Drug-disease association prediction using semantic graph and function similarity representation learning over heterogeneous information networks.

Discovering new indications for existing drugs is a promising development strategy at various stages of drug research and development. However, most of them complete their tasks by constructing a variety of heterogeneous networks without considering available higher-order connectivity patterns in heterogeneous biological information networks, which are believed to be useful for improving the accuracy of new drug discovering. To this end, we propose a computational-based model, called SFRLDDA, for drug-disease association prediction by using semantic graph and function similarity representation learning. Specifically, SFRLDDA first integrates a heterogeneous information network (HIN) by drug-disease, drug-protein, protein-disease associations, and their biological knowledge. Second, different representation learning strategies are applied to obtain the feature representations of drugs and diseases from different perspectives over semantic graph and function similarity graphs constructed, respectively. At last, a Random Forest classifier is incorporated by SFRLDDA to discover potential drug-disease associations (DDAs). Experimental results demonstrate that SFRLDDA yields a best performance when compared with other state-of-the-art models on three benchmark datasets. Moreover, case studies also indicate that the simultaneous consideration of semantic graph and function similarity of drugs and diseases in the HIN allows SFRLDDA to precisely predict DDAs in a more comprehensive manner.

Repurposing sodium stibogluconate as an uracil DNA glycosylase inhibitor against prostate cancer using a time-resolved oligonucleotide-based drug screening platform.

Repurposing drugs can significantly reduce the time and costs associated with drug discovery and development. However, many drug compounds possess intrinsic fluorescence, resulting in aberrations such as auto-fluorescence, scattering and quenching, in fluorescent high-throughput screening assays. To overcome these drawbacks, time-resolved technologies have received increasing attention. In this study, we have developed a rapid and efficient screening platform based on time-resolved emission spectroscopy in order to screen for inhibitors of the DNA repair enzyme, uracil-DNA glycosylase (UDG). From a database of 1456 FDA/EMA-approved drugs, sodium stibogluconate was discovered as a potent UDG inhibitor. This compound showed synergistic cytotoxicity against 5-fluorouracil-resistant cancer cells. This work provides a promising future for time-resolved technologies for high-throughput screening (HTS), allowing for the swift identification of bioactive compounds from previously overlooked scaffolds due to their inherent fluorescence properties.

Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks.

BACKGROUND: As an important task in bioinformatics, clustering analysis plays a critical role in understanding the functional mechanisms of many complex biological systems, which can be modeled as biological networks. The purpose of clustering analysis in biological networks is to identify functional modules of interest, but there is a lack of online clustering tools that visualize biological networks and provide in-depth biological analysis for discovered clusters. RESULTS: Here we present BioCAIV, a novel webserver dedicated to maximize its accessibility and applicability on the clustering analysis of biological networks. This, together with its user-friendly interface, assists biological researchers to perform an accurate clustering analysis for biological networks and identify functionally significant modules for further assessment. CONCLUSIONS: BioCAIV is an efficient clustering analysis webserver designed for a variety of biological networks. BioCAIV is freely available without registration requirements at http://bioinformatics.tianshanzw.cn:8888/BioCAIV/ .

Adjuvant Chemotherapy for Patients with Adenocarcinoma of the Esophagogastric Junction: A Retrospective, Multicenter, Observational Study.

BACKGROUND: Although the incidence of adenocarcinoma of the esophagogastric junction (AEG) has been increasing since the past decade, the proportion of AEG cases in two previous clinical trials (ACTS-GC and CLASSIC) that investigated the efficacy of adjuvant chemotherapy was relatively small. Therefore, whether AEG patients can benefit from adjuvant chemotherapy remains unclear. METHODS: Patients who were diagnosed with pathological stage II/III, Siewert II/III AEG, and underwent curative surgery at three high-volume institutions were assessed. Clinical outcomes were analyzed by using Kaplan-Meier curves, log-rank test, and Cox regression model. Propensity score matching (PSM) was used to reduce the selection bias. RESULTS: A total of 927 patients were included (the chemotherapy group: 696 patients; the surgery-only group: 231 patients). The median follow-up was 39.0 months. The 5-year overall survival was 63.1% (95% confidence interval [CI]: 59.0-67.6%) for the chemotherapy group and 50.2% in the surgery-only group (hazard ratio [HR] = 0.69, 95% CI: 0.54-0.88; p = 0.003). The 5-year, disease-free survival was 35.4% for the chemotherapy group and 16.6% for the surgery-only group (HR = 0.66, 95% CI: 0.53-0.83; p < 0.001). After PSM, the survival benefit of adjuvant chemotherapy for AEG was maintained. Multivariate analysis for overall survival and disease-free survival further demonstrated the survival benefit of adjuvant chemotherapy, with HRs of 0.63 (p < 0.001) and 0.52 (p < 0.001), respectively. CONCLUSIONS: Postoperative adjuvant chemotherapy was associated with improved overall survival and disease-free survival in patients with operable stage II or III AEG after D2 gastrectomy.

The number of cycles of adjuvant chemotherapy in stage III and high-risk stage II rectal cancer: a nomogram and recursive partitioning analysis.

OBJECTIVE: The prognostic role of the number of cycles of adjuvant chemotherapy (ACT) after total mesorectal excision in stage III and high-risk stage II rectal cancer is unknown. As a result of this, our study was designed to assess the effect of the number of cycles of ACT on the prediction of cancer-specific survival. METHODS: Four hundred patients that were diagnosed as stage III and high-risk stage II rectal cancer from January 2012 to January 2018 and who had received total mesorectal excision were enrolled in this study. A nomogram incorporating the number of cycles of ACT was also developed in this study. For internal validation, the bootstrap method was used and the consistency index was used to evaluate the accuracy of the model. The patients were stratified into risk groups according to their tumor characteristics by recursive partitioning analysis. RESULTS: We found that the risk of death was decreased by 26% (HR = 0.74, 95% CI: 0.61-0.89, P = 0.0016) with each increasing ACT cycle. The N stage, positive lymph node ratio (PLNR), carcinoembryonic antigen, neutrophil-to-lymphocyte ratio, and the number of cycles of ACT were chosen and entered into the nomogram model. Recursive partitioning analysis-based risk stratification revealed a significant difference in the prognosis in rectal cancer patients with high-risk, intermediate-risk, and low-risk (3-year cancer-specific survival: 0.246 vs. 0.795 vs. 0.968, P < 0.0001). Seven or more cycles of ACT yielded better survival in patients with PLNR ≥ 0.28 but not in patients with PLNR < 0.28. CONCLUSION: In conclusion, the nomogram prognosis model based on the number of cycles of ACT predicted individual prognosis in rectal cancer patients who had undergone total mesorectal excision. These findings further showed that in patients with PLNR ≥ 0.28, no fewer than 7 cycles of ACT are needed to significantly reduce the patient's risk of death.

[Selection of optimal qRT-PCR reference genes for Aconitum vilmorinianum].

Screening suitable reference genes is the premise of quantitative Real-time PCR(qRT-PCR)for gene expression analysis. To provide stable reference genes for expression analysis of genes in Aconitum vilmorinianum, this study selected 19 candidate re-ference genes(ACT1, ACT2, ACT3, aTUB1, aTUB2, bTUB, 18S rRNA, UBQ, eIF2, eIF3, eIF4, eIF5, CYP, GAPDH1, GAPDH2, PP2A1, PP2A2, ACP, and EF1α) based on the transcriptome data of A. vilmorinianum. qRT-PCR was conducted to profile the expression of these genes in the root, stem, leaf, and flower of A. vilmorinianum. The Ct values showed that 18S rRNA with high expression level and GAPDH2 with large expression difference among organs were not suitable as the reference genes. NormFinder and geNorm showed similar results of the expression stability of the other candidate reference genes and demonstrated PP2A1, EF1α, and CYP as the highly stable ones. However, BestKeeper suggested EF1α, ACT3, and PP2A1 as the top stable genes. In view of the different results from different softwares, the geometric mean method was employed to analyze the expression stability of the candidate re-ference genes, the results of which indicated that PP2A1, EF1α, and ACT3 were the most stable. Based on the comprehensive analysis results of geNorm, NormFinder, BestKeeper, and geometric mean method, PP2A1 and EF1α presented the most stable expression in different organs of A. vilmorinianum. PP2A1 and EF1α were the superior reference genes for gene expression profiling in different organs of A. vilmorinianum.

Ghrelin/GHS-R1a signaling plays different roles in anxiety-related behaviors after acute and chronic caloric restriction.

The brain-gut hormone ghrelin and its receptor GHS-R1a, the growth hormone secretagogue receptor 1a, regulates diverse functions of central nervous system including stress response and mood. Both acute and chronic caloric restrictions (CR) were reported to increase endogenous ghrelin level meanwhile regulate anxiety-related behaviors; however, the causal relationship between CR-induced ghrelin elevation and anxiety are not fully established. Here, we introduced an acute (24 h) and a chronic (10wks) CR procedure to both GHS-R1a KO (Ghsr-/-) mice and WT (Ghsr+/+) littermates, and compared their anxiety-related behaviors. We found that acute CR induced anxiolytic and anti-despairing behaviors in Ghsr+/+ mice but not in Ghsr-/- mice. Ad-libitum refeeding abolished the effect of acute CR on anxiety-related behaviors. In contrast, chronic CR for 10wks facilitated despair-like behavior meanwhile inhibited anxiety-like behavior in Ghsr+/+ mice. GHS-R1a deficiency rescued despair-like behavior while did not affect anxiolytic response induced by chronic CR. In addition, we found elevated interleukin-6 (IL-6) in serum of Ghsr+/+ mice after chronic CR, but not in Ghsr-/- mice. Altogether, our findings indicated that acute CR and chronic CR have different impacts on anxiety-related behaviors, and the former is dependent on ghrelin/GHS-R1a signaling while the latter may not always be. In addition, our findings suggested that GHS-R1a-dependent elevation in serum IL-6 might contribute to increased despair-like behavior in chronic CR state.

Activating Inert, Nonprecious Perovskites with Iridium Dopants for Efficient Oxygen Evolution Reaction under Acidic Conditions.

Simultaneous realization of improved activity, enhanced stability, and reduced cost remains a desirable yet challenging goal in the search of oxygen evolution electrocatalysts in acid. Herein we report iridium-containing strontium titanates (Ir-STO) as active and stable, low-iridium perovskite electrocatalysts for the oxygen evolution reaction (OER) in acid. The Ir-STO contains 57 wt % less iridium relative to the benchmark catalyst IrO2 , but it exhibits more than 10 times higher catalytic activity for OER. It is shown to be among the most efficient iridium-based oxide electrocatalysts for OER in acid. Theoretical results reveal that the incorporation of iridium dopants in the STO matrix activates the intrinsically inert titanium sites, strengthening the surface oxygen adsorption on titanium sites and thereby giving nonprecious titanium catalytic sites that have activities close to or even better than iridium sites.

Cyclin D1 Gene Silencing Promotes IL-1ß-Induced Apoptosis in Rat Chondrocytes.

This study investigated the effects of cyclin D1 gene silencing on cell proliferation and apoptosis of interleukin-1ß (IL-1ß)-induced osteoarthritis (OA) chondrocytes. Chondrocytes from healthy sprague-dawley rats were divided into blank, OA model (chondrocytes underwent IL-1ß inducement), OA trial (chondrocytes underwent IL-1ß inducement with cyclin D1-shRNA treatment), and negative control (NC; chondrocytes underwent IL-1ß inducement and control-shRNA treatment) groups. Cell proliferation was assessed by CCK-8 assay, and cell cycle and apoptosis by flow cytometry. qRT-PCR and Western blotting were performed to detect cyclin D1 and apoptosis-related factors expression levels. Chondrocyte proliferation increased after 72-96 h after incubation. The OA trial group exhibited reduced cell proliferation at 48, 72, and 96 h after treatment. The OA model, OA trial, and NC groups all contained more cells arrested in G1 phase and had higher apoptosis rates than the blank group. Additionally, the OA trial group contained more cells arrested in G1 phase, with increased apoptosis rates compared to the OA model and NC groups. The OA model group had lowest expression of cyclin D1 whereas the blank group contained the highest among the four groups. qRT-PCR also showed that the OA model, OA trial, and NC groups all had increased expression levels of Bax and reduced expression levels of Bcl-2 and P53 compared to the blank group, whereby by the OA group had the most significant change. The combined evidence in our study shows that cyclin D1 gene silencing suppresses proliferation and induces apoptosis of rat chondrocytes in IL-1ß-induced OA. J. Cell. Biochem. 119: 290-299, 2018. © 2017 Wiley Periodicals, Inc.

Super-resolution imaging by anticorrelation of optical intensities.

Photon bunching, a feature of classical thermal fields, has been widely exploited to implement ghost imaging. Here we show that spatial photon antibunching can be experimentally observed via low-pass filtering of the intensities of the two thermal light beams from a beamsplitter correlation system. Through suitable choice of the filter thresholds, the minimum of the measured normalized anti-correlation function, i.e., antibunching dip, can be lower than 0.2, while its full-width-at-half-maximum can be much narrower than that of the corresponding positive correlation peak. Based on this anti-correlation effect, a super-resolution negative ghost image is achieved in a lensless scheme, in which the spatial resolution can exceed the Rayleigh diffraction limit by more than a factor of two. The setup is quite simple and easy to implement, which is an advantage for practical applications.

[Construction of core collection of Psammosilene tunicoides based on polymorphism of ß-AS gene].

Psammosilene tunicoides is one of the main ingredients of the "Yunnan Baiyao". P. tunicoides is an endangered species included in the secondary protection list in China Plant Red Data Book as well as the endemic species in Southwest China. Its natural resources could not meet the needs of pharmaceutical production. Construction of core collection of P. tunicoides will lay the foundation for germplasm improvement and molecular breeding. The sequence variation of the key enzymes gene locus (ß-AS) were carried out to survey the population structure and population history of the species. Among the 11 populations across its geographical range, 36 haplotypes were identified. The levels of haplotype diversity (Hd=0.905) were high, while the levels of population differentiation (GST=0.280) were low. Analysisof molecular variance (AMOVA) indicated that a significantly greater proportion of total genetic variationpartitioned among populations thanwithin populations (values of 77.43% and 22.57%, respectively). These results in combination with the star-like phylogenetic network analysis indicate that Hap1 as an ancestral haplotypewas shared in four populations, Hap2, Hap4, Hap15 and Hap16 are occurred in two populations, the remains as private haplotype only distributed in single population. The strategy of core collection was constructed in order to maximumpreserve genetic diversity of P. tunicoides.

Highly Active, Nonprecious Electrocatalyst Comprising Borophene Subunits for the Hydrogen Evolution Reaction.

Developing nonprecious hydrogen evolution electrocatalysts that can work well at large current densities (e.g., at 1000 mA/cm2: a value that is relevant for practical, large-scale applications) is of great importance for realizing a viable water-splitting technology. Herein we present a combined theoretical and experimental study that leads to the identification of α-phase molybdenum diboride (α-MoB2) comprising borophene subunits as a noble metal-free, superefficient electrocatalyst for the hydrogen evolution reaction (HER). Our theoretical finding indicates, unlike the surfaces of Pt- and MoS2-based catalysts, those of α-MoB2 can maintain high catalytic activity for HER even at very high hydrogen coverage and attain a high density of efficient catalytic active sites. Experiments confirm α-MoB2 can deliver large current densities in the order of 1000 mA/cm2, and also has excellent catalytic stability during HER. The theoretical and experimental results show α-MoB2's catalytic activity, especially at large current densities, is due to its high conductivity, large density of efficient catalytic active sites and good mass transport property.

[Cloning of ß-actin Gene in Psammosilene tunicoides and Its Role as a Reference Gene].

Objective: To establish a real-time quantitative PCR method to detect Psammosilene tunicoides ß-actin, and to provide a reference gene for the detection of Psammosilene tunicoides genes by q PCR. Methods: Specific primers were designed based on the conserved region of the ß-actin gene( Gen Bank) and were used to amplify ß-actin by PCR. ß-actin was also used as a reference gene in the q PCR analysis of glycosyltransferase gene( UGT) expression in the roots,stems,and leaves of Psammosilene tunicoides. Results: The length of the ß-actin gene amplicon from Psammosilene tunicoides was 153 bp and shared relatively high homology with ß-actin found in Vaccaria segetalis, Myosoton aquaticum and Portulaca oleracea. Furthermore, UGT was revealed to be stably expressed in different Psammosilene tunicoides tissues when ß-actin was employed as the reference gene. Conclusion: ß-actin is a reliable and suitable reference gene for studies on the expression of triterpenoid saponin biosynthesis-related genes in Psammosilene tunicoides.

Unique Electronic Structure in a Porous Ga-In Bimetallic Oxide Nano-Photocatalyst with Atomically Thin Pore Walls.

A facile synthetic route is presented that produces a porous Ga-In bimetallic oxide nanophotocatalyst with atomically thin pore walls. The material has an unprecedented electronic structure arising from its ultrathin walls. The bottom of the conduction band and the top of the valence band of the material are distributed on two opposite surfaces separated with a small electrostatic potential difference. This not only shortens the distance by which the photogenerated charges travel from the sites where they are generated to the sites where they catalyze the reactions, but also facilitates charge separations in the material. The porous structure within the walls results in a large density of exposed surface reactive/catalytic sites. Because of these optimized electronic and surface structures, the material exhibits superior photocatalytic activity toward the hydrogen evolution reaction (HER).

[Efficacy of glucocorticoids combined with immunoglobulin in initial treatment of Kawasaki disease: a Meta analysis].

OBJECTIVE: To systematically investigate the efficacy and safety of glucocorticoids (GCs) combined with intravenous injection of immunoglobulin (IVIG) in the initial treatment of Kawasaki disease (KD). METHODS: EDLINE Database, PubMed Database, CNKI, Wanfang Data, and VIP Database were searched to collect prospective or retrospective controlled studies on the combination of GCs and IVIG as the initial treatment of KD, which were published up to March 2016. Two investigators independently screened the literature, extracted data, and assessed the quality of the articles included. Then, a Meta analysis was performed using RevMan 5.2 software. RESULTS: A total of 11 articles in English were included, with 7 prospective studies and 4 retrospective studies. The results of the Meta analysis showed that compared with the group using IVIG alone, the combination group had a significantly lower incidence rate of coronary artery lesion (CAL) (OR=0.44, 95%CI 0.23-0.86, P=0.02) and a significantly shorter duration of fever (MD=-1.66, 95%CI -2.32 to -1.01, P<0.00001). The combination group had a significantly lower rate of no response to initial treatment than the IVIG alone group (OR=0.37, 95%CI 0.27-0.51, P<0.00001). The recurrence rate of KD and the incidence rate of adverse events showed no significant differences between the two groups. CONCLUSIONS: GCs combined with IVIG as the initial treatment for KD can reduce the incidence rate of CAL and the rate of no response to initial treatment and shorten the duration of fever, and does not increase the recurrence rate of KD and the incidence rate of adverse events.

High-index faceted Ni3S2 nanosheet arrays as highly active and ultrastable electrocatalysts for water splitting.

Elaborate design of highly active and stable catalysts from Earth-abundant elements has great potential to produce materials that can replace the noble-metal-based catalysts commonly used in a range of useful (electro)chemical processes. Here we report, for the first time, a synthetic method that leads to in situ growth of {2̅10} high-index faceted Ni3S2 nanosheet arrays on nickel foam (NF). We show that the resulting material, denoted Ni3S2/NF, can serve as a highly active, binder-free, bifunctional electrocatalyst for both the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER). Ni3S2/NF is found to give ∼100% Faradaic yield toward both HER and OER and to show remarkable catalytic stability (for >200 h). Experimental results and theoretical calculations indicate that Ni3S2/NF's excellent catalytic activity is mainly due to the synergistic catalytic effects produced in it by its nanosheet arrays and exposed {2̅10} high-index facets.

Coupling Mo2 C with Nitrogen-Rich Nanocarbon Leads to Efficient Hydrogen-Evolution Electrocatalytic Sites.

In our efforts to obtain electrocatalysts with improved activity for water splitting, meticulous design and synthesis of the active sites of the electrocatalysts and deciphering how exactly they catalyze the reaction are vitally necessary. Herein, we report a one-step facile synthesis of a novel precious-metal-free hydrogen-evolution nanoelectrocatalyst, dubbed Mo2 C@NC that is composed of ultrasmall molybdenum carbide (Mo2 C) nanoparticles embedded within nitrogen-rich carbon (NC) nanolayers. The Mo2 C@NC hybrid nanoelectrocatalyst shows remarkable catalytic activity, has great durability, and gives about 100 % Faradaic yield toward the hydrogen-evolution reaction (HER) over a wide pH range (pH 0-14). Theoretical calculations show that the Mo2 C and N dopants in the material synergistically co-activate adjacent C atoms on the carbon nanolayers, creating superactive nonmetallic catalytic sites for HER that are more active than those in the constituents.

Cysteine substitutions define etomidate binding and gating linkages in the α-M1 domain of γ-aminobutyric acid type A (GABAA) receptors.

Etomidate is a potent general anesthetic that acts as an allosteric co-agonist at GABAA receptors. Photoreactive etomidate derivatives labeled αMet-236 in transmembrane domain M1, which structural models locate in the ß+/α- subunit interface. Other nearby residues may also contribute to etomidate binding and/or transduction through rearrangement of the site. In human α1ß2γ2L GABAA receptors, we applied the substituted cysteine accessibility method to α1-M1 domain residues extending from α1Gln-229 to α1Gln-242. We used electrophysiology to characterize each mutant's sensitivity to GABA and etomidate. We also measured rates of sulfhydryl modification by p-chloromercuribenzenesulfonate (pCMBS) with and without GABA and tested if etomidate blocks modification of pCMBS-accessible cysteines. Cys substitutions in the outer α1-M1 domain impaired GABA activation and variably affected etomidate sensitivity. In seven of eight residues where pCMBS modification was evident, rates of modification were accelerated by GABA co-application, indicating that channel activation increases water and/or pCMBS access. Etomidate reduced the rate of modification for cysteine substitutions at α1Met-236, α1Leu-232 and α1Thr-237. We infer that these residues, predicted to face ß2-M3 or M2 domains, contribute to etomidate binding. Thus, etomidate interacts with a short segment of the outer α1-M1 helix within a subdomain that undergoes significant structural rearrangement during channel gating. Our results are consistent with in silico docking calculations in a homology model that orient the long axis of etomidate approximately orthogonal to the transmembrane axis.

Structural models of ligand-gated ion channels: sites of action for anesthetics and ethanol.

The molecular mechanism(s) of action of anesthetic, and especially, intoxicating doses of alcohol (ethanol [EtOH]) have been of interest even before the advent of the Research Society on Alcoholism. Recent physiological, genetic, and biochemical studies have pin-pointed molecular targets for anesthetics and EtOH in the brain as ligand-gated ion channel (LGIC) membrane proteins, especially the pentameric (5 subunit) Cys-loop superfamily of neurotransmitter receptors including nicotinic acetylcholine (nAChRs), GABAA (GABAA Rs), and glycine receptors (GlyRs). The ability to demonstrate molecular and structural elements of these proteins critical for the behavioral effects of these drugs on animals and humans provides convincing evidence for their role in the drugs' actions. Amino acid residues necessary for pharmacologically relevant allosteric modulation of LGIC function by anesthetics and EtOH have been identified in these channel proteins. Site-directed mutagenesis revealed potential allosteric modulatory sites in both the trans-membrane domain (TMD) and extracellular domain (ECD). Potential sites of action and binding have been deduced from homology modeling of other LGICs with structures known from crystallography and cryo-electron microscopy studies. Direct information about ligand binding in the TMD has been obtained by photoaffinity labeling, especially in GABAA Rs. Recent structural information from crystallized procaryotic (ELIC and GLIC) and eukaryotic (GluCl) LGICs allows refinement of the structural models including evaluation of possible sites of EtOH action.