Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data

CpG islands are typically located in the 5′ end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in order to obtain a similar number of CpG islands in a genome. This approach allows us to systematically compare the methylation and gene expression patterns in the identified CpG islands. We found that Takai and Jones' algorithm tends to identify longer CpG islands but with weaker CpG island features (e.g., lower GC content and lower ratio of the observed over expected CpGs) and higher methylation level. Conversely, the CpG clusters identified by Hackenberg et al.'s algorithm using stringent criteria are shorter and have stronger features and lower methylation level. In addition, we used the genome-wide base-resolution methylation profile in two cell lines to show that genes with a lower methylation level at the promoter-associated CpG islands tend to express in more tissues and have stronger expression. Our results validated that the DNA methylation of promoter-associated CpG islands suppresses gene expression at the genome level

A Novel microRNA and transcription factor mediated regulatory network in schizophrenia

<p>Abstract</p> <p>Background</p> <p>Schizophrenia is a complex brain disorder with molecular mechanisms that have yet to be elucidated. Previous studies have suggested that changes in gene expression may play an important role in the etiology of schizophrenia, and that microRNAs (miRNAs) and transcription factors (TFs) are primary regulators of this gene expression. So far, several miRNA-TF mediated regulatory modules have been verified. We hypothesized that miRNAs and TFs might play combinatory regulatory roles for schizophrenia genes and, thus, explored miRNA-TF regulatory networks in schizophrenia.</p> <p>Results</p> <p>We identified 32 feed-forward loops (FFLs) among our compiled schizophrenia-related miRNAs, TFs and genes. Our evaluation revealed that these observed FFLs were significantly enriched in schizophrenia genes. By converging the FFLs and mutual feedback loops, we constructed a novel miRNA-TF regulatory network for schizophrenia. Our analysis revealed EGR3 and hsa-miR-195 were core regulators in this regulatory network. We next proposed a model highlighting EGR3 and miRNAs involved in signaling pathways and regulatory networks in the nervous system. Finally, we suggested several single nucleotide polymorphisms (SNPs) located on miRNAs, their target sites, and TFBSs, which may have an effect in schizophrenia gene regulation.</p> <p>Conclusions</p> <p>This study provides many insights on the regulatory mechanisms of genes involved in schizophrenia. It represents the first investigation of a miRNA-TF regulatory network for a complex disease, as demonstrated in schizophrenia.</p

The diagnostic value of elastography and ultrasound contrast in papillary thyroid microcarcinoma

目的 评估弹性成像与超声造影（CEUS）两种检查技术对鉴别诊断甲状腺微小乳头状癌（TMC）的价值。方法  对常规超声检测出且定性困难的73例80个甲状腺微小结节进行弹性成像及CEUS检查，所有结节均经手术病理证实。比较两种检查方法的准确性。结果 80个结节中CEUS诊断正确率为85.0%（68/80）,其中6例TMC误诊为良性病变，6例良性结节误诊为TMC；弹性成像5分法诊断正确率为92.5%（74/80）,其中3例TMC误诊为良性结节，3例良性结节误诊为TMC。性成像诊断甲状腺微小癌的敏感性94.0%，特异性90.0%，准确性92.5%；CEUS诊断甲状腺微小癌的敏感性88.0%，特异性80.0%，准确性85.0%。结论 CEUS和弹性成像对于诊断TMC方面均有价值，但弹性评分≥3作为诊断TMC的敏感性、特异性及准确性均高于CEUS。Objective: To assess the value of elastic imaging and CEUS two inspection techniques for differential diagnosis of thyroid papillary carcinoma (TMC). Method: To do elastic imaging and CEUS checks to 73 cases of 80 thyroid nodules which was tested by conventional ultrasonic and difficult to quantify. All nodules were confirmed by surgery and pathologic examination. Comparing the accuracy of both detection methods. Result: Of the 80 nodules, the accuracy of CEUS diagnosis was 85.0%（68/80）,  of which 6 cases were misdiagnosed as benign lesions, and 6cases of benign nodules were misdiagnosed as TMC: the accuracy of 5-point scale criteria of elastography was 92.5%（74/80）, of which 3 TMC were misdiagnosed as benign nodules: and 3 benign nodules were misdiagnosed as TMC. The application of elastography in the diagnosis of thyroid microcarcinoma displayed a sensitivity of 94.0%, a specificity of 90.0% and an accuracy of 92.5%. Elastography detection was more advantagerous than CEUS in the diagnosis of thyroid microcarcinoma, and compared to CEUS , the differences were statistically significant（P &lt;0.05）.Conclusion: Elastography and Ultrasound Contrast have highly practical value to diagnosis of TMC.  The sensitivity specificity and accuracy of using elastic score ≥3 as criteria of diagnosis of TMC was higher than that of CEUS

Atomic-scale combination of germanium-zinc nanofibers for structural and electrochemical evolution

Alloys are recently receiving considerable attention in the community of rechargeable batteries as possible alternatives to carbonaceous negative electrodes; however, challenges remain for the practical utilization of these materials. Herein, we report the synthesis of germanium-zinc alloy nanofibers through electrospinning and a subsequent calcination step. Evidenced by in situ transmission electron microscopy and electrochemical impedance spectroscopy characterizations, this one-dimensional design possesses unique structures. Both germanium and zinc atoms are homogenously distributed allowing for outstanding electronic conductivity and high available capacity for lithium storage. The as-prepared materials present high rate capability (capacity of similar to 50% at 20 C compared to that at 0.2 C-rate) and cycle retention (73% at 3.0 C-rate) with a retaining capacity of 546 mAh g(-1) even after 1000 cycles. When assembled in a full cell, high energy density can be maintained during 400 cycles, which indicates that the current material has the potential to be used in a large-scale energy storage system

Energy-Efficient Opportunistic Transmission Scheduling for Sparse Sensor Networks with Mobile Relays

Wireless sensing devices have been widely used in civilian and military applications over the past decade. In some application scenarios, the sensors are sparsely deployed in the field and are costly or infeasible to have stable communication links for delivering the collected data to the destined server. A possible solution is to utilize the motion of entities that are already present in the environment to provide opportunistic relaying services for sensory data. In this paper, we design and propose a new scheduling scheme that opportunistically schedules data transmissions based on the optimal stopping theory, with a view of minimizing the energy consumption on network probes for data delivery. In fact, by exploiting the stochastic characteristics of the relay motion, we can postpone the communication up to an acceptable time deadline until the best relay is found. Simulation results validate the effectiveness of the derived optimal strategy

Peripheral anti-inflammatory effects explain the ginsenosides paradox between poor brain distribution and anti-depression efficacy

<p>Abstract</p> <p>Background</p> <p>The effectiveness of ginseng in preventing and treating various central nervous system (CNS) diseases has been widely confirmed. However, ginsenosides, the principal components of ginseng, are characterized by poor accessibility to the brain, and this pharmacokinetic-pharmacological paradox remains poorly explained. Anti-inflammatory approaches are becoming promising therapeutic strategies for depression and other CNS diseases; however, previous studies have focused largely on anti-inflammatory therapies directed at the central nervous system. It is thus of interest to determine whether ginsenosides, characterized by poor brain distribution, are also effective in treating lipopolysaccharide- (LPS) induced depression-like behavior and neuroinflammation.</p> <p>Methods</p> <p>In an LPS-induced depression-like behavior model, the antidepressant effects of ginseng total saponins (GTS) were assessed using a forced swimming test, a tail suspension test, and a sucrose preference test. The anti-inflammatory efficacies of GTS in brain, plasma, and LPS-challenged RAW264.7 cells were validated using ELISA and quantitative real-time PCR. Moreover, indoleamine 2,3-dioxygenase (IDO) activity in the periphery and brain were also determined by measuring levels of kynurenine/tryptophan.</p> <p>Results</p> <p>GTS significantly attenuated LPS-induced depression-like behavior. Moreover, LPS-induced increases in 5-HT and tryptophane turnover in the brain were significantly reduced by GTS. IDO activities in brain and periphery were also suppressed after pretreatment with GTS. Furthermore, GTS-associated recovery from LPS-induced depression-like behavior was paralleled with reduced mRNA levels for IL-1β, IL-6, TNF-α, and IDO in hippocampus. Poor brain distribution of ginsenosides was confirmed in LPS-challenged mice. GTS treatment significantly decreased production of various proinflammatory cytokines in both LPS-challenged mice and RAW264.7 cells.</p> <p>Conclusion</p> <p>This study suggests that the anti-depression efficacy of GTS may be largely attributable to its peripheral anti-inflammatory activity. Our study also strengthens an important notion that peripheral anti-inflammation strategies may be useful in the therapy of inflammation-related depression and possibly other CNS diseases.</p