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Article ; Online: A recurrent positional encoding circular attention mechanism network for biomedical image segmentation.

Yu, Xiaoxia / Qin, Yong / Zhang, Fanghong / Zhang, Zhigang

Computer methods and programs in biomedicine

2024 Volume 246, Page(s) 108054

Abstract: Deep-learning-based medical image segmentation techniques can assist doctors in disease diagnosis and rapid treatment. However, existing medical image segmentation models do not fully consider the dependence between feature segments in the feature ... ...

Abstract	Deep-learning-based medical image segmentation techniques can assist doctors in disease diagnosis and rapid treatment. However, existing medical image segmentation models do not fully consider the dependence between feature segments in the feature extraction process, and the correlated features can be further extracted. Therefore, a recurrent positional encoding circular attention mechanism network (RPECAMNet) is proposed based on relative positional encoding for medical image segmentation. Multiple residual modules are used to extract the primary features of the medical images, which are thereafter converted into one-dimensional data for relative positional encoding. The recursive former is used to further extract features from medical images, and decoding is performed using deconvolution. An adaptive loss function is designed to train the model and achieve accurate medical-image segmentation. Finally, the proposed model is used to conduct comparative experiments on the synapse and self-constructed kidney datasets to verify the accuracy of the proposed model for medical image segmentation.
MeSH term(s)	Humans ; Kidney/diagnostic imaging ; Physicians ; Image Processing, Computer-Assisted
Language	English
Publishing date	2024-02-01
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	632564-6
ISSN	1872-7565 ; 0169-2607
ISSN (online)	1872-7565
ISSN	0169-2607
DOI	10.1016/j.cmpb.2024.108054
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Article ; Online: Astragaloside IV ameliorates podocyte apoptosis via inhibiting the PERK-ATF4-CHOP signaling axis.

Yu, Xiaoxia / Dong, He / Gao, Bihu

Asian journal of surgery

2023 Volume 47, Issue 1, Page(s) 776–777

MeSH term(s)	Humans ; Podocytes ; Cells, Cultured ; Saponins/pharmacology ; Apoptosis ; Activating Transcription Factor 4
Chemical Substances	astragaloside A (3A592W8XKE) ; Saponins ; ATF4 protein, human ; Activating Transcription Factor 4 (145891-90-3)
Language	English
Publishing date	2023-10-31
Publishing country	Netherlands
Document type	Letter
ZDB-ID	1068461-x
ISSN	0219-3108 ; 1015-9584
ISSN (online)	0219-3108
ISSN	1015-9584
DOI	10.1016/j.asjsur.2023.10.031
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Article ; Online: The different role of adversity before and after birth in adolescent depression.

Yuan, Yuan / Yu, Xiaoxia / Liang, Zhoujian / Zhang, Li

Journal of affective disorders

2023 Volume 349, Page(s) 116–124

Abstract: Background: Early adversity is strongly linked to adolescent depression, but there is limited research on the impact of indirect exposure to adversity before birth and the distinct role of adversity before and after birth.: Methods: A total of 1911 ... ...

Abstract	Background: Early adversity is strongly linked to adolescent depression, but there is limited research on the impact of indirect exposure to adversity before birth and the distinct role of adversity before and after birth. Methods: A total of 1911 Chinese adolescents (48.8 % males; ages 11 to 19, Mean = 13.96) reported early adversities before and after birth, depression, negative self-cognition and perceived school climate. Structural equation model was used to test the association between early adversity before/after birth and adolescent depression, with negative self-cognition serving as a mediator and school climate as a moderator. Results: Adversity before birth was related to adolescent depression through the full mediating role of negative self-cognition. Furthermore, it was more associated with negative self-cognition in schools with a more favorable climate. Adversity after birth was related to adolescent depression through the partial mediating role of negative self-cognition, and school climate played a nonsignificant moderating role in the mediating path. Limitations: Early adversity was measured through adolescent reports, possibly generating recall bias. The cross-sectional design should be taken into consideration when drawing conclusions about causality. Conclusions: Adversities before and after birth are associated with adolescent depression in distinct ways. The more association between adversity before birth and negative self-cognition in a favorable school climate supports the "healthy context paradox." Interventions that target depression should focus on promoting a positive school climate and helping adolescents who have experienced early adversity bolster positive self-cognition.
MeSH term(s)	Male ; Humans ; Adolescent ; Female ; Depression/epidemiology ; Cross-Sectional Studies ; Schools ; Risk Factors ; Adolescent Behavior
Language	English
Publishing date	2023-12-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	135449-8
ISSN	1573-2517 ; 0165-0327
ISSN (online)	1573-2517
ISSN	0165-0327
DOI	10.1016/j.jad.2023.12.064
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Article ; Online: Non-linear relationship between the body roundness index and metabolic syndrome: data from National Health and Nutrition Examination Survey (NHANES) 1999-2018.

Li, Zhenhan / Fan, Chunhua / Huang, Jun / Chen, Zhongpei / Yu, Xiaoxia / Qian, Jun

The British journal of nutrition

2024 , Page(s) 1–8

Abstract: Obesity is an important characteristic manifestation of metabolic syndrome (MetS), and body roundness index (BRI) is one of the anthropometric indicators associated with obesity. However, studies on the relationship between BRI and MetS risk are limited. ...

Abstract	Obesity is an important characteristic manifestation of metabolic syndrome (MetS), and body roundness index (BRI) is one of the anthropometric indicators associated with obesity. However, studies on the relationship between BRI and MetS risk are limited. We aimed to explore the relationship between baseline BRI and MetS in the USA population. Our study used data from the National Health and Nutrition Examination Survey from 1999 to 2018, ultimately enrolling and analysing 47 303 participants. Data-driven tertiles were used to categorise BRI levels, and multivariate logistic regression models were fitted to investigate the association of BRI with MetS in adults. In addition, receiver operating characteristic curve analysis was used to assess the ability of BRI to predict MetS. The distribution of BRI was different across ethnic groups with a gradual decrease in the proportion of non-Hispanic Whites and other races. In addition, BRI was significantly associated with traditional cardiovascular risk factors. Univariate regression analysis indicated BRI to be a moderate risk factor for MetS, and multivariate logistic regression analysis found that BRI remained an independent risk factor for MetS. After adjusting for confounding variables, a non-linear relationship was found between BRI levels and the prevalence of MetS. More importantly, BRI predicted MetS with the largest AUC among anthropometric measures. In summary, elevated baseline BRI levels are independently associated with the development of MetS, and baseline BRI may assist in identifying patients at risk for MetS, leading to early and optimal treatment to improve their outcomes.
Language	English
Publishing date	2024-02-15
Publishing country	England
Document type	Journal Article
ZDB-ID	280396-3
ISSN	1475-2662 ; 0007-1145
ISSN (online)	1475-2662
ISSN	0007-1145
DOI	10.1017/S0007114524000357
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Article ; Online: Integrative informatics analysis identifies that ginsenoside Re improves renal fibrosis through regulation of autophagy.

Liu, Yingying / Mou, Lingyun / Yi, Zhengzi / Lin, Qisheng / Banu, Khadija / Wei, Chengguo / Yu, Xiaoxia

Journal of natural medicines

2024 Volume 78, Issue 3, Page(s) 722–731

Abstract: We previously demonstrated that ginsenoside Re (G-Re) has protective effects on acute kidney injury. However, the underlying mechanism is still unclear. In this study, we conducted a meta-analysis and pathway enrichment analysis of all published ... ...

Abstract	We previously demonstrated that ginsenoside Re (G-Re) has protective effects on acute kidney injury. However, the underlying mechanism is still unclear. In this study, we conducted a meta-analysis and pathway enrichment analysis of all published transcriptome data to identify differentially expressed genes (DEGs) and pathways of G-Re treatment. We then performed in vitro studies to measure the identified autophagy and fibrosis markers in HK2 cells. In vivo studies were conducted using ureteric obstruction (UUO) and aristolochic acid nephropathy (AAN) models to evaluate the effects of G-Re on autophagy and kidney fibrosis. Our informatics analysis identified autophagy-related pathways enriched for G-Re treatment. Treatment with G-Re in HK2 cells reduced autophagy and mRNA levels of profibrosis markers with TGF-β stimulation. In addition, induction of autophagy with PP242 neutralized the anti-fibrotic effects of G-Re. In murine models with UUO and AAN, treatment with G-Re significantly improved renal function and reduced the upregulation of autophagy and profibrotic markers. A combination of informatics analysis and biological experiments confirmed that ginsenoside Re could improve renal fibrosis and kidney function through the regulation of autophagy. These findings provide important insights into the mechanisms of G-Re's protective effects in kidney injuries.
MeSH term(s)	Ginsenosides/pharmacology ; Ginsenosides/therapeutic use ; Autophagy/drug effects ; Animals ; Fibrosis/drug therapy ; Mice ; Kidney/drug effects ; Kidney/pathology ; Kidney/metabolism ; Humans ; Kidney Diseases/drug therapy ; Male ; Cell Line ; Acute Kidney Injury/drug therapy ; Mice, Inbred C57BL ; Disease Models, Animal ; Ureteral Obstruction/drug therapy
Chemical Substances	ginsenoside Re
Language	English
Publishing date	2024-04-29
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2227540-X
ISSN	1861-0293 ; 1340-3443
ISSN (online)	1861-0293
ISSN	1340-3443
DOI	10.1007/s11418-024-01800-7
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Article: The immunophilin CYCLOPHILIN28 affects PSII‐LHCII supercomplex assembly and accumulation in Arabidopsis thaliana

Zhu, Weining / Xu, Linqing / Yu, Xiaoxia / Zhong, Ying

Journal of integrative plant biology. 2022 Apr., v. 64, no. 4

2022

Abstract: In plant chloroplasts, photosystem II (PSII) complexes, together with light‐harvesting complex II (LHCII), form various PSII‐LHCII supercomplexes (SCs). This process likely involves immunophilins, but the underlying regulatory mechanisms are unclear. ... ...

Abstract	In plant chloroplasts, photosystem II (PSII) complexes, together with light‐harvesting complex II (LHCII), form various PSII‐LHCII supercomplexes (SCs). This process likely involves immunophilins, but the underlying regulatory mechanisms are unclear. Here, by comparing Arabidopsis thaliana mutants lacking the chloroplast lumen‐localized immunophilin CYCLOPHILIN28 (CYP28) to wild‐type and transgenic complemented lines, we determined that CYP28 regulates the assembly and accumulation of PSII‐LHCII SCs. Compared to the wild type, cyp28 plants showed accelerated leaf growth, earlier flowering time, and enhanced accumulation of high molecular weight PSII‐LHCII SCs under normal light conditions. The lack of CYP28 also significantly affected the electron transport rate. Blue native‐polyacrylamide gel electrophoresis analysis revealed more Lhcb6 and less Lhcb4 in M‐LHCII‐Lhcb4‐Lhcb6 complexes in cyp28 versus wild‐type plants. Peptidyl‐prolyl cis/trans isomerase (PPIase) activity assays revealed that CYP28 exhibits weak PPIase activity and that its K113 and E187 residues are critical for this activity. Mutant analysis suggested that CYP28 may regulate PSII‐LHCII SC accumulation by altering the configuration of Lhcb6 via its PPIase activity. Furthermore, the Lhcb6‐P139 residue is critical for PSII‐LHCII SC assembly and accumulation. Therefore, our findings suggest that CYP28 likely regulates PSII‐LHCII SC assembly and accumulation by altering the configuration of P139 of Lhcb6 via its PPIase activity.
Keywords	Arabidopsis thaliana ; chloroplasts ; electron transfer ; gel electrophoresis ; genetically modified organisms ; leaves ; light harvesting complex ; molecular weight ; mutants ; peptidylprolyl isomerase ; photosystem II
Language	English
Dates of publication	2022-04
Size	p. 915-929.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2130095-1
ISSN	1744-7909 ; 1672-9072
ISSN (online)	1744-7909
ISSN	1672-9072
DOI	10.1111/jipb.13235
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Article ; Online: The immunophilin CYCLOPHILIN28 affects PSII-LHCII supercomplex assembly and accumulation in Arabidopsis thaliana.

Zhu, Weining / Xu, Linqing / Yu, Xiaoxia / Zhong, Ying

Journal of integrative plant biology

2022 Volume 64, Issue 4, Page(s) 915–929

Abstract: In plant chloroplasts, photosystem II (PSII) complexes, together with light-harvesting complex II (LHCII), form various PSII-LHCII supercomplexes (SCs). This process likely involves immunophilins, but the underlying regulatory mechanisms are unclear. ... ...

Abstract	In plant chloroplasts, photosystem II (PSII) complexes, together with light-harvesting complex II (LHCII), form various PSII-LHCII supercomplexes (SCs). This process likely involves immunophilins, but the underlying regulatory mechanisms are unclear. Here, by comparing Arabidopsis thaliana mutants lacking the chloroplast lumen-localized immunophilin CYCLOPHILIN28 (CYP28) to wild-type and transgenic complemented lines, we determined that CYP28 regulates the assembly and accumulation of PSII-LHCII SCs. Compared to the wild type, cyp28 plants showed accelerated leaf growth, earlier flowering time, and enhanced accumulation of high molecular weight PSII-LHCII SCs under normal light conditions. The lack of CYP28 also significantly affected the electron transport rate. Blue native-polyacrylamide gel electrophoresis analysis revealed more Lhcb6 and less Lhcb4 in M-LHCII-Lhcb4-Lhcb6 complexes in cyp28 versus wild-type plants. Peptidyl-prolyl cis/trans isomerase (PPIase) activity assays revealed that CYP28 exhibits weak PPIase activity and that its K113 and E187 residues are critical for this activity. Mutant analysis suggested that CYP28 may regulate PSII-LHCII SC accumulation by altering the configuration of Lhcb6 via its PPIase activity. Furthermore, the Lhcb6-P139 residue is critical for PSII-LHCII SC assembly and accumulation. Therefore, our findings suggest that CYP28 likely regulates PSII-LHCII SC assembly and accumulation by altering the configuration of P139 of Lhcb6 via its PPIase activity.
MeSH term(s)	Arabidopsis/genetics ; Immunophilins/analysis ; Light-Harvesting Protein Complexes/analysis ; Light-Harvesting Protein Complexes/chemistry ; Peptidylprolyl Isomerase/analysis ; Photosystem II Protein Complex/analysis ; Photosystem II Protein Complex/chemistry ; Plants ; Thylakoids
Chemical Substances	Light-Harvesting Protein Complexes ; Photosystem II Protein Complex ; Immunophilins (EC 5.2.1.8) ; Peptidylprolyl Isomerase (EC 5.2.1.8)
Language	English
Publishing date	2022-04-05
Publishing country	China (Republic : 1949- )
Document type	Journal Article
ZDB-ID	2130095-1
ISSN	1744-7909 ; 1672-9072
ISSN (online)	1744-7909
ISSN	1672-9072
DOI	10.1111/jipb.13235
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Article ; Online: Uranium bioprecipitation mediated by a phosphate-solubilizing Enterobacter sp. N1-10 and remediation of uranium-contaminated soil.

Yu, Xiaoxia / Xiong, Feng / Zhou, Chenchen / Luo, Zhijian / Zhou, Zhongkui / Chen, Jinying / Sun, Kaixuan

The Science of the total environment

2023 Volume 906, Page(s) 167688

Abstract: Uranium (U) pollution in soils is prevalent worldwide and poses a significant health risk that will require remediation approaches. However, traditional U bioreduction by sulfate reducing bacteria (SRB) are sensitive to oxygen and are not suitable for ... ...

Abstract	Uranium (U) pollution in soils is prevalent worldwide and poses a significant health risk that will require remediation approaches. However, traditional U bioreduction by sulfate reducing bacteria (SRB) are sensitive to oxygen and are not suitable for treating aerobic topsoil. Bioprecipitation of U into uranyl phosphate (UP) mediated by phosphate-solubilizing microorganism (PSM) is not affected by oxygen. In this study, PSM strains were isolated and used for U-contaminated soil remediation. Microbial metabolites and the mechanism of PSM bioprecipitation were revealed. The results showed that strain Enterobacter sp. N1-10 had the highest phosphate-solubilizing capacity (dissolved P was 409.51 ± 8.48 mg/L). Uranium bioprecipitation was investigated by culturing the bacterium in the presence of 50 mg/L U and in the cell-free culture supernatant. The results showed that strain N1-10 had a high U removal rate (99.45 ± 0.43 %) after adding 50 mg/L U to the culture medium. A yellow precipitate was immediately formed when uranyl nitrate solution was added to the cell-free culture supernatant. The analysis indicated that bacterium produced lactic acid (37.58 mg/L), citric acid (4.76 mg/L), succinic acid (2.03 mg/L), and D-glucuronic acid (1.94 mg/L); the four organic acids solubilized Ca
MeSH term(s)	Uranium/metabolism ; Enterobacter ; Biomineralization ; Phosphates/metabolism ; Biodegradation, Environmental ; Soil ; Oxygen
Chemical Substances	hydrogen uranyl phosphate (301YH255RM) ; Uranium (4OC371KSTK) ; Phosphates ; Soil ; Oxygen (S88TT14065)
Language	English
Publishing date	2023-10-11
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.167688
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Article: Genome-wide identification of GATA transcription factors in tetraploid potato and expression analysis in differently colored potato flesh.

Zhang, Xia / Fan, Rong / Yu, Zhuo / Du, Xuerun / Yang, Xinyue / Wang, Huiting / Xu, Wenfeng / Yu, Xiaoxia

Frontiers in plant science

2024 Volume 15, Page(s) 1330559

Abstract: The GATA gene family belongs to a kind of transcriptional regulatory protein featuring a zinc finger motif, which is essential for plant growth and development. However, the identification of the GATA gene family in tetraploid potato is still not ... ...

Abstract	The GATA gene family belongs to a kind of transcriptional regulatory protein featuring a zinc finger motif, which is essential for plant growth and development. However, the identification of the GATA gene family in tetraploid potato is still not performed. In the present research, a total of 88
Language	English
Publishing date	2024-03-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2024.1330559
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Article ; Online: Synergy of surface adsorption and intracellular accumulation for removal of uranium with Stenotrophomonas sp: Performance and mechanisms

Hu, Zhongqiang / Zhou, Zhongkui / Zhou, Yaoyu / Zheng, Lili / Guo, Jianping / Liu, Yong / Sun, Zhanxue / Yang, Zhihui / Yu, Xiaoxia

Environmental Research. 2023 Mar., v. 220 p.115093-

2023

Abstract: Uranium is well-known to have serious adverse effects on the ecological environment and human health. Bioremediation stands out among many remediation methods owing to its being economically feasible and environmentally friendly. This study reported a ... ...

Abstract	Uranium is well-known to have serious adverse effects on the ecological environment and human health. Bioremediation stands out among many remediation methods owing to its being economically feasible and environmentally friendly. This study reported a great promising strategy for eliminating uranium by Stenotrophomonas sp. CICC 23833 in the aquatic environment. The bacterium demonstrated excellent uranium adsorption capacity (qₘₐₓ = 392.9 mg/g) because of the synergistic effect of surface adsorption and intracellular accumulation. Further analysis revealed that hydroxyl, carboxyl, phosphate groups and proteins of microorganisms were essential in uranium adsorption. Intracellular accumulation was closely related to cellular activity, and the efficiency of uranium processing by the permeabilized bacterial cells was significantly improved. In response to uranium stress, the bacterium was found to release multiple ions in conjunction with uranium adsorption, which facilitates the maintenance of bacterial life activities and the conversion of uranyl to precipitates. These above results indicated that Stenotrophomonas sp. Had great potential application value for the remediation of uranium.
Keywords	Stenotrophomonas ; adsorption ; aquatic environment ; bacteria ; bioremediation ; economic feasibility ; human health ; phosphates ; research ; synergism ; uranium ; uranyl ions ; Wastewater ; Stenotrophomonas sp. CICC 23833 ; Biosorption ; Mechanism
Language	English
Dates of publication	2023-03
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	205699-9
ISSN	1096-0953 ; 0013-9351
ISSN (online)	1096-0953
ISSN	0013-9351
DOI	10.1016/j.envres.2022.115093
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