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Article ; Online: A latent profile analysis of tear cytokines and their association with severity of dry eye disease in the Dry Eye Assessment and Management (DREAM) study.

Chen, Yineng / Mallem, Krishna / Asbell, Penny A / Ying, Gui-Shuang

2024 Volume 14, Issue 1, Page(s) 526

Abstract: This study is to identify subgroups of DED patients with different tear cytokine profiles and compare their DED symptoms and signs among subgroups. Baseline tear cytokines (IL-1β, IL-6, IL-8, IL-10, IL-17A, IFN-γ and TNF-α) were measured using a magnetic ...

Abstract	This study is to identify subgroups of DED patients with different tear cytokine profiles and compare their DED symptoms and signs among subgroups. Baseline tear cytokines (IL-1β, IL-6, IL-8, IL-10, IL-17A, IFN-γ and TNF-α) were measured using a magnetic bead assay. DED symptoms were assessed by Ocular Surface Disease Index (OSDI) and signs were assessed by corneal and conjunctival staining, tear break-up time (TBUT), Schirmer's test, tear osmolarity and meibomian gland dysfunction (MGD). Latent profile analysis was performed to identify subgroups, and their scores of DED symptoms and signs were compared using generalized linear regression. Among 131 patients with total tear volume > 4 µl from both eyes, subgroup 1 (n = 23) significantly higher in IL-6 and IL-8 (all p < 0.001) and subgroup 2 (n = 108) significantly higher in IL-10 (p = 0.03), IL-17A (p < 0.001), and IFN-γ (p < 0.001). Both subgroups were similar in demographics and DED symptoms, but subgroup 1 had significantly more severe DED signs: higher conjunctival staining (3.38 vs. 2.69, p = 0.04), corneal staining (4.26 vs. 3.03, p = 0.03), lower Schirmer's test score (8.20 vs. 13.72, p < 0.001), and higher composite severity score of DED sign (0.62 vs. 0.45, p = 0.002). We identified two DED subgroups with different profiles of tear cytokines. Patients in these subgroups differed significantly in DED signs, supporting the inflammation's role in DED development and progression.
MeSH term(s)	Humans ; Cytokines ; Interleukin-10 ; Interleukin-17 ; Interleukin-6 ; Interleukin-8 ; Dry Eye Syndromes/diagnosis ; Tears
Chemical Substances	Cytokines ; Interleukin-10 (130068-27-8) ; Interleukin-17 ; Interleukin-6 ; Interleukin-8
Language	English
Publishing date	2024-01-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-51241-1
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Article ; Online: Association of Tear Cytokine Ratios with Symptoms and Signs of Dry Eye Disease: Biomarker Data from the Dry Eye Assessment and Management Study.

Zhao, Cindy S / Chen, Yineng / Ying, Gui-Shuang / Asbell, Penny A

Current eye research

2024 Volume 49, Issue 1, Page(s) 16–24

Abstract: Purpose: To assess the relationship between tear inflammatory cytokine ratios (CRs) and signs and symptoms of dry eye disease (DED) to investigate the possible use of tear CRs, which may better address the complexity of cytokine interactions than ... ...

Abstract	Purpose: To assess the relationship between tear inflammatory cytokine ratios (CRs) and signs and symptoms of dry eye disease (DED) to investigate the possible use of tear CRs, which may better address the complexity of cytokine interactions than absolute cytokine levels, as a DED biomarker. Methods: Tear concentrations of IL-1b, IL-6, IL-8, IL-10, IL-17A, IFN-g, and TNF-a were measured using standardized procedures, as were DED signs (corneal and conjunctival staining scores, tear break-up time, Schirmer test, Meibomian gland plugging, tear osmolarity, composite sign severity score) and symptoms [Ocular Surface Disease Index (OSDI)]. Ratios between pro-inflammatory (IL-1b, IL-8, IL-17A, IFN-g, and TNF-a) and anti-inflammatory (IL-10) cytokines were calculated. Given its opposing roles in inflammation, IL-6 was tested as both a pro- and anti-inflammatory cytokine. Correlations between CR and DED symptoms and signs were calculated using Spearman correlation coefficients (rho). Results: At baseline, 131 patients, 80.2% female and mean age 54.2 years (SD 14.1, range 20-82), from 10 sites of the Dry Eye Assessment and Management study had sufficient tear volumes ≥4 μL for analysis. IL-6:IL-10, IL-8:IL-10, and TNF-a:IL-10 had some significant correlations, mostly with conjunctival or corneal staining or the composite sign severity score (IL-8:IL-10 and conjunctival staining: rho = 0.19, Conclusions: Pro- to anti-inflammatory CR was weakly correlated with some DED signs and not with symptoms, as measured by OSDI. Future studies in different dry eye populations are needed and should address sampling biases and tear collection techniques.
MeSH term(s)	Humans ; Female ; Middle Aged ; Male ; Cytokines ; Interleukin-10 ; Interleukin-17 ; Interleukin-6 ; Interleukin-8 ; Dry Eye Syndromes/diagnosis ; Tears ; Biomarkers ; Interferon-gamma ; Anti-Inflammatory Agents
Chemical Substances	Cytokines ; Interleukin-10 (130068-27-8) ; Interleukin-17 ; Interleukin-6 ; Interleukin-8 ; Biomarkers ; Interferon-gamma (82115-62-6) ; Anti-Inflammatory Agents
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article
ZDB-ID	82079-9
ISSN	1460-2202 ; 0271-3683
ISSN (online)	1460-2202
ISSN	0271-3683
DOI	10.1080/02713683.2023.2262168
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Article ; Online: Deep Learning-Facilitated Study of the Rate of Change in Photoreceptor Outer Segment Metrics in RPGR-Related X-Linked Retinitis Pigmentosa.

Wang, Yi-Zhong / Juroch, Katherine / Chen, Yineng / Ying, Gui-Shuang / Birch, David G

Investigative ophthalmology & visual science

2024 Volume 64, Issue 14, Page(s) 31

Abstract: Purpose: The aim of this retrospective cohort study was to obtain three-dimensional (3D) photoreceptor outer segment (OS) metrics measurements with the assistance of a deep learning model (DLM) and to evaluate the longitudinal change in OS metrics and ... ...

Abstract	Purpose: The aim of this retrospective cohort study was to obtain three-dimensional (3D) photoreceptor outer segment (OS) metrics measurements with the assistance of a deep learning model (DLM) and to evaluate the longitudinal change in OS metrics and associated factors in retinitis pigmentosa GTPase regulator (RPGR) X-linked retinitis pigmentosa (XLRP). Methods: The study included 34 male patients with RPGR-associated XLRP who had preserved ellipsoid zone (EZ) within their spectral-domain optical coherence tomography volume scans and an approximate 2-year or longer follow-up. Volume scans were segmented using a DLM with manual correction for EZ and apical retinal pigment epithelium (RPE). OS metrics were measured from 3D EZ-RPE layers of volume scans. Linear mixed-effects models were used to calculate the rate of change in OS metrics and the associated factors, including baseline age, baseline OS metrics, and follow-up duration. Results: The mean (standard deviation) of progression rates were -0.28 (0.43) µm/y, -0.73 (0.61) mm2/y, and -0.014 (0.012) mm3/y for OS thickness, EZ area, and OS volume, respectively. In multivariable analysis, the progression rates of EZ area and OS volume were strongly associated with their baseline values, with faster decline in eyes with larger baseline values (P ≤ 0.003), and nonlinearly associated with the baseline age (P ≤ 0.003). OS thickness decline was not associated with its baseline value (P = 0.32). Conclusions: These results provide evidence to support using OS metrics as biomarkers to assess the progression of XLRP and as the outcome measures of clinical trials. Given that their progression rates are dependent on their baseline values, the baseline EZ area and OS volume should be considered in the design and statistical analysis of future clinical trials. Deep learning may provide a useful tool to reduce the burden of human graders to analyze OCT scan images and to facilitate the assessment of disease progression and treatment trials for retinitis pigmentosa.
MeSH term(s)	Humans ; Male ; Deep Learning ; Retrospective Studies ; Retinitis Pigmentosa/diagnosis ; Retinitis Pigmentosa/genetics ; Cilia ; Retinal Pigment Epithelium ; Eye Proteins/genetics
Chemical Substances	RPGR protein, human ; Eye Proteins
Language	English
Publishing date	2024-01-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	391794-0
ISSN	1552-5783 ; 0146-0404
ISSN (online)	1552-5783
ISSN	0146-0404
DOI	10.1167/iovs.64.14.31
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Article: Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species.

Ji, Huiyue / Liu, Junnan / Chen, Yineng / Yu, Xinyi / Luo, Chenlu / Sang, Luxi / Zhou, Jiayu / Liao, Hai

Plants (Basel, Switzerland)

2024 Volume 13, Issue 4

Abstract: Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified ... ...

Abstract	Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified 140
Language	English
Publishing date	2024-02-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants13040468
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Book ; Online: Bidirectional Looking with A Novel Double Exponential Moving Average to Adaptive and Non-adaptive Momentum Optimizers

Chen, Yineng / Li, Zuchao / Zhang, Lefei / Du, Bo / Zhao, Hai

2023

Abstract: Optimizer is an essential component for the success of deep learning, which guides the neural network to update the parameters according to the loss on the training set. SGD and Adam are two classical and effective optimizers on which researchers have ... ...

Abstract	Optimizer is an essential component for the success of deep learning, which guides the neural network to update the parameters according to the loss on the training set. SGD and Adam are two classical and effective optimizers on which researchers have proposed many variants, such as SGDM and RAdam. In this paper, we innovatively combine the backward-looking and forward-looking aspects of the optimizer algorithm and propose a novel \textsc{Admeta} (\textbf{A} \textbf{D}ouble exponential \textbf{M}oving averag\textbf{E} \textbf{T}o \textbf{A}daptive and non-adaptive momentum) optimizer framework. For backward-looking part, we propose a DEMA variant scheme, which is motivated by a metric in the stock market, to replace the common exponential moving average scheme. While in the forward-looking part, we present a dynamic lookahead strategy which asymptotically approaches a set value, maintaining its speed at early stage and high convergence performance at final stage. Based on this idea, we provide two optimizer implementations, \textsc{AdmetaR} and \textsc{AdmetaS}, the former based on RAdam and the latter based on SGDM. Through extensive experiments on diverse tasks, we find that the proposed \textsc{Admeta} optimizer outperforms our base optimizers and shows advantages over recently proposed competitive optimizers. We also provide theoretical proof of these two algorithms, which verifies the convergence of our proposed \textsc{Admeta}.
Keywords	Computer Science - Machine Learning ; Mathematics - Optimization and Control
Subject code	006
Publishing date	2023-07-02
Publishing country	us
Document type	Book ; Online
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Article ; Online: Biomod2 modeling for predicting the potential ecological distribution of three Fritillaria species under climate change.

Huang, Deya / An, Qiuju / Huang, Sipei / Tan, Guodong / Quan, Huige / Chen, Yineng / Zhou, Jiayu / Liao, Hai

Scientific reports

2023 Volume 13, Issue 1, Page(s) 18801

Abstract: The Fritillaria species ranked as a well-known traditional medicine in China and has become rare due to excessive harvesting. To find reasonable strategy for conservation and cultivation, identification of new ecological distribution of Fritillaria ... ...

Abstract	The Fritillaria species ranked as a well-known traditional medicine in China and has become rare due to excessive harvesting. To find reasonable strategy for conservation and cultivation, identification of new ecological distribution of Fritillaria species together with prediction of those responses to climate change are necessary. In terms of current occurrence records and bioclimatic variables, the suitable habitats for Fritillaria delavayi, Fritillaria taipaiensis, and Fritillaria wabuensis were predicted. In comparison with Maxent and GARP, Biomod2 obtained the best AUC, KAPPA and TSS values of larger than 0.926 and was chosen to construct model. Temperature seasonality was indicated to put the greatest influence on Fritillaria taipaiensis and Fritillaria wabuensis, while isothermality was of most importance for Fritillaria delavayi. The current suitable areas for three Fritillaria species were distributed in south-west China, accounting for approximately 17.72%, 23.06% and 20.60% of China's total area, respectively. During 2021-2100 period, the suitable habitats of F. delavayi and F. wabuensis reached the maximum under SSP585 scenario, while that of F. taipaiensis reached the maximum under SSP126 scenario. The high niche overlap among three Fritillaria species showed correlation with the chemical composition (P ≤ 0.05), while no correlation was observed between niche overlap and DNA barcodes, indicating that spatial distribution had a major influence on chemical composition in the Fritillaria species. Finally, the acquisition of species-specific habitats would contribute to decrease in habitat competition, and future conservation and cultivation of Fritillaria species.
MeSH term(s)	Climate Change ; Fritillaria/genetics ; Ecosystem ; China ; Temperature
Language	English
Publishing date	2023-11-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-45887-6
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Article ; Online: Association of Dry Eye Symptoms and Signs in Patients with Dry Eye Disease.

Tawfik, Andrew / Pistilli, Maxwell / Maguire, Maureen G / Chen, Yineng / Yu, Yinxi / Greiner, Jack V / Asbell, Penny A / Ying, Gui-Shuang

Ophthalmic epidemiology

2023 Volume 31, Issue 3, Page(s) 274–282

Abstract: Purpose: To determine the correlations among symptoms and signs of dry eye disease (DED) in the Dry Eye Assessment and Management (DREAM) study.: Methods: A total of 535 patients with moderate-to-severe DED were assessed for symptoms using the Ocular ...

Abstract	Purpose: To determine the correlations among symptoms and signs of dry eye disease (DED) in the Dry Eye Assessment and Management (DREAM) study. Methods: A total of 535 patients with moderate-to-severe DED were assessed for symptoms using the Ocular Surface Disease Index (OSDI) and four DED signs in both eyes (conjunctival lissamine green staining, corneal fluorescein staining, Schirmer's testing, and tear break-up time (TBUT)) following standardized protocols at baseline and follow-up visits (months 3, 6, and 12). Spearman correlation coefficients (rho) were calculated for correlations among symptoms and signs of DED at baseline and among changes in symptoms and signs from baseline at 12 months. The confidence intervals and p-values for correlation coefficients were calculated using a cluster bootstrapping to account for inter-eye correlation. Results: At baseline, OSDI total score was not correlated with signs; however, OSDI subscale score of ocular symptoms was weakly correlated with corneal staining score (rho = 0.14, p = .002) and Schirmer test score (rho = 0.11, p = .01). There were statistically significant correlations among the four signs (p < .001), with absolute correlation coefficient ranging from 0.14 (conjunctival staining score vs. TBUT) to 0.33 (conjunctival staining score vs. cornea staining score). The correlations among changes in symptoms and signs were weaker, with the highest correlation between change in conjunctival staining and corneal staining (rho = 0.21, p < .001). Conclusions: Consistent with previous studies, among DREAM participants with moderate-to-severe DED at baseline, correlations of DED symptoms with signs were low and correlations among four objective signs were low to moderate. The correlations among changes in symptoms and signs were even weaker.
MeSH term(s)	Humans ; Dry Eye Syndromes/diagnosis ; Dry Eye Syndromes/physiopathology ; Female ; Male ; Middle Aged ; Tears/metabolism ; Aged ; Conjunctiva/pathology ; Cornea/pathology ; Adult ; Surveys and Questionnaires ; Fluorescein/metabolism ; Prospective Studies ; Lissamine Green Dyes
Chemical Substances	Fluorescein (TPY09G7XIR) ; Lissamine Green Dyes
Language	English
Publishing date	2023-08-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Multicenter Study
ZDB-ID	1213070-9
ISSN	1744-5086 ; 0928-6586
ISSN (online)	1744-5086
ISSN	0928-6586
DOI	10.1080/09286586.2023.2248629
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Zs.A 4138: Show issues

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Article ; Online: Features Associated with Visible Lamina Cribrosa Pores in Individuals of African Ancestry with Glaucoma: Primary Open-Angle African Ancestry Glaucoma Genetics (POAAGG) Study.

Jordan, Jalin A / Daniel, Ebenezer / Chen, Yineng / Salowe, Rebecca J / Zhu, Yan / Miller-Ellis, Eydie / Addis, Victoria / Sankar, Prithvi S / Zhu, Di / Smith, Eli J / Lee, Roy / Ying, Gui-Shuang / O'Brien, Joan M

Vision (Basel, Switzerland)

2024 Volume 8, Issue 2

Abstract: There are scarce data regarding the rate of the occurrence of primary open-angle glaucoma (POAG) and visible lamina cribrosa pores (LCPs) in the eyes of individuals with African ancestry; the potential impact of these features on disease burden remains ... ...

Abstract	There are scarce data regarding the rate of the occurrence of primary open-angle glaucoma (POAG) and visible lamina cribrosa pores (LCPs) in the eyes of individuals with African ancestry; the potential impact of these features on disease burden remains unknown. We recruited subjects with POAG to the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study. Through regression models, we evaluated the association between the presence of LCPs and various phenotypic features. In a multivariable analysis of 1187 glaucomatous eyes, LCPs were found to be more likely to be present in eyes with cup-to-disc ratios (CDR) of ≥0.9 (adjusted risk ratio (aRR) 1.11, 95%CI: 1.04-1.19,
Language	English
Publishing date	2024-04-18
Publishing country	Switzerland
Document type	Journal Article
ISSN	2411-5150
ISSN (online)	2411-5150
DOI	10.3390/vision8020024
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Article ; Online: Diabetes mellitus in patients with heart failure and reduced ejection fraction: a post hoc analysis from the WARCEF trial.

Romiti, Giulio Francesco / Nabrdalik, Katarzyna / Corica, Bernadette / Bucci, Tommaso / Proietti, Marco / Qian, Min / Chen, Yineng / Thompson, John L P / Homma, Shunichi / Lip, Gregory Y H

Internal and emergency medicine

2024

Abstract: Patients with heart failure with reduced ejection fraction (HFrEF) and diabetes mellitus (DM) have an increased risk of adverse events, including thromboembolism. In this analysis, we aimed to explore the association between DM and HFrEF using data from ... ...

Abstract	Patients with heart failure with reduced ejection fraction (HFrEF) and diabetes mellitus (DM) have an increased risk of adverse events, including thromboembolism. In this analysis, we aimed to explore the association between DM and HFrEF using data from the "Warfarin versus Aspirin in Reduced Cardiac Ejection Fraction" (WARCEF) trial. We analyzed factors associated with DM using multiple logistic regression models and evaluated the effect of DM on long-term prognosis, through adjusted Cox regressions. The primary outcome was the composite of all-cause death, ischemic stroke, or intracerebral hemorrhage; we explored individual components as the secondary outcomes and the interaction between treatment (warfarin or aspirin) and DM on the risk of the primary outcome, stratified by relevant characteristics. Of 2294 patients (mean age 60.8 (SD 11.3) years, 19.9% females) included in this analysis, 722 (31.5%) had DM. On logistic regression, cardiovascular comorbidities, symptoms and ethnicity were associated with DM at baseline, while age and body mass index showed a nonlinear association. Patients with DM had a higher risk of the primary composite outcome (Hazard Ratio [HR] and 95% Confidence Intervals [CI]: 1.48 [1.24-1.77]), as well as all-cause death (HR [95%CI]: 1.52 [1.25-1.84]). As in prior analyses, no statistically significant interaction was observed between DM and effect of Warfarin on the risk of the primary outcome, in any of the subgroups explored. In conclusion, we found that DM is common in HFrEF patients, and is associated with other cardiovascular comorbidities and risk factors, and with a worse prognosis.
Language	English
Publishing date	2024-02-23
Publishing country	Italy
Document type	Journal Article
ZDB-ID	2454173-4
ISSN	1970-9366 ; 1828-0447
ISSN (online)	1970-9366
ISSN	1828-0447
DOI	10.1007/s11739-024-03544-4
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Article ; Online: Retinal Vascular Plexuses Are Unequally Affected in Canine Inherited Retinal Degenerations.

Ripolles-Garcia, Ana / Chen, Yineng / Sato, Yu / Gray, Alexa / Ying, Gui-Shuang / Aguirre, Gustavo D / Beltran, William A

Investigative ophthalmology & visual science

2022 Volume 63, Issue 12, Page(s) 22

Abstract: Purpose: To characterize the progression of vascular changes that occur in each retinal plexus, in three canine models of inherited retinal degeneration.: Methods: In this retrospective cohort study, we examined the retinal imaging records of 44 dogs ...

Abstract	Purpose: To characterize the progression of vascular changes that occur in each retinal plexus, in three canine models of inherited retinal degeneration. Methods: In this retrospective cohort study, we examined the retinal imaging records of 44 dogs from a research colony that had undergone optical coherence tomography angiography (OCTA) imaging. Animals enrolled included crd2/NPHP5 and xlpra2/RPGR mutant dogs imaged at different stages of photoreceptor loss, as well as RHOT4R/+ dogs after acute light-induced rod degeneration. Also included were normal controls imaged at similar ages. OCT angiograms of the superficial vascular plexus combined with the intermediate capillary plexus (SVP + ICP), and the deep capillary plexus (DCP) were analyzed using the AngioTool software to calculate vessel density and other vascular parameters. Results: A reduction in vessel density was seen over time in both the SVP + ICP and DCP in all mutant dogs but was more pronounced in the DCP. Scans were subclassified based on outer nuclear layer (ONL) thinning compared to age-matched normal controls. When ONL loss was 0% to 50%, vessel density in the DCP was significantly lower than in age-matched controls. In all cases, when ONL loss exceeded 87.5%, vessel density in the SVP + ICP was significantly reduced as well. In the acute light-induced rod degeneration model, the vascular regression changes were observed mainly in the DCP. Conclusions: Vessel density reduction in dogs undergoing retinal degeneration is first detected by OCTA in the DCP, and only at later stages in the SVP + ICP.
MeSH term(s)	Dogs ; Animals ; Fluorescein Angiography/methods ; Retinal Vessels ; Retinal Degeneration/genetics ; Retrospective Studies ; Retina ; Tomography, Optical Coherence/methods ; Eye Diseases
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	391794-0
ISSN	1552-5783 ; 0146-0404
ISSN (online)	1552-5783
ISSN	0146-0404
DOI	10.1167/iovs.63.12.22
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