Auto-CORPus: A Natural Language Processing Tool for Standardizing and Reusing Biomedical Literature.

To analyse large corpora using machine learning and other Natural Language Processing (NLP) algorithms, the corpora need to be standardized. The BioC format is a community-driven simple data structure for sharing text and annotations, however there is limited access to biomedical literature in BioC format and a lack of bioinformatics tools to convert online publication HTML formats to BioC. We present Auto-CORPus (Automated pipeline for Consistent Outputs from Research Publications), a novel NLP tool for the standardization and conversion of publication HTML and table image files to three convenient machine-interpretable outputs to support biomedical text analytics. Firstly, Auto-CORPus can be configured to convert HTML from various publication sources to BioC. To standardize the description of heterogenous publication sections, the Information Artifact Ontology is used to annotate each section within the BioC output. Secondly, Auto-CORPus transforms publication tables to a JSON format to store, exchange and annotate table data between text analytics systems. The BioC specification does not include a data structure for representing publication table data, so we present a JSON format for sharing table content and metadata. Inline tables within full-text HTML files and linked tables within separate HTML files are processed and converted to machine-interpretable table JSON format. Finally, Auto-CORPus extracts abbreviations declared within publication text and provides an abbreviations JSON output that relates an abbreviation with the full definition. This abbreviation collection supports text mining tasks such as named entity recognition by including abbreviations unique to individual publications that are not contained within standard bio-ontologies and dictionaries. The Auto-CORPus package is freely available with detailed instructions from GitHub at: https://github.com/omicsNLP/Auto-CORPus.

Imine Gels Based on Ferrocene and Porphyrin and Their Electrocatalytic Property.

A series of porphyrin-based imine gels have been synthesized via dynamic covalent gelation between 5,10,15,20-tetra(4-aminophenyl)-21H,23H-porphyrin (H2 TAPP) derivatives and various aldehyde compounds. The porphyrin-ferrocene imine gels based on MTAPP (M=H2 , Ni2+ , Co2+ , Pd2+ and Zn2+ ) and ferrocene-1,1'-dicarbaldehyde (NA) display efficient HER, OER and ORR activities in alkaline media. Among the gels, CoTAPP-NA shows an HER current density of 10 mA cm-2 at low overpotential of 470 mV and small Tafel slope of 110 mV decade-1 in alkaline media. CoTAPP-NA also exhibits OER catalytic activity with low overpotential (416 mV for 10 mA cm-2 ). CoTAPP-NA shows ability in overall water splitting in alkaline media. In addition, CoTAPP-NA exhibits onset potential (Ep ) of 0.95 V and half-wave potential (E1/2 ) of 0.84 V in 1.0 mol L-1 KOH solution for oxygen reduction. Moreover, the gel catalyst shows good stability.

UiO-67 metal-organic gel material deposited on photonic crystal matrix for photoelectrocatalytic hydrogen production.

Robust UiO-67 metal-organic framework nanoparticles have been precisely and uniformly anchored on the surface of a photonic crystal via metal-organic gelation, resulting in a nanoscale UiO-67 composite. Mott-Schottky measurements indicate that UiO-67/B is an n-type semiconductor with electron conduction, and the band gap significantly decreases with the assistance of the photonic crystal matrix with a band gap of 0.75 eV. Benefiting from the abundant photoelectrons trapped from the photonic crystal, good hydrogen evolution reaction performance is achieved under light irradiation. The current density increases from 3.2 to 7.0 mA cm-2 at -0.6 V (vs. RHE) for UiO-67/B. The optimized carrier density obtained from UiO-67/B is apparently increased 2.15 times under light irradiation for 30 min. This work provides a rational strategy to address the photo-capture and energy transfer issues of metal-organic frameworks under visible light irradiation for H2 production in artificial photosynthesis.

Zirconium-based metal-organic framework gels for selective luminescence sensing.

Metal-organic gelation represents a promising approach to fabricate functional nanomaterials. Herein a series of Zr-carboxylate gels are synthesized from rigid pyrene, porphyrin and tetraphenyl ethylene-derived tetracarboxylate linkers, namely Zr-TBAPy (H4TBAPy = 1,3,6,8-tetrakis(4-carboxylphenyl)pyrene), Zr-TCPE (H4TCPE = 1,1,2,2-tetra(4-carboxylphenyl)ethylene), and Zr-TCPP (H4TCPP = 5,10,15,20-tetrakis(4-carboxyphenyl)porphyrin). The gels are aggregated from metal-organic framework (MOF) nanoparticles. Zr-TBAPy gel consists of NU-901 nanoparticles, and Zr-TCPP gel consists of PCN-224 nanoparticles. The xerogels show high surface areas up to 1203 m2 g-1. MOF gel films are also anchored on the butterfly wing template to yield Zr-MOF/B composites. Zr-TBAPy and Zr-TCPE gels are luminescent for solution-phase sensing and vapour-phase sensing of volatile organic compounds, and exhibit a significant luminescence quenching effect for electron-deficient analytes. Arising from the high porosity and good dispersion of luminescent MOF gels, rapid and effective vapour-sensing of nitrobenzene and 2-nitrotoluene within 30 s has been achieved via Zr-TBAPy film or Zr-TBAPy/B.

Confinement of a Au-N-heterocyclic carbene in a Pd6L12 metal-organic cage.

A Au(i)-N-heterocyclic-carbene (NHC)-edged Pd6L12 molecular metal-organic cage is assembled from a Au(i)-NHC-based bipyridyl bent ligand and Pd2+. The octahedral cage structure is unambiguously established by NMR, electrospray ionization-mass spectrometry and single crystal X-ray crystallography. The electrochemical behaviour was analyzed by cyclic voltammetry. The octahedral cage has a central cavity for guest binding, and is capable of encapsulating PF6 - and BF4 - anions within the cavity.

Serotonergic mechanisms are involved in antidepressant-like effects of bisbenzylisoquinolines liensinine and its analogs isolated from the embryo of Nelumbo nucifera†Gaertner seeds in mice.

OBJECTIVES: We attempted to ascertain if bisbenzylisoquinoline alkaloids, liensinine and isoliensinine from Nelumbo nucifera Gaertner have antidepressant-like effects and compare the effects with those previously obtained by their analogue neferine. METHODS: Using mice, the forced swimming test (FST) was carried out after treatment with liensinine, isoliensinine and neferine. KEY FINDINGS: Liensinine and isoliensinine elicited antidepressant-like effects in mice after the FST. Anti-immobility effects of liensinine and isoliensinine were antagonized by the 5-hydroxytryptamine1 A (5-HT1 A ) receptor antagonist WAY 100635, but not by the α1 -adrenoceptor antagonist prazosin. The anti-immobility effects of liensinine, isoliensinine and neferine were blocked by pretreatment with p-chlorophenylalanine (PCPA), which depletes serotonin (5-HT). CONCLUSIONS: These data suggest that liensinine and isoliensinine from Nelumbo nucifera Gaertner have antidepressant-like effects and that antidepressant-like effects of liensinine and its analogues are closely related to serotonergic mechanisms.

The cumulative damage index method: a new method for evaluating the effectiveness of control measures for Plutella xylostella (Lepidoptera: Plutellidae).

BACKGROUND: All previously and currently used methods for effectiveness evaluation of control measures for the diamondback moth (DBM) do not simultaneously take the actual damage and population size into consideration. Here, we propose a new method, the cumulative damage index method, in which the number of larvae and their amount of food consumption are simultaneously included in the calculation of the theoretical cumulative damage index (T) and actual cumulative damage index (A). Evaluation was based on the reduced degree of damage calculated according to indexes T and A. RESULTS: Based on the new method, the corrected effectiveness of the combined use of biological measures, chemical insecticides, Bacillus thuringiensis (Bt) and P. xylostella granulosis virus (PxGV) on DBM was 35.85, 2.37, 12.50 and 11.77% respectively. Under the action of natural factors, the Population Developmental Index (I) of DBM was 5.1 ± 1.4; under the integrated actions of natural factors and these four types of measure, index I of DBM was 0.34 ± 0.1, 6.1 ± 1.5, 2.1 ± 0.5 and 1.1 ± 0.3 respectively. The sole effectiveness of Trichogramma spp. when integrated with other natural factors, integrated biological measures and chemical insecticides was 21.43 ± 1.69%, 45.27 ± 4.09% and 20.68 ± 2.60% respectively. CONCLUSIONS: There was some difference between the effectiveness evaluated by the new method and index I, and the actual damage caused by DBM could be reflected well by index A. The new method is more scientifically appropriate and practical for effectiveness evaluation than existing methods. © 2014 Society of Chemical Industry.

Antidepressant-like effects of neferine in the forced swimming test involve the serotonin1A (5-HT1A) receptor in mice.

The effects of neferine, an alkaloid of Nelumbo nucifera Gaertner embryos, on immobility in the forced swimming test, which is used to evaluate antidepressants, were investigated in mice. The administration of neferine from 25 to 100 mg/kg i.p. elicited anti-immobility effects in mice. The molecular dose effects of neferine in the forced swimming test were almost equal to those of the typical antidepressants maprotiline and imipramine. The involvement of the 5-HT receptor subtypes was also studied using 5-HT receptor antagonists. Anti-immobility effects of neferine are antagonized by the serotonin1A (5-HT1A) receptor antagonist, N-[2-[4-(2-methoxyphenyl)-1-piperazinyl]ethyl]-N-(2-pyridinyl)cyclohexanecarboxamide (WAY 100635). However, the 5-HT1B receptor antagonist, 3-[3-(dimethylamino)propyl]-4-hydroxy-N-[4-(4-pyridinyl)phenyl] benzamide dihydrochloride (GR 55562), the 5-HT2 receptor antagonist, 6-methyl-1-(methylethyl)-ergoline-8beta-carboxylic acid 2-hydroxy-1-methylpropyl ester (LY 53857), the 5-HT3 receptor antagonist, ondansetron and the 5-HT4 receptor antagonist, 4-amino-5-chloro-2-methoxy-benzoic acid 2-(diethylamino)ethyl ester (SDZ 205,557) did not affect the anti-immobility effects of neferine. The anti-immobility effect of the selective 5-HT1A receptor agonist, 8-hydroxy-2-(di-n-propylamino)tetaralin (8-OH-DPAT) was also antagonized by WAY 100635. Furthermore, co-administration of subactive doses of neferine (10 mg/kg) and 8-OH-DPAT (0.1 mg/kg) produced synergistic antidepressant-like effects. These results suggest that neferine shows antidepressant-like effects in mice similar to typical antidepressants and that these effects are mediated by the 5-HT1A receptor. Therefore, the central effects of neferine are likely to be linked to serotonergic neurotransmission.

Effects of extracts and neferine from the embryo of Nelumbo nucifera seeds on the central nervous system.

The effects of embryos of the seeds of Nelumbo nucifera on the central nervous system were studied in mice. MeOH extracts of embryos of Nelumbo nucifera seeds significantly inhibited locomotor activity in mice. The MeOH extract was successively partitioned between H(2)O and n-hexane, between H(2)O and CHCl(3), and between H(2)O and n-BuOH. CHCl(3) extracts strongly inhibited locomotor activity in mice, although other extracts had no effect on locomotor activity. The main alkaloid of CHCl(3) extracts, neferine, dose-dependently inhibited locomotor activity in mice. Neferine induced hypothermia in mice and apparently potentiated thiopental-induced sleeping time. An anxiolytic, diazepam, decreased locomotor activity, rectal temperature and enhanced sleep elicited by thiopental, similar to neferine. In addition, neferine and diazepam showed anti-anxiety effects in the elevated plus maze test. Neferine did not affect muscle coordination by the rota-rod test. Neferine did not affect strychnine- nor picrotoxin-induced seizure. In contrast, diazepam had apparent muscle relaxant and anti-convulsant effects. These results suggest that neferine has several central effects and that neferine may participate in the efficacy of the sedative effects of embryos of the seeds of Nelumbo nucifera. The mechanisms of the sedative effects of neferine are not similar to those of diazepam.