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2,418 results on '"Shen, Nan"'

9. Molecular pathways identified from single nucleotide polymorphisms demonstrate mechanistic differences in systemic lupus erythematosus patients of Asian and European ancestry.

Author

Owen, Katherine A, Bell, Kristy A, Price, Andrew, Bachali, Prathyusha, Ainsworth, Hannah, Marion, Miranda C, Howard, Timothy D, Langefeld, Carl D, Shen, Nan, Yazdany, Jinoos, Dall'era, Maria, Grammer, Amrie C, and Lipsky, Peter E

Subjects
Humans, Lupus Erythematosus, Systemic, Genetic Predisposition to Disease, Case-Control Studies, Genotype, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Lupus, Clinical Research, Autoimmune Disease, Human Genome, Genetics, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system
Abstract

Systemic lupus erythematosus (SLE) is a multi-organ autoimmune disorder with a prominent genetic component. Individuals of Asian-Ancestry (AsA) disproportionately experience more severe SLE compared to individuals of European-Ancestry (EA), including increased renal involvement and tissue damage. However, the mechanisms underlying elevated severity in the AsA population remain unclear. Here, we utilized available gene expression data and genotype data based on all non-HLA SNP associations in EA and AsA SLE patients detected using the Immunochip genotyping array. We identified 2778 ancestry-specific and 327 trans-ancestry SLE-risk polymorphisms. Genetic associations were examined using connectivity mapping and gene signatures based on predicted biological pathways and were used to interrogate gene expression datasets. SLE-associated pathways in AsA patients included elevated oxidative stress, altered metabolism and mitochondrial dysfunction, whereas SLE-associated pathways in EA patients included a robust interferon response (type I and II) related to enhanced cytosolic nucleic acid sensing and signaling. An independent dataset derived from summary genome-wide association data in an AsA cohort was interrogated and identified similar molecular pathways. Finally, gene expression data from AsA SLE patients corroborated the molecular pathways predicted by SNP associations. Identifying ancestry-related molecular pathways predicted by genetic SLE risk may help to disentangle the population differences in clinical severity that impact AsA and EA individuals with SLE.

Published
2023

24. Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes

Author

Zhang, Jingcheng, Shen, Nan, Li, Chuang, Xiang, Xingjie, Liu, Gaolei, Gui, Ying, Patev, Sean, Hibbett, David S, Barry, Kerrie, Andreopoulos, William, Lipzen, Anna, Riley, Robert, He, Guifen, Yan, Mi, Grigoriev, Igor V, Kwan, Hoi Shan, Cheung, Man Kit, Bian, Yinbing, and Xiao, Yang

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Biotechnology, Human Genome, Agaricales, Genome, Genome-Wide Association Study, Metagenomics, Shiitake Mushrooms, Shiitake, Population genomics, Adaptation, Genetic divergence, GWAS, Phenotypic differentiation
Abstract

IntroductionMushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi.ObjectivesThis study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution.MethodsWe analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution.ResultsWe detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation.ConclusionAdaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.

Published
2022

32. Signal Acquisition of Luojia-1A Low Earth Orbit Navigation Augmentation System with Software Defined Receiver

Author

Chen, Liang, Lu, Xiangchen, Shen, Nan, Wang, Lei, Zhuang, Yuan, Su, Ye, Li, Deren, and Chen, Ruizhi

Subjects
Electrical Engineering and Systems Science - Signal Processing
Abstract

Low earth orbit (LEO) satellite navigation signal can be used as an opportunity signal in case of a Global navigation satellite system (GNSS) outage, or as an enhancement means of traditional GNSS positioning algorithms. No matter which service mode is used, signal acquisition is the prerequisite of providing enhanced LEO navigation service. Compared with the medium orbit satellite, the transit time of the LEO satellite is shorter. Thus, it is of great significance to expand the successful acquisition time range of the LEO signal. Previous studies on LEO signal acquisition are based on simulation data. However, signal acquisition research based on real data is very important. In this work, the signal characteristics of LEO satellite: power space density in free space and the Doppler shift of LEO satellite are individually studied. The unified symbol definitions of several integration algorithms based on the parallel search signal acquisition algorithm are given. To verify these algorithms for LEO signal acquisition, a software-defined receiver (SDR) is developed. The performance of those integration algorithms on expanding the successful acquisition time range is verified by the real data collected from the Luojia-1A satellite. The experimental results show that the integration strategy can expand the successful acquisition time range, and it will not expand indefinitely with the integration duration.

Published
2021

33. Bayesian Information Criterion for Linear Mixed-effects Models

Author

Shen, Nan and González, Bárbara

Subjects
Statistics - Applications
Abstract

The use of Bayesian information criterion (BIC) in the model selection procedure is under the assumption that the observations are independent and identically distributed (i.i.d.). However, in practice, we do not always have i.i.d. samples. For example, clustered observations tend to be more similar within the same group, and longitudinal data is collected by measuring the same subject repeatedly. In these scenarios, the assumption in BIC is not satisfied. The concept of effective sample size is brought up and improved BIC is defined by replacing the sample size in the original BIC expression with the effective sample size, which will give us a better theoretical foundation in the circumstance that mixed-effects models involve. Numerical experiment results are also given by comparing the performance of our new BIC with other widely used BICs.

Published
2021

34. A Location Method of Pole-to-Ground Fault in DC Transmission Lines Based on VSC

Author

Zhang, Ziguang, Guo, Kang, Shen, Nan, Wang, Wenmei, Wang, Xiaonan, Jia, Menghan, Lin, Chao, Li, Dong, Sun, Guoxiang, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Zeng, Pingliang, editor, Zhang, Xiao-Ping, editor, Terzija, Vladimir, editor, Ding, Yi, editor, and Luo, Yunxia, editor

Published
2023
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42. Decoding PPP Corrections from BDS B2b Signals Using a Software-defined Receiver: an Initial Performance Evaluation

Author

Lu, Xiangchen, Chen, Liang, Shen, Nan, Wang, Lei, Jiao, Zhenhang, and Chen, Ruizhi

Subjects
Electrical Engineering and Systems Science - Signal Processing
Abstract

With the rapid development of China's BeiDou Navigation Satellite System(BDS), the application of real-time precise point positioning (RTPPP) based on BDS has become an active research area in the field of Global Navigation Satellite System (GNSS). BDS has provided the service of broadcasting RTPPP information. It indicates that BDS has become the second satellite system that provides RTPPP services, following Galileo among the GNSS, but work based on this direction has yet to be explored. Therefore, this paper evaluates the performance of precise point positioning (PPP) service using a software-defined receiver (SDR). An experiment was carried out tu verify the feasibility of the SDR. The PPP-B2b signal was processed to obtain PPP service information, including orbit corrections, clock corrections, and differential code bias corrections. The time-varying attributes of these corrections of BDS and GPS are evaluated, and the integrity and stability of the PPP service were analyzed. The results show the PPP-B2b signal can stably provide PPP services for staellites in the Asia-Pacific region, including centimeter to decimeter-level orbit corrections and meter-level clock correction for GPS satellites. Finally, detection tip for bitream availability in SDR is proposed. Some content which is not defined in the official document, such as the PPP-B2b frame arrangement, various correction update cycles and the progress of PPP service are discussed.

Published
2020

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