Publications by authors named "Zhiyong Xu"

125 Publications

A novel CRT-IMRT-combined (Co-CRIM) planning technique for peripheral lung stereotactic body radiotherapy in pinnacle treatment planning system.

J Appl Clin Med Phys 2021 Oct 26. Epub 2021 Oct 26.

Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.

Objectives: This study attempts to explore a novel peripheral lung stereotactic body radiotherapy (SBRT) planning technique that can balance the pros and cons of three-dimensional conformal radiotherapy (CRT) and intensity-modulated radiation therapy (IMRT) / volumetric modulated arc therapy (VMAT).

Methods: Treatment plans were retrospectively designed based on CRT, IMRT, VMAT, and the proposed CRT-IMRT-combined (Co-CRIM) techniques using Pinnacle treatment planning system (TPS) for 20 peripheral lung cancer patients. Co-CRIM used an inverse optimization algorithm available in Pinnacle TPS. To develop a Co-CRIM plan, the number of segments in each field was limited to one, the minimum segment area was set to the internal target volume (ITV), and the minimum monitor units (MU) of the segment was the quotient of fractional dose divided by twice the number of total fields. The performance of Co-CRIM was then compared with other techniques.

Results: For conformity index (CI), Co-CRIM performed comparably to IMRT/VMAT but better than CRT. For gradient index (GI), Co-CRIM was similar to IMRT/VMAT or CRT. For heterogeneity index (HI), Co-CRIM was comparable to IMRT/VMAT, higher than CRT. The dosimetric results of spinal cord and lung with Co-CRIM were better than CRT, comparable to IMRT, but inferior to VMAT. The MU resulted from Co-CRIM was lower than IMRT/VMAT but higher than CRT. For plan verification γ passing rate, Co-CRIM was higher than IMRT/VMAT, comparable to CRT. For planning time, Co-CRIM was shorter than CRT or VMAT but similar to IMRT.

Conclusions: The proposed Co-CRIM technique on Pinnacle TPS is an effective planning technique for peripheral lung SBRT.
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http://dx.doi.org/10.1002/acm2.13461DOI Listing
October 2021

Investigation of Predictors to Achieve Acceptable Lung Dose in T-Shaped Upper and Middle Esophageal Cancer With IMRT and VMAT.

Front Oncol 2021 7;11:735062. Epub 2021 Oct 7.

Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.

Purpose: The purpose of this study is to investigate whether there are predictors and cutoff points that can predict the acceptable lung dose using intensity-modulated radiation therapy (IMRT) and volume-modulated arc therapy (VMAT) in radiotherapy for upper ang middle esophageal cancer.

Material And Methods: Eighty-two patients with T-shaped upper-middle esophageal cancer (UMEC) were enrolled in this retrospective study. Jaw-tracking IMRT plan (JT-IMRT), full-arc VMAT plan (F-VMAT), and pactial-arc VMAT plan (P-VMAT) were generated for each patient. Dosimetric parameters such as MLD and V20 of total lung were compared among the three plannings. Ten factors such as PCTV length and PCTV length/total lung length were calculated to find the predictors and cutoff points of the predictors. All patients were divided into two groups according to the cutoff points, and the dosimetric differences between the two groups of the three plans were compared. ANOVA, receiver operating characteristic (ROC) analysis, and Mann-Whitney U-test were performed for comparisons between datasets. A p <0.05 was considered statistically significant.

Result: The quality of the targets of the three plannings was comparable. The total lung dose in P-VMAT was significantly lower than that in JT IMRT and F-VMAT. Monitor unit (MU) of F-VMAT and P-VMAT was significantly lower than that of JT IMRT. ROC analysis showed that among JT IMRT, F-VMAT, and P-VMAT, PCTV, and PCTV/TL had diagnostic power to predict the suitability of RT plans according to lung dose constraints of our department. For JT IMRT, the cutoff points of PCTV and PCTV/TL were 16.6 and 0.59. For F-VMAT, the cutoff points of PCTV and PCTV/TL were 16.75 and 0.62. For P-VMAT, the cutoff points of PCTV and PCTV/TL were 15.15 and 0.59. After Mann-Whitney U-test analysis, it was found that among the three plannings, the group with lower PCTV and PCTV/TL could significantly reduce the dose of total lung and heart (p <0.05).

Conclusion: PCTV16.6 and PCTV/TL <0.59 for JT IMRT, PCTV16.75 and PCTV/TL <0.62 for F-VMAT and PCTV15.15, and PCTV/TL <0.59 for P-VMAT can predict whether patients with T-shaped UMEC can meet the lung dose limits of our department.
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http://dx.doi.org/10.3389/fonc.2021.735062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8529030PMC
October 2021

Error performance optimization utilizing the dynamic detection cycle in a SPAD-based free space optical communication system.

Opt Lett 2021 Oct;46(20):5268-5271

Afterpulsing is a critical non-ideal factor of the single photon avalanche diode (SPAD) at telecommunication wavelength, which limits the performance of a SPAD-based free space optical communication (FSO) system. Afterpulsing probability (AP) is highly dependent on the SPAD detection cycle. In a conventional SPAD-based system, the detection cycle is set to a relatively large constant time length to mitigate afterpulsing. However, it will limit the SPAD counting rate and degrade system performance. In order to improve system performance, a new scheme of the dynamic detection cycle is proposed to adapt to different operation conditions. Then, a multi-exponential model of AP is built and fitted with the test data of the single photon detector QCD-300. Furthermore, based on the joint model of the multi-exponential model of AP and bit error rate (BER) model of the SPAD-based FSO system, a simple and effective optimization algorithm is developed to optimize the detection cycle. And the optimization of the detection cycle under different operation conditions is also investigated. The results indicate that optimal detection cycle is dominated by signal light, background radiation, and SPAD gate length. Compared with a conventional scheme with a constant detection cycle, the proposed scheme with the dynamic detection cycle can improve system error performance effectively.
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http://dx.doi.org/10.1364/OL.438794DOI Listing
October 2021

Filter Pruning via Measuring Feature Map Information.

Sensors (Basel) 2021 Oct 2;21(19). Epub 2021 Oct 2.

Institute of Optics and Electronics, Chinese Academy of Sciences, Chengdu 610200, China.

Neural network pruning, an important method to reduce the computational complexity of deep models, can be well applied to devices with limited resources. However, most current methods focus on some kind of information about the filter itself to prune the network, rarely exploring the relationship between the feature maps and the filters. In this paper, two novel pruning methods are proposed. First, a new pruning method is proposed, which reflects the importance of filters by exploring the information in the feature maps. Based on the premise that the more information there is, more important the feature map is, the information entropy of feature maps is used to measure information, which is used to evaluate the importance of each filter in the current layer. Further, normalization is used to realize cross layer comparison. As a result, based on the method mentioned above, the network structure is efficiently pruned while its performance is well reserved. Second, we proposed a parallel pruning method using the combination of our pruning method above and slimming pruning method which has better results in terms of computational cost. Our methods perform better in terms of accuracy, parameters, and FLOPs compared to most advanced methods. On ImageNet, it is achieved 72.02% top1 accuracy for ResNet50 with merely 11.41M parameters and 1.12B FLOPs.For DenseNet40, it is obtained 94.04% accuracy with only 0.38M parameters and 110.72M FLOPs on CIFAR10, and our parallel pruning method makes the parameters and FLOPs are just 0.37M and 100.12M, respectively, with little loss of accuracy.
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http://dx.doi.org/10.3390/s21196601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8512244PMC
October 2021

Research on the lossless contention MAC protocol and the performance of an ultraviolet communication network.

Opt Express 2021 Sep;29(20):31952-31962

Ultraviolet (UV) communication has been the topic of extensive recent research due to its non-line-of-sight (NLOS) communication, anti-interference, and high confidentiality. Given the lack of the UV Media Access Control (MAC) protocol, this paper proposes a UV lossless contention MAC (UVLLC-MAC) protocol creatively. This MAC protocol is based on the superposition logic of UV power, which effectively reduces the collision loss of multi-node contention access. The basic working mechanism and protocol flow are given in detail, and the network performance is simulated and analyzed mathematically based on a four-node UV network. Comparing with the slotted ALOHA protocol, the simulation results indicate that the network has a higher throughput and lower delay under the protocol. The practical networking of four communication terminals is designed and implemented, and the effectiveness of the new UVLLC-MAC protocol is fully verified.
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http://dx.doi.org/10.1364/OE.436163DOI Listing
September 2021

Isotoxic investigation of F-FDG PET/CT-guided dose escalation with intensity-modulated radiotherapy for LA-NSCLC.

Int J Radiat Biol 2021 Oct 1:1-24. Epub 2021 Oct 1.

Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.

Purpose: This research compared differences of dosimetric and biological parameters between PET/CT-guided isotoxic SIB-IMRT plans and conventional radiotherapy plans for patients with LA-NSCLC, and it also evaluated the factors that affect dose escalation.

Materials And Methods: This study consisted of a retrospective cohort of thirty patients with IIIA-IIIB NSCLC. SIB-IMRT (Plan_iso) and conventional radiotherapy (Plan_primary) plans were generated using auto-planning. Dosimetric parameters such as mean lung dose (MLD) and other indicators were compared. Tumor control probability (TCP) of PTV and normal tissue complication probability (NTCP) of total lung, heart, esophagus and spinal cord were calculated. The relationships between dose escalation and 3D length of PTV and other factors were analyzed. Paired-samples t-test, Mann-Whitney U test, and Chi-Square test were performed for comparisons between datasets. A P < 0.05 was considered statistically significant.

Results: The dosimetric parameters of PTV in Plan_iso were higher than those of PTV in Plan_primary, and there were significant differences (p < 0.05). Compared with Plan_primary, Plan_iso slightly increased dosimetric parameters of total lung, heart, spinal cord, esophagus and MUs. The absolute differences were small. TCPs of PTV in Plan_iso were significantly higher than those in Plan_primary. NTCPs of total lung, esophagus and spinal cord in Plan_iso were higher than those in Plan_primary. There were significant differences, but the absolute differences were small. NTCP of heart in Plan_iso was slightly higher than that in Plan_primary, but there was no statistical difference.

Conclusions: For LA-NSCLC, the SIB based on isotoxic radiotherapy can significantly increase TCP under the premise that the toxicity of OARs is comparable.
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http://dx.doi.org/10.1080/09553002.2021.1987557DOI Listing
October 2021

A 2D-3D hybrid convolutional neural network for lung lobe auto-segmentation on standard slice thickness computed tomography of patients receiving radiotherapy.

Biomed Eng Online 2021 Sep 23;20(1):94. Epub 2021 Sep 23.

Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.

Background: Accurate segmentation of lung lobe on routine computed tomography (CT) images of locally advanced stage lung cancer patients undergoing radiotherapy can help radiation oncologists to implement lobar-level treatment planning, dose assessment and efficacy prediction. We aim to establish a novel 2D-3D hybrid convolutional neural network (CNN) to provide reliable lung lobe auto-segmentation results in the clinical setting.

Methods: We retrospectively collected and evaluated thorax CT scans of 105 locally advanced non-small-cell lung cancer (NSCLC) patients treated at our institution from June 2019 to August 2020. The CT images were acquired with 5 mm slice thickness. Two CNNs were used for lung lobe segmentation, a 3D CNN for extracting 3D contextual information and a 2D CNN for extracting texture information. Contouring quality was evaluated using six quantitative metrics and visual evaluation was performed to assess the clinical acceptability.

Results: For the 35 cases in the test group, Dice Similarity Coefficient (DSC) of all lung lobes contours exceeded 0.75, which met the pass criteria of the segmentation result. Our model achieved high performances with DSC as high as 0.9579, 0.9479, 0.9507, 0.9484, and 0.9003 for left upper lobe (LUL), left lower lobe (LLL), right upper lobe (RUL), right lower lobe (RLL), and right middle lobe (RML), respectively. The proposed model resulted in accuracy, sensitivity, and specificity of 99.57, 98.23, 99.65 for LUL; 99.6, 96.14, 99.76 for LLL; 99.67, 96.13, 99.81 for RUL; 99.72, 92.38, 99.83 for RML; 99.58, 96.03, 99.78 for RLL, respectively. Clinician's visual assessment showed that 164/175 lobe contours met the requirements for clinical use, only 11 contours need manual correction.

Conclusions: Our 2D-3D hybrid CNN model achieved accurate automatic segmentation of lung lobes on conventional slice-thickness CT of locally advanced lung cancer patients, and has good clinical practicability.
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http://dx.doi.org/10.1186/s12938-021-00932-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8461922PMC
September 2021

Dosimetric effect of intensity-modulated radiation therapy for postoperative non-small cell lung cancer with and without air cavity in the planning target volume.

Med Dosim 2021 Sep 19. Epub 2021 Sep 19.

Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China. Electronic address:

To evaluate the dosimetric effect of intensity-modulated radiation therapy (IMRT) for postoperative non-small cell lung cancer (NSCLC), with and without the air cavity in the planning target volume (PTV). Two kinds of IMRT plans were made for 21 postoperative NSCLC patients. In Plan-0: PTV included the tracheal air cavity, and in Plan-1: the air cavity was subtracted from the PTV. For PTV, the dosimetric parameters, including D, D, D, D, D, conformity index (CI), and homogeneity index (HI) were evaluated. For organs at risk (OARs), the evaluation indexes, included the V, V and the mean lung dose (MLD) of total lung, the V, V, and the mean heart dose (MHD) of heart, the spinal cord D, and the V and the mean esophageal dose (MED) of esophagus. The number of segments and MUs were also recorded. Additionally, the correlation between the Plan-1 dosimetric change value relative to Plan-0, the size of air cavity, and the volume proportion of the cavity in the PTV was also analyzed. The D of PTV, D, D, HI and CI in Plan-1 decreased compared with those in Plan-0. For OARs, the V, MHD, and MED also decreased. The CI change value of Plan-1 relative to Plan-0 had a significantly negative correlation with the size and the volume proportion of air cavity, and the MED change value also had a significantly negative correlation with the air cavity size. The IMRT plans for patients with postoperative NSCLC can achieve a better target dose distribution and offer an improved sparing of the heart and esophagus by removing the PTV air cavity, while reducing the target conformity. The change value of CI and MED had a significantly negative correlation with the air cavity size.
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http://dx.doi.org/10.1016/j.meddos.2021.07.005DOI Listing
September 2021

Dosimetric Comparison, Treatment Efficiency Estimation, and Biological Evaluation of Popular Stereotactic Radiosurgery Options in Treating Single Small Brain Metastasis.

Front Oncol 2021 5;11:716152. Epub 2021 Aug 5.

Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.

Objectives: This study aimed to show the advantages of each stereotactic radiosurgery (SRS) treatment option for single small brain metastasis among Gamma Knife (GK), Cone-based VMAT (Cone-VMAT), and MLC-based CRT (MLC-CRT) plans.

Materials And Methods: GK, Cone-VMAT, and MLC-CRT SRS plans were retrospectively generated for 11 patients with single small brain metastasis whose volume of gross tumor volume (GTV) ranged from 0.18 to 0.76 cc (median volume 0.60 cc). Dosimetric parameters, treatment efficiency, and biological parameters of the three techniques were compared and evaluated. The metric variation with the planning target volume (PTV) was also studied.

Results: The conformity index (CI) was similar in GK and MLC-CRT plans, higher than Cone-VMAT. Cone-VMAT achieved comparable volume covered by 12 Gy (V12) and gradient index (GI) as GK, lower than MLC-CRT. The heterogeneity index (HI) of GK, Cone-VMAT, and MLC-CRT decreased sequentially. GK gave the lowest volume covered by 3 Gy (V3) and 6 Gy (V6), while MLC-CRT got the highest. The beam-on time and treatment time of GK, Cone-VMAT, and MLC-CRT decreased in turn. Tumor control probability (TCP) of all three SRS plans was greater than 98%, and normal tissue complication probability (NTCP) of all organs at risk (OARs) was below 0.01%. GK and Cone-VMAT resulted in superior TCP and NTCP of the normal brain tissue than MLC-CRT. The relative value of Cone-VMAT and GK for all metrics hardly changed with the target volume. Except for the unchanged HI and TCP, the other results of MLC-CRT with respect to GK improved as the target volume increased. MLC-CRT could produce higher CI than GK and Cone-VMAT when the target volume increased above 2 and 1.44 cc, respectively.

Conclusion: For single small brain metastases, Cone-VMAT may be used as an alternative to GK-free centers. In addition to the advantage of short treatment time, MLC-CRT showed superiority in CI as the target volume increased. Treatment centers can choose appropriate SRS technique on a case-by-case basis according to institutional conditions and patients' individual needs.
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http://dx.doi.org/10.3389/fonc.2021.716152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8447903PMC
August 2021

Association of plasma branched-chain amino acids with overweight: A Mendelian randomization analysis.

Obesity (Silver Spring) 2021 Oct 7;29(10):1708-1718. Epub 2021 Sep 7.

Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, China.

Objective: A Mendelian randomization (MR) framework was applied to disentangle the causal effect of branched-chain amino acids (BCAAs) and overweight/obesity in Chinese adolescents.

Methods: Circulating BCAA levels were measured by liquid chromatography coupled with mass spectrometry. A total of 7 BCAAs and 12 BMI-associated common variants identified from released genome-wide association study results were genotyped. Furthermore, a bidirectional MR approach was undertaken to disentangle the causal effect of BCAAs and overweight/obesity, using two-stage regression.

Results: Using the inverse variance-weighted strategy and the weighted genetic scoring instruments, the estimated odds ratio per 1-arbitrary-unit increase in the total BCAA level on overweight and obesity odds after adjusting for age and sex was 2.40 (95% CI: 1.38 to 3.42, p < 0.001) and 2.55 (95% CI: 1.35 to 4.82, p = 0.004), respectively. Furthermore, additional MR tests were undertaken using a reversed model, testing the causal effect of increasing BMI variants on total BCAA level. By contrast, no evidence that increased BMI was causally associated with the total BCAA level (estimated β associated with 1-kg/m increase in BMI = 0.05, 95% CI: -0.17 to 0.28, p = 0.642) was observed.

Conclusions: In summary, BCAAs may be causally associated with overweight/obesity or, rather, a congenital dysmetabolism of BCAAs could be a cause of overweight/obesity in adolescents.
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http://dx.doi.org/10.1002/oby.23240DOI Listing
October 2021

Efficacy and Safety of Qinghao Biejia Decoction in the Treatment of Systemic Lupus Erythematosus: A Systematic Review and Meta-Analysis.

Front Pharmacol 2021 6;12:669269. Epub 2021 Aug 6.

Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China.

This meta-analysis aimed to systematically assess the therapeutic efficacy and safety of Qinghao Biejia decoction combined with conventional chemical medicine in patients with systemic lupus erythematosus (SLE), and to provide reference for clinical medication. Multiple databases were retrieved by computer for randomized controlled trials (RCTs) of treating SLE with Qinghao Biejia decoction combining chemical medicine, from the establishment of the database to January 2021. Study screening, data collection, and quality assessment were performed independently by two reviewers. RevMan 5.4 and Stata 15.1 software were used for Meta-analysis. Nine eligible studies, involving 655 SLE participants, were included. Meta-analysis showed that the additional use of Qinghao Biejia decoction superior to chemical medicine alone in people with SLE in improving the overall response rate (RR = 1.30, 95% CI [1.19, 1.41], < 0.00001, heterogeneity = 0.61, = 0%), and can decrease SLE Disease Activity Index (SLEDAI) and TCM symptom scores, improve immunological indexes (C3, C4, IgG, IgA, IFN-γ, IL-4, Th1/Th2), reduce the occurrence of adverse events in treatment ( ≤ 0.05). Based on this meta-analysis, the additional use of Qinghao Biejia decoction has more advantages in the treatment of SLE than conventional chemical medication alone, which could enhance the efficacy and reduce adverse reactions, and is worthy of clinical promotion. However, more and higher quality RCTs are still need to confirm our findings.
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http://dx.doi.org/10.3389/fphar.2021.669269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8378134PMC
August 2021

Dosimetric comparison and biological evaluation of fixed-jaw intensity-modulated radiation therapy for T-shaped esophageal cancer.

Radiat Oncol 2021 Aug 19;16(1):158. Epub 2021 Aug 19.

Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, Xuhui District, Shanghai, 200030, China.

Background: To evaluate the dosimetric and biological benefits of the fixed-jaw (FJ) intensity-modulated radiation therapy (IMRT) technique for patients with T-shaped esophageal cancer.

Methods: FJ IMRT plans were generated for thirty-five patients and compared with jaw tracking (JT) IMRT, static jaw (SJ) IMRT and JT volumetric modulated arc therapy (VMAT). Dosimetric parameters, tumor control probability (TCP) and normal tissue complication probability (NTCP), monitor units (MUs), delivery time and gamma passing rate, as a measure of dosimetric verification, were compared. The correlation between the length of PTV-C below the upper boundary of lung tissue (PTV-C) and dosimetric parameters and NTCP of the lung tissue were analyzed.

Results: The homogeneity and conformity of the target in the four plans were basically equivalent. When compared to the JT IMRT and SJ IMRT plans, FJ IMRT plan led to a statistically significant improvement in the NTCP and low-middle dosimetric parameters of the lung, and the improvement had a moderately positive correlation with the length of PTV-C, with a correlation coefficient ranging from 0.523 to 0.797; the FJ IMRT plan exhibited better lung sparing in low-dose volumes than the JT VMAT plan. The FJ IMRT plan had similar MUs (888 ± 99) and delivery times (516.1 ± 54.7 s) as the JT IMRT plan (937 ± 194, 522 ± 5.6 s) but higher than SJ IMRT (713 ± 137, 488.8 ± 45.2 s) and JT VMAT plan (517 ± 59, 263.7 ± 43.3 s).

Conclusions: The FJ IMRT technique is superior in reducing the low-dose volumes of lung tissues for patients with T-shaped esophageal cancer.
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http://dx.doi.org/10.1186/s13014-021-01882-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8375041PMC
August 2021

Geometric and Dosimetric Changes in Tumor and Lung Tissue During Radiotherapy for Lung Cancer With Atelectasis.

Front Oncol 2021 22;11:690278. Epub 2021 Jul 22.

Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China.

Background And Purpose: This article retrospectively characterized the geometric and dosimetric changes in target and normal tissues during radiotherapy for lung cancer patients with atelectasis.

Materials And Methods: A total of 270 cone beam computed tomography (CBCT) scans of 18 lung patients with atelectasis were collected. The degree and time of resolution or expansion of the atelectasis were recorded. The geometric, dosimetric, and biological changes in the target and lung tissue were also quantified.

Results: There were two patients with expansion, four patients with complete regression, six patients with partial regression, and six patients with no change. The time of resolution or expansion varied. The tumor volume increased by 3.8% in the first seven fractions, then decreased from the 9th fraction, and by 33.4% at the last CBCT. In the LR direction, the average center of mass (COM), boundaries of the tumors gradually shifted mediastinally. In the AP direction, the COM of the tumors was shifted slightly in the posterior direction and then gradually shifted to the anterior direction; the boundaries of the tumors all moved mediastinally. In the SI direction, the COM of the tumors on the right side of the body was substantially shifted toward the head direction. The boundaries of the tumors varied greatly. D, D, D, V, V, and TCP of the PTV were reduced during radiotherapy and were reduced to their lowest values during the last two fractions. The volume of the ipsilateral lung tended to increase gradually. The V, V, V, V, V, and NTCP of the total lung gradually increased with the fraction.

Conclusions: For most patients, regression of the atelectasis occurred, and the volume of the ipsilateral lung tended to increase while the tumor volume decreased, and the COM and boundary of the tumors shifted toward mediastinum, which caused an insufficient dose to the target and an overdose to the lungs. Regression or expansion may occur for any fraction, and it is therefore recommended that CBCT be performed at least every other day.
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http://dx.doi.org/10.3389/fonc.2021.690278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8339992PMC
July 2021

Circular RNA hsa_circ_0081343 promotes trophoblast cell migration and invasion and inhibits trophoblast apoptosis by regulating miR-210-5p/DLX3 axis.

Reprod Biol Endocrinol 2021 Aug 9;19(1):123. Epub 2021 Aug 9.

Department of Obstetrics and Gynecology, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, 518000, Guangdong, China.

Background: Various circular RNAs (circRNAs) are dysregulated in the placenta of fetal growth restriction (FGR) fetuses, but their roles and regulatory mechanisms have not been fully elucidated. Herein, we aimed to elucidate the role of hsa_circ_0081343 in regulating the migration, invasion, and apoptosis of human extravillous trophoblast HTR-8 cells.

Methods: CircRNA and miRNA levels were examined by quantitative reverse transcription PCR (qRT-PCR). Overexpression plasmid constructs and siRNAs were used to overexpress and knockdown hsa_circ_0081343, respectively. Transwell assays and flow cytometry analyses were performed to evaluate the effects of hsa_circ_0081343 or miR-210-5p on migration, invasion, and apoptosis. Protein levels were analyzed by western blotting. Dual luciferase activity and anti-AGO2 RNA immunoprecipitation (RIP) assays were performed to identify the relationship between miR-210-5p and hsa_circ_0081343.

Results: Hsa_circ_0081343 expression was significantly downregulated in 37 FGR placental tissues compared to healthy placental control tissues. Hsa_circ_0081343 overexpression may inhibit apoptosis by downregulating the expression of cleaved caspase 3 and caspase 9 and alleviating the migration and invasion of HTR-8 cells by inducing the expression of MMP2 and MMP9. The dual luciferase activity and anti-AGO2 RIP assay results showed that hsa_circ_0081343 binds to miR-210-5p. miR-210-5p overexpression eliminated the effect of hsa_circ_0081343 overexpression in HTR-8 cells. Finally, DLX3 was identified as a direct target of miR-210-5p.

Conclusions: hsa_circ_0081343 expression levels are significantly downregulated in FGR placental tissues. Hsa_circ_0081343 regulates the migration, invasion, and apoptosis of HTR-8 cells via the hsa-miR-210-5p/DLX3 axis.
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http://dx.doi.org/10.1186/s12958-021-00795-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8351162PMC
August 2021

Tissue distribution and developmental changes of PTEN in the immune organs of chicken and effect of IBDV infection on it.

Poult Sci 2021 Sep 27;100(9):101356. Epub 2021 Jun 27.

College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China. Electronic address:

Phosphatase and tensin homolog (PTEN), a tumor suppressor gene, functions in antiviral innate immunity and regulates the development and function of T cells and B cells. However, limited information about PTEN is available in poultry. In the present study, quantitative real-time polymerase chain reaction and immunohistochemistry staining were used to study the tissue distribution and developmental changes of PTEN in the main immune organs of chicken. The effects of infectious bursal disease virus (IBDV) infection on PTEN mRNA expression in the bursa of Fabricius (BF) of chickens were also investigated. The results are as follows. 1) The order of PTEN mRNA expression levels at the 18th d of hatching (E18) was: muscle and immune organs (spleen and thymus) > visceral organs (heart, lung, kidney, and liver) > hypothalamus and digestive tracts (duodenum, jejunum, ileum, cecum, proventriculus, BF [originates from cloaca], and cecum tonsil [locates at the lamina propria of cecum]). However, at the 15th d of raising (D15), the PTEN mRNA expression in the heart was the highest among all the tissues, followed by those in the liver, proventriculus, and kidney. The PTEN mRNA expression levels in the rest tissues were very low and were only 1.20 to 19.47% as much as that in the heart (P < 0.05). 2) The changes in the expression of PTEN mRNA in the BF, spleen, and thymus from E15 to D15 had no obvious regularity. PTEN-immunopositive (PTEN-ip) cells in the BF were distributed in epithelium mucosa, bursal follicles and interfollicles before hatching, but only in bursal follicles after hatching. PTEN-ip cells in the spleen were expressed in the periarterial lymphatic sheath from E18 to D15. Most of PTEN-ip cells distributed in the thymic medulla and only a few distributed in the thymic cortex during the whole experiment. 3) Chicken with IBDV infection had a remarkable decrease in PTEN mRNA expression from 1 d postinfection (dpi) to 7 dpi. Although PTEN mRNA level was reversed at 7 dpi, it was still significantly lower than that at 0 dpi (P < 0.05). These findings suggest that the PTEN of chicken might play important roles in the development of embryos and T/B lymphocytes, and the downregulation of PTEN in chickens infected with IBDV might be a mechanism of IBDV evasion from host immunity. Strategies designed to restore PTEN expression may be a therapy for preventing chickens from IBDV infection.
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http://dx.doi.org/10.1016/j.psj.2021.101356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8350381PMC
September 2021

Virtual Patient-Specific Quality Assurance of IMRT Using UNet++: Classification, Gamma Passing Rates Prediction, and Dose Difference Prediction.

Front Oncol 2021 20;11:700343. Epub 2021 Jul 20.

Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China.

The dose verification in radiotherapy quality assurance (QA) is time-consuming and places a heavy workload on medical physicists. To provide a clinical tool to perform patient specific QA accurately, the UNet++ is investigated to classify failed or pass fields (the GPR lower than 85% is considered "failed" while the GPR higher than 85% is considered "pass"), predict gamma passing rates (GPR) for different gamma criteria, and predict dose difference from virtual patient-specific quality assurance in radiotherapy. UNet++ was trained and validated with 473 fields and tested with 95 fields. All plans used Portal Dosimetry for dose verification pre-treatment. Planar dose distribution of each field was used as the input for UNet++, with QA classification results, gamma passing rates of different gamma criteria, and dose difference were used as the output. In the test set, the accuracy of the classification model was 95.79%. The mean absolute error (MAE) were 0.82, 0.88, 2.11, 2.52, and the root mean squared error (RMSE) were 1.38, 1.57, 3.33, 3.72 for 3%/3mm, 3%/2 mm, 2%/3 mm, 2%/2 mm, respectively. The trend and position of the predicted dose difference were consistent with the measured dose difference. In conclusion, the Virtual QA based on UNet++ can be used to classify the field passed or not, predict gamma pass rate for different gamma criteria, and predict dose difference. The results show that UNet++ based Virtual QA is promising in quality assurance for radiotherapy.
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http://dx.doi.org/10.3389/fonc.2021.700343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8330420PMC
July 2021

A novel lung-avoidance planning strategy based on 4DCT ventilation imaging and CT density characteristics for stage III non-small-cell lung cancer patients.

Strahlenther Onkol 2021 Aug 5. Epub 2021 Aug 5.

Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, NO.241 West Huaihai Road, Xuhui District, 20030, Shanghai, China.

Background: Functional planning based merely on 4DCT ventilation imaging has limitations. In this study, we proposed a radiotherapy planning strategy based on 4DCT ventilation imaging and CT density characteristics.

Materials And Methods: For 20 stage III non-small-cell lung cancer (NSCLC) patients, clinical plans and lung-avoidance plans were generated. Through deformable image registration (DIR) and quantitative image analysis, a 4DCT ventilation map was calculated. High-, medium-, and low-ventilation regions of the lung were defined based on the ventilation value. In addition, the total lung was also divided into high-, medium-, and low-density areas according to the HU threshold. The lung-avoidance plan aimed to reduce the dose to functional and high-density lungs while meeting standard target and critical structure constraints. Standard and dose-function metrics were compared between the clinical and lung-avoidance plans.

Results: Lung avoidance plans led to significant reductions in high-function and high-density lung doses, without significantly increasing other organ at risk (OAR) doses, but at the expense of a significantly degraded homogeneity index (HI) and conformity index (CI; p < 0.05) of the planning target volume (PTV) and a slight increase in monitor units (MU) as well as in the number of segments (p > 0.05). Compared with the clinical plan, the mean lung dose (MLD) in the high-function and high-density areas was reduced by 0.59 Gy and 0.57 Gy, respectively.

Conclusion: A lung-avoidance plan based on 4DCT ventilation imaging and CT density characteristics is feasible and implementable, with potential clinical benefits. Clinical trials will be crucial to show the clinical relevance of this lung-avoidance planning strategy.
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http://dx.doi.org/10.1007/s00066-021-01821-1DOI Listing
August 2021

Automatic segmentation of lung tumors on CT images based on a 2D & 3D hybrid convolutional neural network.

Br J Radiol 2021 Oct 4;94(1126):20210038. Epub 2021 Aug 4.

Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.

Objective: A stable and accurate automatic tumor delineation method has been developed to facilitate the intelligent design of lung cancer radiotherapy process. The purpose of this paper is to introduce an automatic tumor segmentation network for lung cancer on CT images based on deep learning.

Methods: In this paper, a hybrid convolution neural network (CNN) combining 2D CNN and 3D CNN was implemented for the automatic lung tumor delineation using CT images. 3D CNN used V-Net model for the extraction of tumor context information from CT sequence images. 2D CNN used an encoder-decoder structure based on dense connection scheme, which could expand information flow and promote feature propagation. Next, 2D features and 3D features were fused through a hybrid module. Meanwhile, the hybrid CNN was compared with the individual 3D CNN and 2D CNN, and three evaluation metrics, Dice, Jaccard and Hausdorff distance (HD), were used for quantitative evaluation. The relationship between the segmentation performance of hybrid network and the GTV volume size was also explored.

Results: The newly introduced hybrid CNN was trained and tested on a dataset of 260 cases, and could achieve a median value of 0.73, with mean and stand deviation of 0.72 ± 0.10 for the Dice metric, 0.58 ± 0.13 and 21.73 ± 13.30 mm for the Jaccard and HD metrics, respectively. The hybrid network significantly outperformed the individual 3D CNN and 2D CNN in the three examined evaluation metrics ( < 0.001). A larger GTV present a higher value for the Dice metric, but its delineation at the tumor boundary is unstable.

Conclusions: The implemented hybrid CNN was able to achieve good lung tumor segmentation performance on CT images.

Advances In Knowledge: The hybrid CNN has valuable prospect with the ability to segment lung tumor.
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http://dx.doi.org/10.1259/bjr.20210038DOI Listing
October 2021

Vomifoliol isolated from mangrove plant Ceriops tagal inhibits the NFAT signaling pathway with CN as the target enzyme in vitro.

Bioorg Med Chem Lett 2021 Sep 30;48:128235. Epub 2021 Jun 30.

Key Laboratory of Advanced Materials of Tropical Island Resources of Ministry of Education, School of Chemical Engineering and Technology, Hainan University, Haikou 570228, PR China. Electronic address:

Vomifoliol, a natural sesquiterpene compound, is a secondary metabolite isolated from the mangrove plant Ceriops tagal. The present study aimed to determine the immunosuppressive effects and underlying mechanisms of vomifoliol on Jurkat cells in vitro. The results show that vomifoliol significantly inhibited calcineurin (CN) at concentrations resulting in relatively low cytotoxicity. Moreover, vomifoliol was found to exert an inhibitory effect on phorbol 12-myristate 13-acetate (PMA)/ ionomycin (Io) -induced Jurkat cells and the dephosphorylation of NFAT1. In addition, it reduced the expression of IL-2. Based on these results, we concluded that vomifoliol may inhibit the immune response of Jurkat cells, and vomifoliol may use CN as the target enzyme to inhibit NFAT signaling pathway. Therefore, vomifoliol may be promising as a low-toxic natural immunosuppressant.
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http://dx.doi.org/10.1016/j.bmcl.2021.128235DOI Listing
September 2021

Regression models for predicting physical and EQD plan parameters of two methods of hybrid planning for stage III NSCLC.

Radiat Oncol 2021 Jun 27;16(1):119. Epub 2021 Jun 27.

Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China.

Background/purpose: To establish regression models of physical and equivalent dose in 2 Gy per fraction (EQD) plan parameters of two kinds of hybrid planning for stage III NSCLC.

Methods: Two kinds of hybrid plans named conventional fraction radiotherapy & stereotactic body radiotherapy (C&S) and conventional fraction radiotherapy & simultaneous integrated boost (C&SIB) were retrospectively made for 20 patients with stage III NSCLC. Prescription dose of C&S plans was 2 Gy × 30f for planning target volume of lymph node (PTV) and 12.5 Gy × 4f for planning target volume of primary tumor (PTV), while prescription dose of C&SIB plans was 2 Gy × 26f for PTV and sequential 2 Gy × 4f for PTV combined with 12.5 Gy × 4f for PTV. Regression models of physical and EQD plan parameters were established based on anatomical geometry features for two kinds of hybrid plans. The features were mainly characterized by volume ratio, min distance and overlapping slices thickness of two structures. The possibilities of regression models of EQD plan parameters were verified by spearman's correlation coefficients between physical and EQD plan parameters, and the influence on the consistence of fitting goodness between physical and EQD models was investigated by the correlations between physical and EQD plan parameters. Finally, physical and EQD models predictions were compared with plan parameters for two new patients.

Results: Physical and EQD plan parameters of PTV CI have shown strong positive correlations with PTV volume and min distance, and strong negative correlations with PTV volume for two kinds of hybrid plans. PTV CI is not only correlated with above three geometry features, but also negatively correlated with overlapping slices thickness. When neck lymph node metastasis was excluded from PTV volume, physical and EQD total lung V showed a high linear correlation with corrected volume ratio Meanwhile, physical total lung mean dose (MLD) had a high linear correlation with corrected volume ratio, while EQD total lung MLD was not only affected by corrected volume ratio but also volume ratio Heart D, D and mean dose (MHD) would be more susceptible to overlapping structure. Min distance may be an important feature for predicting EQD esophageal max dose for hybrid plans. It's feasible for regression models of EQD plan parameters, and the consistence of the fitting goodness of physical and EQD models had a positive correlation with spearman's correlation coefficients between physical and EQD plan parameters. For total lung V, ipsilateral lung V, and ipsilateral lung MLD, the models could predict that C&SIB plans were higher than C&S plans for two new patients.

Conclusion: The regression models of physical and EQD plan parameters were established with at least moderate fitting goodness in this work, and the models have a potential to predict physical and EQD plan parameters for two kinds of hybrid planning.
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http://dx.doi.org/10.1186/s13014-021-01848-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8237456PMC
June 2021

A novel specific grading standard study of auto-segmentation of organs at risk in thorax: subjective-objective-combined grading standard.

Biomed Eng Online 2021 Jun 3;20(1):54. Epub 2021 Jun 3.

Department of Radiation Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China.

Background: To develop a novel subjective-objective-combined (SOC) grading standard for auto-segmentation for each organ at risk (OAR) in the thorax.

Methods: A radiation oncologist manually delineated 13 thoracic OARs from computed tomography (CT) images of 40 patients. OAR auto-segmentation accuracy was graded by five geometric objective indexes, including the Dice similarity coefficient (DSC), the difference of the Euclidean distance between centers of mass (ΔCMD), the difference of volume (ΔV), maximum Hausdorff distance (MHD), and average Hausdorff distance (AHD). The grading results were compared with those of the corresponding geometric indexes obtained by geometric objective methods in the other two centers. OAR auto-segmentation accuracy was also graded by our subjective evaluation standard. These grading results were compared with those of DSC. Based on the subjective evaluation standard and the five geometric indexes, the correspondence between the subjective evaluation level and the geometric index range was established for each OAR.

Results: For ΔCMD, ΔV, and MHD, the grading results of the geometric objective evaluation methods at our center and the other two centers were inconsistent. For DSC and AHD, the grading results of three centers were consistent. Seven OARs' grading results in the subjective evaluation standard were inconsistent with those of DSC. Six OARs' grading results in the subjective evaluation standard were consistent with those of DSC. Finally, we proposed a new evaluation method that combined the subjective evaluation level of those OARs with the range of corresponding DSC to determine the grading standard. If the DSC ranges between the adjacent levels did not overlap, the DSC range was used as the grading standard. Otherwise, the mean value of DSC was used as the grading standard.

Conclusions: A novel OAR-specific SOC grading standard in thorax was developed. The SOC grading standard provides a possible alternative for evaluation of the auto-segmentation accuracy for thoracic OARs.
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http://dx.doi.org/10.1186/s12938-021-00890-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8173789PMC
June 2021

Blind Deblurring Based on Sigmoid Function.

Sensors (Basel) 2021 May 17;21(10). Epub 2021 May 17.

Key Laboratory of Optical Engineering, Chinese Academy of Sciences, Chengdu 610209, China.

Blind image deblurring, also known as blind image deconvolution, is a long-standing challenge in the field of image processing and low-level vision. To restore a clear version of a severely degraded image, this paper proposes a blind deblurring algorithm based on the sigmoid function, which constructs novel blind deblurring estimators for both the original image and the degradation process by exploring the excellent property of sigmoid function and considering image derivative constraints. Owing to these symmetric and non-linear estimators of low computation complexity, high-quality images can be obtained by the algorithm. The algorithm is also extended to image sequences. The sigmoid function enables the proposed algorithm to achieve state-of-the-art performance in various scenarios, including natural, text, face, and low-illumination images. Furthermore, the method can be extended naturally to non-uniform deblurring. Quantitative and qualitative experimental evaluations indicate that the algorithm can remove the blur effect and improve the image quality of actual and simulated images. Finally, the use of sigmoid function provides a new approach to algorithm performance optimization in the field of image restoration.
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http://dx.doi.org/10.3390/s21103484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8156062PMC
May 2021

Robust Global Motion Estimation for Video Stabilization Based on Improved K-Means Clustering and Superpixel.

Sensors (Basel) 2021 Apr 3;21(7). Epub 2021 Apr 3.

Institute of Optics and Electronics, Chinese Academy of Sciences, Chengdu 610200, China.

Obtaining accurate global motion is a crucial step for video stabilization. This paper proposes a robust and simple method to implement global motion estimation. We don't extend the framework of 2D video stabilization but add a "plug and play" module to motion estimation based on feature points. Firstly, simple linear iterative clustering (SLIC) pre-segmentation is used to obtain superpixels of the video frame, clustering is performed according to the superpixel centroid motion vector and cluster center with large value is eliminated. Secondly, in order to obtain accurate global motion estimation, an improved K-means clustering is proposed. We match the feature points of the remaining superpixels between two adjacent frames, establish a feature points' motion vector space, and use improved K-means clustering for clustering. Finally, the richest cluster is being retained, and the global motion is obtained by homography transformation. Our proposed method has been verified on different types of videos and has efficient performance than traditional approaches. The stabilization video has an average improvement of 0.24 in the structural similarity index than the original video and 0.1 higher than the traditional method.
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http://dx.doi.org/10.3390/s21072505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8038417PMC
April 2021

Low-Cost and Scalable Platform with Multiplexed Microwell Array Biochip for Rapid Diagnosis of COVID-19.

Research (Wash D C) 2021 12;2021:2813643. Epub 2021 Mar 12.

Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China.

Sensitive detection of SARS-CoV-2 is of great importance for inhibiting the current pandemic of COVID-19. Here, we report a simple yet efficient platform integrating a portable and low-cost custom-made detector and a novel microwell array biochip for rapid and accurate detection of SARS-CoV-2. The instrument exhibits expedited amplification speed that enables colorimetric read-out within 25 minutes. A polymeric chip with a laser-engraved microwell array was developed to process the reaction between the primers and the respiratory swab RNA extracts, based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP). To achieve clinically acceptable performance, we synthesized a group of six primers to identify the conserved regions of the ORF1ab gene of SARS-CoV-2. Clinical trials were conducted with 87 PCR-positive and 43 PCR-negative patient samples. The platform demonstrated both high sensitivity (95.40%) and high specificity (95.35%), showing potentials for rapid and user-friendly diagnosis of COVID-19 among many other infectious pathogens.
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http://dx.doi.org/10.34133/2021/2813643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7982056PMC
March 2021

Simulation Insight into the Synergic Role of Citrate and Polyaspartic Peptide in Biomineralization.

Langmuir 2021 03 10;37(11):3410-3419. Epub 2021 Mar 10.

School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou 510640, P. R. China.

Hydroxyapatite (HAP) is one of the most important inorganic components in biological minerals such as bones and teeth. More than 90% of the total citrate is accumulated in human bones and other biomineralized tissues. In addition, mineralizing proteins are enriched in glutamate and aspartate residues, which are important for their mineral-regulating properties. However, how citrate ions (CITs) and/or acidic amino acids regulate the formation of HAP is still unclear. In this work, molecular dynamics simulations were performed to study how CIT regulates the adsorption behavior of polyaspartic acid (PASP) on the HAP surface in the calcium phosphate solution. The simulation results indicate that PASP can be used as an ion chelator to complex Ca and can serve as templates for HAP mineralization by templating the distribution of Ca on its surface, which are attributed to the -COO and α-helix structure. Most importantly, the orientation distributions of PASP in all systems are narrower with the help of CIT, thereby PASP can be adsorbed on the HAP surface stably with a "lying-down" orientation. This indicates that CIT can be used as a bridging agent to bond the acidic peptide to the HAP surface in biomineralization. Thus, the synergic role of CIT and the acidic peptide on the HAP surface were revealed in this work, which can provide new insights into the interfacial phenomena during the biomineralization.
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http://dx.doi.org/10.1021/acs.langmuir.0c03626DOI Listing
March 2021

Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response.

Cell Host Microbe 2021 03 29;29(3):489-502.e8. Epub 2021 Jan 29.

Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China.

The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-β levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-β responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.
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http://dx.doi.org/10.1016/j.chom.2021.01.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7846228PMC
March 2021

Roles of TNF receptor-associated and Fas-associated death domain proteins in the apoptosis of Eimeria tenella host cells.

Vet Parasitol 2021 Feb 7;290:109351. Epub 2021 Jan 7.

College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, China.

The present study aimed to investigate the effects of death receptor adapter proteins, namely, TNF receptor-associated death domain (TRADD) and Fas-associated death domain (FADD) proteins, on Eimeria tenella-induced host cell apoptosis. Gene silencing, culture technique for primary chick embryo cecal epithelial cells, enzyme-linked immunosorbent assay, Hoechst-Annexin V/PI apoptosis staining, fluorescence quantitative PCR, and flow cytometry were used to detect the E. tenella host cell apoptotic rate, RIP1 and FADD protein expression levels, and caspase-8 activity of the TRADD siRNA-treated and FADD siRNA-treated groups. Results showed that the apoptotic rate in the TRADD siRNA group was significantly higher than that in the NC siRNA group at 4 h post-infection with E. tenella (P < 0.05). The RIP1 protein expression level in the TRADD siRNA group was significantly lower than that in the NC siRNA group at 4-24 h (P < 0.05). The FADD expression and apoptotic rates in the TRADD siRNA group were significantly lower than those in the NC siRNA group at 24-120 h (P < 0.05). The caspase-8 activity and apoptotic rates in the FADD siRNA group were significantly lower than those in the NC siRNA group (P < 0.05) at 24-120 h. These findings indicated that E. tenella inhibited the host cell apoptosis through the TRADD-RIP1 pathway at the early developmental stage and promoted host cell apoptosis via the TRADD-FADD-caspase-8 apoptotic pathway at the middle and late developmental stages.
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http://dx.doi.org/10.1016/j.vetpar.2021.109351DOI Listing
February 2021

Deep learning-based automatic delineation of the hippocampus by MRI: geometric and dosimetric evaluation.

Radiat Oncol 2021 Jan 14;16(1):12. Epub 2021 Jan 14.

Department of Radiation Oncology, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, China.

Background: Whole brain radiotherapy (WBRT) can impair patients' cognitive function. Hippocampal avoidance during WBRT can potentially prevent this side effect. However, manually delineating the target area is time-consuming and difficult. Here, we proposed a credible approach of automatic hippocampal delineation based on convolutional neural networks.

Methods: Referring to the hippocampus contouring atlas proposed by RTOG 0933, we manually delineated (MD) the hippocampus on the MRI data sets (3-dimensional T1-weighted with slice thickness of 1 mm, n = 175), which were used to construct a three-dimensional convolutional neural network aiming for the hippocampus automatic delineation (AD). The performance of this AD tool was tested on three cohorts: (a) 3D T1 MRI with 1-mm slice thickness (n = 30); (b) non-3D T1-weighted MRI with 3-mm slice thickness (n = 19); (c) non-3D T1-weighted MRI with 1-mm slice thickness (n = 11). All MRIs confirmed with normal hippocampus has not been violated by any disease. Virtual radiation plans were created for AD and MD hippocampi in cohort c to evaluate the clinical feasibility of the artificial intelligence approach. Statistical analyses were performed using SPSS version 23. P < 0.05 was considered significant.

Results: The Dice similarity coefficient (DSC) and Average Hausdorff Distance (AVD) between the AD and MD hippocampi are 0.86 ± 0.028 and 0.18 ± 0.050 cm in cohort a, 0.76 ± 0.035 and 0.31 ± 0.064 cm in cohort b, 0.80 ± 0.015 and 0.24 ± 0.021 cm in cohort c, respectively. The DSC and AVD in cohort a were better than those in cohorts b and c (P < 0.01). There is no significant difference between the radiotherapy plans generated using the AD and MD hippocampi.

Conclusion: The AD of the hippocampus based on a deep learning algorithm showed satisfying results, which could have a positive impact on improving delineation accuracy and reducing work load.
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http://dx.doi.org/10.1186/s13014-020-01724-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7807715PMC
January 2021

Shallow Graph Convolutional Network for Skeleton-Based Action Recognition.

Sensors (Basel) 2021 Jan 11;21(2). Epub 2021 Jan 11.

Key Laboratory of Optical Engineering, Institute of Optics and Electronics, Chinese Academy of Sciences, Chengdu 610209, China.

Graph convolutional networks (GCNs) have brought considerable improvement to the skeleton-based action recognition task. Existing GCN-based methods usually use the fixed spatial graph size among all the layers. It severely affects the model's abilities to exploit the global and semantic discriminative information due to the limits of receptive fields. Furthermore, the fixed graph size would cause many redundancies in the representation of actions, which is inefficient for the model. The redundancies could also hinder the model from focusing on beneficial features. To address those issues, we proposed a plug-and-play channel adaptive merging module (CAMM) specific for the human skeleton graph, which can merge the vertices from the same part of the skeleton graph adaptively and efficiently. The merge weights are different across the channels, so every channel has its flexibility to integrate the joints. Then, we build a novel shallow graph convolutional network (SGCN) based on the module, which achieves state-of-the-art performance with less computational cost. Experimental results on NTU-RGB+D and Kinetics-Skeleton illustrates the superiority of our methods.
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http://dx.doi.org/10.3390/s21020452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7827280PMC
January 2021

Phylogenetic Diversity, Antimicrobial and Antioxidant Potential and Identification of Bioactive Compounds from Culturable Endophytic Fungi Associated with Mangrove Bruguiera sexangula (Lour.) Poir.

Curr Microbiol 2021 Feb 2;78(2):479-489. Epub 2021 Jan 2.

Key Laboratory of Advanced Materials of Tropical Island Resources of Ministry of Education, School of Chemical Engineering and Technology, Hainan University, Haikou, 570228, People's Republic of China.

A total of 96 isolates were obtained from 375 segments, isolated from the healthy roots, stems, leaves, hypocotyls and flowers of Bruguiera sexangula (Lour.) Poir. collected at the Dong Zhai Gang Mangrove Garden on Hainan Island, and 20 independent representative isolates were identified using a combination of morphological and molecular approaches. The most frequent endophytic fungal species isolated were Diaporthe phaseolorum (relative frequency = 31.2%). The Shannon-Wiener diversity and Simpson's diversity index both showed that stems possessed the highest diversity compared to the other tissues estimated. Ethyl acetate extracts and the isolated metabolites were tested for antimicrobial activity using the serial dilution technique and for antioxidant activity using 2,2'-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonicacid) (ABTS) radical-scavenging capacity assays, respectively. The fungal isolate HL18 (Gelasinospora endodonta) cultured on Czapek's agar (CA) displayed a broad spectrum of antimicrobial activities and was significantly active against Escherichia coli (MIC = 0.0625 mg ml). Antioxidant assays showed that most of the fungal isolates (60.0%) exhibited some degree of antioxidant capacity (%RSA > 50%). The stain HL14 (Pestalotiopsis mangiferae) grown on potato dextrose agar (PDA) exhibited the highest DPPH and ABTS radical-scavenging capability with IC values of 0.717 ± 0.012 mg ml and 0.787 ± 0.027 mg ml, respectively. Furthermore, five known secondary metabolites 1-5 were isolated and identified from HL-14. Compounds 1 and 5 exhibited weak antioxidant activity.
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http://dx.doi.org/10.1007/s00284-020-02314-7DOI Listing
February 2021
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