Biomedical Field Research Articles

Data augmentation and transfer learning for cross-lingual Named Entity Recognition in the biomedical domain

AbstractGiven the increase in production of data for the biomedical field and the unstoppable growth of the internet, the need for Information Extraction (IE) techniques has skyrocketed. Named Entity Recognition (NER) is one of such IE tasks useful for professionals in different areas. There are several settings where biomedical NER is needed, for instance, extraction and analysis of biomedical literature, relation extraction, organisation of biomedical documents, and knowledge-base completion. However, the computational treatment of entities in the biomedical domain has faced a number of challenges including its high cost of annotation, ambiguity, and lack of biomedical NER datasets in languages other than English. These difficulties have hampered data development, affecting both the domain itself and its multilingual coverage. The purpose of this study is to overcome the scarcity of biomedical data for NER in Spanish, for which only two datasets exist, by developing a robust bilingual NER model. Inspired by back-translation, this paper leverages the progress in Neural Machine Translation (NMT) to create a synthetic version of the Colorado Richly Annotated Full-Text (CRAFT) dataset in Spanish. Additionally, a new CRAFT dataset is constructed by replacing 20% of the entities in the original dataset generating a new augmented dataset. We evaluate two training methods: concatenation of datasets and continuous training to assess the transfer learning capabilities of transformers using the newly obtained datasets. The best performing NER system in the development set achieved an F-1 score of 86.39%. The novel methodology proposed in this paper presents the first bilingual NER system and it has the potential to improve applications across under-resourced languages.

Green Synthesis of Silver Nanoparticles and their Potential Applications in Mitigating Cancer.

In recent years, the field of nanotechnology has brought about significant advancements that have transformed the landscape of disease diagnosis, prevention, and treatment, particularly in the realm of medical science. Among the various approaches to nanoparticle synthesis, the green synthesis method has garnered increasing attention. Silver nanoparticles (AgNPs) have emerged as particularly noteworthy nanomaterials within the spectrum of metallic nanoparticles employed for biomedical applications. AgNPs possess several key attributes that make them highly valuable in the biomedical field. They are biocompatible, cost-effective, and environmentally friendly, rendering them suitable for various bioengineering and biomedical applications. Notably, AgNPs have found a prominent role in the domain of cancer diagnosis. Research investigations have provided evidence of AgNPs' anticancer activity, which involves mechanisms such as DNA damage, cell cycle arrest, induction of apoptosis, and the regulation of specific cytokine genes. The synthesis of AgNPs primarily involves the reduction of silver ions by reducing agents. Interestingly, natural products and living organisms have proven to be effective sources for the generation of precursor materials used in AgNP synthesis. This comprehensive review aims to summarize the key aspects of AgNPs, including their characterization, properties, and recent advancements in the field of biogenic AgNP synthesis. Furthermore, the review highlights the potential applications of these nanoparticles in combating cancer.

The elimination of two restriction enzyme genes allows for electroporation-based transformation and CRISPR-Cas9-based base editing in the non-competent Gram-negative bacterium Acinetobacter sp. Tol 5

ABSTRACT Environmental isolates are promising candidates for new chassis of synthetic biology because of their inherent capabilities, which include efficiently converting a wide range of substrates into valuable products and resilience to environmental stresses; however, many remain genetically intractable and unamenable to established genetic tools tailored for model bacteria. Acinetobacter sp. Tol 5, an environmentally isolated Gram-negative bacterium, possesses intriguing properties for use in synthetic biology applications. Despite the previous development of genetic tools for the engineering of strain Tol 5, its genetic manipulation has been hindered by low transformation efficiency via electroporation, rendering the process laborious and time-consuming. This study demonstrated the genetic refinement of the Tol 5 strain, achieving efficient transformation via electroporation. We deleted two genes encoding type I and type III restriction enzymes. The resulting mutant strain not only exhibited marked efficiency of electrotransformation but also proved receptive to both in vitro and in vivo DNA assembly technologies, thereby facilitating the construction of recombinant DNA without reliance on intermediate Escherichia coli constructs. In addition, we successfully adapted a CRISPR-Cas9-based base-editing platform developed for other Acinetobacter species. Our findings provide genetic modification strategies that allow for the domestication of environmentally isolated bacteria, streamlining their utilization in synthetic biology applications. IMPORTANCE Recent synthetic biology has sought diverse bacterial chassis from environmental sources to circumvent the limitations of laboratory Escherichia coli strains for industrial and environmental applications. One of the critical barriers in cell engineering of bacterial chassis is their inherent resistance to recombinant DNA, propagated either in vitro or within E. coli cells. Environmental bacteria have evolved defense mechanisms against foreign DNA as a response to the constant threat of phage infection. The ubiquity of phages in natural settings accounts for the genetic intractability of environmental isolates. The significance of our research is in demonstrating genetic modification strategies for the cell engineering of such genetically intractable bacteria. This research marks a pivotal step in the domestication of environmentally isolated bacteria, promising candidates for emerging synthetic biology chassis. Our work thus significantly contributes to advancing their applications across industrial, environmental, and biomedical fields.

Ultrasound-triggered three dimensional hyaluronic acid hydrogel promotes in vitro and in vivo reprogramming into induced pluripotent stem cells

Cellular reprogramming technologies have been developed with different physicochemical factors to improve the reprogramming efficiencies of induced pluripotent stem cells (iPSCs). Ultrasound is a clinically applied noncontact biophysical factor known for regulating various cellular behaviors but remains uninvestigated for cellular reprogramming. Here, we present a new reprogramming strategy using low-intensity ultrasound (LIUS) to improve cellular reprogramming of iPSCs in vitro and in vivo. Under 3D microenvironment conditions, increased LIUS stimulation shows enhanced cellular reprogramming of the iPSCs. The cellular reprogramming process facilitated by LIUS is accompanied by increased mesenchymal to epithelial transition and histone modification. LIUS stimulation transiently modulates the cytoskeletal rearrangement, along with increased membrane fluidity and mobility to increase HA/CD44 interactions. Furthermore, LIUS stimulation with HA hydrogel can be utilized in application of both human cells and in vivo environment, for enhanced reprogrammed cells into iPSCs. Thus, LIUS stimulation with a combinatorial 3D microenvironment system can improve cellular reprogramming in vitro and in vivo environments, which can be applied in various biomedical fields.

Hydroxide‐derived Nanostructures: Scalable Synthesis, Characterization, Properties and Potential Applications

AbstractMetal oxide nanostructures have received an increasing attention owing to their unique chemical and physical properties along with their widespread applications in various fields. In this article, we provide an overview of our recent discovery – christened Hydroxides‐Derived Nanostructures, or HDNs – in which we react hydroxide aqueous solutions (mostly tetramethylammonium hydroxide, TMAH) at temperatures < 100 °C and under atmospheric pressure with various metal‐containing precursors to scalably prepare novel metal oxide nanostructures. In one case, we converted a dozen commercial and earth abundant Ti‐containing powders such as binary carbides, nitrides, borides, among others, into new, one‐dimensional TiO2–based lepidocrocite (1DL) nanofilaments (NFs). Application‐wise, 1DLs show outstanding performance in a number of energy, environmental, and biomedical fields such as photo‐ and electrocatalysis, water splitting, lithium‐sulfur and lithium‐ion batteries, water purification, dye degradation, cancer therapy, and polymer composites. In addition to 1DL, the HDNs family encompasses other metal oxides nanostructures including magnetic Fe3O4 nanoparticles and MnO2 birnessite‐based crystalline two‐dimensional (2D) flakes. The latter showed promise as a bifunctional electrocatalyst for water oxidation and oxygen reduction, as well as cathodes in aqueous asymmetric supercapacitor and in an aqueous ammonium ion battery. Our developed recipe provides a new vista in the molecular self‐assembly synthesis of metal oxide nanomaterials that can advance the field with a library of novel nanostructures with substantial implications in a multitude of fields.This article is protected by copyright. All rights reserved

Plant-assisted green preparation of silver nanoparticles using leaf extract of Dalbergia sissoo and their antioxidant, antibacterial and catalytic applications.

Plant-mediated preparation of silver nanoparticles (AgNPs) is thought to be a more economical and environmentally benign process in comparison to physical and chemical synthesis methods. In the present study, the aqueous leaf extract of Dalbergia sissoo was prepared and utilized to reduce silver ion (Ag+) during the green synthesis of silver nanoparticles (DL-AgNPs). The formation of DL-AgNPs was verified using UV-Vis spectra, exhibiting the surface plasmon resonance (SPR) band at around 450nm. FT-IR analysis revealed the kinds of phytochemicals that serve as reducing and capping agents while DL-AgNPs are being synthesized. Analysis of scanning electron microscope (SEM) and high-resolution transmission electron microscopy (HR-TEM) images verified the development of spherical and oval-shaped DL-AgNPs, with sizes ranging from 10 to 25nm. The stability and particle size distribution of synthesized DL-AgNPs were ensured by zeta potential and DLS (dynamic light scattering) investigations. Additionally, X-ray diffraction (XRD) analysis confirmed the crystalline nature of DL-AgNPs. In antioxidant experiments, DL-AgNPs demonstrated significant scavenging capacities of DPPH and ABTS radicals with EC50 values of 51.32 and 33.32μg/mL, respectively. The antibacterial activity of DL-AgNPs was shown to be significant against harmful bacteria, with a maximum zone of inhibition (21.5 ± 0.86mm) against Staphylococcus aureus. Furthermore, DL-AgNPs exhibited effective catalytic activity to degrade environment-polluting dyes (methylene blue, methyl orange, and Congo red) and toxic chemicals (p-nitrophenol). The results of all these studies suggested that DL-AgNPs made from the leaf extract of Dalbergia sissoo have merit for application in the environmental and biomedical fields.

Revolution in Cancer Treatment: How Are Intelligently Designed Nanostructures Changing the Game?

Nanoparticles (NPs) are extremely important tools to overcome the limitations imposed by therapeutic agents and effectively overcome biological barriers. Smart designed/tuned nanostructures can be extremely effective for cancer treatment. The selection and design of nanostructures and the adjustment of size and surface properties are extremely important, especially for some precision treatments and drug delivery (DD). By designing specific methods, an important era can be opened in the biomedical field for personalized and precise treatment. Here, we focus on advances in the selection and design of nanostructures, as well as on how the structure and shape, size, charge, and surface properties of nanostructures in biological fluids (BFs) can be affected. We discussed the applications of specialized nanostructures in the therapy of head and neck cancer (HNC), which is a difficult and aggressive type of cancer to treat, to give an impetus for novel treatment approaches in this field. We also comprehensively touched on the shortcomings, current trends, and future perspectives when using nanostructures in the treatment of cancer.

The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples

Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.

Terahertz Spectroscopic Insight into the Hydrogelation of Copper Ion-Coordinated Poly(vinyl alcohol)

Metal-coordinated hydrogels are becoming increasingly popular in the biomedical field due to their unique properties. However, the mechanism behind gel forming involving metal ions is not yet fully understood. In this work, terahertz spectroscopy was used to investigate the role of interfacial water in the gelation process of copper ion-coordinated poly(vinyl alcohol) hydrogels. The results showed that the binding of copper ions could alter the interfacial hydration dynamics of the poly(vinyl alcohol) polymers. Combined with the results of differential scanning calorimetry (DSC), we propose a possible hydration layer-mediated mechanism for the formation of cooper ion-coordinated hydrogel during the freeze–thaw cycle. These results highlight the value of terahertz spectroscopy as a sensor for studying the hydration process in hydrogels and provide an important clue for understanding the mechanism of hydrogelation in ion-coordinated hydrogels.

Quantum dots and their potential biomedical applications

Quantum dots (QDs) are semiconductor-based nanocrystals. These nanoparticles have exhibited their unique optical and electronic properties. With these characteristics, QDs attracted scientists interest in biomedical areas such as bioimaging, drug delivery and biosensors apart from other applications like photocatalysis, light-emitting, and solar cells in recent years, and plenty of QDs and QD-based materials have exhibited their unique properties in their applications of biomedical areas. Nevertheless, the potential toxicity of QDs becomes the limitation of QDs application in biomedical areas. The toxicity of QDs might come from: the toxicity core material of QDs; the toxicity substances from the surface of QDs; the free radicals or reactive species released from QDs; the biological environment induced QDs toxicity. In this article, we review the properties of QDs, the applications of QDs in different biomedical fields, how QDs cause toxicity, and how to reduce or prevent QDs potential toxicity. In the future, we expect the improvement and further application of QDs in biomedical areas.

Enhanced fabrication of size-controllable chitosan-genipin nanoparticles using orifice-induced hydrodynamic cavitation: Process optimization and performance evaluation

Chitosan nanoparticles (NPs) possess great potential in biomedical fields. Orifice-induced hydrodynamic cavitation (HC) has been used for the enhancement of fabrication of size-controllable genipin-crosslinked chitosan (chitosan-genipin) NPs based on the emulsion cross-linking (ECLK). Experiments have been performed using various plate geometries, chitosan molecular weight and under different operational parameters such as inlet pressure (1–3.5 bar), outlet pressure (0–1.5 bar) and cross-linking temperature (40–70 °C). Orifice plate geometry was a crucial factor affecting the properties of NPs, and the optimized geometry of orifice plate was with single hole of 3.0 mm diameter. The size of NPs with polydispersity index of 0.359 was 312.6 nm at an optimized inlet pressure of 3.0 bar, and the maximum production yield reached 84.82 %. Chitosan with too high or too low initial molecular weight (e.g., chitosan oligosaccharide) was not applicable for producing ultra-fine and narrow-distributed NPs. There existed a non-linear monotonically-increasing relationship between cavitation number (Cv) and chitosan NP size. Scanning electron microscopy (SEM) test indicated that the prepared NPs were discrete with spherical shape. The study demonstrated the superiority of HC in reducing particle size and size distribution of NPs, and the energy efficiency of orifice type HC-processed ECLK was two orders of magnitude than that of ultrasonic horn or high shear homogenization-processed ECLK. In vitro drug-release studies showed that the fabricated NPs had great potential as a drug delivery system. The observations of this study can offer strong support for HC to enhance the fabrication of size-controllable chitosan-genipin NPs.

Application of hyperbranched polysiloxanes in biomedical materials based on AIE polymer properties

Application of hyperbranched polysiloxanes in biomedical materials based on AIE polymer properties

Exploring drug release performance of hollow‐structured CS/SA/POSS composite gel spheres employing hydrophilic polymerizable AS‐POSS as crosslinker

AbstractThis study prepares a series of hollow‐structured CS/SA/POSS composite gel spheres with a diameter of ~2.5 mm by using hydrophilic Janus‐type polyhedral oligomeric silsesquioxane (AS‐POSS) as a crosslinking agent in combination with sodium alginate and chitosan via electrostatic adsorption/free radical polymerization. As the content of POSS increases, the wall thickness of the gel spheres also increases from 20 to 30 μm, leading to a more compact and smooth wall structure in the polymerized CS/SA/POSS composite gel spheres. Additionally, the introduction and polymerization of POSS significantly enhance the stability, drug loading rate, and entrapment rate of the gel spheres, providing them with improved drug release capabilities. For hydrophilic drug doxorubicin, the loading rate and encapsulation rate reach 41.2% and 79.9%, respectively, while for the hydrophobic drug ibuprofen, they are 14.7% and 76.3%. Compared to some previously reported drug‐loaded gel materials, the gels prepared in this study demonstrate relatively higher drug loading performance. Thus, these hollow‐structured CS/SA/POSS composite gel spheres hold promise as innovative drug carriers in the biomedical field.

Designing Pathway-Controlled Multicomponent Ultrashort Peptide Hydrogels with Diverse Functionalities at the Nanoscale for Directing Cellular Behavior.

Tuning self-assembling pathways by implementing different external stimuli has been extensively studied, owing to their effective control over structural and mechanical properties. Consequently, multicomponent peptide hydrogels with high structural tunability and stimuli responsiveness are crucial in dictating cellular behavior. Herein, we have implemented both coassembly approach and pathway-dependent self-assembly to design nonequilibrium nanostructures to understand the thermodynamic and kinetic aspects of peptide self-assembly toward controlling cellular response. Our system involved an ultrashort peptide gelator and a hydrophilic surfactant which coassembled through different pathways, i.e., heat-cool and sonication methods with variable energy input. Interestingly, it was possible to access diverse structural and mechanical properties at the nanoscale in a single coassembled system. Further, the hydrophilic surfactant provided additional surface functionalities, thus creating an efficient hydrophilic matrix for cellular interaction. Such diverse functionalities in a single coassembled system could lead to the development of advanced scaffolds, with applications in various biomedical fields.

Hydrogen bond‐reinforced double‐network hydrogels with enhanced mechanical strength: Preparation, characterization and swelling behavior

AbstractRecently, double network (DN) gels with dynamic non‐covalent interaction such as hydrogen bonds has drawn much attention as an innovative material having both high water content and high mechanical strength. Research efforts have identified DN gels as a promising class of materials due to their unique network architecture. These gels comprise two interpenetrating networks formed by different types of polymer. Herein, we report a tough DN hydrogel with high mechanical strength and high swelling ability. The DN gel is synthesized via a two‐step network formation. The first network gel was synthesized via frontal polymerization. Then, the first gel is immersed in an aqueous solution of a second monomer and carrying out a second polymerization in the presence of first network. The spectroscopic analysis and thermal behavior with differential scanning calorimeter measurements corroborated the existence of hydrogen bonds. The mechanical test and microscopic morphology were further explored to explain the strength and high imbibing characteristics. We expect that this facile strategy may explore a dynamic and tunable hydrogel to expand its potential applications in biomedical field.

Design and Synthesis of Biomedical Polymer Materials

Due to their biocompatibility and non-toxic nature, biomedical polymer materials have found widespread applications and significantly propelled the progress of the biomedical field [...]

Biologically active sodium pentaborate pentahydrate and Hypericum perforatum oil loaded poly vinyl alcohol: chitosan membranes

In this study, sodium pentaborate pentahydrate (NaB) and Hypericum perforatum (HP) oil were incorporated into polyvinyl alcohol (PVA) and chitosan (CH) polymer blend to obtain membranes by solution casting method. In order to see the synergistic effects of NaB and HP oil on the biological and physical properties of the membranes NaB and HP oil were incorporated into membrane matrix in different ratios. Fourier-transform infrared spectroscopy (FTIR) results showed that no significant bond formation between the bioactive components and the PVA:CH matrix. According to mechanical test results, Young's Modulus and elongation at break decreased from 426 MPa to 346 MPa and 52.23 % to 15.11 % for neat PVA:CH membranes and NaB and HP oil incorporated PVA:CH (PVA:CH@35NaB:HP) membranes, respectively. Antimicrobial activity tests have shown the membranes were over 99 % effective against Escherichia coli, Staphylococcus aureus, and Candida albicans, underlining their potential for infection control. Cytocompatibility assay performed with Human Dermal Fibroblast (HDFa) cells highlight the biocompatibility of the membranes, revealing 74.84 % cell viability after 72 h. The properties of NaB and HP oil doped PVA:CH based membranes obtained from these experiments reveal the promise of a versatile membrane for applications in wound healing, tissue engineering and other biomedical fields.

Identification of an affordable and printable metastable β Ti alloy with outstanding deformation behaviour for use in laser powder bed fusion

Research on metastable β Ti alloys has recently shown the possibility to achieve outstanding ductility and work hardening behaviours by engineering the materials’ unique strain transformable attributes and responses to heat treatment. As quenching is central to the development of the metastable phase in these alloys, it is of interest to understand how these materials could be designed and developed for use in laser additive manufacturing where feedstocks experience numerous rapid thermal cycles. In this context, we first propose a material design framework to identify printable metastable Ti alloys for laser powder bed fusion (L-PBF). We focus on the ternary Ti-Cr-Sn system for both its affordable character and interest in the biomedical field. The design framework combines criteria based on well-established empirical parameters that we use to compare stability of β phase and resistance to cracking during L-PBF, i.e. its printability. The design work is supported by series of microstructural investigations on arc-melted buttons of selected compositions. Using such methodology we identify Ti-7.5Cr-4.5Sn as strain transformable alloy of good printability and we then characterise this alloy in depth in a series of laser powder bed fusion experiments. Printability of this alloy is further demonstrated via printing experiments using a variety of processing conditions while the deformation character is studied using compressive testing. It was found that the identified Ti-7.5Cr-4.5Sn alloy can achieve a high compressive strain exceeding 70 % thanks to deformation mechanisms that combine dislocation slip and {3 3 2}<1 1 3> twinning. This research paves the way towards the identification of novel Ti alloys for L-PBF beyond those used in the aerospace sector, opening the way for a broader field of applications.

Metal-polyphenol coordination nanosheets with synergistic peroxidase-like and photothermal properties for efficient antibacterial treatment

Bacterial infections pose a serious threat to human health and socioeconomics worldwide. In the post-antibiotic era, the development of novel antimicrobial agents remains a challenge. Polyphenols are natural compounds with a variety of biological activities such as intrinsic antimicrobial activity and antioxidant properties. Metal-polyphenol obtained by chelation of polyphenol ligands with metal ions not only possesses efficient antimicrobial activity but also excellent biocompatibility, which has great potential for application in biomedical and food packaging fields. Herein, we developed metal-polyphenol coordination nanosheets named copper oxidized tannic acid quinone (CuTAQ) possessing efficient antibacterial and anti-biofilm effects, which was synthesized by a facile one-pot method. The synthesis was achieved by chelation of partially oxidized tannic acid (TA) with Cu2+ under mild conditions, which supports low-cost and large-scale production. It was demonstrated that CuTAQ exhibited high antibacterial activity via disrupting the integrity of bacterial cell membranes, inducing oxidative stress, and interfering with metabolism. In addition, CuTAQ exhibits excellent peroxidase catalytic activity and photothermal conversion properties, which play a significant role in enhancing its bactericidal and biofilm scavenging abilities. This study provides insights for rational design of innovative metal-polyphenol nanomaterials with efficient antimicrobial properties.

Influence of Silsesquioxane-Containing Ultra-Thin Polymer Films on Metal Oxide Gas Sensor Performance for the Tunable Detection of Biomarkers

Certain biomarkers in exhaled breath are indicators of diseases in the human body. The non-invasive detection of such biomarkers in human breath increases the demand for simple and cost-effective gas sensors to replace state-of-the-art gas chromatography (GC) machines. The use of metal oxide (MOX) gas sensors based on thin-film structures solves the current limitations of breath detectors. However, the response at high humidity levels, i.e., in the case of exhaled human breath, significantly decreases the sensitivity of MOX sensors, making it difficult to detect small traces of biomarkers. We have introduced, in previous work, the concept of a hybrid gas sensor, in which thin-film-based MOX gas sensors are combined with an ultra-thin (20–30 nm) polymer top layer deposited by solvent-free initiated chemical vapor deposition (iCVD). The hydrophobic top layer enables sensor measurement in high-humidity conditions as well as the precise tuning of selectivity and sensitivity. In this paper, we present a way to increase the hydrogen (H2) sensitivity of hybrid sensors through chemical modification of the polymer top layer. A poly(1,3,5,7-tetramethyl-tetravinylcyclotetrasiloxane) (PV4D4) thin film, already applied in one of our previous studies, is transformed into a silsesquioxane-containing top layer by a simple heating step. The transformation results in a significant increase in the gas response for H2 ~709% at an operating temperature of 350 °C, which we investigate based on the underlying sensing mechanism. These results reveal new pathways in the biomedical application field for the analysis of exhaled breath, where H2 indicates gastrointestinal diseases.