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

POLYMERIC MICRO/NANOSTRUCTURES AND BIOAPPLICATIONS

Ph.DDOCTOR OF PHILOSOPH

The binding interface of kindlin-2 and ILK involves Asp344/Asp352/Thr356 in kindlin-2 and Arg243/Arg334 in ILK

Focal adhesion (FA) proteins, kindlin‐2 and integrin‐linked kinase (ILK), regulate cell adhesion and migration. ILK interacts with and promotes kindlin‐2 targeting to FAs. Leu353 and Leu357 in kindlin‐2 have been reported to be important for the interaction between kindlin‐2 and ILK. However, the binding interface between kindlin‐2 and ILK remains unclear. Using molecular modeling and molecular dynamics simulations, we show that Asp344, Asp352, and Thr356 in kindlin‐2 and Arg243 and Arg334 in ILK kinase domain (KD) are important in kindlin‐2/ILK complex formation. Mutations that disrupt these interactions abrogate kindlin‐2 and ILK colocalization in HeLa cells. The interactions are direct based on data from pull‐down assays using purified recombinant kindlin‐2 F2‐pleckstrin homology and ILK KDs. These data provide additional insights into the binding interface between kindlin‐2 and ILK.ASTAR (Agency for Sci., Tech. and Research, S’pore)MOE (Min. of Education, S’pore)Accepted versio

Recent Progress in Energy-Driven Water Splitting

Hydrogen is readily obtained from renewable and non-renewable resources via water splitting by using thermal, electrical, photonic and biochemical energy. The major hydrogen production is generated from thermal energy through steam reforming/gasification of fossil fuel. As the commonly used non-renewable resources will be depleted in the long run, there is great demand to utilize renewable energy resources for hydrogen production. Most of the renewable resources may be used to produce electricity for driving water splitting while challenges remain to improve cost-effectiveness. As the most abundant energy resource, the direct conversion of solar energy to hydrogen is considered the most sustainable energy production method without causing pollutions to the environment. In overall, this review briefly summarizes thermolytic, electrolytic, photolytic and biolytic water splitting. It highlights photonic and electrical driven water splitting together with photovoltaic-integrated solar-driven water electrolysis.Published versio

Upconversion luminescence of Gd2O3:Ln3+ nanorods for white emission and cellular imaging via surface charging and crystallinity control

In this paper, an oxide upconversion nanomaterial, Gd2O3:Ln3+, as an alternative counterpart of NaGdF4:Ln3+ was developed via controlled surfactant-free synthesis, flexible lanthanide loading, compositional/size tuning, hexagonal-to-cubic lattice refinement, and positive surface charging to achieve a substantial enhancement of upconversion luminescence (∼30 times upon calcination at 1000 vs 600 °C; ∼4000 times versus its hydroxide form) due to high crystallinity and extremely low residual impurities for white emission and cellular imaging.Nanyang Technological UniversityAccepted versionThis work is supported by School of Materials Science and Engineering of Nanyang Technological University and Institute of Materials Research and Engineering for funding support. Electron microscopy and XRD were performed at the Facility for Analysis, Characterization, Testing and Simulation, Nanyang Technological University, Singapore

Oral Administration and Selective Uptake of Polymeric Nanoparticles in <i>Drosophila</i> Larvae as an <i>in Vivo</i> Model

In this article, <i>Drosophila</i> larvae are applied as an <i>in vivo</i> model to investigate the transport and uptake of polymeric nanoparticles in the larval digestive tract after oral administration. After feeding the larvae with food containing bare and chitosan-coated Poly­(d,l-lactic-<i>co</i>-glycolic acid) (PLGA) nanoparticles encapsulated with BODIPY, time-lapse imaging of live larvae is used to monitor the movement of fluorescent nanoparticles in the anterior, middle, and posterior midgut of the digestive tract. Also, the dissection of the digestive tract enables the analysis of cellular uptake in the midgut. Bare PLGA nanoparticles travel through the whole midgut smoothly while chitosan-coated PLGA nanoparticles have a long retention time in the posterior midgut. We identify that this retention occurs in the posterior segment of the posterior midgut, and it is termed as the retention segment. During transport in the midgut, chitosan-coated nanoparticles pass through the near-neutral anterior midgut and become highly positively charged when entering into the highly acidic middle midgut. After traveling through the near-neutral anterior segment of the posterior midgut, chitosan-coated nanoparticles have a long retention time of ∼10 h in the retention segment, indicating that the chitosan coating greatly enhances mucoadhesive ability and promotes cellular uptake in this part of the midgut. The dynamic behavior of orally administered nanoparticles in <i>Drosophila</i> larvae is in agreement with studies in other animal models. A <i>Drosophila</i> larva has the potential to evolve into a low-cost drug screening model through real time imaging, which will accelerate the development of improved nanoparticle formulations for oral drug delivery

Epidemiology and outcomes of older trauma patients in Singapore: a multicentre study

10.1016/j.injury.2022.08.018Injur

Comparing Comorbidity Polypharmacy Score and Charlson Comorbidity Index in predicting outcomes in older trauma patients.

10.1016/j.injury.2023.02.031InjuryS0020-1383(23)00163-8

Protein Induces Layer-by-Layer Exfoliation of Transition Metal Dichalcogenides

Here, we report a general and facile method for effective layer-by-layer exfoliation of transition metal dichalcogenides (TMDs) and graphite in water by using protein, bovine serum albumin (BSA) to produce single-layer nanosheets, which cannot be achieved using other commonly used bio- and synthetic polymers. Besides serving as an effective exfoliating agent, BSA can also function as a strong stabilizing agent against reaggregation of single-layer nanosheets for greatly improving their biocompatibility in biomedical applications. With significantly increased surface area, single-layer MoS₂ nanosheets also exhibit a much higher binding capacity to pesticides and a much larger specific capacitance. The protein exfoliation process is carefully investigated with various control experiments and density functional theory simulations. It is interesting to find that the nonpolar groups of protein can firmly bind to TMD layers or graphene to expose polar groups in water, facilitating the effective exfoliation of single-layer nanosheets in aqueous solution. The present work will enable to optimize the fabrication of various 2D materials at high yield and large scale, and bring more opportunities to investigate the unique properties of 2D materials and exploit their novel applications