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2. GA-HQS: MRI reconstruction via a generically accelerated unfolding approach

Author

Jiang, Jiawei, Feng, Yuchao, Xu, Honghui, Chen, Wanjun, and Zheng, Jianwei

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Deep unfolding networks (DUNs) are the foremost methods in the realm of compressed sensing MRI, as they can employ learnable networks to facilitate interpretable forward-inference operators. However, several daunting issues still exist, including the heavy dependency on the first-order optimization algorithms, the insufficient information fusion mechanisms, and the limitation of capturing long-range relationships. To address the issues, we propose a Generically Accelerated Half-Quadratic Splitting (GA-HQS) algorithm that incorporates second-order gradient information and pyramid attention modules for the delicate fusion of inputs at the pixel level. Moreover, a multi-scale split transformer is also designed to enhance the global feature representation. Comprehensive experiments demonstrate that our method surpasses previous ones on single-coil MRI acceleration tasks.

Published
2023

7. Transcription factor Tox2 is required for metabolic adaptation and tissue residency of ILC3 in the gut

Author

Das, Arundhoti, Martinez-Ruiz, Gustavo Ulises, Bouladoux, Nicolas, Stacy, Apollo, Moraly, Josquin, Vega-Sendino, Maria, Zhao, Yongge, Lavaert, Marieke, Ding, Yi, Morales-Sanchez, Abigail, Harly, Christelle, Seedhom, Mina O., Chari, Raj, Awasthi, Parirokh, Ikeuchi, Tomoko, Wang, Yueqiang, Zhu, Jinfang, Moutsopoulos, Niki M., Chen, WanJun, Yewdell, Jonathan W., Shapiro, Virginia Smith, Ruiz, Sergio, Taylor, Naomi, Belkaid, Yasmine, and Bhandoola, Avinash

Published
2024
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9. Characterizing genetic transmission networks among newly diagnosed HIV-1 infected individuals in eastern China: 2012–2016

Author

Ding, Xiaobei, Chaillon, Antoine, Pan, Xiaohong, Zhang, Jiafeng, Zhong, Ping, He, Lin, Chen, Wanjun, Fan, Qin, Jiang, Jun, Luo, Mingyu, Xia, Yan, Guo, Zhihong, and Smith, Davey M

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Clinical Research, HIV/AIDS, Infection, Good Health and Well Being, China, Genotype, HIV Infections, HIV Seropositivity, HIV-1, Homosexuality, Male, Humans, Male, Phylogeny, Sexual and Gender Minorities, General Science & Technology
Abstract

We aimed to elucidate the characteristics of HIV molecular epidemiology and identify transmission hubs in eastern China using genetic transmission network and lineage analyses. HIV-TRACE was used to infer putative relationships. Across the range of epidemiologically-plausible genetic distance (GD) thresholds (0.1-2.0%), a sensitivity analysis was performed to determine the optimal threshold, generating the maximum number of transmission clusters and providing reliable resolution without merging different small clusters into a single large cluster. Characteristics of genetically linked individuals were analyzed using logistic regression. Assortativity (shared characteristics) analysis was performed to infer shared attributes between putative partners. 1,993 persons living with HIV-1 were enrolled. The determined GD thresholds within subtypes CRF07_BC, CRF01_AE, and B were 0.5%, 1.2%, and 1.7%, respectively, and 826 of 1,993 (41.4%) sequences were linked with at least one other sequence, forming 188 transmission clusters of 2-80 sequences. Clustering rates for the main subtypes CRF01_AE, CRF07_BC, and B were 50.9% (523/1027), 34.2% (256/749), and 32.1% (25/78), respectively. Median cluster sizes of these subtypes were 2 (2-52, n = 523), 2 (2-80, n = 256), and 3 (2-6, n = 25), respectively. Subtypes in individuals diagnosed and residing in Hangzhou city (OR = 1.423, 95% CI: 1.168-1.734) and men who have sex with men (MSM) were more likely to cluster. Assortativity analysis revealed individuals were more likely to be genetically linked to individuals from the same age group (AIage = 0.090, P

Published
2022

12. Author Correction: Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver

Subjects
General Science & Technology
Abstract

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

Published
2021

16. Zfp335 establishes eTreg lineage and neonatal immune tolerance by targeting Hadha-mediated fatty acid oxidation

Author

Wang, Xin, Sun, Lina, Yang, Biao, Li, Wenhua, Zhang, Cangang, Yang, Xiaofeng, Sun, Yae, Shen, Xiaonan, Gao, Yang, Ju, Bomiao, Gao, Yafeng, Liu, Dan, Song, Jiapeng, Jia, Xiaoxuan, Su, Yanhong, Jiao, Anjun, Liu, Haiyan, Zhang, Lianjun, He, Lan, Lei, Lei, Chen, WanJun, and Zhang, Baojun

Subjects
T cells -- Analysis, Inflammation -- Analysis, Autoimmunity -- Analysis, B cells -- Analysis, Fatty acids -- Analysis, Enzymes -- Analysis, Infants (Newborn) -- Analysis, Oxidation-reduction reaction -- Analysis, Health care industry
Abstract

Regulatory T cells (Tregs) are instrumental in maintaining immune tolerance and preventing destructive autoimmunity, but how heterogeneous Treg populations are established remains largely unknown. Here, we show that Zfp335 deletion in Tregs failed to differentiate into effector Tregs (eTregs) and lose Treg-suppressive function and that KO mice exhibited early-onset lethal autoimmune inflammation with unrestricted activation of conventional T cells. Single-cell RNASeq analyses revealed that Zfp335-deficient Tregs lacked a eTreg population and showed dramatic accumulation of a dysfunctional Treg subset. Mechanistically, Zfp335-deficient Tregs displayed reduced oxidative phosphorylation and dysfunctional mitochondrial activity. Further studies revealed that Zfp335 controlled eTreg differentiation by regulating fatty acid oxidation (FAO) through direct targeting of the FAO enzyme Hadha. Importantly, we demonstrate a positive correlation between ZNF335 and HADHA expression in human eTregs. Our findings reveal that Zfp335 controls FAO-driven eTreg differentiation to establish immune tolerance., Introduction Regulatory T cells (Tregs) expressing forkhead box P3 (Foxp3) play a key role in the establishment and maintenance of peripheral immune tolerance through the prevention and suppression of autoimmunity [...]

Published
2023
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19. Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Life on Land, Animals, Birds, Chickens, Conservation of Natural Resources, Datasets as Topic, Finches, Genome, Genomics, Humans, Phylogeny, Selection, Genetic, Synteny, General Science & Technology
Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Published
2020

20. Structure fusion based on graph convolutional networks for semi-supervised classification

Author

Lin, Guangfeng, Wang, Jing, Liao, Kaiyang, Zhao, Fan, and Chen, Wanjun

Subjects
Computer Science - Machine Learning, Computer Science - Computer Vision and Pattern Recognition, Statistics - Machine Learning
Abstract

Suffering from the multi-view data diversity and complexity for semi-supervised classification, most of existing graph convolutional networks focus on the networks architecture construction or the salient graph structure preservation, and ignore the the complete graph structure for semi-supervised classification contribution. To mine the more complete distribution structure from multi-view data with the consideration of the specificity and the commonality, we propose structure fusion based on graph convolutional networks (SF-GCN) for improving the performance of semi-supervised classification. SF-GCN can not only retain the special characteristic of each view data by spectral embedding, but also capture the common style of multi-view data by distance metric between multi-graph structures. Suppose the linear relationship between multi-graph structures, we can construct the optimization function of structure fusion model by balancing the specificity loss and the commonality loss. By solving this function, we can simultaneously obtain the fusion spectral embedding from the multi-view data and the fusion structure as adjacent matrix to input graph convolutional networks for semi-supervised classification. Experiments demonstrate that the performance of SF-GCN outperforms that of the state of the arts on three challenging datasets, which are Cora,Citeseer and Pubmed in citation networks.

Published
2019
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21. Transfer feature generating networks with semantic classes structure for zero-shot learning

Author

Lin, Guangfeng, Chen, Wanjun, Liao, Kaiyang, Kang, Xiaobing, and Fan, Caixia

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Feature generating networks face to the most important question, which is the fitting difference (inconsistence) of the distribution between the generated feature and the real data. This inconsistence further influence the performance of the networks model, because training samples from seen classes is disjointed with testing samples from unseen classes in zero-shot learning (ZSL). In generalization zero-shot learning (GZSL), testing samples come from not only seen classes but also unseen classes for closer to the practical situation. Therefore, most of feature generating networks difficultly obtain satisfactory performance for the challenging GZSL by adversarial learning the distribution of semantic classes. To alleviate the negative influence of this inconsistence for ZSL and GZSL, transfer feature generating networks with semantic classes structure (TFGNSCS) is proposed to construct networks model for improving the performance of ZSL and GZSL. TFGNSCS can not only consider the semantic structure relationship between seen and unseen classes, but also learn the difference of generating features by transferring classification model information from seen to unseen classes in networks. The proposed method can integrate the transfer loss, the classification loss and the Wasserstein distance loss to generate enough CNN features, on which softmax classifiers are trained for ZSL and GZSL. Experiments demonstrate that the performance of TFGNSCS outperforms that of the state of the arts on four challenging datasets, which are CUB,FLO,SUN, AWA in GZSL.

Published
2019
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27. Analytically Modeling the Effect of Buffer Charge on the 2DEG Density in AlGaN/GaN HEMT

Author

Wang, Fangzhou, primary, Chen, Wanjun, additional, Wang, Yang, additional, Sun, Ruize, additional, Ding, Guojian, additional, Yu, Ping, additional, Wang, Xiaohui, additional, Feng, Qi, additional, Xu, Wenjun, additional, Xu, Xiaorui, additional, Liu, Chao, additional, Wang, Zeheng, additional, Jia, Haiqiang, additional, Chen, Hong, additional, and Zhang, Bo, additional

Published
2024
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30. Class label autoencoder for zero-shot learning

Author

Lin, Guangfeng, Fan, Caixia, Chen, Wanjun, Chen, Yajun, and Zhao, Fan

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Existing zero-shot learning (ZSL) methods usually learn a projection function between a feature space and a semantic embedding space(text or attribute space) in the training seen classes or testing unseen classes. However, the projection function cannot be used between the feature space and multi-semantic embedding spaces, which have the diversity characteristic for describing the different semantic information of the same class. To deal with this issue, we present a novel method to ZSL based on learning class label autoencoder (CLA). CLA can not only build a uniform framework for adapting to multi-semantic embedding spaces, but also construct the encoder-decoder mechanism for constraining the bidirectional projection between the feature space and the class label space. Moreover, CLA can jointly consider the relationship of feature classes and the relevance of the semantic classes for improving zero-shot classification. The CLA solution can provide both unseen class labels and the relation of the different classes representation(feature or semantic information) that can encode the intrinsic structure of classes. Extensive experiments demonstrate the CLA outperforms state-of-art methods on four benchmark datasets, which are AwA, CUB, Dogs and ImNet-2.

Published
2018

33. Exploration and Practice of University Students Health Education Promotion Model Under Big Data Information

Author

Chen, Wanjun, Akan, Ozgur, Editorial Board Member, Bellavista, Paolo, Editorial Board Member, Cao, Jiannong, Editorial Board Member, Coulson, Geoffrey, Editorial Board Member, Dressler, Falko, Editorial Board Member, Ferrari, Domenico, Editorial Board Member, Gerla, Mario, Editorial Board Member, Kobayashi, Hisashi, Editorial Board Member, Palazzo, Sergio, Editorial Board Member, Sahni, Sartaj, Editorial Board Member, Shen, Xuemin (Sherman), Editorial Board Member, Stan, Mircea, Editorial Board Member, Jia, Xiaohua, Editorial Board Member, Zomaya, Albert Y., Editorial Board Member, Jan, Mian Ahmad, editor, and Khan, Fazlullah, editor

Published
2021
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34. Research on College Students’ Health Education Based on Feature Extraction Algorithm

Author

Chen, Wanjun, Akan, Ozgur, Editorial Board Member, Bellavista, Paolo, Editorial Board Member, Cao, Jiannong, Editorial Board Member, Coulson, Geoffrey, Editorial Board Member, Dressler, Falko, Editorial Board Member, Ferrari, Domenico, Editorial Board Member, Gerla, Mario, Editorial Board Member, Kobayashi, Hisashi, Editorial Board Member, Palazzo, Sergio, Editorial Board Member, Sahni, Sartaj, Editorial Board Member, Shen, Xuemin (Sherman), Editorial Board Member, Stan, Mircea, Editorial Board Member, Jia, Xiaohua, Editorial Board Member, Zomaya, Albert Y., Editorial Board Member, Jan, Mian Ahmad, editor, and Khan, Fazlullah, editor

Published
2021
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35. Factors associated with casual sexual behavior among college students in Zhejiang Province, China: A cross-sectional survey.

Author

Yang, Zhongrong, Chen, Wanjun, Chen, Weiyong, Ma, Qiaoqin, Wang, Hui, Jiang, Tingting, Fu, Yun, and Zhou, Xin

Subjects
*CONDOM use, *HUMAN sexuality, *UNSAFE sex, *COLLEGE students, *SEXUAL intercourse, *ATTITUDES toward sex
Abstract

This study aimed to analyze the characteristics and risk factors associated with casual sexual behavior among sexually active college students and to contribute to AIDS prevention and control efforts among this demographic. A cross-sectional survey was conducted using a stratified cluster sampling technique. Self-reported sexually active college students were selected as respondents from 11 cities in Zhejiang Province from October 8 to November 30, 2018. A questionnaire was used to collect variables such as demographic information, sexual attitudes, intervention acceptance, and self-efficacy of condom use. Univariate and multivariate analyses were performed. Among 3,771 college students who reported engaging in sexual activity, 675 (17.90%) reported engaging in casual sexual encounters. The multivariate analysis revealed multiple factors associated with casual sexual behavior among students: being male, originating from a city/town, having pursued HIV testing education in the last year, seeking HIV risk self-assessment within the last year, accepting to engage in one-night stand behavior, accepting to partake in commercial sexual activity, having conducted HIV antibody tests within the last year, homosexual partner or homosexual/heterosexual partner, demonstrating self-efficacy in condom usage, and monthly living expenses falling within the range of 1001–1500 yuan. Additionally, students with knowledge that appearance does not determine HIV infection, a proclivity for seeking HIV counseling and testing following high-risk sexual behavior and awareness that the centers for disease control provides HIV diagnosis were found to have significant associations with casual sexual activity. Casual sex is significantly prevalent among college students, with male, students from urban areas, those who accepted to engage in one-night stand behavior and partook in commercial sexual activity demonstrating a higher propensity for such behavior. This tendency can be attributed to several factors including a more liberal sexual attitude, a rudimentary understanding of HIV risk, and a low adoption rate of HIV testing. Therefore, it is imperative to enhance HIV prevention and education among college students. [ABSTRACT FROM AUTHOR]

Published
2024
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42. Insights into the Molecular Network Characteristics of Major HIV-1 Subtypes in Developed Eastern China: A Study Based on In-Depth Molecular Surveillance Data

Author

Fan, Qin, primary, Zhang, Jiafeng, additional, Pan, Xiaohong, additional, Ding, Xiaobei, additional, Xing, Hui, additional, Feng, Yi, additional, Li, Xingguang, additional, Zhong, Ping, additional, Zhao, Hehe, additional, Cheng, Wei, additional, Jiang, Jun, additional, Chen, Wanjun, additional, Zhou, Xin, additional, Guo, Zhihong, additional, Xia, Yan, additional, Chai, Chengliang, additional, and Jiang, Jianmin, additional

Published
2024
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43. Effect of Pore Size on Carbon Dioxide Adsorption and Specific Capacity as Supercapacitors Electrode by Activated Carbon Fibers Prepared from Natural Cotton Fibers

Author

Wang, Peiyu, primary, Liu, Hang, additional, Zhu, Wenting, additional, Zhang, Guoheng, additional, Chen, Wanjun, additional, Wang, Xiangli, additional, Chen, Qiong, additional, Deng, Xiaoyan, additional, Yang, Bao, additional, Limao, Cairang, additional, and Cairang, Zuoma, additional

Published
2024
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