hand, foot and mouth disease in children under 7 years old, Nanjing, China, 2010–2019

Junjun Wang, Songning Ding, Weijia Xie, Taiwu Wang, Ying Qin, Jiandong Zheng, Xiaokun Yang, Hongting Zhao, Zhibin Peng & Tao Ma
Additional file 1: Supplementary Table 1. Spatial cluster scan of mild hand, foot, and mouth disease cases aged < 7 years in Nanjing, China, 2010-2019. Supplementary Table 2. Enterovirus serotypes distribution for mild hand, foot, and mouth disease cases aged < 7 years in Nanjing, China, 2010-2019.

Theoretical analysis of 60-W solar-pumped single crystal fiber laser

Pengfei Xiang, Lanling Lan, Yan Liu, Hongfei Qi, Yulong Tang & xiuhua ma
In order to improve the output power of solar-pumped single-crystal fiber (SCF) lasers, a novel solar concentrating system is proposed, which consists of a parabolic mirror, a 3D-CPC, and a hollow-core reflector. By ray tracing with TracePro, influence of the fiber’s diameter and the hollow reflector’s shape on the solar absorption efficiency is theoretically investigated. A typical Nd:YAG SCF with a core-diameter of 1 mm, length of 150 mm and doping concentration of 1 at.%...

Supplementary document for Theoretical analysis of 60-W solar-pumped single crystal fiber laser - 6067286.pdf

Pengfei Xiang, Lanling Lan, Yan Liu, Hongfei Qi, Yulong Tang & xiuhua ma
supplemental document of the manuscript

Additional file 2 of Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study

Yan Liu, Polonca Štefanič, Youzhi Miao, Yansheng Xue, Weibing Xun, Nan Zhang, Qirong Shen, Ruifu Zhang, Zhihui Xu & Ines Mandic-Mulec
Additional file 2: TableS1 The information of 127 strains for colony PCR. TableS2 The genomes information for nucleotide variability analysis of gyrA gene and 16S rRNA gene in inter- and intraspecies Bacillus. TableS3 The gyrA gene database information of Bacillus for computer simulation. TableS4 The general primers converted from degenerate primer pair gyrA3. TableS5 The genomes information for SNP analysis of gyrA gene and 16S rRNA gene in four Bacillus species. TableS6 The information of...

Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study

Yan Liu, Polonca Štefanič, Youzhi Miao, Yansheng Xue, Weibing Xun, Nan Zhang, Qirong Shen, Ruifu Zhang, Zhihui Xu & Ines Mandic-Mulec
Abstract Bacillus is a genus of microorganisms (bacteria) and contains many important commercial species used in industry, agriculture and healthcare. Many different Bacilli are relatively well understood at the single-cell level; however, molecular tools that determine the diversity and ecology of Bacillus community are limited, which limits our understanding of how the Bacillus community works. In the present study, we investigated the potential of the housekeeping gene gyrA as a molecular marker for determining the...

Specific triacylglycerol, diacylglycerol, and lyso-phosphatidylcholine species for the prediction of type 2 diabetes: a ~ 16-year prospective study in Chinese

Junda Zhong, Chloe Y. Y. Cheung, Xiuli Su, Chi-Ho Lee, Yi Ru, Carol H. Y. Fong, Yan Liu, Cynthia K. Y. Cheung, Karen S. L. Lam, Zongwei Cai & Aimin Xu
Abstract Background Bioactive lipids play an important role in insulin secretion and sensitivity, contributing to the pathophysiology of type 2 diabetes (T2D). This study aimed to identify novel lipid species associated with incident T2D in a nested case–control study within a long-term prospective Chinese community-based cohort with a median follow-up of ~ 16 years. Methods Plasma samples from 196 incident T2D cases and 196 age- and sex-matched non-T2D controls recruited from the Hong Kong Cardiovascular...

Additional file 1 of High-yield production of protopanaxadiol from sugarcane molasses by metabolically engineered Saccharomyces cerevisiae

Yuan Zhu, Jianxiu Li, Longyun Peng, Lijun Meng, Mengxue Diao, Shuiyuan Jiang, Jianbin Li & Nengzhong Xie
Additional file 1: Table S1. PPD production of engineering Saccharomyces cerevisiae. Table S2. Plasmids used in this study. Table S3. Primers used in this study. Table S4. Primers used for RT-PCR in this study. Table S5. gRNA target sequences used in this study. Figure S1. High-throughput screening of PPD-producing strains. Figure S2. RT-qPCR of PPD-producing strains. Figure S3. PPD production of strain BY-V with glucose/molasses feeding. Figure S4. Construction of Cas9 expression plasmid. Figure S5....

Additional file 1 of High-yield production of protopanaxadiol from sugarcane molasses by metabolically engineered Saccharomyces cerevisiae

Yuan Zhu, Jianxiu Li, Longyun Peng, Lijun Meng, Mengxue Diao, Shuiyuan Jiang, Jianbin Li & Nengzhong Xie
Additional file 1: Table S1. PPD production of engineering Saccharomyces cerevisiae. Table S2. Plasmids used in this study. Table S3. Primers used in this study. Table S4. Primers used for RT-PCR in this study. Table S5. gRNA target sequences used in this study. Figure S1. High-throughput screening of PPD-producing strains. Figure S2. RT-qPCR of PPD-producing strains. Figure S3. PPD production of strain BY-V with glucose/molasses feeding. Figure S4. Construction of Cas9 expression plasmid. Figure S5....

Two new terpenoids with anti-inflammatory activity from the fruits of Arenga pinnata (Wurmb) Merr.

Jia-Tong Wu, Adnan Mohammed Algradi, Yan Liu, Jin-Hai Huo, Xiao-Mao Li, Bing-You Yang & Wei-Ming Wang
Two new terpenoids (1 and 2), arenterpenoid D (1) and pinnasesquiterpene A (2), along with 16 phenylpropanoids (3–18) and 8 known terpenoids (19–26) were isolated from 70% EtOH extract of the Arenga pinnata (Wurmb) Merr. fruits. Their structures were elucidated by spectroscopic methods including HR-ESI-MS, 1D, and 2D NMR. The absolute configuration of arenterpenoid D (1) was defined by X-ray crystallographic analysis. Furthermore, we evaluated the anti-inflammatory activity of all compounds, and outcomes showed that...

Two new terpenoids with anti-inflammatory activity from the fruits of Arenga pinnata (Wurmb) Merr.

Jia-Tong Wu, Adnan Mohammed Algradi, Yan Liu, Jin-Hai Huo, Xiao-Mao Li, Bing-You Yang & Wei-Ming Wang
Two new terpenoids (1 and 2), arenterpenoid D (1) and pinnasesquiterpene A (2), along with 16 phenylpropanoids (3–18) and 8 known terpenoids (19–26) were isolated from 70% EtOH extract of the Arenga pinnata (Wurmb) Merr. fruits. Their structures were elucidated by spectroscopic methods including HR-ESI-MS, 1D, and 2D NMR. The absolute configuration of arenterpenoid D (1) was defined by X-ray crystallographic analysis. Furthermore, we evaluated the anti-inflammatory activity of all compounds, and outcomes showed that...

Data from: Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China

Fabien L. Condamine, A.J. Harris, Junlin Chen, Bo Pan, Michael Moeller, Van Sam Hoang, Ming Kang, Hanghui Kong & AJ Harris
Karst ecosystems in southern China are species-rich and have high levels of endemism, yet little is known regarding the evolutionary processes responsible for the origin and diversification of karst biodiversity. The genus Primulina (Gesneriaceae) comprises ca. 170 species endemic to southern China with high levels of ecological (edaphic) specialization, providing an exceptional model to study the plant diversification in karsts. We used molecular data from nine chloroplast and 11 nuclear regions and macroevolutionary analyses to...

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