EGFAFS: A Novel Feature Selection Algorithm Based on Explosion Gravitation Field Algorithm

Feature selection (FS) is a vital step in data mining and machine learning, especially for analyzing the data in high-dimensional feature space. Gene expression data usually consist of a few samples characterized by high-dimensional feature space. As a result, they are not suitable to be processed by simple methods, such as the filter-based method. In this study, we propose a novel feature selection algorithm based on the Explosion Gravitation Field Algorithm, called EGFAFS. To reduce the dimensions of the feature space to acceptable dimensions, we constructed a recommended feature pool by a series of Random Forests based on the Gini index. Furthermore, by paying more attention to the features in the recommended feature pool, we can find the best subset more efficiently. To verify the performance of EGFAFS for FS, we tested EGFAFS on eight gene expression datasets compared with four heuristic-based FS methods (GA, PSO, SA, and DE) and four other FS methods (Boruta, HSICLasso, DNN-FS, and EGSG). The results show that EGFAFS has better performance for FS on gene expression data in terms of evaluation metrics, having more than the other eight FS algorithms. The genes selected by EGFAGS play an essential role in the differential co-expression network and some biological functions further demonstrate the success of EGFAFS for solving FS problems on gene expression data.     

基因编辑与人的尊严—关于基因技术革命的伦理学思考

生物技术革命所带来的基因编辑技术,使人类充当“上帝”的角色,成为自身的造物主,具有“设计生命”和“人的再造”的能力,但这一技术革命却带来了对人类尊严的存在论根基的严重挑战,引发了最深刻的伦理学新问题。当代自由主义优生学者提出,人类能够以“玩弄上帝”的方式去改变和重新创造人类自身,而这一再创造的存在论后果却是一个悖谬：人类在获得极度自由的同时,却摧毁了人之为人的尊严的根基,从而彻底失去生命存在的自由本性。按照康德的教诲,尊严是人之为人的最高伦理价值,尊严并不仅仅是出于个体自主性的“权利”和“自尊”,而是出于普遍道德自主性之上的“责任”和“敬重”,人的自由本性的道德自律才是人的尊严和崇高所在。后形而上学思想家进一步发展了康德的尊严观点,在他者和公共性维度上提出一种建立在承认、交互性和交往共同体基础之上的新尊严理论。面对生物技术的滥用和人类尊严受到的挑战,伦理学需要保卫和重建尊严概念,在“自由者的共在关系”中寻求尊严的基础和规范性的力量,从开放的“我们”推演出对“未来人”的责任。     

Molecular approach to human leukemia: Isolation and characterization of the first human retrovirus HTLV-1 and its impact on tumorigenesis in Adult T-cell Leukemia

Molecular biology of mouse and chicken retroviruses had identified oncogenes and provided a revolutionary concept in understanding of cancers. A human retrovirus was established during 1980–1982 in linkage with a unique human leukemia, concurrently in Japan and USA. This review covers our efforts on the discovery of new retrovirus, Human T-cell Leukemia Virus Type 1 (HTLV-1), first introducing to a new class of retroviruses with a unique regulatory factors, Tax and Rex. Then it is followed by analyses of molecular interaction of the vial Tax with cellular machineries involved in the pathogenesis of Adult T-cell Leukemia (ATL). And then a probable mechanism of pathogenesis of ATL is proposed including recent findings on HBZ after our efforts.     

Retrovirus-mediated transduction of a cytosine deaminase gene preserves the stemness of mesenchymal stem cells

Human mesenchymal stem cells (MSCs) have emerged as attractive cellular vehicles to deliver therapeutic genes for ex-vivo therapy of diverse diseases; this is, in part, because they have the capability to migrate into tumor or lesion sites. Previously, we showed that MSCs could be utilized to deliver a bacterial cytosine deaminase (CD) suicide gene to brain tumors. Here we assessed whether transduction with a retroviral vector encoding CD gene altered the stem cell property of MSCs. MSCs were transduced at passage 1 and cultivated up to passage 11. We found that proliferation and differentiation potentials, chromosomal stability and surface antigenicity of MSCs were not altered by retroviral transduction. The results indicate that retroviral vectors can be safely utilized for delivery of suicide genes to MSCs for ex-vivo therapy. We also found that a single retroviral transduction was sufficient for sustainable expression up to passage 10. The persistent expression of the transduced gene indicates that transduced MSCs provide a tractable and manageable approach for potential use in allogeneic transplantation.     

Self‐Assembled PAA‐Based Nanoparticles as Potential Gene and Protein Delivery Systems

A series of nanoparticles is prepared via layer‐by‐layer assembly of oppositely charged, synthetic biocompatible polyamidoamine polymers as potential carriers. Particle size, surface charge and internal chain mobility are quantified as a function of the polymer type and number of layers. The effect of addition of surfactant is examined to simulate the effects of nanoparticle dissolution. The cyctotoxicity of these particles (in epithelia and murine cell lines) are orders of magnitude lower than polyethyleneimine controls. Stable nanoparticles may be prepared from mixtures of strongly, oppositely charged polymers, but less successfully from weakly charged polymers, and, given their acceptable toxicity characteristics, such modularly designed constructs show promise for drug and gene delivery.

     

Synthesis of Cholesterylated Thiogalactosides for Gene Delivery

A series of cholesterylated thiogalactosides L₁ –L₆ the cell targeting ligands for gene delivery to hepatocytes, was synthesized. Related poly(ethylene glycol) chain was used as a bridge for the attachment of galactoside on one hydroxyl end, while the other hydroxyl end was linked with cholesterol. This design provided an effective entry for the synthesis of a poly(ethylene glycol) compound with the hepatocyte targeting.     

Thermo-responsive gelatin-functionalized PCL film surfaces for improvement of cell adhesion and intelligent recovery of gene-transfected cells

Efficient local gene transfection on a tissue scaffold is dependent on good cell-adhesion characteristics. In this work, the thermo-responsive gelatin-functionalized polycaprolactone (PCL) films were proposed for improvement of cell adhesion and intelligent recovery of gene-transfected cells. Functional copolymer brushes (PCL-g-P(NIPAAm-co-MAAS)) were first prepared via surface-initiated ATRP of N-isopropylacrylamide (NIPAAm) and methacrylic acid sodium salt (MAAS) from the initiator-funcationalized PCL surfaces. The pendant carboxyl end-groups of the PCL-g-P(NIPAAm-co-MAAS) surface were subsequently coupled with gelatin via carbodiimide chemistry to produce the thermo-responsive gelatin-functionalized PCL surface. The thermo-responsive gelatin-functionalized PCL film surface can improve cell adhesion and proliferation above the LCST of P(NIPAAm) without destroying cell detachment properties at lower temperatures. The dense transfected cells can be recovered simply by lowering culture temperature. The thermo-responsive gelatin-functionalized PCL films are potentially useful as intelligent adhesion modifiers for directing cellular functions within tissue scaffolds.     

Duplex dual-labeled fluorescence probe-based melting curve and endpoint genotyping assays for genotyping of rs2000999 and haptoglobin gene deletion

Haptoglobin (Hp) is a hemoglobin-binding serum glycoprotein. Some variations in the Hp gene (HP) or Hp-related gene (HPR), including a single-nucleotide polymorphism in intron 2 of HRP, rs2000999, and a complete deletion of the HP gene (HP^del), one of the rare variants of HP, have been reported to correlate with the serum cholesterol concentration as well as the serum Hp concentration. In this study, we developed a duplex dual-labeled fluorescence probe-based method to simultaneously determine the rs2000999 G > A polymorphism by melting curve genotyping and the zygosity of HP^del by endpoint genotyping. This method was then validated by using the genomic DNA from 94 Japanese subjects for whom genotypes of rs2000999 and HP^del zygosity had already been determined. The results obtained with this method were in perfect agreement with the previous ones. Thus, the present method enables us to estimate these two polymorphisms in relatively large-scale groups of subjects, especially in Asian populations where the HP^del is distributed.     

DCE-MRI参数联合IFIT1基因对腰椎间盘突出患者椎间盘退变程度的评估价值

探讨DCE-MRI参数及IFIT1基因对腰椎间盘突出症(LDH)患者椎间盘退变(IDD)程度的评估价值。随机选取确诊的66例LDH患者作为研究对象,根据改良Pfirrmann分级法将患者分为2组:轻中度IDD(Ⅰ~Ⅲ级)组(46例)和重度IDD(Ⅳ~Ⅴ级)组20例。通过DCE-MRI检查考察患者的K-trans值,采用日本骨科学会评分(JOA)评估腰椎功能,采用视觉模拟评分法(VAS)评估腰部疼痛,采用RT-PCR检测外周血单个核细胞(PBMC)中IFIT1的mRNA表达。轻中度IDD组的K-trans值显著低于重度IDD组。轻中度IDD组患者PBMC中的IFIT1 mRNA相对表达量显著低于重度IDD组。K-trans值与PBMC中的IFIT1 mRNA水平和VAS评分正相关,与JOA评分负相关(P<0.05)。PBMC中的IFIT1 mRNA水平与VAS评分正相关,与JOA评分负相关(P<0.05)。K-trans值和PBMC中的IFIT1 mRNA水平联合诊断重度IDD的AUC值、敏感性和特异性分别为0.991、91.3%和100.0%,AUC值和特异性均高于单独诊断。DCE-MRI检查中的K-trans值联合PBMC中的IFIT1 mRNA水平可用于LDH患者IDD程度的诊断。