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1. Statistics, machine learning and deep learning for population genetic inference

Author

Qin, Xinghu and Gaggiotti, Oscar E.

Subjects
576.5, Machine learning, Deep learning, Population genetics, Population structure, Detection of natural selection, Information-based summary statistics, Genome scan, Genome wide association study
Abstract

Deciphering the evolutionary changes from raw DNA data effectively without the loss of intrinsic information has been the fundamental and core work in population genetics. However, some statistical challenges still restrict the inferential performance in population genetics, for example, the undue emphasis on rare or common alleles measured by different statistics, the ubiquitous multimodal genetic structure within populations, and complex genotype-by-environment associations. In this thesis, I propose to integrate the information-based statistics with machine learning approaches to address these problems and challenges for population genetic inference. First, I evaluated the performance of the information-based summary statistics for spatial demography inference. I showed that the summary statistics based on Shannon differentiation and the transformed diversity of order q=1 had higher power to discriminate spatially-structured scenarios than the traditional allelic richness and heterozygosity-based summary statistics. This provides guidelines for using summary statistics to make inference of spatial demography and for developing new statistical methods to detect signatures of evolutionary changes. Second, I proposed to use Kernel Local Fisher Discriminant Analysis of Principal Components (KLFDAPC) for population genetic structure inference considering the nonlinear and multimodal genetic information between individuals. KLFDAPC outperformed both PCA and DAPC in discriminatory power and in predicting individual geographic origin. KLFDAPC is useful for geographic ancestry inference and correction of population stratification in GWAS. Finally, I proposed a deep learning-based approach (DeepGenomeScan) to detect signals of selection. DeepGenomeScan had higher power than the commonly used machine learning approaches such as pcadapt and RDA in identifying signatures of selection. Furthermore, DeepGenomeScan can be extended to implement various genome-wide association studies (GWAS, TWAS, PWAS, and MWAS) by performing a systematic scanning on genome-wide variants to detect the genetic variations responsible for complex traits or involved in adaptation. In summary, this dissertation addresses several foundational questions in statistics-based and machine learning-based inference, contributing several the-state-of-the-art statistical tools for population genetic inference.

Published
2021

3. The third Intensive Care Bundle with Blood Pressure Reduction in Acute Cerebral Haemorrhage Trial (INTERACT3): an international, stepped wedge cluster randomised controlled trial

Author

Robinson, Thompson, Miranda, J. Jaime, Anderson, Craig S., You, Chao, Song, Lili, Parry-Jones, Adrian, Sprigg, Nikola, Durrans, Sophie, Harris, Caroline, Bamford, Ann, Smith, Olivia, Herbert, Robert, Chen, Christopher, Whiteley, William, Hu, Rong, Billot, Laurent, Li, Qiang, Mysore, Jayanthi, Hu, Xin, Zhang, Yao, Liu, Feifeng, Sakamoto, Yuki, You, Shoujiang, Han, Qiao, Crutzen, Bernard, Li, Yunke, Cheung, Emily, Jan, Stephen, Liu, Hueiming, Ouyang, Menglu, Sun, Lingli, Chu, Honglin, Anjum, Anila, Gonzalez Mc Cawley, Francisca, Del Rio, Alejandra, Rimoli, Bruna, Cerantola, Rodrigo, Jeevarajah, Thanushanthan, Kannangara, Madhushani, Joseph, Andrene, Nanayakkara, Chamath, Chen, Xiaoying, Malavera, Alejandra, Zhang, Chunmiao, Yang, Zhao, Li, Brook, Meng, Zhuo, Liu, Leibo, Ning, Yi, Dong, Le, Armenis, Manuela, Lim, Joyce, Monaghan, Helen, Ma, Lu, Li, Xi, Luo, Rui, Cheng, Guojuan, Dong, Yilin, Liu, Ziqin, Wang, Shuihong, Zhang, Ying, Cheng, Jipeng, Shi, Hui, Li, Wenjing, Mou, Langming, Yi, Ping, Chen, Chen, Chen, Xue, Weerawardena, Shalomi, Ellawala, Poornima, Ranasinghe, Enalee, Rodrigo, Chrishmi, Wahab, Kolawala, Adeniyi, Sunday, Pandian, Jeyaraj, Khanna, Megha, Muñoz Venturelli, Paula, González, Francisca, Urrutia Goldsack, Francisca, Wasay, Mohammad, Begum, Dilshad, Pontes-Neto, Octavio, Camilo, Millene, Dias, Francisco, Vincenzi, Octavio, Moro, Carla, Santos, Renata, Texeira, Nara, Longo, Alexandre, Liberato, Rafaela, Martins, Sheila, Pille, Arthur, Chwal, Bruna, Silva, Isabel, Titton, Natacha, Weiss, Gustavo, Mora, Daissy, Ouriques, Magda, Carbonera, Leonardo, Bazan, Rodrigo, Modolo, Gabriel, Winckler, Fernanda, Miranda, Luana, Souza, Juli, Rojo, Alexis, Uslar, Wilhelm, Medel, Lorena, Lopez, Javiera, Herrero, Diego, Lavados, Pablo, Vargas Latorre, Barbara, Conejan, Nathalie, Esparza, Tomas, Sotomayor, Patricio, Wenger, Denisse, Gigoux, Juan Pablo, Letelier, Aldo, Acevedo, Lilian, Moya, Vivianne, Figueroa, Cristian, Vallejos, Nicol, Guerrero, Rodrigo, Velasquez, Mauricio, Vallejos, Jose, Pallauta, Kimerly, Santibanez, Tamara, Queirolo, Angelo, Lobos, Andrea, Jiang, Yongming, Li, Weimin, Huang, Wei, Luo, Ke, Liu, Gangying, Tang, Guanghai, Yang, Guang, Jiang, Hongtao, Zhang, Xu, Jing, Hongyan, Zhu, Sheng, Pu, Bo, Lv, Dong, Kang, Hui, Hu, Qiuping, She, Xiaochun, Jiang, Xiaoming, Chen, Yanli, Yang, Shenghua, He, Jianjun, Li, Zongping, Cheng, Gang, Huang, Hailin, Wang, Xiaoyi, Lin, Jianqiong, Chen, Minhui, Yang, Chenghao, Ding, Hao, Deng, Yunliang, Luo, Fei, Zhang, Rongjun, Wang, Xiaofeng, Zhang, Hongbing, Yang, Xiaoliang, Zhang, Yang, Yang, Chengyi, He, Yu, Liu, Feng, Wang, Rongjie, Zhang, Yuhui, Xin, Xiaodong, Feng, Bin, Hao, Wanru, Song, Chang, Guo, Yun, Jiang, Dehua, Chen, Jie, Tang, Changtong, Zhu, Hongliang, Li, Xin, Cui, Jin, Xu, Haidong, Li, Boyang, Tang, Fusheng, Li, Yuanbin, Gao, Min, Yang, Bo, Xu, Xuejun, Deng, Bing, Zheng, Yi, Ge, Yuanhong, Chen, Keyu, Liu, Yang, Li, Xinshen, Zhong, Tingting, Xu, Jianfeng, Zhang, Hai, Wang, Jiyue, Zhu, Jianxin, Sun, Hanyu, Yu, Fuhua, Zhang, Xueguang, Xu, Jianguo, Zhang, Mingsen, Wang, Bin, Ma, Yiming, Jiang, Donglin, Zhou, Jun, Liu, Cong, Nie, Wenhong, Li, Mingguo, Tian, Tao, Li, Yong, He, Mingfang, Tu, Xiaolong, Wu, Zhengjun, Liu, Hong, Zhong, Dongsheng, Jiang, Rongcai, Sun, Jian, Tian, Ye, Wei, Yingsheng, An, Shuo, Wei, Pingbo, Luo, Le, Lin, Bin, Liu, Gang, Wen, Yan, Cai, Qiang, Chen, Qianxue, Lei, Pan, Li, Zhiyang, Zhang, Meifang, He, Jiaquan, Chen, Yan, Liu, Jun, Liu, Xinghai, Li, Junyan, Chen, Min, Wang, Jing, Zhou, Bingzhi, Ye, Baichun, Zhang, Jiancheng, Zhang, Manyuan, Pan, Xuming, Yu, Xiaoxiang, Xu, Jian, Xiao, Qingbao, Wang, Yuefei, Tao, Liang, Shi, Lin, Zheng, Niandong, You, Guoliang, Lei, Bo, Chen, Shu, Wu, Honggang, Hu, Jin, Zhao, Jianlan, Yu, Jian, Yuan, Qiang, Du, Zhuoying, Tang, Xielin, Li, Qianke, Liu, Shenghua, Yang, Feilong, Xiao, Kui, Luo, Chao, Wang, Guang, Che, Xudong, Teng, Zhipeng, Wan, Wenwu, Li, Jun, Liu, Yu, Fan, Mingbo, Zhang, Tao, Cai, Lun, Ma, Yuan, Ma, Zhifeng, Li, Bin, He, Linlin, Li, Jinghui, Zhang, Weibing, Zhang, Shuxin, Zhang, Hongzhen, Dai, Yingguang, Lei, Jun, Mao, Lei, Huang, Yiyang, Zhou, Zhi, Chen, Ping, Chen, Fang, Wei, Pan, Li, Tiangui, Chen, Honglin, Zeng, Mengfei, Mou, Kejie, Xue, Jun, Jiang, Yong, Tang, Xiaoping, Chen, Tao, Zhang, Yalan, Xu, Yanbing, Gu, Yuchen, Chen, Lei, Zhao, Yujun, Yang, Bin, Kuai, Peng, Wang, Xi, Yang, Yuwang, Hu, Xueling, Zhang, Huitian, Yang, Yintao, Wang, Weifeng, Zhang, Junyi, Cheng, Wei, Zhang, Xiaoxue, Ma, Xiaowen, He, Qin, Zhang, Li, Gao, Rong, Liu, Huixiang, Ye, Jingwei, Xu, Ping, Wu, Xin, Yuan, Yuan, Zou, Peng, Zhang, Zhen, Cheng, Jiyong, Zhou, Zhangming, Zeng, Yijun, Liang, Zhang, Du, Deming, Yu, Shui, Cao, Yongjun, Xu, Jiaping, Huang, Zhichao, Chen, Dongqin, Xiao, Wenfeng, Zhu, Li, Yuan, Miao, Wang, Yuhai, Shi, Dongliang, Hu, Xu, Xiang, Dingchao, Shi, Like, Wang, Hongqin, Yang, Liu, Miao, Wang, Hu, Yiyi, Zhao, Yuchun, Hu, Xi, Zhou, Weiduo, Sun, Chao, Tang, Dong, Yao, Kun, You, Jin, Chen, Shishi, Yao, Jianmin, Li, Huanmei, Liu, Jinmei, Bai, Ailin, Yi, Yong, Deng, Qingshan, Luo, Peng, Wang, Han, Jiang, Jingcheng, Yang, Qingwei, He, Shunpo, Wang, Jun, Chen, Yu, He, Hua, Deng, Yuyang, Cao, Zhikai, Yi, Xuxia, Luo, Jinbiao, Luo, Shuang, Gong, Min, Liu, Li, Gao, Xuejun, Liu, Jia, Wu, Li'e, Zhang, Jia, Sun, Hongying, Li, Xinhui, Jia, Lu, Wu, Jianbing, Zhang, Jie, Zhang, Huajun, Du, Chunfu, Li, Shun, Yang, Xiaobin, He, Jie, Liao, Lei, Zhou, Gezhi, Dong, Wentao, Chen, Yunxiang, Lin, Xiaofeng, Shui, Xujian, Zhang, Peng, Zhao, Yuan, Yang, Hongli, Zhao, Wenbin, Zhang, Xiaoyi, Chen, Jincao, Wu, Qian, Dai, Xuan, Tang, Baogui, Wang, Yinjuan, Liu, Tao, Zhang, Haixia, Duan, Faliang, Luo, Ming, Jiao, Qingfang, Lei, Guoliang, Wang, Dong, Song, Chunwang, Tan, Haopeng, Ye, Feng, Qin, Xinghu, Liang, Xiaolong, Liu, Junling, Yang, Lang, Yang, Jie, Lin, Yapeng, Yang, Qian, Ma, Xuntai, Qi, Yinkuang, Pan, Baogen, Jiang, Caixia, Ye, Zhanying, Dong, Ce, Yue, Xiongfei, Yang, Xiaopeng, Maimaitiyiming, Tuoheti, Dong, Jun, Wu, Yonggang, Gao, Feng, Zhao, Deqiang, Zhang, Xinghai, Wang, PengJun, Jiang, Hongbo, Li, Jianping, Zhang, Wei, Chen, Jing, Tong, Haibo, Wang, Yonghong, Qiao, Kaipeng, Guo, Fuyou, Zhang, Mingchu, Hu, Yan, Feng, Mengzhao, Song, Dengpan, Zuo, Yi, Chen, Shangjun, Qian, Chao, Li, Baoming, Ma, Jingku, Zhang, Sunfu, Kong, Bin, Dong, Xingyu, Fang, Sheng, Lu, Bin, Li, Yang, Yang, Yongling, Yu, Hong, Sun, Huaiyu, Wang, Yue, Wang, Weimin, Li, Tong, Li, Shengli, Xu, Zhiming, Wang, Yongyi, Dong, Qiang, Tang, Yuping, Chu, Heling, Lu, Ying, Wang, Zhong, Sun, Xiaoou, Zhao, Jianhua, Yang, Shuaifeng, Qian, Xiying, Saroja, Aralikatte Onkarappa, Naik k, Ravishankar, Chindhi, Sandip, Pampaniya, Nakul, Amaresh, Kurubara, Iype, Thomas, R, Dileep, Rajan, Reeja, Panicker, Praveen, Das, Rupjyoti, Choudhury, Nupur, Gohain, Pankaja, Webster, Jemin, Pakma, Biyol, Sangi, Lalbiak, Sebastian, Ivy, Aggrawal, Gaurav, Raj, Komal, Rajoura, Deepankshi, Singh, Sulena, Aggrawal, Varun, Narang, Amit, Arauz, Antonio, Cano-Nigenda, Vanesa, López-Mena, Diego, Valdez-Ruvalcaba, Héctor, Toledo-Treviño, Roberto, Obiako, Reginald, Abubakar, Sani, Emeka, Oguike, Olayemi, Balogun, Lois, Melika, Philip, Ibinaiye, Comfort O, Olurishe, Okubadejo, Njideka, Agabi, Osigwe, Ojo, Oluwadamilola, Wahab, Kolawole, Bello, Abiodun, Ibukun, Oyinloye, Sanayaolu, Olufemi, Jimoh, Abdulraheem, Waheed, Shahid, Kamal, Dr.Ayeesha, Shoaib, Raja Farhat, Orooj, Fizza, Majid, Sadaf, Zehra, Taskeen, Khan, Abdus Salam, Shanker, Ravi, Syed, Nadir Ali, Ahmad, Nashwa, Abanto, Carlos, Valencia, Ana, Barrientos, Danny, Ramirez, Jorge, Calle, Pilar, Palliyeguruge, Dilum, Muthucumarana, Sumudu, Ratnayaka, Shiroma, Ganihiarachchi, Dilhara, Bandaranayake, Arundathi, Somaratne, S.D.B, Narayana, Saumya, Gallage, Sithara, Senanayake, Bimsara, Samarasiri, Udari, Luke, Dunya, Sivapathasundaram, Mythily, Sahadevan, Vithoosan, Rasmi, Amani, Deshaka, Yuran, Fernando, Nilukshi, Munasinghe, Aruna, Rathnapriya, Kapilanga, Nissanka, A.S, Karunathilake, Kanchana, Gayan, Isuru, Wijenayake, Kaminda, Gunasekara, Hasitha, Vidyarathne, Jagath, Keshavaraj, Ajantha, Janarthanan, Kanagasabapathy, Gerald Jeevathasan, Arhivalaky, Sivamainthan, Sivaram, John Priyanth, Mathyamuthan, John Priyanth, Abirami, Rajendiran, Thambippillai, Alwis, Sanjeewa, Gunasekare, Nushara, Liyanarachchi, Vasundara, Dissanayake, Athula, Uluwattage, Wimalasiri Mewa, Ratnayake, Gimhani, Rajinee, Charika, Jayawardana, Sakura, Peiris, Janaka, Wicramasinghe, Ranjith, Fernando, Chamila, Abbas, Jessie, Withanage, Nethmini, Bandara, Makaranda, Mai, Duy Ton, Nguyen, Van Chi, Dao, Viet Phuong, Vuong, Xuan Trung, Nguyen, Tien Dung, Dinh, Trung Hieu, Phan, Ha Quan, Bui, Quoc Viet, Phung, Dinh Tho, Pham, Quang Tho, Pham, Dinh Dai, Do, Duc Thuan, Dang, Phuc Duc, Dang, Minh Duc, Nguyen, Dang Hai, Nguyen, Thi Phuong Nga, Nguyen, Quoc Huy, Pham, Quoc Dai, Chau, Quoc Vinh, Tai, Vinh Thy Van, Le, Tran Vinh, Le, Cong Tri, Tran, Ha Mai Khuong, Nguyen, Huu Khanh, Ngyen, Hoang Minh Thao, Vo, Duc Chien, Nguyen, Thai My Phuong, Tran, Trung Thanh, Vo, Thi Hanh Vi, Cao, Hao Nhien, Nguyen, Ba Thang, Le, Thi Ngoc Suong, La, Thien Duc, Pham, Chi Duc, Thai, Huy, Muñoz-Venturelli, Paula, de Silva, Asita, Thang, Nguyen Huy, Wahab, Kolawole W, Pandian, Jeyaraj D, Pontes-Neto, Octavio M, Shi, Haiping, Wang, Xia, Zhao, Yang, Li, Hao, Liu, Yi, Jiang, Yan, Wu, Bo, Liu, Ming, and Anderson, Craig S

Published
2023
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4. DeepGenomeScan of 15 Worldwide Bovine Populations Detects Spatially Varying Positive Selection Signals.

Author

Kumar, Harshit, Qin, Xinghu, Bhushan, Bharat, Dutt, Triveni, and Panigrahi, Manjit

Subjects
*LOCUS (Genetics), *NATURAL selection, *DEEP ecology, *MILK proteins, *MILKFAT
Abstract

Identifying genomic regions under selection is essential for understanding the genetic mechanisms driving species evolution and adaptation. Traditional methods often fall short in detecting complex, spatially varying selection signals. Recent advances in deep learning, however, present promising new approaches for uncovering subtle selection signals that traditional methods might miss. In this study, we utilized the deep learning framework DeepGenomeScan to detect spatially varying selection signatures across 15 bovine populations worldwide. Our analysis uncovered novel insights into selective sweep hotspots within the bovine genome, revealing key genes associated with physiological and adaptive traits that were previously undetected. We identified significant quantitative trait loci linked to milk protein and fat percentages. By comparing the selection signatures identified in this study with those reported in the Bovine Genome Variation Database, we discovered 38 novel genes under selection that were not identified through traditional methods. These genes are primarily associated with milk and meat yield and quality. Our findings enhance our understanding of spatially varying selection's impact on bovine genomic diversity, laying a foundation for future research in genetic improvement and conservation. This is the first deep learning-based study of selection signatures in cattle, offering new insights for evolutionary and livestock genomics research. [ABSTRACT FROM AUTHOR]

Published
2024
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9. The third Intensive Care Bundle with Blood Pressure Reduction in Acute Cerebral Haemorrhage Trial (INTERACT3): an international, stepped wedge cluster randomised controlled trial

Author

Ma, Lu, primary, Hu, Xin, additional, Song, Lili, additional, Chen, Xiaoying, additional, Ouyang, Menglu, additional, Billot, Laurent, additional, Li, Qiang, additional, Malavera, Alejandra, additional, Li, Xi, additional, Muñoz-Venturelli, Paula, additional, de Silva, Asita, additional, Thang, Nguyen Huy, additional, Wahab, Kolawole W, additional, Pandian, Jeyaraj D, additional, Wasay, Mohammad, additional, Pontes-Neto, Octavio M, additional, Abanto, Carlos, additional, Arauz, Antonio, additional, Shi, Haiping, additional, Tang, Guanghai, additional, Zhu, Sheng, additional, She, Xiaochun, additional, Liu, Leibo, additional, Sakamoto, Yuki, additional, You, Shoujiang, additional, Han, Qiao, additional, Crutzen, Bernard, additional, Cheung, Emily, additional, Li, Yunke, additional, Wang, Xia, additional, Chen, Chen, additional, Liu, Feifeng, additional, Zhao, Yang, additional, Li, Hao, additional, Liu, Yi, additional, Jiang, Yan, additional, Chen, Lei, additional, Wu, Bo, additional, Liu, Ming, additional, Xu, Jianguo, additional, You, Chao, additional, Anderson, Craig S, additional, Robinson, Thompson, additional, Miranda, J. Jaime, additional, Anderson, Craig S., additional, Parry-Jones, Adrian, additional, Sprigg, Nikola, additional, Durrans, Sophie, additional, Harris, Caroline, additional, Bamford, Ann, additional, Smith, Olivia, additional, Herbert, Robert, additional, Chen, Christopher, additional, Whiteley, William, additional, Hu, Rong, additional, Mysore, Jayanthi, additional, Zhang, Yao, additional, Jan, Stephen, additional, Liu, Hueiming, additional, Sun, Lingli, additional, Chu, Honglin, additional, Anjum, Anila, additional, Gonzalez Mc Cawley, Francisca, additional, Del Rio, Alejandra, additional, Rimoli, Bruna, additional, Cerantola, Rodrigo, additional, Jeevarajah, Thanushanthan, additional, Kannangara, Madhushani, additional, Joseph, Andrene, additional, Nanayakkara, Chamath, additional, Zhang, Chunmiao, additional, Yang, Zhao, additional, Li, Brook, additional, Meng, Zhuo, additional, Ning, Yi, additional, Dong, Le, additional, Armenis, Manuela, additional, Lim, Joyce, additional, Monaghan, Helen, additional, Ma, Lu, additional, Luo, Rui, additional, Cheng, Guojuan, additional, Dong, Yilin, additional, Liu, Ziqin, additional, Wang, Shuihong, additional, Zhang, Ying, additional, Cheng, Jipeng, additional, Shi, Hui, additional, Li, Wenjing, additional, Mou, Langming, additional, Yi, Ping, additional, Chen, Xue, additional, Weerawardena, Shalomi, additional, Ellawala, Poornima, additional, Ranasinghe, Enalee, additional, Rodrigo, Chrishmi, additional, Wahab, Kolawala, additional, Adeniyi, Sunday, additional, Pandian, Jeyaraj, additional, Khanna, Megha, additional, Muñoz Venturelli, Paula, additional, González, Francisca, additional, Urrutia Goldsack, Francisca, additional, Begum, Dilshad, additional, Pontes-Neto, Octavio, additional, Camilo, Millene, additional, Dias, Francisco, additional, Vincenzi, Octavio, additional, Moro, Carla, additional, Santos, Renata, additional, Texeira, Nara, additional, Longo, Alexandre, additional, Liberato, Rafaela, additional, Martins, Sheila, additional, Pille, Arthur, additional, Chwal, Bruna, additional, Silva, Isabel, additional, Titton, Natacha, additional, Weiss, Gustavo, additional, Mora, Daissy, additional, Ouriques, Magda, additional, Carbonera, Leonardo, additional, Bazan, Rodrigo, additional, Modolo, Gabriel, additional, Winckler, Fernanda, additional, Miranda, Luana, additional, Souza, Juli, additional, Rojo, Alexis, additional, Uslar, Wilhelm, additional, Medel, Lorena, additional, Lopez, Javiera, additional, Herrero, Diego, additional, Lavados, Pablo, additional, Vargas Latorre, Barbara, additional, Conejan, Nathalie, additional, Esparza, Tomas, additional, Sotomayor, Patricio, additional, Wenger, Denisse, additional, Gigoux, Juan Pablo, additional, Letelier, Aldo, additional, Acevedo, Lilian, additional, Moya, Vivianne, additional, Figueroa, Cristian, additional, Vallejos, Nicol, additional, Guerrero, Rodrigo, additional, Velasquez, Mauricio, additional, Vallejos, Jose, additional, Pallauta, Kimerly, additional, Santibanez, Tamara, additional, Queirolo, Angelo, additional, Lobos, Andrea, additional, Jiang, Yongming, additional, Li, Weimin, additional, Huang, Wei, additional, Luo, Ke, additional, Liu, Gangying, additional, Yang, Guang, additional, Jiang, Hongtao, additional, Zhang, Xu, additional, Jing, Hongyan, additional, Pu, Bo, additional, Lv, Dong, additional, Kang, Hui, additional, Hu, Qiuping, additional, Jiang, Xiaoming, additional, Chen, Yanli, additional, Yang, Shenghua, additional, He, Jianjun, additional, Li, Zongping, additional, Cheng, Gang, additional, Huang, Hailin, additional, Wang, Xiaoyi, additional, Lin, Jianqiong, additional, Chen, Minhui, additional, Yang, Chenghao, additional, Ding, Hao, additional, Deng, Yunliang, additional, Luo, Fei, additional, Zhang, Rongjun, additional, Wang, Xiaofeng, additional, Zhang, Hongbing, additional, Yang, Xiaoliang, additional, Zhang, Yang, additional, Yang, Chengyi, additional, He, Yu, additional, Liu, Feng, additional, Wang, Rongjie, additional, Zhang, Yuhui, additional, Xin, Xiaodong, additional, Feng, Bin, additional, Hao, Wanru, additional, Song, Chang, additional, Guo, Yun, additional, Jiang, Dehua, additional, Chen, Jie, additional, Tang, Changtong, additional, Zhu, Hongliang, additional, Li, Xin, additional, Cui, Jin, additional, Xu, Haidong, additional, Li, Boyang, additional, Tang, Fusheng, additional, Li, Yuanbin, additional, Gao, Min, additional, Yang, Bo, additional, Xu, Xuejun, additional, Deng, Bing, additional, Zheng, Yi, additional, Ge, Yuanhong, additional, Chen, Keyu, additional, Liu, Yang, additional, Li, Xinshen, additional, Zhong, Tingting, additional, Xu, Jianfeng, additional, Zhang, Hai, additional, Wang, Jiyue, additional, Zhu, Jianxin, additional, Sun, Hanyu, additional, Yu, Fuhua, additional, Zhang, Xueguang, additional, Zhang, Mingsen, additional, Wang, Bin, additional, Ma, Yiming, additional, Jiang, Donglin, additional, Zhou, Jun, additional, Liu, Cong, additional, Nie, Wenhong, additional, Li, Mingguo, additional, Tian, Tao, additional, Li, Yong, additional, He, Mingfang, additional, Tu, Xiaolong, additional, Wu, Zhengjun, additional, Liu, Hong, additional, Zhong, Dongsheng, additional, Jiang, Rongcai, additional, Sun, Jian, additional, Tian, Ye, additional, Wei, Yingsheng, additional, An, Shuo, additional, Wei, Pingbo, additional, Luo, Le, additional, Lin, Bin, additional, Liu, Gang, additional, Wen, Yan, additional, Cai, Qiang, additional, Chen, Qianxue, additional, Lei, Pan, additional, Li, Zhiyang, additional, Zhang, Meifang, additional, He, Jiaquan, additional, Chen, Yan, additional, Liu, Jun, additional, Liu, Xinghai, additional, Li, Junyan, additional, Chen, Min, additional, Wang, Jing, additional, Zhou, Bingzhi, additional, Ye, Baichun, additional, Zhang, Jiancheng, additional, Zhang, Manyuan, additional, Pan, Xuming, additional, Yu, Xiaoxiang, additional, Xu, Jian, additional, Xiao, Qingbao, additional, Wang, Yuefei, additional, Tao, Liang, additional, Shi, Lin, additional, Zheng, Niandong, additional, You, Guoliang, additional, Lei, Bo, additional, Chen, Shu, additional, Wu, Honggang, additional, Hu, Jin, additional, Zhao, Jianlan, additional, Yu, Jian, additional, Yuan, Qiang, additional, Du, Zhuoying, additional, Tang, Xielin, additional, Li, Qianke, additional, Liu, Shenghua, additional, Yang, Feilong, additional, Xiao, Kui, additional, Luo, Chao, additional, Wang, Guang, additional, Che, Xudong, additional, Teng, Zhipeng, additional, Wan, Wenwu, additional, Li, Jun, additional, Liu, Yu, additional, Fan, Mingbo, additional, Zhang, Tao, additional, Cai, Lun, additional, Ma, Yuan, additional, Ma, Zhifeng, additional, Li, Bin, additional, He, Linlin, additional, Li, Jinghui, additional, Zhang, Weibing, additional, Zhang, Shuxin, additional, Zhang, Hongzhen, additional, Dai, Yingguang, additional, Lei, Jun, additional, Mao, Lei, additional, Huang, Yiyang, additional, Zhou, Zhi, additional, Chen, Ping, additional, Chen, Fang, additional, Wei, Pan, additional, Li, Tiangui, additional, Chen, Honglin, additional, Zeng, Mengfei, additional, Mou, Kejie, additional, Xue, Jun, additional, Jiang, Yong, additional, Tang, Xiaoping, additional, Chen, Tao, additional, Zhang, Yalan, additional, Xu, Yanbing, additional, Gu, Yuchen, additional, Zhao, Yujun, additional, Yang, Bin, additional, Kuai, Peng, additional, Wang, Xi, additional, Yang, Yuwang, additional, Hu, Xueling, additional, Zhang, Huitian, additional, Yang, Yintao, additional, Wang, Weifeng, additional, Zhang, Junyi, additional, Cheng, Wei, additional, Zhang, Xiaoxue, additional, Ma, Xiaowen, additional, He, Qin, additional, Zhang, Li, additional, Gao, Rong, additional, Liu, Huixiang, additional, Ye, Jingwei, additional, Xu, Ping, additional, Wu, Xin, additional, Yuan, Yuan, additional, Zou, Peng, additional, Zhang, Zhen, additional, Cheng, Jiyong, additional, Zhou, Zhangming, additional, Zeng, Yijun, additional, Liang, Zhang, additional, Du, Deming, additional, Yu, Shui, additional, Cao, Yongjun, additional, Xu, Jiaping, additional, Huang, Zhichao, additional, Chen, Dongqin, additional, Xiao, Wenfeng, additional, Zhu, Li, additional, Yuan, Miao, additional, Wang, Yuhai, additional, Shi, Dongliang, additional, Hu, Xu, additional, Xiang, Dingchao, additional, Shi, Like, additional, Wang, Hongqin, additional, Yang, Liu, additional, Miao, Wang, additional, Hu, Yiyi, additional, Zhao, Yuchun, additional, Hu, Xi, additional, Zhou, Weiduo, additional, Sun, Chao, additional, Tang, Dong, additional, Yao, Kun, additional, You, Jin, additional, Chen, Shishi, additional, Yao, Jianmin, additional, Li, Huanmei, additional, Liu, Jinmei, additional, Bai, Ailin, additional, Yi, Yong, additional, Deng, Qingshan, additional, Luo, Peng, additional, Wang, Han, additional, Jiang, Jingcheng, additional, Yang, Qingwei, additional, He, Shunpo, additional, Wang, Jun, additional, Chen, Yu, additional, He, Hua, additional, Deng, Yuyang, additional, Cao, Zhikai, additional, Yi, Xuxia, additional, Luo, Jinbiao, additional, Luo, Shuang, additional, Gong, Min, additional, Liu, Li, additional, Gao, Xuejun, additional, Liu, Jia, additional, Wu, Li'e, additional, Zhang, Jia, additional, Sun, Hongying, additional, Li, Xinhui, additional, Jia, Lu, additional, Wu, Jianbing, additional, Zhang, Jie, additional, Zhang, Huajun, additional, Du, Chunfu, additional, Li, Shun, additional, Yang, Xiaobin, additional, He, Jie, additional, Liao, Lei, additional, Zhou, Gezhi, additional, Dong, Wentao, additional, Chen, Yunxiang, additional, Lin, Xiaofeng, additional, Shui, Xujian, additional, Zhang, Peng, additional, Zhao, Yuan, additional, Yang, Hongli, additional, Zhao, Wenbin, additional, Zhang, Xiaoyi, additional, Chen, Jincao, additional, Wu, Qian, additional, Dai, Xuan, additional, Tang, Baogui, additional, Wang, Yinjuan, additional, Liu, Tao, additional, Zhang, Haixia, additional, Duan, Faliang, additional, Luo, Ming, additional, Jiao, Qingfang, additional, Lei, Guoliang, additional, Wang, Dong, additional, Song, Chunwang, additional, Tan, Haopeng, additional, Ye, Feng, additional, Qin, Xinghu, additional, Liang, Xiaolong, additional, Liu, Junling, additional, Yang, Lang, additional, Yang, Jie, additional, Lin, Yapeng, additional, Yang, Qian, additional, Ma, Xuntai, additional, Qi, Yinkuang, additional, Pan, Baogen, additional, Jiang, Caixia, additional, Ye, Zhanying, additional, Dong, Ce, additional, Yue, Xiongfei, additional, Yang, Xiaopeng, additional, Maimaitiyiming, Tuoheti, additional, Dong, Jun, additional, Wu, Yonggang, additional, Gao, Feng, additional, Zhao, Deqiang, additional, Zhang, Xinghai, additional, Wang, PengJun, additional, Jiang, Hongbo, additional, Li, Jianping, additional, Zhang, Wei, additional, Chen, Jing, additional, Tong, Haibo, additional, Wang, Yonghong, additional, Qiao, Kaipeng, additional, Guo, Fuyou, additional, Zhang, Mingchu, additional, Hu, Yan, additional, Feng, Mengzhao, additional, Song, Dengpan, additional, Zuo, Yi, additional, Chen, Shangjun, additional, Qian, Chao, additional, Li, Baoming, additional, Ma, Jingku, additional, Zhang, Sunfu, additional, Kong, Bin, additional, Dong, Xingyu, additional, Fang, Sheng, additional, Lu, Bin, additional, Li, Yang, additional, Yang, Yongling, additional, Yu, Hong, additional, Sun, Huaiyu, additional, Wang, Yue, additional, Wang, Weimin, additional, Li, Tong, additional, Li, Shengli, additional, Xu, Zhiming, additional, Wang, Yongyi, additional, Dong, Qiang, additional, Tang, Yuping, additional, Chu, Heling, additional, Lu, Ying, additional, Wang, Zhong, additional, Sun, Xiaoou, additional, Zhao, Jianhua, additional, Yang, Shuaifeng, additional, Qian, Xiying, additional, Saroja, Aralikatte Onkarappa, additional, Naik k, Ravishankar, additional, Chindhi, Sandip, additional, Pampaniya, Nakul, additional, Amaresh, Kurubara, additional, Iype, Thomas, additional, R, Dileep, additional, Rajan, Reeja, additional, Panicker, Praveen, additional, Das, Rupjyoti, additional, Choudhury, Nupur, additional, Gohain, Pankaja, additional, Webster, Jemin, additional, Pakma, Biyol, additional, Sangi, Lalbiak, additional, Sebastian, Ivy, additional, Aggrawal, Gaurav, additional, Raj, Komal, additional, Rajoura, Deepankshi, additional, Singh, Sulena, additional, Aggrawal, Varun, additional, Narang, Amit, additional, Cano-Nigenda, Vanesa, additional, López-Mena, Diego, additional, Valdez-Ruvalcaba, Héctor, additional, Toledo-Treviño, Roberto, additional, Obiako, Reginald, additional, Abubakar, Sani, additional, Emeka, Oguike, additional, Olayemi, Balogun, additional, Lois, Melika, additional, Philip, Ibinaiye, additional, Comfort O, Olurishe, additional, Okubadejo, Njideka, additional, Agabi, Osigwe, additional, Ojo, Oluwadamilola, additional, Wahab, Kolawole, additional, Bello, Abiodun, additional, Ibukun, Oyinloye, additional, Sanayaolu, Olufemi, additional, Jimoh, Abdulraheem, additional, Waheed, Shahid, additional, Kamal, Dr.Ayeesha, additional, Shoaib, Raja Farhat, additional, Orooj, Fizza, additional, Majid, Sadaf, additional, Zehra, Taskeen, additional, Khan, Abdus Salam, additional, Shanker, Ravi, additional, Syed, Nadir Ali, additional, Ahmad, Nashwa, additional, Valencia, Ana, additional, Barrientos, Danny, additional, Ramirez, Jorge, additional, Calle, Pilar, additional, Palliyeguruge, Dilum, additional, Muthucumarana, Sumudu, additional, Ratnayaka, Shiroma, additional, Ganihiarachchi, Dilhara, additional, Bandaranayake, Arundathi, additional, Somaratne, S.D.B, additional, Narayana, Saumya, additional, Gallage, Sithara, additional, Senanayake, Bimsara, additional, Samarasiri, Udari, additional, Luke, Dunya, additional, Sivapathasundaram, Mythily, additional, Sahadevan, Vithoosan, additional, Rasmi, Amani, additional, Deshaka, Yuran, additional, Fernando, Nilukshi, additional, Munasinghe, Aruna, additional, Rathnapriya, Kapilanga, additional, Nissanka, A.S, additional, Karunathilake, Kanchana, additional, Gayan, Isuru, additional, Wijenayake, Kaminda, additional, Gunasekara, Hasitha, additional, Vidyarathne, Jagath, additional, Keshavaraj, Ajantha, additional, Janarthanan, Kanagasabapathy, additional, Gerald Jeevathasan, Arhivalaky, additional, Sivamainthan, Sivaram, additional, John Priyanth, Mathyamuthan, additional, John Priyanth, Abirami, additional, Rajendiran, Thambippillai, additional, Alwis, Sanjeewa, additional, Gunasekare, Nushara, additional, Liyanarachchi, Vasundara, additional, Dissanayake, Athula, additional, Uluwattage, Wimalasiri Mewa, additional, Ratnayake, Gimhani, additional, Rajinee, Charika, additional, Jayawardana, Sakura, additional, Peiris, Janaka, additional, Wicramasinghe, Ranjith, additional, Fernando, Chamila, additional, Abbas, Jessie, additional, Withanage, Nethmini, additional, Bandara, Makaranda, additional, Mai, Duy Ton, additional, Nguyen, Van Chi, additional, Dao, Viet Phuong, additional, Vuong, Xuan Trung, additional, Nguyen, Tien Dung, additional, Dinh, Trung Hieu, additional, Phan, Ha Quan, additional, Bui, Quoc Viet, additional, Phung, Dinh Tho, additional, Pham, Quang Tho, additional, Pham, Dinh Dai, additional, Do, Duc Thuan, additional, Dang, Phuc Duc, additional, Dang, Minh Duc, additional, Nguyen, Dang Hai, additional, Nguyen, Thi Phuong Nga, additional, Nguyen, Quoc Huy, additional, Pham, Quoc Dai, additional, Chau, Quoc Vinh, additional, Tai, Vinh Thy Van, additional, Le, Tran Vinh, additional, Le, Cong Tri, additional, Tran, Ha Mai Khuong, additional, Nguyen, Huu Khanh, additional, Ngyen, Hoang Minh Thao, additional, Vo, Duc Chien, additional, Nguyen, Thai My Phuong, additional, Tran, Trung Thanh, additional, Vo, Thi Hanh Vi, additional, Cao, Hao Nhien, additional, Nguyen, Ba Thang, additional, Le, Thi Ngoc Suong, additional, La, Thien Duc, additional, Pham, Chi Duc, additional, and Thai, Huy, additional

Published
2023
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28. DA: Population structure inference using discriminant analysis.

Author

Qin, Xinghu, Lock, Thomas Ryan, and Kallenbach, Robert L.

Subjects
INFERENTIAL statistics, GENETIC variation, SPATIAL variation
Abstract

Genetic variations in a species across geographic areas typically exhibit spatial clines. There is increasing interest in inferring population genetic structure to understand the patterns of genetic variation and the evolution of a species.Here, we present the da package and propose to infer population structure using discriminant analysis (DA). We incorporate five supervised learning approaches (DAPC, LDAKPC, LFDA, LFDAKPC and KLFDA) into da package within the same DA family, but with different linear and nonlinear properties.We tested the performance and properties of these five approaches for population structure inference using both simulated and empirical data. Results showed that these five approaches preserved the same global genetic structure under each genetic scenario. Notably, genetic features produced from KLFDA and LFDA had higher correlations with FST under isolation‐by‐distance model and higher discriminatory power in population structure identification, with KLFDA achieving the best performance. The applications to empirical data indicated that all these methods could intuitively capture the continuous genetic gradients while LFDA and KLFDA could discriminate nuanced population structures that the other approaches cannot.These DA methods can be applied to other statistical inferences in genetics and beyond. The da package is available at https://cran.r‐project.org/web/packages/DA/index.html. We recommend users choosing these approaches appropriately depending on their scientific questions and target data. [ABSTRACT FROM AUTHOR]

Published
2022
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30. Molecular Ecological Basis of Grasshopper (Oedaleus asiaticus) Phenotypic Plasticity under Environmental Selection

Author

Qin, Xinghu, primary, Hao, Kun, additional, Ma, Jingchuan, additional, Huang, Xunbing, additional, Tu, Xiongbing, additional, Ali, Md. Panna, additional, Pittendrigh, Barry R., additional, Cao, Guangchun, additional, Wang, Guangjun, additional, Nong, Xiangqun, additional, Whitman, Douglas W., additional, and Zhang, Zehua, additional

Published
2017
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31. Large manipulative experiments revealed variations of insect abundance and trophic levels in response to the cumulative effects of sheep grazing

Author

Ma, Jingchuan, primary, Huang, Xunbing, additional, Qin, Xinghu, additional, Ding, Yong, additional, Hong, Jun, additional, Du, Guilin, additional, Li, Xinyi, additional, Gao, Wenyuan, additional, Zhang, Zhuoran, additional, Wang, Guangjun, additional, Wang, Ning, additional, and Zhang, Zehua, additional

Published
2017
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34. High-Throughput Sequencing and Co-Expression Network Analysis of lncRNAs and mRNAs in Early Brain Injury Following Experimental Subarachnoid Haemorrhage

Author

Peng, Jianhua, primary, Wu, Yue, additional, Tian, Xiaocui, additional, Pang, Jinwei, additional, Kuai, Li, additional, Cao, Fang, additional, Qin, Xinghu, additional, Zhong, Jianjun, additional, Li, Xinshen, additional, Li, Yong, additional, Sun, Xiaochuan, additional, Chen, Ligang, additional, and Jiang, Yong, additional

Published
2017
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35. Apolipoprotein E Mimetic Peptide Increases Cerebral Glucose Uptake by Reducing Blood–Brain Barrier Disruption after Controlled Cortical Impact in Mice: An 18F-Fluorodeoxyglucose PET/CT Study

Author

Qin, Xinghu, primary, You, Hong, additional, Cao, Fang, additional, Wu, Yue, additional, Peng, Jianhua, additional, Pang, Jinwei, additional, Xu, Hong, additional, Chen, Yue, additional, Chen, Ligang, additional, Vitek, Michael P., additional, Li, Fengqiao, additional, Sun, Xiaochuan, additional, and Jiang, Yong, additional

Published
2017
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37. Potential implications of Apolipoprotein E in early brain injury after experimental subarachnoid hemorrhage: Involvement in the modulation of blood-brain barrier integrity

Author

Pang, Jinwei, primary, Wu, Yue, additional, Peng, Jianhua, additional, Yang, Ping, additional, Kuai, Li, additional, Qin, Xinghu, additional, Cao, Fang, additional, Sun, Xiaochuan, additional, Chen, Ligang, additional, Vitek, Michael P., additional, and Jiang, Yong, additional

Published
2016
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39. Effectiveness of Bacillus pumilusPDSLzg-1, an innovative Hydrocarbon-Degrading Bacterium conferring antifungal and plant growth-promoting function

Author

Hao, Kun, Ullah, Hidayat, Qin, Xinghu, Li, Hongna, Li, Feng, and Guo, Ping

Abstract

Genome of the hydrocarbon-degrading bacterium Bacillus pumilusPDSLzg-1 was analyzed. A group of gene clusters and pathways associated with nitrogen fixation, plant-bacterial interactions, plant growth-promoting hormone synthesis, antibiotics, secondary metabolite, and disease resistance were identified. In addition, 0.06 mg/L of 3-indoleacrylic acid (IAA) and 2 mg/L of gibberellin (GA) were, respectively, detected in PDSLzg-1 fermentation broth by high-performance liquid chromatography (HPLC). Up-regulated expression levels of 11 key genes related to GA and IAA biosynthesis pathways were detected after the induction of 0.2% n-hexadecane. Furthermore, bioassays showed that PDSLzg-1 fermentation could significantly promote the length and biomass of the stems and roots of Triticum aestivumL., while inhibited Colletotrichum truncatumcolonization. Results indicated that B. pumilusPDSLzg-1 had plant growth-promoting and antifungal functions, besides its potential applications in phyto-microbial bioremediation combinations for oil-contaminated soil.

Published
2019
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40. Apolipoprotein E Mimetic Peptide Increases Cerebral Glucose Uptake by Reducing Blood-Brain Barrier Disruption after Controlled Cortical Impact in Mice: An 18F-Fluorodeoxyglucose PET/CT Study.

Author

Qin, Xinghu, You, Hong, Cao, Fang, Wu, Yue, Peng, Jianhua, Pang, Jinwei, Xu, Hong, Chen, Yue, Chen, Ligang, Vitek, Michael P., Li, Fengqiao, Sun, Xiaochuan, and Jiang, Yong

Subjects
*APOLIPOPROTEIN E, *PEPTIDES, *BLOOD-brain barrier, *LABORATORY mice, *FLUORODEOXYGLUCOSE F18, *VASCULAR endothelial growth factors
Abstract

Traumatic brain injury (TBI) disrupts the blood-brain barrier (BBB) and reduces cerebral glucose uptake. Vascular endothelial growth factor (VEGF) is believed to play a key role in TBI, and COG1410 has demonstrated neuroprotective activity in several models of TBI. However, the effects of COG1410 on VEGF and glucose metabolism following TBI are unknown. The current study aimed to investigate the expression of VEGF and glucose metabolism effects in C57BL/6J male mice subjected to experimental TBI. The results showed that controlled cortical impact (CCI)-induced vestibulomotor deficits were accompanied by increases in brain edema and the expression of VEGF, with a decrease in cerebral glucose uptake. COG1410 treatment significantly improved vestibulomotor deficits and glucose uptake and produced decreases in VEGF in the pericontusion and ipsilateral hemisphere of injury, as well as in brain edema and neuronal degeneration compared with the control group. These data support that COG1410 may have potential as an effective drug therapy for TBI. [ABSTRACT FROM AUTHOR]

Published
2017
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41. Apolipoprotein E Mimetic Peptide Increases Cerebral Glucose Uptake by Reducing Blood-Brain Barrier Disruption after Controlled Cortical Impact in Mice: An 18 F-Fluorodeoxyglucose PET/CT Study.

Author

Qin X, You H, Cao F, Wu Y, Peng J, Pang J, Xu H, Chen Y, Chen L, Vitek MP, Li F, Sun X, and Jiang Y

Subjects
Animals, Apolipoproteins E administration & dosage, Brain Edema metabolism, Brain Edema physiopathology, Brain Injuries, Traumatic metabolism, Brain Injuries, Traumatic physiopathology, Disease Models, Animal, Fluorodeoxyglucose F18, Male, Mice, Mice, Inbred C57BL, Neuroprotective Agents administration & dosage, Positron Emission Tomography Computed Tomography, Apolipoproteins E pharmacology, Blood-Brain Barrier drug effects, Brain Edema drug therapy, Brain Injuries, Traumatic drug therapy, Glucose metabolism, Neuroprotective Agents pharmacology, Vascular Endothelial Growth Factor A metabolism
Abstract

Traumatic brain injury (TBI) disrupts the blood-brain barrier (BBB) and reduces cerebral glucose uptake. Vascular endothelial growth factor (VEGF) is believed to play a key role in TBI, and COG1410 has demonstrated neuroprotective activity in several models of TBI. However, the effects of COG1410 on VEGF and glucose metabolism following TBI are unknown. The current study aimed to investigate the expression of VEGF and glucose metabolism effects in C57BL/6J male mice subjected to experimental TBI. The results showed that controlled cortical impact (CCI)-induced vestibulomotor deficits were accompanied by increases in brain edema and the expression of VEGF, with a decrease in cerebral glucose uptake. COG1410 treatment significantly improved vestibulomotor deficits and glucose uptake and produced decreases in VEGF in the pericontusion and ipsilateral hemisphere of injury, as well as in brain edema and neuronal degeneration compared with the control group. These data support that COG1410 may have potential as an effective drug therapy for TBI.

Published
2017
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