352 Works

sj-rar-2-chl-10.1177_17475198221145838 – Supplemental material for Palladium-catalyzed transfer hydrogenation of terminal alkynes using ethanol as the hydrogen donor

Jie Hui & Feng Wang
Supplemental material, sj-rar-2-chl-10.1177_17475198221145838 for Palladium-catalyzed transfer hydrogenation of terminal alkynes using ethanol as the hydrogen donor by Jie Hui and Feng Wang in Journal of Chemical Research

Genome-wide identification of genes critical for in vivo fitness of multi-drug resistant porcine extraintestinal pathogenic Escherichia coli by transposon-directed insertion site sequencing using a mouse infection model

Fan Yin, Yan Hu, Zixuan Bu, Yuying Liu, Hui Zhang, Yawen Hu, Ying Xue, Shaowen Li, Chen Tan, Xiabing Chen, Lu Li, Rui Zhou & Qi Huang
Extraintestinal pathogenic Escherichia coli (ExPEC) is an important zoonotic pathogen. Recently, ExPEC has been reported to be an emerging problem in pig farming. However, the mechanism of pathogenicity of porcine ExPEC remains to be revealed. In this study, we constructed a transposon (Tn) mutagenesis library covering Tn insertion in over 72% of the chromosome-encoded genes of a virulent and multi-drug resistant porcine ExPEC strain PCN033. By using a mouse infection model, a transposon-directed insertion site...

Additional file 2 of Bacteriomes in lesions of pulmonary tuberculosis and its association with status of Mycobacterium tuberculosis excretion

Weili Du, Yingli Zhao, Li Zhang, Jialu Che, Zichen Liu, Kun Li & Nanying Che
Additional file 2: Supplemental Table 2. Bacterial metabolic pathways that are significantly down/up regulated in TB-E compared to TB-NE.

Additional file 6 of NLRP3 inflammasome regulates astrocyte transformation in brain injury induced by chronic intermittent hypoxia

Ningning She, Yewen Shi, Yani Feng, Lina Ma, Yuqi Yuan, Yitong Zhang, Zine Cao, Xi Chen, Bingjie Zhao, Haiqin Liu & Xiaoyong Ren
Additional file 6: Table S1. The primer sequences uesd in RT-qPCR.

Additional file 4 of The effect of SNPs in lncRNA as ceRNA on the risk and prognosis of hepatocellular carcinoma

Han Mo, Xi Wang, Guohua Ji, Xiao Liang, Yi Yang, Wenjing Sun, Xueyuan Jia, Lidan Xu, Yuandong Qiao, Henan Zhou, Wenhui Zhao, Songbin Fu & Xuelong Zhang
Additional file 4:

Additional file 3 of The effect of SNPs in lncRNA as ceRNA on the risk and prognosis of hepatocellular carcinoma

Han Mo, Xi Wang, Guohua Ji, Xiao Liang, Yi Yang, Wenjing Sun, Xueyuan Jia, Lidan Xu, Yuandong Qiao, Henan Zhou, Wenhui Zhao, Songbin Fu & Xuelong Zhang
Additional file 3:

Additional file 2 of Enhanced transcriptome-wide RNA G-quadruplex sequencing for low RNA input samples with rG4-seq 2.0

Jieyu Zhao, Eugene Yui-Ching Chow, Pui Yan Yeung, Qiangfeng Cliff Zhang, Ting-Fung Chan & Chun Kit Kwok
Additional file 2. Details of identified rG4 in each rG4-seq library.

Additional file 7 of Enhanced transcriptome-wide RNA G-quadruplex sequencing for low RNA input samples with rG4-seq 2.0

Jieyu Zhao, Eugene Yui-Ching Chow, Pui Yan Yeung, Qiangfeng Cliff Zhang, Ting-Fung Chan & Chun Kit Kwok
Additional file 7. The commands and configurations of the respective tools used in the bioinformatic analysis.

Zinc finger protein 521 attenuates osteoarthritis via the histone deacetylases 4 in the nucleus

Lingan Huang, Pengcui Li, Li Guo, Lu Li, Jie Yuan, Ruipeng Zhao, Haoqian Li & Xiaochun Wei
To determine whether zinc finger protein 521 (Zfp521) has a chondroprotective effect by maintaining extracellular matrix (ECM) homeostasis to attenuate osteoarthritis (OA). In chondrocytes, Zfp521 was overexpressed or silenced to detect its effects on proliferation, apoptosis, and ECM homeostasis. Adenovirus encoding Zfp521 was injected into the knee joints of anterior cruciate ligament transection rats to test its efficacy against OA. Combined with proteomic analysis, the molecular mechanism of Zfp521 in cartilage degeneration was further explored....

Erxian herbal pair enhances bone formation in infected bone nonunion models and attenuates lipopolysaccharide-induced osteoblastinhibition by regulating miRNA-34a-5p

Li Zhang, Yang Zhang, Maomao Miao, Shaoqi Hu, Xuping Wang, Lisha Zhao, Xiaowen Huang, Gang Cao & Dan Shou
Bacterium-induced inflammatory responses cause bone nonunion. Although antibiotics suppress infection, bone loss after antibacterial treatment remains a critical challenge. Erxian herbal pair (EHP) has been proven effective in promoting bone formation. Our study aimed to investigate the effect of EHP on bone repair after anti-infection treatment, explore its effect on a lipopolysaccharide (LPS)-induced osteoblast. We evaluated effects of EHP on bone repair with Micro-CT, and morphology detecting. Chemical constituents of EHP and EHP-containing serum (EHP-CS)...

Identification of major hub genes involved in high-fat diet-induced obese visceral adipose tissue based on bioinformatics approach

Yu Jiang, Rui Zhang, Jia-Qi Guo, Ling-Lin Qian, Jing-Jing Ji, Ya Wu, Zhen-Jun Ji, Zi-Wei Yang, Yao Zhang, Xi Chen, Gen-Shan Ma & Yu-Yu Yao
High-fat diet (HFD) can cause obesity, inducing dysregulation of the visceral adipose tissue (VAT). This study aimed to explore potential biological pathways and hub genes involved in obese VAT, and for that, bioinformatic analysis of multiple datasets was performed. The expression profiles (GSE30247, GSE167311 and GSE79434) were downloaded from Gene Expression Omnibus. Overlapping differentially expressed genes (ODEGs) between normal diet and HFD groups in GSE30247 and GSE167311 were selected to run protein–protein interaction network, GO...

Efficient Approximation of Gromov-Wasserstein Distance Using Importance Sparsification

Mengyu Li, Jun Yu, Hongteng Xu & Cheng Meng
As a valid metric of metric-measure spaces, Gromov-Wasserstein (GW) distance has shown the potential for matching problems of structured data like point clouds and graphs. However, its application in practice is limited due to the high computational complexity. To overcome this challenge, we propose a novel importance sparsification method, called Spar-GW, to approximate GW distance efficiently. In particular, instead of considering a dense coupling matrix, our method leverages a simple but effective sampling strategy to...

Efficient Approximation of Gromov-Wasserstein Distance Using Importance Sparsification

Mengyu Li, Jun Yu, Hongteng Xu & Cheng Meng
As a valid metric of metric-measure spaces, Gromov-Wasserstein (GW) distance has shown the potential for matching problems of structured data like point clouds and graphs. However, its application in practice is limited due to the high computational complexity. To overcome this challenge, we propose a novel importance sparsification method, called Spar-GW, to approximate GW distance efficiently. In particular, instead of considering a dense coupling matrix, our method leverages a simple but effective sampling strategy to...

A plant virus hijacks phosphatidylinositol-3,5-bisphosphate to escape autophagic degradation in its insect vector

Haitao Wang, Jianhua Zhang, Haoqiu Liu, Man Wang, Yan Dong, Yijun Zhou, Sek-Man Wong, Kai Xu & Qiufang Xu
Hosts can initiate macroautophagy/autophagy as an antiviral defense response, while viruses have developed multiple ways to evade the host autophagic degradation. However, little is known as to whether viruses can target lipids to subvert autophagic degradation. Here, we show that a low abundant signaling lipid, phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2), is required for rice black-streaked dwarf virus (RBSDV) to evade the autophagic degradation in the insect vector Laodelphax striatellus. RBSDV binds to PtdIns(3,5)P2 and elevates its level...

A plant virus hijacks phosphatidylinositol-3,5-bisphosphate to escape autophagic degradation in its insect vector

Haitao Wang, Jianhua Zhang, Haoqiu Liu, Man Wang, Yan Dong, Yijun Zhou, Sek-Man Wong, Kai Xu & Qiufang Xu
Hosts can initiate macroautophagy/autophagy as an antiviral defense response, while viruses have developed multiple ways to evade the host autophagic degradation. However, little is known as to whether viruses can target lipids to subvert autophagic degradation. Here, we show that a low abundant signaling lipid, phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2), is required for rice black-streaked dwarf virus (RBSDV) to evade the autophagic degradation in the insect vector Laodelphax striatellus. RBSDV binds to PtdIns(3,5)P2 and elevates its level...

LncRNA KCNQ1OT1 inhibits the radiosensitivity and promotes the tumorigenesis of hepatocellular carcinoma via the miR-146a-5p/ACER3 axis

Ganghua Yang, Lijing Zhou, Qinhong Xu, Fandi Meng, Yong Wan, Xiankui Meng, Lin Wang & Lei Zhang
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death, and radiotherapy is currently one of the main treatments. Long non-coding RNAs (lncRNAs) are associated with the radiosensitivity and tumorigenesis of HCC. However, the role and molecular mechanism of potassium voltage-gated channel subfamily Q member 1 overlapping transcript 1 (KCNQ1OT1) in HCC are still unclear. The relative expression of KCNQ1OT1, microRNA-146a-5p (miR-146a-5p) and alkaline ceramidase 3 (ACER3) was quantified by quantitative real-time polymerase chain...

BMI1 promotes steroidogenesis through maintaining redox homeostasis in mouse MLTC-1 and primary Leydig cells

Tingting Gao, Meng Lin, Binbin Shao, Qiao Zhou, Yufeng Wang, Xia Chen, Dan Zhao, Xiuliang Dai, Cong Shen, Hongbo Cheng, Shenmin Yang, Hong Li, Bo Zheng, Xingming Zhong, Jun Yu, Li Chen & Xiaoyan Huang
In males, aging is accompanied by decline in serum testosterone levels due to impairment of testicular Leydig cells. The polycomb protein BMI1 has recently been identified as an anti-aging factor. In our previous study, BMI1 null mice showed decreased serum testosterone and Leydig cell population, excessive oxidative stress and p16/p19 signaling activation. However, a cause-and-effect relationship between phenotypes and pathways was not investigated. Here, we used the rescue approach to study the role of oxidative...

Exogenous brassinosteroids promotes root growth, enhances stress tolerance, and increases yield in maize

Hao Zhang, Dan Zhao, Ziyan Tang, Ying Zhang, Ke Zhang, Jingao Dong & Fengru Wang
Brassinosteroids (BRs) regulate of maize (Zea mays L.) growth, but the underlying molecular mechanism remains unclear. In this study, we used a multi-disciplinary approach to determine how BRs regulate maize morphology and physiology during development. Treatment with the BRs promoted primary root the elongation and growth during germination, and the early development of lateral roots. BRs treatment during the middle growth stage increased the levels of various stress resistance factors, and enhanced resistance to lodging,...

Data from: Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

Jin Sun, Yu Zhang, Ting Xu, Yang Zhang, Huawei Mu, Yanjie Zhang, Yi Lan, Christopher J. Fields, Jerome H. L. Hui, Wei-Peng Zhang, Runsheng Li, Wenyan Nong, Fiona K. M. Cheung, Jian-Wen Qiu & Pei-Yuan Qian
Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialised macrobenthos such as mussels. But lack of genome information hinders understanding of the adaptation of these animals to such inhospitable environment. Here we report the genomes of a deep-sea vent/seep mussel Bathymodiolus platifrons and a shallow-water mussel Modiolus philippinarum. Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilising protein...

Development of an automatic integrated gene detection system for novel severe acute respiratory syndrome-related coronavirus (SARS-CoV2)

Yuchang Li, Jing Li, Ying Zhang, Lizhong Dai, Lin Li, Juan Liu, Sen Zhang, Xiaoyan Wu, Yi Hu, Chenfeng Qin, Tao Jiang & Xiaoping Kang
In December 2019, Wuhan, China suffered a serious outbreak of a novel coronavirus infectious disease (COVID) caused by novel severe acute respiratory syndrome-related coronavirus (SARS-CoV 2). To quickly identify the pathogen, we designed and screened primer sets, and established a sensitive and specific qRT-PCR assay for SARS-CoV 2; the lower limit of detection (LOD) was 14.8 (95% CI: 9.8–21) copies per reaction. We combined this qRT-PCR assay with an automatic integration system for nucleic acid...

First-order Newton-type Estimator for Distributed Estimation and Inference

Xi Chen, Weidong Liu & Yichen Zhang
This paper studies distributed estimation and inference for a general statistical problem with a convex loss that could be non-differentiable. For the purpose of efficient computation, we restrict ourselves to stochastic first-order optimization, which enjoys low per-iteration complexity. To motivate the proposed method, we first investigate the theoretical properties of a straightforward Divide-and-Conquer Stochastic Gradient Descent (DC-SGD) approach. Our theory shows that there is a restriction on the number of machines and this restriction becomes...

First-Order Newton-Type Estimator for Distributed Estimation and Inference

Xi Chen, Weidong Liu & Yichen Zhang
This article studies distributed estimation and inference for a general statistical problem with a convex loss that could be nondifferentiable. For the purpose of efficient computation, we restrict ourselves to stochastic first-order optimization, which enjoys low per-iteration complexity. To motivate the proposed method, we first investigate the theoretical properties of a straightforward divide-and-conquer stochastic gradient descent approach. Our theory shows that there is a restriction on the number of machines and this restriction becomes more...

IncRNA ZFAS1 contributes to the radioresistance of nasopharyngeal carcinoma cells by sponging hsa-miR-7-5p to upregulate ENO2

Jiaojiao Peng, Feng Liu, Hong Zheng, Qi Wu & Shixi Liu
Previous research revealed that lncRNA ZFAS1 could promote nasopharyngeal carcinoma (NPC) by inhibiting its downstream target axis. However, the association between ZFAS1 and radioresistant NPC cells is unclear. This study aimed to explore the roles of ZFAS1 in the radioresistance of NPC. Bioinformatics analysis was conducted to identify the significant factors (ENO2 and miR-7-5p) that contributed to the radioresistance of NPC cells. After performing qRT-PCR analysis, we found that the expression of ZFAS1 and ENO2...

Novel insights into clear cell renal cell carcinoma prognosis by comprehensive characterization of aberrant alternative splicing signature: a study based on large-scale sequencing data

Dong Zhang, Wenjie Zhang, Rui Sun & Zhongxian Huang
Clear cell renal cell carcinoma (ccRCC) is the most common type with poor prognosis in kidney tumor. Growing evidence has indicated that aberrant alternative splicing (AS) events are efficacious signatures for tumor prognosis prediction and therapeutic targets. However, the detailed roles of AS events in ccRCC are largely unknown. In our study, level 3 RNA-seq data was acquired from The Cancer Genome Atlas dataset and corresponding AS profiles were detected with the assistance of SpliceSeq...

Novel insights into clear cell renal cell carcinoma prognosis by comprehensive characterization of aberrant alternative splicing signature: a study based on large-scale sequencing data

Dong Zhang, Wenjie Zhang, Rui Sun & Zhongxian Huang
Clear cell renal cell carcinoma (ccRCC) is the most common type with poor prognosis in kidney tumor. Growing evidence has indicated that aberrant alternative splicing (AS) events are efficacious signatures for tumor prognosis prediction and therapeutic targets. However, the detailed roles of AS events in ccRCC are largely unknown. In our study, level 3 RNA-seq data was acquired from The Cancer Genome Atlas dataset and corresponding AS profiles were detected with the assistance of SpliceSeq...

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