物理模型試驗應用於順向坡板岩變形特性之研究

本文主要探討臺灣板岩順向坡變形特性，藉由現場調查、地形分析與物理模型試驗說明板岩不同條件下之重力變形特性，並推估板岩變形過程與潛在崩壞機制。結果顯示，坡趾侵蝕透空與降雨入滲機制為板岩變形之關鍵，其將造成板岩材料強度弱化加速發生變形。此外，板岩變形初始發生於崖頂張力區，坡體將沿著高角度葉理滑移，並於侵蝕弱化帶附近形成剪切破壞或複合型破壞。而變形範圍內具有相當多葉理張開之現象，其將有助於地表水與地下水滲入，促使板岩變形區加速變形至崩壞。This paper focuses on characterizing the deformation of consequent slate slopes in Taiwan. Onsite surveys, terrain analysis, and a physical model test are used to describe the characteristics of gravity-driven deformation under various conditions and identify the process of slate deformation as well as potential failure mechanisms. Slate deformation is shown to begin in the tension zone at cliff tops, wherein the slope body slips along the highly inclined foliation, contributing to shear failure or composite failure near the eroded zone of weakness. The phenomenon of foliation opening is widespread within the area of deformation, enabling surface water and groundwater to seep in, thereby accelerating deformation and failure in the slate deformation zone

Sequence variants of the aging gene CISD2 and the risk for Alzheimer's disease

Background/PurposeThe CISD2 gene has been related to life span control and mitochondrial dysfunction in animals. In addition, inhibition of mitochondrial enzymes due to an accumulation of beta-amyloid peptide has been related to Alzheimer's disease (AD). This study aimed to explore the association between sequence variants of the CISD2 gene and risk for AD, which has not been explored previously.MethodsThis was a case–control study involving a total of 276 patients with AD who were recruited from three teaching hospitals in Taiwan from 2007 to 2010; 460 controls were recruited from elderly individuals attending for health check-ups and volunteers in the hospital during the same period of time. All participants were aged 60 years or older. Two haplotype-tagging single nucleotide polymorphisms (htSNPs), rs223330 and rs223331, were selected from the CISD2 gene to test the association between their polymorphisms and the risk for dementia, and how ApoE ɛ4 status, sex, hypertension, and type 2 diabetes mellitus might modify this association.Resultsrs223330 variant carriage was not associated with risk for AD [TT versus CC: adjusted odds ratio (AOR) = 0.98, 95% confidence interval (CI) = 0.59–1.62; TC versus CC: AOR = 0.72, 95% CI = 0.47–1.11]. Similar findings were observed for rs223331 (AA versus TT: AOR = 1.12; AT versus TT: AOR = 0.99). In addition, hypertension significantly modified the association between rs223331 and risk for AD (p = 0.005).Three common haplotypes (with a frequency of 99.8%) were observed for CISD2. Common CISD2 haplotypes were not associated with the risk for AD.ConclusionOur findings suggested that CISD2 htSNPs are not associated with AD risk

Polymorphisms of an Innate Immune Gene, Toll-Like Receptor 4, and Aggressive Prostate Cancer Risk: A Systematic Review and Meta-Analysis

Background: Toll-like receptor 4 (TLR4) is one of the best known TLR members expressed on the surface of several leukocytes and tissue cells and has a key function in detecting pathogen and danger-associated molecular patterns. The role of TLR4 in the pathophysiology of several age-related diseases is also well recognized, such as prostate cancer (PCa). TLR4 polymorphisms have been related to PCa risk, but the relationship between TLR4 genotypes and aggressive PCa risk has not been evaluated by any systematic reviews. Methods: We performed a systematic review and meta-analysis of candidate-gene and genome-wide association studies analyzing this relationship and included only white population. Considering appropriate criteria, only nine studies were analyzed in the meta-analysis, including 3,937 aggressive PCa and 7,382 controls. Results: Using random effects model, no significant association was found in the ten TLR4 SNPs reported by at least four included studies under any inheritance model (rs2737191, rs1927914, rs10759932, rs1927911, rs11536879, rs2149356, rs4986790, rs11536889, rs7873784, and rs1554973). Pooled estimates from another ten TLR4 SNPs reported by three studies also showed no significant association (rs10759930, rs10116253, rs11536869, rs5030717, rs4986791, rs11536897, rs1927906, rs913930, rs1927905, and rs7045953). Meta-regression revealed that study type was not a significant source of between-study heterogeneity. Conclusions: TLR4 polymorphisms were not significantly associated with the risk of aggressive PCa

CHRNA7 Polymorphisms and Response to Cholinesterase Inhibitors in Alzheimer's Disease

Background: CHRNA7 encodes the alpha 7 nicotinic acetylcholine receptor subunit, which is important to Alzheimer's disease (AD) pathogenesis and cholinergic neurotransmission. Previously, CHRNA7 polymorphisms have not been related to cholinesterase inhibitors (ChEI) response. Methods: Mild to moderate AD patients received ChEIs were recruited from the neurology clinics of three teaching hospitals from 2007 to 2010 (n = 204). Nine haplotype-tagging single nucleotide polymorphisms of CHRNA7 were genotyped. Cognitive responders were those showing improvement in the Mini-Mental State Examination score >= 2 between baseline and 6 months after ChEI treatment. Results: AD women carrying rs8024987 variants [GG+GC vs. CC: adjusted odds ratio (AOR) = 3.62, 95% confidence interval (CI) = 1.47-8.89] and GG haplotype in block1 (AOR = 3.34, 95% CI = 1.38-8.06) had significantly better response to ChEIs (false discovery rate <0.05). These variant carriers using galantamine were 11 times more likely to be responders than female non-carriers using donepezil or rivastigmine. Conclusion: For the first time, this study found a significant association between CHRNA7 polymorphisms and better ChEI response. If confirmed by further studies, CHRNA7 polymorphisms may aid in predicting ChEI response and refining treatment choice

Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers

Abstract Background RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule amplifies equally, causing some to be overrepresented. Unique molecular identifiers (UMIs) can be used to distinguish undesirable PCR duplicates derived from a single molecule and identical but biologically meaningful reads from different molecules. Results We have incorporated UMIs into RNA-seq and small RNA-seq protocols and developed tools to analyze the resulting data. Our UMIs contain stretches of random nucleotides whose lengths sufficiently capture diverse molecule species in both RNA-seq and small RNA-seq libraries generated from mouse testis. Our approach yields high-quality data while allowing unique tagging of all molecules in high-depth libraries. Conclusions Using simulated and real datasets, we demonstrate that our methods increase the reproducibility of RNA-seq and small RNA-seq data. Notably, we find that the amount of starting material and sequencing depth, but not the number of PCR cycles, determine PCR duplicate frequency. Finally, we show that computational removal of PCR duplicates based only on their mapping coordinates introduces substantial bias into data analysis

Cyclic Vomiting Syndrome and Migraine in Children

Cyclic vomiting syndrome (CVS) is an episodic nausea and non-bilious vomiting disorder characterized by recurrent stereotypic symptoms with disease-free intervals. CVS in children is associated with a high prevalence of migraine, and is commonly considered a precursor to migraine. This study aimed to investigate the clinical manifestations of pediatric CVS and its prognosis, and to clarify its relationship with the risk of migraine development in children. Methods: The clinical features of children diagnosed with CVS before the age of 18 years at the designated hospital were retrospectively studied over the past 30 years (1976–2006) based on the Rome III or ICHD II criteria. Clinical evaluations, including age of onset, sex, family history, symptoms and duration during attacks, frequency, trigger events, electroencephalogram, treatment and subsequent development of migraine were assessed from chart records and telephone interviews. Results: Thirty-five children (17 males and 18 females) were enrolled. Their age of onset ranged from 2 to 17 years (mean, 6.8 ± 3.1 years) and frequency of attacks ranged from once to 36 times per year (mean, 8.2 ± 7.6 times). Duration of symptoms during each attack ranged from 1 to 45 days (mean, 5.9 ± 7.3 days). Of 20 children assessed for migraine development, seven subsequently developed typical migraine symptoms. There was younger onset age in the migraine-positive subgroup (5 ± 1.7 years) than in the migraine-negative subgroup (8.9 ± 3 years; p = 0.001). Co-morbid headache during CVS attack was also more evident in the migraine-positive subgroup (28.6% vs. 0%). Conclusion: Results of the study show that younger onset age and headache during CVS attacks may have increased risk of migraine development. Large-scale prospective studies are warranted to further clarify the relationship between CVS and migraine

Additional file 1: of Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers

Mapping and UMI statistics of (A) RNA-seq and (B) small RNA-seq data generated in this study. (XLSX 112 kb

Additional file 2: of Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers

Figure S1. Accuracy and fraction of duplicates for simulated data varying (A) sequencing error rate, (B) UMI length, (C) PCR error rate, or (D) minimum amplification probability. Each dotted line indicates the value for this parameter used in other simulations. (PDF 868 kb

Additional file 3: of Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers

UMI method comparison. (XLSX 11 kb