Link-Prediction and its Application in Online Social Networks

Alongside the continuous development of Internet technologies, traditional social networks are running online to provide more services so as to unite the community. In the meantime, conventional web-based information systems are trying hard to utilise social networking elements to develop a virtual community so as to increase their popularity. The combination of these two domains has become what people knew as the ‘online social networks’. There is much to do to reveal the knowledge behind the screen as massive amounts of user-generated data is created every second. Many people from different disciplines are using their tools and techniques to analyse and build knowledge to try understanding the evolution of it. Link Prediction, with the essence of calculating similarities of two nodes, is one of the most common techniques to analyse an online social network. It is worth mentioning that while using Link Prediction to explain online social network, we consider it as a graph with nodes and edges connecting one another where nodes represent individuals and edges represent the relations between them. Link Prediction can be utilised in many ways in this domain, where one of the most common ways is predicting links/edges that may appear in the future of an evolving network where links/edges represent connections. The meaning of these connections vary under different circumstance, such as an academia social network where they may represent co-author relationships among researchers. Therefore, one of the most common applications of Link Prediction in an online social network will be the recommendation system. Many works have been done to analyse social-oriented online networks and many turns into applications with great success such as Facebook and Twitter. However, this thesis concentrates on investigating a particular type of online social network where there is still a large gap waiting to be filled - the online academia social network. The objective of this thesis is to provide a more sensible way for people to understand the evolution of this network and develop models and algorithms that solving issues in regards to the needs of the users in this system of finding valuable research partners. Further the object is to building up an environment for future researchers to share knowledge and to carry on the work as a community. To be specific, this thesis contains four main chapters, and they are connected in some ways to develop solutions for the issues coming out during the research processes

Genome-Wide Identification and Analysis of <i>ZF-HD</i> Gene Family in Moso Bamboo (<i>Phyllostachys edulis</i>)

Zinc finger-homeodomain (ZF-HD) proteins play essential roles in plant growth, development and stress responses. However, knowledge of the expression and evolutionary history of ZF-HD genes in moso bamboo remains limited. In this study, a total of 24 ZF-HD genes were found unevenly distributed on 12 chromosomes in moso bamboo (Phyllostachys edulis). Phylogenetic analysis indicated that PeZF-HDs were divided into two subfamilies: ZHD and MIF. The ZHD subfamily genes were further classified into seven groups according to their orthologous relationships among the rice and Arabidopsis ZF-HD gene family. The gene structures and conserved motifs of PeZF-HDs were analyzed. Whole-genome duplication (WGD) or segmental duplication promoted the evolution and expansion of the moso bamboo ZF-HD gene family. Ka/Ks ratios suggested that the twenty-four duplication pairs had undergone purifying selection. Promoter analysis showed that most PeZF-HDs contained cis-elements associated with stress responses and hormones. Expression analysis demonstrated that many PeZF-HDs were responsive to abiotic stress treatment. Overall, this work investigated PeZF-HD genes in moso bamboo using bioinformatic approaches. The evolutionary research on gene structure, motif distribution and cis-regulatory elements indicated that PeZF-HDs play distinct roles in biological processes, which provides a theoretical basis for exploring the physiological functions of ZF-HDs and selecting candidate stress-related genes in moso bamboo

Single-cell gene regulatory network analysis for mixed cell populations with applications to COVID-19 single cell data

Gene regulatory network (GRN) refers to the complex network formed by regulatory interactions between genes in living cells. In this paper, we consider inferring GRNs in single cells based on single cell RNA sequencing (scRNA-seq) data. In scRNA-seq, single cells are often profiled from mixed populations and their cell identities are unknown. A common practice for single cell GRN analysis is to first cluster the cells and infer GRNs for every cluster separately. However, this two-step procedure ignores uncertainty in the clustering step and thus could lead to inaccurate estimation of the networks. To address this problem, we propose to model scRNA-seq by the mixture multivariate Poisson log-normal (MPLN) distribution. The precision matrices of the MPLN are the GRNs of different cell types and can be jointly estimated by maximizing MPLN's lasso-penalized log-likelihood. We show that the MPLN model is identifiable and the resulting penalized log-likelihood estimator is consistent. To avoid the intractable optimization of the MPLN's log-likelihood, we develop an algorithm called VMPLN based on the variational inference method. Comprehensive simulation and real scRNA-seq data analyses reveal that VMPLN performs better than the state-of-the-art single cell GRN methods.Comment: 95 pages,28 figure

Identification, evolution and functional inference on the cold-shock domain protein family in Pak-choi (Brassica rapa ssp. chinensis) and Chinese cabbage (Brassica rapa ssp. pekinensis)

The cold shock domain proteins (CSPs) play important roles in plant developmental processes and stress responses. Multiple sequence alignments found that these CSPs all have a cold shock domain fragment. Phylogenetic tree analysis found that most BcCSPs were more closely related to BrCSPs than other crops. Furthermore, we observed the conserved intron/exon structural patterns of these CSP genes in Pak-choi, Chinese cabbage and Arabidopsis, all motif were observed to be conserved among several boxes subgroups. Comparative analysis of expression patterns of CSP genes in Pak-choi, Chinese cabbage and Arabidopsis suggest that the CSP genes play various roles in plants through qRT-PCR analysis. Further, the CSP expression pattern in different tissues (roots, stems and leaves) of Chinese cabbage was also studied. This study showed that these gene family members might play roles in abiotic stresses responses, and might benefit from their functional characterization and utilization in the resistance engineering of Pak-choi and Chinese cabbage

Design, Synthesis, and Antitumor Activity of Olmutinib Derivatives Containing Acrylamide Moiety

Two series of olmutinib derivatives containing an acrylamide moiety were designed and synthesized, and their IC50 values against cancer cell lines (A549, H1975, NCI-H460, LO2, and MCF-7) were evaluated. Most of the compounds exhibited moderate cytotoxic activity against the five cancer cell lines. The most promising compound, H10, showed not only excellent activity against EGFR kinase but also positive biological activity against PI3K kinase. The structure–activity relationship (SAR) suggested that the introduction of dimethylamine scaffolds with smaller spatial structures was more favorable for antitumor activity. Additionally, the substitution of different acrylamide side chains had different effects on the activity of compounds. Generally, compounds H7 and H10 were confirmed as promising antitumor agents

High-Energy Transsyndesmotic Ankle Fracture Dislocation: A Case Report and Systematic Literature Review

High-energy trauma can cause transsyndesmotic ankle fracture dislocation. These fractures are quite rare. Here we present a clinical case of a male patient with this type of injury. A systematic review of PubMed, Ovid MEDLINE, and Embase electronic databases revealed only two prior publications on a similar topic. We discuss the typical clinical features of these injuries, the treatment of high-energy trauma which can cause transsyndesmotic ankle fracture dislocation, and its prognosis