mTreeIllustrator: A Mixed-Initiative Framework for Visual Exploratory Analysis of Multidimensional Hierarchical Data

Multidimensional hierarchical (mTree) data are very common in daily life and scientific research. However, mTree data exploration is a laborious and time-consuming process due to its structural complexity and large dimension combination space. To address this problem, we present mTreeIllustrator, a mixed-initiative framework for exploratory analysis of multidimensional hierarchical data with faceted visualizations. First, we propose a recommendation pipeline for the automatic selection and visual representation of important subspaces of mTree data. Furthermore, we design a visual framework and an interaction schema to couple automatic recommendations with human specifications to facilitate progressive exploratory analysis. Comparative experiments and user studies demonstrate the usability and effectiveness of our framework

Host Lipids in Positive-Strand RNA Virus Genome Replication

Membrane association is a hallmark of the genome replication of positive-strand RNA viruses [(+)RNA viruses]. All well-studied (+)RNA viruses remodel host membranes and lipid metabolism through orchestrated virus-host interactions to create a suitable microenvironment to survive and thrive in host cells. Recent research has shown that host lipids, as major components of cellular membranes, play key roles in the replication of multiple (+)RNA viruses. This review focuses on how (+)RNA viruses manipulate host lipid synthesis and metabolism to facilitate their genomic RNA replication, and how interference with the cellular lipid metabolism affects viral replication

Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood

Caffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuable timber tree species in China . We performed a comprehensive analysis of COMT genes in the C. bungei genome by describing the gene structure and phylogenetic relationships of each family member using bioinformatics-based methods. A total of 23 putative COMT genes were identified using the conserved domain sequences and amino acid sequences of COMTs from Arabidopsis thaliana and Populus trichocarpa as probes. Phylogenetic analysis showed that 23 CbuCOMTs can be divided into three groups based on their structural characteristics; five conserved domains were found in the COMT family. Promoter analysis indicated that the CbuCOMT promoters included various cis-acting elements related to growth and development. Real-time quantitative polymerase chain reaction (PCR) analysis showed differential expression among CbuCOMTs. CbuCOMT2, 7, 8, 9, 10, 12, 13, 14, 21, and 23 were mainly expressed in xylem. Only CbuCOMT23 was significantly downregulated in tension wood and upregulated in opposite wood compared to normal wood. Our study provides new information about the CbuCOMT gene family and will facilitate functional characterisation in further research

Jianpi Bushen, a Traditional Chinese Medicine Therapy, Combined with Chemotherapy for Gastric Cancer Treatment: A Meta-Analysis of Randomized Controlled Trials

Objective. To investigate the effects of Jianpi Bushen (JPBS), a traditional Chinese medicine that is used to invigorate the spleen and tonify the kidney, combined with chemotherapy for the treatment of gastric cancer. Methods. Literature retrieval was performed in PubMed, EMBASE, Cochrane Library, MEDLINE, CNKI, Wanfang Data Information Site, and VIP from inception to October 2017. Randomized controlled trials to evaluate the effects of JPBS combined with chemotherapy were identified. The primary reported outcomes were KPS (Karnofsky Performance Status), clinical curative efficiency, immune function, blood system, and nonhematologic system. Review Manager 5.3 (RevMan 5.3) was used for data analysis, and the quality of the studies was also appraised. Results. A total of 26 studies were included with 3098 individuals. The results of the meta-analysis indicated that treatment of gastric cancer with the combination of JPBS and chemotherapy resulted in better outcomes compared to chemotherapy alone. Conclusion. Evidence from the meta-analysis suggested that JPBS combined with chemotherapy has a positive effect on gastric cancer treatment. However, additional rigorously designed and large sample randomized controlled trials are required to confirm the efficacy and safety of this treatment

Metabolomics profiling reveals new aspects of dolichol biosynthesis in Plasmodium falciparum

The cis-polyisoprenoid lipids namely polyprenols, dolichols and their derivatives are linear polymers of several isoprene units. In eukaryotes, polyprenols and dolichols are synthesized as a mixture of four or more homologues of different length with one or two predominant species with sizes varying among organisms. Interestingly, co-occurrence of polyprenols and dolichols, i.e. detection of a dolichol along with significant levels of its precursor polyprenol, are unusual in eukaryotic cells. Our metabolomics studies revealed that cis-polyisoprenoids are more diverse in the malaria parasite Plasmodium falciparum than previously postulated as we uncovered active de novo biosynthesis and substantial levels of accumulation of polyprenols and dolichols of 15 to 19 isoprene units. A distinctive polyprenol and dolichol profile both within the intraerythrocytic asexual cycle and between asexual and gametocyte stages was observed suggesting that cis-polyisoprenoid biosynthesis changes throughout parasite’s development. Moreover, we confirmed the presence of an active cis-prenyltransferase (PfCPT) and that dolichol biosynthesis occurs via reduction of the polyprenol to dolichol by an active polyprenol reductase (PfPPRD) in the malaria parasite

Antisynchronization of the Hyperchaotic Systems with Uncertainty and Disturbance Using the UDE-Based Control Method

In this paper, we investigate the antisynchronization problem of a class of hyperchaotic systems with both model uncertainty and external disturbance. Firstly, combining the dynamic feedback control method and the uncertainty and disturbance estimation (UDE)-based control method, we propose a new UDE-based dynamic feedback control method. Secondly, we take the 4D hyperchaotic system as an example and realize the antisynchronization problem of such system. Finally, the effectiveness and correctness of the proposed method is verified by numerical simulation

Complete Synchronization and Partial Anti-Synchronization of Complex Lü Chaotic Systems by the UDE-Based Control Method

The presence of uncertainty and disturbance can lead to asymmetric control of nonlinear systems, and this asymmetric control can lead to a decrease in the productivity of the engineered system. In order to improve the control speed of the improved nonlinear system, complete synchronization and partial anti-synchronization of complex Lü chaotic systems with uncertainty and disturbance are investigated in the present paper. First, a new UDE-based dynamic feedback control method is proposed for the complete synchronization problem of the system. The method unites the dynamic gain feedback control method and the uncertainty and perturbation estimator (UDE) control method, where the dynamic gain feedback controller is used to achieve asymptotic stability of the nominal system and the UDE controller is used to handle a given controlled system with uncertainty and disturbance. Second, for the partial desynchronization problem of this system, a new UDE-based linear-like feedback control method is proposed, which consists of two controllers: a linear-like feedback controller used to achieve the asymptotic stabilization of the nominal system and the other UDE controller is designed to handle the given controlled system with uncertainty and disturbance. Finally, numerical simulations are performed to verify the correctness and stability of the theoretical results

Projection Synchronization of a Class of Complex Chaotic Systems with Both Uncertainty and Disturbance

This paper mainly investigates the projection synchronization of complex chaotic systems with both uncertainty and disturbance. Using the linear feedback method and the uncertainty and disturbance estimation- (UDE-) based control method, the projection synchronization of such systems is realized by two steps. In the first step, a linear feedback controller is designed to control the nominal complex chaotic systems to achieve projection synchronization. An UDE-based controller is proposed to estimate the whole of uncertainty and disturbance in the second step. Finally, numerical simulations verify the feasibility and effectiveness of the control method