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Article ; Online: Long-term (2003-2021) evolution trend of water quality in the Three Gorges Reservoir: An evaluation based on an enhanced water quality index.

Sang, Chong / Tan, Lu / Cai, Qinghua / Ye, Lin

2024 Volume 915, Page(s) 169819

Abstract: The degradation of water quality induced by the construction of large-scale hydraulic projects is one of the primary public concerns; however, it is rarely addressed with long-term field observation data. Here, we reported the long-term (2003-2021) ... ...

Abstract	The degradation of water quality induced by the construction of large-scale hydraulic projects is one of the primary public concerns; however, it is rarely addressed with long-term field observation data. Here, we reported the long-term (2003-2021) trends, seasonal patterns, and overall condition of water quality of the Three Gorges Reservoir (TGR) with an enhanced water quality index (WQI). Specifically, to emphasize the importance of the biological role in water quality assessment, chlorophyll-a (Chla) was incorporated into WQI, and then a novel workflow using machine learning approach based on Random Forest (RF) model was constructed to develop a minimal water quality index (WQI
Language	English
Publishing date	2024-01-06
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.2023.169819
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Zs.A 949: Show issues

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Article ; Online: The landscape of pathophysiology guided therapeutic strategies for gout treatment.

Hao, Sai Heng / Ye, Lin Yan / Yang, Chang

Expert opinion on pharmacotherapy

2024 Volume 24, Issue 18, Page(s) 1993–2003

Abstract: Introduction: Gout is a common autoinflammatory disease caused by hyperuricemia with acute and/or chronic inflammation as well as tissue damage. Currently, urate-lowering therapy (ULT) and anti-inflammatory therapy are used as first-line strategies for ... ...

Abstract	Introduction: Gout is a common autoinflammatory disease caused by hyperuricemia with acute and/or chronic inflammation as well as tissue damage. Currently, urate-lowering therapy (ULT) and anti-inflammatory therapy are used as first-line strategies for gout treatment. However, traditional drugs for gout treatment exhibit some unexpected side effects and are not suitable for certain patients due to their comorbidity with other chronic disease. Areas covered: In this review, we described the pathophysiology of hyperuricemia and monosodium urate (MSU) crystal induced inflammatory response during gout development in depth and comprehensively summarized the advances in the investigation of promising ULT drugs as well as anti-inflammatory drugs that might be safer and more effective for gout treatment. Expert opinion: New drugs that are developed based on these molecular mechanisms exhibited great efficacy on reduction of disease burden both in vitro and in vivo, implying their potential for clinical application. Moreover, hyperthermia also showed regulation effect on MSU crystals formation and the signaling pathways involved in inflammation.
MeSH term(s)	Humans ; Hyperuricemia/drug therapy ; Uric Acid/pharmacology ; Uric Acid/therapeutic use ; Gout/drug therapy ; Inflammation/drug therapy ; Anti-Inflammatory Agents/therapeutic use
Chemical Substances	Uric Acid (268B43MJ25) ; Anti-Inflammatory Agents
Language	English
Publishing date	2024-01-05
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2001535-5
ISSN	1744-7666 ; 1465-6566
ISSN (online)	1744-7666
ISSN	1465-6566
DOI	10.1080/14656566.2023.2291073
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Zs.A 5130: Show issues

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Article ; Online: Vectorgastrogram: dynamic trajectory and recurrence quantification analysis to assess slow wave vector movement in healthy subjects.

Prats-Boluda, Gema / Martinez-de-Juan, Jose L / Nieto-Del-Amor, Felix / Termenon, María / Varón, Cristina / Ye-Lin, Yiyao

Physical and engineering sciences in medicine

2024

Abstract: Functional gastric disorders entail chronic or recurrent symptoms, high prevalence and a significant financial burden. These disorders do not always involve structural abnormalities and since they cannot be diagnosed by routine procedures, ... ...

Abstract	Functional gastric disorders entail chronic or recurrent symptoms, high prevalence and a significant financial burden. These disorders do not always involve structural abnormalities and since they cannot be diagnosed by routine procedures, electrogastrography (EGG) has been proposed as a diagnostic alternative. However, the method still has not been transferred to clinical practice due to the difficulty of identifying gastric activity because of the low-frequency interference caused by skin-electrode contact potential in obtaining spatiotemporal information by simple procedures. This work attempted to robustly identify the gastric slow wave (SW) main components by applying multivariate variational mode decomposition (MVMD) to the multichannel EGG. Another aim was to obtain the 2D SW vectorgastrogram VGG
Language	English
Publishing date	2024-03-04
Publishing country	Switzerland
Document type	Journal Article
ISSN	2662-4737
ISSN (online)	2662-4737
DOI	10.1007/s13246-024-01396-y
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Article ; Online: The progression of obstructive renal fibrosis in rats is regulated by ADAMTS18 gene methylation in the embryonic kidney through the AKT/Notch pathway.

Xu, Ben / Zhang, Jia-En / Ye, Lin / Yuan, Chang-Wei

Journal of biochemical and molecular toxicology

2024 Volume 38, Issue 1, Page(s) e23628

Abstract: This study aimed to explore the mechanism by which postembryonic renal ADAMTS18 methylation influences obstructive renal fibrosis in rats. After exposure to transforming growth factor (TGF)-β1 during the embryonic period, analysis of postembryonic renal ... ...

Abstract	This study aimed to explore the mechanism by which postembryonic renal ADAMTS18 methylation influences obstructive renal fibrosis in rats. After exposure to transforming growth factor (TGF)-β1 during the embryonic period, analysis of postembryonic renal ADAMTS18 methylation and expression levels was conducted. Histological analysis was performed to assess embryonic kidney lesions and damage. Western blot analysis was used to determine the expression of renal fibrosis markers. Rats with ureteral obstruction and a healthy control group were selected. The methylation levels of ADAMTS18 in the different groups were analyzed. Western blot analysis and immunohistochemistry were performed to analyze the expression of renal fibrosis markers, and kidney-related indicators were measured. Treatment with TGF-β1 resulted in abnormal development of the postembryonic kidney, which was characterized by rough kidney surfaces with mild depressions and irregularities on the outer surface. TGF-β1 treatment significantly promoted ADAMTS18 methylation and activated the protein kinase B (AKT)/Notch pathway. Ureteral obstruction was induced to establish a renal hydronephrosis model, which led to renal fibrotic injury in newborn rats. Overexpression of the ADAMTS18 gene alleviated renal fibrosis. The western blot results showed that compared to that in the control group, the expression of renal fibrosis markers was significantly decreased after ADAMTS18 overexpression, and there was a thicker renal parenchymal tissue layer and significantly reduced p-AKT/AKT and Notch1 levels. TGF-β1 can induce ADAMTS18 gene methylation in the postembryonic kidney, and the resulting downregulation of ADAMTS18 expression has long-term effects on kidney development, potentially leading to increased susceptibility to obstructive renal fibrosis. This mechanism may involve activation of the AKT/Notch pathway. Reversing ADAMTS18 gene methylation may reverse this process.
MeSH term(s)	Animals ; Rats ; Fibrosis ; Kidney ; Kidney Diseases/metabolism ; Methylation ; Proto-Oncogene Proteins c-akt/metabolism ; Signal Transduction ; Transforming Growth Factor beta1/genetics ; Transforming Growth Factor beta1/metabolism ; Ureteral Obstruction/metabolism ; Ureteral Obstruction/pathology ; ADAMTS Proteins/genetics
Chemical Substances	Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Transforming Growth Factor beta1 ; ADAMTS Proteins (EC 3.4.24.-)
Language	English
Publishing date	2024-01-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	1410020-4
ISSN	1099-0461 ; 1095-6670
ISSN (online)	1099-0461
ISSN	1095-6670
DOI	10.1002/jbt.23628
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Zs.A 2201: Show issues

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Article: The Role of the ADAMTS18 Gene-Induced Immune Microenvironment in Mouse Kidney Development.

Xu, Ben / Zhang, Jia-En / Ye, Lin / Yuan, Chang-Wei

Biomedicines

2024 Volume 12, Issue 2

Abstract: The aim of this study is to investigate the role of the ADAMTS18 gene in regulating the renal development of mice. PAS staining was used to observe the kidney development of E12.5-E17.5 mice, while immunofluorescence staining and RT-PCR were used to ... ...

Abstract	The aim of this study is to investigate the role of the ADAMTS18 gene in regulating the renal development of mice. PAS staining was used to observe the kidney development of E12.5-E17.5 mice, while immunofluorescence staining and RT-PCR were used to observe the expression of ADAMTS18. Ureteric bud (UB) branches were observed using immunofluorescence staining using the UB marker E-cadherin, and the apoptosis and proliferation of posterior renal mesenchymal cells were analyzed using TUNEL and PH3 fluorescence staining. Flow cytometry was used to analyze the immune cell infiltration, and western blotting (WB) was used to analyze the expression of PD-1/PD-L1 and CTLA-4. As a result, the ADAMTS18 gene expression gradually increased as the kidney continued to mature during embryonic development. Compared with that in the control and vector groups, UB branching was significantly reduced in the ADAMTS18 deletion group (
Language	English
Publishing date	2024-02-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines12020396
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Article ; Online: Swimming exercise reverses transcriptomic changes in aging mouse lens.

Ye, Lin / Yuan, Jiayue / Zhu, Shijie / Ji, Shunmei / Dai, Jinhui

BMC medical genomics

2024 Volume 17, Issue 1, Page(s) 67

Abstract: Background: The benefits of physical activity for the overall well-being of elderly individuals are well-established, the precise mechanisms through which exercise improves pathological changes in the aging lens have yet to be fully understood.: ... ...

Abstract	Background: The benefits of physical activity for the overall well-being of elderly individuals are well-established, the precise mechanisms through which exercise improves pathological changes in the aging lens have yet to be fully understood. Methods: 3-month-old C57BL/6J mice comprised young sedentary (YS) group, while aging mice (18-month-old) were divided into aging sedentary (AS) group and aging exercising (AE) group. Mice in AE groups underwent sequential stages of swimming exercise. H&E staining was employed to observe alterations in lens morphology. RNA-seq analysis was utilized to examine transcriptomic changes. Furthermore, qPCR and immunohistochemistry were employed for validation of the results. Results: AE group showed alleviation of histopathological aging changes in AS group. By GSEA analysis of the transcriptomic changes, swimming exercise significantly downregulated approximately half of the pathways that underwent alterations upon aging, where notable improvements were 'calcium signaling pathway', 'neuroactive ligand receptor interaction' and 'cell adhesion molecules'. Furthermore, we revealed a total of 92 differentially expressed genes between the YS and AS groups, of which 10 genes were observed to be mitigated by swimming exercise. The result of qPCR was in consistent with the transcriptome data. We conducted immunohistochemical analysis on Ciart, which was of particular interest due to its dual association as a common aging gene and its significant responsiveness to exercise. The Protein-protein Interaction network of Ciart showed the involvement of the regulation of Rorb and Sptbn5 during the process. Conclusion: The known benefits of exercise could extend to the aging lens and support further investigation into the specific roles of Ciart-related pathways in aging lens.
MeSH term(s)	Humans ; Aged ; Animals ; Mice ; Infant ; Mice, Inbred C57BL ; Transcriptome ; Swimming ; Gene Expression Profiling ; Aging/genetics
Language	English
Publishing date	2024-03-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2411865-5
ISSN	1755-8794 ; 1755-8794
ISSN (online)	1755-8794
ISSN	1755-8794
DOI	10.1186/s12920-024-01839-1
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Article ; Online: The Effect of Lens Shape, Zonular Insertion and Finite Element Model on Simulated Shape Change of the Eye Lens.

Ye, Lin / Wang, Kehao / Grasa, Jorge / Pierscionek, Barbara K

Annals of biomedical engineering

2024

Abstract: The process of lens shape change in the eye to alter focussing (accommodation) is still not fully understood. Modelling approaches have been used to complement experimental findings in order to determine how constituents in the accommodative process ... ...

Abstract	The process of lens shape change in the eye to alter focussing (accommodation) is still not fully understood. Modelling approaches have been used to complement experimental findings in order to determine how constituents in the accommodative process influence the shape change of the lens. An unexplored factor in modelling is the role of the modelling software on the results of simulated shape change. Finite element models were constructed in both Abaqus and Ansys software using biological parameters from measurements of shape and refractive index of two 35-year-old lenses. The effect of zonular insertion on simulated shape change was tested on both 35-year-old lens models and with both types of software. Comparative analysis of shape change, optical power, and stress distributions showed that lens shape and zonular insertion positions affect the results of simulated shape change and that Abaqus and Ansys show differences in their respective models. The effect of the software package used needs to be taken into account when constructing finite element models and deriving conclusions.
Language	English
Publishing date	2024-03-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	185984-5
ISSN	1573-9686 ; 0191-5649 ; 0090-6964
ISSN (online)	1573-9686
ISSN	0191-5649 ; 0090-6964
DOI	10.1007/s10439-024-03491-3
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Zs.A 1018: Show issues

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Article ; Online: Causal relationship between gut microbiota and diabetic nephropathy: a two-sample Mendelian randomization study.

Yan, Shuxiang / Wang, Hua / Feng, Baiyu / Ye, Lin / Chen, Anqun

Frontiers in immunology

2024 Volume 15, Page(s) 1332757

Abstract: Objective: Emerging evidence has provided compelling evidence linking gut microbiota (GM) and diabetic nephropathy (DN) via the "gut-kidney" axis. But the causal relationship between them hasn't been clarified yet. We perform a Two-Sample Mendelian ... ...

Abstract	Objective: Emerging evidence has provided compelling evidence linking gut microbiota (GM) and diabetic nephropathy (DN) via the "gut-kidney" axis. But the causal relationship between them hasn't been clarified yet. We perform a Two-Sample Mendelian randomization (MR) analysis to reveal the causal connection with GM and the development of DN, type 1 diabetes nephropathy (T1DN), type 2 diabetes nephropathy (T2DN), type 1 diabetes mellitus (T1DM), and type 2 diabetes mellitus (T2DM). Methods: We used summary data from MiBioGen on 211 GM taxa in 18340 participants. Generalized MR analysis methods were conducted to estimate their causality on risk of DN, T1DN, T2DN, T1DM and T2DM from FinnGen. To ensure the reliability of the findings, a comprehensive set of sensitivity analyses were conducted to confirm the resilience and consistency of the results. Results: It was showed that Class Conclusions: At the gene prediction level, we identified the specific GM that is causally linked to DN in both T1DM and T2DM patients. Moreover, we identified distinct microbial changes in T1DN that differed from those seen in T2DN, offering valuable insights into GM signatures associated with subtype of nephropathy.
MeSH term(s)	Humans ; Diabetic Nephropathies ; Gastrointestinal Microbiome ; Diabetes Mellitus, Type 1 ; Diabetes Mellitus, Type 2 ; Mendelian Randomization Analysis ; Reproducibility of Results
Language	English
Publishing date	2024-03-08
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1332757
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Article ; Online: Expectation maximization based framework for joint localization and parameter estimation in single particle tracking from segmented images.

Ye Lin / Sean B Andersson

PLoS ONE, Vol 16, Iss 5, p e

2021 Volume 0243115

Abstract: Single Particle Tracking (SPT) is a well known class of tools for studying the dynamics of biological macromolecules moving inside living cells. In this paper, we focus on the problem of localization and parameter estimation given a sequence of segmented ...

Abstract	Single Particle Tracking (SPT) is a well known class of tools for studying the dynamics of biological macromolecules moving inside living cells. In this paper, we focus on the problem of localization and parameter estimation given a sequence of segmented images. In the standard paradigm, the location of the emitter inside each frame of a sequence of camera images is estimated using, for example, Gaussian fitting (GF), and these locations are linked to provide an estimate of the trajectory. Trajectories are then analyzed by using Mean Square Displacement (MSD) or Maximum Likelihood Estimation (MLE) techniques to determine motion parameters such as diffusion coefficients. However, the problems of localization and parameter estimation are clearly coupled. Motivated by this, we have created an Expectation Maximization (EM) based framework for simultaneous localization and parameter estimation. We demonstrate this framework through two representative methods, namely, Sequential Monte Carlo combined with Expectation Maximization (SMC-EM) and Unscented Kalman Filter combined with Expectation Maximization (U-EM). Using diffusion in two-dimensions as a prototypical example, we conduct quantitative investigations on localization and parameter estimation performance across a wide range of signal to background ratios and diffusion coefficients and compare our methods to the standard techniques based on GF-MSD/MLE. To demonstrate the flexibility of the EM based framework, we do comparisons using two different camera models, an ideal camera with Poisson distributed shot noise but no readout noise, and a camera with both shot noise and the pixel-dependent readout noise that is common to scientific complementary metal-oxide semiconductor (sCMOS) camera. Our results indicate our EM based methods outperform the standard techniques, especially at low signal levels. While U-EM and SMC-EM have similar accuracy, U-EM is significantly more computationally efficient, though the use of the Unscented Kalman Filter limits U-EM to lower ...
Keywords	Medicine ; R ; Science ; Q
Subject code	620
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Chinese herbal compound SanHuang decoction reverses axitinib resistance in ccRCC through regulating immune cell infiltration by affecting ADAMTS18 expression.

Xu, Ben / Zhang, Jiaen / Ye, Lin / Yuan, Changwei

American journal of cancer research

2023 Volume 13, Issue 7, Page(s) 2841–2860

Abstract: This investigation aims to study the reversal effect of the Chinese herbal compound SanHuang decoction on axitinib resistance in clear cell renal cell carcinoma (ccRCC) cells and its mechanistic role by employing cellular and mouse models. Axitinib- ... ...

Abstract	This investigation aims to study the reversal effect of the Chinese herbal compound SanHuang decoction on axitinib resistance in clear cell renal cell carcinoma (ccRCC) cells and its mechanistic role by employing cellular and mouse models. Axitinib-resistant ccRCC cell lines (A498-DR and 786-O-DR) were cultured and treated with SanHuang decoction. The apoptosis and migration of tumor cells were observed by flow cytometry and wound healing assays, respectively, and the expression of a disintegrin-like and metalloprotease with thrombospondin type 1 motif 18 (ADAMTS18) was evaluated by reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting (WB). In addition, A498-DR cells were inoculated into mice to establish tumorigenic models, and the models were treated with normal saline, axitinib, or different concentrations of SanHuang decoction plus axitinib. Then, the tumor diameter in each group was measured, and the expression of ADAMTS18 was evaluated by RT-PCR, WB and immunohistochemistry. In addition, the distribution of T cells (CD45+, CD4+, CD8+) and PD-L1 expression was analyzed by flow cytometry to evaluate the level of immune cell infiltration. SanHuang decoction significantly reduced the proliferative activity of axitinib-resistant tumor cells and enhanced the sensitivity of tumors to axitinib
Language	English
Publishing date	2023-07-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2589522-9
ISSN	2156-6976
ISSN	2156-6976
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