Three-dimensional pseudo-continuous arterial spin-labelled perfusion imaging for diagnosing upper cervical lymph node metastasis in patients with nasopharyngeal carcinoma: a whole-node histogram analysis

AIM

To evaluate whole-node histogram parameters of blood flow (BF) maps derived from three-dimensional pseudo-continuous arterial spin-labelled (3D pCASL) imaging in discriminating metastatic from benign upper cervical lymph nodes (UCLNs) for nasopharyngeal carcinoma (NPC) patients.

MATERIALS AND METHODS

Eighty NPC patients with a total of 170 histologically confirmed UCLNs (67 benign and 103 metastatic) were included retrospectively. Pre-treatment 3D pCASL imaging was performed and whole-node histogram analysis was then applied. Histogram parameters and morphological features, such as minimum axis diameter (MinAD), maximum axis diameter (MaxAD), and location of UCLNs, were assessed and compared between benign and metastatic lesions. Predictors were identified and further applied to establish a combined model by multivariate logistic regression in predicting the probability of metastatic UCLNs. Receiver operating characteristic (ROC) curves were used to analyse the diagnostic performance.

RESULTS

Metastatic UCLNs had larger MinAD and MinAD/MaxAD ratio, greater energy and entropy values, and higher incidence of level II (upper jugular group), but lower BF10th value than benign nodes (all p<0.05). MinAD, BF10th, energy, and entropy were validated as independent predictors in diagnosing metastatic UCLNs. The combined model yielded an area under the curve (AUC) of 0.932, accuracy of 84.42 %, sensitivity of 80.6 %, and specificity of 90.29 %.

CONCLUSIONS

Whole-node histogram analysis on BF maps is a feasible tool to differentiate metastatic from benign UCLNs in NPC patients, and the combined model can further improve the diagnostic efficacy.

[Incidence of diabetes and influencing factors in HIV-infected individuals after antiretroviral therapy in Dehong Dai and Jingpo Autonomous Prefecture]

Objective: To understand the incidence of diabetes and influencing factors, the trend of FPG change and risk for mortality in HIV-infected individuals after antiretroviral therapy (ART) in Dehong Dai and Jingpo Autonomous Prefecture (Dehong). Methods: The HIV/AIDS treatment database was collected from China Information System for Disease Control and Prevention. This retrospective cohort study was conducted in HIV-infected individuals with access to ART in Dehong during 2004-2020.The Cox proportional hazard regression model was used to analyze the incidence density of diabetes, the influencing factors and risk for mortality in HIV-infected individuals with access to ART, mixed linear effects model was used to analyze the trend of FPG change and predict FPG in those with different glucose metabolic status at baseline survey. Statistical analysis was performed using software SAS 9.4. Results: A total of 8 763 HIV-infected individuals were included, in whom 8 432 (96.2%) had no diabetes, 331 had diabetes. The incidence density of diabetes was 2.31/1 000 person years. Multivariate Cox proportional hazard regression analysis revealed that 30- 59 years old, BMI ≥24.0 kg/m2, Efavirenz (EFV) based initial treatment regimen and impaired fasting glucose (IFG) at baseline survey were significantly and positively associated with incidence of diabetes. Mixed effect model revealed that FPG was positively correlated with the duration of ART, age and baseline FPG. Suffering from diabetes was a risk factor for mortality in HIV-infected individuals both at baseline survey and during follow-up. Conclusions: The risk for diabetes increased in HIV-infected individuals who were 30-59 years old, baseline BMI ≥24.0 kg/m2, received EFV based initial treatment, and IFG in HIV-infected individuals after antiretroviral therapy in Dehong, 2004-2020. It is important to pay close attention to their blood glucose, and patients with high blood glucose should receive treatment as early as possible.

CT-based radiomics nomogram for the preoperative prediction of microsatellite instability and clinical outcomes in colorectal cancer: a multicentre study

AIM

To develop and validate a computed tomography (CT)-based radiomics nomogram for preoperative prediction of microsatellite instability (MSI) status and clinical outcomes in colorectal cancer (CRC) patients.

MATERIALS AND METHODS

This retrospective study enrolled 497 CRC patients from three centres. Least absolute shrinkage and selection operator regression was utilised for feature selection and constructing the radiomics signature. Univariate and multivariate logistic regression analyses were employed to identify significant clinical variables. The radiomics nomogram was constructed by integrating the radiomics signature and the identified clinical variables. The performance of the nomogram was evaluated through receiver operating characteristic curves, calibration curves, and decision curve analysis. Kaplan-Meier analysis was performed to investigate the prognostic value of the nomogram.

RESULTS

The radiomics signature comprised 10 radiomics features associated with MSI status. The nomogram, integrating the radiomics signature and independent predictors (age, location, and thickness), demonstrated favourable calibration and discrimination, achieving areas under the receiver operating characteristic (ROC) curves (AUCs) of 0.89 (95% confidence interval [CI]: 0.83-0.95), 0.87 (95% CI: 0.79-0.95), 0.88 (95% CI: 0.81-0.96), and 0.86 (95% CI: 0.78-0.93) in the training cohort, internal validation cohort, and two external validation cohorts, respectively. The nomogram exhibited superior performance compared to the clinical model (p<0.05). Additionally, survival analysis demonstrated that the nomogram successfully stratified stage II CRC patients based on prognosis (hazard ratio [HR]: 0.357, p=0.022).

CONCLUSION

The radiomics nomogram demonstrated promising performance in predicting MSI status and stratifying the prognosis of patients with CRC.

Dual domestications and origin of traits in grapevine evolution

We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused by continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.

Predictive value of peritumour radiomics in the diagnosis of benign and malignant pulmonary nodules with halo sign

AIM

To evaluate peritumour radiomics in predicting benign and malignant pulmonary nodules with halo sign.

MATERIALS AND METHODS

In this retrospective study, 305 pulmonary nodules with halo sign (benign, 120; adenocarcinoma, 185) were collected. Manual segmentation was used to mark the gross tumour volume (GTV) and the peritumour volume (PTV) was established by uniform dilation (1 cm) of the tumour area in three dimensions. The GTV and PTV radiomic features were combined to produce the gross tumour and peritumour volume (GPTV). The minimum-redundancy maximum-relevance (mRMR) feature ranking method and least absolute shrinkage and selection operator (LASSO) algorithm were used to eliminate redundant radiomic features. Predictive models combined with clinical features and radiomic signatures were established. Multivarible logistic regression analysis was used to establish the combined model and develop a nomogram. Receiver operating characteristic (ROC) curve analysis was used to evaluate the predictive performance of the model.

RESULTS

In the testing cohort, the area under the ROC curve (AUC) of the GTV, PTV, and GPTV radiomic models was 0.701 (95% CI: 0.589-0.814), 0.674 (95% CI: 0.557-0.791) and 0.755 (95% CI: 0.643-0.867), respectively. The AUC of the nomogram model based on clinical and GPTV radiomic signatures was 0.804 (95% CI: 0.707-0.901).

CONCLUSION

The nomogram model based on clinical and GPTV radiomic signatures can better predict benign and malignant pulmonary nodules with halo signs, demonstrating that the model has potential as a convenient and effective auxiliary diagnostic tool for radiologists.

Whole-genome resequencing reveals the origin of tea in Lincang

Phylogeographic, population genetics and diversity analysis are crucial for local tea resource conservation and breeding programs. Lincang in Yunnan has been known as the possible place of domestication for tea worldwide, yet, its genetic makeup and unique Lincang origin are little understood. Here, we reported a large-scale whole-genome resequencing based population genomic analysis in eight main tea-producing areas of Lincang in Yunnan (1,350 accessions), and the first comprehensive map of tea genome variation in Lincang was constructed. Based on the population structure, tea sample in Lincang was divided into three subgroups, and inferred Xigui and Nahan Tea Mountain in Linxiang, Baiying Mountain Ancient Tea Garden in Yun, and Jinxiu Village of Xiaowan Town in Fengqing, which belong to the birthplace of the three subgroups, were all likely to be the origin center of Lincang tea. Meanwhile, the history population sizes analysis show that similar evolutionary patterns were observed for the three subgroups of Lincang. It also was observed that the hybrid among eight areas of Lincang was noticeable, resulting in insignificant genetic differentiation between geographical populations and low genetic diversity. The findings of this study clarified the genetic make-up and evolutionary traits of the local population of tea, which gave some insight into the development of Lincang tea.

Preoperative prediction of the degree of differentiation of lung adenocarcinoma presenting as sub-solid or solid nodules with a radiomics nomogram

AIM

To develop and validate a radiomics nomogram for prediction of degree of differentiation in lung adenocarcinoma presenting as sub-solid or solid nodules.

MATERIALS AND METHODS

A total of 438 patients with histopathologically confirmed adenocarcinoma (248 non-poorly differentiated and 190 poorly differentiated) were divided into training cohort (n=235) and internal validation cohort (n=203) according to surgery sequence. Sixty patients form public TCIA dataset were selected for external validation. One thousand, two hundred and eighteen radiomics features were extracted from each volumetric region of interest and a least absolute shrinkage and selection operator logistic regression was applied to select meaningful radiomic features for building a radiomics score (Rad-score) model. A nomogram model incorporating the Rad-score and type was established after multivariable logistic regression. The discrimination efficiency, calibration efficacy, and clinical utility value of the nomogram were evaluated.

RESULTS

The Rad-score model could predict the differentiation degree of lung adenocarcinoma with an area under the curve (AUC) of 0.83 (95% confidence interval [CI]: 0.78-0.89) in the internal validation cohort. The AUC of the nomogram and radiographic model was 0.86 (95% CI: 0.80-0.91), 0.78 (95% CI: 0.72-0.84) in the internal validation cohort respectively. The AUC of the nomogram in the external validation cohort was 0.73 (95% CI: 0.58-0.88). Delong's test showed that the nomogram performed better than radiographic features alone (p=0.001).

CONCLUSIONS

The proposed radiomics nomogram has the potential to predict the differentiation degree of lung adenocarcinoma preoperatively.

[Dynamic changes and influencing factors of HIV-1 DNA load in HIV-1 infected individuals under antiretroviral therapy]

Objective: To analyze the dynamic changes and influencing factors of HIV-1 DNA load in HIV-1 infected individuals under antiretroviral therapy (ART) in Dehong Dai and Jingpo autonomous prefecture, Yunnan province, and provide information support for the clinical use of HIV-1 DNA quantitative detection. Methods: The HIV infection cases in recent infection cohort from Dehong Center for Disease Control and Prevention during 2009-2018 were selected as study subjects. The dynamic curve of HIV-1 DNA load varrying with time was generated and logistic regression analysis was conducted to identify the risk factors for HIV-1 load in the recent follow up after ART and statistical analysis was performed by using SPSS 17.0. Results: Among the 113 HIV infection cases detected from the recent infection cohort, the recent HIV infection rate were 49.6%(56/113) males, sexual transmission cases and drug injection transmission cases accounted for 53.1% (60/113), 80.5% (91/113) and 19.5% (22/113), respectively. The dynamic changes curve showed that HIV-1 DNA load was relatively high (>800 copies /10⁶ PBMCs) before ART, and droped rapidly (<400 copies /10⁶ PBMCs) after ART for 1 year. However, HIV-1 DNA load decreased insignificantly from the second year of ART, and remained to be 269 copies/10⁶ PBMCs after ART for 6 years. Univariable logistic regression analysis indicated that OR (95%CI) of CD8, CD4/CD8 and HIV-1 DNA load were 1.00 (1.00-1.00), 0.30 (0.09-1.05) and 1.01 (1.00-1.01), respectively. Multivariable logistic regression analysis showed that OR value of HIV-1 DNA load base was 1.00 (1.00-1.01). Conclusions: HIV-1 DNA load decreased significantly in the first year of ART, then remained stable for years. HIV-1 DNA load base was the key factor associated with the decrease of HIV-1 DNA load, the lower the HIV-1 DNA load base, the lower HIV-1 DNA load. Therefore, earlier ART can contribute to the decrease of HIV-1 DNA load.

[A longitudinal analysis on dynamic change of platelet count in HIV-infected patients with access to antiretroviral therapy in Dehong Dai and Jingpo Autonomous Prefecture]

Objective: To explore the dynamic change of platelet count and related factors in HIV-infected patients with access to antiretroviral therapy (ART) in Dehong Dai and Jingpo autonomous prefecture of Yunnan province. Methods: A longitudinal analysis was used to analyze the dynamic change of platelet count in HIV-infected patients with access to ART. Linear mixed model (LMM) was used to analyze factors associated with the dynamic change of platelet count. Stratified analysis and sensitivity analysis were also conducted. Results: A total of 761 HIV-infected patients were recruited and 608 cases had at least one follow-up record (80.0%,608/761). 374, 555 and 233 cases were investigated in follow-up visits at month 6, 12 and 24, respectively. The mean platelet count and the proportion of higher platelet count (>300×10⁹/L) were significantly higher in women than in men at both baseline survey and each follow-up visit (P<0.05). Among patients with no obvious liver fibrosis, the mean platelet count was significantly higher in women than in men at baseline survey and each follow-up visit; while in the patients with liver fibrosis, the mean baseline platelet count was still significantly higher in women than in men, but the difference had no significance at follow-up visits. Results of LMM revealed that follow-up platelet count was positively correlated with gender (β=5.90, 95%CI: 1.09-10.70, P=0.016), baseline platelet count (β=0.82, 95%CI: 0.79-0.86, P<0.001) and time (β=1.76, 95%CI: 1.52-2.01, P<0.001). Sensitivity analysis among 220 cases who had both 12- and 24-month follow-up visits further confirmed that follow-up platelets count was still positively associated with gender (β=10.50, 95%CI: 2.24-18.74, P=0.013), baseline platelet count (β=0.71, 95%CI: 0.65-0.77, P<0.001) and time (β=1.60, 95%CI: 1.20-1.99, P<0.001) but negatively associated with age (β=-0.42, 95%CI: -0.78--0.06, P=0.021). Conclusions: The platelet count of HIV-infected patients gradually increased after ART. The mean platelet count was consistently higher in women than in men. Attention should be paid to the gender specific difference in platelet count in HIV-infected patients and timely intervention should be given to reduce the morbidity and mortality of platelet-related diseases.

[A retrospective cohort study of incidence of anemia and risk factors in HIV/AIDS patients with access to antiretroviral therapy in Dehong Jingpo and Dai Autonomous Prefecture in Yunnan province, 2004-2018]

Objective: To investigate the incidence of anemia and risk factors in HIV/AIDS patients with access to antiretroviral therapy (ART) during 2004-2018 in Dehong Jingpo and Dai Autonomous Prefecture (Dehong). Methods: A retrospective cohort study was conducted in HIV/AIDS patients receiving ART in Dehong during 2004-2018 based on the data extracted from the National HIV/AIDS antiretroviral therapy database. Cox proportional risk model was used to analyze the factors associated with the incidences of anemia and moderate or severe anemia in the HIV/AIDS patients. And the piecewise linear mixed-effects model was used to depict the trajectory of hemoglobin changes over time after initiating ART according to baseline level. Results: A total of 8 044 HIV/AIDS patients were included, in whom 6 337 (78.8%) were without anemia at baseline survey and had a median follow up time of 4.43 (P₂₅, P₇₅: 1.50, 6.71) years. The median follow up time for 1 291 new anemia cases and 293 new moderate or severe anemia cases was 0.16 (P₂₅, P₇₅: 0.07, 1.99) years and 0.48 (P₂₅, P₇₅:0.09, 2.97) years, respectively. The incidence rate of anemia and moderate or severe anemia was 4.40 per 100 person-years and 0.41 per 100 person-years respectively. In multivariable Cox regression analysis, older age, being female, being in Dai and Jingpo ethnic group, baseline BMI <18.5 kg/m², baseline CD4⁺T lymphocyte cell counts (CD4) <200 cells/μl, and zidovudine (AZT) -based initial treatment regimen were factors significantly and positively associated with incidence of anemia after treatment. Factors as being female, being in Dai ethnic group, baseline BMI <18.5 kg/m², mild baseline anemia, and AZT-based initial treatment regimen were significantly and positively associated with incidence of moderate or severe anemia after treatment. Conclusion: The risk for anemia was higher in HIV/AIDS patients with specific characteristics, such as age ≥60 years , being female, being in Dai and Jingpo ethnic groups, lower BMI, CD4 <200 cells/μl, and treatment of AZT, after initiation of ART in Dehong during 2004-2018. Additional efforts are needed to strengthen the screening, prevention and treatment of anemia in this population.

[Prevalence and related factors of CD4+T lymphocytes immune recovery among adult HIV/AIDS on antiretroviral therapy in Dehong Dai and Jingpo Autonomous Prefecture]

Objective: To analyze the longitudinal characteristics of CD4⁺T lymphocytes (CD4) among the adult HIV/AIDS on antiretroviral therapy (ART) and the related factors. Methods: A retrospective cohort of adult HIV/AIDS starting ART in Dehong Dai and Jingpo Autonomous Prefecture (Dehong) in 2007-2016 was followed up to December 31, 2018. Group-based trajectory models were utilized to identify CD4 subgroups based on immune recovery (whether and when CD4 reached the average level of >500 cells/μl). The demographics and information at ART baseline were described, and the related factors were analyzed with polytomous logistic regression. The SAS 9.4 software was used for statistical analysis. Results: A total of 7 605 adults with HIV/AIDS were included, of which the median (P₂₅,P₇₅) age at ART were 36 (30,43) years old, 61.0% were male, 42.5% were Han nationality, and 60.8% with the education of primary school or below. The follow-up duration M (P₂₅, P₇₅) was 6.1 (4.1,8.1) years. HIV/AIDS in Dehong showed four CD4 trajectory subgroups from low to high: below the average level, primary recovery to a normal level, full recovery to a moderate level, and normal steady level, accounting for 34.4%, 39.8%, 20.6%, and 5.2%, respectively. When compared with corresponding control groups, age <35 years at ART, female, education of middle school or above, sexual transmission, no opportunistic infection, CD4 ≥200 cells/μl, baseline regimen with tenofovir (TDF) and time from HIV diagnosis to ART <1 year were the related factors facilitating the higher CD4 subgroups. Conclusions: The various CD4 immune recoveries of HIV/AIDS were changing patterns after ART. Starting ART with a high CD4 level was beneficial to CD4 recovery to normal level during the follow-up period. Early initiation of ART and exceptional attention to CD4 immune recovery should be encouraged after the ART.

Genomic Analyses of Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa

Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

[Prevalence and correlates of HIV infection among cross-border families in Dehong Dai and Jingpo Autonomous Prefecture]

Objective: To study the prevalence and correlations of HIV infection among cross-border couples in the Dehong prefecture. Methods: A cross-sectional mass screening study with questionnaire interview and HIV testing was conducted among 17 594 registered cross-border couples from May 2017 through June 2018. Results: Among 32 400 participants, the overall prevalence of HIV infection was 2.27% (736/32 400), 2.44% (375/15 372) for Chinese citizens, and 2.12% (361/17 028) for foreign spouses. Among all the 13 853 couples with both spouses receiving HIV testing, 13 415(96.84%) were seroconcordant-negative couples, 142(1.03%) were serocondordant-positive couples, and 296(2.13%) were serodiscordant couples, including 167(1.20%) couples with positive husband and negative wife and 129(0.93%) couples with positive wife and negative husband. Multiple logistic regression analyses indicated that HIV infection was associated with drug use and risky sexual behaviors for male spouses. In contrast, HIV infection was associated with risky sexual behaviors for female spouses. Conclusion: The prevalence of HIV among cross-border couples in Dehong prefecture is high, underscoring the urgent need to scale up HIV testing, prevention, and behavioral intervention.

[Incidence and influencing factors of AIDS-related and non-AIDS-related deaths after receiving antiretroviral therapy among HIV-positive individuals in Dehong Dai and Jingpo Autonomous Prefecture, 2010-2019]

Objective: To explore the changing trends and influencing factors of AIDS-related and non-AIDS-related deaths after receiving antiretroviral therapy (ART) among HIV-positive individuals in Dehong Dai Jingpo autonomous prefecture (Dehong) from 2010 to 2019. Methods: Based on the Chinese National treatment database, HIV patients who initiated ART from 2010 to 2019 were included in the analysis. The cumulative incidence function was used to estimate the cumulative incidence of AIDS-related death and non-AIDS-related death, respectively. The Fine-Grey model was used to compare the differences between AIDS-related and non-AIDS-related deaths and analyze its influencing factors. Results: A total of 7 068 HIV-positive individuals were included, of which 388 were AIDS-related deaths and 570 were non-AIDS-related deaths. The cumulative mortality rate at years 1, 2, 3, 4, 5, 7 and 9 after receiving ART were 2.27%, 3.46%, 4.47%, 5.03%, 5.84%, 6.61%, 7.40% for AIDS-related deaths, and 1.63%, 3.11%, 4.68%, 6.02%, 7.42%, 10.49%, 12.75% for non-AIDS-related deaths, respectively. In the Fine-Grey model, older age at ART initiation, male, unmarried, injection drug use as the transmission route, lower baseline BMI, lower baseline CD4⁺ T cell counts, baseline FIB-4 score >3.25, and baseline anemia were risk factors for AIDS-related death. In contrast, age at ART initiation ≥45 years, male, Dai, and Jingpo minority ethnicities, unmarried, injection drug use as the transmission route, lower baseline BMI, baseline FIB-4 score >3.25, baseline eGFR <60 ml·min^-1·1.73 m^-2, and baseline anemia were risk factors for non-AIDS-related deaths. Conclusions: The cumulative mortality rate was low among HIV-positive individuals after receiving ART in Dehong during 2010-2019. The mortality of non-AIDS-related deaths was higher than that of AIDS-related deaths. There were also differences in the factors influencing AIDS-related and non-AIDS-related deaths and interventions should be intensified to target the influencing factors for non-AIDS-related deaths.

HGFDB: a collective database of helmeted guinea fowl genomics

As a vigorous and hardy and an almost disease-free game bird, the domestic helmeted guinea fowl (Numida meleagris, hereafter HGF) has attracted considerable attention in a large number of genetic study projects. However, none of the current/recent avian databases are related to this agriculturally and commercially important poultry species. To address this data gap, we developed Helmeted Guinea Fowl Database (HGFDB), which manages and shares HGF genomic and genetic data. By processing the data of genome assembly, sequencing reads and genetic variations, we organized them into eight modules, which correspond to ‘Home’, ‘Genome’, ‘Re-sequence’, ‘Gene’, ‘Variation’, ‘Download’, ‘Tools’ and ‘Help’, HGFDB provides the most comprehensive view of the HGF genome to date and will be relevant for future studies on HGF structural and functional genomics and genetic improvement.

Database URL:http://hgfdb.ynau.edu.cn/

High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae

Erigeron breviscapus is an important medicinal plant in Compositae and the first species to realize the whole process from the decoding of the draft genome sequence to scutellarin biosynthesis in yeast. However, the previous low‐quality genome assembly has hindered the optimization of candidate genes involved in scutellarin synthesis and the development of molecular‐assisted breeding based on the genome. Here, the E. breviscapus genome was updated using PacBio RSII sequencing data and Hi‐C data, and increased in size from 1.2 Gb to 1.43 Gb, with a scaffold N50 of 156.82 Mb and contig N50 of 140.95 kb, and a total of 43,514 protein‐coding genes were obtained and oriented onto nine pseudo‐chromosomes, thus becoming the third plant species assembled to chromosome level after sunflower and lettuce in Compositae. Fourteen genes with evidence for positive selection were identified and found to be related to leaf morphology, flowering and secondary metabolism. The number of genes in some gene families involved in flavonoid biosynthesis in E. breviscapus have been significantly expanded. In particular, additional candidate genes involved in scutellarin biosynthesis, such as flavonoid‐7‐O‐glucuronosyltransferase genes (F7GATs) were identified using updated genome. In addition, three candidate genes encoding indole‐3‐pyruvate monooxygenase YUCCA2 (YUC2), serine carboxypeptidase‐like 18 (SCPL18), and F‐box protein (FBP), respectively, were identified to be probably related to leaf development and flowering by resequencing 99 individuals. These results provided a substantial genetic basis for improving agronomic and quality traits of E. breviscapus, and provided a platform for improving other draft genome assemblies to chromosome‐level.

Chromosome Level Genome Assembly of Andrographis paniculata

Andrographis paniculata (Chinese name: Chuanxinlian) is an annual dicotyledonous medicinal plant widely grown in China and Southeast Asia. The dried plant has a highly acclaimed usage in the traditional Chinese medicine for its antipyretic, anti-inflammatory, and analgesic effects. In order to help delineate the biosynthetic pathways of various secondary metabolites, we report in this study a high-quality reference genome for A. paniculata. With the help of both PacBio single molecule real time sequencing and Illumina sequencing reads for error correction, the A. paniculata genome was assembled into a total size of 284 Mb with a contig N50 size of 5.14 Mb. The contigs were further assembled into 24 pseudo-chromosomes by the Hi-C technique. We also analyzed the gene families (e.g., KSL, and CYP450) whose protein products are essential for synthesizing bioactive compounds in A. paniculata. In conclusion, the high-quality A. paniculata genome assembly builds the foundation for decoding the biosynthetic pathways of various medicinal compounds.

Identification of Selective Sweeps in the Domesticated Table and Wine Grape (Vitis vinifera L.)

Grapevine (Vitis vinifera) is one of the most important fruit species in the Classical Mediterranean world. It is thought to have been domesticated 6,000-8,000 years ago in the Near East. However, the domestication of its wild relative into wine grapes or table grapes remains largely unknown. In this study, we analyzed 30 table grapes, 30 wine grapes, 30 dual-purpose grape accessions, as well as 30 wild relatives (Vitis vinifera ssp. sylvestris). The phenotypic comparison showed striking differences in berry weight, acidity and the content of aroma. Based on a total of 7,522,958 single-nucleotide polymorphisms, we identified several significant selective sweep regions for table and wine grapes. Besides the well-known sex-determination locus on chromosome 2, the other four highest signals shared by table and wine grapes could not be linked to the known QTLs. The identification of these genomic regions under selection sweep may reveal agronomically important traits that have been selected during grape domestication. This information not only sheds light on the mechanisms of adaptions and diversification, but also guide the genetic improvement in breeding programs.

A Chromosome-Scale Reference Assembly of a Tibetan Loach, Triplophysa siluroides

Cobitoidea is one of the two superfamilies in Cypriniformes; however, few genomes have been sequenced for Cobitoidea fishes. Here, we obtained a total of 252.90 Gb of short Illumina reads and 31.60 Gb of long PacBio Sequel reads, representing approximate genome coverage of 256× and 50×, respectively. The final assembled genome is about 583.47 Mb with contig N50 sizes of 2.87 Mb, which accounts for 91.44% of the estimated genome size of 638.07 Mb. Using Hi-C-based chromatin contact maps, 99.31% of the genome assembly was placed into 25 chromosomes, and the N50 is 22.3 Mb. The gene annotation completeness was evaluated by BUSCO, and 2,470 of the 2,586 conserved genes (95.5%) could be found in our assembly. Repetitive elements were calculated to reach 33.08% of the whole genome. Moreover, we identified 25,406 protein-coding genes, of which 92.59% have been functionally annotated. This genome assembly will be a valuable genomic resource to understand the biology of the Tibetan loaches and will also set a stage for comparative analysis of the classification, diversification, and adaptation of fishes in Cobitoidea.

A new reliable test for crossmatching: microplate hydrogel immunoassay technology

OBJECTIVES

To provide a novel assay to detect incomplete antibodies in the crossmatching test.

BACKGROUND

There is a requirement in China that both major and minor crossmatch tests are required. Among all methods of crossmatching, the tube anti-human globulin test requires tedious washing steps and is time-consuming, whereas the microcolumn gel immunoassay anti-human globulin test is susceptible to sample quality.

METHODS

The process of the microplate hydrogel immunoassay anti-human globulin test involves the use of our patented hydrogel chromatography medium and U-bottom microplates pre-coated with goat anti-human globulin (AHG). A mixture of red blood cells (RBCs) and serum is centrifuged through the hydrogel under precise conditions. In incompatible reactions, the sensitised RBCs are captured by the pre-coated AHG and form a layer over the bottom of the well, whereas in compatible reactions, the unbound RBCs form a button at the bottom of the well. The sensitivity of this new approach and the performance when testing old specimens were evaluated.

RESULTS

This approach was more convenient and slightly more sensitive than the tube anti-human globulin test and was superior to the microcolumn gel immunoassay when testing old specimens.

CONCLUSION

In general, this assay is suitable for the routine clinical use of crossmatching to detect incomplete antibodies.

[Experimental study on the effect of acid stimulation on human cell characteristics]

Objective:The purpose of the present study was to explore the characteristics and differentiation of somatic cells in vitro undergoing a low pH treatment, so as to provide new therapeutic strategies for treating sensorineural hearing loss.Method: The human mature somatic cells were selected as the target cells, and the cells were treated with different pH values to observe the cell morphology. The cell characteristics were identified from alkaline phosphatase (AKP) activity, immunohistochemical staining and molecular biology, and the most suitable pH value was selected. In addition, a mouse model of the cochlear lesion was constructed using bilirubin. Subsequently, the characteristics and therapeutic effect of somatic cells undergoing low pH treatment were examined by morphology, AKP activity, immunofluorescence assay and Q-PCR.Result:The cell growth of the experimental group was significantly better than those in the control group. The activity of AKP in the experimental group was higher than that in the control group. The expression of Nanog and Oct4 was both positive in the two groups. When the cells were changed to neurobasol medium, the marker of Nestin was positive.Conclusion:The human somatic cells undergoing a low pH treatment showed the similar characteristics as those of induced pluripotent stem (iPS) cells; although the functions and therapeutic effect of these altered human somatic cells need to be further studied.

Effects of aging, baseline renal function and stage of HIV infection on post-treatment changes in renal function among HIV-infected patients: a retrospective cohort study

OBJECTIVES

The use of combination antiretroviral therapy (cART) increases clinical uncertainty about changes in renal function. Specifically, little is known regarding the interaction of the effects of aging, baseline renal impairment, and stages of HIV infection on post-treatment changes in renal function.

METHODS

This analysis included 5533 HIV-infected patients on cART in 2004-2016. Progression to chronic kidney disease (CKD) was defined as either two consecutive estimated glomerular filtration rate (eGFR) measurements < 60 mL/min/1.73 m² for baseline eGFR ≥ 60 mL/min/1.73 m² (mild renal impairment or normal renal function) or a 25% decline for baseline eGFR < 60 mL/min/1.73 m² (moderate renal impairment).

RESULTS

During follow-up (median 4.8 years), 130 (2.3%) of the patients progressed to CKD. A total of 20.1% of patients with baseline normal renal function progressed to mild renal impairment, while 74.0% of patients with baseline mild or moderate renal impairment improved to normal renal function. In multivariable analysis, a significant positive baseline-eGFR-by-World Health Organization (WHO)-stage interaction effect on progression to CKD in all patients was identified, indicating a cross-over effect from a reduced risk to an increased risk. A significant negative baseline-age-by-WHO-stage interaction effect on progression to mild renal impairment in patients with baseline normal renal function was identified, with adjusted hazard ratios progressively lower at older ages. In addition, there were significant associations with older age, lower baseline eGFR, Dai ethnic minority, and anaemia for both outcomes, hyperglycaemia for CKD only, and higher CD4 count, tenofovir and ritonavir-boosted lopinavir use for mild renal impairment only.

CONCLUSIONS

Our data suggest a complex pattern of renal function dynamics in patients on cART, which requires precise management with systematic monitoring of the interaction of the effects of sociodemographic, nephrological and HIV-specific clinical characteristics.

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.

[Molecular transmission clusters on HCV genotypes among newly reported HIV/HCV co-infection in Dehong Dai and Jingpo autonomous prefecture of Yunnan province, 2016]

Objective: To understand the characteristics on major strain subtypes of hepatitis C virus among HIV/HCV co-infected patients, so as to explore the molecular transmission clusters and related risk factors of HCV strains. Methods: A total of 336 newly reported HIV-infected patients were diagnosed as HIV/HCV co-infection in Dehong Dai and Jingpo autonomous prefecture (Dehong) in 2016. We used Nested PCR to amplify CE1 and NS5B genes among 318 samples with plasma levels above 200 μl, before using the combining phylogenetic tree and constructing molecular propagation network method to analyze the related data. Results: A total of 267 HIV/HCV co-infection patients who had met the HCV genotyping requirements were screened the gene subtypes were diversified. Among these genotypes, proportions of 3b, 6n, 6u, 1a, 3a and other subtypes appeared as 32.6% (87/267), 18.4% (49/267), 15.7%(42/267), 13.1%(35/267), 11.2%(30/267) and 9.0%(24/267) respectively. Molecular transmission network of five major HCV genotypes was constructed with a clustering rate of 39.1% (95/243). The clustering rate of subtype 1a was the highest, as 71.4% (25/35). Results from the multivariate logistic regression showed that ethnic minorities other than the Yi and Jingpo (vs. the Han, OR=0.17, 95%CI: 0.04-0.71), the married spouses (vs. the unmarried, OR=0.42, 95%CI: 0.18-0.94), the 6n and 3a subtype (vs. the 3b subtype, OR=0.34, 95%CI: 0.12-0.95; OR=0.22, 95%CI: 0.05-0.93) were more difficult to form transmission clusters. However, the 6u and 1a subtype (vs. the 3b subtype, OR=3.10, 95%CI: 1.21-7.94; OR=4.00, 95%CI: 1.32-12.11) seemed more likely to form the transmission clusters. Conclusion: Ethnicity, marital status and genetic subtypes were factors significantly associated with the formation of transmission clusters related to the major HCV gene subtypes among newly reported HIV/HCV co-infection in Dehong.

Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses

Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement.

Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.

[HIV-1 drug resistance transmission threshold survey in Dehong prefecture of Yunnan province, 2015]

Objective: To study the HIV-1 drug resistance transmission level in HIV infected persons receiving no antiviral therapy in Dehong prefecture of Yunnan province in 2015. Methods: A total of 72 plasma samples were collected from recently reported HIV-infected persons aged 16-25 years in Dehong from January to July 2015 for drug resistance gene detection. Results: Forty eight samples were successfully sequenced and analyzed. Among them, 31.2% (15/48) were from Chinese, and 68.8% (33/48) were from Burmese. Based on pol sequences, HIV genotypes included URF (52.08%, 25/48), CRF01_AE (16.67%, 8/48), RF07_BC (10.42%, 5/48), subtype B (6.25%, 3/48), subtype C (6.25%, 3/48), CRF57_BC (6.25%, 3/48) and CRF08_BC (2.08%, 1/48). One drug resistant mutation site to non-nucleoside analog reverse transcriptase inhibitor (NNRTI) and two drug resistant mutation site to nucleoside analog reverse transcriptase inhibitor (NRTI) were detected in four sequences. Based on the statistical method of HIV drug resistance threshold survey, the prevalence of HIV-1 drug resistant strain was 5%-15%. Conclusions: The proportion of Burmese among newly reported HIV-infected individuals aged 16-25 years in Dehong in 2015 was higher. HIV-1 genetic diversity was found in Dehong. The prevalence of HIV-1 drug resistant strain had reached a moderate level in Dehong.

[Estimation of HIV diagnosis rate with CD4(+) T-lymphocyte level and infected-time model in Dehong Prefecture, Yunnan Province]

Objective: To estimate the total number of people infected with HIV and to calculate the diagnosis rate of HIV in Dehong Prefecture, Yunnan Province. Methods: Through the comprehensive AIDS prevention and treatment information system, we collected and analyzed the relevant information of the new diagnosis report of HIV in Dehong Prefecture, Yunnan Province in 2006-2015, mainly including age, sex, infected transmission, CD4(+) T-lymphocyte counts, diagnostic time and so on. The content of the study was to establish a model method for estimating the diagnosis rate of HIV in Dehong. First, used the first CD4(+) T-lymphocyte count after HIV diagnosis to estimate the date of infection. Then based on the estimated time from HIV infection to diagnosis we can estimate the diagnosis delay distribution which in turn can be used to account for individuals infected but not yet diagnosed and thus estimated the total number of HIV infections (diagnosed and undiagnosed). Finally, the number of new infections in each year was added to estimate the total number of infected people, and the number of people who had been diagnosed was divided by the total number of infected persons to obtain the proportion of HIV diagnosis rate. Results: There were 8 215 reported cases in Dehong from 2006 to 2015, of which 1 297 cases were reported in 2007 (15. 8%) and 361 cases (4.4%) in 2015. The diagnosis rate of newly infected persons were 88% in 2005 and before. And from 2006 to 2015, the diagnosis rate of newly infected persons were 75%, 71%, 68%, 66%, 61%, 58%, 53%, 45%, 40% and 33%, respectively. The total number of newly infected persons in 2005 and before was 11 197 cases. The annual new infected number from 2006 to 2015 was 653, 671, 723, 640, 509, 468, 369, 375, 285 and 224 cases. The total number of people infected with HIV in Dehong was 16 114 cases, and the diagnosis rate was 87.7%. Conclusion: The diagnosis rate of HIV in Dehong was at a high level. Since 2008, the annual number of new infections in Dehong has been declining.

[Estimating HIV incidence among female sex workers and injection drug users in Dehong Prefecture, 2009-2017]

Objective: To obtain HIV incidence among injection drug users (IDU) and female sex workers (FSW) in Dehong Prefecture, Yunnan Province during 2009-2017. Methods: We recruited drug users and female sex workers from all sentinel surveillance sites across Dehong Prefecture during 2009-2017. A total of 10 480 IDU and 18 126 FSW in Dehong Prefecture were recruited by fingerprint technique. Data about drug uses, commercial sexual behavior, sociodemographic characteristics was collected by structured questionnaire. HIV-positive patients who were long-term infected or with CD4(+) T cell count was ≤200 were not included for further HIV incidence testing. Also, those who self-identified as on antiretroviral treatment (ART) or AIDS cases were also excluded. A total of 841 and 157 plasma specimens from IDU and FSW that met the inclusion criterion were finally included, respectively. Limiting antigen avidity enzyme immunoassay(LAg-Avidity EIA) were performed to calculate the HIV incidence among these two sub-populations. Results: A total of 3 444 IDU were HIV-positive, among which 884 (25.7%) were Burmese with age of (30.4±7.7), and 2 560 were Chinese with age of (36.6±7.3). Among 228 HIV-positive FSW, 109 (47.8%) were Burmese with age of (27.1±6.3), 119 (52.5%) were Chinese with age of (29.9±11.1). For IDU, the estimated HIV incidence among Burmese in 2009-2010, 2011-2012, 2013-2014, 2015-2017 was 4.20% (95%CI: -0.55%-8.95%), 7.75% (95%CI: 2.95%-12.55%), 11.79% (95%CI: 5.38%-18.20%), 10.30% (95%CI: 5.67%-14.94%), respectively, while Chinese were 3.11% (95%CI: 1.59%-4.64%), 0.03% (95%CI: -0.03%-0.08%), 1.55% (95%CI: 0.54%-2.57%), 0.58% (95%CI: -0.06%-1.04%), respectively. In 2009-2011, 2012-2014, 2015-2017, estimated HIV incidence among Burmese FSW was 0.22% (95%CI: -0.21%-0.64%), 1.24%(95%CI: 0.15%-2.32%), 0.55%(95%CI: 0.01%-1.08%). Whereas, estimated HIV incidence among Chinese FSW was 0.62% (95%CI: 0.25%-0.98%), 0.11% (95%CI: -0.04%-0.26%), 0.22% (95%CI: 0-0.44%). Conclusion: HIV incidences among Chinese IDU and FSW are on the downward trend, while Burmese IDU and FSW seem to be gaining momentum.

Serum Stem Cell Factor Level Predicts Decline in Kidney Function in Healthy Aging Adults

BACKGROUND AND OBJECTIVES

Stem cell factor (SCF), the ligand of the c-kit receptor, actively participates in the organ reconstruction and fibrosis associated with various diseases, including kidney disease. However, it remains unclear whether SCF plays a role in kidney aging.

DESIGN, SETTING, PARTICIPANTS, AND MEASUREMENTS

In the present study, we measured the serum SCF level, estimated glomerular filtration rate (eGFR), and other biological parameters in a Chinese Han group of 892 subjects, and explored the relationship between SCF level and renal function during aging; we sought to define novel biomarkers of kidney aging.

RESULTS

Multiple linear regression was used to select potential indicators of decline in renal function. Only age, SCF level, and 25% maximum expiratory flow (25% MEF) were significant predictors after redundancy analysis (|r| > 0.70 and P < 0.05). Multiple linear regression showed that the relationship among eGFR, SCF level, and age could be described as follows: eGFR = 154.486 - (0.846 × age) - (0.011 × SCF level).

CONCLUSIONS

We found no between-gender difference in the effect of SCF on kidney aging. In conclusion, the SCF level is an ideal biomarker of renal aging and may help to predict changes in eGFR during aging.

[HIV gene subtypes of newly reported HIV/AIDS cases in Dehong Dai and Jingpo autonomous prefecture of Yunnan province, 2016]

Objective: To explore distribution of HIV gene subtypes among newly reported HIV/AIDS cases from China and Myanmar in Dehong Dai and Jingpo prefecture of Yunnan province in 2016. Methods: We conducted DNA extractions from newly reported HIV/AIDS cases in 2016. The gag, env and pol genes were amplified by using reverse transcription-PCR (RT-PCR) and sequenced to identify HIV subtypes. Results: A total of 1 112 newly diagnosed HIV cases were reported in Dehong in 2016, and the HIV subtypes were identified for 860 cases. Subtype C was predominant (33.6%), followed by unique recombinant forms (URFs) (28.4%), CRF01_AE (18.6%) and so on. URFs include four recombination, among which the recombination of CRF01_AE and C subtype were predominant. The HIV subtype distribution was associated with nationality and transmission route in HIV/AIDS cases from Myanmar. Conclusions: The gene subtypes of C, URFs and CRF01_AE were mainly distributed; distribution of URFs remained complex and diverse among newly reported HIV/AIDS cases in Dehong in 2016.

The Genome Sequences of 90 Mushrooms

Macrofungus is defined as the fungus that grows an observable sporocarp. The sporocarps of many species are commonly called mushrooms and consumed by people all around the world as food and/or medicine. Most macrofungi belong to the divisions Basidiomycetes and Ascomycetes, which are estimated to contain more than 80,000 species in total. We report the draft genome assemblies of macrofungi (83 Basidiomycetes species and 7 Ascomycetes species) based on Illumina sequencing. The genome sizes of these species ranged from 27.4 Mb (Hygrophorus russula) to 202.2 MB (Chroogomphus rutilus). The numbers of protein-coding genes were predicted in the range of 9,511 (Hygrophorus russula) to 52,289 (Craterellus lutescens). This study provides the largest genomic dataset for macrofungi species. This resource will facilitate the artificial cultivation of edible mushrooms and the discovery of novel drug candidates.

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

Phytophthora cactorum is a homothallic oomycete pathogen, which has a wide host range and high capability to adapt to host defense compounds and fungicides. Here we report the 121.5 Mb genome assembly of the P. cactorum using the third-generation single-molecule real-time (SMRT) sequencing technology. It is the second largest genome sequenced so far in the Phytophthora genera, which contains 27,981 protein-coding genes. Comparison with other Phytophthora genomes showed that P. cactorum had a closer relationship with P. parasitica, P. infestans and P. capsici. P. cactorum has similar gene families in the secondary metabolism and pathogenicity-related effector proteins compared with other oomycete species, but specific gene families associated with detoxification enzymes and carbohydrate-active enzymes (CAZymes) underwent expansion in P. cactorum. P. cactorum had a higher utilization and detoxification ability against ginsenosides-a group of defense compounds from Panax notoginseng-compared with the narrow host pathogen P. sojae. The elevated expression levels of detoxification enzymes and hydrolase activity-associated genes after exposure to ginsenosides further supported that the high detoxification and utilization ability of P. cactorum play a crucial role in the rapid adaptability of the pathogen to host plant defense compounds and fungicides.

[Epidemiological characteristics of newly reported HIV infections in Chinese and Burmese residents, during 2012-2016 in Dehong Dai and Jingpo Autonomous Prefecture, Yunnan province]

Objective: To understand the epidemiological characteristics of newly reported HIV infections in Chinese and Burmese residents during 2012-2016 in Dehong Dai and Jingpo Autonomous Prefecture of Yunnan province (Dehong) and to provide evidence for the development of related programs on prevention and control. Methods: All the HIV infections who were newly reported during 2012-2016 in Dehong, were recruited as the study subjects, with epidemiological characteristics of the cases analyzed by using the software SPSS 22.0. Results: A total of 5 692 HIV infections were newly reported between 2012 and 2016 (including 5 592 in this study), in which the Chinese patients accounted for 43.3% (2 419) and the rest 56.7% (3 173) were Burmese. Differences in age, gender and other social characteristics of these newly reported HIV infections were statistically significant between the Chinese and the Burmese (all p-values <0.05). Most cases were males and between the age of 20-49 years old. Other characteristics of the patients would include: having had primary school education, married, being farmers, and with CD(4)(+)T cells counts ≥350 cells/μl. HIV infection was mainly transmitted through sexual contact among the Chinese patients but through injecting drug use among the Burmese patients. Conclusions: Epidemiological characteristics of the newly reported HIV infections were different between the Chinese and the Burmese, between 2012 and 2016 in Dehong. Targeted prevention and control programs should be taken.

[Radiological analysis of coronal and sagittal spinopelvic parameters in patients with degenerative lumbar kyphoscoliosis]

Objective: To review and compare radiological parameters between degenerative lumbar kyphoscoliosis (DLKS) and degenerative lumbar kyphosis (DLK), and analyze the relationships between coronal and sagittal deformities and compensatory mechanisms of sagittal balance. Methods: A total of 82 patients with lumbar degenerative deformities were enrolled for our radiographic study at Department of Spinal Surgery, Peking University People's Hospital from January 2016 to May 2017. These patients were divided into two groups: DLKS group (39 patients) with lumbar coronal and sagittal deformities, and DLK group (43 patients) just with lumbar sagittal deformity. Complete spinopelvic radiographic parameters were compared. Results: The Cobb angle and lumbar lordosis of DLKS group were (23.0±11.8)° and (18.2±12.1)°, while the lumbar lordosis of DLK group was (20.4±10.2)°. In DLKS group, Cobb angle had correlations with lumbar lordosis(r=-0.338, P=0.035), and central sacral vertical line distance had significant correlations with thoracolumbar junctional angle (r=0.488, P=0.002) . Moreover, no significant differences of all sagittal spinopelvic parameters were found between two groups (P>0.05). In DLKS group, significant correlations between lumbar lordosis and sacral slope (r=0.617, P=0.000), and correlations between lumbar lordosis and thoracic kyphosis(r=-0.363, P=0.023) were observed. In DLK group, lumbar lordosis showed significant correlations with thoracic kyphosis(r=-0.341, P=0.025) and sacral slope (r=0.772, P=0.000). According to Nash-Moe grading scale of apical vertebral rotation, 10 patients were with Ⅰ-Ⅱ grade while 29 patients with Ⅲ-Ⅴ grade in DLKS group. Conclusions: Both as typical lumbar degenerative deformities, there are some correlations between scoliosis and kyphosis. However, coronal scoliosis may not influent sagittal morphological parameters for DLKS patients. Thoracic curve changes and pelvic backtilt are both important for maintaining the sagittal balance in patients with degenerative lumbar kyphoscoliosis.

Brassica napusGLABRA3-1 promotes anthocyanin biosynthesis and trichome formation in true leaves when expressed in Arabidopsis thaliana

Previous studies have shown that GLABRA3 (AtGL3), a bHLH transcription factor, plays essential roles in anthocyanin biosynthesis and trichome formation in Arabidopsis thaliana. However, there have been no such studies of a homologue, BnGL3, from the closely related crop, Brassica napus. Here, we analysed the BnGL3-1 coding domain sequence from the B. napus cultivar QINYOU Seven, identified conserved protein domains and performed a phylogenetic analysis to elucidate its relationship with homologues form a range of plant species. When expressed in tobacco leaves as a fusion protein with green fluorescent protein, BnGL3-1 accumulated in the nucleus, consistent with its predicted function as a transcription factor. Ectopic expression of the BnGL3-1 gene in the A. thaliana gl3-3 mutant resulted in levels of anthocyanins and numbers of trichomes in true leaves that were higher than in wild-type plants. Moreover, overexpression of BnGL3-1 in gl3-3 compensated for the promotion and repression of genes involved in anthocyanin biosynthesis and trichome formation, respectively, that has been reported in gl3-3 young shoots and expanding true leaves. This study provides new insights into GL3 function in anthocyanin biosynthesis and trichome formation in crucifers, and represents a promising target for genetic manipulation of B. napus.

UV-curable ladder-like diphenylsiloxane-bridged methacryl-phenyl-siloxane for high power LED encapsulation

A UV curable ladder-like diphenylsiloxane-bridged methacryl-phenyl-siloxane (L-MPS) was synthesized from phenyltrichlorosilane, diphenylsilanediol and methacryloxypropyldimethylmethoxysilane via dehydrochlorination precoupling, supramolecular architecture-directed hydrolysis-condensation and end-capping reactions. The L-MPS has a condensation degree of ∼100%, and can be complete crosslinked by UV curing. XRD, TEM and molecular simulation suggest that the ladder-like molecules are close packed with a periodic distance of ca. 1.2 nm. The L-MPS shows transmittance of 98% and a refractive index of ca. 1.61 at 450 nm. The cured L-MPS with a T_d5% value of 465.5 °C showed excellent anti-yellowing and anti-sulfidation properties. The cured L-MPS film and the encapsulated LED samples were compared with those of Dow Corning OE-6630 and OE-7662. It is believed that the dense nano-ladder unit also contributes to the thermal, gas barrier and even optical properties. L-MPS shows promising potential as a high power LED encapsulant and optical coating for use in harsh environments. This work provides an approach to integrate this novel ladder structure with advanced properties.

UV-curable ladder-like polysiloxane was constructed to integrate high RI (1.61/450 nm) with high thermal stability etc. for high power LED encapsulation.

[A cohort study of HIV incidence among injecting drug users in Dehong Prefecture, Yunnan Province]

Objective: To investigate the incidence rates of HIV among injection drug users (IDU) in Dehong Prefecture, Yunnan Province. Methods: We recruited 1 413 HIV-negative IDU attending drug rehabilitation centers and identified a further 1 830 potential participants from a historical database from 2004-2009 using the same criteria. Fingerprint recognition technology was used to confirm the identity of all participants. A total of 3 243 HIV-negative IDU were recruited by the end of 2015, of which 2 546 (78.5%) had been followed up at least once since the initial data collection and 697 (21.5%) were lost to follow-up. Epidemiological data were collected through structured face-to-face interviews which included items on knowledge of AIDS, drug use, sexual activity and history of HIV testing. We collected 3-5 ml of venous blood from each subject for HIV testing. The Chi-squared test was used to compare the characteristics of those IDUs successfully followed up and those lost to follow-up. Results: We identified 226 new HIV cases among the 2 546 respondents-representing 13 907.1 person-years of follow-up and implying an average HIV incidence rate of 1.6 per 100 person-years over the entire study period (95%CI: 1.4-1.9). The incidence rate (per 100 person-years) was 2.6 (95%CI: 2.2-3.1) for the period 2004-2009 and 1.6 (95%CI: 1.0-2.3), 1.7 (95%CI: 1.1-2.4), 1.2 (95%CI: 0.8-1.9), 0.6 (95%CI: 0.3-1.1), 0.2 (95%CI:0.0-0.7), 0.5 (95%CI: 0.1-1.4) for each year from 2010 to 2015 respectively. Conclusion: Although the incidence rate of HIV remains high among IDUs in Dehong, there was a declining trend over the period studied.

[Comparative study on the HIV epidemic between the Chinese and Burmese drug users in drug rehabilitation places in Dehong Prefecture, Yunnan Province]

Objective: To compare the prevalence of HIV infection and its risk factors among Chinese and Burmese drug users living in Dehong Prefecture, Yunnan Province. Methods: We obtained plasma specimens and gathered demographic data from 7 867 drug users with Chinese or Burmese nationality attending rehabilitation clinics in Dehong Prefecture from October 2014 to September 2015. Of these, 7 756 individuals who gave valid questionnaire responses, including 5 389 Chinese and 2 367 Burmese, were enrolled in the study after giving informed consent. We used the Chi-squared test to compare the demographic characteristics and HIV prevalence between the Chinese and Burmese drug users. Logistic regression was then used to identify risk factors for HIV infection. Results: The HIV infection rate of 7 756 subjects (aged (35.45 ± 10.91) years old) was 7.18%, in which Burmese with higher HIV infection rate (9.38%, 222/2 367) than Chinese (6.22%, 335/5 389) (χ²=24.21, P<0.001). In chinese drug users, OR (95%CI) of HIV infection of those aged 25-34 years old, 35-44 years old and ≥45 years old were 2.88 (1.46-5.69), 5.72 (2.87-11.40) and 3.48 (1.66-7.27),compared with those aged below 25 years;Compared with married participants, OR (95% CI) of those unmarried and divorced were 1.44 (1.08-1.93) and 1.56 (1.09-2.24); Jingpo drug users were 1.47 (1.07-2.04) times to get HIV infection,compared with Han ethnicity; OR (95%CI) of HIV infection for IDUs was 11.48 (9.73-16.01) compared with NIDUs.In Burmese drug users, OR (95% CI) of HIV infection for females was 0.50 (0.26-0.93) compared with men;Compared with those aged below 25 years,those aged 25-34,35-44 and ≥45 years had OR (95% CI) of 1.82 (1.18-2.77), 2.90 (1.82-4.62) and 2.31 (1.24-4.30), respectively; OR (95% CI) of Jingpo participants was 2.22 (1.44-3.41) compared with Han nationality; OR (95%CI) of HIV infection for IDUs was 10.61 (7.68-14.64) compared with NIDUs. Conclusion: The HIV infection rate of Burmese drug users was higher than that of Chinese drug users. Measures of HIV prevention and control should be mainly allocated in those 25 years above, non-married, Jingpo ethnicity and IDU in Chinese drug users, while in Burmese drug users,those females, 25 years above, Jingpo ethnicity and IDU should be higlighted in HIV prevention and control.

[A cross-sectional survey of receiving no methadone maintenance treatment in HIV infected injecting drug users in Dehong Dai and Jingpo autonomous prefecture, Yunnan province]

Objective: To understand the current status of receiving no methadone maintenance treatment (MMT) and influencing factors in HIV infected injecting drug users (IDUs) in Dehong Dai and Jingpo autonomous prefectures, Yunnan province. Methods: Data of survival of IDUs with AIDS in Dehong were collected from " Chinese National Comprehensive HIV/AIDS and Care Information System" in December, 2014. Results: There were 987 IDUs who should receive MMT, the majority of them were males (94.6%, 934/987), aged 35-44 years (53.0%, 523/987) and farmers (77.2%, 762/987). Among the 987 IDUs, 60.2% (592/987) received no MMT. Multivariate logistic regression analysis showed that being female (OR=2.66, 95%CI: 1.21-5.87), in Jingpo ethnic group (OR=3.05, 95% CI: 1.97-4.71) were the major risk factors for receiving no MMT; not being farmers (OR=0.46, 95%CI: 0.31-0.70), in Dai ethnic group (OR=0.53, 95%CI: 0.36-0.79), diagnosed HIV infection history ≥10 years (OR=0.60, 95%CI: 0.45-0.81) were the major protective factors for receiving no MMT. The reasons for receiving no MMT included long distance journey (289, 48.8%), fear of exposure (124, 20.9%), poor daily medication compliance (59, 10.0%), fear of side effects (47, 7.9%), others (73, 12.3%). Conclusions: The proportion of receiving no MMT in IDUs with AIDS in Dehong was high. Being female and farmer, in Jingpo ethnic group, low educational level, short diagnosed HIV infection history were influencing factors for receiving no MMT. The effective intervention measures should be taken to further improve MMT coverage according to the different characteristics of the patients.

[Comparison of genotypes of hepatitis C virus between Chinese and Burmese drug users living in Dehong Prefecture, Yunnan Province]

Objective: To analyze the distribution of hepatitis C virus (HCV) genotypes among Chinese and Burmese drug users in Dehong Prefecture, Yunnan Province. Methods: Plasma specimens and relevant epidemiological data were collected from 7 545 drug users attending rehabilitation centers and methadone clinics in Dehong Prefecture from January to September in 2015, of which 752 were positive for HCV antibodies. HCV RNA was then extracted from 139 random specimens (64 Burmese and 75 Chinese) and the CE1 and NS5B regions were amplified by nested PCR. The sequences of these HCV genes were aligned, a phylogenetic tree was constructed using MEGA 6.0.6 and the average genetic discrete rate of each subtype group was calculated. We used Fisher's exact test to compare distribution of HCV subtypes from different people, using analysis of variance to compare the discrete rates of different CE1 and NS5B subtypes. Results: While we successfully amplified RNA from 43 specimens provided by Burmese patients (67%), including 31 with CE1 region and 38 with NS5B region, 52 from Chinese patients (69%) were successfully amplified including 43 with CE1 region and 45 with NS5B region. We found that 3b and 6n were the predominant subtypes and were found in 27% (n=14) and 37% (n=19) of Chinese and 28% (n=12) and 33%(n=14) of Burmese specimens. Subtypes 6u, 3a, 1a and 1b were present in 14%(n=7), 19%(n=10), 2% (n=1) and 2%(n=1) of Chinese specimens and 16%(n=7), 5%(n=2), 16%(n=7) and 2%(n=1) of Burmese specimens respectively. While the prevalence of subtype 1a was higher among samples from Burmese patients than Chinese patients (P=0.015), the presence of subtype 3a was higher among the latter (P=0.031). The discrete rates of CE1 region subtypes 1a, 1b, 3a, 3b, 6n and 6u were 0.048±0.007, 0.091±0.013, 0.074± 0.008, 0.061 ± 0.006, 0.136 ± 0.009 and 0.031 ± 0.005 (F=516.26, P<0.001). The discrete rates for NS5B region subtypes 1a, 1b, 3a, 3b, 6n and 6u, meanwhile, were 0.032±0.006, 0.065±0.012, 0.058±0.008, 0.041± 0.005, 0.059 ± 0.008, 0.045 ± 0.006 (F=45.11, P<0.001). Conclusion: Six HCV subtypes were identified among drug users in Dehong Prefecture, of which 6n and 3b were predominant. There were statistically significant differences in the distribution of subtypes 1a and 3b, which have been circulating for a long time in this population, between samples from Chinese and Burmese participants.

More improvement than progression of liver fibrosis following antiretroviral therapy in a longitudinal cohort of HIV-infected patients with or without HBV and HCV co-infections

We examined the effect of combination antiretroviral therapy (cART) on liver fibrosis among HIV-infected patients with or without hepatitis B (HBV) or C virus (HCV) co-infection. This was a retrospective cohort study of HIV-infected patients receiving cART during 2004-2016. Liver fibrosis was assessed using Fibrosis-4 (FIB-4) score with three classifications: Class 1, <1.45; Class 2, 1.45-3.25; Class 3, >3.25. Of 3900 participants, 68.6% were HIV mono-infected, 5.3% were HIV/HBV co-infected, 23.8% were HIV/HCV co-infected and 2.3% were HIV/HBV/HCV co-infected. Participants received follow-up treatment (median was 3.3 years). Improvement to a lower class was observed in Class 2 (52.6%) and Class 3 (74.2%), respectively. Progression to a higher class was observed in 12.8% and 5.0% in Class 1 and Class 2, respectively, and with a median time of 5.7 months. For improvement to lower classes, older age, male, Dai ethnicity, injection drug use, HCV co-infection and tenofovir for treatment were negative predictors, but in Class 3 of FIB-4 and time-updated increases in CD4 count from baseline were positive predictors. For progression to higher classes, older age, male, Jingpo ethnicity and HCV co-infection were positive predictors, while baseline CD4 count and in Class 2 of FIB-4 were negative predictors. Improvement to lower class linked with decreased mortality risk among patients in Class 3. Early cART initiation for HIV-infected patients with and without hepatitis co-infections may mitigate or slow down some of liver fibrosis, but special attention should be given to those who are older, male, co-infected with HCV.

[Tracing hepatitis C virus transmission by using high-throughput sequencing technique]

OBJECTIVE

An approach for analysis of hepatitis C virus (HCV) quasispecies using Hiseq high-throughput sequencing (hereinafter referred to as Hiseq sequencing) technique was developed and then applied to investigate a possible case of HCV needle sharing transmission.

METHODS

One case of HCV antibody seroconversion (P1) was found in a methadone clinic on January 15, 2015. Four HCV antibody positive injecting drug users (IDUs), P2 to P5, suspected to be involved in needle sharing transmission with P1 during the period (after March 24, 2014) that P1 may be infected with HCV were investigated, and another 28 HCV antibody positive IDUs were selected as controls (C1 to C28). These controls came from the same methadone clinic or lived in the same town with P1. The RNAs were extracted from the plasma specimens and then reverse-transcribed into cDNA. After HCV subtyping, Hiseq sequencing was performed to detect and sequence the HCV quasispecies (263 bp) in the specimens with the same subtype as P1. The frequency of quasispecies was counted and ranked. Intrapersonal and interpersonal genetic distance and phylogenetic tree were calculated.

RESULTS

The HCV subtype of specimen P1 was 3b. All the other specimens with the same subtype were P2, C7, C12, C14, C15, C16, C19, C20 and C28. Hiseq sequencing was successfully performed in 9 out of these 10 specimens, and 249 753 to 1 086 333 (average 869 608) cleaned sequences representing 3 to 172 (average 48) unique HCV quasispecies were obtained. The medians (P50) of intrapersonal genetic diversities from the 9 specimens were 0.4% to 12.3%. The P50 (P25, P75) of genetic diversities between P1 and the other 8 specimens were 19.0% (18.4%, 19.8%), 10.4% (2.8%, 18.3%), 19.6% (17.8%, 21.4%),24.9% (23.8%, 26.1%), 19.8% (18.7%, 20.7%), 20.1% (18.9%, 21.2%), 20.6% (20.0%, 21.1%), 23.6% (22.4%, 24.8%). There were no significant difference between the genetic diversities of P1 and P2 and those of P1 and other 7 specimens (H=9.40, P=0.100). The genetic diversities between few HCV quasispecies from P1 and few ones from C7 were 0. Phylogenetic tree analysis indicated that there was no HCV transmission relationship between P1 and P2, but there was HCV transmission relationship between P1 and C7.

CONCLUSION

With the feature of high-throughput, easier operation and lower cost, Hiseq sequencing technique has high practical value in tracing HCV transmission at the quasispecies level.

[Drug resistance and influencing factors in adult AIDS patients receiving antiretroviral treatment in Dehong, Yunnan province]

OBJECTIVE

To investigate the incidence of drug resistance in adult AIDS patients receiving antiretroviral treatment(ART)and influencing factors in Dehong prefecture, Yunnan province during 2012-2014.

METHODS

For this cohort study, all the AIDS patients aged over 15 and receiving ART in Dehong were screened for HIV drug resistance in 2012, and 3 715 patients who had received ART for more than 6 months were enrolled for 12 months and 24 months follow up.

RESULTS

Among the 3 715 patients, 56.6% were males, 72.6% were aged 26-45 years and 76.0% were married. The main treatment regimen was nevirapine(NVP)+ lamivudine(3TC)+ zidovudine(AZT)(38.2%). A total of 3 556 patients(95.7%)received at least one viral load testing during the two years follow-up, among them 253(7.1%)patients had VL≥1 000 copies/ml, in which 211(83.4%)received drug resistance related gene mutation testing, the results indicated that the drug resistance developed in 52 and 39 patients in 2013 and 2014(1.43 per 100 person years and 0.88 per 100 person years)respectively. The overall HIV drug incidence was 1.13 per 100 person years. Multivariate regression analysis indicated that age ≤25 years, to be infected through drug use, treatment regimen as D4T+ 3TC +NVP and baseline CD4(+) T cells ≤200 cells/μl were the risk factor of HIV drug resistance. Eleven HIV gene subtypes were detected in the 82 patients with newly developed drug resistance, CRF_BC was predominant(31.7%), followed by CRF01_AE(22.0%)and C(19.5%). Ten patients were infected with mixed subtypes of CRF_BC/B', CRF_BC/CRF_01B and CRF_BC/C. Most of the 82 patients were resistant to NRTIs and NNRTIs, the main mutation loci were M184V and K103N.

CONCLUSIONS

The incidence of drug resistance in adult AIDS patients receiving ART was relatively low in Dehong. However, it is necessary to conduct the health education in young people and drug users to improve the treatment compliance and strengthen the surveillance for HIV drug resistance.