Discovery and Analysis of MicroRNAs in Leymus chinensis under Saline-Alkali and Drought Stress Using High-Throughput Sequencing

Leymus chinensis (Trin.) Tzvel. is a perennial rhizome grass of the Poaceae (also called Gramineae) family, which adapts well to drought, saline and alkaline conditions. However, little is known about the stress tolerance of L. chinensis at the molecular level. microRNAs (miRNAs) are known to play critical roles in nutrient homeostasis, developmental processes, pathogen responses, and abiotic stress in plants. In this study, we used Solexa sequencing technology to generate high-quality small RNA data from three L. chinensis groups: a control group, a saline-alkaline stress group (100 mM NaCl and 200 mM NaHCO₃), and a drought stress group (20% polyethylene glycol 2000). From these data we identified 132 known miRNAs and 16 novel miRNAs candidates. For these miRNAs we also identified target genes that encode a broad range of proteins that may be correlated with abiotic stress regulation. This is the first study to demonstrate differentially expressed miRNAs in L. chinensis under saline-alkali and drought stress. These findings may help explain the saline-alkaline and drought stress responses in L. chinensis.     

Contourlet Textual Features: Improving the Diagnosis of Solitary Pulmonary Nodules in Two Dimensional CT Images

Objective

To determine the value of contourlet textural features obtained from solitary pulmonary nodules in two dimensional CT images used in diagnoses of lung cancer.

Materials and Methods

A total of 6,299 CT images were acquired from 336 patients, with 1,454 benign pulmonary nodule images from 84 patients (50 male, 34 female) and 4,845 malignant from 252 patients (150 male, 102 female). Further to this, nineteen patient information categories, which included seven demographic parameters and twelve morphological features, were also collected. A contourlet was used to extract fourteen types of textural features. These were then used to establish three support vector machine models. One comprised a database constructed of nineteen collected patient information categories, another included contourlet textural features and the third one contained both sets of information. Ten-fold cross-validation was used to evaluate the diagnosis results for the three databases, with sensitivity, specificity, accuracy, the area under the curve (AUC), precision, Youden index, and F-measure were used as the assessment criteria. In addition, the synthetic minority over-sampling technique (SMOTE) was used to preprocess the unbalanced data.

Results

Using a database containing textural features and patient information, sensitivity, specificity, accuracy, AUC, precision, Youden index, and F-measure were: 0.95, 0.71, 0.89, 0.89, 0.92, 0.66, and 0.93 respectively. These results were higher than results derived using the database without textural features (0.82, 0.47, 0.74, 0.67, 0.84, 0.29, and 0.83 respectively) as well as the database comprising only textural features (0.81, 0.64, 0.67, 0.72, 0.88, 0.44, and 0.85 respectively). Using the SMOTE as a pre-processing procedure, new balanced database generated, including observations of 5,816 benign ROIs and 5,815 malignant ROIs, and accuracy was 0.93.

Conclusion

Our results indicate that the combined contourlet textural features of solitary pulmonary nodules in CT images with patient profile information could potentially improve the diagnosis of lung cancer.     

HIF-1α Signaling Activation by Post-Ischemia Treatment with Astragaloside IV Attenuates Myocardial Ischemia-Reperfusion Injury

In this study, we evaluated the effect of astragaloside IV (Ast IV) post-ischemia treatment on myocardial ischemia-reperfusion (IR) injury (IRI). We also examined whether hypoxia inducible factor-1α (HIF-1α) and its downstream gene-inducible nitric oxide (NO) synthase (iNOS) play roles in the cardioprotective effect of Ast IV. Cultured cardiomyocytes and perfused isolated rat hearts were exposed to Ast IV during reperfusion in the presence or absence of the HIF-1α inhibitor 2-methoxyestradiol (2-MeOE2). The post-ischemia treatment with Ast IV protected cardiomyocytes from the apoptosis and death induced by simulated IRI (SIRI). Additionally, in cardiomyocytes, 2-MeOE2 and HIF-1α siRNA treatment each not only abolished the anti-apoptotic effect of post-ischemia treatment with Ast IV but also reversed the upregulation of HIF-1α and iNOS expression. Furthermore, after treatment with Ast IV, post-ischemic cardiac functional recovery and lactate dehydrogenase (LDH) release in the coronary flow (CF) were improved, and the myocardial infarct size was decreased. Moreover, the number of apoptotic cells was reduced, and the upregulation of the anti-apoptotic protein Bcl2 and downregulation of the pro-apoptotic protein Caspase3 were reversed. 2-MeOE2 reversed these effects of Ast IV on IR-injured hearts. These results suggest that post-ischemia treatment with Ast IV can attenuate IRI by upregulating HIF-1α expression, which transmits a survival signal to the myocardium.     

A Survey of Overlooked Viral Infections in Biological Experiment Systems

It is commonly accepted that there are many unknown viruses on the planet. For the known viruses, do we know their prevalence, even in our experimental systems? Here we report a virus survey using recently published small (s)RNA sequencing datasets. The sRNA reads were assembled and contigs were screened for virus homologues against the NCBI nucleotide (nt) database using the BLASTn program. To our surprise, approximately 30% (28 out of 94) of publications had highly scored viral sequences in their datasets. Among them, only two publications reported virus infections. Though viral vectors were used in some of the publications, virus sequences without any identifiable source appeared in more than 20 publications. By determining the distributions of viral reads and the antiviral RNA interference (RNAi) pathways using the sRNA profiles, we showed evidence that many of the viruses identified were indeed infecting and generated host RNAi responses. As virus infections affect many aspects of host molecular biology and metabolism, the presence and impact of viruses needs to be actively investigated in experimental systems.     

Breast Contrast-Enhanced Ultrasound: Is a Scoring System Feasible? ----A Preliminary Study in China

Objectives

Although many studies about breast contrast-enhanced ultrasound had been conducted, clear diagnostic criteria for evaluating enhancement patterns are still lacking. This study aims to identify significant indicators for breast contrast-enhanced ultrasound and to establish an initial scoring system.

Materials and Methods

Totally 839 patients were included in the study. This study was divided into two parts. 364 patients were included in part 1 while 475 in part 2. Conventional ultrasound and contrast-enhanced ultrasound were used to examine each lesion. Only the cases in part 2 were also examined by elastography. In part 1, Logistic regression analysis was performed to predict significant variables. A 5-point scoring system was developed based on the results. In part 2, the scoring system was used to evaluate all the breast lesions. To evaluate the diagnostic efficacy of the new scoring system, it was compared with the system established for elastography and conventional ultrasound (BI-RADS).

Results

Three independent variables, namely, lesion scope, margin, and shape were selected in the final step of the logistic regression analysis in part 1. In part 2, the area under the ROC (receiver operating characteristic) curve for the contrast-enhanced scoring system was 0.912. The difference in the diagnostic capabilities of the contrast-enhanced scoring system and elastography was not statistically significant (P = 0.17). The difference in the diagnostic capabilities of the contrast-enhanced scoring system and BI-RADS was statistically significant (P<0.001).

Conclusions

The contrast-enhanced patterns of benign and malignant breast tumors are different. The application of a 5-point scoring system for contrast-enhanced ultrasound is clinically promising.     

Measurement Properties of the Chinese Version of the Youth Quality of Life Instrument–Weight Module (YQOL-W)

Background

Childhood obesity is a growing public health concern in China. It not only compromises physical health, but also has negative impacts on psychosocial well-being. As obesity rates increase, finding out what the perceptions of Chinese youth are regarding their weight is important for intervention planning and evaluation. However, there is a paucity of available obesity-specific instruments for children and adolescents in China and youth weight-specific quality of life (QOL) has been little reported. This study aimed to evaluate the measurement properties of the Chinese version of the Youth Quality of Life Instrument – Weight Module (YQOL-W).

Methods

The Chinese version of the YQOL-W was administered to 840 youth aged 11–18 from nine schools. Measurement properties including measurement model, reliability, validity and burden were evaluated.

Results

Confirmatory factor analysis showed that a three-factor model had acceptable model fit. The instrument had robust internal consistency reliability with Cronbach''s α ranging from 0.84 to 0.96 and acceptable test-retest reliability with the intraclass correlation coefficients (ICCs) all higher than 0.7. The standard error of measurement (SEM) values for the Self, Social and Environment factors and total score were 10.352, 9.526, 12.086 and 8.425, respectively. The small real differences (SRDs) for the Self, Social and Environment factors and total score were 28.675, 26.387, 33.478, and 23.337, respectively. The Pearson''s correlation coefficients between the YQOL-W and the PedsQL4.0 General Core Scales were stronger between comparable dimensions than those between less comparable dimensions, demonstrating convergent and discriminant evidence of construct validity. Significant differences were found in subscale and total scores across weight status, age and genders (P<0.01), supporting the known-groups validity of the instrument.

Conclusion

The Chinese version of the YQOL-W has acceptable measurement properties and can be used to assess the weight-specific QOL of children and adolescents in China.     

A Meta-Analysis of Parental Smoking and the Risk of Childhood Brain Tumors

Objective

Previous studies regarding the association between parental smoking and the risk of childhood brain tumors (CBT) have reported inconsistent results. We performed a meta-analysis to summarize evidence on this association and to quantify the potential dose-response relationship.

Methods

A systematic literature search was conducted in the Medline and Embase databases. The summary relative risks (RRs) with 95% confidence intervals (CIs) were calculated. Dose–response meta-analysis was also performed for studies that reported categorical risk estimates for a series of smoking exposure levels.

Results

A total of 17 studies fulfilled the inclusion criteria. In the meta-analyses, the summary RRs (95% CIs) of CBT for maternal smoking during pregnancy, paternal smoking during pregnancy, maternal smoking before pregnancy, and paternal smoking before pregnancy were 0.96 (0.86–1.07), 1.09 (0.97–1.22), 0.93 (0.85–1.00), and 1.09 (1.00–1.20), respectively. Dose-response meta-analysis also showed no significant association between parental smoking and the risk of CBT.

Conclusions

Findings from our meta-analysis indicate that parental smoking may not be associated with a risk of CBT.     

Discovering Social Events through Online Attention

Twitter is a major social media platform in which users send and read messages (“tweets”) of up to 140 characters. In recent years this communication medium has been used by those affected by crises to organize demonstrations or find relief. Because traffic on this media platform is extremely heavy, with hundreds of millions of tweets sent every day, it is difficult to differentiate between times of turmoil and times of typical discussion. In this work we present a new approach to addressing this problem. We first assess several possible “thermostats” of activity on social media for their effectiveness in finding important time periods. We compare methods commonly found in the literature with a method from economics. By combining methods from computational social science with methods from economics, we introduce an approach that can effectively locate crisis events in the mountains of data generated on Twitter. We demonstrate the strength of this method by using it to locate the social events relating to the Occupy Wall Street movement protests at the end of 2011.     

上皮组织特异性表达N-LMP1和CR2转基因猪胚胎成纤维细胞的构建与鉴定

目的 构建上皮组织特异性表达鼻咽癌来源潜伏膜蛋白1（N-LMP1）和人补体受体2（CR2）真核表达载体,转染猪胚胎成纤维细胞并筛选整合有N-LMP1和CR2基因的细胞克隆,为构建与EBV感染相关的猪鼻咽癌模型奠定基础.方法 通过直接合成ED-L2启动子和N-LMP1,从人B淋巴细胞中的RNA经RT-PCR扩增出CR2,将上述3个片段逐个连接到真核表达载体pN1上,构建上皮组织特异性表达N-LMP1和CR2的载体pN1-ED-L2-N-LMP1-CR2;用脂质体转染猪胚胎成纤维细胞,经药物G418 筛选和PCR鉴定阳性克隆.结果 成功构建上皮组织特异性表达N-LMP1和CR2的真核表达载体pN1-ED-L2-N-LMP1-CR2,并成功整合到猪胚胎成纤维细胞的基因组中,获得了整合有目的 基因N-LMP1和CR2的猪胚胎成纤维细胞克隆.结论 获得了上皮组织特异性表达N-LMP1和CR2 的猪胚胎成纤维细胞克隆,为通过细胞核移植方法获得表达N-LMP1和CR2转基因猪提供了供体细胞.