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Liu X, Marin T, Vafay Eslahi S, Tiss A, Chemli Y, Johson KA, El Fakhri G, Ouyang J. Subject-aware PET Denoising with Contrastive Adversarial Domain Generalization. IEEE NUCLEAR SCIENCE SYMPOSIUM CONFERENCE RECORD. NUCLEAR SCIENCE SYMPOSIUM 2024; 2024:10.1109/nss/mic/rtsd57108.2024.10656150. [PMID: 39445307 PMCID: PMC11497478 DOI: 10.1109/nss/mic/rtsd57108.2024.10656150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Recent advances in deep learning (DL) have greatly improved the performance of positron emission tomography (PET) denoising performance. However, DL model performance can vary a lot across subjects, due to the large variability of the count levels and spatial distributions. A generalizable DL model that mitigates the subject-wise variations is highly expected toward a reliable and trustworthy system for clinical application. In this work, we propose a contrastive adversarial learning framework for subject-wise domain generalization (DG). Specifically, we configure a contrastive discriminator in addition to the UNet-based denoising module to check the subject-related information in the bottleneck feature, while the denoising module is adversarially trained to enforce the extraction of subject-invariant features. The sampled low-count realizations from the list-mode data are used as anchor-positive pairs to be close to each other, while the other subjects are used as negative samples to be distributed far away. We evaluated on 97 18F-MK6240 tau PET studies, each having 20 noise realizations with 25% fractions of events. Training, validation, and testing were implemented using 1400, 120, and 420 pairs of 3D image volumes in a subject-independent manner. The proposed contrastive adversarial DG demonstrated superior denoising performance than conventional UNet without subject-wise DG and cross-entropy-based adversarial DG.
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Liu X, Woo J, Ma C, Ouyang J, El Fakhri G. Point-supervised Brain Tumor Segmentation with Box-prompted Medical Segment Anything Model. IEEE NUCLEAR SCIENCE SYMPOSIUM CONFERENCE RECORD. NUCLEAR SCIENCE SYMPOSIUM 2024; 2024:10.1109/nss/mic/rtsd57108.2024.10656071. [PMID: 39445308 PMCID: PMC11497479 DOI: 10.1109/nss/mic/rtsd57108.2024.10656071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Delineating lesions and anatomical structure is important for image-guided interventions. Point-supervised medical image segmentation (PSS) has great potential to alleviate costly expert delineation labeling. However, due to the lack of precise size and boundary guidance, the effectiveness of PSS often falls short of expectations. Although recent vision foundational models, such as the medical segment anything model (MedSAM), have made significant advancements in bounding-box-prompted segmentation, it is not straightforward to utilize point annotation, and is prone to semantic ambiguity. In this preliminary study, we introduce an iterative framework to facilitate semantic-aware point-supervised MedSAM. Specifically, the semantic box-prompt generator (SBPG) module has the capacity to convert the point input into potential pseudo bounding box suggestions, which are explicitly refined by the prototype-based semantic similarity. This is then succeeded by a prompt-guided spatial refinement (PGSR) module that harnesses the exceptional generalizability of MedSAM to infer the segmentation mask, which also updates the box proposal seed in SBPG. Performance can be progressively improved with adequate iterations. We conducted an evaluation on BraTS2018 for the segmentation of whole brain tumors and demonstrated its superior performance compared to traditional PSS methods and on par with box-supervised methods.
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Huang Y, Liu X, Miyazaki T, Omachi S, El Fakhri G, Ouyang J. Ablation Study of Diffusion Model with Transformer Backbone for Low-count PET Denoising. IEEE NUCLEAR SCIENCE SYMPOSIUM CONFERENCE RECORD. NUCLEAR SCIENCE SYMPOSIUM 2024; 2024:10.1109/nss/mic/rtsd57108.2024.10655179. [PMID: 39445309 PMCID: PMC11497477 DOI: 10.1109/nss/mic/rtsd57108.2024.10655179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Diffusion models (DM) built from a hierarchy of denoising autoencoders have achieved remarkable progress in image generation, and are increasingly influential in the field of image restoration (IR) tasks. In the meantime, its backbone of autoencoders also evolved from UNet to vision transformer, e.g. Restormer. Therefore, it is important to disentangle the contribution of backbone networks and the additional generative learning scheme. Notably, DM shows varied performance across IR tasks, and the performance of recent advanced transformer-based DM on PET denoising is under-explored. In this study, we further raise an intuitive question, "{if we have a sufficiently powerful backbone, whether DM can be a general add-on generative learning scheme to further boost PET denoising}". Specifically, we investigate one of the best-in-class IR models, i.e., DiffIR, which is a latent DM based on the Restormer backbone. We provide a qualitative and quantitative comparison with UNet, SR3 (UNet+pixel DM), and Restormer, on the 25% low dose 18F-FDG whole-body PET denoising task, aiming to identify the best practices. We trained and tested on 93 and 12 subjects, and each subject has 644 slices. It appears that Restormer outperforms UNet in terms of PSNR and MSE. However, additional latent DM over Restormer does not contribute to better MSE, SSIM, or PSNR in our task, which is even inferior to the conventional UNet. In addition, SR3 with pixel space DM is not stable to synthesize satisfactory results. The results are consistent with the natural image super-resolution tasks, which also suffer from limited spatial information. A possible reason would be the denoising iteration at latent feature space cannot well support detailed structure and texture restoration. This issue is more crucial in the IR tasks taking inputs with limited details, e.g., SR and PET denoising.
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Xu PP, Zhou T, Xu YY, Peng MX, Du Y, Xie T, Yang YG, Ouyang J, Chen B. [Ruxolitinib combined with venetoclax and azacitidine in the treatment of refractory T-ALL patients with JAK1, JAK3, and STAT5B gene mutations: a case report and literature review]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2024; 45:872-875. [PMID: 39414615 PMCID: PMC11518909 DOI: 10.3760/cma.j.cn121090-20240412-00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Indexed: 10/18/2024]
Abstract
Refractory acute T-lymphoblastic leukemia (T-ALL), which is characterized by a low sensitivity to conventional induction therapy and poor prognosis, poses significant challenges during treatment. This study reported a case of refractory T-ALL patient with mutations in the JAK1, JAK3, and STAT5B genes from Nanjing University's Gulou Hospital. Following an unsuccessful course of standard VDLP regimen chemotherapy, the treatment was modified to include ruxolitinib in combination with venetoclax and azacitidine. Subsequent to this therapy, the patient achieved bone marrow minimal residual disease (MRD) negativity. Notably, pleural effusion and mediastinal mass significantly improved the post-chest cavity infusion of dexamethasone combined with etoposide at the same stage. The patient also underwent allogeneic hematopoietic stem cell transplantation upon achieving bone marrow remission and was followed up until January 2024. Ruxolitinib combined with venetoclax and azacytidine has shown promising efficacy and safety in treating refractory T-ALL harboring the JAK1, JAK3, and STAT5B mutations, providing a novel therapeutic approach for such patients.
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Ouyang J, Gao Y, Yang Y. PCP-GC-LM: single-sequence-based protein contact prediction using dual graph convolutional neural network and convolutional neural network. BMC Bioinformatics 2024; 25:287. [PMID: 39223474 PMCID: PMC11370006 DOI: 10.1186/s12859-024-05914-3] [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: 05/04/2023] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Recently, the process of evolution information and the deep learning network has promoted the improvement of protein contact prediction methods. Nevertheless, still remain some bottleneck: (1) One of the bottlenecks is the prediction of orphans and other fewer evolution information proteins. (2) The other bottleneck is the method of predicting single-sequence-based proteins mainly focuses on selecting protein sequence features and tuning the neural network architecture, However, while the deeper neural networks improve prediction accuracy, there is still the problem of increasing the computational burden. Compared with other neural networks in the field of protein prediction, the graph neural network has the following advantages: due to the advantage of revealing the topology structure via graph neural network and being able to take advantage of the hierarchical structure and local connectivity of graph neural networks has certain advantages in capturing the features of different levels of abstraction in protein molecules. When using protein sequence and structure information for joint training, the dependencies between the two kinds of information can be better captured. And it can process protein molecular structures of different lengths and shapes, while traditional neural networks need to convert proteins into fixed-size vectors or matrices for processing. RESULTS Here, we propose a single-sequence-based protein contact map predictor PCP-GC-LM, with dual-level graph neural networks and convolution networks. Our method performs better with other single-sequence-based predictors in different independent tests. In addition, to verify the validity of our method against complex protein structures, we will also compare it with other methods in two homodimers protein test sets (DeepHomo test dataset and CASP-CAPRI target dataset). Furthermore, we also perform ablation experiments to demonstrate the necessity of a dual graph network. In all, our framework presents new modules to accurately predict inter-chain contact maps in protein and it's also useful to analyze interactions in other types of protein complexes.
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Djebra Y, Liu X, Marin T, Tiss A, Dhaynaut M, Guehl N, Johnson K, El Fakhri G, Ma C, Ouyang J. DIFFUSION MODEL-BASED POSTERIOR DISTRIBUTION PREDICTION FOR KINETIC PARAMETER ESTIMATION IN DYNAMIC PET. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2024; 2024:10.1109/isbi56570.2024.10635805. [PMID: 39530051 PMCID: PMC11554386 DOI: 10.1109/isbi56570.2024.10635805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
Positron Emission Tomography (PET) is a valuable imaging method for studying molecular-level processes in the body, such as hyperphosphorylated tau (p-tau) protein aggregates, a hallmark of several neurodegenerative diseases including Alzheimer's disease. P-tau density and cerebral perfusion can be quantified from PET data using tracer kinetic modeling techniques. However, noise in PET images leads to uncertainty in the estimated kinetic parameters. This can be quantified in a Bayesian framework by the posterior distribution of kinetic parameters given PET measurements. Markov Chain Monte Carlo (MCMC) techniques can be employed to estimate the posterior distribution, although with significant computational needs. In this paper, we propose to leverage deep learning inference efficiency to infer the posterior distribution. A novel approach using denoising diffusion probabilistic model (DDPM) is introduced. The performance of the proposed method was evaluated on a [18F]MK6240 study and compared to an MCMC method. Our approach offered significant reduction in computation time (over 30 times faster than MCMC) and consistently predicted accurate (< 0.8 % mean error) and precise (< 5.77 % standard deviation error) posterior distributions.
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Guo QJ, Ouyang J, Rao JQ, Zhang YZ, Yu LL, Xu WY, Long JH, Gao XH, Wu XY, Gu Y. [Construction and preliminary validation of a risk prediction model for the recurrence of diabetic foot ulcer in diabetic patients]. ZHONGHUA SHAO SHANG YU CHUANG MIAN XIU FU ZA ZHI 2023; 39:1149-1157. [PMID: 38129301 DOI: 10.3760/cma.j.cn501225-20231101-00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Objective: To develop a risk prediction model for the recurrence of diabetic foot ulcer (DFU) in diabetic patients and primarily validate its predictive value. Methods: Meta-analysis combined with retrospective cohort study was conducted. The Chinese and English papers on risk factors related to DFU recurrence publicly published in China Biology Medicine disc, China National Knowledge Infrastructure, Wanfang Database, VIP Database, and PubMed, Embase, Cochrane Library, and Web of Science, and the search time was from the establishment date of each database until March 31st, 2022. The papers were screened and evaluated, the data were extracted, a meta-analysis was performed using RevMan 5.4.1 statistical software to screen risk factors for DFU recurrence, and Egger's linear regression was used to assess the publication bias of the study results. Risk factors for DFU recurrence mentioned in ≥3 studies and with statistically significant differences in the meta-analysis were selected as the independent variables to develop a logistic regression model for risk prediction of DFU recurrence. The medical records of 101 patients with DFU who met the inclusion criteria and were admitted to Affiliated Hospital of Guizhou Medical University from January 2019 to June 2022 were collected. There were 69 males and 32 females, aged (63±14) years. The receiver operating characteristic (ROC) curve of the predictive performance of the above constructed predictive model for DFU recurrence was drawn, and the area under the ROC curve, maximum Youden index, and sensitivity and specificity at the point were calculated. Dataset including data of 8 risk factors for DFU recurrence and the DFU recurrence rates of 10 000 cases was simulated using RStudio software and a scatter plot was drawn to determine two probabilities for risk division of DFU recurrence. Using the β coefficients corresponding to 8 DFU recurrence risk factors ×10 and taking the integer as the score of coefficient weight of each risk factor, the total score was obtained by summing up, and the cutoff scores for risk level division were calculated based on the total score × two probabilities for risk division of DFU recurrence. Results: Finally, 20 papers were included, including 3 case-control studies and 17 cohort studies, with a total of 4 238 cases and DFU recurrence rate of 22.7% to 71.2%. Meta-analysis showed that glycosylated hemoglobin >7.5% and with plantar ulcer, diabetic peripheral neuropathy, diabetic peripheral vascular disease, smoking, osteomyelitis, history of amputation/toe amputation, and multidrug-resistant bacterial infection were risk factors for the recurrence of DFU (with odds ratios of 3.27, 3.66, 4.05, 3.94, 1.98, 7.17, 11.96, 3.61, 95% confidence intervals of 2.79-3.84, 2.06-6.50, 2.50-6.58, 2.65-5.84, 1.65-2.38, 2.29-22.47, 4.60-31.14, 3.13-4.17, respectively, P<0.05). There were no statistically significant differences in publication biases of diabetic peripheral neuropathy, diabetic peripheral vascular disease, glycosylated hemoglobin >7.5%, plantar ulcer, smoking, multidrug-resistant bacterial infection, or osteomyelitis (P>0.05), but there was a statistically significant difference in the publication bias of amputation/toe amputation (t=-30.39, P<0.05). The area under the ROC curve of the predictive model was 0.81 (with 95% confidence interval of 0.71-0.91) and the maximum Youden index was 0.59, at which the sensitivity was 72% and the specificity was 86%. Ultimately, 29.0% and 44.8% were identified respectively as the cutoff for dividing the probability of low risk and medium risk, and medium risk and high risk for DFU recurrence, while the corresponding total scores of low, medium, and high risks of DFU recurrence were <37, 37-57, and 58-118, respectively. Conclusions: Eight risk factors for DFU recurrence are screened through meta-analysis and the risk prediction model for DFU recurrence is developed, which has moderate predictive accuracy and can provide guidance for healthcare workers to take interventions for patient with DFU recurrence risk.
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Chen KT, Tesfay R, Koran MEI, Ouyang J, Shams S, Young CB, Davidzon G, Liang T, Khalighi M, Mormino E, Zaharchuk G. Generative Adversarial Network-Enhanced Ultra-Low-Dose [ 18F]-PI-2620 τ PET/MRI in Aging and Neurodegenerative Populations. AJNR Am J Neuroradiol 2023; 44:1012-1019. [PMID: 37591771 PMCID: PMC10494955 DOI: 10.3174/ajnr.a7961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 07/11/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND AND PURPOSE With the utility of hybrid τ PET/MR imaging in the screening, diagnosis, and follow-up of individuals with neurodegenerative diseases, we investigated whether deep learning techniques can be used in enhancing ultra-low-dose [18F]-PI-2620 τ PET/MR images to produce diagnostic-quality images. MATERIALS AND METHODS Forty-four healthy aging participants and patients with neurodegenerative diseases were recruited for this study, and [18F]-PI-2620 τ PET/MR data were simultaneously acquired. A generative adversarial network was trained to enhance ultra-low-dose τ images, which were reconstructed from a random sampling of 1/20 (approximately 5% of original count level) of the original full-dose data. MR images were also used as additional input channels. Region-based analyses as well as a reader study were conducted to assess the image quality of the enhanced images compared with their full-dose counterparts. RESULTS The enhanced ultra-low-dose τ images showed apparent noise reduction compared with the ultra-low-dose images. The regional standard uptake value ratios showed that while, in general, there is an underestimation for both image types, especially in regions with higher uptake, when focusing on the healthy-but-amyloid-positive population (with relatively lower τ uptake), this bias was reduced in the enhanced ultra-low-dose images. The radiotracer uptake patterns in the enhanced images were read accurately compared with their full-dose counterparts. CONCLUSIONS The clinical readings of deep learning-enhanced ultra-low-dose τ PET images were consistent with those performed with full-dose imaging, suggesting the possibility of reducing the dose and enabling more frequent examinations for dementia monitoring.
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Guo QJ, Gu Y, Ouyang J, Yu LL, Zhang YZ, Rao JQ, Luo SS, Xu WY. [Summary of the best evidence on exercise for the prevention and treatment of diabetic foot]. ZHONGHUA SHAO SHANG YU CHUANG MIAN XIU FU ZA ZHI 2023; 39:671-678. [PMID: 37805697 DOI: 10.3760/cma.j.cn501225-20220822-00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Abstract
Objective: To summarize the best evidence on exercise for the prevention and treatment of diabetic foot. Methods: A bibliometric approach was used. Systematic searches were carried out to retrieve all the publicly published evidences till July 2022 on exercise for the prevention and treatment of diabetic foot, including guidelines, evidence summary, recommended practices, expert consensus, systematic review, and original research, from foreign language databases including BMJ Best Practice, UpToDate, Joanna Briggs Institute Evidence-Based Practice Database, Cochrane Library, Embase, PubMed, Guideline International Network, National Guideline Clearinghouse, Chinese databases including China National Knowledge Infrastructure, Wanfang Database, VIP Database, China Biology Medicine disc, China Clinical Guidelines Library, and the official websites of relevant academic organizations including National Institute for Health and Care Excellence of the United Kingdom, Registered Nurses' Association of Ontario of Canada, the International Working Group on the Diabetic Foot, International Diabetes Federation, American College of Sports Medicine, American Diabetes Association, and Chinese Diabetes Society. The literature was screened and evaluated for the quality, from which the evidences were extracted and evaluated to summarize the best evidences. Results: Nine guidelines, three expert consensuses, one evidence summary (with two systematic reviews being traced), two systematic reviews, 6 randomized controlled trials were retrieved and included, with good quality of literature. Totally 33 pieces of best evidences on exercise for the prevention and treatment of diabetic foot were summarized from the aspects of appropriate exercise prevention of diabetic foot, exercise therapy of diabetic foot, precautions for exercise, health education, and establishment of a multidisciplinary limb salvage team. Conclusions: Totally 33 pieces of best evidences on exercise for the prevention and treatment of diabetic foot were summarized from 5 aspects, providing decision-making basis for clinical guidance on exercise practice for patients with diabetic foot.
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Lin L, Tao JP, Li M, Peng J, Zhou C, Ouyang J, Si YY. Mechanism of ALDH2 improves the neuronal damage caused by hypoxia/reoxygenation. EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2022; 26:2712-2720. [PMID: 35503616 DOI: 10.26355/eurrev_202204_28601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To investigate the protective effect and mechanism of ALDH2 on PC12 cells and brain nerve tissue injury under hypoxia. MATERIALS AND METHODS The hypoxia model of PC12 cells with low ALDH2 expression was established and screened. The eukaryotic expression vector of wild type pEGFP-N1-ALDH2 and blank plasmid pEGFP-N1 were constructed and transfected into PC12 hypoxia cells respectively. After reoxygenation culture, the morphology, quantity, ALDH2 expression level and apoptosis rate of the two groups were observed, and the role of ALDH2 in cell hypoxia injury was analyzed. Eighty SD rats were randomly divided into model group (ischemia-reperfusion injury group), Alda-1 group (intraperitoneal injection of alda-1 12 hours before and after modeling), DMSO group (intraperitoneal injection of dimethyl sulfoxide) and sham operation group, with 20 rats in each group. The neurobehavioral score, apoptosis rate of nerve cells, the content and activity of ALDH2 in active cerebral cortex and hippocampal CA1 area were compared. RESULTS The number of PC12 cells in hypoxia group was lower than that in control group. The expression level of ALDH2 protein in PC12 cells after 4 hours of hypoxia was lower than that in normal culture group. The number of PC12 cells transfected with wild-type recombinant plasmid was significantly more than that of blank plasmid group. Compared with the hypoxia group, the pre apoptotic and post apoptotic cells in wild type transfection group decreased after hypoxia treatment. Compared with sham operation group, nerve injury and apoptosis were increased in group M and DMSO, while ALDH2 activity and expression did not change significantly. Compared with M group and DMSO group, the nerve injury and apoptosis in Alda-1 group were improved, ALDH2 activity was increased, and ALDH2 expression was not significantly changed in Alda-1 group. CONCLUSIONS Increasing the expression of ALDH2 or enhancing the activity of ALDH2 can improve the injury of neurons induced by hypoxia/reoxygenation.
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Liang G, He Y, Zhao L, Ouyang J, Geng W, Zhang X, Han X, Jiang Y, Ding H, Xiong Y, Dong J, Liu M, Shang H. CTNNBL1 restricts HIV-1 replication by suppressing viral DNA integration into the cell genome. Cell Rep 2022; 38:110533. [PMID: 35294870 DOI: 10.1016/j.celrep.2022.110533] [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: 04/11/2021] [Revised: 10/17/2021] [Accepted: 02/25/2022] [Indexed: 11/03/2022] Open
Abstract
Retroviral integration is mediated by a unique enzymatic process shared by all retroviruses and retrotransposons. During integration, double-stranded linear viral DNA is inserted into the host genome in a process catalyzed by viral-encoded integrase (IN). However, host cell defenses against HIV-1 integration are not clear. This study identifies β-catenin-like protein 1 (CTNNBL1) as a potent inhibitor of HIV-1 integration via association with viral-encoded integrase (IN) and its cofactor, lens epithelium-derived growth factor/p75. CTNNBL1 overexpression blocks HIV-1 integration and inhibits viral replication, whereas CTNNBL1 depletion significantly upregulates HIV-1 integration into the genome of various target cells. Further, CTNNBL1 expression is downregulated in CD4+ T cells by activation, and CTNNBL1 depletion also facilitates HIV-1 integration in resting CD4+ T cells. Thus, host cells may employ CTNNBL1 to inhibit HIV-1 integration into the genome. This finding suggests a strategy for the treatment of HIV infections.
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Ren W, Yu Y, He Z, Mao L, Chen Y, Ouyang W, Tan Y, Li C, Chen K, Ouyang J, Hu Q, Xie C, Yao H. 133P Magnetic resonance imaging radiomics predicts high and low recurrence risk and is associated with LncRNAs in early-stage invasive breast cancer. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Yu Y, Xie Y, Thamm T, Gong E, Ouyang J, Christensen S, Marks MP, Lansberg MG, Albers GW, Zaharchuk G. Tissue at Risk and Ischemic Core Estimation Using Deep Learning in Acute Stroke. AJNR Am J Neuroradiol 2021; 42:1030-1037. [PMID: 33766823 DOI: 10.3174/ajnr.a7081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/28/2020] [Indexed: 01/21/2023]
Abstract
BACKGROUND AND PURPOSE In acute stroke patients with large vessel occlusions, it would be helpful to be able to predict the difference in the size and location of the final infarct based on the outcome of reperfusion therapy. Our aim was to demonstrate the value of deep learning-based tissue at risk and ischemic core estimation. We trained deep learning models using a baseline MR image in 3 multicenter trials. MATERIALS AND METHODS Patients with acute ischemic stroke from 3 multicenter trials were identified and grouped into minimal (≤20%), partial (20%-80%), and major (≥80%) reperfusion status based on 4- to 24-hour follow-up MR imaging if available or into unknown status if not. Attention-gated convolutional neural networks were trained with admission imaging as input and the final infarct as ground truth. We explored 3 approaches: 1) separate: train 2 independent models with patients with minimal and major reperfusion; 2) pretraining: develop a single model using patients with partial and unknown reperfusion, then fine-tune it to create 2 separate models for minimal and major reperfusion; and 3) thresholding: use the current clinical method relying on apparent diffusion coefficient and time-to-maximum of the residue function maps. Models were evaluated using area under the curve, the Dice score coefficient, and lesion volume difference. RESULTS Two hundred thirty-seven patients were included (minimal, major, partial, and unknown reperfusion: n = 52, 80, 57, and 48, respectively). The pretraining approach achieved the highest median Dice score coefficient (tissue at risk = 0.60, interquartile range, 0.43-0.70; core = 0.57, interquartile range, 0.30-0.69). This was higher than the separate approach (tissue at risk = 0.55; interquartile range, 0.41-0.69; P = .01; core = 0.49; interquartile range, 0.35-0.66; P = .04) or thresholding (tissue at risk = 0.56; interquartile range, 0.42-0.65; P = .008; core = 0.46; interquartile range, 0.16-0.54; P < .001). CONCLUSIONS Deep learning models with fine-tuning lead to better performance for predicting tissue at risk and ischemic core, outperforming conventional thresholding methods.
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Bai CQ, Ouyang J, Su CH, Cui QQ, Liu D, Gao ZH, Chen SY, Zhao YY. [Association of hyperuricemia-induced renal damage with sirtuin 1 and endothelial nitric oxide synthase in rats]. ZHONGHUA YI XUE ZA ZHI 2021; 101:429-434. [PMID: 33611893 DOI: 10.3760/cma.j.cn112137-20200620-01900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the association of hyperuricemia-induced renal damage with sirtuin 1 (SIRT1) and endothelial nitric oxide synthase (eNOS) in rats. Methods: Using the random number table method, 32 Sprague-Dawley rats were randomly divided into 4 groups: control group, model A group (the model was generated using oxonic acid potassium salt alone), model B group (hyperuricemia model was generated using oxonic acid potassium salt combined with uric acid) and resveratrol group, with 8 rats in each group. The experiment lasted 12 weeks. Serum uric acid and cystatin C levels were monitored regularly. In week 12, serum creatinine and urea nitrogen levels were measured, and the kidneys were extracted. The expression of SIRT1 and eNOS in renal tissues was measured and determined by immunohistochemistry, quantitative reverse-transcription polymerase chain reaction (RT-qPCR) and western blotting. Immunohistochemistry of alpha-smooth muscle actin combined with Masson staining was employed to evaluate the degree of renal fibrosis, and pathological changes were observed based on hematoxylin and eosin staining. Results: In week 12, the uric acid levels in both the model A and model B groups were higher than those in the control group [(316±43) μmol/L, (297±40) μmol/L vs (118±44) μmol/L, both P<0.05]. The levels of cystatin C in the model A, model B, and resveratrol groups were all higher than those in the control group [(156±20) ng/ml, (143±29) ng/ml, (128±26) ng/ml vs (62±18) ng/ml, all P<0.05]. Creatinine levels were higher in the model A and model B groups than those in the control group [(68.5±10.3) μmol/L, (64.5±13.9) μmol/L vs (43.2±10.6) μmol/L, both P<0.05]. The levels of uric acid, cystatin C and creatinine in the resveratrol group were lower than those in the model A group (all P<0.05). Immunohistochemistry, RT-qPCR, and Western blotting for renal SIRT1 and eNOS showed that the expression in the model A and model B groups was inhibited, while the expression in the resveratrol group was not significantly inhibited, compared with that in the control group. Microscopically, obvious abnormalities were not found in the renal tissue of the control group. Renal inflammatory cell aggregation and edema occurred, and interstitial fibrosis was obvious in both the model A and model B groups, while these lesions in the resveratrol group were significantly improved. Conclusions: Hyperuricemia may cause renal injury by inhibiting the expression of SIRT1 and eNOS.
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Ren W, Yu Y, Tan Y, Chen Y, Liu J, He Z, Li A, Ma J, Lu N, Li C, Li X, Ou Q, Chen K, Hu Q, Ouyang J, Su F, Xie C, Song E, Yao H. 4MO Machine learning intratumoral and peritumoral magnetic resonance imaging radiomics for predicting disease-free survival in patients with early-stage breast cancer (RBC-01 Study). Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.10.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Yu Y, Tan Y, Hu Q, Ouyang J, Chen Y, Yang G, Li A, Lu N, He Z, Yang Y, Chen K, Ou Q, Zhang Y, Wu Z, Su F, Xie C, Song E, Yao H. 169MO Development and validation of a magnetic resonance imaging radiomics-based signature to predict axillary lymph node metastasis and disease-free survival in patients with breast cancer: A multicenter cohort study. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Gao B, Zhang Y, Ouyang J, Tai B, Cao X, Hu S. Surgical removal of a retained lumbar-drainage catheter. Neurochirurgie 2020; 66:408-409. [PMID: 32777232 DOI: 10.1016/j.neuchi.2020.06.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/28/2020] [Indexed: 11/25/2022]
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Liu M, Yuan X, Ouyang J, Chaisson J, Bergeron T, Cantrell D, Washington V, Zhang Y, Nigam S. Evaluation of four disease management programs: evidence from blue cross blue shield of Louisiana. J Med Econ 2020; 23:557-565. [PMID: 31990232 DOI: 10.1080/13696998.2020.1722677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Aims: Chronic diseases impose a substantial healthcare burden. This study sought to evaluate the clinical and economic impact of new disease management (DM) programs, targeting four major chronic disease groups: diabetes, coronary heart disease (CHD)/hypertension (HTN), asthma/chronic obstructive pulmonary disease (COPD), and congestive heart failure (CHF)/chronic kidney disease (CKD).Materials and methods: Between March 1, 2015, and February 28, 2018, members with Blue Cross Blue Shield of Louisiana insurance were contacted and enrolled in a DM program if they were aged 18 years through 64 years, eligible for a DM program, and had not been previously enrolled in a DM program. Active enrollees of a DM program ("IN" group) were compared to members who were not yet enrolled ("OUT" group). Average per member per month (PMPM) costs were aggregated annually to document any descriptive trends. Multivariable model estimates were used to compare PMPM costs for all IN subjects and all OUT subjects. Total medical savings were evaluated for the following time intervals: 1-12 months, 13-24 months, and 25-36 months.Results: For all four DM programs, average costs PMPM trended upward over time for the OUT cohort, while they remained relatively stable for the IN cohort. Some evidence also showed that DM programs improved clinical outcomes, such as hemoglobin A1c values. A difference in difference analysis showed PMPM savings for all four programs combined of $31.61, $50.45, and $53.72 after 1, 2, and 3 years, respectively. Multivariable modeling results showed total savings after 3 years of $14,460,174 for all DM programs combined.Limitations: Although multivariable models adjusted for several clinical, demographic, and economic characteristics; it is possible that some important confounders were missing due to lack of data.Conclusions: DM programs implemented to control diabetes, CHD/HTN, CHF/CKD, and asthma/COPD are cost-effective and show some evidence of improved clinical outcomes.
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Feng PN, Liang YR, Lin WB, Yao ZR, Chen DB, Chen PS, Ouyang J. Homocysteine induced oxidative stress in human umbilical vein endothelial cells via regulating methylation of SORBS1. EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2019; 22:6948-6958. [PMID: 30402861 DOI: 10.26355/eurrev_201810_16164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE The aim of the present study was to investigate the mechanism of homocysteine (Hcy) induced oxidative stress in the human umbilical vein endothelial cells (HUVECs). PATIENTS AND METHODS The HUVECs were isolated from umbilical vein vascular wall of 12 patients and treated with Hcy. The malondialdehyde (MDA) level was measured using the thiobarbituric acid (TBA) method. The expressions of superoxide dismutase 2 (SOD2), endothelial nitric oxide synthase (eNOS), and intercellular adhesion molecule 1 (ICAM-1) were detected by Western blot and RT-PCR. The genome-wide DNA methylation assay was performed using the Infinium Human Methylation 450 BeadChip. The specific DNA methylation was determined using bisulfite sequencing analysis. To evaluate the role of sorbin and SH3 domain-containing protein 1 (SORBS1), the HUVECs were transfected with small interfere RNA (siRNA) targeting SORBS1 (SORBS1-siRNA). RESULTS Hcy induced MDA level in HUVECs, and increased ICAM-1 expression both in protein and mRNA levels. The protein and mRNA levels of SOD2 and eNOS were inhibited by Hcy induction. However, the effects of Hcy on MDA level and expressions of SOD2, eNOS, and ICAM-1 were attenuated by folic acid (Fc) and vitamin B12 (B12) treatment. DNA total methylation level in Hcy treated cells was significantly decreased compared to the control group, while the DNA total methylation levels were increased after treatment with Fc and B12. The methylation level of SORBS1 in Hcy treatment group was higher than that of control group. And the methylation level of SORBS1 induced by Hcy was attenuated by Fc and B12 treatment. SORBS1-siRNA transfection induced the MDA levels and reduced the expressions of SOD2 in HUVECs. CONCLUSIONS We indicated that Hcy induced oxidative stress in HUVECs via regulating methylation of SORBS1. We also found that Fc and B12 treatment attenuated the oxidative stress and inflammation induced by Hcy in HUVECs. The findings indicated that Fc and B12 might be effective agents for the treatment of Hcy induced AS.
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Petibon Y, Sun T, Han PK, Ma C, Fakhri GE, Ouyang J. MR-based cardiac and respiratory motion correction of PET: application to static and dynamic cardiac 18F-FDG imaging. Phys Med Biol 2019; 64:195009. [PMID: 31394518 PMCID: PMC7007962 DOI: 10.1088/1361-6560/ab39c2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Motion of the myocardium deteriorates the quality and quantitative accuracy of cardiac PET images. We present a method for MR-based cardiac and respiratory motion correction of cardiac PET data and evaluate its impact on estimation of activity and kinetic parameters in human subjects. Three healthy subjects underwent simultaneous dynamic 18F-FDG PET and MRI on a hybrid PET/MR scanner. A cardiorespiratory motion field was determined for each subject using navigator, tagging and golden-angle radial MR acquisitions. Acquired coincidence events were binned into cardiac and respiratory phases using electrocardiogram and list mode-driven signals, respectively. Dynamic PET images were reconstructed with MR-based motion correction (MC) and without motion correction (NMC). Parametric images of 18F-FDG consumption rates (Ki) were estimated using Patlak's method for both MC and NMC images. MC alleviated motion artifacts in PET images, resulting in improved spatial resolution, improved recovery of activity in the myocardium wall and reduced spillover from the myocardium to the left ventricle cavity. Significantly higher myocardium contrast-to-noise ratio and lower apparent wall thickness were obtained in MC versus NMC images. Likewise, parametric images of Ki calculated with MC data had improved spatial resolution as compared to those obtained with NMC. Consistent with an increase in reconstructed activity concentration in the frames used during kinetic analyses, MC led to the estimation of higher Ki values almost everywhere in the myocardium, with up to 18% increase (mean across subjects) in the septum as compared to NMC. This study shows that MR-based motion correction of cardiac PET results in improved image quality that can benefit both static and dynamic studies.
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Liu M, Dong J, Ouyang J, Zhao L, Liang G, Shang H. Metalloprotease TRABD2A Restriction of HIV-1 Production in Monocyte-Derived Dendritic Cells. AIDS Res Hum Retroviruses 2019; 35:887-889. [PMID: 31282173 DOI: 10.1089/aid.2019.0140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Zhao L, Liu M, Ouyang J, Zhu Z, Geng W, Dong J, Xiong Y, Wang S, Zhang X, Qiao Y, Ding H, Sun H, Liang G, Shang H, Han X. The Per-1 Short Isoform Inhibits de novo HIV-1 Transcription in Resting CD4+ T-cells. Curr HIV Res 2019; 16:384-395. [PMID: 30774045 PMCID: PMC6446521 DOI: 10.2174/1570162x17666190218145048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/02/2019] [Accepted: 02/11/2019] [Indexed: 12/24/2022]
Abstract
Background: Understanding of the restriction of HIV-1 transcription in resting CD4+ T-cells is critical to find a cure for AIDS. Although many negative factors causing HIV-1 transcription blockage in resting CD4+ T-cells have been found, there are still unknown mechanisms to explore. Objective: To explore the mechanism for the suppression of de novo HIV-1 transcription in resting CD4+ T-cells. Methods: In this study, a short isoform of Per-1 expression plasmid was transfected into 293T cells with or without Tat's presence to identify Per-1 as a negative regulator for HIV-1 transcription. Silenc-ing of Per-1 was conducted in resting CD4+ T-cells or monocyte-derived macrophages (MDMs) to evaluate the antiviral activity of Per-1. Additionally, we analyzed the correlation between Per-1 expres-sion and viral loads in vivo, and silenced Per-1 by siRNA technology to investigate the potential anti-HIV-1 roles of Per-1 in vivo in untreated HIV-1-infected individuals. Results: We found that short isoform Per-1 can restrict HIV-1 replication and Tat ameliorates this in-hibitory effect. Silencing of Per-1 could upregulate HIV-1 transcription both in resting CD4+ T-cells and MDMs. Moreover, Per-1 expression is inversely correlated with viral loads in Rapid progressors (RPs) in vivo. Conclusion: These data together suggest that Per-1 is a novel negative regulator of HIV-1 transcrip-tion. This restrictive activity of Per-1 to HIV-1 replication may contribute to HIV-1 latency in resting CD4+ T-cells.
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Xu YY, Ouyang J, Zhou M, Xu Y, Li P, Shao XY, Chen B, Zhou RF. [A case report of Kasabach-Merritt syndrome treated with vindesine sulfate]. ZHONGHUA NEI KE ZA ZHI 2019; 58:143-145. [PMID: 30704202 DOI: 10.3760/cma.j.issn.0578-1426.2019.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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Zhu L, Jin F, Zhu YQ, Wang JC, Dong KF, Mo WQ, Song JL, Ouyang J. Giant Magneto-Impedance (GMI) Effect in Single-Layer Soft Magnetic Film Under Stress. JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY 2018; 18:8195-8200. [PMID: 30189937 DOI: 10.1166/jnn.2018.15799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The stress-induced magnetic anisotropy can significantly affect giant magneto-impedance (GMI) effect of the soft magnetic film. This paper is devoted to the GMI effect of the single layer soft magnetic film implied without and with a stress. By simulating a physical model with MATLAB and COMSOL software, the impedance expression of the single layer soft magnetic film and the relation between external magnetic field and magnetic permeability are deduced. We observed that, without a stress, the sensitive region increased firstly and then decreased with the increasing of the excitation current frequency from 1 MHz to 200 MHz. While the film was subjected to the stress in the direction of the current with one end stressed, the stress on the film was gradually reduced from stressed end to free end. Also, the impedance change rate of the film changed when the stress was added, which is similar to the effect of adding a bias magnetic field on the film. More importantly, the addition of stress σ can induce the bias of the GMI measurement range and improve its sensitivity near zero magnetic fields. This may provide a new way for designing a GMI sensor with higher sensitivity and adjustable measurement range.
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Zhou JR, Zhang X, Zhao YL, Yang JF, Zhang JP, Cao XY, Lu Y, Liu DY, Lyu FY, Ouyang J, Lu PH. [Clinical characteristics and prognosis of 34 cases of acute myeloid leukemia with FLT3 internal tandem duplication and MLL gene rearrangement]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2018; 39:751-756. [PMID: 30369187 PMCID: PMC7342257 DOI: 10.3760/cma.j.issn.0253-2727.2018.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Indexed: 11/05/2022]
Abstract
Objective: To analyze the clinical characteristics and prognosis of 34 cases of acute myeloid leukemia (AML) with FLT3 internal tandem duplication (FLT3-ITD) and MLL gene rearrangement. Methods: The clinical data of 34 AML patients with FLT3-ITD and MLL gene rearrangement was compared and analyzed for the therapeutic efficacy, prognostic factors when treated with chemotherapy, chemotherapy combined with targeted therapy or allogenic hematopoietic stem cell transplantation (allo-HSCT). Results: Of the thirty-four cases with median age 41 (4-71) years old, 63.6% presented with white blood cells (WBC) greater than 30×10(9)/L, 39.4% greater than 50 × 10(9)/L respectively on admission. M(5) (35.3%) made up the highest proportion. The cytogenetic abnormality reached 61.8%, of which the complex cytogenetic abnormality accounted for 11.8%. Eleven patients (32.35%) had both FLT3-ITD and MLL gene abnormalities. In addition to FLT3 and MLL abnormalities, 23 patients (67.6%) had one or more other gene abnormalities (multiple gene abnormalities). Of the 34 cases, 29.4% patients went into complete remission (CR) after two courses of chemotherapy. 20.6% (7 patients) went into CR after 3 or more courses of chemotherapy. The rate of early relapse in the CR group was 52.9%. Patients with WBC>50×10(9)/L or multiple gene abnormalities had a lower remission rate (7.7%, 5.4%) after two courses of chemotherapy. CR rate for the patients with more than three gene abnormalities was 0. The total 2-year overall survival (OS) in the 34 patients was 28.8% (95% CI 13.5%-46.0%) and the disease-free survival (DFS) was 27.1% (95% CI 12.5%-44.0%). Of the 18 patients treated with chemotherapy alone or chemotherapy combined with targeted therapy, 17 cases died within 2 years and 1 lost follow-up after giving up treatment. For the 16 patients received allo-HSCT, the 3-year OS was 43.4% (95% CI 13.7%-70.4%) and DFS 42.7% (95% CI 13.4%-69.7%). Conclusion: AML patients with FLT3-ITD and MLL gene rearrangement often presented with M(5), accompanied by hyperleukocytosis, cytogenetic or multiple gene abnormalities. Those patients were observed to have low response rate and high early relapse when treated with chemotherapy without allo-HSCT. Patients had multiple gene abnormalities may be an important poor prognostic factor. Allo-HSCT is an effective treatment which could significantly improve the prognosis and survival of AML patients with FLT3-ITD and MLL gene abnormalities.
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