Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

New Method Based on the Direct Analysis in Real Time Coupled with Time-of-Flight Mass Spectrometry to Investigate the Thermal Depolymerization of Poly(methyl methacrylate)

In this work, the isothermal decomposition of poly(methyl methacrylate) synthesized in bulk by the radical route of methyl methacrylate in the presence of azobisisobutyronitrile as the initiator was carried out and monitored for the first time with the DART-Tof-MS technique at different temperatures. Nuclear magnetic resonance (NMR) analysis revealed a predominantly atactic microstructure, and size-exclusion chromatography (SEC) analysis indicated a number average molecular weight of 3 × 105 g·mol−1 and a polydispersity index of 2.47 for this polymer. Non-isothermal decomposition of this polymer carried out with thermogravimetry analysis (TGA) showed that the weight loss process occurs in two steps. The first one starts at approximately 224 °C and the second at 320 °C. The isothermal decomposition of this polymer carried out and monitored with the DART-Tof-MS method revealed only one stage of weight loss in this process, which begins at approximately 250 °C, not far from that of the second step observed in the case of the non-isothermal process conducted with the TGA method. The results obtained with the MS part of this technique revealed that the isothermal decomposition of this polymer regenerates a significant part of methyl methacrylate monomer, which increases with temperature. This process involves radical chain reactions leading to homolytic chain scissions and leading to the formation of secondary and tertiary alkyl radicals, mainly regenerating methyl methacrylate monomer through an unzipping rearrangement. Although they are in the minority, other fragments, such as the isomers of 2-methyl carboxyl, 4-methyl, penta-2,4-diene and dimethyl carbate, are also among the products detected. At 200 °C, no trace of monomer was observed, which coincides with the first step of the weight loss observed in the TGA. These compounds are different to those reported by other researchers using TGA coupled with mass spectrometry in which methyl isobutyrate, traces of methyl pyruvate and 2,3-butanonedione were detected

Antimicrobial Activity of Novel Ni(II) and Zn(II) Complexes with (E)-2-((5-Bromothiazol-2-yl)imino)methyl)phenol Ligand: Synthesis, Characterization and Molecular Docking Studies

In order to address the challenges associated with antibiotic resistance by bacteria, two new complexes, Ni(II) and Zn(II), have been synthesized using the conventional method based on Schiff base ligand (E)-2-((5-bromothiazol-2-yl) imino) methyl) phenol. The Schiff base ligand (HL) was synthesized using salicylaldehyde and 5-(4-bromophenyl)thiazol-2-amine in both traditional and efficient, ecologically friendly, microwave-assisted procedures. The ligand and its complexes were evaluated by elemental analyses, FTIR spectroscopy, UV-Vis spectroscopy, nuclear magnetic resonance (NMR), thermogravimetric analysis (TGA) and magnetic susceptibility. The ligand and its complexes were tested for antibacterial activity against three Gram-positive bacteria (Staphylococcus aureus ATCC 25923, Methicillin-resistant Staphylococcus aureus ATCC 43300 and Enterococcus faecalis ATCC 29212) and three Gram-negative bacteria (Pseudomonas aeruginosa ATCC 27853, Escherichia coli ATCC 25922 and Klebsiella pneumoniae ATCC 700603). The findings demonstrate the potent activity of the ligand and its complexes against selective bacteria but the Ni(II) complex with MIC values ranging from 1.95 to 7.81 µg/mL outperformed all other compounds, including the widely used antibiotic Streptomycin. Furthermore, the docking study provided evidence supporting the validity of the antimicrobial results, since the Ni complex showed superior binding affinity against to E. coli NAD synthetase, which had a docking score (−7.61 kcal/mol)

Poly(ethylene-Co-vinyl Alcohol)/Titanium Dioxide Nanocomposite: Preparation and Characterization of Properties for Potential Use in Bone Tissue Engineering

A series of poly(ethylene-co-vinyl alcohol)/titanium dioxide (PEVAL/TiO2) nanocomposites containing 1, 2, 3, 4 and 5 wt% TiO2 were prepared by the solvent casting method. These prepared hybrid materials were characterized by Fourier-transform infrared (FT-IR), X-ray diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and scanning electron microscopy (SEM). The pores and their interconnections inside these nanocomposites were created using naphthalene microparticles used as a porogen after having been extracted by sublimation under a high vacuum at temperatures slightly below the glass transition temperature. A cellular activity test of these hybrid materials was performed on human gingival fibroblast cells (HGFs) in accordance with ISO 10993-5 and ISO 10993-12 standards. The bioviability (cell viability) of HGFs was evaluated after 1, 4 and 7 days using Alamar Blue®. The results were increased cell activity throughout the different culture times and a significant increase in cell activity in all samples from Day 1 to Day 7, and all systems tested showed significantly higher cell viability than the control group on Day 7 (p < 0.002). The adhesion of HGFs to the scaffolds studied by SEM showed that HGFs were successfully cultured on all types of scaffolds

Copolymer Involving 2-Hydroxyethyl Methacrylate and 2-Chloroquinyl Methacrylate: Synthesis, Characterization and In Vitro 2-Hydroxychloroquine Delivery Application

The Poly(2-chloroquinyl methacrylate-co-2-hydroxyethyl methacrylate) (CQMA-co-HEMA) drug carrier system was prepared with different compositions through a free-radical copolymerization route involving 2-chloroquinyl methacrylate (CQMA) and 2-hydroxyethyl methacrylate) (HEMA) using azobisisobutyronitrile as the initiator. 2-Chloroquinyl methacrylate monomer (CQMA) was synthesized from 2-hydroxychloroquine (HCQ) and methacryloyl chloride by an esterification reaction using triethylenetetramine as the catalyst. The structure of the CQMA and CQMA-co-HEMA copolymers was confirmed by a CHN elementary analysis, Fourier transform infra-red (FTIR) and nuclear magnetic resonance (NMR) analysis. The absence of residual aggregates of HCQ or HCQMA particles in the copolymers prepared was confirmed by a differential scanning calorimeter (DSC) and XR-diffraction (XRD) analyses. The gingival epithelial cancer cell line (Ca9-22) toxicity examined by a lactate dehydrogenase (LDH) assay revealed that the grafting of HCQ onto PHEMA slightly affected (4.2–9.5%) the viability of the polymer carrier. The cell adhesion and growth on the CQMA-co-HEMA drug carrier specimens carried out by the (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) (MTT) assay revealed the best performance with the specimen containing 3.96 wt% HCQ. The diffusion of HCQ through the polymer matrix obeyed the Fickian model. The solubility of HCQ in different media was improved, in which more than 5.22 times of the solubility of HCQ powder in water was obtained. According to Belzer, the in vitro HCQ dynamic release revealed the best performance with the drug carrier system containing 4.70 wt% CQMA

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press