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14,053 results on '"Zhu, Yong"'

1. Birth of protein folds and functions in the virome

Author

Nomburg, Jason, Doherty, Erin E, Price, Nathan, Bellieny-Rabelo, Daniel, Zhu, Yong K, and Doudna, Jennifer A

Subjects
Biochemistry and Cell Biology, Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Emerging Infectious Diseases, Immunization, Genetics, Infectious Diseases, Biodefense, 1.1 Normal biological development and functioning, 2.2 Factors relating to the physical environment, Generic health relevance, Infection, Animals, Humans, Bacteriophages, Hydrolysis, Immune Evasion, Immunity, Innate, Models, Molecular, Nucleotides, Cyclic, Phosphoric Diester Hydrolases, Protein Folding, Viral Proteins, Virome, Databases, Protein, Host Microbial Interactions, General Science & Technology
Abstract

The rapid evolution of viruses generates proteins that are essential for infectivity and replication but with unknown functions, due to extreme sequence divergence1. Here, using a database of 67,715 newly predicted protein structures from 4,463 eukaryotic viral species, we found that 62% of viral proteins are structurally distinct and lack homologues in the AlphaFold database2,3. Among the remaining 38% of viral proteins, many have non-viral structural analogues that revealed surprising similarities between human pathogens and their eukaryotic hosts. Structural comparisons suggested putative functions for up to 25% of unannotated viral proteins, including those with roles in the evasion of innate immunity. In particular, RNA ligase T-like phosphodiesterases were found to resemble phage-encoded proteins that hydrolyse the host immune-activating cyclic dinucleotides 3',3'- and 2',3'-cyclic GMP-AMP (cGAMP). Experimental analysis showed that RNA ligase T homologues encoded by avian poxviruses similarly hydrolyse cGAMP, showing that RNA ligase T-mediated targeting of cGAMP is an evolutionarily conserved mechanism of immune evasion that is present in both bacteriophage and eukaryotic viruses. Together, the viral protein structural database and analyses presented here afford new opportunities to identify mechanisms of virus-host interactions that are common across the virome.

Published
2024

2. Enhancing Taobao Display Advertising with Multimodal Representations: Challenges, Approaches and Insights

Author

Sheng, Xiang-Rong, Yang, Feifan, Gong, Litong, Wang, Biao, Chan, Zhangming, Zhang, Yujing, Cheng, Yueyao, Zhu, Yong-Nan, Ge, Tiezheng, Zhu, Han, Jiang, Yuning, Xu, Jian, and Zheng, Bo

Subjects
Computer Science - Information Retrieval, Computer Science - Machine Learning
Abstract

Despite the recognized potential of multimodal data to improve model accuracy, many large-scale industrial recommendation systems, including Taobao display advertising system, predominantly depend on sparse ID features in their models. In this work, we explore approaches to leverage multimodal data to enhance the recommendation accuracy. We start from identifying the key challenges in adopting multimodal data in a manner that is both effective and cost-efficient for industrial systems. To address these challenges, we introduce a two-phase framework, including: 1) the pre-training of multimodal representations to capture semantic similarity, and 2) the integration of these representations with existing ID-based models. Furthermore, we detail the architecture of our production system, which is designed to facilitate the deployment of multimodal representations. Since the integration of multimodal representations in mid-2023, we have observed significant performance improvements in Taobao display advertising system. We believe that the insights we have gathered will serve as a valuable resource for practitioners seeking to leverage multimodal data in their systems., Comment: Accepted at CIKM 2024

Published
2024

3. SDSAT: Accelerating LLM Inference through Speculative Decoding with Semantic Adaptive Tokens

Author

Liu, Chengbo and Zhu, Yong

Subjects
Computer Science - Computation and Language
Abstract

We propose an acceleration scheme for large language models (LLMs) through Speculative Decoding with Semantic Adaptive Tokens (SDSAT). The primary objective of this design is to enhance the LLM model's ability to generate draft tokens more accurately without compromising the model's accuracy. The core strategies involve: 1) Fine-tune the model by incorporating semantic adaptive tokens that possess flexible decoding capabilities without changing its structure, allowing them to generate high-quality draft tokens. 2) By employing a training method that does not affect the standard tokens, the model can acquire parallel decoding abilities atop its original framework with minimal training overhead. 3) We have designed the "two-step-draft-then-verify" generation strategies using both greedy search and nucleus sampling. Experiments conducted on the CodeLlama-13B and 7B models have yielded speed increases of over 3.5X and 3.0X, respectively. Please refer to https://github.com/hasuoshenyun/SDSAT., Comment: 12 pages, 7 figures

Published
2024

12. Optimizing single-photon quantum radar detection through partially postselected filtering

Author

Li, Liangsheng, Liu, Maoxin, You, Wen-Long, Zhang, Chengjie, Zhang, Shengli, Yin, Hongcheng, Xiao, Zhihe, and Zhu, Yong

Subjects
Quantum Physics
Abstract

In this study, we explore an approach aimed at enhancing the transmission or reflection coefficients of absorbing materials through the utilization of joint measurements of entangled photon states. On the one hand, through the implementation of photon catalysis in the reflected channel, we can effectively modify the state of the transmission channel, leading to a notable improvement in the transmission ratio. Similarly, this approach holds potential for significantly amplifying the reflection ratio of absorbing materials, which is useful for detecting cooperative targets. On the other hand, employing statistical counting methods based on the technique of heralding on zero photons, we evaluate the influence of our reflection enhancement protocol for detecting noncooperative targets, which is validated through Monte Carlo simulations of a quantum radar setup affected by Gaussian white noise. Our results demonstrate a remarkable enhancement in the signal-to-noise ratio of imaging, albeit with an increase in mean-square error. These findings highlight the potential practical applications of our approach in the implementation of quantum radar., Comment: 11 pages, 10 figures

Published
2024
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13. Biogeographic patterns and drivers of soil viromes

Author

Ma, Bin, Wang, Yiling, Zhao, Kankan, Stirling, Erinne, Lv, Xiaofei, Yu, Yijun, Hu, Lingfei, Tang, Chao, Wu, Chuyi, Dong, Baiyu, Xue, Ran, Dahlgren, Randy A, Tan, Xiangfeng, Dai, Hengyi, Zhu, Yong-Guan, Chu, Haiyan, and Xu, Jianming

Subjects
Microbiology, Environmental Sciences, Biological Sciences, Ecology, Infection, Soil, Ecosystem, Virome, Soil Microbiology, Viruses, Evolutionary biology, Environmental management
Abstract

Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.

Published
2024

18. Building resilience in Asian mega-deltas

Author

Chan, Faith Ka Shun, Paszkowski, Amelie, Wang, Zilin, Lu, Xiaohui, Mitchell, Gordon, Tran, Duc Dung, Warner, Jeroen, Li, Jianfeng, Chen, Yongqin David, Li, Nan, Pal, Indrajit, Griffiths, James, Chen, Jiannan, Chen, Wei-Qiang, and Zhu, Yong-Guan

Published
2024
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30. Dioscin protects against chronic prostatitis through the TLR4/NF-κB pathway

Author

Long Yan, Ge Xiaodong, Ma Liangliang, Guo Junhua, and Zhu Yong

Subjects
dioscin, chronic prostatitis, tlr4/nf-κb pathway, Medicine
Abstract

This study aimed to elucidate the effects and potential mechanisms of dioscin on chronic prostatitis (CP) in vivo and in vitro. CP models were constructed in vivo and in vitro and treated with different concentrations of dioscin. Hematoxylin and eosin staining was used to investigate the morphology of the prostate tissues. The concentration of inflammatory factors in prostate tissues was determined by enzyme-linked immunosorbent assay. The release of reactive oxygen species, malondialdehyde, superoxide dismutase, and catalase was measured using detection kits. P69 cell proliferation was assessed by 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide. Furthermore, the activity of the TLR4/NF-κB signaling pathway was determined by quantitative reverse transcriptase polymerase chain reaction or Western blot assay. Histopathological data suggested that dioscin exerted protective effects against prostate morphological changes. Dioscin inhibits inflammatory cytokines and oxidative stress (OS) in prostate tissues in a concentration-dependent manner. Moreover, dioscin notably inhibited the activation of the TLR4/NF-κB signaling pathway in CP rats. In vitro, dioscin remarkably reduced lipopolysaccharide-induced P69 proliferation, inflammation, OS, and TLR4/NF-κB pathway activation in a dose-dependent manner. In conclusion, dioscin exerts a protective effect in CP by decreasing the inflammatory response and OS through the TLR4/NF-κB pathways. Our findings provide a novel latent therapy for dioscin for the treatment and prevention of CP.

Published
2024
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31. Targeting the non-coding genome and temozolomide signature enables CRISPR-mediated glioma oncolysis.

Author

Tan, I-Li, Perez, Alexendar, Lew, Rachel, Sun, Xiaoyu, Baldwin, Alisha, Zhu, Yong, Shah, Mihir, Berger, Mitchel, Doudna, Jennifer, and Fellmann, Christof

Subjects
CP: Cancer, CRISPR-Cas9, cancer shredding, genome shredding, glioblastoma, hypermutated glioma, Humans, Temozolomide, Brain Neoplasms, Cell Line, Tumor, Drug Resistance, Neoplasm, Neoplasm Recurrence, Local, Glioblastoma, Glioma, Antineoplastic Agents, Alkylating
Abstract

Glioblastoma (GBM) is the most common lethal primary brain cancer in adults. Despite treatment regimens including surgical resection, radiotherapy, and temozolomide (TMZ) chemotherapy, growth of residual tumor leads to therapy resistance and death. At recurrence, a quarter to a third of all gliomas have hypermutated genomes, with mutational burdens orders of magnitude greater than in normal tissue. Here, we quantified the mutational landscape progression in a patients primary and recurrent GBM, and we uncovered Cas9-targetable repeat elements. We show that CRISPR-mediated targeting of highly repetitive loci enables rapid elimination of GBM cells, an approach we term genome shredding. Importantly, in the patients recurrent GBM, we identified unique repeat sequences with TMZ mutational signature and demonstrated that their CRISPR targeting enables cancer-specific cell ablation. Cancer shredding leverages the non-coding genome and therapy-induced mutational signatures for targeted GBM cell depletion and provides an innovative paradigm to develop treatments for hypermutated glioma.

Published
2023

43. Continuous and low-carbon production of biomass flash graphene

Author

Zhu, Xiangdong, Lin, Litao, Pang, Mingyue, Jia, Chao, Xia, Longlong, Shi, Guosheng, Zhang, Shicheng, Lu, Yuanda, Sun, Liming, Yu, Fengbo, Gao, Jie, He, Zhelin, Wu, Xuan, Li, Aodi, Wang, Liang, Wang, Meiling, Cao, Kai, Fu, Weiguo, Chen, Huakui, Li, Gang, Zhang, Jiabao, Wang, Yujun, Yang, Yi, and Zhu, Yong-Guan

Published
2024
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44. Towards an actionable One Health approach

Author

Zhang, Xiao-Xi, Lederman, Zohar, Han, Le-Fei, Schurer, Janna M., Xiao, Li-Hua, Zhang, Zhi-Bing, Chen, Qiu-Lan, Pfeiffer, Dirk, Ward, Michael P., Sripa, Banchob, Gabriël, Sarah, Dhama, Kuldeep, Acharya, Krishna Prasad, Robertson, Lucy J., Deem, Sharon L., Aenishaenslin, Cécile, Dantas-Torres, Filipe, Otranto, Domenico, Grace, Delia, Wang, Yang, Li, Peng, Fu, Chao, Poeta, Patrícia, Md. Tanvir Rahman, Kassegne, Kokouvi, Zhu, Yong-Zhang, Yin, Kun, Liu, Jiming, Wang, Zhao-Jun, Guo, Xiao-Kui, Gong, Wen-Feng, Schwartländer, Bernhard, Ren, Ming-Hui, and Zhou, Xiao-Nong

Published
2024
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47. Lactobacillus rhamnosus GG ameliorates hyperuricemia in a novel model

Author

Fu, Yang, Chen, Yong-Song, Xia, Dai-Yang, Luo, Xiao-Dan, Luo, Hao-Tong, Pan, Jie, Ma, Wei-Qing, Li, Jin-Ze, Mo, Qian-Yuan, Tu, Qiang, Li, Meng-Meng, Zhao, Yue, Li, Yu, Huang, Yi-Teng, Chen, Zhi-Xian, Li, Zhen-Jun, Bernard, Lukuyu, Dione, Michel, Zhang, You-Ming, Miao, Kai, Chen, Jian-Ying, Zhu, Shan-Shan, Ren, Jie, Zhou, Ling-Juan, Jiang, Xian-Zhi, Chen, Juan, Lin, Zhen-Ping, Chen, Jun-Peng, Ye, Hui, Cao, Qing-Yun, Zhu, Yong-Wen, Yang, Lin, Wang, Xue, and Wang, Wen-Ce

Published
2024
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