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A Novel Method for Gene Regulatory Network Inference with Pseudotime Data Using Information Criterion 基于信息准则的伪时间数据基因调控网络推断新方法
Pub Date : 2022-07-01 DOI: 10.17706/ijbbb.2022.12.3.43-52
Shuhei Yao, Kaito Uemura, S. Seno, H. Matsuda
: Trajectory inference has been used to model cellular dynamic processes by using single-cell RNA sequence data. The inference often computes pseudotime representing the progression through the process along the trajectory. Several methods to infer gene regulatory networks have been proposed using the gene expression profiles of the cells ordered with the pseudotime to elucidate the regulatory relationships between genes in a dynamic process. In this paper, we propose a novel method for the inference of such gene regulatory networks. To predict highly accurate gene regulatory relationships in the network, we introduce an edge-scoring scheme with bootstrap sampling. We demonstrate the accuracy of the proposed methods by comparing the results with those of existing methods using synthetic and real single-cell RNA-seq data. a type in which the regulatory relationships of genes are connected in a long straight line [6]. Each network was generated with five different patterns of cell numbers: 100, 200, 500, 2000, and 5000. In each condition, 10 networks were generated and evaluated as described in [6]. For the actual data, we extracted the expression data of 10 genes from the network of transcription factors experimentally confirmed in the report of [11] from the expression data of cells in the differentiation lineage from pluripotent progenitor cells to monocytes as described above. 315 cells in which at least 3 of the 10 genes were expressed. The same time point was defined as the number truncated after the decimal point of the pseudotime. Using these data as input, network inference was performed using the DBN approach of SiGN-BN, and edge gain was calculated using the approach described above. We performed 100 bootstrap sampling for the synthetic data and 1000 bootstrap sampling for the real data. For each edge of the obtained network, the bootstrap probability, which means the probability that a regulated edge appears in the network inferred from multiple data sets generated by the bootstrap method, was calculated separately from the proposed method. The results obtained by the bootstrap probabilities and SINCERITIES were compared with the proposed method. The AUROC (area under the receiver operating characteristic curve) and AUPRC for each method were computed with the PRROC package [12], and all graphs were plotted in R. For the network visualization, Cytoscape was used.
轨迹推理已被用于利用单细胞RNA序列数据来模拟细胞动态过程。推理通常计算伪时间,表示沿着轨迹的过程的进展。人们提出了几种利用细胞的基因表达谱来推断基因调控网络的方法,以阐明在一个动态过程中基因之间的调控关系。在本文中,我们提出了一种新的方法来推断这种基因调控网络。为了准确预测网络中的基因调控关系,我们引入了一种带自举采样的边缘评分方案。我们通过将结果与使用合成和真实单细胞RNA-seq数据的现有方法的结果进行比较,证明了所提出方法的准确性。一种基因调控关系以一条长直线连接的类型。每个网络都由五种不同的单元号码模式生成:100、200、500、2000和5000。在每种情况下,生成10个网络,并按照[6]的描述进行评估。对于实际数据,我们从上述多能祖细胞向单核细胞分化谱系中细胞的表达数据中提取了[11]报告中实验证实的转录因子网络中10个基因的表达数据。315个细胞至少表达了10个基因中的3个。同一时间点被定义为在伪时间小数点后截断的数字。使用这些数据作为输入,使用SiGN-BN的DBN方法进行网络推理,并使用上述方法计算边缘增益。我们对合成数据进行了100次自举抽样,对真实数据进行了1000次自举抽样。对于得到的网络中的每条边,分别计算自举概率(bootstrap probability),即从自举方法生成的多个数据集推断出网络中出现一条调节边的概率。将自举概率和自举诚恳度得到的结果与所提方法进行了比较。使用proroc软件包[12]计算每种方法的AUROC(接收者工作特征曲线下面积)和AUPRC,所有图形以r绘制。网络可视化使用Cytoscape。
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引用次数: 0
A Personalized Diagnostic Tool for Microbiome-Related Morbidities 微生物组相关疾病的个性化诊断工具
Pub Date : 2022-07-01 DOI: 10.17706/ijbbb.2022.12.3.53-62
Olympia Giannou
: A model-driven approach suitable for classifying microbiome-related morbidities such as ulcerative colitis on smart mobile devices is investigated in this manuscript. A novel scheme is proposed, which consists of a pre-trained image classifier on ImageNet and is deployed into the presented Android mobile application for this purpose. Endoscopic images of mouse colitis were used as input datasets for our experiments. The proposed approach offers an efficient classifier, based on the average of all its performance metrics: confusion matrix, accuracy, recall, precision, cross entropy, f1-score. The results are compared with these of the most representative image classifiers for the kind of classification we target, in terms of performance, as well as the size of the retrained frozen graph on our dataset. Such a classification could serve as a valuable tool in clinical medicine offering an automated, diagnostic tool for microbiome-related morbidities, thus allowing accurate early diagnosis and the design of personalized and targeted therapeutic approaches.
一种模型驱动的方法适合于分类微生物组相关的发病率,如溃疡性结肠炎在智能移动设备上进行了研究。提出了一种基于ImageNet的预训练图像分类器的新方案,并将其部署到Android移动应用程序中。小鼠结肠炎的内镜图像被用作我们实验的输入数据集。该方法提供了一个高效的分类器,基于其所有性能指标的平均值:混淆矩阵,准确性,召回率,精度,交叉熵,f1-score。将结果与我们目标分类类型的最具代表性的图像分类器进行比较,在性能方面,以及在我们的数据集中重新训练的冻结图的大小。这种分类可以作为临床医学中有价值的工具,为微生物组相关疾病提供自动化诊断工具,从而实现准确的早期诊断和个性化和靶向治疗方法的设计。
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引用次数: 0
a 一个
Pub Date : 2022-01-01 DOI: 10.33545/26646536.2022.v4.i1a.30
Debeli Tadesse Amente, Shimellis Hailu Dessie, Dinaol Belina Kitila, Adem Hiko Washie, Sufiyan Abdi Musa
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引用次数: 0
Review on microbial genetics and virulence factors of mycobacterium bovis 牛分枝杆菌的微生物遗传学及毒力因子研究进展
Pub Date : 2022-01-01 DOI: 10.33545/26646536.2022.v4.i1a.31
Darge Lulu, Dr. Mohammed Hussen
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引用次数: 0
Repurposing of Known Drugs as Potential Therapeutics for Cancer Immunotherapy for Patients with Solid Tumors: Modeling Small Molecule Interactions with PD-1 Binding Sites 利用已知药物作为实体瘤患者癌症免疫治疗的潜在疗法:模拟PD-1结合位点的小分子相互作用
Pub Date : 2022-01-01 DOI: 10.17706/ijbbb.2022.12.4.71-84
A. Huang
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引用次数: 0
Identification of Lineage Markers for T Cell Immune Dysregulation in Sarcoidosis Using Single-Cell RNA-seq 单细胞RNA-seq鉴定结节病T细胞免疫失调的谱系标记
Pub Date : 2022-01-01 DOI: 10.17706/ijbbb.2022.12.4.63-70
A. Nomura, H. Matsuda
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引用次数: 1
Pirin, a Multifunction Protein with Quercetinase Activity and Involvement in Transcription Regulation 具有槲皮素酶活性并参与转录调控的多功能蛋白Pirin
Pub Date : 2022-01-01 DOI: 10.17706/ijbbb.2022.12.4.85-92
Yifei Wang
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引用次数: 0
Next-Generation Sequencing on COVID-19 Pandemic COVID-19大流行的新一代测序
Pub Date : 2022-01-01 DOI: 10.17706/ijbbb.2022.12.2.30-38
Jiahuan He
: Next-generation sequencing (NGS), with Illumina sequencing being the most well-known and most widely used NGS platform, is a high-throughput DNA (or RNA) sequencing technology that allows massive parallel sequencing. There are numerous applications of NGS, with some of them being related to the pandemics or epidemics caused by viral infection, and an example of that is the coronavirus disease 2019 (COVID-19), which is a pandemic that began in December 2019 caused by a novel coronavirus—the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This review then focuses on the discussion of how NGS technology has been applied to the study of the COVID-19 pandemic. Specifically, the review describes the applications of NGS in whole-genome sequencing of SARS-CoV-2, identification of novel COVID-19 viral mutations, tracking the variant viral lineages, and providing insights into the origin and transmission pattern of the current pandemic.
下一代测序(NGS)是一种高通量DNA(或RNA)测序技术,可以进行大规模并行测序,Illumina测序是最知名和最广泛使用的NGS平台。NGS有许多应用,其中一些应用与病毒感染引起的大流行或流行病有关,其中一个例子是2019年冠状病毒病(COVID-19),这是一种新型冠状病毒-严重急性呼吸综合征冠状病毒2 (SARS-CoV-2) -于2019年12月开始的大流行。然后,本文重点讨论了NGS技术如何应用于COVID-19大流行的研究。具体而言,综述描述了NGS在SARS-CoV-2全基因组测序、鉴定新型COVID-19病毒突变、追踪变异病毒谱系以及了解当前大流行的起源和传播模式方面的应用。
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引用次数: 0
a 一个
Pub Date : 2022-01-01 DOI: 10.33545/26646536.2022.v4.i1a.29
Prasanna Dhondi, Javeria Uzma, S. Talla, Kiranmayee Kasula
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引用次数: 0
Novel Thiazolyl-Pyrazoline Analogs: Potential Role for Tyrosine Kinase Inhibition in Colorectal Cancer 新型噻唑基吡唑啉类似物:在结直肠癌中酪氨酸激酶抑制的潜在作用
Pub Date : 2022-01-01 DOI: 10.17706/ijbbb.2022.12.2.22-29
Ayat Fayez, S. Hammad, D. Ghareeb, M. A. Demellawy, Ahmed M Osman
: Colorectal cancer (CRC) ranked the third and the second in the onset and mortality rates, respectively, among all types of cancer (GLOBOCAN 2020). In this study, we targeted epidermal growth factor receptor (EGFR) using two synthesized thiazolyl pyrazoline analogs in presence and absence of berberine as an adjuvant remedy. Preliminary results showed that these compounds exert anti-neoplastic and tyrosine kinase inhibitory effects against lung cancer cell lines. We assessed the anticancer activities of these compounds via quantitative determination of transcripts levels (qRT-PCR) of some apoptotic and proliferative markers in Caco-2 cell line. Our data showed a synergistic augmented effect between the tested compounds and berberine on the pro-apoptotic markers (BAX and p53). Furthermore, the oncogenes EGFR and c-MYC, as well as the anti-apoptotic gene ARC, exhibited downregulation trend. In conclusion, the novel compounds show promising results as potential TKI that inhibit malignant cell growth and restore cancer cells' apoptotic capacity. strategy to hinder the signaling pathways associated with EGFR by binding to its ATP binding sites. We aimed to investigate the potential of novel thiazolyl pyrazolines to inhibit EGFR expression and apoptosis induction when added with the natural isoquinoline berberine. Our results showed a good synergism where P53 was upregulated with its downstream transcription targets BAX and Fas, indicating apoptosis activation. Furthermore, EGFR and TGF-b were downregulated post-treatment suggesting a decline in cell proliferation and migration. Overall, we recommend combining berberine and thiazolyl pyrazoline derivatives to enhance colorectal cancer treatment.
在所有类型的癌症中,结直肠癌(CRC)的发病率和死亡率分别排名第三和第二(GLOBOCAN 2020)。在这项研究中,我们使用两种合成的噻唑基吡唑啉类似物在小檗碱存在和不存在的情况下靶向表皮生长因子受体(EGFR)作为辅助治疗。初步结果表明,这些化合物对肺癌细胞株具有抗肿瘤和酪氨酸激酶抑制作用。我们通过定量测定Caco-2细胞系中一些凋亡和增殖标记物的转录本水平(qRT-PCR)来评估这些化合物的抗癌活性。我们的数据显示,所测试的化合物和小檗碱对促凋亡标志物(BAX和p53)具有协同增强效应。此外,癌基因EGFR、c-MYC以及抗凋亡基因ARC均呈现下调趋势。总之,这些新化合物作为抑制恶性细胞生长和恢复癌细胞凋亡能力的潜在TKI具有很好的前景。通过与EGFR的ATP结合位点结合来阻碍与EGFR相关的信号通路。我们的目的是研究新型噻唑基吡唑啉与天然异喹啉小檗碱添加后抑制EGFR表达和诱导细胞凋亡的潜力。我们的研究结果显示P53与其下游转录靶点BAX和Fas存在良好的协同作用,表明凋亡激活。此外,EGFR和TGF-b在处理后下调,表明细胞增殖和迁移能力下降。总之,我们建议联合使用小檗碱和噻唑基吡唑啉衍生物来加强结直肠癌的治疗。
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International Journal of Bioscience, Biochemistry and Bioinformatics
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