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Article ; Online: Generalizing factors of COVID-19 vaccine attitudes in different regions

Yang Liu / Jiale Shi / Chenxu Zhao / Chengzhi Zhang

Digital Health, Vol

A summary generation and topic modeling approach

2023 Volume 9

Abstract: Objective The goal of this study is to use summary generation and topic modeling to identify factors contributing to vaccine attitudes for three different vaccine brands, with the aim of generalizing these factors across different regions. Methods A ... ...

Abstract	Objective The goal of this study is to use summary generation and topic modeling to identify factors contributing to vaccine attitudes for three different vaccine brands, with the aim of generalizing these factors across different regions. Methods A total of 5562 tweets about three vaccine brands (Sinovac, AstraZeneca, and Pfizer) were collected from 14 December 2020 to 30 December 2021. BERTopic clustering is used to group the tweets into topics, and then contrastive learning (CL) is adopted to generate summaries of each topic. The main content of each topic is generalized into three factors that contribute to vaccine attitudes: vaccine-related factors, health system-related factors, and individual social attributes. Results BERTopic clustering outperforms Latent Dirichlet Allocation clustering in our analysis. It can also be found that using CL for summary generation helped to better model the topics, particularly at the center-point of the clustering. Our model identifies three main factors contributing to vaccine attitudes that are consistent across different regions. Conclusions Our study demonstrates the effectiveness of deep learning methods for identifying factors contributing to vaccine attitudes in different regions. By determining these factors, policymakers and medical institutions can develop more effective strategies for addressing concerns related to the vaccination process.
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	006
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Immune evasion strategy involving propionylation by the KSHV interferon regulatory factor 1 (vIRF1).

Jiale Shi / Xuemei Jia / Yujia He / Xinyue Ma / Xiaoyu Qi / Wan Li / Shou-Jiang Gao / Qin Yan / Chun Lu

PLoS Pathogens, Vol 19, Iss 4, p e

2023 Volume 1011324

Abstract: Post-translational modifications (PTMs) are essential for host antiviral immune response and viral immune evasion. Among a set of novel acylations, lysine propionylation (Kpr) has been detected in both histone and non-histone proteins. However, whether ... ...

Abstract	Post-translational modifications (PTMs) are essential for host antiviral immune response and viral immune evasion. Among a set of novel acylations, lysine propionylation (Kpr) has been detected in both histone and non-histone proteins. However, whether protein propionylation occurs in any viral proteins and whether such modifications regulate viral immune evasion remain elusive. Here, we show that Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded viral interferon regulatory factor 1 (vIRF1) can be propionylated in lysine residues, which is required for effective inhibition of IFN-β production and antiviral signaling. Mechanistically, vIRF1 promotes its own propionylation by blocking SIRT6's interaction with ubiquitin-specific peptidase 10 (USP10) leading to its degradation via a ubiquitin-proteasome pathway. Furthermore, vIRF1 propionylation is required for its function to block IRF3-CBP/p300 recruitment and repress the STING DNA sensing pathway. A SIRT6-specific activator, UBCS039, rescues propionylated vIRF1-mediated repression of IFN-β signaling. These results reveal a novel mechanism of viral evasion of innate immunity through propionylation of a viral protein. The findings suggest that enzymes involved in viral propionylation could be potential targets for preventing viral infections.
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Tenuazonic Acid-Triggered Cell Death Is the Essential Prerequisite for Alternaria alternata (Fr.) Keissler to Infect Successfully Host Ageratina adenophora

Jiale Shi / Min Zhang / Liwen Gao / Qian Yang / Hazem M. Kalaji / Sheng Qiang / Reto Jörg Strasser / Shiguo Chen

Cells, Vol 10, Iss 1010, p

2021 Volume 1010

Abstract: The necrotrophic fungus Alternaria alternata contains different pathotypes that produce different mycotoxins. The pathotype Ageratina adenophora secretes the non-host-selective toxin tenuazonic acid (TeA), which can cause necrosis in many plants. ... ...

Abstract	The necrotrophic fungus Alternaria alternata contains different pathotypes that produce different mycotoxins. The pathotype Ageratina adenophora secretes the non-host-selective toxin tenuazonic acid (TeA), which can cause necrosis in many plants. Although TeA is thought to be a central virulence factor of the A. adenophora pathotype, the precise role of TeA in different stages of host infection by pathogens remains unclear. Here, an A. alternata wild-type and the toxin-deficient mutant ΔHP001 with a 75% reduction in TeA production were used. It was observed that wild-type pathogens could induce the reactive oxygen species (ROS) bursts in host leaves and killed photosynthetic cells before invading hyphae. The ROS interceptor catalase remarkably inhibited hyphal penetration and invasive hyphal growth and expansion in infected leaves and suppressed necrotic leaf lesion. This suggests that the production of ROS is critical for pathogen invasion and proliferation and disease symptom formation during infection. It was found that the mutant pathogens did not cause the formation of ROS and cell death in host leaves, showing an almost complete loss of disease susceptibility. In addition, the lack of TeA resulted in a significant reduction in the ability of the pathogen to penetrate invasive hyphal growth and spread. The addition of exogenous TeA, AAL-toxin, and bentazone to the mutant ΔHP001 pathogens during inoculation resulted in a significant restoration of pathogenicity by increasing the level of cell death, frequency of hyphal penetration, and extent of invasive hyphal spread. Our results suggest that cell death triggered by TeA is the essential requirement for successful colonization and disease development in host leaves during infection with A. adenophora pathogens.
Keywords	necrotrophic pathogen ; mycotoxin ; reactive oxygen species ; disease susceptibility ; Biology (General) ; QH301-705.5
Subject code	580 ; 630
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An identified PfHMGB1 promotes microcystin-LR-induced liver injury of yellow catfish (Pelteobagrus fulvidraco)

Yun Wang / Xiaoxue Xiao / Feijie Wang / Zupeng Yang / Jingkai Yue / Jiale Shi / Fei Ke / Zhaohui Xie / Yanru Fan

Ecotoxicology and Environmental Safety, Vol 207, Iss , Pp 111266- (2021)

2021

Abstract: Microcystin-LR (MC-LR) is a potent hepatotoxin that can cause liver inflammation and injury. However, the mode of action of related inflammatory factors is not fully understood. PfHMGB1 is an inflammatory factor induced at the mRNA level in the liver of ... ...

Abstract	Microcystin-LR (MC-LR) is a potent hepatotoxin that can cause liver inflammation and injury. However, the mode of action of related inflammatory factors is not fully understood. PfHMGB1 is an inflammatory factor induced at the mRNA level in the liver of juvenile yellow catfish (Pelteobagrus fulvidraco) that were intraperitoneally injected with 50 μg/kg MC-LR. The PfHMGB1 mRNA level was highest in the liver and muscle among 11 tissues examined. The full-length cDNA sequence of PfHMGB1 was cloned and overexpressed in E. coli, and the purified protein rPfHMGB1 demonstrated DNA binding affinity. Endotoxin-free rPfHMGB1 (6–150 μg/mL) also showed dose-dependent hepatotoxicity and induced inflammatory gene expression of primary hepatocytes. PfHMGB1 antibody (anti-PfHMGB1) in vitro reduced MC-LR (30 and 50 μmol/L)-induced hepatotoxicity, suggesting PfHMGB1 is important in the toxic effects of MC-LR. In vivo study showed that MC-LR upregulated PfHMGB1 protein in the liver. The anti-PfHMGB1 blocked its counterpart and reduced ALT/AST activities after MC-LR exposure. Anti-PfHMGB1 partly neutralized MC-LR-induced hepatocyte disorganization, nucleus shrinkage, mitochondria, and rough endoplasmic reticula destruction. These findings suggest that PfHMGB1 promotes MC-LR-induced liver damage in the yellow catfish. HMGB1 may help protect catfish against widespread microcystin pollution.
Keywords	PfHMGB1 ; MC-LR ; Hepatotoxicity ; Liver injury ; Yellow catfish ; anti-PfHMGB1 ; Environmental pollution ; TD172-193.5 ; Environmental sciences ; GE1-350
Subject code	570 ; 610
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ependymal polarity defects coupled with disorganized ciliary beating drive abnormal cerebrospinal fluid flow and spine curvature in zebrafish.

Haibo Xie / Yunsi Kang / Junjun Liu / Min Huang / Zhicheng Dai / Jiale Shi / Shuo Wang / Lanqin Li / Yuan Li / Pengfei Zheng / Yi Sun / Qize Han / Jingjing Zhang / Zezhang Zhu / Leilei Xu / Pamela C Yelick / Muqing Cao / Chengtian Zhao

PLoS Biology, Vol 21, Iss 3, p e

2023 Volume 3002008

Abstract: Idiopathic scoliosis (IS) is the most common spinal deformity diagnosed in childhood or early adolescence, while the underlying pathogenesis of this serious condition remains largely unknown. Here, we report zebrafish ccdc57 mutants exhibiting scoliosis ... ...

Abstract	Idiopathic scoliosis (IS) is the most common spinal deformity diagnosed in childhood or early adolescence, while the underlying pathogenesis of this serious condition remains largely unknown. Here, we report zebrafish ccdc57 mutants exhibiting scoliosis during late development, similar to that observed in human adolescent idiopathic scoliosis (AIS). Zebrafish ccdc57 mutants developed hydrocephalus due to cerebrospinal fluid (CSF) flow defects caused by uncoordinated cilia beating in ependymal cells. Mechanistically, Ccdc57 localizes to ciliary basal bodies and controls the planar polarity of ependymal cells through regulating the organization of microtubule networks and proper positioning of basal bodies. Interestingly, ependymal cell polarity defects were first observed in ccdc57 mutants at approximately 17 days postfertilization, the same time when scoliosis became apparent and prior to multiciliated ependymal cell maturation. We further showed that mutant spinal cord exhibited altered expression pattern of the Urotensin neuropeptides, in consistent with the curvature of the spine. Strikingly, human IS patients also displayed abnormal Urotensin signaling in paraspinal muscles. Altogether, our data suggest that ependymal polarity defects are one of the earliest sign of scoliosis in zebrafish and disclose the essential and conserved roles of Urotensin signaling during scoliosis progression.
Keywords	Biology (General) ; QH301-705.5
Subject code	571
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correction

Wan Li / Fei Wang / Jiale Shi / Qi Feng / Yuheng Chen / Xiaoyu Qi / Cong Wang / Hongmei Lu / Zhongmou Lu / Xuemei Jia / Qin Yan / Shou-Jiang Gao / Chun Lu

PLoS Pathogens, Vol 18, Iss 1, p e

Sperm associated antigen 9 promotes oncogenic KSHV-encoded interferon regulatory factor-induced cellular transformation and angiogenesis by activating the JNK/VEGFA pathway.

2022 Volume 1010232

Abstract: This corrects the article DOI:10.1371/journal.ppat.1008730.]. ...

Abstract	[This corrects the article DOI:10.1371/journal.ppat.1008730.].
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correction

Wan Li / Fei Wang / Jiale Shi / Qi Feng / Yuheng Chen / Xiaoyu Qi / Cong Wang / Hongmei Lu / Zhongmou Lu / Xuemei Jia / Qin Yan / Shou-Jiang Gao / Chun Lu

PLoS Pathogens, Vol 18, Iss

Sperm associated antigen 9 promotes oncogenic KSHV-encoded interferon regulatory factor-induced cellular transformation and angiogenesis by activating the JNK/VEGFA pathway

2022 Volume 1

Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Effect of compressive strength and chloride diffusion on life cycle CO2 assessment of concrete containing supplementary cementitious materials

Zhang, Yurong / Junzhi Zhang / Wei Luo / Jiandong Wang / Jiale Shi / Huaxia Zhuang / Yuanfeng Wang

Journal of cleaner production. 2019 May 01, v. 218

2019

Abstract: Using supplementary cementitious materials (SCMs) in concrete is considered as one of the possible solutions to making green concrete. Previous research often analyzed the environmental impact of concrete without considering the influences of compressive ...

Abstract	Using supplementary cementitious materials (SCMs) in concrete is considered as one of the possible solutions to making green concrete. Previous research often analyzed the environmental impact of concrete without considering the influences of compressive strength and durability simultaneously. Such a practice will lead to less rational life cycle assessment (LCA) results, since the service life of concrete could be shortened when durability is poor, especially if concrete is exposed to marine dry-wet environment where chloride ion is intensive. Moreover, Fick’s second law of diffusion was always used to determine the chloride diffusion coefficient of concrete, without considering the influences of convection zone and peak value of chloride concentration. Therefore, this paper proposed an integrated functional unit combining durability (resistance to chloride ion diffusion), compressive strength and volume to evaluate the environmental impact of concrete containing SCMs. The chloride diffusion coefficient was calculated by re-scaling the ‘‘zero’’ of penetration axis to calibrate Fick’s second law of diffusion. In addition, three other functional units (volume, combining volume and compressive strength, combing volume and durability) were also proposed and compared. Results indicate that the selection of functional unit has a significant influence on the LCA results of the studied concrete. Despite the variation with different functional units, concrete containing silica fume or silica fume as well as fly ash shows a consistently superior environmental performance over the ordinary concrete.
Keywords	carbon dioxide ; compression strength ; concrete ; convection ; diffusivity ; durability ; environmental impact ; environmental performance ; fly ash ; life cycle assessment ; silica
Language	English
Dates of publication	2019-0501
Size	p. 450-458.
Publishing place	Elsevier Ltd
Document type	Article
ISSN	0959-6526
DOI	10.1016/j.jclepro.2019.01.335
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Sperm associated antigen 9 promotes oncogenic KSHV-encoded interferon regulatory factor-induced cellular transformation and angiogenesis by activating the JNK/VEGFA pathway.

Wan Li / Fei Wang / Jiale Shi / Qi Feng / Yuheng Chen / Xiaoyu Qi / Cong Wang / Hongmei Lu / Zhongmou Lu / Xuemei Jia / Qin Yan / Shou-Jiang Gao / Chun Lu

PLoS Pathogens, Vol 16, Iss 8, p e

2020 Volume 1008730

Abstract: Kaposi's sarcoma (KS), caused by Kaposi's sarcoma-associated herpesvirus (KSHV), is a highly angioproliferative disseminated tumor of endothelial cells commonly found in AIDS patients. We have recently shown that KSHV-encoded viral interferon regulatory ... ...

Abstract	Kaposi's sarcoma (KS), caused by Kaposi's sarcoma-associated herpesvirus (KSHV), is a highly angioproliferative disseminated tumor of endothelial cells commonly found in AIDS patients. We have recently shown that KSHV-encoded viral interferon regulatory factor 1 (vIRF1) mediates KSHV-induced cell motility (PLoS Pathog. 2019 Jan 30;15(1):e1007578). However, the role of vIRF1 in KSHV-induced cellular transformation and angiogenesis remains unknown. Here, we show that vIRF1 promotes angiogenesis by upregulating sperm associated antigen 9 (SPAG9) using two in vivo angiogenesis models including the chick chorioallantoic membrane assay (CAM) and the matrigel plug angiogenesis assay in mice. Mechanistically, vIRF1 interacts with transcription factor Lef1 to promote SPAG9 transcription. vIRF1-induced SPAG9 promotes the interaction of mitogen-activated protein kinase kinase 4 (MKK4) with JNK1/2 to increase their phosphorylation, resulting in enhanced VEGFA expression, angiogenesis, cell proliferation and migration. Finally, genetic deletion of ORF-K9 from KSHV genome abolishes KSHV-induced cellular transformation and impairs angiogenesis. Our results reveal that vIRF1 transcriptionally activates SPAG9 expression to promote angiogenesis and tumorigenesis via activating JNK/VEGFA signaling. These novel findings define the mechanism of KSHV induction of the SPAG9/JNK/VEGFA pathway and establish the scientific basis for targeting this pathway for treating KSHV-associated cancers.
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cryo-EM analysis of the HCoV-229E spike glycoprotein reveals dynamic prefusion conformational changes

Xiyong Song / Yuejun Shi / Wei Ding / Tongxin Niu / Limeng Sun / Yubei Tan / Yong Chen / Jiale Shi / Qiqi Xiong / Xiaojun Huang / Shaobo Xiao / Yanping Zhu / Chongyun Cheng / Zhen F. Fu / Zhi-Jie Liu / Guiqing Peng

Nature Communications, Vol 12, Iss 1, Pp 1-

2021 Volume 9

Abstract: The spike protein of coronaviruses (S-protein) is an envelope-anchored trimeric type I transmembrane glycoprotein that mediates receptor binding and the fusion of the viral and host cell membranes. Here the authors report the conformational states of ... ...

Abstract	The spike protein of coronaviruses (S-protein) is an envelope-anchored trimeric type I transmembrane glycoprotein that mediates receptor binding and the fusion of the viral and host cell membranes. Here the authors report the conformational states of HCoV-229E S trimer and observe the conformational changes in S1 subunit from closed state to activated state for receptor binding.
Keywords	Science ; Q
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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