1.EvoNB: A protein language model-based workflow for nanobody mutation prediction and optimization.
Danyang XIONG ; Yongfan MING ; Yuting LI ; Shuhan LI ; Kexin CHEN ; Jinfeng LIU ; Lili DUAN ; Honglin LI ; Min LI ; Xiao HE
Journal of Pharmaceutical Analysis 2025;15(6):101260-101260
The identification and optimization of mutations in nanobodies are crucial for enhancing their therapeutic potential in disease prevention and control. However, this process is often complex and time-consuming, which limit its widespread application in practice. In this study, we developed a workflow, named Evolutionary-Nanobody (EvoNB), to predict key mutation sites of nanobodies by combining protein language models (PLMs) and molecular dynamic (MD) simulations. By fine-tuning the ESM2 model on a large-scale nanobody dataset, the ability of EvoNB to capture specific sequence features of nanobodies was significantly enhanced. The fine-tuned EvoNB model demonstrated higher predictive accuracy in the conserved framework and highly variable complementarity-determining regions of nanobodies. Additionally, we selected four widely representative nanobody-antigen complexes to verify the predicted effects of mutations. MD simulations analyzed the energy changes caused by these mutations to predict their impact on binding affinity to the targets. The results showed that multiple mutations screened by EvoNB significantly enhanced the binding affinity between nanobody and its target, further validating the potential of this workflow for designing and optimizing nanobody mutations. Additionally, sequence-based predictions are generally less dependent on structural absence, allowing them to be more easily integrated with tools for structural predictions, such as AlphaFold 3. Through mutation prediction and systematic analysis of key sites, we can quickly predict the most promising variants for experimental validation without relying on traditional evolutionary or selection processes. The EvoNB workflow provides an effective tool for the rapid optimization of nanobodies and facilitates the application of PLMs in the biomedical field.
2.Preliminary application of participatory bilingual teaching in nuclear medicine teaching
Dong DUAN ; Xiaomei PAN ; Hua PANG ; Lili GUAN ; Jie WANG
Chinese Journal of Medical Education Research 2024;23(8):1046-1049
Objective:To investigate the feasibility and value of participatory bilingual teaching in nuclear medicine teaching.Methods:With the same chapter of Nuclear Medicine as the teaching contents, the traditional method of cramming bilingual teaching was used for the clinical medical students in the class of 2014 of the seven-year program and the five-year program, and the method of participatory bilingual teaching was used for the students in the class of 2015. The methods of periodical achievement test, questionnaire survey, and final examination were used to evaluate the teaching effect of the above two teaching modes.Results:In the periodical achievement test, the participatory bilingual teaching group had significantly higher scores than the cramming teaching group in terms of mean score, case analysis, and English questions [seven-year program: (82.13±10.72), (35.74±4.13), and (23.03±3.40) vs. (79.21±11.31), (33.86±5.23), and (22.12±2.75), P<0.05; five-year program: (78.66±12.75), (34.30±5.59), and (22.45±2.91) vs. (75.29±10.81), (32.70±6.04), and (21.36±3.09), P<0.05]. The questionnaire survey showed that participatory bilingual teaching had a better degree of satisfaction than cramming teaching. The participatory bilingual teaching group had a better score than the cramming teaching group in the final examination, but with no significant difference between the two groups. Conclusions:In the teaching of nuclear medicine, the participatory bilingual teaching mode can significantly improve teaching effect and achieve the teaching goal efficiently.
3.Real situational teaching in "simulated traditional chinese medicine nursing clinic" based on the cultivation of syndrome differentiation ability
Jiaojiao YANG ; Lili PENG ; Yilan LI ; Aoqi LI ; Yuan JIANG ; Lina DUAN ; Dongmei PENG ; Chaosheng LIU
Chinese Journal of Medical Education Research 2024;23(10):1425-1429
Objective:To investigate the effect of "simulated Chinese medicine nursing clinic" teaching on syndrome differentiation ability among nursing students and the teaching effect of this method.Methods:A total of 325 students were randomly divided into conventional teaching group with 163 students (receiving conventional nursing teaching) and real situational teaching group with 162 students (receiving "simulated Chinese medicine nursing nursing clinic" teaching at the same time). A self-made questionnaire for syndrome differentiation-based nursing ability, assessment scores of traditional Chinese medicine nursing theories and skills, and a teaching satisfaction questionnaire were used for evaluation.Results:After intervention, the real situational teaching group (the treatment group and the experience group) had significantly higher socres of syndrome differentiation-based nursing ability (mastery of four diagnostic methods, diagnosis of syndromes, analysis of syndromes, determination of nursing principles, and development of nursing regimens) than the conventional teaching group (the treatment group and the conventional teaching group: 8.97±1.00/8.47±1.20/8.33±1.06/8.30±1.26/7.89±1.13 and 7.96±1.14/7.29±1.36/7.14±1.18/7.39±1.30/7.26±1.18, P<0.05; the experience group and the conventional teaching group: 8.39±1.10/8.17±1.15/8.07±1.06/7.97±1.26/7.73±1.38 and 7.96±1.14/7.29±1.36/7.14±1.18/7.39±1.30/7.26±1.18, P<0.05). The real situational teaching group had a significantly higher overall degree of satisfaction with teaching than the conventional teaching group [160 (97.6%) and 150 (92.0%), P<0.05]. Conclusions:The "simulated Chinese medicine nursing clinic" teaching program effectively enhances the thinking of syndrome differientiation and related abilities for nursing, improves the learning effect of traditional Chinese medicine nursing theories and skills, and increases the learning interest in traditional Chinese medicine nursing among nursing students.
4.Analysis of factors influencing the treatment outcome of pulmonary tuberculosis patients in Xinjiang Production and Construction Corps
YANG Liugen ; MA Xiaoling ; FAN Ben ; ZHAO Yongnian ; DONG Gaimei ; DUAN Lili ; Delina Sairike ; LI Fanka
China Tropical Medicine 2024;24(4):456-
Abstract: Objective To investigate the treatment outcomes of patients with pulmonary tuberculosis (PTB) in Xinjiang Production and Construction Corps and to explore the risk factors affecting these outcomes, so as to provide a scientific basis for the prevention and treatment of pulmonary tuberculosis in the corps region. Methods TB patients registered in the Corps from 2016 to 2022 were selected, and the basic demographic and clinical data of the research objects were collected by retrospective method. Log-rank test was used for univariate analysis and the Cox multivariate regression model was used to analyze the influencing factors of treatment outcomes of patients with pulmonary tuberculosis. Results From 2016 to 2022, a total of 8 838 TB patients were registered in the TB Management Information System of Xinjiang Production and Construction Corps, of which 495 cases were untreated, 43 cases had changed diagnoses, 301 cases had no treatment outcomes, 6 cases were diagnosed as extrapulmonary tuberculosis, 11 cases were diagnosed as tracheobronchial tuberculosis, and finally 7 982 TB patients were included in the study. Of the 7 982 patients, 7 578 (94.94%) were treated successfully, while 404 (5.06%) had adverse outcomes (including 32 cases of failure, 13 cases of TB death, 173 cases of non-TB death, 12 cases lost to follow-up, 94 cases of adverse reactions, 10 cases transferred to multi-drug resistance treatment, and 70 other cases). Multivariate Cox regression analysis showed that the >30 to 60-year-old and >60-year-old age groups (OR=1.565, P=0.009; OR=2.960, P<0.001), belonging to ethnic minorities (OR=1.526, P<0.001), being a patients with diabetes mellitus (OR=1.696, P=0.002), current address being in other areas of the province or patients from other provinces (OR=1.419, P=0.004; OR=1.624, P=0.001), receiving retreatment (OR=1.910, P<0.001), and absence of primary care management (OR=1.351, P=0.003) were the risk factors for unsuccessful treatment outcomes in the corps' pulmonary tuberculosis patients. Conclusions The treatment success rate of pulmonary tuberculosis patients in the Corps region is relatively high, but there is still a need to strengthen the treatment and management of the elderly, ethnic minorities, diabetes patients, non-local floating population, retreatment patients and patients who did not receive primary management.
5.Surveillance of bacterial resistance in tertiary hospitals across China:results of CHINET Antimicrobial Resistance Surveillance Program in 2022
Yan GUO ; Fupin HU ; Demei ZHU ; Fu WANG ; Xiaofei JIANG ; Yingchun XU ; Xiaojiang ZHANG ; Fengbo ZHANG ; Ping JI ; Yi XIE ; Yuling XIAO ; Chuanqing WANG ; Pan FU ; Yuanhong XU ; Ying HUANG ; Ziyong SUN ; Zhongju CHEN ; Jingyong SUN ; Qing CHEN ; Yunzhuo CHU ; Sufei TIAN ; Zhidong HU ; Jin LI ; Yunsong YU ; Jie LIN ; Bin SHAN ; Yunmin XU ; Sufang GUO ; Yanyan WANG ; Lianhua WEI ; Keke LI ; Hong ZHANG ; Fen PAN ; Yunjian HU ; Xiaoman AI ; Chao ZHUO ; Danhong SU ; Dawen GUO ; Jinying ZHAO ; Hua YU ; Xiangning HUANG ; Wen'en LIU ; Yanming LI ; Yan JIN ; Chunhong SHAO ; Xuesong XU ; Wei LI ; Shanmei WANG ; Yafei CHU ; Lixia ZHANG ; Juan MA ; Shuping ZHOU ; Yan ZHOU ; Lei ZHU ; Jinhua MENG ; Fang DONG ; Zhiyong LÜ ; Fangfang HU ; Han SHEN ; Wanqing ZHOU ; Wei JIA ; Gang LI ; Jinsong WU ; Yuemei LU ; Jihong LI ; Qian SUN ; Jinju DUAN ; Jianbang KANG ; Xiaobo MA ; Yanqing ZHENG ; Ruyi GUO ; Yan ZHU ; Yunsheng CHEN ; Qing MENG ; Shifu WANG ; Xuefei HU ; Wenhui HUANG ; Juan LI ; Quangui SHI ; Juan YANG ; Abulimiti REZIWAGULI ; Lili HUANG ; Xuejun SHAO ; Xiaoyan REN ; Dong LI ; Qun ZHANG ; Xue CHEN ; Rihai LI ; Jieli XU ; Kaijie GAO ; Lu XU ; Lin LIN ; Zhuo ZHANG ; Jianlong LIU ; Min FU ; Yinghui GUO ; Wenchao ZHANG ; Zengguo WANG ; Kai JIA ; Yun XIA ; Shan SUN ; Huimin YANG ; Yan MIAO ; Mingming ZHOU ; Shihai ZHANG ; Hongjuan LIU ; Nan CHEN ; Chan LI ; Jilu SHEN ; Wanqi MEN ; Peng WANG ; Xiaowei ZHANG ; Yanyan LIU ; Yong AN
Chinese Journal of Infection and Chemotherapy 2024;24(3):277-286
Objective To monitor the susceptibility of clinical isolates to antimicrobial agents in tertiary hospitals in major regions of China in 2022.Methods Clinical isolates from 58 hospitals in China were tested for antimicrobial susceptibility using a unified protocol based on disc diffusion method or automated testing systems.Results were interpreted using the 2022 Clinical &Laboratory Standards Institute(CLSI)breakpoints.Results A total of 318 013 clinical isolates were collected from January 1,2022 to December 31,2022,of which 29.5%were gram-positive and 70.5%were gram-negative.The prevalence of methicillin-resistant strains in Staphylococcus aureus,Staphylococcus epidermidis and other coagulase-negative Staphylococcus species(excluding Staphylococcus pseudintermedius and Staphylococcus schleiferi)was 28.3%,76.7%and 77.9%,respectively.Overall,94.0%of MRSA strains were susceptible to trimethoprim-sulfamethoxazole and 90.8%of MRSE strains were susceptible to rifampicin.No vancomycin-resistant strains were found.Enterococcus faecalis showed significantly lower resistance rates to most antimicrobial agents tested than Enterococcus faecium.A few vancomycin-resistant strains were identified in both E.faecalis and E.faecium.The prevalence of penicillin-susceptible Streptococcus pneumoniae was 94.2%in the isolates from children and 95.7%in the isolates from adults.The resistance rate to carbapenems was lower than 13.1%in most Enterobacterales species except for Klebsiella,21.7%-23.1%of which were resistant to carbapenems.Most Enterobacterales isolates were highly susceptible to tigecycline,colistin and polymyxin B,with resistance rates ranging from 0.1%to 13.3%.The prevalence of meropenem-resistant strains decreased from 23.5%in 2019 to 18.0%in 2022 in Pseudomonas aeruginosa,and decreased from 79.0%in 2019 to 72.5%in 2022 in Acinetobacter baumannii.Conclusions The resistance of clinical isolates to the commonly used antimicrobial agents is still increasing in tertiary hospitals.However,the prevalence of important carbapenem-resistant organisms such as carbapenem-resistant K.pneumoniae,P.aeruginosa,and A.baumannii showed a downward trend in recent years.This finding suggests that the strategy of combining antimicrobial resistance surveillance with multidisciplinary concerted action works well in curbing the spread of resistant bacteria.
6.3D print-guided fenestration/branch stent treatment of abdominal aortic disease: a national multicenter retrospective study
Yuexue HAN ; Yi JIN ; Dongsheng FU ; Jianhang HU ; Jianfeng DUAN ; Lili SUN ; Mian WANG ; Hao YU ; Yiming SU ; Zhengdong HUA ; Zhidan CHEN ; Shikui GUO ; Zhaohui HUA ; Xiaoqiang LI ; Zhao LIU
Chinese Journal of General Surgery 2024;39(7):527-533
Objective:To study the application of 3D printing technology in multi-center fenestrated/branched endovascular repair (F/B-EVAR) for endovascular repair of abdominal aortic diseases.Methods:From Feb 2018 to Mar 2023, The clinical and followup data of 316 cases of abdominal aortic lesions undergoing repair with F/B-EVAR at 69 medical centers nationwide using 3D printing technology to guide physician-modified stent graft were retrospectively analyzed.Results:The mean follow-up time of the patients was 23 months (2-60 months), and 24 cases were lost to follow up, the follow-up rate was 92.4% (292/316), the mean postoperative hospitalization time was (8.2±4.9) days. A total of 944 main abdominal branch arteries were reconstructed. Intraoperative reconstruction of 11 branches failed, with a success rate of 98.8% (933/944). Within 30 days after surgery, 8 patients died (2.5%), and 6 patients died during follow-up, a total of 14 patients died (4.4%). There were 11 cases (3.5%) of spinal cord ischemia and no patient suffered from permanent paraplegia. There were 19 patients (6.0%) with postoperative renal function injury. Internal leakage was found in 26 patients, and the rate of internal leakage was 8.2%.Conclusion:3D printing technology can accurately locate the location of branch arteries, simplifing the surgical process, shortening the learning curve , and improving clinical efficacy.
7.Risk factors of postoperative complications after fenestrated /branched TEVAR for aortic arch lesions: a multicenter retrospective analysis
Yuexue HAN ; Zhao LIU ; Chen LIU ; Wendong LI ; Nan HU ; Jianhang HU ; Yu ZHOU ; Jianfeng DUAN ; Lili SUN ; Hao YU ; Yiming SU ; Zhengdong HUA ; Zhidan CHEN ; Zhaohui HUA ; Xiaoqiang LI
Chinese Journal of General Surgery 2024;39(9):667-672
Objective:To review the risk factors for early and medium-term complications of fenestration-branch endovascular thoracic aortic repair (F/B-TEVAR) in patients with complex aortic arch disease.Methods:The clinical and follow-up data of 202 patients undergoing F/B-TEVAR treatment from Feb 2019 to Sep 2023 in these centers were retrospectively analyzed .Results:There were 46 cases suffering from postoperative complications (22.8%). The risk factors with statistical significance included aortic atherosclerotic plaque [ OR=2.843; 95% CI (1.4-5.6); P<0.01], aortic intramural thrombosis [ OR=2.358; 95% CI (1.2-4.6), P=0.011], the aortic dilatation [ OR=4.219; 95% CI (1.6-11.3), P<0.01], the history of stroke [ OR=2.088; 95% CI (1.1-4.1), P=0.032], smoking history [ OR=2.680; 95% CI: (1.3-5.5); P<0.01], duration of surgery [ OR=1.9; 95% CI: (1.2-2.9); P=0.042].While the application of 3D printing assistive technology [ OR=0.392; 95% CI: (0.2-0.9); P=0.048] was in a negative correlation with postoperative complication. Conclusions:The independent risk factors for complications after F/B-TVAR included aortic atherosclerotic plaque, aortic intramural thrombosis, the aortic dilatation, the history of stroke, smoking history,duration of surgery.The application of 3D printing technology can effectively reduce the complication rate.
8.Clinical study on osteoporosis in male patients with alcoholic cirrhosis
Nan LIU ; Xuesong GAO ; Yaonan ZHANG ; Hongjie LI ; Yijin ZHANG ; Lili GAO ; Ping GAO ; Yaping LIU ; Xuefei DUAN
Chinese Journal of General Practitioners 2024;23(7):709-715
Objective:To investigate the incidence of abnormal bone mineral density (BMD) in male patients with alcoholic cirrhosis.Methods:Clinical data of 72 patients with alcoholic cirrhosis admitted in Beijing Ditan Hospital, Capital Medical University from March 2017 to July 2023 were enrolled as study group, and 40 age-and BMI-matched non-hepatopathy subjects were selected as control group.The incidence of abnormal BMD were compared between two groups. The serum levels of osteocalcin (OC), total procollagen type 1 amino-terminal propeptide (TP1NP), β-C-terminal telopeptide of typeⅠcollagen (CTX) and 25-hydroxy vitamin D [25-(OH)VD] were measured and compared among patients with different Child-Pugh grades.Results:Among 72 alcoholic cirrhosis patients, there were 54 cases (75.0%) complicated with abnormal BMD, including 21 cases (29.2%) of bone loss and 33 cases (45.8%) of osteoporosis. In control group there were 15 subjects with abnormal bone mineral density, including 9 cases (22.5%) of bone loss and 6 cases (15.0%) of osteoporosis( χ2=5.623 and 15.900,both P<0.05). The average BMDs of L1-L4, femoral neck, intertrochanteric region and trochanter of the femur in patients with alcoholic cirrhosis were significantly lower than those in control group ( t=3.574, 8.640, 7.282, 7.958, 3.755, 5.573, 5.026,all P<0.05); the average BWDs of L1-L3 and hip joint in patients with Child-Pugh C were significantly lower than those in patients with Child-Pugh A and B ( t=1.414, 1.699, 3.786, 2.590, 8.763, 2.581, 1.392, 6.232,all P<0.05). The serum levels of 25-(OH)VD in alcoholic cirrhosis patients with Child-Pugh C grade were significantly lower than those with Child-Pugh A and B ( t=3.969 and 2.911, P<0.05); the serum calcium levels in patients with Child-Pugh C grade were lower than those with Child-Pugh A( t=3.627, P<0.05); while the TP1NP levels in patients with Child-Pugh C were higher than those with Child-Pugh A and B grades( t=6.722 and 5.034, P<0.05).The Child-Pugh grade was negatively correlated with 25-(OH)VD level( β=-0.767, P<0.05)and positively correlated with TP1NP level ( β=2.186, P<0.05). Conclusion:The incidence of bone loss and osteoporosis in patients with alcoholic cirrhosis is increased significantly, and the deterioration of their liver function is closely associated with an increased TP1NP level and decreased 25-(OH)VD levels.
9.Study on recombinant adenovirus vector vaccine in G protein conserved domain of respiratory syncytial virus
Yi SHI ; Pengdi CHAI ; Zhaojun DUAN ; Qing ZHANG ; Xiangyu KONG ; Hong WANG ; Lili PANG ; Dandi LI
Chinese Journal of Experimental and Clinical Virology 2024;38(5):497-505
Objective:A recombinant adenoviral vector vaccine based on non-replicating human adenovirus type 5 (Ad5), encoding the conserved domain of respiratory syncytial virus G protein (RSV-G) was constructed. The immunogenicity and protective efficacy of this vaccine were subsequently evaluated in mice.Methods:The recombinant Ad5 vector plasmid (Ad5-Gbcc-Gacc) was constructed by inserted conserved domains of RSV A and RSV B. The recombinant adenovirus Ad5-Gbcc-Gacc was rescued in HEK293A cells. The genome of virus Ad5-Gbcc-Gacc was identified by multi-enzyme digestion, and the expression of Ad5-Gbcc-Gacc was verified by Western blot. Recombinant adenovirus was used to immunize BALB/c mice via intramuscular injection with signal dose, and then challenged with RSV Long strain at week 6. The levels of G specific IgG and antibody subtypes in serum were detected by enzyme-linked immunosorbent assay, the level of neutralizing antibodies was determined by micro-neutralization assay. After challenge, the mice′s weight was recorded daily, the copies of RSV virus in the lung and nasal tissues were detected. Pathological changes in lung tissue were also examined.Results:Western blot and multi-enzyme digestion identification confirmed the successful rescue of the recombinant adenovirus. Ad5-Gbcc-Gacc elicit high titers of specific IgG, robust neutralizing antibodies, and a balanced Th1/Th2 immune response in mice. In comparison to unimmunized controls, mice immunized with Ad5-Gbcc-Gacc reduced the viral copies in both lung and nasal tissue, and exhibited only minimal pathological damage of lung tissue following RSV challenge. In conclusion, Ad5-Gbcc-Gacc induced robust immunogenicity and offers protective effects against RSV infection in murine models.Conclusions:Ad5-Gbcc-Gacc induce robust immunogenicity and can protect mice from RSV challenge, which lays a foundation for further development of RSV vaccine based on G protein.
10.Analysis of language and influencing factors of children with speech disorder in Beijing
Jianhong WANG ; Qi XU ; Haifeng DUAN ; Lei WANG ; Bo ZHOU ; Lili ZHANG ; Xi WANG ; Lijun ZHOU ; Xueman LIU ; Lin WANG
Chinese Journal of Pediatrics 2024;62(5):438-443
Objective:To investigate the features and influencing factors of language in children with various types of speech disorders.Methods:A case-control study was carried out, 262 children with speech disorder had been diagnosed at the language-speech clinic of the Center of Children′s Healthcare, Children′s Hospital, Capital Institute of Pediatrics from January 2021 to November 2023, the children with speech sound disorder as the speech sound disorder group, the children with developmental stuttering as the stuttering group. There were 100 typically-developed children who underwent physical checkups at the Center of Healthcare during the same period as the healthy group. All children experienced a standardized evaluation of language with diagnostic receptive and expressive assessment of mandarin‐comprehensive(DREAM-C) and questionnaire, One-way ANOVA and LSD test were conducted to compare the differences in overall language, receptive language, expressive language, semantics, and syntax scores among 3 groups of children. According to the results of DREAM-C, the children with speech disorder were divided into language normal group and language delay group. Chi‐square test and multivariate Logistic regression were implemented to analyze the association between the linguistic development of children with speech disorder and potential influential factors.Results:There were 145 children in the speech sound disorder group, including 110 males and 35 females respectively, with an age of (5.9±1.0) years; 117 children in the stuttering group, including 91 males and 26 females, with an age of (5.8±1.0) years; 100 children in the healthy group, including 75 males and 25 females, with an age of (5.7±1.2) years. The variations in overall language, expressive language, and syntax scores among 3 groups of children were statistically significant (92±18 vs.96±11 vs. 98±11, 81±18 vs. 84±14 vs. 88±13, 87±16 vs. 89±11 vs. 91±10, F=5.46, 4.69, 3.68, all P<0.05). Pairwise comparison revealed that the speech sound disorder group had lower scores in overall language, expressive language, and syntactic compared to the healthy group, and the differences were statistically significant (all P<0.01) and the overall language score was lower than that of children with stuttering ( P<0.05). In terms of overall language and expressive language, there was a statistically significant difference in the incidence of language delay among the three groups of children (15.9% (23/145) vs. 20.5% (24/117) vs. 7.0% (7/100), 46.2% (67/145) vs. 39.3% (46/117) vs. 26.0% (26/100); χ2=7.93, 10.28; both P<0.05). In terms of overall language, the stuttering group took up the highest proportion. In terms of expressive language, the speech sound disorder group accounted for the highest amount. The incidence of language delay in children with speech disorder was 44.3% (116/262). Non-parent-child reading, daily screen time ≥1 hour and screen exposure before 1.5 years of age are risk factors for the development of language in children with speech disorder ( OR=1.87, 2.18, 2.01; 95% CI 1.07-3.27, 1.23-3.86, 1.17-3.45; all P<0.01). Negative family history are protective factors for the progress of language ability ( OR=0.37, 95% CI 0.17-0.81, P<0.05). Conclusions:Children with speech disorder tend to have easy access to language delay, especially in expressive language and syntax. The occurrence of language delay in children with speech disorder is tightly connected with factors such as the family medical history, parent-child reading, screen time, etc. Attention should be paid to the development of language in children who suffer from speech disorder.

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