New Intraclass Helitrons Classification Using DNA-Image Sequences and Machine Learning Approaches

Helitrons, eukaryotic transposable elements (TEs) transposed by rolling-circle mechanism, have been found in various species with highly variable copy numbers and sometimes with a large portion of their genomes. The impact of helitrons sequences in the genome is to frequently capture host genes during their transposition. Since their discovery, 18 years ago, by computational analysis of whole genome sequences of Arabidopsis thaliana plant and Caenorhabditis elegans (C. elegans) nematode, the identification and classification of these mobile genetic elements remain a challenge due to the fact that the wide majority of their families are non-autonomous. In C. elegans genome, DNA helitrons sequences possess great variability in terms of length that varies between 11 and 8965 base pairs (bps) from one sequence to another. In this work, we develop a new method to predict helitrons DNA-sequences, which is particularly based on Frequency Chaos Game Representation (FCGR) DNA-images. Thus, we introduce an automatic system in order to classify helitrons families in C. elegans genome, based on a combination between machine learning approaches and features extracted from DNA-sequences. Consequently, the new set of helitrons features (the FCGR images and K-mers) are extracted from DNA sequences. These helitrons features consist of the frequency apparition number of K nucleotides pairs (Tandem Repeat) in the DNA sequences. Indeed, three different classifiers are used for the classification of all existing helitrons families. The results have shown potential global score equal to 72.7% due to FCGR images which constitute helitrons features and the pre-trained neural network as a classifier. The two other classifiers demonstrate that their efficiency reaches 68.7% for Support Vector Machine (SVM) and 91.45% for Random Forest (RF) algorithms using the K-mers features corresponding to the genomic sequences.     

Identification of a Trypsin-Like Site Associated with Acetylcholinesterase by Affinity Labelling with [3H]Diisopropyl Fluorophosphate

Neuritic plaque core amyloid protein in Alzheimer's disease brain tissue was investigated for the extent of amino acid racemization. Long-lived human proteins exhibit racemization of certain amino acids over the course of a human lifetime. Purified core amyloid was found to contain relatively large proportions of D-aspartate and D-serine, suggesting that neuritic plaque amyloid is derived from a long-lived precursor protein. Alternatively, racemization of protein amino acids may be abnormally accelerated in Alzheimer's disease.     

A Computationally Efficient Correlational Neural Network for Automated Prediction of Chronic Kidney Disease

ObjectivesIn this paper, we propose a computationally efficient Correlational Neural Network (CorrNN) learning model and an automated diagnosis system for detecting Chronic Kidney Disease (CKD). A Support Vector Machine (SVM) classifier is integrated with the CorrNN model for improving the prediction accuracy.Material and methodsThe proposed hybrid model is trained and tested with a novel sensing module. We have monitored the concentration of urea in the saliva sample to detect the disease. Experiments are carried out to test the model with real-time samples and to compare its performance with conventional Convolutional Neural Network (CNN) and other traditional data classification methods.ResultsThe proposed method outperforms the conventional methods in terms of computational speed and prediction accuracy. The CorrNN-SVM combined network achieved a prediction accuracy of 98.67%. The experimental evaluations show a reduction in overall computation time of about 9.85% compared to the conventional CNN algorithm.ConclusionThe use of the SVM classifier has improved the capability of the network to make predictions more accurately. The proposed framework substantially advances the current methodology, and it provides more precise results compared to other data classification methods.     

动脉粥样硬化斑块的微区拉曼光谱检测

为探讨动脉粥样硬化斑块的微区拉曼光谱特征,以球囊损伤日本长耳白兔右侧颈总动脉后予以高脂饮食喂养,在实验过程中监测体重和血脂变化情况。3个月后,以中国斑点蝰蛇毒和组胺加以触发使斑块破裂,将动物处死并查找动脉硬化斑块,动脉组织经大体病理分类后,进行微区拉曼光谱及病理检测。结果显示:动脉粥样硬化斑块的拉曼光谱图在1450及1660cm-1处均有明显的胆固醇等脂质特征峰。特征峰曲线下相对面积统计结果表明:明显动脉粥样硬化斑块的谱峰下相对面积(5.80×10-3±3.51×10-3)显著高于轻度动脉粥样硬化组织(2.01×10-3±1.49×10-3)及正常动脉组织(1.01×10-3±0.94×10-3),P<0.05。正常动脉组织拉曼光谱曲线较光滑,无明显特征峰。血栓形成处拉曼光谱图荧光背底较强,未见特征谱峰。该研究结果证明微区拉曼光谱可以对动脉粥样硬化斑块的胆固醇等脂质含量进行特异性定量检测,表明微区拉曼光谱是评估动脉粥样硬化程度及斑块稳定性的可行方法。     

中老年人动脉粥样硬化性脑卒中血清CRP与血脂水平关系分析

目的:探讨中老年人动脉粥样硬化性脑卒中血清CRP与血脂水平关系。方法:2011年3月至2013年2月选择我院收治的中老年人动脉粥样硬化性脑卒中120例作为观察组,同期门诊选择健康中老年人120例作为对照组,两组都进行血清CRP与血脂的测定并进行相关分析。结果:多因素logistic回归分析结果显示TC、CRP、LDL-C与HDL-C是导致中老年人动脉粥样硬化性脑卒中发病的独立危险因素(P0.05)。观察组的血清CRP含量明显高于对照组,TC、TG与LDL-C含量明显高于对照组,而HDL-C含量明显低于对照组,对比差异都有统计学意义(P0.05)。血清CRP≥3 mg/L患者(n=80)的TC、TG与LDL-C含量也明显高于血清CRP3 mg/L患者(n=40),对比差异也有统计学意义(P0.05)。结论:中老年人动脉粥样硬化性脑卒中患者表现为血清CRP、TG、LDL-C和TC的升高,它们也是脑卒中的独立危险因素,同时CRP水平可以预测相关血脂指标的变化。     

Mechanical analysis of arterial plaques in native geometry with OCT wall motion analysis

The mechanical behavior of an atherosclerotic plaque may encode information about the type, composition, and vulnerability to rupture. Human arterial segments with varying plaque burden were analyzed ex vivo with optical coherence tomography (OCT) to determine plaque type and to determine compliance during pulsatile inflation in their native geometry. Calcifications and lipid filled plaques showed markedly different compliance when analyzed with OCT wall motion analysis. There was also a trend towards increased circumferential variation in arterial compliance with increasing plaque burden.     

Uniaxial tensile testing approaches for characterisation of atherosclerotic plaques

The pathological changes associated with the development of atherosclerotic plaques within arterial vessels result in significant alterations to the mechanical properties of the diseased arterial wall. There are several methods available to characterise the mechanical behaviour of atherosclerotic plaque tissue, and it is the aim of this paper to review the use of uniaxial mechanical testing. In the case of atherosclerotic plaques, there are nine studies that employ uniaxial testing to characterise mechanical behaviour. A primary concern regarding this limited cohort of published studies is the wide range of testing techniques that are employed. These differing techniques have resulted in a large variance in the reported data making comparison of the mechanical behaviour of plaques from different vasculatures, and even the same vasculature, difficult and sometimes impossible. In order to address this issue, this paper proposes a more standardised protocol for uniaxial testing of diseased arterial tissue that allows for better comparisons and firmer conclusions to be drawn between studies. To develop such a protocol, this paper reviews the acquisition and storage of the tissue, the testing approaches, the post-processing techniques and the stress–strain measures employed by each of the nine studies. Future trends are also outlined to establish the role that uniaxial testing can play in the future of arterial plaque mechanical characterisation.     

Variable Deposition of Amyloid β-Protein (Aβ) with the Carboxy-Terminus that Ends at Residue Valine40 (Aβ40) in the Cerebral Cortex of Patients with Alzheimer's Disease: A Double-Labeling Immunohistochemical Study with Antibodies Specific for Aβ40 and the Aβ that Ends at Residues Alanine42/Threonine43 (Aβ42)

Amyloid -protein (A) deposits in the cerebral cortices of patients with Alzheimer's disease (AD) were investigated immunohistochemically to determine their carboxy terminal sequences. Antibodies specific for A terminating at residue valine₄₀ (A40) and at residues alanine₄₂/threonine₄₃ (A42) were used. Virtually all parenchymal A deposits were positive for A42. Many of these deposits were also partially or completely labeled for A40. The degree of A40 labeling varied from area to area within a given brain and from AD case to AD case. In contrast to parenchymal deposits, A40 labeled essentially all the vascular deposits which constitute amyloid angiopathy (AA), with A42 occurring variably in some of these deposits. Occasional AA was found, however, in which A42 predominated or was exclusively deposited. Such a diversity of A species, both in brain parenchyma and in AA, suggests that multiple C-terminal processing mechanisms occur in the cell types responsible for these deposits.     

Novel biomarkers with potential for cardiovascular risk reclassification

Precise estimation of the absolute risk for CVD events is necessary when making treatment recommendations for patients. A number of multivariate risk models have been developed for estimation of cardiovascular risk in asymptomatic individuals based upon assessment of multiple variables. Due to the inherent limitation of risk models, several novel risk markers including serum biomarkers have been studied in an attempt to improve the cardiovascular risk prediction above and beyond the established risk factors. In this review, we discuss the role of underappreciated biomarkers such as red cell distribution width (RDW), cystatin C (cysC), and homocysteine (Hcy) as well as imaging biomarkers in cardiovascular risk reclassification, and highlight their utility as additional source of information in patients with intermediate risk.     

胆固醇结晶激活动脉粥样硬化斑块巨噬细胞NLRP3炎症体的途径

动脉粥样硬化既是胆固醇在血管壁聚集的疾病,也是发生在动脉壁的一种低强度慢性炎症形式。近年来有研究证实胆固醇结晶在动脉粥样硬化发生发展中具有重要作用。新的显微技术证实,胆固醇结晶在动脉粥样硬化斑块形成的早期即已出现,并与早期炎症有关。胆固醇结晶通过诱发局部炎症,促进大的脂质核心形成;刺破纤维帽,导致斑块破裂进而促进动脉粥样硬化斑块的进展。在影响斑块进程中,NLRP3炎症体的激活对此发挥了重要的作用。NLRP3炎症体是研究最多最明确的炎症体,其与非炎症性疾病的发生发展密切相关。以胆固醇结晶激活NLRP3炎症体的途径作为研究靶点,为动脉粥样硬化的诊断和治疗提供了新的思路和方法。该文就胆固醇结晶在动脉粥样硬化斑块中激活巨噬细胞NLRP3炎症体的两种途径做一综述。     

Plasma ornithine carbamyl transferase level as an indicator of ischaemic injury of rat liver

The activity of ornithine carbamyl transferase (OCT) and glutamate pyruvate transaminase (GPT) in serum has been correlated with the extent of necrosis 24 h after different periods of ischaemia in rat liver. The extent of necrosis has been quantified as the volume density of necrosis in the total ischaemic liver lobes using tetranitro BT. The GPT-activity in serum is maximal between 1 and 5 h after different periods of ischaemia, whereas OCT reaches its maximum between 5 and 12 h after ischaemia. The total amount of leaked enzyme-activity as well as the peak value give a linear correlation with the extent of necrosis for OCT and GPT. There is a difference between the character of these two enzymes in that a small leakage of GPT does not indicate liver cell necrosis later on. However, the appearance of OCT in the blood, an enzyme localized in the mitochondrial matrix, has a predictive value for the extent of necrosis, likely to occur later on. GPT, an enzyme from the cytoplasm, can also occur in the blood during the reversible stage of liver cell damage.