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  1. Article ; Online: Stability of dosiomic features against variations in dose calculation: An analysis based on a cohort of prostate external beam radiotherapy patients.

    Sun, Lingyue / Smith, Wendy / Kirkby, Charles

    Journal of applied clinical medical physics

    2023  Volume 24, Issue 5, Page(s) e13904

    Abstract: Introduction: Interest in using higher order features of the planned 3D dose distributions (i.e., dosiomics) to predict radiotherapy outcomes is growing. This is driving many retrospective studies where historical data are mined to train machine ... ...

    Abstract Introduction: Interest in using higher order features of the planned 3D dose distributions (i.e., dosiomics) to predict radiotherapy outcomes is growing. This is driving many retrospective studies where historical data are mined to train machine learning models; however, recent decades have seen considerable advances in dose calculation that could have a direct impact on the dosiomic features such studies seek to extract. Is it necessary to recalculate planned dose distributions using a common algorithm if retrospective datasets from different institutions are included? Does a change in dose calculation grid size part way through a retrospective cohort, introduce bias in the extracted dosiomic features? The purpose of this study is to assess the stability of dosiomic features against variations in three factors: the dose calculation algorithm type, version, and dose grid size.
    Methods: Dose distributions for 27 prostate patients who received EBRT were recalculated in the Eclipse Treatment Planning System (Varian Medical Systems, Palo Alto, California, USA) using two algorithms (AAA and Acuros XB), two versions (version 13.6 and 15.6), and three dose grids (2, 2.5 s, and 3 mm) - 12 dose distributions for each patient. Ninety-three dosiomic features were extracted from each dose distribution and each of the following regions-of-interest: high dose PTV (PTV_High), 1 cm rind around PTV_High (PTV_Ring), low dose PTV (PTV_Low), rectum, and bladder using PyRadiomics. The coefficient of variation (CV) was calculated for each dosiomic feature. Hierarchical clustering was used to group features with high and low variability. Three-way repeated measures ANOVA was performed to investigate the effect of the three different factors on dosiomic features that were classified with high variation. Additionally, CVs were calculated for cumulative dose volume histograms (DVHs) to test their ability to detect the variations in dose distributions.
    Results: For PTV_Ring, PTV_Low, and rectum, all the dosiomic features had low CV (average CV ≤ 0.26) across the varying dose calculation conditions. For PTV_High, six dosiomic features showed CV > 0.26, and dose calculation algorithm type and grid size were the major sources of within-patient variation. For bladder, one dosiomic feature had average CV > 0.26, but none of the three dose calculation-related factors led to a statistically significant variation. The CVs for all the DVHs were very small (CV < 0.05).
    Conclusion: For all the regions-of-interest examined in this study, the majority of the dosiomic features were stable against variations in dose calculation; however, some of the dosiomic features for PTV_High and bladder had significant variations due to differences in dose calculation details. DVHs were detecting less variation than dosiomic features.
    MeSH term(s) Male ; Humans ; Prostate ; Retrospective Studies ; Radiotherapy Dosage ; Radiotherapy, Intensity-Modulated ; Radiotherapy Planning, Computer-Assisted ; Algorithms
    Language English
    Publishing date 2023-01-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2010347-5
    ISSN 1526-9914 ; 1526-9914
    ISSN (online) 1526-9914
    ISSN 1526-9914
    DOI 10.1002/acm2.13904
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  2. Article ; Online: Response by Sun et al to Letter Regarding Article, "Nuclear Receptor NR1D1 Regulates Abdominal Aortic Aneurysm Development by Targeting the Mitochondrial Tricarboxylic Acid Cycle Enzyme Aconitase-2".

    Sun, Ling-Yue / Lyu, Yu-Yan / Pu, Jun

    Circulation

    2023  Volume 147, Issue 20, Page(s) 1562–1563

    MeSH term(s) Humans ; Nuclear Receptor Subfamily 1, Group D, Member 1 ; Citric Acid Cycle ; Aortic Aneurysm, Abdominal ; Aconitate Hydratase/metabolism
    Chemical Substances Nuclear Receptor Subfamily 1, Group D, Member 1 ; Aconitate Hydratase (EC 4.2.1.3) ; NR1D1 protein, human
    Language English
    Publishing date 2023-05-15
    Publishing country United States
    Document type Letter ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 80099-5
    ISSN 1524-4539 ; 0009-7322 ; 0069-4193 ; 0065-8499
    ISSN (online) 1524-4539
    ISSN 0009-7322 ; 0069-4193 ; 0065-8499
    DOI 10.1161/CIRCULATIONAHA.123.064232
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  3. Article: Do Dosiomic Features Extracted From Planned 3-Dimensional Dose Distribution Improve Biochemical Failure-Free Survival Prediction: an Analysis Based on a Large Multi-Institutional Data Set.

    Sun, Lingyue / Burke, Ben / Quon, Harvey / Swallow, Alec / Kirkby, Charles / Smith, Wendy

    Advances in radiation oncology

    2023  Volume 8, Issue 5, Page(s) 101227

    Abstract: Purpose: The objective of this work was to investigate whether including additional dosiomic features can improve biochemical failure-free survival prediction compared with models with clinical features only or with clinical features as well as ... ...

    Abstract Purpose: The objective of this work was to investigate whether including additional dosiomic features can improve biochemical failure-free survival prediction compared with models with clinical features only or with clinical features as well as equivalent uniform dose and tumor control probability.
    Methods and materials: This retrospective study included 1852 patients who received diagnoses of localized prostate cancer between 2010 and 2016 and were treated with curative external beam radiation therapy in Albert, Canada. A total of 1562 patients from 2 centers were used for developing 3 random survival forest models: Model A included only 5 clinical features; Model B included 5 clinical features, equivalent uniform dose, and tumor control probability; and Model C considered 5 clinical features and 2074 dosiomic features derived from the planned dose distribution of the clinical target volume and planning target volume with further feature selection to determine prognostic features. No feature selection was performed for models A and B. Two hundred ninety patients from another 2 centers were used for independent validation. Individual model-based risk stratification was examined, and the log-rank tests were performed to test statistically significant differences between the risk groups. The 3 models' performances were evaluated using Harrell's concordance index (C-index) and compared using one-way repeated-measures analysis of variance with post hoc paired
    Results: Model C selected 6 dosiomic features and 4 clinical features to be prognostic. There were statistically significant differences between the 4 risk groups for both training and validation data sets. The C-index for the out-of-bag samples of the training data set was 0.650, 0.648, and 0.669 for models A, B, and C, respectively. The C-index for the validation data set for models A, B, and C was 0.653, 0.648, and 0.662, respectively. Although gains were modest, Model C was statistically significantly better than models A and B.
    Conclusions: Dosiomics contain information beyond common dose-volume histogram metrics from planned dose distributions. Incorporation of prognostic dosiomic features in biochemical failure-free survival outcome models can lead to statistically significant although modest improvement in performance.
    Language English
    Publishing date 2023-03-27
    Publishing country United States
    Document type Journal Article
    ISSN 2452-1094
    ISSN 2452-1094
    DOI 10.1016/j.adro.2023.101227
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  4. Article ; Online: LXRα Promotes Abdominal Aortic Aneurysm Formation Through UHRF1 Epigenetic Modification of miR-26b-3p.

    Guo, Xiao / Zhong, Jianmei / Zhao, Yichao / Fu, Yanan / Sun, Ling-Yue / Yuan, Ancai / Liu, Junling / Chen, Alex F / Pu, Jun

    Circulation

    2024  

    Abstract: Background: Abdominal aortic aneurysm (AAA) is a severe aortic disease without effective pharmacological approaches. The nuclear hormone receptor LXRα (liver X receptor α), encoded by the : Methods: Through integrated analyses of human and murine AAA ...

    Abstract Background: Abdominal aortic aneurysm (AAA) is a severe aortic disease without effective pharmacological approaches. The nuclear hormone receptor LXRα (liver X receptor α), encoded by the
    Methods: Through integrated analyses of human and murine AAA gene expression microarray data sets, we identified
    Results: Upregulated LXRα was observed in the aortas of patients with AAA and in angiotensin II- or CaCl
    Conclusions: Our study reveals a pivotal role of the LXRα/UHRF1/miR-26b-3p axis in AAA and provides potential biomarkers and therapeutic targets for AAA.
    Language English
    Publishing date 2024-04-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 80099-5
    ISSN 1524-4539 ; 0009-7322 ; 0069-4193 ; 0065-8499
    ISSN (online) 1524-4539
    ISSN 0009-7322 ; 0069-4193 ; 0065-8499
    DOI 10.1161/CIRCULATIONAHA.123.065202
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: External beam radiation therapy treatment factors prognostic of biochemical failure free survival: A multi-institutional retrospective study for prostate cancer.

    Sun, Lingyue / Quon, Harvey / Tran, Vicki / Kirkby, Charles / Smith, Wendy

    Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology

    2022  Volume 173, Page(s) 109–118

    Abstract: Background and purpose: The goal of this work is to identify specific treatment planning and delivery features that are prognostic of biochemical failure-free survival (BFFS) for prostate cancer patients treated with external beam radiotherapy (EBRT).!## ...

    Abstract Background and purpose: The goal of this work is to identify specific treatment planning and delivery features that are prognostic of biochemical failure-free survival (BFFS) for prostate cancer patients treated with external beam radiotherapy (EBRT).
    Materials and methods: This study reviewed patients diagnosed with localized prostate adenocarcinoma between 2005 and 2016, and treated with EBRT on a Varian linear accelerator at one of the four cancer centers in Alberta, Canada. BFFS was calculated using the Kaplan-Meier estimator. Patient demographics, tumor characteristics, and EBRT treatment planning and delivery factors, were collected for each patient. The patient cohort was split into a training dataset with patients from two centers and a validation dataset with patients from another two centers. A random survival forest was used to identify features associated with BFFS.
    Results: This study included 2827 patients with a median follow-up of 6.4 years. The BFFS for this cohort collectively was 84.9% at 5 years and 69.3% at 10 years. 2519 patients from two centers were used for model training and 308 patients from two different centers were used for model validation. The prognostic features were Gleason score, prostate-specific antigen (PSA) at diagnosis, clinical T stage, CTV D99, pelvic irradiation, IGRT frequency, and PTV V98. Variables including bladder volume, dose calculation algorithm, PTV D99, age at diagnosis, hip prosthesis, number of malignancies, fiducial marker usage, PTV volume, RT modality, PTV HI, rectal volume, hormone treatment, PTV D1cc, equivalent PTV margin, IGRT type, and EQD2_1.5 were unlikely to be prognostic. A random survival forest using only the seven prognostic variables was built. The Harrell's concordance index for the model was 0.65 for the whole training dataset, 0.62 for out-of-bag samples of the training dataset, and 0.62 for the validation dataset.
    Conclusion: EBRT features prognostic of BFFS were identified and a random survival forest was developed for predicting prostate cancer patients' BFFS after EBRT.
    MeSH term(s) Adenocarcinoma/mortality ; Adenocarcinoma/pathology ; Adenocarcinoma/radiotherapy ; Alberta/epidemiology ; Humans ; Male ; Prognosis ; Prostate-Specific Antigen ; Prostatic Neoplasms/mortality ; Prostatic Neoplasms/pathology ; Prostatic Neoplasms/radiotherapy ; Retrospective Studies
    Chemical Substances Prostate-Specific Antigen (EC 3.4.21.77)
    Language English
    Publishing date 2022-06-02
    Publishing country Ireland
    Document type Journal Article ; Multicenter Study ; Research Support, Non-U.S. Gov't
    ZDB-ID 605646-5
    ISSN 1879-0887 ; 0167-8140
    ISSN (online) 1879-0887
    ISSN 0167-8140
    DOI 10.1016/j.radonc.2022.05.030
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  6. Article ; Online: Variation in Interinstitutional Plan Quality When Adopting a Hypofractionated Protocol for Prostate Cancer External Beam Radiation Therapy.

    Sun, Lingyue / Smith, Wendy / Kirkby, Charles

    International journal of radiation oncology, biology, physics

    2020  Volume 107, Issue 2, Page(s) 243–252

    Abstract: Purpose: This study quantified plan quality differences across the 4 cancer centers in Alberta, Canada for plans that followed the PROstate Fractionated Irradiation Trial protocol.: Methods and materials: Prostate plans of 235 patients were ... ...

    Abstract Purpose: This study quantified plan quality differences across the 4 cancer centers in Alberta, Canada for plans that followed the PROstate Fractionated Irradiation Trial protocol.
    Methods and materials: Prostate plans of 235 patients were retrospectively reviewed. Interinstitutional plan quality comparisons were made based on distributions of protocol-specified parameters using 1-way analysis of variance with Games-Howell post hoc analysis. Dosimetrically representative cases were selected from each center using k-medoid clustering, enabling side-by-side comparison of dose-volume histograms and dose distributions. Fourteen anatomic features were investigated to explore interinstitutional patient population differences. Anatomically representative cases were selected from each center to explore differences in planning practices. Tumor control probability (TCP), as well as rectal wall and bladder wall normal tissue complication probabilities (NTCPs), were calculated to quantify the clinical effect of the differences in plan quality.
    Results: Comparing the mean value of each center to the other 3, statistically significant differences were observed for bladder wall D30% and D50%, left and right femoral heads D5%, planning target volume D99% and D1cc, and clinical target volume D99%. Dosimetrically representative cases demonstrated consistent results. Although anatomic differences were observed between the center-specific populations, an analysis using anatomically similar cases demonstrated consistent trends in the dosimetric differences, suggesting the dosimetric variation is not exclusively due to anatomic differences. Minimal differences (<1%) among the 4 centers were noted for TCP and NTCPs, suggesting the reported differences in plan quality may not have any clinical significance.
    Conclusions: Despite common guidelines, statistically significant differences in plan quality metrics occurred among the 4 investigated centers. The differences are due at least in part to variation in local planning practices. TCP and NTCP calculations suggest that the clinical significance of the differences is minimal. These results can serve as a reference for the degree of variation among centers that can be accepted when a common protocol is adopted.
    MeSH term(s) Humans ; Male ; Organs at Risk/radiation effects ; Prostatic Neoplasms/radiotherapy ; Quality Control ; Radiation Dose Hypofractionation ; Radiometry ; Radiotherapy Planning, Computer-Assisted/methods ; Radiotherapy, Conformal/adverse effects
    Language English
    Publishing date 2020-02-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 197614-x
    ISSN 1879-355X ; 0360-3016
    ISSN (online) 1879-355X
    ISSN 0360-3016
    DOI 10.1016/j.ijrobp.2020.02.026
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  7. Article ; Online: In Vivo

    Sun, Lingyue / Zhang, Shuzhen / Wan, Zhe / Li, Ruoyu / Yu, Jin

    Infection and immunity

    2021  Volume 89, Issue 5

    Abstract: ... Mucor ... ...

    Abstract Mucor irregularis
    MeSH term(s) Animals ; CARD Signaling Adaptor Proteins/deficiency ; Disease Models, Animal ; Disease Susceptibility ; Genetic Predisposition to Disease ; Mice ; Mucor/immunology ; Mucormycosis/genetics ; Mucormycosis/immunology ; Mucormycosis/microbiology ; Neutrophils/immunology ; Neutrophils/metabolism ; T-Lymphocytes, Helper-Inducer/immunology ; T-Lymphocytes, Helper-Inducer/metabolism ; Th1 Cells/immunology ; Th1 Cells/metabolism ; Th17 Cells/immunology ; Th17 Cells/metabolism
    Chemical Substances CARD Signaling Adaptor Proteins ; Card9 protein, mouse
    Language English
    Publishing date 2021-04-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218698-6
    ISSN 1098-5522 ; 0019-9567
    ISSN (online) 1098-5522
    ISSN 0019-9567
    DOI 10.1128/IAI.00040-21
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  8. Article ; Online: Dosimetric effect of body contour changes for prostate and head and neck volumetric modulated arc therapy plans.

    Sun, Lingyue / Kirkby, Charles / Smith, Wendy

    Journal of applied clinical medical physics

    2019  Volume 20, Issue 4, Page(s) 115–124

    Abstract: Body contour changes are commonly seen in prostate and head and neck (H&N) patients undergoing volumetric modulated arc therapy (VMAT) treatments, which may cause a discrepancy between the planned dose and the delivered dose. Dosimetrists, radiation ... ...

    Abstract Body contour changes are commonly seen in prostate and head and neck (H&N) patients undergoing volumetric modulated arc therapy (VMAT) treatments, which may cause a discrepancy between the planned dose and the delivered dose. Dosimetrists, radiation oncologists or medical physicists sometimes are required to visually assess the dosimetric impact of body contour changes and make a judgment call on whether further re-assessment of the plan is needed. However, an intuitive judgment cannot always be made in a timely manner due to the complexity of VMAT plans as well as the complicated forms of body contour changes. This study evaluated the dosimetric effect of body contour changes for prostate and H&N patients to help with clinical decision-making. By analyzing the one-dimensional spatial dose profiles from the original body and the body with different body contour deformations, rules of thumb for dose percentage change and isodose line shift due to body contour changes were ascertained. Moreover, based on dose distribution comparison using three-dimensional gamma analysis, the response of the clinical prostate and H&N VMAT plans to body contour changes was assessed. Within center specific dose deviation tolerances, prostate patients who had less than 2 cm single side body contour change or less than 1 cm uniform body contour change were unlikely to need plan re-assessment; H&N VMAT plans with less than 1 cm uniform body contour change or less than 1 cm shoulder superior-inferior positional change were also unlikely to trigger further evaluation. Dose percentage change and isodose line shift were considered independently from the problem of volume changes in this study, but clinically, both aspects must be considered.
    MeSH term(s) Abdomen/diagnostic imaging ; Algorithms ; Body Contouring/methods ; Head and Neck Neoplasms/diagnostic imaging ; Head and Neck Neoplasms/physiopathology ; Head and Neck Neoplasms/radiotherapy ; Humans ; Image Processing, Computer-Assisted/methods ; Male ; Prostatic Neoplasms/diagnostic imaging ; Prostatic Neoplasms/physiopathology ; Prostatic Neoplasms/radiotherapy ; Radiotherapy Dosage ; Radiotherapy Planning, Computer-Assisted/methods ; Radiotherapy, Intensity-Modulated/methods ; Tomography, X-Ray Computed/methods
    Language English
    Publishing date 2019-03-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2010347-5
    ISSN 1526-9914 ; 1526-9914
    ISSN (online) 1526-9914
    ISSN 1526-9914
    DOI 10.1002/acm2.12571
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  9. Article: Mulberry and

    Zhou, Xiao-Ting / Zhu, An-Qi / Li, Xiao-Min / Sun, Ling-Yue / Yan, Jian-Gang / Luo, Nin / Chen, Shi-Sheng / Huang, Zebo / Mao, Xin-Liang / Li, Kun-Ping

    Frontiers in endocrinology

    2024  Volume 15, Page(s) 1344262

    Abstract: Obesity, a multifactorial disease with many complications, has become a global epidemic. Weight management, including dietary supplementation, has been confirmed to provide relevant health benefits. However, experimental evidence and mechanistic ... ...

    Abstract Obesity, a multifactorial disease with many complications, has become a global epidemic. Weight management, including dietary supplementation, has been confirmed to provide relevant health benefits. However, experimental evidence and mechanistic elucidation of dietary supplements in this regard are limited. Here, the weight loss efficacy of MHP, a commercial solid beverage consisting of mulberry leaf aqueous extract and
    MeSH term(s) Rats ; Animals ; PPAR gamma/genetics ; PPAR gamma/metabolism ; Hippophae/metabolism ; Morus/metabolism ; Diet, High-Fat/adverse effects ; Obesity/metabolism ; Adipose Tissue, White/metabolism ; Signal Transduction ; Weight Loss
    Chemical Substances PPAR gamma
    Language English
    Publishing date 2024-03-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2592084-4
    ISSN 1664-2392
    ISSN 1664-2392
    DOI 10.3389/fendo.2024.1344262
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  10. Article ; Online: In vitro

    Sun, Lingyue / Wan, Zhe / Li, Ruoyu / Yu, Jin

    Journal of medical microbiology

    2019  Volume 68, Issue 11, Page(s) 1664–1670

    Abstract: Purpose. ...

    Abstract Purpose.
    MeSH term(s) Amphotericin B/pharmacology ; Antifungal Agents/pharmacology ; Drug Resistance, Fungal ; Fluconazole/pharmacology ; Fungi/classification ; Fungi/drug effects ; Fungi/genetics ; Fungi/isolation & purification ; Humans ; Itraconazole/pharmacology ; Microbial Sensitivity Tests ; Mycoses/microbiology ; Triazoles/pharmacology ; Voriconazole/pharmacology
    Chemical Substances Antifungal Agents ; Triazoles ; Itraconazole (304NUG5GF4) ; posaconazole (6TK1G07BHZ) ; Amphotericin B (7XU7A7DROE) ; Fluconazole (8VZV102JFY) ; Voriconazole (JFU09I87TR)
    Language English
    Publishing date 2019-09-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 218356-0
    ISSN 1473-5644 ; 0022-2615
    ISSN (online) 1473-5644
    ISSN 0022-2615
    DOI 10.1099/jmm.0.001083
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