143 Works

Additional file 2 of 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
Additional file 2: Table S1. Stepwise model selection coefficients and Wald-Z tests. Table S2. List of measured lipid species. Table S3. Weighted gene co-expression network analysis module components. Table S4. Boruta analysis result.

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...

Additional file 1 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 1: Figure S1 The agarose gel electrophoresis of DNA amplification products of three gyrA gene primer pairs: gyrA1 (A), gyrA2 (B) and gyrA3 (C). 1-7 indicates strains LY18, LY25, LY37, FZB42, SXL408, SXL277 and ACCC01043. Figure S2 The amplification ability of the primer pair gyrA1 and gyrA2 in Bacillus species by computer simulation. The eight Bacillus species were amplified by gyrA1 and nine Bacillus species were amplified by gyrA2. The phylogenetic trees were...

A Gentle Introduction to Bayesian Network Meta-Analysis Using an Automated R Package

Yan Liu, Audrey Béliveau, Yaguang Wei, Michelle Y. Chen, Rosalynn Record-Lemon, Pei-Lun Kuo, Elizabeth Pritchard, Xuyan Tang & Guanyu Chen
Network meta-analysis is an extension of standard meta-analysis. It allows researchers to build a network of evidence to compare multiple interventions that may have not been compared directly in existing publications. With a Bayesian approach, network meta-analysis can be used to obtain a posterior probability distribution of all the relative treatment effects, which allows for the estimation of relative treatment effects to quantify the uncertainty of parameter estimates, and to rank all the treatments in...

MicroRNA-455-3p accelerate malignant progression of tumor by targeting H2AFZ in colorectal cancer

Lizhen Ye, Tingting Fan, Ying Qin, Cheng Qiu, Lulu Li, Mengmeng Dai, Yaoyao Zhou, Yan Chen & Yuyang Jiang
Colorectal cancer (CRC) becomes the second leading cause of cancer-related deaths in 2020. Emerging studies have indicated that microRNAs (miRNAs) play a key role in tumorigenesis and progression. The dysfunctions of miR-455-3p are observed in many cancers. However, its biological function in CRC remains to be confirmed. By sequencing serum sample, miR-455-3p was found to be up-regulated in CRC patients. RT-qPCR demonstrated that the miR-455-3p expression was both higher in the serum and tumor tissues...

The complete mitochondrial genome and phylogenetic analysis of the ocellated angelshark: Squatina tergocellatoides Chen, 1963

Chunbin Jia, Binbin Shan, Yan Liu, Changping Yang, Liangming Wang & Dianrong Sun
The ocellated angelshark (Squatina tergocellatoides Chen, 1963) is a threatened shark within the family Squatinidae. In the present study, we reported the mitochondrial genome sequence of the ocellated angelshark. The complete mitochondrial genome is 16,683 bp in length and contains 37 mitochondrial genes and a control region as similar to most fishes. In addition, we constructed a maximum-likelihood phylogenetic tree of S. tergocellatoides and its relative species. This work will provide molecular data for further...

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

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.%...

Additional file 1 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 1: Figure S1 The agarose gel electrophoresis of DNA amplification products of three gyrA gene primer pairs: gyrA1 (A), gyrA2 (B) and gyrA3 (C). 1-7 indicates strains LY18, LY25, LY37, FZB42, SXL408, SXL277 and ACCC01043. Figure S2 The amplification ability of the primer pair gyrA1 and gyrA2 in Bacillus species by computer simulation. The eight Bacillus species were amplified by gyrA1 and nine Bacillus species were amplified by gyrA2. The phylogenetic trees were...

The circadian timing of noise exposure influences noise-induced inflammatory responses in the mouse cochlea

Shichang Li, Hongwei Zheng, Zhimin Xing, Yan Liu, Lin Han, Zijing Wang & Lisheng Yu
Abstract Introduction: Noise-induced hearing loss is one of the most common forms of sensorineural hearing loss. Nevertheless, the mechanisms of noise-induced hearing loss are still not fully understood. Objective: To investigate the dynamics of inflammatory responses in the mammalian cochlea following noise trauma at two different times, once during the light cycle and once during the dark. Methods: We challenged C57BL/6J mice with moderate, continuous noise trauma at either 9 a.m. or 9 p.m. Auditory...

Deep learning-enabled volumetric cone photoreceptor segmentation in adaptive optics optical coherence tomography images of normal and diseased eyes

Somayyeh Soltanian-Zadeh, Zhuolin Liu, Yan Liu, Ayoub Lassoued, Catherine Cukras, Donald Miller, Daniel Hammer & Sina Farsiu
Objective quantification of photoreceptor cell morphology, such as cell diameter and outer segment length, is crucial for early, accurate, and sensitive diagnosis and prognosis of retinal neurodegenerative diseases. Adaptive optics optical coherence tomography (AO-OCT) provides three-dimensional (3-D) visualization of photoreceptor cells in the living human eye. The current gold standard for extracting cell morphology from AO-OCT images involves the tedious process of 2-D manual marking. To automate this process and extend to 3-D analysis of...

Supplementary document for Deep learning-enabled volumetric cone photoreceptor segmentation in adaptive optics optical coherence tomography images of normal and diseased eyes - 6129718.pdf

Somayyeh Soltanian-Zadeh, Zhuolin Liu, Yan Liu, Ayoub Lassoued, Catherine Cukras, Donald Miller, Daniel Hammer & Sina Farsiu
Supplementary Information

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...

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...

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....

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 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 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.

Registration Year

  • 2023
    13
  • 2022
    115
  • 2021
    9
  • 2020
    2
  • 2019
    1
  • 2017
    2
  • 2015
    1

Resource Types

  • Text
    85
  • Dataset
    36
  • Collection
    20
  • Other
    2

Affiliations

  • Guangxi Institute of Botany
    143
  • Shanghai Jiao Tong University
    125
  • Peking University
    123
  • Sun Yat-sen University
    120
  • Henan University
    119
  • Capital Medical University
    119
  • Inner Mongolia Agricultural University
    119
  • Southern Medical University
    119
  • Huazhong Agricultural University
    119
  • Wuhan University
    119