A Hybrid Approach for CpG Island Detection in the Human Genome

Background

CpG islands have been demonstrated to influence local chromatin structures and simplify the regulation of gene activity. However, the accurate and rapid determination of CpG islands for whole DNA sequences remains experimentally and computationally challenging.

Methodology/Principal Findings

A novel procedure is proposed to detect CpG islands by combining clustering technology with the sliding-window method (PSO-based). Clustering technology is used to detect the locations of all possible CpG islands and process the data, thus effectively obviating the need for the extensive and unnecessary processing of DNA fragments, and thus improving the efficiency of sliding-window based particle swarm optimization (PSO) search. This proposed approach, named ClusterPSO, provides versatile and highly-sensitive detection of CpG islands in the human genome. In addition, the detection efficiency of ClusterPSO is compared with eight CpG island detection methods in the human genome. Comparison of the detection efficiency for the CpG islands in human genome, including sensitivity, specificity, accuracy, performance coefficient (PC), and correlation coefficient (CC), ClusterPSO revealed superior detection ability among all of the test methods. Moreover, the combination of clustering technology and PSO method can successfully overcome their respective drawbacks while maintaining their advantages. Thus, clustering technology could be hybridized with the optimization algorithm method to optimize CpG island detection.

Conclusion/Significance

The prediction accuracy of ClusterPSO was quite high, indicating the combination of CpGcluster and PSO has several advantages over CpGcluster and PSO alone. In addition, ClusterPSO significantly reduced implementation time.     

Pre-Dialysis Visits to a Nephrology Department and Major Cardiovascular Events in Patients Undergoing Dialysis

Background and Objectives

Pre-dialysis care by a nephrology out-patient department (OPD) may affect the outcomes of patients who ultimately undergo maintenance dialysis. This study examined the effect of pre-dialysis care by a nephrology OPD on the incidence of one-year major cardiovascular events after initiation of dialysis.

Design, Setting Participants, & Measurements

The study consisted of Taiwanese patients with chronic kidney disease (CKD) who commenced dialysis from 2006 to 2008. The number of nephrology OPD visits during the critical care period (within 6 months of initiation of dialysis) and the early care period (6–36 months before initiation of dialysis) were analyzed. The primary outcome measure was one-year major cardiovascular events.

Results

A total of 1191 CKD patients who initiated dialysis from 2006 to 2008 were included. Binary logistic regression showed that patients with ≧3 visits during the critical care period and those with ≧11 visits during the early care period had fewer composite major cardiovascular events than those with 0 visits. Patients with early referral are less likely to experience composite major cardiovascular events than those with late referral, with aOR 0.574 (95% CI = 0.43–0.77, P<0.001). Patients with both ≧3 visits during critical care period and ≧11 visits during early care period were less likely to experience composite major cardiovascular events (aOR = 0.25, 95% CI = 0.16–0.39, P < 0.001).

Conclusions

Patients with adequate pre-dialysis nephrology OPD visits, not just early referral, may had fewer one-year composite major cardiovascular events after initiation of dialysis. This information may be important to medical care providers and public health policy makers in their efforts to improve the well-being of CKD patients.     

Altered plasma acylcarnitine and amino acid profiles in type 2 diabetic kidney disease

Introduction

Dysregulation of acylcarnitines (AcylCNs) and amino acids metabolism have implicated in abnormality of fatty acid oxidation in type 2 diabetes (T2D). However, it is not well known whether altered plasma AcylCN, and amino acid profiles are associated with albuminuria or diabetic nephropathy (DN) in T2D.

Objective

The aim of this study was to elucidate alterations in plasma levels of AcylCNs and amino acids with respect to the T2D patients with various stages of albuminuria.

Methods

We recruited 52 healthy subjects as control, and 156 T2D patients which were divided into 52 normoalbuminuria, 52 microalbuminuria, and 52 macroalbuminuria. Plasma 37 AcylCNs and 12 amino acids were analyzed by tandem mass spectrometry.

Results

We found that T2D with normoalbuminuria and microalbuminuria had lower shot-, medium-, and long-chain AcylCNs, whereas T2D with macroalbuminuria had higher short-and medium-chain AcylCNs and lower long-chain AcylCNs than healthy subjects. Moreover, estimated glomerular filtration rate (eGFR) was a negative, independent and significant predictor of albumin to creatinine ratio (ACR) levels (β = ?0.376, P < 0.001), whereas plasma Low-density lipoprotein cholesterol (LDL-C) was significantly and positively associated with ACR levels (β = 0.169, P = 0.049). Furthermore, multivariate ordinal logistic regression analysis revealed that isobutyrylcarnitine (C4) was a positive, independent, and significant predictor of ACR levels with higher odds of having T2D patients with progression normoalbuminuria to microalbuminuria [OR = 9.93, 95 % CI (3.51–28.05), P < 0.001].

Conclusions

The findings suggest that plasma C4 may serve as a potential biomarker for the early stages of DN.

     

犬小孢子菌致女性外阴脓癣1例

报道1例犬小孢子菌感染引起的女性外阴脓癣。患者女,25岁,耻骨外阴红肿疼痛半年,加重2周。皮肤科检查:耻骨外阴境界清楚的红色肿胀性斑块,触之浸润,疼痛明显;可见密集的毛囊性丘疹、脓疱,局部有波动感及脓液溢出,毛发松动,极易拔出。双侧腹股沟可及肿大触痛的淋巴结。组织病理学检查符合感染性肉芽肿表现。真菌镜检及培养鉴定为犬小孢子菌。诊断:脓癣。治疗:特比萘芬片250 mg,口服,每日1次,连续4周。服药2周后炎症基本消退,部分毛囊瘢痕形成。     

我国中医人才培养状况与趋势的可视化分析研究

文章借助信息可视化工具,以中国知网建库时间--2017年12月31日期间发表的文献为样本数据,对CNKI(中国知识资源总库)收录的中医人才培养领域的相关文献进行可视化分析,借助文献作者、机构、基金项目的分布来分析中医人才培养研究主体的构成;通过绘制关键词共现图谱并结合词频与中心度来解析我国中医人才培养的研究主题与热点,旨在为大家直观展示我国中医人才培养研究现状、研究热点和未来的研究趋势,从而辨识和探测我国中医人才培养的基本动向和整体发展脉络。     

泌桐高速公路生态护坡不同草灌混播10a后的植被群落特征

稳定的边坡群落是公路边坡生态防护的目标,为探究高速公路生态护坡工程10 a演替后群落特征,该研究以泌桐高速公路为依托,布设自然恢复、单一狗牙根播种和5个不同播种密度的草灌混播生态防护措施,分析不同恢复方式对边坡群落组成、生活型和物种多样性的影响。结果表明:(1)调查样方内共有52种植物,分属于17科49属。禾本科、菊科和豆科植物共26属29种,占种总数的55.77%,表明这三大科植物在边坡群落演替过程中起着重要作用。(2) 10 a演替后不同恢复方式下群落中多年生植物比例高于一年生草本植物。(3)在草灌混播样地中,群落物种多样性指数随着播种密度的增加呈先增加后降低的单峰变化趋势,在播种密度为每平方米500株时达到最大。(4)草灌混播的生态恢复效果优于纯草本种植和自然恢复方式。(5)播种密度对草灌混播群落类型,地上生物量和物种多样性指数没有显著影响。从植物的生长效果及成本方面考虑,初播密度每平方米为500~600株的草灌混播可构建较为稳定的边坡植物群落,实现最佳的边坡恢复效果,可应用于类似区域边坡生态恢复工程。     

丙酮丁醇梭菌的基因编辑工具及代谢工程改造

丙酮丁醇梭菌作为极具潜力的新型生物燃料丁醇的生产菌,受到各国研究学者的广泛关注。通过丙酮丁醇梭菌(ABE)发酵生产丁醇,由于生产成本高,限制了其工业化应用。随着基因组学和分子生物学的快速发展,适用于丙酮丁醇的基因编辑工具不断发展并应用于提高菌株的发酵性能。本文对丙酮丁醇梭菌基因编辑工具和代谢工程改造取得的进展进行综述。