Quick Way to Port Existing C/C++ Chemoinformatics Toolkits to the Web Using Emscripten

Emscripten is a special open source compiler that compiles C and C++ code into JavaScript. By utilizing this compiler, some typical C/C++ chemoinformatics toolkits and libraries are quickly ported to to web. The compiled JavaScript files have sizes similar to native programs, and from a series of constructed benchmarks, the performance of the compiled JavaScript codes is also close to that of the native codes and is better than the handwritten JavaScript codes. Therefore, we believe that Emscripten is a feasible and practical tool for reusing existing C/C++ codes on the web, and many other chemoinformatics or molecular calculation software tools can also be easily ported by Emscripten

Kekule.js: An Open Source JavaScript Chemoinformatics Toolkit

Kekule.js is an open-source, object-oriented JavaScript toolkit for chemoinformatics. It provides methods for many common tasks in molecular informatics, including chemical data input/output (I/O), two- and three-dimensional (2D/3D) rendering of chemical structure, stereo identification, ring perception, structure comparison, and substructure search. Encapsulated widgets to display and edit chemical structures directly in web context are also supplied. Developed with web standards, the toolkit is ideal for building chemoinformatics applications over the Internet. Moreover, it is highly platform-independent and can also be used in desktop or mobile environments. Some initial applications, such as plugins for inputting chemical structures on the web and uses in chemistry education, have been developed based on the toolkit

Characterization of Morphology and Structure of Wax Crystals in Waxy Crude Oils by Terahertz Time-Domain Spectroscopy

The content, morphology, and structure of precipitated wax crystals are major factors affecting crude oil rheology. In this paper, model oils obtained by dissolving a realistic mixture of long-chain <i>n</i>-octacosane in diesel fuels were studied using terahertz time-domain spectroscopy (THz-TDS) and microscopy to gain insight into clusters composed of asphaltene and wax with increasing wax content. The fractal dimension was used for quantitative characterization of the morphology and structure of clusters in the model oils. From the measured absorption and extinction coefficients in the THz region, dynamic processes of the clusters in the model oils were analyzed and identified. The extinction coefficient in the THz region strongly depended on the dispersed and aggregated states of the asphaltene and wax crystals. These observations suggest that the aggregation state of the particles in model oils can be monitored with THz-TDS. In the future, THz-TDS technology may be used to effectively analyze particle dispersion or the aggregation state in crude oil and may thus be useful for rapid assessment of the effect of pour-point depressant on wax crystal aggregates

A surrogate-assisted particle swarm optimization algorithm based on efficient global optimization for expensive black-box problems

<p>Evolutionary algorithms cannot effectively handle computationally expensive problems because of the unaffordable computational cost brought by a large number of fitness evaluations. Therefore, surrogates are widely used to assist evolutionary algorithms in solving these problems. This article proposes an improved surrogate-assisted particle swarm optimization (ISAPSO) algorithm, in which a hybrid particle swarm optimization (PSO) is combined with global and local surrogates. The global surrogate is not only used to predict fitness values for reducing computational burden but also regarded as a global searcher to speed up the global search process of PSO by using an efficient global optimization algorithm, while the local one is constructed for a local search in the neighbourhood of the current optimal solution by finding the predicted optimal solution of the local surrogate. Empirical studies on 10 widely used benchmark problems and a real-world structural design optimization problem of a driving axle show that the ISAPSO algorithm is effective and highly competitive.</p

DataSheet_1_Three-dimensional and single-cell sequencing of liver cancer reveals comprehensive host-virus interactions in HBV infection.docx

BackgroundsHepatitis B virus (HBV) infection is a major risk factor for chronic liver diseases and liver cancer (mainly hepatocellular carcinoma, HCC), while the underlying mechanisms and host-virus interactions are still largely elusive.MethodsWe applied HiC sequencing to HepG2 (HBV-) and HepG2-2.2.15 (HBV+) cell lines and combined them with public HCC single-cell RNA-seq data, HCC bulk RNA-seq data, and both genomic and epigenomic ChIP-seq data to reveal potential disease mechanisms of HBV infection and host-virus interactions reflected by 3D genome organization.ResultsWe found that HBV enhanced overall proximal chromatin interactions (CIs) of liver cells and primarily affected regional CIs on chromosomes 13, 14, 17, and 22. Interestingly, HBV altered the boundaries of many topologically associating domains (TADs), and genes nearby these boundaries showed functional enrichment in cell adhesion which may promote cancer metastasis. Moreover, A/B compartment analysis revealed dramatic changes on chromosomes 9, 13 and 21, with more B compartments (inactive or closed) shifting to A compartments (active or open). The A-to-B regions (closing) harbored enhancers enriched in the regulation of inflammatory responses, whereas B-to-A regions (opening) were enriched for transposable elements (TE). Furthermore, we identified large HBV-induced structural variations (SVs) that disrupted tumor suppressors, NLGN4Y and PROS1. Finally, we examined differentially expressed genes and TEs in single hepatocytes with or without HBV infection, by using single-cell RNA-seq data. Consistent with our HiC sequencing findings, two upregulated genes that promote HBV replication, HNF4A and NR5A2, were located in regions with HBV-enhanced CIs, and five TEs were located in HBV-activated regions. Therefore, HBV may promote liver diseases by affecting the human 3D genome structure.ConclusionOur work promotes mechanistic understanding of HBV infection and host-virus interactions related to liver diseases that affect billions of people worldwide. Our findings may also have implications for novel immunotherapeutic strategies targeting HBV infection.</p

DataSheet_1_High-quality chromosome-level genome assembly of Pacific cod, Gadus macrocephalus.docx

The full text of this article can be freely accessed on the publisher's website

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<p>Purpose: The anti-inflammatory activities of protein glucocorticoid-induced leucine zipper (GILZ) have been demonstrated in vivo and in vitro. Here, we examined the potential effect of a synthetic peptide derived from the leucine zipper motif and proline-rich region of GILZ on suppressing inflammatory responses in primary cultured rat Müller cells.</p><p>Methods: Peptides were selected from amino acids 98–134 of the GILZ protein (GILZ-p). Solid-phase peptide synthesis was used to generate the cell-penetrating peptide TAT, which was bound to the amino terminus of GILZ-p. Primary cultured retinal Müller cells were stimulated with lipopolysaccharide (LPS) alone or in combination with different concentrations of GILZ-p, and the interaction of GILZ-p with nuclear factor (NF)-κB p65 in Müller cells was investigated by western blotting, immunoprecipitation, and immunofluorescence. The expression of the Müller cell gliosis marker glial fibrillary acidic protein (GFAP), functional protein aquaporin (AQP)-4, and the inflammatory cytokines interleukin (IL)-1β, tumor necrosis factor (TNF) α, intercellular adhesion molecule (ICAM)-1, and monocyte chemoattractant protein (MCP)-1 was measured by Western Blotting. The concentration of those cytokines in culture medium was measured by using Enzyme-Linked Immunosorbent Assay.</p><p>Results: The synthesized GILZ-p, which was water-soluble, entered cells and bound with NF-κB p65, inhibiting p65 nuclear translocation. GILZ-p inhibited the LPS-induced expression of GFAP, IL-1β, TNFα, ICAM-1, and MCP-1 in Müller cells and prevented the LPS-induced downregulation of AQP4.</p><p>Conclusions: These results indicate that GILZ-p interacted with NF-κB p65 and suppressed p65 nuclear translocation, thereby inhibiting inflammatory cytokine release and Müller cell gliosis.</p

Additional file 1 of L-Fucose promotes enteric nervous system regeneration in type 1 diabetic mice by inhibiting SMAD2 signaling pathway in enteric neural precursor cells

Additional file 1: Figure S1. (A) Immunostaining showed the co-expressed of GFP (green), Nestin (red), and Ngfr (purple) in colonic myenteric plexus in Nestin-creERT2 × Ngfr-DreERT2: DTRGFP triple transgenic mice. (B-D) The effects of L-Fucose on gastrointestinal motility in diabetic mice by oral gavage for continuous 14 days (n = 5), including defecation frequency (B), The total intestinal transmission time (C), and bead expulsion time (D). (E) The expression level of SMAD2 signaling in control and Fuc groups. (F) Densitometric analysis of SMAD2 signaling in control and Fuc groups. Con: the control mice; Fuc: control mice administrated with L-Fucose; DM: diabetic mice; DM + Fuc: diabetic mice administrated with L-Fucose. Results were expressed as mean ± standard deviation. *p  0.0

Isolation Strategies and Transformation Behaviors of Spironolactone Forms

Spironolactone (SPI) is one kind of potassium-sparing diuretic, and two polymorphs (form I and form II) along with five solvates (methanol, ethanol, acetonitrile, ethyl acetate, and benzene) of SPI have been reported in the literature. However, no detailed information about the stability, solubility, and transformation behaviors of SPI forms has been reported. In this paper, two new forms of SPI, 1-propanol solvate and 2-propanol solvate, were found and characterized. The thermodynamic stability and solubility of form II and four alcohol solvates of SPI were investigated and determined. It was found that methanol solvate and ethanol solvate of SPI are relatively stable while 1-propanol solvate and 2-propanol solvate of SPI are metastable in corresponding solvents, and 1-propanol solvate and 2-propanol solvate of SPI would transform to form II in corresponding solvents. Furthermore, the transformation processes of 1-propanol solvate and 2-propanol solvate were in situ monitored by attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and Raman spectroscopy and some offline tools such as microscopy and powder X-ray diffraction (PXRD). The reasons behind the transformation were explained by the enthalpy data of different solvates

Genome-Wide Identification of Hsp40 Genes in Channel Catfish and Their Regulated Expression after Bacterial Infection

<div><p>Heat shock proteins (HSPs) consist of a large group of chaperones whose expression is induced by high temperature, hypoxia, infection and a number of other stresses. Among all the HSPs, Hsp40 is the largest HSP family, which bind to Hsp70 ATPase domain in assisting protein folding. In this study, we identified 57 hsp40s in channel catfish (<i>Ictalurus punctatus</i>) through <i>in silico</i> analysis using RNA-Seq and genome databases. These genes can be classified into three different types, Type I, II and III, based on their structural similarities. Phylogenetic and syntenic analyses provided strong evidence in supporting the orthologies of these HSPs. Meta-analyses of RNA-Seq datasets were conducted to analyze expression profile of Hsp40s following bacterial infection. Twenty seven hsp40s were found to be significantly up- or down-regulated in the liver after infection with <i>E. ictaluri</i>; 19 hsp40s were found to be significantly regulated in the intestine after infection with <i>E. ictaluri</i>; and 19 hsp40s were found to be significantly regulated in the gill following infection with <i>F. columnare</i>. Altogether, a total of 42 Hsp40 genes were regulated under disease situations involving three tissues and two bacterial infections. The significant regulated expression of Hsp40 genes after bacterial infection suggested their involvement in disease defenses in catfish.</p></div