A Survey on Graph Neural Networks and Graph Transformers in Computer Vision: A Task-Oriented Perspective.

Graph Neural Networks (GNNs) have gained momentum in graph representation learning and boosted the state of the art in a variety of areas, such as data mining (e.g., social network analysis and recommender systems), computer vision (e.g., object detection and point cloud learning), and natural language processing (e.g., relation extraction and sequence learning), to name a few. With the emergence of Transformers in natural language processing and computer vision, graph Transformers embed a graph structure into the Transformer architecture to overcome the limitations of local neighborhood aggregation while avoiding strict structural inductive biases. In this paper, we present a comprehensive review of GNNs and graph Transformers in computer vision from a task-oriented perspective. Specifically, we divide their applications in computer vision into five categories according to the modality of input data, i.e., 2D natural images, videos, 3D data, vision + language, and medical images. In each category, we further divide the applications according to a set of vision tasks. Such a task-oriented taxonomy allows us to examine how each task is tackled by different GNN-based approaches and how well these approaches perform. Based on the necessary preliminaries, we provide the definitions and challenges of the tasks, in-depth coverage of the representative approaches, as well as discussions regarding insights, limitations, and future directions.

Nano-vibration exciter: Hypoxia-inducible factor 1 signaling pathway-mediated extracellular vesicles as bioactive glass substitutes for bone regeneration.

Bioactive glasses (BG) play a vital role in angiogenesis and osteogenesis through releasing functional ions. However, the rapid ion release in the early stage will cause excessive accumulation of metal ions, which in turn leads to obvious cytotoxicity, long-term inflammation, and bone repair failure. Inspired by the vibration exciter, small extracellular vesicles (sEVs) obtained by treating mesenchymal stem cells with copper-doped bioactive glass (CuBG-sEVs), is prepared as a nano-vibration exciter. The nano-vibration exciter can convert the ion signals of CuBG into biochemical factor signals through hypoxia-inducible factor 1 (HIF-1) signaling pathway and its activated autophagy, so as to better exert the osteogenic activity of BG. The results showed that CuBG extracts could significantly improve the enrichment of key miRNAs and increase the yield of CuBG-sEVs by activating HIF-1 signaling pathway and its activated autophagy. Cell experiments showed that CuBG-sEVs are favor to cell recruitment, vascularization and osteogenesis as the enrichment of key miRNAs. The animal experiments results showed that CuBG-sEVs stimulated angiogenesis mediated by CD31 and promoted bone regeneration by activating signaling pathways related to osteogenesis. These findings underscored the significant potential of sEVs as alternative strategies to better roles of BG.

High performance injectable Mg doped bioactive glass bone cement for the regulation of osteogenic immune microenvironment.

Although calcium phosphate has been extensively utilized in orthopedic applications such as spine, limbs, dentistry, and maxillofacial surgery, the lack of osteoinductive properties often hinders its effectiveness in treating bone defects resulting from pathological micro-environment such as tumor surgery, osteoporosis, osteomyelitis, and diabetic. Therefore, a novel bone cement based on magnesium-doped bioactive glass was developed in this study. The moderate release of magnesium ions improved the mechanical properties by controlling the crystal size of hydroxyapatite. Through detailed discussion of element content and heat treatment temperature, it was found that 2Mg-BG-800 was suitable for the construction of bone cement. 2Mg-BG-BC exhibited favorable initial (15 min) and final (30 min) setting time, compressive strength (29.45 MPa), compressive modulus (1851.49 MPa), injectability, and shape-adaptability. Furthermore, Mg-BG-BC demonstrated the ability to enhance the osteogenic differentiation of BMSCs, and induce macrophage polarization towards the M2 phenotype, suggesting its potential for osteoporotic fracture regeneration.

Enhancement and quenching of plasmon-enhanced spectroscopy of single molecule confined in metallic nanoparticle dimers.

We present a theoretical analysis of plasmon-enhanced fluorescence (PEF) and Raman scattering (PERS) spectroscopy of a single molecule confined in the laser-irradiated metallic nanoparticles (NPs) dimer, focusing on the origin of the spectral enhancement and quenching effects. The theoretical method ofD-parameters has been used to calculate the dimer distance-dependent nonlocal dielectric effect in Ag and Au NPs. Meanwhile, other damping rates and electric field enhancements are quantitatively computed by finite element method. Moreover, PEF and PERS spectra of rhodamine 6G are obtained within the density-functional theory. Our calculated results show that the PERS mainly depend on the excitation and emission field enhancements, and thus it occurs at the narrower dimer gap due to the stronger localized plasmon coupling. The PEF is related to fluorescence rate caused by the competition between excitation electric field and quantum efficiency, and the increase of former may enhance the fluorescence intensity while the lower latter lead to reduce the intensity as decreasing the dimer distance. The contribution of nonlocal dielectric effect can significantly reduce the quantum efficiency at smaller distance so that it overcomes the excitation field enhancement, leading to the fluorescence quenching for Au NPs dimer. Furthermore, by optimizing the dimer distance and NPs size, the maximum PERS and PEF cross sections reach 10-14and 10-15under 2.45 eV laser excitation for Ag NPs dimer, and 10-18for Au NPs. Our study finely explains the experiment results showed either fluorescence enhancement or quenching with the change of molecule-NPs distance, and better guidance for optimizing the experiments.

Phosphoserine enhanced Cu-doped bioactive glass dynamic dual-network hydrogel for craniofacial bone defect repair.

Flexible hydrogels containing various osteogenic inorganic constituents, which can accommodate complicated shape variations, are considered as ideal grafts for craniofacial bone defect reconstruction. However, in most hybrid hydrogels, poor interaction between the polymer network and particles has detrimental effects on hydrogel rheological and structural properties, clinical manipulation and repair efficacy. In this article, we designed and prepared a series of hyaluronic acid composite hydrogel containing Cu-doped bioactive glass (CuBG) and phosphoserine (PS), in which hyaluronic acid was modified by methacrylate groups and phenylboronic acid groups to form a double crosslinked network. PS acted as an interaction bridge of CuBG particles and HAMA-PBA network to improve the mechanical properties of the composite hydrogels. The CuBG/PS hydrogels exhibited suitable rheological properties (injectable, self-healing, shape-adaptable), bone tissue integrating ability and anti-bacterial property. Meanwhile, we found that CuBG and PS have synergistic effect on improving osteogenic efficiency both in vitro and in vivo, particularly when the ratio of CuBG to PS is lower than 3 (9CB/3PS). This work provided a versatile and scalable approach to enhanced the interaction within inorganic particles and polymer network in hydrogels without extra modification on components.

Quantum tunneling effect on the surface enhanced Raman process in molecular systems.

In this paper, we theoretically study the effect of quantum tunneling on the surface enhanced Raman scattering (SERS) of a generic molecule confined in sub-nanometer nanocavities formed by metallic dimers. The tunneling effect was described by the quantum corrected model in combination with finite element simulations. The SERS spectra were calculated by a density matrix method. Simulation results demonstrate that both the field enhancement and the molecular SERS spectra are very sensitive to the size of the cavity. By decreasing the gap size, the local field enhancement first increases then starts to be significantly suppressed as a result of the tunneling effect which neutralizes the positive and negative induced charges in the nanocavity. Consequently, the SERS intensity also experienced dramatic decrease in the short gap distance region. We also show that both the plasmonic enhancement to the local field and the enhanced molecular decay rates have to be taken into account to understand the SERS properties of the molecule in such sub-nanometer nanocavities. These results could be helpful for the understanding of the surface enhanced spectral properties of molecular systems at sub-nanometer nanocavities.

Study of the characteristics of combined insulation in compact pulse transformers.

One of the important research directions in pulse power technology is to increase power density and operational stability of compact high-power pulse transformers. In this paper, the research object is a high-power pulse transformer using combined insulation, and the operating characteristics are obtained using simulation and experiment methods. The experimental results show that the maximum output voltage of the transformer increases by 30% in the combined insulation. At the same time, the combined insulation transformers are safer and have better insulation holding capacity. Moreover, multiple breakdowns have less effect on the subsequent breakdown voltage of the combined insulation transformer. The average subsequent breakdown voltage after 30 breakdowns of combination insulated transformers is still higher than the first breakdown voltage of non-combined insulation transformers. In addition, the energy storage density of combined insulation transformers is ∼40% higher than that of non-combined insulation transformers because of the higher permittivity of Midel 7131 than transformer oil.

3D printing of Cu-doped bioactive glass composite scaffolds promotes bone regeneration through activating the HIF-1α and TNF-α pathway of hUVECs.

The increasing insight into the molecular and cellular processes within the angiogenic cascade assists in enhancing the survival and integration of engineered bone constructs. Copper-doped bioactive glass (Cu-BG) is now a potential structural component of the novel scaffolds and implants used in orthopedic and dental repairs. However, it is difficult for BG, especially micro-nano particles, to be printed into scaffolds and still retain its biological activity and ability to biodegrade. Additionally, the mechanisms of the copper-stimulating autocrine and paracrine effects of human umbilical vein endothelial cells (hUVECs) during repair and regeneration of bone are not yet clear. Therefore, in this study, we created monodispersed micro-nano spherical Cu-BG particles with varying copper content through a sol-gel process. Through in vitro tests, we found that Cu-BG enhanced angiogenesis by activating the pro-inflammatory environment and the HIF-1α pathway of hUVECs. Furthermore, 2Cu-BG diluted extracts directly promoted the osteogenic differentiation of mouse bone mesenchymal stem cells (BMSCs) in vitro. Then, a new 3D-printed tyramine-modified gelatin/silk fibroin/copper-doped bioactive glass (Gel/SF/Cu-BG) scaffold for rat bone defects was constructed, and the mechanism of the profound angiogenesis effect regulated by copper was explored in vivo. Finally, we found that hydrogel containing 1 wt% 2Cu-BG effectively regulated the spatiotemporal coupling of vascularization and osteogenesis. Therefore, Cu-BG-containing scaffolds have great potential for a wide range of bone defect repairs.

3D printed silk-gelatin hydrogel scaffold with different porous structure and cell seeding strategy for cartilage regeneration.

Hydrogel scaffolds are attractive for tissue defect repair and reorganization because of their human tissue-like characteristics. However, most hydrogels offer limited cell growth and tissue formation ability due to their submicron- or nano-sized gel networks, which restrict the supply of oxygen, nutrients and inhibit the proliferation and differentiation of encapsulated cells. In recent years, 3D printed hydrogels have shown great potential to overcome this problem by introducing macro-pores within scaffolds. In this study, we fabricated a macroporous hydrogel scaffold through horseradish peroxidase (HRP)-mediated crosslinking of silk fibroin (SF) and tyramine-substituted gelatin (GT) by extrusion-based low-temperature 3D printing. Through physicochemical characterization, we found that this hydrogel has excellent structural stability, suitable mechanical properties, and an adjustable degradation rate, thus satisfying the requirements for cartilage reconstruction. Cell suspension and aggregate seeding methods were developed to assess the inoculation efficiency of the hydrogel. Moreover, the chondrogenic differentiation of stem cells was explored. Stem cells in the hydrogel differentiated into hyaline cartilage when the cell aggregate seeding method was used and into fibrocartilage when the cell suspension was used. Finally, the effect of the hydrogel and stem cells were investigated in a rabbit cartilage defect model. After implantation for 12 and 16 weeks, histological evaluation of the sections was performed. We found that the enzymatic cross-linked and methanol treatment SF5GT15 hydrogel combined with cell aggregates promoted articular cartilage regeneration. In summary, this 3D printed macroporous SF-GT hydrogel combined with stem cell aggregates possesses excellent potential for application in cartilage tissue repair and regeneration.

Tough thermoplastic hydrogels with re-processability and recyclability for strain sensors.

Tough hydrogels with the ability to be repeatedly processed into various shapes as thermoplastics are highly desired in advanced medical devices and tissue engineering. Here, we have developed a kind of versatile supramolecular hydrogel with a network cross-linked by double hydrogen bonds from poly(N-acryloyl glycinamide) (PNAGA). The resulting PNAGA-30 hydrogels (30 wt% solid content) are tough, re-processable, and recyclable similar to thermoplastics. The hydrogels in the form of fragments can be easily re-processed into various shapes including sheet, filament, cylinder and other complex shapes by using simple stamping and injection methods. The mechanical properties of the re-programed hydrogels are comparable to the properties of the original hydrogels. The re-processability and robust mechanical properties of the PNAGA hydrogels are promising for practical applications in soft materials, tissue engineering and wearable devices. Furthermore, the PNAGA-30&LiCl ionic hydrogels can be fabricated by simply compositing LiCl into thermoplastic hydrogels. The PNAGA-30&LiCl hydrogels can function as multifunctional strain sensors to monitor large human movements and tiny vibrations, thereby showing great application potential in robotics, biomedical prosthetics, personal healthcare monitoring and so on.

Influence of nonlocal dielectric response on the Au tip-enhanced fluorescence effect.

Tip-enhanced fluorescence (TEF) with ultra-high detection sensitivity and spatial resolution has been a powerful characterization technique in the study of surface science and life science. Herein, a systematically theoretical investigation in the visible range had been performed to study TEF properties of a single molecule located inside a nanogap formed by Au tip and substrate. In the strong localized surface plasmon coupling effect, the contribution of nonlocal dielectric response to the fluorescence quantum yield as well as radiative and energy dissipated decay rates were calculated. It is found that the nonlocal dielectric effects become comparable to the radiative and energy dissipated decay rates with the increasing of the tip-molecule distance, as a result, the nonlocal dielectric effect significantly suppresses the fluorescence process. The huge excitation enhancement at the shorter tip-molecule distance can efficiently compensate the low quantum yield, leading to the great fluorescence enhancement. The results show that the maximum enhancement obtained from the calculations can reach as high as four orders of magnitude by optimizing the tip-molecule distance. These results are not only helpful to our understanding of the TEF mechanism but also valuable for its further applications.

Tubular Silk Fibroin/Gelatin-Tyramine Hydrogel with Controllable Layer Structure and Its Potential Application for Tissue Engineering.

In recent years, biomimetic tubular scaffolds have been widely used to repair various human tissue defects, due to their hollow structure similar to the native tissues such as blood vessel, trachea, ureter, and bone marrow cavity. However, there are still many challenges in manufacturing a tubular hydrogel scaffold with suitable mechanical properties, specific microstructure, and good biocompatibility. In this study, we exploited an enzymatic cross-linking method using horseradish peroxidase (HRP) as an enzyme and hydrogen peroxide (H2O2) as a substrate, and combining with gelatin's thermal sensitivity to produce an enzymatically cross-linked silk fibroin/gelatin-tyramine (E-SF/GT) tubular hydrogel. Through further treatment with methanol, we fabricated an EM-SF/GT tubular hydrogel with fine-wall architecture that consists of two different layers (inner and outer, dense and porous). Mechanical measurement showed that the compressive moduli values were up to 4.82 MPa and the tensile moduli values were up to 4.79 kPa under the static loading conditions. Also, degradation test showed that the hydrogel's degradation time was prolonged. Finally, the bioactivity was tested by seeding mouse bone marrow mesenchymal stem cells (mBMSCs) in the lumen of a small-diameter (2 mm) EM-SF/GT tubular hydrogel. Cell morphology and immunofluorescence test indicated that mBMSCs differentiated into endothelial cells and lined the inner surface of the tubular hydrogel under induction. This work provided a feasible strategy for developing tubular hydrogels, which could be potentially used as scaffolds for hollow multilayer tissue engineering, such as blood vessels.

A medical adhesive used in a wet environment by blending tannic acid and silk fibroin.

A multifunctional and effective medical adhesive with a combination of high toughness and superior adhesion is highly desired in biomedical fields. However, clinical application of medical adhesives is still limited due to their weak adhesion to wet tissue. In this study, a novel medical adhesive called TASK composed of tannic acid (TA) and silk fibroin (SF) based on polyphenol-gel systems was developed. TASK powder was prepared by a simple physical mixture of pyrogallol-rich tannic acid and silk fibroin in aqueous solution and further freeze drying, which was stable and convenient for sterilization before clinical application. The TASK composite gel was formed by just adding water to the TASK powder. TASK showed improved wet-adhesive properties and stability; its adhesion strength after 5 h in water reached 180.9 ± 27.4 kPa. ATR-FTIR results indicated that the plentiful phenolic hydroxyl groups in TA allowed TASK to maintain adhesion to tissue in a wet environment. Furthermore, no chemical modification or covalent cross-linking was required for this wet-adhesive TASK which may facilitate its clinical application.

Pathogen escape from host immunity by a genome program for antigenic variation.

The vector-borne bacterium Borrelia hermsii, a relapsing fever agent, switches gene expression of a surface protein between different antigenic variants, thereby causing sequential waves of immune escape within hosts and increasing the likelihood of transmission. Analogous programmed systems of antigenic variation occur in African trypanosomes and Plasmodium falciparum. In these examples, switch rates to individual variants differ over a wide range. We studied how B. hermsii determines switch rates in two experimental infections: one where variants were identified by specific antisera and one based on identification by DNA sequence. Unexpressed loci of variant antigens copy into a single expression site at rates determined by extragenic features of silent loci rather than similarity between coding sequences of variants at silent sites and the single expression site. Two elements, in particular, determine switch rates. One set of elements overlaps the 5' ends of the expressed gene and the silent loci; greater sequence identity between elements was associated with a higher switch rate. The second set of elements flanks the expression site on the 3' side and occurs at variable distances downstream from silent loci; the nearer an element to a silent locus, the greater the switch rate of that locus into the expression site. In combination, these two features of the genome provide a simple mechanism to modulate switch rate whereby silent loci form a hierarchy of switch rates into the expression site. Although the switching hierarchy causes changes in individual cells that are stochastic, ordering of variants within hosts is semipredictable.

Antigenic variation by Borrelia hermsii occurs through recombination between extragenic repetitive elements on linear plasmids.

The relapsing fever agent Borrelia hermsii undergoes multiphasic antigenic variation through gene conversion of a unique expression site on a linear plasmid by an archived variable antigen gene. To further characterize this mechanism we assessed the repertoire and organization of archived variable antigen genes by sequencing approximately 85% of plasmids bearing these genes. Most archived genes shared with the expressed gene a

Function and evolution of plasmid-borne genes for pyrimidine biosynthesis in Borrelia spp.

The thyX gene for thymidylate synthase of the Lyme borreliosis (LB) agent Borrelia burgdorferi is located in a 54-kb linear plasmid. In the present study, we identified an orthologous thymidylate synthase gene in the relapsing fever (RF) agent Borrelia hermsii, located it in a 180-kb linear plasmid, and demonstrated its expression. The functions of the B. hermsii and B. burgdorferi thyX gene products were evaluated both in vivo, by complementation of a thymidylate synthase-deficient Escherichia coli mutant, and in vitro, by testing their activities after purification. The B. hermsii thyX gene complemented the thyA mutation in E. coli, and purified B. hermsii ThyX protein catalyzed the conversion of dTMP from dUMP. In contrast, the B. burgdorferi ThyX protein had only weakly detectable activity in vitro, and the B. burgdorferi thyX gene did not provide complementation in vivo. The lack of activity of B. burgdorferi's ThyX protein was associated with the substitution of a cysteine for a highly conserved arginine at position 91. The B. hermsii thyX locus was further distinguished by the downstream presence in the plasmid of orthologues of nrdI, nrdE, and nrdF, which encode the subunits of ribonucleoside diphosphate reductase and which are not present in the LB agents B. burgdorferi and Borrelia garinii. Phylogenetic analysis suggested that the nrdIEF cluster of B. hermsii was acquired by horizontal gene transfer. These findings indicate that Borrelia spp. causing RF have a greater capability for de novo pyrimidine synthesis than those causing LB, thus providing a basis for some of the biological differences between the two groups of pathogens.

Opioid activity of C8813, a novel and potent opioid analgesic.

Compound trans-4-(p-bromophenyl)-4-(dimethylamino)-1-(2-thiophen-2-yl-ethyl)-cyclohexanol (C8813), structurally unrelated to morphine, is a novel analgesic. The present study examined the antinociception, opioid receptor selectivity and in vitro activity of C8813. The antinociceptive activity was evaluated using mouse hot plate and acetic acid writhing tests. In mouse hot plate test, the antinociceptive ED(50) of C8813 was 11.5 microg/kg, being 591 times and 3.4 times more potent than morphine and fentanyl respectively. In mouse writhing test, the antinociceptive ED(50) of C8813 was 16.9 microg/kg, being 55 times and 2.3 times more active than morphine and fentanyl respectively. In the opioid receptor binding assay, C8813 showed high affinity for mu-opioid receptor (K(i) = 1.37 nM) and delta-opioid receptor (K(i) = 3.24 nM) but almost no affinity for kappa-opioid receptor (at 1 microM). In the bioassay, the inhibitory effect of C8813 in the guinea-pig ileum (GPI) was 16.5 times more potent than in the mouse vas deferens (MVD). The inhibitory effects of C8813 in the GPI and MVD could be antagonized by mu-opioid receptor antagonist naloxone and delta-opioid receptor antagonist ICI174,864 respectively. However, the inhibitory effect of C8813 in the rabbit vas deferens was very weak. These results indicated that C8813 was a potent analgesic and a high affinity agonist for the mu- and delta-opioid receptors.