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

Injectable Interpenetrating Network Hydrogels via Kinetically Orthogonal Reactive Mixing of Functionalized Polymeric Precursors

The enhanced mechanics, unique chemistries, and potential for domain formation in interpenetrating network (IPN) hydrogels have attracted significant interest in the context of biomedical applications. However, conventional IPNs are not directly injectable in a biological context, limiting their potential utility in such applications. Herein, we report a fully injectable and thermoresponsive interpenetrating polymer network formed by simultaneous reactive mixing of hydrazone cross-linked poly­(<i>N</i>-isopropylacrylamide) (PNIPAM), and thiosuccinimide cross-linked poly­(<i>N</i>-vinylpyrrolidone) (PVP). The resulting IPN gels rapidly (<1 min) after injection without the need for heat, UV irradiation, or small-molecule cross-linkers. The IPNs, cross-linked by kinetically orthogonal mechanisms, showed a significant synergistic enhancement in shear storage modulus compared to the individual component networks as well as distinctive pore morphology, degradation kinetics, and thermal swelling; in particular, significantly lower hysteresis was observed over the thermal phase transition relative to single-network PNIPAM hydrogels

pH-Ionizable <i>in Situ</i> Gelling Poly(oligo ethylene glycol methacrylate)-Based Hydrogels: The Role of Internal Network Structures in Controlling Macroscopic Properties

The incorporation of charge within <i>in situ</i> covalently gelling poly­(oligo ethylene glycol methacrylate) (POEGMA) precursor polymers enables the fabrication of hydrogels that exhibit both pH-responsive swelling and tunable network structures due to multimechanism cross-linking interactions. The gelation times, swelling responses, degradation kinetics, and mechanics of the resulting gels were strongly influenced by both the type of charge(s) incorporated and pH, with both amphoteric gels and anionic gels showing clear evidence of dual network formation. While the amphoteric dual network was anticipated due to charge interactions, the mechanism of the 5-fold enhancement in mechanical properties observed with the anionic gel relative to the neutral gel was revealed by isothermal titration calorimetry and small-angle neutron scattering to relate to the formation of a zippered chain structure based on dipole–dipole interactions. Consequently, rational design of the chemistry and the microscopic network structure results in controllable macroscopic properties amenable to potential biomedical applications

Probing the Internal Morphology of Injectable Poly(oligoethylene glycol methacrylate) Hydrogels by Light and Small-Angle Neutron Scattering

While injectable, <i>in situ</i> gelling hydrogels have attracted increasing attention in the biomedical literature due to their minimally invasive administration potential, little is known about the internal morphology of these hydrogels and thus how to engineer precursor polymer compositions to achieve desired hydrogel properties. In this paper, the internal morphology of injectable <i>in situ</i> gelling hydrogels based on hydrazide and aldehyde-functionalized poly­(oligoethylene glycol methacrylate) precursors with varying lower critical solution temperatures (LCSTs) is investigated using a combination of spectrophotometry, small-angle neutron scattering, and light scattering. If two precursor polymers with similar LCSTs are used to prepare the hydrogel, relatively homogeneous hydrogels are produced (analogous to conventional step-growth polymerized hydrogels); this result is observed provided that gelation is sufficiently slow for diffusional mixing to compensate for any incomplete mechanical mixing in the double-barrel syringe and the volume phase transition temperature (VPTT) of the hydrogel is sufficiently high that phase separation does not occur on the time scale of gelation. Hydrogels prepared from precursor polymers with different LCSTs (1 polymer/barrel) also retain transparency, although their internal morphology is significantly less homogeneous. However, if functionalized polymers with different LCSTs are mixed in each barrel (i.e., 2 polymers/barrel, such that a gelling pair of precursors with both low and high LCSTs is present), opaque hydrogels are produced that contain significant inhomogeneities that are enhanced as the temperature is increased; this suggests phase separation of the hydrogel into lower and higher LCST domains. Based on this work, the internal morphology of injectable hydrogels can be tuned by engineering the gelation time and the physical properties (i.e., miscibility) of the precursor polymers, insight that can be applied to improve the design of such hydrogels for biomedical applications

Poly(oligoethylene glycol methacrylate) Dip-Coating: Turning Cellulose Paper into a Protein-Repellent Platform for Biosensors

The passivation of nonspecific protein adsorption to paper is a major barrier to the use of paper as a platform for microfluidic bioassays. Herein we describe a simple, scalable protocol based on adsorption and cross-linking of poly­(oligoethylene glycol methacrylate) (POEGMA) derivatives that reduces nonspecific adsorption of a range of proteins to filter paper by at least 1 order of magnitude without significantly changing the fiber morphology or paper macroporosity. A lateral-flow test strip coated with POEGMA facilitates effective protein transport while also confining the colorimetric reporting signal for easier detection, giving improved performance relative to bovine serum albumin (BSA)-blocked paper. Enzyme-linked immunosorbent assays based on POEGMA-coated paper also achieve lower blank values, higher sensitivities, and lower detection limits relative to ones based on paper blocked with BSA or skim milk. We anticipate that POEGMA-coated paper can function as a platform for the design of portable, disposable, and low-cost paper-based biosensors

Injectable On-Demand Pulsatile Drug Delivery Hydrogels Using Alternating Magnetic Field-Triggered Polymer Glass Transitions

Remote-controlled pulsatile or staged release has significant potential in a wide range of therapeutic treatments. However, most current approaches are hindered by the low resolution between the on- and off-states of drug release and the need for surgical implantation of larger controlled-release devices. Herein, we describe a method that addresses these limitations by combining injectable hydrogels, superparamagnetic iron oxide nanoparticles (SPIONs) that heat when exposed to an alternating magnetic field (AMF), and polymeric nanoparticles with a glass transition temperature (Tg) just above physiological temperature. Miniemulsion polymerization was used to fabricate poly(methyl methacrylate-co-butyl methacrylate) (p(MMA-co-BMA)) nanoparticles loaded with a model hydrophobic drug and tuned to have a Tg value just above physiological temperature (∼43 °C). Co-encapsulation of these drug-loaded nanoparticles with SPIONs inside a carbohydrate-based injectable hydrogel matrix (formed by rapid hydrazone cross-linking chemistry) enables injection and immobilization of the nanoparticles at the target site. Temperature cycling facilitated a 2.5:1 to 6:1 on/off rhodamine release ratio when the nanocomposites were switched between 37 and 45 °C; release was similarly enhanced by exposing the nanocomposite hydrogel to an AMF to drive heating, with enhanced release upon pulsing observed even 1 week after injection. Coupled with the apparent cytocompatibility of all of the nanocomposite components, these injectable nanocomposite hydrogels are promising as minimally invasive but remotely actuated release delivery vehicles capable of complex release kinetics with high on–off resolution

A Highly Sensitive Immunosorbent Assay Based on Biotinylated Graphene Oxide and the Quartz Crystal Microbalance

A high-sensitivity flow-based immunoassay is reported based on a gold-coated quartz crystal microbalance (QCM) chip functionalized directly in the QCM without requiring covalent conjugation steps. Specifically, the irreversible adsorption of a biotinylated graphene oxide-avidin complex followed by loading of a biotinylated capture antibody is applied to avoid more complex conventional surface modification chemistries and enable chip functionalization and sensing all within the QCM instrument. The resulting immunosensors exhibit significantly lower nonspecific protein adsorption and stronger signal for antigen sensing relative to simple avidin-coated sensors. Reproducible quantification of rabbit IgG concentrations ranging from 0.1 ng/mL to 10 μg/mL (6 orders of magnitude) can be achieved depending on the approach used to quantify the binding with simple mass changes used to detect higher concentrations and a horseradish peroxidase-linked detection antibody that converts its substrate to a measurable precipitate used to detect very low analyte concentrations. Sensor fabrication and assay performance take ∼5 h in total, which is on par with or faster than other techniques. Quantitative sensing is possible in the presence of complex protein mixtures, such as human plasma. Given the broad availability of biotinylated capture antibodies, this method offers both an easy and flexible platform for the quantitative sensing of a variety of biomolecule targets