1.Genomic Epidemiology of SARS-CoV-2 in Pakistan
Song SHUHUI ; Li CUIPING ; Kang LU ; Tian DONGMEI ; Badar NAZISH ; Ma WENTAI ; Zhao SHILEI ; Jiang XUAN ; Wang CHUN ; Sun YONGQIAO ; Li WENJIE ; Lei MENG ; Li SHUANGLI ; Qi QIUHUI ; Ikram AAMER ; Salman MUHAMMAD ; Umair MASSAB ; Shireen HUMA ; Batool FATIMA ; Zhang BING ; Chen HUA ; Yang YUN-GUI ; Abbasi Ali AMIR ; Li MINGKUN ; Xue YONGBIAO ; Bao YIMING
Genomics, Proteomics & Bioinformatics 2021;19(5):727-740
COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,2020.We identified a total of 347 mutated positions,31 of which were over-represented in Pakistan.Meanwhile,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or coevolution.Some of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying selections.The genomic epidemiology revealed five distinctive spreading clusters.The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF 1ab)of this cluster.Further-more,28 putative international introductions were identified,several of which are consistent with the epidemiological investigations.In all,this study has inferred the possible pathways of introduc-tions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control.
2.The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR
Song SHUHUI ; Ma LINA ; Zou DONG ; Tian DONGMEI ; Li CUIPING ; Zhu JUNWEI ; Chen MEILI ; Wang ANKE ; Ma YINGKE ; Li MENGWEI ; Teng XUFEI ; Cui YING ; Duan GUANGYA ; Zhang MOCHEN ; Jin TONG ; Shi CHENGMIN ; Du ZHENGLIN ; Zhang YADONG ; Liu CHUANDONG ; Li RUJIAO ; Zeng JINGYAO ; Hao LILI ; Jiang SHUAI ; Chen HUA ; Han DALI ; Xiao JINGFA ; Zhang ZHANG ; Zhao WENMING ; Xue YONGBIAO ; Bao YIMING
Genomics, Proteomics & Bioinformatics 2020;18(6):749-759
On January 22, 2020, China National Center for Bioinformation (CNCB) released the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access information resource for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 2019nCoVR features a comprehensive integra-tion of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline. Of particular note, 2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and their detailed statistics for each virus isolate, and congregates the quality score, functional annotation,and population frequency for each variant. Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019 (COVID-19), including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC. Furthermore, by linking with relevant databases in CNCB, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with NCBI. Collectively, SARS-CoV-2 is updated daily to collect the latest information on genome sequences, variants, hap-lotypes, and literature for a timely reflection, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.
3. Ultrasound in diagnosis of malignant and benign thyroid nodules in children
Chinese Journal of Medical Imaging Technology 2019;35(3):337-340
Objective: To investigate the value of ultrasound in differential diagnosis of benign and malignant thyroid nodules in children. Methods Ultrasonic manifestations of 120 children with thyroid nodules confirmed by pathology were retrospectively analyzed, and ultrasonic features of benign and malignant thyroid nodules were compared. Results Among 120 cases, malignant nodules were detected in 71 cases (71/120, 59.17%), while benign nodules were found in 49 cases (49/120, 40.83%). There were significant differences of the shape, boundary, margin, composition, echo and calcification types between benign and malignant thyroid nodules (all P<0.05). The accuracy of the above ultrasonic features in diagnosis of malignant thyroid nodules was 80.00%(112/140), 78.57%(110/140), 78.57%(110/140), 81.43%(114/140), 82.86%(116/140), 87.86%(123/140), the sensitivity was 68.29%(56/82), 70.73%(58/82), 73.17%(60/82), 97.56%(80/82), 90.24%(74/82), 79.27%(65/82), and the specificity was 96.55%(56/58), 89.66%(52/58), 86.21%(50/58), 58.62%(34/58), 72.41%(42/58), 100%(58/58). Among 71 cases of malignant thyroid nodules, 60 cases (60/71, 84.51%) were associated with cervical lymph node metastasis, 14 cases (14/71, 19.72%) were associated with central region lymph node metastasis, 46 cases (46/71, 64.79%) were simultaneously involved in the lateral compartment. Conclusion Ultrasound can effectively differentiate benign and malignant thyroid nodules in children.
4.Diagnostic value of mammographic calcification for ductal carcinoma in situ without palpable lumps
Peng XU ; Hua XU ; Cuiping WANG ; Zhengshuai TAN ; Kun FANG ; Peiying LI ; Qitang WANG
Chinese Journal of Endocrine Surgery 2018;12(5):386-390
Objective To explore the diagnostic value of calcification by full field digital mammography in cases without breast palpable lumps or nodules in ductal carcinoma in situ(DC1S).Methods Based on breast imaging-reporting and data system (BI-RADS)proposed by the American College of Radiology (ACR),the cases without palpable lumps or nodules,but with calcification (over Category 4a)found by full field digital mammography admitted from Oct.2014 to Oct.2016 were analyzed.They underwent excisional biopsy after three-dimensional guide wire positioning or three-dimensional vacuum rotary cutting.After being filmed again to make sure the resection was complete,the isolated specimen were sent to pathological examination.The pathology and calcification were analyzed and summarized.Results Among 126 cases,71 (56.3%)were breast adenosis,41 (32.5%) were DCIS,6(4.8%) were infiltrating ductal carcinoma (IDC),and 8 (6.3%)were other types.The detection rate of DCIS in younger group was higher.The calcifications in DCIS were mostly linear-branching,segmental calcification,and those in IDC were mostly pleomorphic,clustering or regional calcification.Conclusion Full field digital mammography has great diagnostic value for DCIS in cases with calcification but without palpable breast lumps or nodules.
5.Ultrasonography in the diagnosis of benign and malignant thyroid nodules with rim calcification
Cuiping HUA ; Jianwei WANG ; Zhixing GUO ; Qingguang LIN ; Xuebin ZOU ; Zimin LAI ; Jueming CHEN ; Feng HAN
Chinese Journal of Medical Ultrasound (Electronic Edition) 2017;14(10):755-759
Objective The aim of this study was to investigate the value of ultrasound in diagnosis of benign and malignant thyroid nodules with rim calcification. Methods Sixty thyroid nodules with rim calcifications from Sun Yat-sen University Cancer center which were detected on ultrasound from January 2008 to December 2015 were included in this study, and all the thyroid nodules had pathological results. Ultrasonic features of thyroid nodules, including the size, border, internal echo, growth pattern, rear echo, interruption or inner sink of the rim calcification and hypoechoic soft tissue extrusion around rim calcification were analyzed. Results Thirty-seven nodules (61.7%) were confirmed to be benign, and twenty-three nodules (38.3%) were malignant. The ultrasonic features of interruption or inner sink of rim calcifications and hypoechoic soft tissue extrusion around rim calcification, were more often in malignant nodules than benign nodules. The sensitivity, specificity, the positive predictive values and the negative predictive values for interruption or inner sink of rim calcifications were 85.7%, 89.4%, 85.7% and 89.4%, respectively. The sensitivity, specificity, the positive predictive values and the negative predictive values for hypoechoic soft tissue extrusion around rim calcification were 81.3%, 94.4%, 92.9% and 85.0%, respectively. Internal hypoechogenicity was more frequently observed in the malignant nodules (82.6%) than in benign nodules (40.5%). The longitudinal growth pattern of thyroid was more frequently observed in malignant nodules (30.4%) than in benign nodules (2.7%). The differences of this two ultrasound features were statistically significant(χ2=9.958 and 9.440,both P<0.01).There were no significant differences in size,border and the rear echo between malignant and benign nodules (all P>0.05). Conclusion The interruption or inner sink of the rim calcification could be useful in differential diagnosis of thyroid nodules with rim calcification.
6.Expression of integrin-linked kinase and E-cadherin in primary gallbladder cancer and its significance
Hua XU ; Shengshui LI ; Xiuqing LI ; Li LI ; Cuiping LI ; Shuangbiao LI ; Fengmei ZHANG ; Yan LIU
Chinese Journal of Clinical Oncology 2013;(19):1170-1173
Objective: To detect the protein expression and relationship between integrin-linked kinase (ILK) and E-cadherin (E-cad) in primary gallbladder cancer (PGC), as well as to evaluate their clinical significance. Methods:ILK and E-cad were examined in 48 cases with PGC, 25 with gallbladder adenoma and 25 with chronic cholecystitis tissues by immunohistochemistry. Then, the corre-lation between clinical and pathological features, as well as their relationship, was investigated. Results:The positive rate of ILK was significantly higher in the gallbladder cancer group (66.7%;32/48) than in the gallbladder adenoma (36.0%;9/25) and chronic cholecys-titis groups (24.0%;6/25) (P<0.05). However, the positive rate of E-cad, namely, 45.8%(22/48), was significantly lower than those of the benign groups (P<0.05). When the depth of invasion was aggravated and lymph node metastasis had occurred, the ILK expression level became significantly higher. Nevertheless, negative E-cad results were produced (P<0.05). A negative correlation between the ex-pression of ILK and E-cad in gallbladder cancer existed (r=-0.411, P<0.05). Conclusion:The expression of ILK and E-cad is signifi-cantly correlated with tumor invasion and metastasis. A negative correlation exists between these expressions. Detection of these two in-dexes is useful in predicting tumor progression and prognosis.
7.Exploration of formative evaluation as the center examination in principles of medical equipment
Cuiping WANG ; Chao MENG ; Jiazhen YAN ; Zhilong WANG ; Hua WANG ; Yonghong DU ; Shihe MENG
Chinese Journal of Medical Education Research 2012;11(4):422-425
Principles of medical equipment course were explored of formative evaluation as the center examination,constructed an examination reform scheme as” One center (formative evaluation as the center),three systems (content system,operation system,monitoring system).” Made students to learn from the center of focus scores change to autonomous learning and culture analysis,solves the question ability and practical ability.At the same time,strengthen the teaching process of teaching and learning to communicate and exchange,Get the students learning feedback information to improve teaching and learning in time,Strengthen the students′ ability of autonomous learning and lifelong learning ability.
8.An epidemiological analysis of pituitary apoplexy
He LIU ; Xijiang LI ; Shu LI ; Hua JIANG ; Cuiping CAO ; Yiji ZHANG ; Guoliang LIU
Chinese Journal of Endocrinology and Metabolism 2012;(12):998-1000
Objective To analyze the epidemiological characteristics of pituitary apoplexy and investigate the changes and features of endocrine hormones caused by pituitary apoplexy.Methods A retrospective analysis of the clinical and laboratory data of pituitary tumor and pituitary apoplexy was carried out.Results (1) The incidence of pituitary apoplexy was 31.78%,patients were 15-75 (47.5 ± 11.7) year old,most patients were female.(2)Diabetes,coronary heart disease,menopausal hormone therapy,radiotherapy,surgery,and bromocriptine administration may be related to pituitary apoplexy.(3) There was high incidence of apoplexy in nonfunctioning adenoma.(4) According to the relationship between apoplexy and pituitary tumor,cases with pituitary apoplexy were divided into 5 types.(5) Pituitary apoplexy was associated with low serum creatinine,hypernatremia,hyperchloremia,hypoeosinophilia,and hypobasophilia.(6) 61.61% of the patients had pituitary hormone deficiency,especially the GnH deficiency.(7)98.10% of the patients were treated by surgery.Conclusion Pituitary apoplexy has its own clinical characteristics,and more attention should be paid in clinical practice.
9.Regulation of claudin-4 gene expression in endometrial adenocarcinoma Ishikawa cell line by progesterone
Yan JIN ; Cuiping FENG ; Yanan WANG ; Hua LIN ; Huajun LI ; Xiaoyu PAN
Chinese Journal of Obstetrics and Gynecology 2012;47(5):368-372
ObjectiveTo explore the regulation of claudin-4 expression in endometrial adenocarcinoma cell lines by progesterone.Methods Ishikawa cells were treated with various concentrations of megestrol acetate (MA:2,5,10,15,20 mg/L).After cultured for 24,48 and 72 hours,cells growth were measured by methyl thiazolyl tetrazolium (MTT).The group of Ishikawa cells incubated with MA at the 50% inhibitory concentration ( IC50 ) was selected for cell apoptosis assay by using transmission electron microscopy and flow cytometry method.Real-time PCR and western blot were used for detecting the mRNA and protein expression levels of claudin-4.The localization of claudin-4 was examined by immunofluorescent staining.Results The inhibitory effects of megestrol acetate on the growth of Ishikawa cells were dosedependent and time-dependent.IC50 of MA on Ishikawa cells was 15 mg/L after incubated for 72 hours.After MA treatment,Ishikawa cells showed shrinkage,nuclear chromatin condensation,fractures of nuclear membrane and endoplasmic reticulum expansion,even round apoptotic bodies were found.The apoptosis rate of cells before MA treatment was (0.076 ±0.024)%,and the rate was (3.934 ±0.816)% by MA treated for 72 hours,in which there were signicant difference( P < 0.05 ).The relative quantification of claudin-4 mRNA and protein of the cells before MA treatment were 0.64 ± 0.20 and 0.94 ± 0.18,while they were 0.47 -0.15 and 0.62 ±0.15 after MA treated.The expression of claudin-4 was significantly decreased after MA treatment ( P < 0.05 ).The localization of claudin-4 transferred from cytomembrane to cytoplasm and nucleus after MA treatment.Conclusions MA could inhibite the growth of Ishikawa cells,in which the mechanism may be decrease the expression of claudin-4 and the apoptosis of cells.The distribution change of claudin-4 may be related to the anti-cancer effect of progesterone.
10.Anterior pituitary hypofunction: a clinical analysis of 117 cases
He LIU ; Hua JIANG ; Cuiping CAO ; Guoliang LIU
Chinese Journal of Endocrinology and Metabolism 2011;27(11):883-886
Objective To investigate the clinical features of anterior pituitary hypofunction.Methods A retrospective analysis was carried out on the data of 117 patients with anterior pituitary hypofunction during 1994-2010.Results There were 60.68% male and 39.32% female patients respectively.The onset age was from 13 to 79 years,with 79.12% of the patients more than 40 years old.There were 57 cases with sellar tumors ( 40.17% ),in which 55 cases( 96.49% )were operated and (or) treated with radiotherapy.35 cases were operated via the frontal approaches( 66.04% ) and 18 cases underwent transsphenoidal surgery ( 33.96% ).There were 108 cases with hyponatremia with the first symptoms of weakness,anorexia,nausea,and vomiting induced by ACTH deficiency (92.31% ).There were 23 cases accompanied with central diabetes insipidus( 19.66% )and 82 cases with coronary heart disease( 70.09% ).Conclusion Owing to the difference in etiological factors,the incidence,early symptoms,and the hormones involved are greatly different.The main cause is pituitary tumor,which occured more in aged person,more in males than females.

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