Xiping Shen

Computational Identification of Antigenicity-Associated Sites in the Hemagglutinin Protein of A/H1N1 Seasonal Influenza Virus.

The antigenic variability of influenza viruses has always made influenza vaccine development challenging. The punctuated nature of antigenic drift of influenza virus suggests that a relatively small number of genetic changes or combinations of genetic changes may drive changes in antigenic phenotype. The present study aimed to identify antigenicity-associated sites in the hemagglutinin protein of A/H1N1 seasonal influenza virus using computational approaches. Random Forest Regression (RFR) and Support Vector Regression based on Recursive Feature Elimination (SVR-RFE) were applied to H1N1 seasonal influenza viruses and used to analyze the associations between amino acid changes in the HA1 polypeptide and antigenic variation based on hemagglutination-inhibition (HI) assay data. Twenty-three and twenty antigenicity-associated sites were identified by RFR and SVR-RFE, respectively, by considering the joint effects of amino acid residues on antigenic drift. Our proposed approaches were further validated with the H3N2 dataset. The prediction models developed in this study can quantitatively predict antigenic differences with high prediction accuracy based only on HA1 sequences. Application of the study results can increase understanding of H1N1 seasonal influenza virus antigenic evolution and accelerate the selection of vaccine strains.

Etiological epidemiology of viral diarrhea on the basis of sentinel surveillance in children younger than 5 years in Gansu, northwest China, 2009–2013

To explore the etiological spectrum of diarrhea and its epidemiological characteristics in diarrhea symptoms surveillance cases younger than 5 years from 2009 to 2013 in Gansu province, northwest China. Systematic diarrhea symptoms surveillance were conducted in 27 sentinel sites in Gansu province and outpatients with three or more loose, watery, or sticky pus stools per day were defined as surveillance cases. All stool specimens were tested for Rotavirus, Human calicivirus, Adenovirus, and Astrovirus. Totally, 1,119 cases (51.54%) were identified as any enteric virus. The average isolation rate of Rotavirus was 51.13%, Astrovirus was 10.84%, Adenovirus was 6.94%, and Human calicivirus was 6.60% (P < 0.01). Rotavirus was identified with the highest frequency among these enteric pathogens except in 2011, with a notable downward trend over time (P < 0.01). Rotavirus A was the most proportion in rotavirus, G3P[8] and G9P[8] were the most common combination. Rotavirus mixed Human calicivirus infections was the most common mixed infected patterns. Viral‐positive rate was higher among children aged group of 0–12 and 13–24 months (P < 0.01, respectively). The isolation rates of four enteric viral pathogens showed a similar distinct seasonal variation with a higher rate in spring, autumn, and winter months. Rotavirus was the major epidemiological viral pathogen in diarrhea symptom surveillance cases in Gansu province, northwest China, during period 2009–2013. Seasonal and age‐related variations were observed in enteric viral pathogen isolation rate. The comprehensive and continuous surveillance is needed to identify the prevalence of different enteric viral pathogens. J. Med. Virol. 87:2048–2053, 2015.

Dose-response analyses of uric acid and risk of type 2 diabetes in a Chinese occupational population: a cohort study and meta-analysis

Abstract Background The link between hyperuricaemia and risk of type 2 diabetes has long been hypothesised, although the debate about the causality of this is unresolved. To better understand the causal role of high concentrations of serum uric acid in the development of diabetes, we comprehensively assessed the association between serum uric acid concentration and the risk of incident diabetes in an occupational population of Chinese men and women. Methods We used Restricted Cubic Splines functions and Cox proportional hazards models to estimate the association between serum uric acid measured at baseline and the risk of incident diabetes in the Jinchang cohort study, an ongoing occupational-based prospective study of 42 122 metal-exposed workers aged 20 years or older at baseline (2011–13). Only those who participated in the baseline survey and first follow-up with repeat medical examinations were eligible. Serum uric acid was measured with the uricase-peroxidase enzymatic method. We also performed a meta-analysis of ongoing and completed studies in both the occupational and general populations to summarise this association. Findings Among 30 917 participants without diagnosed diabetes at baseline, there were 934 incident diabetes cases during a median of 2·2 years (IQR 1·8–2·5) of follow-up. We observed a positive linear dose–response association between serum uric acid concentration and incident diabetes by spline analyses (p overall association =0·001; p non-linearity =0·90). After multiple adjustments such as age, BMI, and occupation, the hazard ratio (HR) for incident diabetes was 1·62 (95% CI 1·26–2·08) for the fourth and highest quartile concentration of serum uric acid (p trend trend =0·01), but was not associated in women (p trend =0·06). However, when modelled as a continuous variable, serum uric acid concentration was significantly associated with the risk of diabetes both in men and women. In a meta-analysis of 14 studies comprising a total of 137 485 participants and 9351 cases of type 2 diabetes, comparing the highest versus lowest quartile of serum uric acid concentration, the HR for incident diabetes was 1·44 (95% CI 1·34–1·55). Interpretation Our findings from the Jinchang cohort show a positive linear dose–response association between serum uric acid concentration and risk of incident type 2 diabetes in both Chinese men and women. These findings were substantiated in an updated meta-analysis, suggesting that high serum uric acid concentration might identify individuals at risk of diabetes. More studies, such as Mendelian randomisation studies and conventional epidemiological studies, are needed to establish causality. Funding Project of Science and Technology of the Jinchang Nonferrous Metals Corporation (Grant JKB20120013) and US National Institutes of Health (D43TW 008323, D43Tw 007864–01, and DK66401).

Viral etiologies and epidemiology of patients with acute respiratory infections based on sentinel hospitals in Gansu Province, Northwest China, 2011-2015

Understanding etiological role and epidemiological profile is needed to improve clinical management and prevention of acute respiratory infections (ARIs). A 5‐year prospective study about active surveillance for outpatients and inpatients with ARIs was conducted in Gansu province, China, from January 2011 to November 2015. Respiratory specimens were collected from patients and tested for eight respiratory viruses using polymerase chain reaction (PCR) or reverse transcription polymerase chain reaction (RT‐PCR). In this study, 2768 eligible patients with median age of 43 years were enrolled including pneumonia (1368, 49.2%), bronchitis (435, 15.7%), upper respiratory tract infection or URTI (250, 9.0%), and unclassified ARI (715, 25.8%). Overall, 29.2% (808/2768) were positive for any one of eight viruses, of whom 130 cases were identified with two or more viruses. Human rhinovirus (HRV) showed the highest detection rate (8.6%), followed by influenza virus (Flu, 7.3%), respiratory syncytial virus (RSV, 6.1%), human coronavirus (hCoV, 4.3%), human parainfluenza (PIV, 4.0%), adenovirus (ADV, 2.1%), human metapneumovirus (hMPV, 1.6%), and human bocavirus (hBoV, 0.7%). Compared with URTI, RSV was more likely identified in pneumonia (χ2 = 12.720, P < 0.001) and hCoV was more commonly associated with bronchitis than pneumonia (χ2 = 15.019, P < 0.001). In patients aged less than 5 years, RSV showed the highest detection rate and hCoV was the most frequent virus detected in adults and elderly. The clear epidemical seasons were observed in HRV, Flu, and hCoV infections. These findings could serve as a reference for local health authorities in drawing up further plans to prevent and control ARIs associated with viral etiologies.

Optimal-combined model for air quality index forecasting: 5 cities in North China

Air pollution forecasting is significant for public health and controlling pollution, and statistical methods are important air pollution forecasting techniques. Nevertheless, the research of AQI (air quality index) forecasting is very rare. So an accurate and stable AQI forecasting model is very urgent and necessary. For the high complex, volatile and nonlinear AQI series, this research presents a novel optimal-combined model based on CEEMD (complementary ensemble empirical mode decomposition), PSOGSA (particle swarm optimization and gravitational search algorithm), PSO (particle swarm optimization) and combined forecasting method. The proposed model effectively solves the blind combined forecasting. AQI series forecasts of five cities in North China show that the proposed model has the highest correct rate of forecasting classifications compared with the candidates. Totally, the presented model has the following advantages compared with the candidates: more robust forecasting performance, smaller forecasting error and better generalization ability.

Liver Enzymes, Fatty Liver and Type 2 Diabetes Mellitus in Jinchang Cohort: a Prospective Study in Adults

OBJECTIVES It is unclear whether liver enzymes or the interactions of various liver enzymes is a predictor of type 2 diabetes mellitus (T2DM), which is independent of fatty liver. METHODS A total of 48,001 subjects participated in baseline examinations. Among the subjects, 33,355 were followed for an average of 2.2 years. Cox proportional hazard models were used to examine the adjusted associations of AST, GGT and ALT with T2DM. RESULTS The cumulative incidence of T2DM was 8.05% to 9.02% for fatty liver and 2.25% to 4.10% for non-fatty liver, both showing statistically significant differences. Compared with the normal liver enzyme levels in the group with fatty liver, the adjusted incident hazard ratios in T2DM were: ALT 1.23 (95% CI 1.10 to 1.50); AST 1.30 (95% CI 1.07-1.59); and GGT 1.34 (95% CI 1.08 to 1.65). In addition, compared with the normal liver enzyme levels in the group with non-fatty liver, the adjusted incident hazard ratios in type 2 diabetes were: ALT 1.27 (95% CI 1.02 to 1.59); AST 1.33 (95% CI 1.02 to 1.59); and GGT 1.53 (95% CI 1.19 to 1.98). There are significant interactions of T2DM hazard ratios between GGT and ALT and between GGT and AST in addition to ALT and AST. CONCLUSIONS Our results suggest that the incidence of T2DM in the group with fatty liver is significantly higher than that in the normal population, and the rise of serum AST, GGT and ALT levels are risk factors independent of fatty liver for the development of T2DM after adjusting for confounding factors.

Disease burden of liver cancer in Jinchang cohort

OBJECTIVE To understand the current status of lung cancer disease burden in Jinchang cohort. METHODS In this historical cohort study, the mortality data of the lung cancer from 2001 to 2013 and medical records of the lung cancer cases from 2001 to 2010 in Jinchang cohort were used, analyze mortality, direct economic burden, potential years of life lost (PYLL) and working PYLL (WPYLL) associated with lung cancer. RESULTS A total of 434 lung cancer deaths occurred in Jinchang cohort from 2001 to 2013. The crude mortality rate of lung cancer was 78.06 per 100,000 from 2001 to 2013, with the increasing rate of 4.77%. The mortality rate of lung cancer in males and females were about 108.90 per 100,000 and 26.08 per 100,000 with the increasing rate of 4.24% and 6.91%, respectively. During the thirteen years, the PYLL and average PYLL (APYLL) of lung cancer were 3 721.71 person-years and 8.58 years. The APYLL of lung cancer in females (15.94 years) was higher than that in males (7.87 years). The WPYLL and the average WPYLL (AWPYLL) of lung cancer were 1161.00 person-years and 2.68 years, respectively. The AWPYLL of lung cancer was also higher in females than in males. The direct economic burden of lung cancer from 2001 to 2010 in Jinchang cohort was 6309.39 Yuan per case with no increased trend. CONCLUSION Lung cancer is the main health problem in Jinchang cohort, causing heavy disease burden.