Genetic and Epigenomic Modifiers of Diabetic Neuropathy

Diabetic neuropathy (DN), the most common chronic and progressive complication of diabetes mellitus (DM), strongly affects patients’ quality of life. DN could be present as peripheral, autonomous or, clinically also relevant, uremic neuropathy. The etiopathogenesis of DN is multifactorial, and genetic components play a role both in its occurrence and clinical course. A number of gene polymorphisms in candidate genes have been assessed as susceptibility factors for DN, and most of them are linked to mechanisms such as reactive oxygen species production, neurovascular impairments and modified protein glycosylation, as well as immunomodulation and inflammation. Different epigenomic mechanisms such as DNA methylation, histone modifications and non-coding RNA action have been studied in DN, which also underline the importance of “metabolic memory” in DN appearance and progression. In this review, we summarize most of the relevant data in the field of genetics and epigenomics of DN, hoping they will become significant for diagnosis, therapy and prevention of DN.     

In Silico Analysis of the Molecular-Level Impact of SMPD1 Variants on Niemann-Pick Disease Severity

Sphingomyelin phosphodiesterase (SMPD1) is a key enzyme in the sphingolipid metabolism. Genetic SMPD1 variants have been related to the Niemann-Pick lysosomal storage disorder, which has different degrees of phenotypic severity ranging from severe symptomatology involving the central nervous system (type A) to milder ones (type B). They have also been linked to neurodegenerative disorders such as Parkinson and Alzheimer. In this paper, we leveraged structural, evolutionary and stability information on SMPD1 to predict and analyze the impact of variants at the molecular level. We developed the SMPD1-ZooM algorithm, which is able to predict with good accuracy whether variants cause Niemann-Pick disease and its phenotypic severity; the predictor is freely available for download. We performed a large-scale analysis of all possible SMPD1 variants, which led us to identify protein regions that are either robust or fragile with respect to amino acid variations, and show the importance of aromatic-involving interactions in SMPD1 function and stability. Our study also revealed a good correlation between SMPD1-ZooM scores and in vitro loss of SMPD1 activity. The understanding of the molecular effects of SMPD1 variants is of crucial importance to improve genetic screening of SMPD1-related disorders and to develop personalized treatments that restore SMPD1 functionality.     

基于神经网络和遗传算法的锭子弹性管性能优化

为得到减振弹性管对下锭胆的支承弹性和锭子高速运动下的稳定性等性能的最优匹配效率,依据减振弹性管的等效抗弯刚度及底部等效刚度系数公式,利用MatLab数值分析软件构建弹性管抗弯刚度和底部挠度数学模型。首先,结合Isight优化软件基于径向基神经网络构建其近似模型,且使精度达到可接受水平,并以模型的关键结构参数弹性模量、螺距、槽宽、壁厚为设计变量,结合遗传算法对弹性管抗弯刚度和底部挠度进行多目标优化设计,得到Pareto最优解集和Pareto前沿图,确定出减振弹性管结构工艺参数的优化方案。通过对优化数据进行分析发现,该方案在保证减振弹性管弹性的同时,其底部振幅明显减弱。     

Digital Microfluidics for Manipulation and Analysis of a Single Cell

The basic structural and functional unit of a living organism is a single cell. To understand the variability and to improve the biomedical requirement of a single cell, its analysis has become a key technique in biological and biomedical research. With a physical boundary of microchannels and microstructures, single cells are efficiently captured and analyzed, whereas electric forces sort and position single cells. Various microfluidic techniques have been exploited to manipulate single cells through hydrodynamic and electric forces. Digital microfluidics (DMF), the manipulation of individual droplets holding minute reagents and cells of interest by electric forces, has received more attention recently. Because of ease of fabrication, compactness and prospective automation, DMF has become a powerful approach for biological application. We review recent developments of various microfluidic chips for analysis of a single cell and for efficient genetic screening. In addition, perspectives to develop analysis of single cells based on DMF and emerging functionality with high throughput are discussed.     

ATSP:时态网络可视化的自适应时间片划分方法

现有的时态网络可视化方法大多采用等量时间片来可视化网络的演变，不利于时态模式的快速挖掘和发现。为此，根据时态网络固有的特征提出自适应时间片划分方法（Adaptive Time Slice Partition method，ATSP）。在时态网络的两种表示方式（基于事件的表示方式和基于快照的表示方式）的基础上，构建了ATSP的基础模型，同时提出了一种改进模型用来描述事件间隔时间服从长尾分布的时态网络。为了实现时间片的不等量划分，针对探索任务的不同提出了基于时态模式的ATSP规则和基于中心节点的ATSP规则，并提出了实现算法--层次划分算法（Hierarchical Partition algorithm，HP）和增量划分算法（Incremental Partition algorithm，IP）。实验结果表明，ATSP方法比传统的时间片划分方法更能准确地表示网络的时态特征，且该方法应用于可视化时，能有效归纳并展示网络的特征，明显提高了视觉分析的效率。     

Update on the Diagnostic Pitfalls of Autopsy and Post-Mortem Genetic Testing in Cardiomyopathies

Inherited cardiomyopathies are frequent causes of sudden cardiac death (SCD), especially in young patients. Despite at the autopsy they usually have distinctive microscopic and/or macroscopic diagnostic features, their phenotypes may be mild or ambiguous, possibly leading to misdiagnoses or missed diagnoses. In this review, the main differential diagnoses of hypertrophic cardiomyopathy (e.g., athlete’s heart, idiopathic left ventricular hypertrophy), arrhythmogenic cardiomyopathy (e.g., adipositas cordis, myocarditis) and dilated cardiomyopathy (e.g., acquired forms of dilated cardiomyopathy, left ventricular noncompaction) are discussed. Moreover, the diagnostic issues in SCD victims affected by phenotype-negative hypertrophic cardiomyopathy and the relationship between myocardial bridging and hypertrophic cardiomyopathy are analyzed. Finally, the applications/limits of virtopsy and post-mortem genetic testing in this field are discussed, with particular attention to the issues related to the assessment of the significance of the genetic variants.     

User activities and the heterogeneity of urban space:The case of Dahiyat Al Hussein park

Urban researchers have maintained a constant interest in the complexity and continuity of urban space usage. Some have applied actor–network theory (ANT) to investigate the heterogeneity of spaces and present them through the networks of their users’ activities. However, these accounts are predominantly limited in examining the extent to which these spaces may be heterogeneous when exploring such networks. This paper draws on recent ANT scholarship, which employs an ethnographic research conducted in a main park in a housing project at Dahiyat Al Hussein in Amman, Jordan. The findings describe the complex and unpredictable negotiations that occur within spaces by documenting the varieties and interrelations among user activity networks within this common and shared urban space. This research reveals the extent to which spaces, parks in this case, may be heterogeneous by unpacking their usage. The conclusions and insights assert the necessity of paying attention to design detail and creating designs that are responsive to evolving user activities.     

Sofosbuvir Selects for Drug-Resistant Amino Acid Variants in the Zika Virus RNA-Dependent RNA-Polymerase Complex In Vitro

The nucleotide analog sofosbuvir, licensed for the treatment of hepatitis C, recently revealed activity against the Zika virus (ZIKV) in vitro and in animal models. However, the ZIKV genetic barrier to sofosbuvir has not yet been characterized. In this study, in vitro selection experiments were performed in infected human hepatoma cell lines. Increasing drug pressure significantly delayed viral breakthrough (p = 0.029). A double mutant in the NS5 gene (V360L/V607I) emerged in 3 independent experiments at 40–80 µM sofosbuvir resulting in a 3.9 ± 0.9-fold half- maximal inhibitory concentration (IC₅₀) shift with respect to the wild type (WT) virus. A triple mutant (C269Y/V360L/V607I), detected in one experiment at 80 µM, conferred a 6.8-fold IC₅₀ shift with respect to the WT. Molecular dynamics simulations confirmed that the double mutant V360L/V607I impacts the binding mode of sofosbuvir, supporting its role in sofosbuvir resistance. Due to the distance from the catalytic site and to the lack of reliable structural data, the contribution of C269Y was not investigated in silico. By a combination of sequence analysis, phenotypic susceptibility testing, and molecular modeling, we characterized a double ZIKV NS5 mutant with decreased sofosbuvir susceptibility. These data add important information to the profile of sofosbuvir as a possible lead for anti-ZIKV drug development.     

一种基于Spark的不确定数据集频繁模式挖掘算法

如何在海量不确定数据集中提高频繁模式挖掘性能是目前研究的热点.传统算法大多是以期望、概率或者权重等单一指标为数据项集支持度，在大数据背景下，同时考虑概率和权重支持度的算法难以兼顾其执行效率.为此，本文提出一种基于Spark的不确定数据集频繁模式挖掘算法（UWEFP），首先，为了同时兼顾数据项的概率和权重，计算一项集的最大概率权重值并进行剪枝；然后，为了减少对数据集的多次扫描，结合Spark框架的优点，设计了一种具有FP-tree特征的新颖的UWEFP-tree结构进行模式树的构建及挖掘；最后在Spark环境下，以UCI数据集进行实验验证.实验结果表明本文的方法在保证挖掘结果的同时，提高了效率.