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The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery

Genomics, Proteomics & Bioinformatics 2020年第5期18卷 516-524页

作者： Jing Sun Yanfang Zhang Minhui Wang Qian Guan xiujia yang Jin Xia Ou Mingchen Yan Chengrui Wang Yan Zhang Zhi-Hao Li Chunhong Lan Chen Mao Hong-Wei Zhou Bingtao Hao Zhenhai Zhang State Key Laboratory of Organ Failure Research National Clinical Research Center for Kidney DiseaseDivision of NephrologyNanfang HospitalSouthern Medical UniversityGuangzhou 510515China Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China Key Laboratory of Mental Health of the Ministry of Education Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired IntelligenceSouthern Medical UniversityGuangzhou 510515China Center for Precision Medicine Shunde Hospital of Southern Medical UniversityFoshan 528399China Microbiome Medicine Center Division of Laboratory MedicineZhujiang HospitalSouthern Medical UniversityGuangzhou 510282China Division of Epidemiology School of Public HealthSouthern Medical UniversityGuangzhou 510515China

Identification of genetic variants via high-throughput sequencing(HTS)technologies has been essential for both fundamental and clinical ***,to what extent the genome sequence composition affects variant calling remains *** this study,we identified 63,897 multi-copy sequences(MCSs)with a minimum length of 300 bp,each of which occurs at least twice in the human *** 151,749 genomic loci(multi-copy regions,or MCRs)harboring these MCSs account for 1.98% of the genome and are distributed unevenly across *** containing the same MCS tend to be located on the same *** Ontology(GO)analyses revealed that 3800 genes whose UTRs or exons overlap with MCRs are enriched for Golgirelated cellular component terms and various enzymatic activities in the GO biological function *** are also enriched for loci that are sensitive to neocarzinostatin-induced double-strand ***,genetic variants discovered by genome-wide association studies and recorded in dbSNP are significantly underrepresented in *** simulated HTS datasets,we show that false variant discovery rates are significantly higher in MCRs than in other genomic *** results suggest that extra caution must be taken when identifying genetic variants in the MCRs via HTS technologies.

关键词： Multi-copy sequence Multi-copy region Genetic study Variant discovery High-throughput sequencing

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Antibody upstream sequence diversity and its biological implications revealed by repertoire sequencing

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Journal of Genetics and Genomics 2021年第10期48卷 936-945页

作者： Yan Zhu xiujia yang Cuiyu Ma Haipei Tang Qilong Wang Junjie Guan Wenxi Xie Sen Chen Yuan Chen Minhui Wang Chunhong Lan Deqiang Sun Lai Wei Caijun Sun Xueqing Yu Zhenhai Zhang State Key Laboratory of Organ Failure Research National Clinical Research Center for Kidney DiseaseDivision of NephrologyNanfang HospitalSouthern Medical UniversityGuangzhou 510515China Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhou 510515China Center for Precision Medicine Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Key Laboratory of Mental Health of the Ministry of Education Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired IntelligenceSouthern Medical UniversityGuangzhou 510515China Department of Nephrology Hainan Affiliated Hospital of Hainan Medical CollegeHaikou 570311China Department of Nephrology Hainan General HospitalHaikou 570311China Department of Center Laboratory The Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510700China State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat-sen UniversityGuangzhou 510060China School of Public Health Sun Yat-sen UniversityShenzhen 510006China Division of Nephrology Guangdong Provincial People's HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China

The sequence upstream of the antibody variable region(antibody upstream sequence[AUS])consists of a 5′untranslated region(5′UTR)and a preceding leader *** sequence variations in AUS affect antibody engineering and PCR based antibody quantification and may also be implicated in mRNA transcription and ***,the diversity of AUSs remains *** 5′rapid amplification of cDNA ends and high-throughput antibody repertoire sequencing technique,we acquired full-length AUSs for human,rhesus macaque,cynomolgus macaque,mouse,and *** designed a bioinformatics pipeline and identified 3307 unique AUSs,corresponding to 3026 and 1457 unique sequences for 5′UTR and leader region,*** analysis indicated that 928(63.69%)leader sequences are novel relative to those recorded in the international ImMunoGeneTics information ***,leader sequences are more conserved than 5′UTR and seem to coevolve with their downstream V ***,single-nucleotide polymorphisms are position dependent for leader regions and may contribute to the functional reversal of the downstream V ***,the AUGs in AUSs were found to have little impact on gene *** together,our findings can facilitate primer design for capturing antibodies efficiently and provide a valuable resource for antibody engineering and molecule-level antibody studies.

关键词： Antibody upstream sequences 5′UTR Leader sequences Antibody repertoire sequencing Antibody repertoire

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TMED3 promotes prostate cancer via FOXO1a and FOXO3a phosphorylation

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Oncology Research 2025年第1期33卷 161-169页

作者： XIUWANG WEI JIANBO LIANG HUANWEN HUANG DAMING yang XINXIN WANG xiujia WANG CHANGSHENG CHEN KAIQIANG LI TAISEN PANG BIN HU FENGNING WU Department of Urology The People’s Hospital of Guangxi Zhuang Autonomous RegionNanning530000China Department of Rehabilitation The People’s Hospital of Guangxi Zhuang Autonomous RegionNanning530000China

Background:Transmembrane emp24 trafficking protein 3(TMED3)is associated with the development of several tumors;however,whether TMED3 regulates the progression of prostate cancer remains *** and Methods:Short hairpin RNA was performed to repress TMED3 in prostate cancer cells(DU145 cells)and in a prostate cancer mice model to determine its function in prostate cancer in vitro and in ***:In the present study,we found that TMED3 was highly expressed in prostate cancer *** vitro,shTMED3 treatment suppressed the proliferation,invasion,and migration and promoted the apoptosis of DU145 ***,the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed a strong correlation between TMED3 and forkhead box O transcription factor(FOXO)***,TMED3 inhibition efficiently decreased FOXO1a and FOXO3a *** vivo,TMED3 downregulation suppressed the apoptosis,growth,and metastasis of prostate cancer cells via FOXO1a and ***:The present findings show that TMED3 participates in the regulation of prostate cancer progression via FOXO1a and FOXO3a phosphorylation,thereby revealing a novel mechanism underlying prostate cancer development and suggesting that TMED3 inhibition may serve as a novel strategy for prostate cancer treatment.

关键词： Prostate cancer Transmembrane emp24 trafficking protein 3(TMED3) forkhead box O transcription factor(FOXO) Proliferation Apoptosis

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牛病毒性腹泻综合防控

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畜牧兽医科学（电子版） 2021年第12期 60-61页

作者：杨秀佳广西贵港市港北区中里乡农业农村中心贵港537113

牛病毒性腹泻属于国家二类动物疫病,是由病毒性腹泻病毒感染引发的一种临床复杂的传染性疾病。牛群一旦受到病毒侵染,一方面会引发严重的腹泻症状和黏膜病变,另一方面还会对牛群免疫功能造成严重破坏,具有很强传染性,并且很容易和多种... 详细信息

牛病毒性腹泻属于国家二类动物疫病,是由病毒性腹泻病毒感染引发的一种临床复杂的传染性疾病。牛群一旦受到病毒侵染,一方面会引发严重的腹泻症状和黏膜病变,另一方面还会对牛群免疫功能造成严重破坏,具有很强传染性,并且很容易和多种细菌性疾病和病毒性疾病,继发感染混合感染,表现出极其复杂的临床症状。虽然牛病毒性腹泻造成的死亡率相对较低,但是感染牛后会引发牛出现一系列的呼吸系统、生殖系统和消化道疾病,影响牛的正常生长发育,使牛群生产能力显著下降,对养殖场造成的经济损失不可估量。

关键词：牛病毒性腹泻诊断综合防控

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猪衣原体病临床症状与防控

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畜牧兽医科学（电子版） 2021年第9期 172-173页

作者：杨秀佳广西贵港市港北区中里乡农业农村中心贵港537113

在生猪养殖中,常会受到一些传染病的侵袭,猪衣原体病正是其中之一,该病主要是由衣原体所引起的一种接触性传染病,对生猪养殖的水平提升造成极大程度的损害,不得不对此予以高度重视。猪衣原体病发病主要表现为慢性,但是在某些外在因素的... 详细信息

在生猪养殖中,常会受到一些传染病的侵袭,猪衣原体病正是其中之一,该病主要是由衣原体所引起的一种接触性传染病,对生猪养殖的水平提升造成极大程度的损害,不得不对此予以高度重视。猪衣原体病发病主要表现为慢性,但是在某些外在因素的刺激下,常可能会造成急性爆发的问题,不同猪龄的猪群都会感染此类病症,尤其会严重威胁到仔猪和母猪。该文主要论述猪衣原体病症状及防控。

关键词：猪衣原体病临床病症防控

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Starch grain evidence reveals early pottery function cooking plant foods in North China

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Chinese Science Bulletin 2014年第32期59卷 4352-4358页

作者： Xiaoyan yang Zhikun Ma Tao Wang Linda Perry Quan Li xiujia Huan Jincheng Yu Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences University of Chinese Academy of Sciences School of Geography Beijing Normal University Department of Archaeology and Museology Capital Normal University The Foundation for Archaeobotanical Research in Microfossils Fairfax VA 22038 USA Department of Geography and Geoinformation Science Center for Earth Observing and Space Research George Mason University Fairfax VA 22030 USA Beijing Institute of Cultural Relics

Early pottery sherds excavated in northern China date back to more than 11,000 cal a BP,and are presumed to have been used as cooking *** has been,however,no direct evidence to demonstrate this *** we report ancient starch grains recovered from carbonized residues adhering to the bases of flatbottomed vessels excavated from the Zhuannian site dating more than 10,000 cal a BP in the North China *** evidence demonstrates that early pottery was being used to cook cereal grains,particularly millets,and *** millets were in the process of domestication at thistime,we propose that pottery invention in northern China may have been related to early farming activities.

关键词：中国北方烹饪器皿淀粉粒植物性食物陶器早期证据 CAL

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Compensatory Growth of Juvenile Brown Flounder Paralichthys olivaceus Following Low Temperature Treatment for Different Periods

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Journal of Ocean University of China 2017年第2期16卷 326-332页

作者： PENG Yinhui LIU xiujia HUANG Guoqiang WEI Liuzhi ZHANG Xiumei Guangxi Key Laboratory of Marine Biotechnology Guangxi Institute of Oceanology Key Laboratory of Mariculture of Ministry of Education Ocean University of China

We investigated the effects of low temperature(8.5℃) on the growth and feeding rates and feed conversion efficiency of juvenile *** with an average initial weight of 3.87 ± 0.06 g(mean ± SE).Fish were exposed to 8.5℃ for 0(control),1,2,3 and 4 weeks,and then to 20℃ for 10,9,8,7 and 6 weeks,*** temperature clearly led to growth *** weight of fish exposed to low temperature for 1 week was restored to that of control,while that of fish exposed to low temperature longer was significantly decreased(P 0.05).Feeding rate and feed conversion efficiency were reduced at low temperature in juvenile *** compensatory growth of juvenile *** may therefore be attributed to the improvement of feeding *** results suggested that growth depression occurs when juvenile *** are exposed to low temperature for more than one week.

关键词： Paralichthys olivaceus compensatory growth low temperature exposure feeding rate

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Correlation of hair risperidone concentration and serum level among patients with schizophrenia

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General Psychiatry 2019年第1期32卷 35-42页

作者： xiujia Sun Lihua Wang Fuzhong yang Juanjuan Ren Ping Jiang Hongmei Liu Huafang Li Chunbo Li Chen Zhang Shanghai Key Laboratory of Psychotic Disorders Shanghai Mental Health CenterShanghai Jiaotong University School of MedicineShanghai200030China Shanghai Mental Health Center Shanghai Jiaotong University School of MedicineShanghai200030China

Background Risperidone (RSP) has a rapid onset in vivo, low dosage and high plasma protein binding rate, therefore therapeutic drug monitoring (TDM) is needed to ensure safety in clinical treatment. However, compared with blood, hair is non-invasive, safe, non-infectious and easy to transport and store. Aims This study aims to investigate the correlations among the drug concentrations of RSP in hair and serum, which provides an experimental basis to explore hair as a novel biomaterial to meet the needs of clinical detection. Methods 34 patients with schizophrenia treated with RSP for more than 3 months were enrolled in this study. About 1 cm section of hair near the scalp was taken from the subjects, pretreated and detected by liquid chromatography-mass spectrometry. A correlation analysis was conducted among the drug concentrations in hair, the serum concentrations and the daily dosage. The data were analysed usi叩 SPSS 20.0 software. Results There was significant correlation between the hair concentration of RSP (two-tailed test, r=0.440, p=0.009) with the serum concentration of RSP, and the hair concentration of 9-hydroxyrisperidone (9-HR) with the serum concentration of 9-HR had no significant correlation (two-tailed test, r=-0.217, p=0.217);the total concentration of the RSP and 9-HR had no significant correlation between hair and serum (r=0.227, p=0.196). The dosage had no statistically significant correlation with the concentration of RSP in hair (r=0.207, p=0.241), 9-HR in hair (r=-0.194, p=0.271) and the total concentration of RSP and 9-HR in hair (r=0.188, p=0.288). There was no statistical correlation between the dosage and the concentration of RSP in serum (r=-0.059, p=0.741), but significant correlation between the dosage and 9-HR in serum (r=0.581 p<0.001) was found, and the correlation between the dosage and the total concentration of the two drugs RSP and 9-HR in serum was also significant (r=0.437, p=0.01). Conclusion The correlation analysis showed

关键词： Correlation of hair risperidone concentration serum level among patients schizophrenia

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Effects of the combination of second-generation antipsychotics on serum concentrations of aripiprazole and dehydroaripiprazole in Chinese patients with schizophrenia

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General Psychiatry 2021年第2期34卷 87-98页

作者： Ping Jiang xiujia Sun Juanjuan Ren Hongmei Liu Zhiguang Lin Junwen Liu Xinyu Fang Chen Zhang Department of Biochemistry and Psychopharmacology Shanghai Mental Health CenterShanghaiChina Shanghai Key Laboratory of Psychotic Disorders ShanghaiChina

Background Aripiprazole(ARI)is often prescribed alone or in combination with other second-generation antipsychotics(SGAs)to treat patients with ***,this may increase the potential clinical significance of drug-drug *** drug monitoring(TDM)is an important and fundamental tool both when administering ARI alone and in combination with other SGAs to monitor ARI pharmacokinetics,adjust the dosage and thereby achieve more effective and safer *** This study retrospectively investigated the effects of four SGA comedications(clozapine,risperidone,quetiapine(QTP)and olanzapine)and other potential factors(sex,age and ARI dose)on the serum concentrations of ARI and dehydroaripiprazole(DARI)in Chinese patients with schizophrenia using TDM *** High-performance liquid chromatography was used to test the serum concentrations of ARI,DARI and ARI+*** addition,steady-state dose-adjusted serum concentrations(ie,concentration-to dose ratios,C:D ratios)of ARI,DARI and ARI+DARI;sex;age;ARI dose and SGA comedication dose between 299 inpatients with schizophrenia who received ARI or SGA comedication were all collected and ***’s correlation and multiple linear regression analysis were used to evaluate bivariate associations between ARI dose and serum ARI and DARI concentrations and describe the effect of independent variables on serum ARI and DARI concentrations,*** There were significant differences in the C:D ratios of ARI(χ^(2)=−3.21,p=0.001)and ARI+DARI(χ^(2)=−2.50,p=0.01)between the ARI and SGA groups,as well as in the C:D ratios of ARI(χ^(2)=−3.59,p<0.001)and ARI+DARI(χ^(2)=−3.10,p=0.002)between the female patients in the two *** the four SGAs,only QTP had significant effects on the C:D ratios of ARI(Z=−4.12,p<0.001)and ARI+DARI(Z=−3.62,p<0.001)when compared with the ARI group in the whole sample and on the C:D ratios of ARI,DARI and ARI+DARI(Z=−3.96,p<0.001;Z=−2.22,p=0.03;Z=−3.75,p<0.00

关键词： dosage patients schizophrenia

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Magnetic-field-induced deflection of nonlocal light bullets in a Rydberg atomic gas

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Chinese Optics Letters 2022年第4期20卷 60-64页

作者： xiujia Dong Yao Ding Zhengyang Bai Guoxiang Huang State Key Laboratory of Precision Spectroscopy Shanghai 200062China NYU-ECNU Institute of Physics at NYU Shanghai Shanghai 200062China

Light bullets(LBs)are localized nonlinear waves propagating in high spatial *** stable LBs and realizing their control are desirable due to the interesting physics and potential ***,we show that nonlocal LBs generated in a cold Rydberg atomic gas via the balance among the dispersion,diffraction,and giant nonlocal Kerr nonlinearity contributed by long-range Rydberg-Rydberg interaction can be actively manipulated by using a weak gradient magnetic *** LBs are generated by a balance among dispersion,diffraction,and large nonlocal Kerr nonlinearities contributed by long-range Rydberg-Rydberg ***,we find that active manipulation can be achieved by weak gradient magnetic fields in cold Rydberg atomic ***,the LBs may undergo significant Stern-Gerlach deflections,and their motion trajectories can be controlled by adjusting the magnetic-field *** results reported here are helpful not only for understanding unique properties of LBs in nonlocal optical media but also for finding ways for precision measurements of magnetic fields.

关键词： nonlinear optics optical soliton Rydberg atom

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