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Liang Y, Cao M, Zhang S. NeuroPred-ResSE: Predicting neuropeptides by integrating residual block and squeeze-excitation attention mechanism. Anal Biochem 2024; 695:115648. [PMID: 39154878 DOI: 10.1016/j.ab.2024.115648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/31/2024] [Accepted: 08/15/2024] [Indexed: 08/20/2024]
Abstract
Neuropeptides play crucial roles in regulating neurological function acting as signaling molecules, which provide new opportunity for developing drugs for the treatment of neurological diseases. Therefore, it is very necessary to develop a rapid and accurate prediction model for neuropeptides. Although a few prediction tools have been developed, there is room for improvement in prediction accuracy by using deep learning approach. In this paper, we establish the NeuroPred-ResSE model based on residual block and squeeze-excitation attention mechanism. Firstly, we extract multi-features by using one-hot coding based on the NT5CT5 sequence, dipeptide deviation from expected mean and natural vector. Then, we integrate residual block and squeeze-excitation attention mechanism, which can capture and identify the most relevant attribute features. Finally, the accuracies of the training set and test set are 97.16 % and 96.60 % based on the 5-fold cross-validation and independent test, respectively, and other evaluation metrics have also obtained satisfactory results. The experimental results show that the performance of the NeuroPred-ResSE model outperforms those of existing state-of-the-art models, and our model is an effective, intelligent and robust prediction tool. The datasets and source codes are available at https://github.com/yunyunliang88/NeuroPred-ResSE.
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Sun J, Wei J, Pan Y, Cao M, Li X, Xiao J, Yang G, Yu T. Improving genomic prediction accuracy of pig reproductive traits based on genotype imputation using preselected markers with different imputation platforms. Animal 2024; 19:101387. [PMID: 39708733 DOI: 10.1016/j.animal.2024.101387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 11/21/2024] [Accepted: 11/22/2024] [Indexed: 12/23/2024] Open
Abstract
Genomic prediction has been widely applied to the pig industry and has greatly accelerated the progress of genetic improvement in pigs. With the development of sequencing technology and price reduction, more and more genotype imputation panels of pig have been investigated, providing an effective and economical method to further study the genetic variation of pig economic traits. In this study, the imputation from 80 k Single Nucleotide Polymorphism chip data of 832 Large White pigs to whole-genome sequencing genotypes was performed by Swine Imputation Server, Pig Haplotypes Reference Panel (PHARP), Animal Genotype Imputation Database and 1k-pig-genomes four thousand-pig imputation panels. Then, linkage disequilibrium (LD) pruning and genome-wide association study (GWAS) preselected markers strategies were utilised to compare the genomic prediction accuracy of the different imputation data for reproductive traits, respectively. Our results showed that the PHARP panel exhibited the best genomic prediction accuracy among the four imputation panels. Meanwhile, the genomic prediction accuracy of the imputation data can be further improved by utilising the LD pruning and GWAS preselected marker strategies. In conclusion, our study provides insights into imputation data for pig genetic breeding.
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Heppert JK, Awori RM, Cao M, Chen G, McLeish J, Goodrich-Blair H. Analyses of Xenorhabdus griffiniae genomes reveal two distinct sub-species that display intra-species variation due to prophages. BMC Genomics 2024; 25:1087. [PMID: 39548374 PMCID: PMC11566119 DOI: 10.1186/s12864-024-10858-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 10/01/2024] [Indexed: 11/17/2024] Open
Abstract
BACKGROUND Nematodes of the genus Steinernema and their Xenorhabdus bacterial symbionts are lethal entomopathogens that are useful in the biocontrol of insect pests, as sources of diverse natural products, and as research models for mutualism and parasitism. Xenorhabdus play a central role in all aspects of the Steinernema lifecycle, and a deeper understanding of their genomes therefore has the potential to spur advances in each of these applications. RESULTS Here, we report a comparative genomics analysis of Xenorhabdus griffiniae, including the symbiont of Steinernema hermaphroditum nematodes, for which genetic and genomic tools are being developed. We sequenced and assembled circularized genomes for three Xenorhabdus strains: HGB2511, ID10 and TH1. We then determined their relationships to other Xenorhabdus and delineated their species via phylogenomic analyses, concluding that HGB2511 and ID10 are Xenorhabdus griffiniae while TH1 is a novel species. These additions to the existing X. griffiniae landscape further allowed for the identification of two subspecies within the clade. Consistent with other Xenorhabdus, the analysed X. griffiniae genomes each encode a wide array of antimicrobials and virulence-related proteins. Comparative genomic analyses, including the creation of a pangenome, revealed that a large amount of the intraspecies variation in X. griffiniae is contained within the mobilome and attributable to prophage loci. In addition, CRISPR arrays, secondary metabolite potential and toxin genes all varied among strains within the X. griffiniae species. CONCLUSIONS Our findings suggest that phage-related genes drive the genomic diversity in closely related Xenorhabdus symbionts, and that these may underlie some of the traits most associated with the lifestyle and survival of entomopathogenic nematodes and their bacteria: virulence and competition. This study establishes a broad knowledge base for further exploration of not only the relationships between X. griffiniae species and their nematode hosts but also the molecular mechanisms that underlie their entomopathogenic lifestyle.
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Li J, Liu L, Gu J, Cao M, Lei J, Li H, He J, He J. The impact of air pollutants on spontaneous abortion: a case-control study in Tongchuan City. Public Health 2024; 227:267-273. [PMID: 38320452 DOI: 10.1016/j.puhe.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024]
Abstract
OBJECTIVES Studies related to air pollutants and spontaneous abortion in urban northwestern China are scarce, and the main exposure windows of pollutants acting on pregnant women are unclear. STUDY DESIGN Case-control study. METHODS Data were collected from pregnant women in Tongchuan City from 2018 to 2019. A total of 289 cases of spontaneous abortion and 1156 cases of full-term labor were included and analyzed using a case-control study. Logistic regression models were developed to explore the relationship between air pollutants and spontaneous abortion after Chi square analysis and Air pollutant description. RESULTS O3 (odds ratio [OR] = 1.028) is a risk factor for spontaneous abortion throughout pregnancy. PM2.5 (OR = 1.015), PM10 (OR = 1.010), SO2 (OR = 1.026), and NO2 (OR = 1.028) are risk factors for spontaneous abortion in the 30 days before the last menstrual period. PM2.5 (OR = 1.015), PM10 (OR = 1.013), SO2 (OR = 1.036), and NO2 (OR = 1.033) are risk factors for spontaneous abortion in the 30-60 days before the last menstrual period. PM2.5 (OR = 1.028), PM10 (OR = 1.013), SO2 (OR = 1.035), and NO2 (OR = 1.059) are risk factors for spontaneous abortion in the 60-90 days before the last menstrual period. CONCLUSION Exposure to high levels of air pollutants may be a cause of increased risk of spontaneous abortion, especially in the first trimester of the last menstrual period.
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Cao M. CRISPR-Cas9 genome editing in Steinernema entomopathogenic nematodes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.24.568619. [PMID: 38045388 PMCID: PMC10690278 DOI: 10.1101/2023.11.24.568619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Molecular tool development in traditionally non-tractable animals opens new avenues to study gene functions in the relevant ecological context. Entomopathogenic nematodes (EPN) Steinernema and their symbiotic bacteria of Xenorhabdus spp are a valuable experimental system in the laboratory and are applicable in the field to promote agricultural productivity. The infective juvenile (IJ) stage of the nematode packages mutualistic symbiotic bacteria in the intestinal pocket and invades insects that are agricultural pests. The lack of consistent and heritable genetics tools in EPN targeted mutagenesis severely restricted the study of molecular mechanisms underlying both parasitic and mutualistic interactions. Here, I report a protocol for CRISPR-Cas9 based genome-editing that is successful in two EPN species, S. carpocapsae and S. hermaphroditum . I adapted a gonadal microinjection technique in S. carpocapsae , which created on-target modifications of a homologue Sc-dpy-10 (cuticular collagen) by homology-directed repair. A similar delivery approach was used to introduce various alleles in S. hermaphroditum including Sh-dpy-10 and Sh-unc-22 (a muscle gene), resulting in visible and heritable phenotypes of dumpy and twitching, respectively. Using conditionally dominant alleles of Sh-unc-22 as a co-CRISPR marker, I successfully modified a second locus encoding Sh-Daf-22 (a homologue of human sterol carrier protein SCPx), predicted to function as a core enzyme in the biosynthesis of nematode pheromone that is required for IJ development. As a proof of concept, Sh-daf-22 null mutant showed IJ developmental defects in vivo ( in insecta) . This research demonstrates that Steinernema spp are highly tractable for targeted mutagenesis and has great potential in the study of gene functions under controlled laboratory conditions within the relevant context of its ecological niche.
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Naumann LM, Lauria M, Kishan AU, Kaprealian TB, Cao M, Savjani RR, Iwamoto K, Sandstrom RE, Strause L, Steinberg ML, Low D. Clinical Implementation of Weak Magnetic Field Generator in Radiation Therapy. Int J Radiat Oncol Biol Phys 2023; 117:e701-e702. [PMID: 37786058 DOI: 10.1016/j.ijrobp.2023.06.2188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The application of weak magnetic fields may improve radiation therapy efficacy by manipulating the free radical activity induced by radiation to optimize tumor death. Once the device is commercially available, we will conduct clinical trials to determine the clinical impact of the weak magnetic field. However, the magnetic field generator (MFG) restricts Linac gantry rotation to approximately 180° and this limitation may limit treatment plan quality. This work is a continuation of an ongoing study to determine if the gantry angle restrictions can be compensated for during treatment planning. MATERIALS/METHODS Previous work has demonstrated the feasibility for GBM cases. For this work, 10 prostate cancer treatment plans were retrospectively replanned using only coplanar arcs that spanned from 90° to 270° (half-arcs). The prescriptions were 60 Gy for 6 patients, 55.8 Gy for 2 patients, 54 Gy for 1 patient, and 40.05 Gy for 1 patient. The prescription doses were delivered to 95% of the planning target volume (PTV = GTV + 2 cm). The critical structure doses were compared to determine if clinically equivalent plans could be delivered using half-arcs. RESULTS The dose criteria that were met by the clinical plans were also met by the half-arc plans except for the cases shown in Table 1. Table 1: Doses that did not meet criteria CONCLUSION: The half-arc plans were able to deliver clinically equivalent dose distributions as the clinical treatment plans. This provides continuing evidence that clinical trials will be able to be developed to evaluate the use of weak magnetic fields for radiation therapy.
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Jiang T, Valle L, Steinberg ML, Reiter RE, Rettig M, Nickols NG, Casado M, Lamb JM, Cao M, Raman S, Sung KH, Romero T, Kishan AU. One Year Radiographic Response Following Prostrate SBRT: An Exploratory Analysis of a Phase III Randomized Trial. Int J Radiat Oncol Biol Phys 2023; 117:e396-e397. [PMID: 37785326 DOI: 10.1016/j.ijrobp.2023.06.1524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Radiographic MRI response following prostate radiotherapy, particularly stereotactic body radiotherapy (SBRT), remains poorly understood. Our objective was to describe radiographic changes to the prostate gland and prostate tumor following SBRT of men treated on a prospective, randomized trial. MATERIALS/METHODS MIRAGE (NCT04384770) is a single center, randomized phase III trial of patients receiving either CT or MRI guided SBRT for localized prostate cancer. Patients underwent pre-treatment and annual post-treatment MRIs, in addition to routine PSA surveillance. Outcomes reported include percent gland shrinkage, percent PSA response at one year, and presence of residual tumor based on radiographic interpretation. Patient characteristics were compared via two-sample t-test or Fischer's exact test. Both univariate and multivariable logistical analysis were employed to identify potential clinical predictors of residual tumor on 1-year follow up MRI. RESULTS This study cohort included 94 eligible patients with baseline characteristics in Table 1. Residual lesions were seen in 13 patients (14%), 5/27 (18.5%) treated without ADT and 8/67 (12%) with ADT. PSA ablation was deep, with a 79% median decrease without ADT and 98% median decrease with ADT. Patients receiving ADT showed more gland shrinkage (17% vs. 34% shrinkage, p = 0.0001), while radiographic non-responders and responders experienced similar gland shrinkage (median 21% vs 29% shrinkage, p > 0.05). No significant clinical predictors of residual tumor were identified on univariate and multivariate analysis. No patient had any clinical or biochemical evidence of failure. CONCLUSION A total of 14% of patients were found to have residual tumor detected on MRI one year after SBRT. These data highlight the protracted nature of radiographic tumor response to radiation therapy, even with ablative radiation techniques. The analysis is limited by the lack of biopsy data to quantify whether visualized residual tumor harbor active cancer.
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Ma TM, Neylon JP, Savjani RR, Low D, Steinberg ML, Cao M, Kishan AU. Treatment Delivery Gating of MRI-Guided Stereotactic Radiotherapy for Prostate Cancer: An Exploratory Analysis of a Phase III Randomized Trial of CT-Vs. MR-Guided Radiotherapy (MIRAGE). Int J Radiat Oncol Biol Phys 2023; 117:e692-e693. [PMID: 37786034 DOI: 10.1016/j.ijrobp.2023.06.2168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Compared to CT-guided radiotherapy, MRI-guided radiotherapy (MRgRT) has been shown to reduce acute physician-scored and patient-reported gastrointestinal and genitourinary (GU) toxicities associated with prostate stereotactic body radiotherapy (SBRT) in the MIRAGE randomized trial (NCT04384770). We hypothesize that real-time intrafraction tracking/gating is important and is a critical enabler of aggressive margin reduction with MRgRT. MATERIALS/METHODS 79 patients received MRgRT on the MIRAGE trial with a planning margin of 2mm around the prostate and proximal seminal vesicles, which were treated to 40 Gy in five fractions on an MR-Linac. Tracking was performed at 4 frames/second in the sagittal plane during treatment with a gating boundary of 3mm for automatic beam hold. An in-house tool was developed to extract treatment time and beam gating status based on treatment logs and real-time cine images. The ratio of the time that the target was within the gating window/total time of target inside or outside the gating boundary was defined as the duty cycle (DC). Target contours were extracted from each frame of tracking and overlaid to create a motion-convolved target occupancy map. Minimum isotropic expansions of the prostate to cover 85%, 90% and 95% of the intrafraction motion were calculated with and without gating. RESULTS Median treatment time per fraction including image guidance procedure and beam delivery was 24.3 min (IQR: 22.2-27.7 min). The median time for image guidance 5.4 min (IQR: 4.2-6.7 min). A total of 391 treatment fractions were analyzed and the median DC per fraction was 0.974 (IQR: 0.926 -0.983). 89 (22.8%) and 35 (9.0%) of fractions had DC<90% and <80%, respectively, corresponding to 50/79 (62.3%) and 24/79 (30.4%) of patients having at least one fraction with a DC<90% and <80%, respectively. The minimum duty cycle of all fractions was lower among patients with grade ≥2 GU toxicity compared to those with grade 0-1 GU toxicity (mean 79.8% vs. 85.9%, p = 0.06). The proportion of patients with grade ≥2 GU toxicity was also greater in patients with a minimum gating cycle <80% (37.5% vs. 18.2%, p = 0.06). Gating significantly decreased the minimum isotropic expansion of the prostate to cover 85%, 90% and 95% of the intrafraction motion (p<0.0001 for all). Prostate intrafraction motion tended to be along the bladder-rectum axis secondary to bladder filling, rectal gas and bulk motion. Fractions with large prostate motion were mostly stochastic. CONCLUSION A large fraction (30%) of patients had at least of one treatment fraction with DC<80%, which correlated with increased acute GU toxicity. Gating effectively reduces the expansion needed to cover prostate intrafraction motion, and is necessary for real-time motion management given the unpredictable nature of prostate motion.
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Jiang T, Smith LM, Valle L, Ballas LK, Steinberg ML, Reiter RE, Nikitas J, Cao M, Kishan AU. Dosimetric Implications of Prostate Bed Deformability: An Analysis of the SCIMITAR Clinical Trial. Int J Radiat Oncol Biol Phys 2023; 117:e396. [PMID: 37785325 DOI: 10.1016/j.ijrobp.2023.06.1523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The post-operative prostate bed is a dynamic target volume due to the deformable nature of the bladder and rectum. These changes can lead to incorrect dosing of the prostate bed and organs at risk (OARs). Our objective was to quantify the dosimetric impact of prostate bed and OAR deformation. MATERIALS/METHODS SCIMITAR (NCT03541850) is a prospective phase II clinical trial evaluating stereotactic body radiotherapy (SBRT) in the post-prostatectomy setting. This analysis included a subset of patients who received 5 fractions of 6-6.8 Gy to the prostate bed under CT-based image guidance. The clinical target volume (CTV) and OARs were contoured on fractional CBCT images. Changes in volume, shape (via the dice similarity coefficient [DSC]), and dosimetry were quantified. Student's t-test was used to analyze the differences between planning and daily treatment outcomes. RESULTS A total of 29 patients (145 fractional images) were analyzed. We found the CTV volume remained stable (median change 1.1%; IQR: -15.1% - 16.1%), whereas the CTV shape was deformable (DSC of 0.76 [IQR: 0.71 - 0.79]). The bladder and rectum exhibited changes with median volume change of 5.7% (IQR: -24.3% - 51.0%) and 5.5% (IQR: -8.7% - 21.9%), respectively and median DSC of 0.77 (IQR: 0.68 - 0.84) and 0.74 (IQR: 0.69 - 0.80) respectively. The CTV received less radiation dose than planned (volume receiving 95%: 93.2% actual vs 99.6% planned, p < 0.01). 39% (56/145) of total fractions and 52% (15/29) of patients met criteria for CTV under-coverage (volume receiving 95% of the prescription dose < 93%). The rectum received higher dose than planned on several parameters (e.g., V27.5 Gy increased from 15.4% to 21.0% [p = 0.009] and V32.5 Gy increased from 6.0% to 10.9% [p = 0.006]) (Table 1). CONCLUSION We found underdosing of the prostate CTV and overdosing of the rectum in patients receiving CT-guided postoperative SBRT. While future work will correlate these dosimetric consequences with toxicity, these data suggest that approaches such as adaptive radiotherapy may be beneficial.
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Liu H, Neilsen BK, Xu D, Pham J, Cao M, Ruan D, Kishan AU, Sheng K. Towards Automated Dosimetric Analysis of the Bladder Trigone: Deep-Learning-Based Joint Segmentation and Landmark Localization. Int J Radiat Oncol Biol Phys 2023; 117:S118. [PMID: 37784306 DOI: 10.1016/j.ijrobp.2023.06.452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The bladder trigone dosimetry is hypothesized to have a stronger correlation with post-SBRT urinary toxicity than that of the entire bladder. However, the trigone tends to move significantly between simulation and daily treatment. Its small size, large daily motion, and proximity to the target lead to potentially consequential but unaccounted-for dosimetric uncertainties. Manual segmentation of the structure can be inconsistent and time-consuming, even with MR-guided RT. Here, we propose and demonstrate a deep-learning-based framework for joint segmentation and landmark localization to support deformable registration and comprehensive dosimetric analysis. MATERIALS/METHODS A total of 30 patients were randomly selected for training, and 20 were held out for testing. Each patient had 1 simulation and 5 daily pre-treatment images obtained from a clinical 0.35T MR Linac. The trigone is defined as the triangular bladder section among three landmarks (2 ureteral orifices and the internal urethral orifice). In the manual contouring process, the 3 landmarks were identified first, followed by trigone segmentation. The proposed joint method uses a modified 3D nnU-Net with 2 decoders, one for segmentation and the other for landmark localization. The shared encoder is expected to extract features useful for both tasks. The joint framework was compared with a baseline method using two separate 3D nnU-Nets for landmark localization and trigone segmentation, respectively. Since the trigone is small (∼2% of the bladder volume), we further experimented with a second-stage prediction mimicking the human contouring process. The predicted landmarks from the first stage were used to crop the trigone region, and a second network was trained on cropped images. Evaluation metrics included the Dice score, 95% Hausdorff distance (HD95), and average surface distance (ASD) for segmentation, and Euclidean distance (ED) between the predicted and ground truth landmarks for localization. RESULTS The quantification metrics are summarized in the table below. The joint approach shows similar Dice performance to the baseline method but markedly better HD95 by 13%. For landmark localization, the proposed method is similar to the baseline, but the integration of the segmentation task stabilizes the training process. The two-stage approach further improves HD95, ASD, and ED by 27%, 24%, and 19%. CONCLUSION Combining segmentation and landmark localization exhibits a synergistic effect. The proposed two-stage approach provided additional improvement. Future studies will explore the deformable registration of the trigone based on the segmentation and landmark detection, as well as analyze cumulated dose distribution.
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Lan W, Yao J, Cao M, Wang Z, Xiang B, Zhou J, Liao W, Liu X, Yang M, Zhang S, Zhao Y. Bifunctional Role of Monocyte Subsets in Modulating Radiotherapy Combined Intra-Tumor αCD40 Agonist Induced Abscopal Effect. Int J Radiat Oncol Biol Phys 2023; 117:S121. [PMID: 37784314 DOI: 10.1016/j.ijrobp.2023.06.459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Abscopal effect induced by radiotherapy and immune checkpoint blockade is a promising yet far from satisfactory strategy in clinical. The underlying immune mechanism, especially driven by monocytes remains poorly undefined. Monocytes consist of two phenotypically and functionally distinct subsets distinguished by expression of chemokine receptors CCR2 and CX3CR1: classical inflammatory Ly6ChiCCR2hi monocytes and nonclassical patrolling Ly6CloCCR2loCX3CR1hi monocytes. Monocytes differentiate and transit to other myeloid cells such as dendritic cells and macrophages according to various environmental cues. Herein we investigated the roles of monocyte subsets in modulating tumor control consisting of combination RT and myeloid checkpoint agonist αCD40 to specifically ignite myeloid cell activation. MATERIALS/METHODS To establish abscopal model, contralateral tumors were implanted in each mouse, while only one side were treated with RT (8 Gy × 3) + αCD40 agonist (50 μg, intra-tumor). Tumor volume and mice survival were compared in each group (control, RT, αCD40 and RT + αCD40). Ccr2RFP/+ Cx3cr1GFP/+ (R2 × 3), Ccr2RFP/RFPCx3cr1+/+ (R2-KO) and Ccr2+/+Cx3cr1GFP/GFP (X3-KO) mice were used for cell tracking and to dissect chemokine receptor CCR2 and CX3CR1 on monocyte. Tumor infiltrating immune cells were analyzed by flowcytometry and RNA-seq. RESULTS RT combined with αCD40 significantly dampened tumor growth on both ipsilateral and contralateral sides in abscopal model (p< 0.01), accompanied by upregulation of chemokine receptors CCR2 and CX3CR1 on myeloid cells were both increased in tumor and peripheral blood. Chemokine ligands CCL2, CCL3, CCL5, CCL7, CCL12 and CX3CL1 were upregulated in tumor after RT and αCD40 treatment, recruiting CCR2 and CX3CR1 expressing monocytes in situ. To elucidate the roles of CCR2 and CX3CR1 in mediating local and systemic anti-tumor immunity, R2 × 3, R2-KO and X3-KO mice with combined treatment were used. Tumor size on ipsilateral leg were similar among groups. However, tumor growth was significantly delayed on contralateral side in X3-KO mice while accelerated in R2-KO mice compared with that in R2 × 3 mice. Mechanistically, remarkable decrease of antigen presenting dendritic cells (MHCII+Ly6ChiCD11c+) were observed in R2-KO mice. Moreover, phagocytosis was strengthened in macrophages (F4/80+CD11b+) of X3-KO mice. CONCLUSION CX3CR1 deletion ignite anti-tumor immunity elicited by RT and αCD40 through enhanced phagocytosis in macrophages, while CCR2 deletion renders inferior tumor control through reduction of dendritic cells. Preferential targeting nonclassical patrolling monocyte may lead to enhanced local and systemic tumor control.
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Zou RY, Zhao Q, Tian YQ, Yan X, Qiu XH, Gao YJ, Liu Y, Huang M, Cao M, Dai JH, Cai HR. [Clinical characteristics and prognostic factors of patients with anti-melanoma differentiation-associated gene 5 antibody-positive dermatomyositis associated interstitial lung disease]. ZHONGHUA JIE HE HE HU XI ZA ZHI = ZHONGHUA JIEHE HE HUXI ZAZHI = CHINESE JOURNAL OF TUBERCULOSIS AND RESPIRATORY DISEASES 2023; 46:781-790. [PMID: 37536988 DOI: 10.3760/cma.j.cn112147-20221017-00821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Objective: To analyze the clinical characteristics and prognostic factors of patients with anti-melanoma differentiation-associated gene 5 (anti-MDA5)-positive dermatomyositis associated interstitial lung disease (DM-ILD). Methods: The patients with MDA5+DM-ILD who were admitted to Department of Respiratory Medicine, Nanjing Drum Tower Hospital from January 2017 to March 2021 were enrolled. The clinical data and survival information were analyzed retrospectively. Patients were divided into survival group or death group, and rapid progressive ILD (RP-ILD) group or non-rapid progressive ILD group, according to their survival status and clinical progression. Results: A total of 105 patients with anti-MDA5+DM-ILD (median age of onset 54 years) were enrolled, 58% being female (61 cases). The main sub-type of dermatomyositis was amyopathic dermatomyositis (n=74, 70%), followed by dermatomyositis (n=31, 30%). The main extrapulmonary manifestations were skin lesions (n=60, 57.1%), muscle manifestations(n=20, 19%) and arthralgia/arthritis (n=20, 19%). 15.4% of the patients had positive ANA (antibody titer≥1∶320), and 61.9% of the patients had anti-RO-52 kDa antibody. A total of 66 patients (62.8%) developed RP-ILD, and 58 patients (56.3%) died. Lower oxygenation index (OR=0.974, 95%CI:0.954-0.994, P=0.012) and no joint pain (OR=0.032, 95%CI: 0.002-0.663 P=0.026) were independent risk factors for RP-ILD. Cox regression analysis showed that RP-ILD (HR=3.194, 95%CI:1.025-9.954, P=0.045), older than 53 years (HR=3.450, 95%CI: 1.388-8.577, P=0.008), ferritin level more than 1 330.5 ng/ml (HR=3.032, 95%CI 1.208-7.610, P=0.018) and C-reactive protein (CRP) above 16.95 mg/L (HR=2.794, 95%CI:1.102-7.084, P=0.030) were independent predictors of mortality. Conclusions: The clinical manifestations of patients with anti-MDA5+DM-ILD presenting to the respiratory department were heterogeneous, with most being amyopathic dermatomyositis, and both the incidence of RP-ILD and the risk of death were high. Even in the absence of associated rash, joint, or muscle manifestations, anti-MDA5 antibody screening should be considered in patients with rapidly progressive ILD who were negative on baseline autoantibody screening but positive for anti-RO52kDa antibody.
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Cao M, Xu Q, Zhang QR, Su XQ, Ye YL, Zhu WS, Yin XD, Zhang ZQ. [Exploration of the effect of blood lipids on the lesion distribution pattern in acute ischemic stroke based on MRI study with population standard spatial analysis]. ZHONGHUA YI XUE ZA ZHI 2023; 103:1739-1745. [PMID: 37305932 DOI: 10.3760/cma.j.cn112137-20230424-00663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Objective: To explore the effect of blood lipids on the lesion distribution pattern in patients with acute ischemic stroke by using MRI technology based on population standard spatial analysis. Methods: The MRI data of 1 202 patients with acute ischemic stroke in General Hospital of Eastern Theater Command from January 2015 to December 2020 and Nanjing First Hospital from January 2013 to December 2021 were retrospectively collected, including 871 males and 331 females, aged 26 to 94 (64±11) years. According to the condition of blood lipids, they were divided into the dyslipidemia group (n=683) and the normal blood lipids group (n=519). After the automatic segmentation of diffusion-weighted imaging (DWI) images by artificial intelligence, the infarct sites were registered to the standard space which was used to draw the frequency heat map. The chi-square test was used to compare the difference in lesion location between the two groups. Generalized linear model regression analysis was used to observe the correlation between each blood lipid index and lesion site, and inter-group comparison and correlation analysis were used to observe the relationship between each blood lipid index and lesion volume. Results: Compared with the normal blood lipid group, the lesions in the dyslipidemia group were more extensive, mostly distributed in the occipital temporal region of the right posterior cerebral artery and the frontal region of the left middle cerebral artery. The brain regions of higher triglyceride(TG) and higher low-density lipoprotein cholesterol(LDL-C) groups were concentrated in the posterior circulation. The brain regions in the higher total cholesterol(TC) and lower high-density lipoprotein cholesterol(HDL-C) groups were concentrated in the anterior circulation(all P<0.05). In the anterior circulation infarct volume, the higher TC group was significantly higher than the normal TC group[(27.58±5.34) vs (17.73±1.18)ml, P=0.029]. In the posterior circulation infarct volume, the higher LDL-C group and the TG group were significantly higher than the normal LDL-C and TG groups[(7.55±2.51) vs (3.55±0.31) ml; (5.76±1.19) vs (3.36±0.30) ml](both P<0.05). Correlation analysis showed that TC and LDL-C were non-linearly (U-shaped) correlated with anterior circulation infarct volume (both P<0.05). Conclusions: Different blood lipids have effects on the distribution pattern and volume of ischemic stroke infarcts. Different hyperlipidemia is related to the specific distribution site and the larger extent of infarction.
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Liu B, Liu L, Ran J, Xie N, Li J, Xiao H, Yang X, Tian C, Wu H, Lu J, Gao J, Hu X, Cao M, Shui Z, Hu ZY, Ouyang Q. A randomized trial of eribulin monotherapy versus eribulin plus anlotinib in patients with locally recurrent or metastatic breast cancer. ESMO Open 2023; 8:101563. [PMID: 37285718 DOI: 10.1016/j.esmoop.2023.101563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Eribulin mesylate is a novel, nontaxane, microtubule dynamics inhibitor. In this study, we assessed the efficacy and safety of eribulin versus eribulin plus the oral small-molecule tyrosine kinase inhibitor anlotinib in patients with locally recurrent or metastatic breast cancer. PATIENTS AND METHODS In this single-center, open-label, phase II clinical study (NCT05206656) conducted in a Chinese hospital, patients with human epidermal growth factor receptor 2 (HER2)-negative, locally recurrent or metastatic breast cancer previously treated with anthracycline- or taxane-based chemotherapy were randomized (1 : 1) to receive eribulin alone or in combination with anlotinib. The primary efficacy endpoint was investigator-assessed progression-free survival (PFS). RESULTS From June 2020 to April 2022, a total of 80 patients were randomly assigned to either eribulin monotherapy or eribulin plus anlotinib combination therapy, with 40 patients in each group. The data cut-off was 10 August 2022. The median PFS was 3.5 months [95% confidence interval (CI) 2.8-5.5 months] for eribulin and 5.1 months (95% CI 4.5-6.9 months) for eribulin plus anlotinib (hazard ratio = 0.56, 95% CI 0.32-0.98; P = 0.04). The objective response rates were 32.5% versus 52.5% (P = 0.07), respectively, and disease control rates were 67.5% versus 92.5% (P = 0.01), respectively. Patients <50 years of age, with an Eastern Cooperative Oncology Group performance status score of 0, visceral metastasis, number of treatment lines of four or more, hormone receptor negative (triple-negative), and HER2 low expression appeared to benefit more from combined treatment. The most common adverse events in both groups were leukopenia (n = 28, 70.0%, patients in the eribulin monotherapy group versus n = 35, 87.5%, patients in the combination therapy group), aspartate aminotransferase elevations (n = 28, 70.0%, versus n = 35, 87.5%), neutropenia (n = 25, 62.5%, versus n = 31, 77.5%), and alanine aminotransferase elevations (n = 25, 62.5%, versus n = 30, 75.0%). CONCLUSION Eribulin plus anlotinib can be considered an alternative treatment option for HER2-negative locally advanced or metastatic breast cancer.
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Alani OS, Cao M, Goodrich-Blair H, Heppert JK. Conjugation and transposon mutagenesis of Xenorhabdus griffiniae HGB2511, the bacterial symbiont of the nematode Steinernema hermaphroditum (India). MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000772. [PMID: 37179970 PMCID: PMC10170317 DOI: 10.17912/micropub.biology.000772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/05/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023]
Abstract
Symbiosis, the beneficial interactions between two organisms, is a ubiquitous feature of all life on Earth, including associations between animals and bacteria. However, the specific molecular and cellular mechanisms which underlie the diverse partnerships formed between animals and bacteria are still being explored. Entomopathogenic nematodes transport bacteria between insect hosts, together they kill the insect, and the bacteria consume the insect and serve as food source for the nematodes. These nematodes, including those in the Steinernema genus, are effective laboratory models for studying the molecular mechanisms of symbiosis because of the natural partnership they form with Xenorhabdus bacteria and their straightforward husbandry. Steinernema hermaphroditum nematodes and their Xenorhabdus griffiniae symbiotic bacteria are being developed as a genetic model pair for studying symbiosis. Our goal in this project was to begin to identify bacterial genes that may be important for symbiotic interactions with the nematode host. Towards this end, we adapted and optimized a protocol for delivery and insertion of a lacZ- promoter-probe transposon for use in the S. hermaphroditum symbiont, X. griffiniae HGB2511 (Cao et al., 2022). We assessed the frequencies at which we obtained exconjugants, metabolic auxotrophic mutants, and active promoter- lacZ fusions. Our data indicate that the Tn 10 transposon inserted relatively randomly based on the finding that 4.7% of the mutants exhibited an auxotrophic phenotype. Promoter-fusions with the transposon-encoded lacZ , which resulted in expression of β-galactosidase activity, occurred in 47% of the strains. To our knowledge, this is the first mutagenesis protocol generated for this bacterial species, and will facilitate the implementation of large scale screens for symbiosis and other phenotypes of interest in X. griffiniae .
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Jin S, Shang S, Jiang S, Cao M, Wang Y. Sensitivity Analysis of RV Reducer Rotation Error Based on Deep Gaussian Processes. SENSORS (BASEL, SWITZERLAND) 2023; 23:3579. [PMID: 37050638 PMCID: PMC10098658 DOI: 10.3390/s23073579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
The rotation error is the most important quality characteristic index of a rotate vector (RV) reducer, and it is difficult to accurately optimize the design of a RV reducer, such as the Taguchi type, due to the many factors affecting the rotation error and the serious coupling effect among the factors. This paper analyzes the RV reducer rotation error and each factor based on the deep Gaussian processes (DeepGP) model and Sobol sensitivity analysis(SA) method. Firstly, using the optimal Latin hypercube sampling (OLHS) approach and the DeepGP model, a high-precision regression prediction model of the rotation error and each affecting factor was created. On the basis of the prediction model, the Sobol method was used to conduct a global SA of the factors influencing the rotation error and to compare the coupling relationship between the factors. The results show that the OLHS method and the DeepGP model are suitable for predicting the rotation error in this paper, and the accuracy of the prediction model constructed based on both of them is as high as 95%. The rotation error mainly depends on the influencing factors in the second stage cycloidal pinwheel drive part. The primary involute planetary part and planetary output carrier's rotation error factors have little effect. The coupling effects between the matching clearance between the pin gear and needle gear hole (δJ) and the circular position error of the needle gear hole (δt) is noticeably stronger.
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Jin S, Cao M, Qian Q, Zhang G, Wang Y. Study on an Assembly Prediction Method of RV Reducer Based on IGWO Algorithm and SVR Model. SENSORS (BASEL, SWITZERLAND) 2022; 23:366. [PMID: 36616963 PMCID: PMC9824458 DOI: 10.3390/s23010366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
This paper proposes a new method for predicting rotation error based on improved grey wolf-optimized support vector regression (IGWO-SVR), because the existing rotation error research methods cannot meet the production beat and product quality requirements of enterprises, because of the disadvantages of its being time-consuming and having poor calculation accuracy. First, the grey wolf algorithm is improved based on the optimal Latin hypercube sampling initialization, nonlinear convergence factor, and dynamic weights to improve its accuracy in optimizing the parameters of the support vector regression (SVR) model. Then, the IGWO-SVR prediction model between the manufacturing error of critical parts and the rotation error is established with the RV-40E reducer as a case. The results show that the improved grey wolf algorithm shows better parameter optimization performance, and the IGWO-SVR method shows better prediction performance than the existing back propagation (BP) neural network and BP neural network optimized by the sparrow search algorithm rotation error prediction methods, as well as the SVR models optimized by particle swarm algorithm and grey wolf algorithm. The mean squared error of IGWO-SVR model is 0.026, the running time is 7.843 s, and the maximum relative error is 13.5%, which can meet the requirements of production beat and product quality. Therefore, the IGWO-SVR method can be well applied to the rotate vector (RV) reducer parts-matching model to improve product quality and reduce rework rate and cost.
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Nikitas J, Gao Y, Smith L, Ma T, Sachdeva A, Yoon S, Steinberg M, Ballas L, Cao M, Kishan A. Dosimetric Implications of Margin-Reduced MRI-Guided Stereotactic Body Radiotherapy to the Prostate Bed Following Radical Prostatectomy: Post-Hoc Analysis of a Phase II Study. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Naumann L, Kaprealian T, Cao M, Savjani R, Iwamoto K, Sandstrom R, Strause L, Steinberg M, Low D. Dosimetric Evaluation of Physical Radiation Delivery Limits of a Weak Magnetic Field Generator on GBM Dose Distributions. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.2151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sang Y, McNitt-Gray M, Yang Y, Cao M, Low D, Ruan D. Inference-Time Adaptation for Improved Transfer Ability and Generalization in Deformable Image Registration Deep Learning. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kishan A, Ma T, Lamb J, Casado M, Wilhame H, Low D, Yang Y, Gao Y, Neylon J, Basehart V, Cao M, Steinberg M. Magnetic Resonance Imaging-Guided vs. Computed Tomography-Guided Stereotactic Body Radiotherapy for Prostate Cancer (MIRAGE): Primary Endpoint Analysis of a Phase III Randomized Trial. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Sonni I, Pra AD, O'Connell D, Benz M, Nguyen K, Yoon S, Deng J, Smith C, Nickols N, Cao M, Kishan A, Calais J. PSMA PET/CT–Based Atlas for Prostatic Bed Recurrence of Prostate Cancer after Radical Prostatectomy: Clinical Implications for Salvage Radiation Therapy. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Cao M, Ong MTY, Yung PSH, Tuan RS, Jiang Y. Role of synovial lymphatic function in osteoarthritis. Osteoarthritis Cartilage 2022; 30:1186-1197. [PMID: 35487439 DOI: 10.1016/j.joca.2022.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/01/2022] [Accepted: 04/20/2022] [Indexed: 02/02/2023]
Abstract
BACKGROUND Osteoarthritis (OA) affects the entire joint, initially with a low degree of inflammation. Synovitis is correlated with the severity of OA clinical symptoms and cartilage degradation. The synovial lymphatic system (SLS) plays a prominent role in clearing macromolecules within the joint, including the pro-inflammatory cytokines in arthritic status. Scattered evidence shows that impaired SLS drainage function leads to the accumulation of inflammatory factors in the joint and aggravates the progression of OA, and the role of SLS function in OA is less studied. DESIGN This review summarizes the current understanding of synovial lymphatic function in OA progression and potential regulatory pathways and aims to provide a framework of knowledge for the development of OA treatments targeting lymphatic structure and functions. RESULTS SLS locates in the subintima layer of the synovium and consists of lymphatic capillaries and lymphatic collecting vessels. Vascular endothelial growth factor C (VEGF-C) is the most critical regulating factor of lymphatic endothelial cells (LECs) and SLS. Nitric oxide production-induced impairment of lymphatic muscle cells (LMCs) and contractile function may attribute to drainage dysfunction. Preclinical evidence suggests that promoting lymphatic drainage may help restore intra-articular homeostasis to attenuate the progression of OA. CONCLUSION SLS is actively involved in the homeostatic maintenance of the joint. Understanding the drainage function of the SLS at different stages of OA development is essential for further design of therapies targeting the function of these vessels.
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Shi M, Chang Y, Cao M, Zhang J, Zhang L, Xie H, Miao Z. Effects of dietary yam polysaccharide on growth performance and
intestinal microflora in growing Huoyan geese. JOURNAL OF ANIMAL AND FEED SCIENCES 2022. [DOI: 10.22358/jafs/151561/2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Lu M, Zhao HJ, Li WX, Zhang H, Cao M. [Orthodontic and surgical treatment of a patient with skeletal class Ⅲ subdivision malocclusion and mandibular asymmetry accompanied by an maxillary horizontal impacted canine]. ZHONGHUA KOU QIANG YI XUE ZA ZHI = ZHONGHUA KOUQIANG YIXUE ZAZHI = CHINESE JOURNAL OF STOMATOLOGY 2022; 57:745-748. [PMID: 35790515 DOI: 10.3760/cma.j.cn112144-20211221-00560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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