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  1. Article ; Online: Deep reinforcement learning and its applications in medical imaging and radiation therapy: a survey.

    Xu, Lanyu / Zhu, Simeng / Wen, Ning

    Physics in medicine and biology

    2022  Volume 67, Issue 22

    Abstract: Reinforcement learning takes sequential decision-making approaches by learning the policy through trial and error based on interaction with the environment. Combining deep learning and reinforcement learning can empower the agent to learn the ... ...

    Abstract Reinforcement learning takes sequential decision-making approaches by learning the policy through trial and error based on interaction with the environment. Combining deep learning and reinforcement learning can empower the agent to learn the interactions and the distribution of rewards from state-action pairs to achieve effective and efficient solutions in more complex and dynamic environments. Deep reinforcement learning (DRL) has demonstrated astonishing performance in surpassing the human-level performance in the game domain and many other simulated environments. This paper introduces the basics of reinforcement learning and reviews various categories of DRL algorithms and DRL models developed for medical image analysis and radiation treatment planning optimization. We will also discuss the current challenges of DRL and approaches proposed to make DRL more generalizable and robust in a real-world environment. DRL algorithms, by fostering the designs of the reward function, agents interactions and environment models, can resolve the challenges from scarce and heterogeneous annotated medical image data, which has been a major obstacle to implementing deep learning models in the clinic. DRL is an active research area with enormous potential to improve deep learning applications in medical imaging and radiation therapy planning.
    MeSH term(s) Humans ; Neural Networks, Computer ; Reinforcement, Psychology ; Algorithms ; Radiography ; Diffusion Magnetic Resonance Imaging
    Language English
    Publishing date 2022-11-11
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 208857-5
    ISSN 1361-6560 ; 0031-9155
    ISSN (online) 1361-6560
    ISSN 0031-9155
    DOI 10.1088/1361-6560/ac9cb3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The 2021 landscape of FDA-approved artificial intelligence/machine learning-enabled medical devices: An analysis of the characteristics and intended use.

    Zhu, Simeng / Gilbert, Marissa / Chetty, Indrin / Siddiqui, Farzan

    International journal of medical informatics

    2022  Volume 165, Page(s) 104828

    Abstract: Background: Machine learning (ML), a type of artificial intelligence (AI) technology that uses a data-driven approach for pattern recognition, has been shown to be beneficial for many tasks across healthcare. To characterize the commercial availability ... ...

    Abstract Background: Machine learning (ML), a type of artificial intelligence (AI) technology that uses a data-driven approach for pattern recognition, has been shown to be beneficial for many tasks across healthcare. To characterize the commercial availability of AI/ML applications in the clinic, we performed a detailed analysis of AI/ML-enabled medical devices approved/cleared by the US Food and Drug Administration (FDA) by June 2021.
    Methods/materials: The publicly available approval letters by the FDA on 343 AI/ML-enabled medical devices compiled by the agency were reviewed. The characteristics of the devices and the patterns of their intended use were analyzed, and basic descriptive statistical analysis was performed on the aggregated data.
    Results: Most devices were reviewed by radiology (70.3%) and cardiovascular (12.0%) medical specialty panels. The growth of these devices sharply rose since the mid-2010s. Most (95.0%) devices were cleared under the 510(k) premarket notification pathway, and 69.4% were software as a medical device (SaMD). Of the 241 radiology-related devices, the most common applications were for diagnostic assistance (48.5%) and image reconstruction (14.1%). Of the 117 radiology-related devices for diagnostic assistance, 20.5% were developed for breast lesion assessment and 14.5% for cardiac function assessment on echocardiogram. Of the 41 cardiology-related devices, the most common applications were electrocardiography-based arrhythmia detection (46.3%) and hemodynamics & vital signs monitoring (26.8%).
    Conclusion: In this study, we characterized the patterns and trends of AI/ML-enabled medical devices approved or cleared by the FDA. To our knowledge, this is the most up-to-date and comprehensive analysis of the landscape as of 2021.
    MeSH term(s) Artificial Intelligence ; Cardiology ; Device Approval ; Humans ; Machine Learning ; United States ; United States Food and Drug Administration
    Language English
    Publishing date 2022-07-01
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 1466296-6
    ISSN 1872-8243 ; 1386-5056
    ISSN (online) 1872-8243
    ISSN 1386-5056
    DOI 10.1016/j.ijmedinf.2022.104828
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Transcriptomic profiling and regulatory pathways of cardiac resident macrophages in aging.

    Xia, Guofang / Zhu, Simeng / Liu, Yujia / Pan, Jingwei / Wang, Xiaoqing / Shen, Chengxing / Du, Ailian / Xu, Congfeng

    Cellular and molecular life sciences : CMLS

    2024  Volume 81, Issue 1, Page(s) 220

    Abstract: Cardiovascular diseases are an array of age-related disorders, and accumulating evidence suggests a link between cardiac resident macrophages (CRMs) and the age-related disorders. However, how does CRMs alter with aging remains elusive. In the present ... ...

    Abstract Cardiovascular diseases are an array of age-related disorders, and accumulating evidence suggests a link between cardiac resident macrophages (CRMs) and the age-related disorders. However, how does CRMs alter with aging remains elusive. In the present study, aged mice (20 months old) have been employed to check for their cardiac structural and functional alterations, and the changes in the proportion of CRM subsets as well, followed by sorting of CRMs, including C-C Motif Chemokine Receptor 2 (CCR2)
    MeSH term(s) Animals ; Macrophages/metabolism ; Aging/genetics ; Aging/metabolism ; Mice ; Receptors, CCR2/metabolism ; Receptors, CCR2/genetics ; Gene Expression Profiling ; Mice, Inbred C57BL ; Transcriptome ; Myocardium/metabolism ; Male ; Single-Cell Analysis ; Inflammation/genetics ; Inflammation/metabolism ; Inflammation/pathology ; Signal Transduction ; Phagocytosis
    Chemical Substances Ccr2 protein, mouse
    Language English
    Publishing date 2024-05-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1358415-7
    ISSN 1420-9071 ; 1420-682X
    ISSN (online) 1420-9071
    ISSN 1420-682X
    DOI 10.1007/s00018-024-05235-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Enhancing Precision in Cardiac Segmentation for MR-Guided Radiation Therapy through Deep Learning.

    Summerfield, Nicholas / Morris, Eric / Banerjee, Soumyanil / He, Qisheng / Ghanem, Ahmed I / Zhu, Simeng / Zhao, Jiwei / Dong, Ming / Glide-Hurst, Carri

    International journal of radiation oncology, biology, physics

    2024  

    Abstract: Introduction: Cardiac substructure dose metrics are more strongly linked to late cardiac morbidities than whole-heart metrics. MR-guided radiation therapy (MRgRT) enables substructure visualization during daily localization, allowing potential for ... ...

    Abstract Introduction: Cardiac substructure dose metrics are more strongly linked to late cardiac morbidities than whole-heart metrics. MR-guided radiation therapy (MRgRT) enables substructure visualization during daily localization, allowing potential for enhanced cardiac sparing. We extend a publicly available state-of-the-art deep learning (DL) framework, nnU-Net, to incorporate self-distillation (nnU-Net.wSD) for substructure segmentation for MRgRT.
    Methods: Eighteen (Institute A) patients who underwent thoracic or abdominal radiation therapy on a 0.35 T MR-guided linac were retrospectively evaluated. On each image, one of two radiation oncologists delineated reference contours of 12 cardiac substructures (chambers, great vessels, and coronary arteries) used to train (n=10), validate (n=3), and test (n=5) nnU-Net.wSD leveraging a teacher-student network and comparing to standard 3D U-Net. The impact of using simulation data or including 3-4 daily images for augmentation during training was evaluated for nnU-Net.wSD. Geometric metrics (Dice similarity coefficient (DSC), mean distance to agreement (MDA), and 95% Hausdorff distance (HD95)), visual inspection, and clinical dose volume histograms (DVHs) were evaluated. To determine generalizability, Institute A's model was tested on an unlabeled dataset from Institute B (n=22) and evaluated via consensus scoring and volume comparisons.
    Results: nnU-Net.wSD yielded a DSC (reported mean ± standard deviation) of 0.65±0.25 across the 12 substructures (Chambers: 0.85±0.05, Great Vessels: 0.67±0.19, and Coronary Arteries 0.33±0.16, mean MDA <3 mm, and mean HD95 <9 mm) while outperforming the 3D U-Net (0.583±0.28, p<0.01). Leveraging fractionated data for augmentation improved over a single MR-SIM timepoint (0.579±0.29, p<0.01). Predicted contours yielded DVHs that closely matched the clinical treatment plans where mean and D
    Conclusions: This work is a critical step to rapid and reliable cardiac substructure segmentation to improve cardiac sparing in low-field MRgRT.
    Language English
    Publishing date 2024-05-24
    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.2024.05.013
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  5. Article: Efficient peroxymonosulfate (PMS) activation by visible-light-driven formation of polymorphic amorphous manganese oxides

    Zhu, Simeng / Xiao, Pengyu / Wang, Xue / Liu, Yang / Yi, Xianliang / Zhou, Hao

    Journal of hazardous materials. 2022 Apr. 05, v. 427

    2022  

    Abstract: Heterogeneous sulfate radical-based advanced oxidation processes (SR-AOPs) have been widely reported over the last decade as a promising technology for pollutant removal from wastewater. In this study, a novel peroxymonosulfate (PMS) activator was ... ...

    Abstract Heterogeneous sulfate radical-based advanced oxidation processes (SR-AOPs) have been widely reported over the last decade as a promising technology for pollutant removal from wastewater. In this study, a novel peroxymonosulfate (PMS) activator was obtained by visible-light-driven Mn(II) oxidation in the presence of nitrate. The photochemically synthesized manganese oxides (PC-MnOₓ) were polymorphic amorphous nanoparticles and nanorods, with an average oxidation state of approximately 3.0. It possesses effective PMS activation capacity and can remove 20 mg L⁻¹ acid organic II (AO7) within 30 min. The AO7 removal performance of PC-MnOₓ was slightly decreased in natural waterbodies and in the presence of CO₃²⁻, while it showed an anti-interference capacity for Cl⁻, NO₃⁻ and humic acid. Chemical quenching, reactive oxygen species (ROS) trapping, X-ray photoelectric spectroscopy (XPS), in-situ Raman spectroscopy, and electrochemical experiments supported a nonradical mechanism, i.e., electron transfer from AO7 to the metastable PC-MnOₓ-PMS complex, which was responsible for AO7 oxidation. The PC-MnOₓ-PMS system also showed substrate preferences based on their redox potentials. Moreover, PC-MnOₓ could activate periodate (PI) but not peroxydisulfate (PDS) or H₂O₂. Overall, this study provides a new catalyst for PMS activation through a mild and green synthesis approach.
    Keywords Raman spectroscopy ; X-radiation ; catalysts ; electrochemistry ; electron transfer ; humic acids ; manganese ; nanorods ; nitrates ; oxidation ; pollution control ; sulfates ; surface water ; wastewater
    Language English
    Dates of publication 2022-0405
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 1491302-1
    ISSN 1873-3336 ; 0304-3894
    ISSN (online) 1873-3336
    ISSN 0304-3894
    DOI 10.1016/j.jhazmat.2021.127938
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  6. Article: Superoxide radical mediated Mn(III) formation is the key process in the activation of peroxymonosulfate (PMS) by Mn-incorporated bacterial-derived biochar

    Gao, Bixia / Zhu, Simeng / Gu, Jialiang / Liu, Yang / Yi, Xianliang / Zhou, Hao

    Journal of hazardous materials. 2022 June 05, v. 431

    2022  

    Abstract: Biochar was used as a heterogeneous activator for peroxymonosulfate (PMS), and the activation performance strongly depended on the structure, functional groups, and modification of the biochar. In this study, a new type of modified biochar was ... ...

    Abstract Biochar was used as a heterogeneous activator for peroxymonosulfate (PMS), and the activation performance strongly depended on the structure, functional groups, and modification of the biochar. In this study, a new type of modified biochar was synthesized by utilizing the Mn(II) adsorption capacity of bacteria. After one-step pyrolysis of Mn(II)-adsorbed bacterial cells at 800 °C, a Mn-incorporated bacterial-derived biochar (Mn-BBC) was successfully produced. It exhibited structural heterogeneity, with MnO located at the surface of the BBC matrix, as shown on the result of SEM and XRD. Compared to BBC, Mn-BBC showed a 10-fold increase (0.0727 min⁻¹ versus 0.0069 min⁻¹) of pollutant removal rate. In addition, it also showed anti-interference capacity against common water matrix (except 10 mM CO₃²⁻) and great stability/reusability. Chemical quenching, electron spin resonance, and pyrophosphate trapping indicated an indirect but important role of the superoxide, formed during the self-decomposition of PMS. The MnO on Mn-BBC can be oxidized by superoxide to produce surface Mn(III), which then binds to PMS and forms a surface complex. This complex promotes electron transfer from the pollutant to the Mn-BBC, facilitating the oxidation of the contaminants. Overall, this study confirmed the PMS activation capacity and mechanism of Mn-BBC, which expands the application of BBC-based materials derived from metal-adsorbed microbes.
    Keywords adsorption ; biochar ; electron paramagnetic resonance spectroscopy ; electron transfer ; manganese monoxide ; oxidation ; pollutants ; pollution control ; pyrolysis ; superoxide anion
    Language English
    Dates of publication 2022-0605
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 1491302-1
    ISSN 1873-3336 ; 0304-3894
    ISSN (online) 1873-3336
    ISSN 0304-3894
    DOI 10.1016/j.jhazmat.2022.128549
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  7. Article ; Online: Radiotherapy for Melanoma with Perineural Invasion: University of Florida Experience.

    Zhu, Simeng / Mendenhall, William M

    Cancer investigation

    2018  Volume 36, Issue 7, Page(s) 389–394

    Abstract: Purpose: Outcomes after adjuvant radiotherapy for cutaneous melanoma with perineural invasion (PNI).: Methods: Seven patients (5 cutaneous, 2 recurrent nerve lesions) received radiotherapy.: Results: At a median 4.5 years: Two patients did not ... ...

    Abstract Purpose: Outcomes after adjuvant radiotherapy for cutaneous melanoma with perineural invasion (PNI).
    Methods: Seven patients (5 cutaneous, 2 recurrent nerve lesions) received radiotherapy.
    Results: At a median 4.5 years: Two patients did not recur; no local failures occurred. Three patients who omitted nodal irradiation developed regional failures (2 out-of-field, 1 in-field). Three patients developed distant metastases. Four died with disease (median, 3.6 years); 1 died from intercurrent disease (13.0 years). Two are alive without disease (6.8 and 11.6 years). No patient experienced grade ≥3 toxicity.
    Conclusions: Postoperative radiotherapy can reduce local recurrences; primary radiotherapy for unresectable disease is recommended.
    MeSH term(s) Adult ; Aged ; Aged, 80 and over ; Disease Progression ; Disease-Free Survival ; Female ; Florida ; Humans ; Male ; Melanoma/drug therapy ; Melanoma/mortality ; Melanoma/secondary ; Middle Aged ; Neoplasm Invasiveness ; Neoplasm Recurrence, Local ; Peripheral Nerves/pathology ; Peripheral Nerves/radiation effects ; Radiotherapy, Adjuvant ; Retrospective Studies ; Skin Neoplasms/mortality ; Skin Neoplasms/pathology ; Skin Neoplasms/radiotherapy ; Time Factors ; Treatment Outcome ; Universities
    Language English
    Publishing date 2018-09-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 604942-4
    ISSN 1532-4192 ; 0735-7907
    ISSN (online) 1532-4192
    ISSN 0735-7907
    DOI 10.1080/07357907.2018.1504055
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  8. Article ; Online: Superoxide radical mediated Mn(III) formation is the key process in the activation of peroxymonosulfate (PMS) by Mn-incorporated bacterial-derived biochar.

    Gao, Bixia / Zhu, Simeng / Gu, Jialiang / Liu, Yang / Yi, Xianliang / Zhou, Hao

    Journal of hazardous materials

    2022  Volume 431, Page(s) 128549

    Abstract: Biochar was used as a heterogeneous activator for peroxymonosulfate (PMS), and the activation performance strongly depended on the structure, functional groups, and modification of the biochar. In this study, a new type of modified biochar was ... ...

    Abstract Biochar was used as a heterogeneous activator for peroxymonosulfate (PMS), and the activation performance strongly depended on the structure, functional groups, and modification of the biochar. In this study, a new type of modified biochar was synthesized by utilizing the Mn(II) adsorption capacity of bacteria. After one-step pyrolysis of Mn(II)-adsorbed bacterial cells at 800 °C, a Mn-incorporated bacterial-derived biochar (Mn-BBC) was successfully produced. It exhibited structural heterogeneity, with MnO located at the surface of the BBC matrix, as shown on the result of SEM and XRD. Compared to BBC, Mn-BBC showed a 10-fold increase (0.0727 min
    MeSH term(s) Bacteria ; Charcoal ; Environmental Pollutants ; Peroxides ; Superoxides
    Chemical Substances Environmental Pollutants ; Peroxides ; biochar ; Superoxides (11062-77-4) ; Charcoal (16291-96-6) ; peroxymonosulfate (22047-43-4)
    Language English
    Publishing date 2022-02-23
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1491302-1
    ISSN 1873-3336 ; 0304-3894
    ISSN (online) 1873-3336
    ISSN 0304-3894
    DOI 10.1016/j.jhazmat.2022.128549
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Catalytic performance and periodate activation mechanism of anaerobic sewage sludge-derived biochar

    Xiao, Pengyu / Yi, Xianliang / Wu, Minghuo / Wang, Xue / Zhu, Simeng / Gao, Bixia / Liu, Yang / Zhou, Hao

    Journal of hazardous materials. 2022 Feb. 15, v. 424

    2022  

    Abstract: Periodate (PI)-based advanced oxidation processes are a newly discovered approach for effective pollutant elimination. In this study, we demonstrated that biochar obtained from pyrolysis of anaerobic sewage sludge without any pretreatment can be used for ...

    Abstract Periodate (PI)-based advanced oxidation processes are a newly discovered approach for effective pollutant elimination. In this study, we demonstrated that biochar obtained from pyrolysis of anaerobic sewage sludge without any pretreatment can be used for PI activation. The biochar obtained at 800 °C (SBC-800) exhibited the best PI activation capacity using acid organic II (AO7) as substrate. The PI activation was strongly dependent on pH and exhibited the highest AO7 removal rate at pH 3.0. Meanwhile, the anti-interference capacity with common wastewater components and reusability of the SBC-800/PI system were confirmed. Combined with the results of chemical quenching, reactive oxygen species (ROS) trapping, X-ray photoelectric spectroscopy (XPS), electrochemical and density function theory (DFT)-based calculations, singlet oxygen production and electron transfer mediated by the SBC-800-PI complex were the dominant AO7 oxidation mechanisms. This study provides easily prepared catalysts for PI activation and paves the way for solid waste recycling and reuse.
    Keywords X-radiation ; biochar ; catalytic activity ; electrochemistry ; electron transfer ; oxidation ; oxygen production ; pH ; pollutants ; pyrolysis ; sewage ; sewage sludge ; singlet oxygen ; solid wastes ; wastewater
    Language English
    Dates of publication 2022-0215
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 1491302-1
    ISSN 1873-3336 ; 0304-3894
    ISSN (online) 1873-3336
    ISSN 0304-3894
    DOI 10.1016/j.jhazmat.2021.127692
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  10. Article ; Online: Matched-pair Analysis for Survival Endpoints Between Women With Early-stage Uterine Carcinosarcoma and Uterine Serous Carcinoma.

    Yahya, Jehan B / Zhu, Simeng / Burmeister, Charlotte / Hijaz, Miriana Y / Elshaikh, Mohamed A

    American journal of clinical oncology

    2021  Volume 44, Issue 9, Page(s) 463–468

    Abstract: Objective: The objective of this study was to compare survival endpoints between women with uterine carcinosarcoma and those with uterine serous carcinoma utilizing matching analysis.: Methods: Patients with stages I to II who underwent hysterectomy ... ...

    Abstract Objective: The objective of this study was to compare survival endpoints between women with uterine carcinosarcoma and those with uterine serous carcinoma utilizing matching analysis.
    Methods: Patients with stages I to II who underwent hysterectomy at our institution were included in this analysis. Patients with carcinosarcoma were then matched to patients with serous carcinoma based on stage, and adjuvant management received (observation, radiation treatment alone, chemotherapy alone, or combined modality with radiotherapy and chemotherapy. Recurrence-free survival, disease-specific survival, and overall survival were calculated for the 2 groups.
    Results: A total of 134 women were included (67 women with carcinosarcoma and 67 with serous carcinoma, matched 1:1). There was no statistically significant difference between the 2 groups regarding 5-year recurrence-free survival (59% vs. 62%), disease-specific survival (66% vs. 67%), or overall survival (53% vs. 57%), respectively. The only independent predictor of shorter recurrence-free survival for the entire cohort was the lack of adjuvant combined modality therapy, while lower uterine segment involvement was the only independent predictor for shorter disease-specific survival. Lack of lymph node dissection and lack of adjuvant combined modality therapy were independent predictors of shorter overall survival.
    Discussion: When matched based on stage and adjuvant treatment, our study suggests that there is no statistically significant difference in survival endpoints between women with early-stage carcinosarcoma and serous carcinoma. Adjuvant combined modality treatment is an independent predictor of longer recurrence-free survival and overall survival.
    MeSH term(s) Adult ; Aged ; Aged, 80 and over ; Carcinosarcoma/mortality ; Carcinosarcoma/pathology ; Carcinosarcoma/therapy ; Chemotherapy, Adjuvant ; Combined Modality Therapy ; Cystadenocarcinoma, Serous/mortality ; Cystadenocarcinoma, Serous/therapy ; Female ; Humans ; Hysterectomy ; Lymph Node Excision ; Matched-Pair Analysis ; Middle Aged ; Ovariectomy ; Radiotherapy Dosage ; Uterine Neoplasms/mortality ; Uterine Neoplasms/pathology ; Uterine Neoplasms/therapy
    Language English
    Publishing date 2021-06-29
    Publishing country United States
    Document type Comparative Study ; Journal Article
    ZDB-ID 604536-4
    ISSN 1537-453X ; 0277-3732
    ISSN (online) 1537-453X
    ISSN 0277-3732
    DOI 10.1097/COC.0000000000000851
    Database MEDical Literature Analysis and Retrieval System OnLINE

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