Meta-DHGNN: method for CRS-related cytokines analysis in CAR-T therapy based on meta-learning directed heterogeneous graph neural network.

Chimeric antigen receptor T-cell (CAR-T) immunotherapy, a novel approach for treating blood cancer, is associated with the production of cytokine release syndrome (CRS), which poses significant safety concerns for patients. Currently, there is limited knowledge regarding CRS-related cytokines and the intricate relationship between cytokines and cells. Therefore, it is imperative to explore a reliable and efficient computational method to identify cytokines associated with CRS. In this study, we propose Meta-DHGNN, a directed and heterogeneous graph neural network analysis method based on meta-learning. The proposed method integrates both directed and heterogeneous algorithms, while the meta-learning module effectively addresses the issue of limited data availability. This approach enables comprehensive analysis of the cytokine network and accurate prediction of CRS-related cytokines. Firstly, to tackle the challenge posed by small datasets, a pre-training phase is conducted using the meta-learning module. Consequently, the directed algorithm constructs an adjacency matrix that accurately captures potential relationships in a more realistic manner. Ultimately, the heterogeneous algorithm employs meta-photographs and multi-head attention mechanisms to enhance the realism and accuracy of predicting cytokine information associated with positive labels. Our experimental verification on the dataset demonstrates that Meta-DHGNN achieves favorable outcomes. Furthermore, based on the predicted results, we have explored the multifaceted formation mechanism of CRS in CAR-T therapy from various perspectives and identified several cytokines, such as IFNG (IFN-γ), IFNA1, IFNB1, IFNA13, IFNA2, IFNAR1, IFNAR2, IFNGR1 and IFNGR2 that have been relatively overlooked in previous studies but potentially play pivotal roles. The significance of Meta-DHGNN lies in its ability to analyze directed and heterogeneous networks in biology effectively while also facilitating CRS risk prediction in CAR-T therapy.

Giant nonreciprocal second-harmonic generation from antiferromagnetic bilayer CrI3.

Layered antiferromagnetism is the spatial arrangement of ferromagnetic layers with antiferromagnetic interlayer coupling. The van der Waals magnet chromium triiodide (CrI3) has been shown to be a layered antiferromagnetic insulator in its few-layer form1, opening up opportunities for various functionalities2-7 in electronic and optical devices. Here we report an emergent nonreciprocal second-order nonlinear optical effect in bilayer CrI3. The observed second-harmonic generation (SHG; a nonlinear optical process that converts two photons of the same frequency into one photon of twice the fundamental frequency) is several orders of magnitude larger than known magnetization-induced SHG8-11 and comparable to the SHG of the best (in terms of nonlinear susceptibility) two-dimensional nonlinear optical materials studied so far12,13 (for example, molybdenum disulfide). We show that although the parent lattice of bilayer CrI3 is centrosymmetric, and thus does not contribute to the SHG signal, the observed giant nonreciprocal SHG originates only from the layered antiferromagnetic order, which breaks both the spatial-inversion symmetry and the time-reversal symmetry. Furthermore, polarization-resolved measurements reveal underlying C2h crystallographic symmetry-and thus monoclinic stacking order-in bilayer CrI3, providing key structural information for the microscopic origin of layered antiferromagnetism14-18. Our results indicate that SHG is a highly sensitive probe of subtle magnetic orders and open up possibilities for the use of two-dimensional magnets in nonlinear and nonreciprocal optical devices.

Epitaxial growth of a 100-square-centimetre single-crystal hexagonal boron nitride monolayer on copper.

The development of two-dimensional (2D) materials has opened up possibilities for their application in electronics, optoelectronics and photovoltaics, because they can provide devices with smaller size, higher speed and additional functionalities compared with conventional silicon-based devices1. The ability to grow large, high-quality single crystals for 2D components-that is, conductors, semiconductors and insulators-is essential for the industrial application of 2D devices2-4. Atom-layered hexagonal boron nitride (hBN), with its excellent stability, flat surface and large bandgap, has been reported to be the best 2D insulator5-12. However, the size of 2D hBN single crystals is typically limited to less than one millimetre13-18, mainly because of difficulties in the growth of such crystals; these include excessive nucleation, which precludes growth from a single nucleus to large single crystals, and the threefold symmetry of the hBN lattice, which leads to antiparallel domains and twin boundaries on most substrates19. Here we report the epitaxial growth of a 100-square-centimetre single-crystal hBN monolayer on a low-symmetry Cu (110) vicinal surface, obtained by annealing an industrial copper foil. Structural characterizations and theoretical calculations indicate that epitaxial growth was achieved by the coupling of Cu <211> step edges with hBN zigzag edges, which breaks the equivalence of antiparallel hBN domains, enabling unidirectional domain alignment better than 99 per cent. The growth kinetics, unidirectional alignment and seamless stitching of the hBN domains are unambiguously demonstrated using centimetre- to atomic-scale characterization techniques. Our findings are expected to facilitate the wide application of 2D devices and lead to the epitaxial growth of broad non-centrosymmetric 2D materials, such as various transition-metal dichalcogenides20-23, to produce large single crystals.

PrCRS: a prediction model of severe CRS in CAR-T therapy based on transfer learning.

BACKGROUND: CAR-T cell therapy represents a novel approach for the treatment of hematologic malignancies and solid tumors. However, its implementation is accompanied by the emergence of potentially life-threatening adverse events known as cytokine release syndrome (CRS). Given the escalating number of patients undergoing CAR-T therapy, there is an urgent need to develop predictive models for severe CRS occurrence to prevent it in advance. Currently, all existing models are based on decision trees whose accuracy is far from meeting our expectations, and there is a lack of deep learning models to predict the occurrence of severe CRS more accurately. RESULTS: We propose PrCRS, a deep learning prediction model based on U-net and Transformer. Given the limited data available for CAR-T patients, we employ transfer learning using data from COVID-19 patients. The comprehensive evaluation demonstrates the superiority of the PrCRS model over other state-of-the-art methods for predicting CRS occurrence. We propose six models to forecast the probability of severe CRS for patients with one, two, and three days in advance. Additionally, we present a strategy to convert the model's output into actual probabilities of severe CRS and provide corresponding predictions. CONCLUSIONS: Based on our findings, PrCRS effectively predicts both the likelihood and timing of severe CRS in patients, thereby facilitating expedited and precise patient assessment, thus making a significant contribution to medical research. There is little research on applying deep learning algorithms to predict CRS, and our study fills this gap. This makes our research more novel and significant. Our code is publicly available at https://github.com/wzy38828201/PrCRS . The website of our prediction platform is: http://prediction.unicar-therapy.com/index-en.html .

Contrast-enhanced phase-resolved second harmonic generation microscopy.

The characterization of inverted structures (crystallographic, ferroelectric, or magnetic domains) is crucial in the development and application of novel multi-state devices. However, determining these inverted structures needs a sensitive probe capable of revealing their phase correlation. Here a contrast-enhanced phase-resolved second harmonic generation (SHG) microscopy is presented, which utilizes a phase-tunable Soleil-Babinet compensator and the interference between the SHG fields from the inverted structures and a homogeneous reference. By this means, such inverted structures are correlated through the π-phase difference of SHG, and the phase difference is ultimately converted into the intensity contrast. As a demonstration, we have applied this microscopy in two scenarios to determine the inverted crystallographic domains in two-dimensional van der Waals material MoS2. Our method is particularly suitable for applying in vacuum and cryogenic environments while providing optical diffraction-limited resolution and arbitrarily adjustable contrast. Without loss of generality, this contrast-enhanced phase-resolved SHG microscopy can also be used to resolve other non-centrosymmetric inverted structures, e.g. ferroelectric, magnetic, or multiferroic phases.

Gate-tunable room-temperature ferromagnetism in two-dimensional Fe3GeTe2.

Materials research has driven the development of modern nano-electronic devices. In particular, research in magnetic thin films has revolutionized the development of spintronic devices1,2 because identifying new magnetic materials is key to better device performance and design. Van der Waals crystals retain their chemical stability and structural integrity down to the monolayer and, being atomically thin, are readily tuned by various kinds of gate modulation3,4. Recent experiments have demonstrated that it is possible to obtain two-dimensional ferromagnetic order in insulating Cr2Ge2Te6 (ref. 5) and CrI3 (ref. 6) at low temperatures. Here we develop a device fabrication technique and isolate monolayers from the layered metallic magnet Fe3GeTe2 to study magnetotransport. We find that the itinerant ferromagnetism persists in Fe3GeTe2 down to the monolayer with an out-of-plane magnetocrystalline anisotropy. The ferromagnetic transition temperature, Tc, is suppressed relative to the bulk Tc of 205 kelvin in pristine Fe3GeTe2 thin flakes. An ionic gate, however, raises Tc to room temperature, much higher than the bulk Tc. The gate-tunable room-temperature ferromagnetism in two-dimensional Fe3GeTe2 opens up opportunities for potential voltage-controlled magnetoelectronics7-11 based on atomically thin van der Waals crystals.

Twist Phase Matching in Two-Dimensional Materials.

Optical phase matching involves establishing a proper phase relationship between the fundamental excitation and generated waves to enable efficient optical parametric processes. It is typically achieved through birefringence or periodic polarization. Here, we report that the interlayer twist angle in two-dimensional (2D) materials creates a nonlinear geometric phase that can compensate for the phase mismatch, and the vertical assembly of the 2D layers with a proper twist sequence generates a nontrivial "twist-phase-matching" (twist-PM) regime. The twist-PM model provides superior flexibility in the design of optical crystals, which can be applied for twisted layers with either periodic or random thickness distributions. The designed crystal from the twisted rhombohedral boron nitride films within a thickness of only 3.2 µm is capable of producing a second-harmonic generation with conversion efficiency of ∼8% and facile polarization controllability that is absent in conventional crystals. Our methodology establishes a platform for the rational design and atomic manufacturing of nonlinear optical crystals based on abundant 2D materials.

Mechanisms of Actinidia chinensis Planch in treating colon cancer based on the integration of network pharmacology, molecular docking, and experimental verification.

BACKGROUND: As an anticancer Chinese herbal medicine, the effective components and mechanism of Actinidia chinensis Planch (ACP, Tengligen) in the treatment of colon cancer are still unclear. In the present study, the integration of network pharmacology, molecular docking, and cell experiments was employed to study the effective mechanism of ACP against colon cancer. METHODS: The Venn diagram and STRING database were used to construct the protein-protein interaction network (PPI) of ACP-colon cancer, and further topological analysis was used to obtain the key target genes of ACP in colon cancer. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to visualize the related functions and pathways. Molecular docking between key targets and compounds was determined using software such as AutoDockTools. Finally, the effect of ACP on CT26 cells was observed in vitro. RESULTS: The study identified 40 ACP-colon key targets, including CASP3, CDK2, GSK3B, and PIK3R1. GO and KEGG enrichment analyses found that these genes were involved in 211 biological processes and 92 pathways, among which pathways in cancer, PI3K-Akt, p53, and cell cycle might be the main pathways of ACP against colon cancer. Molecular docking verified that the key components of ACP could stably bind to the corresponding targets. The experimental results showed that ACP could inhibit proliferation, induce apoptosis, and downregulate the phosphorylation of PIK3R1, Akt, and GSK3B in CT26 cells. CONCLUSION: ACP is an anti-colon cancer herb with multiple components, and involvement of multiple target genes and signaling pathways. ACP can significantly inhibit proliferation and induce apoptosis of colon cancer cells, which may be closely related to the regulation of PI3K/AKT/GSK3B signal transduction.

Selective excitation of four-wave mixing by helicity in gated graphene.

Gapless Dirac fermions in monolayer graphene give rise to an abundance of peculiar physical properties, including exceptional broadband nonlinear optical responses. By tuning the chemical potential, stacking order, and photonic structures, the effective modulation of nonlinear optical phenomena in graphene has been demonstrated in recent years. Here, we demonstrate that optical helicity can be used as an extra tuning knob for four-wave mixing in gated graphene. Our results reveal the helicity selection rule for four-wave mixing in monolayer graphene, revealing nearly perfect circular polarization. Corresponding theoretical interpretations of the helicity selection rule that are also applicable to other nonlinear optical processes and materials are presented.

Probing the Chiral Domains and Excitonic States in Individual WS2 Tubes by Second-Harmonic Generation.

Distinct from carbon nanotubes, transition-metal dichalcogenide (TMD) nanotubes are noncentrosymmetric and polar and can exhibit some intriguing phenomena such as nonreciprocal superconductivity, chiral shift current, bulk photovoltaic effect, and exciton-polaritons. However, basic characterizations of individual TMD nanotubes are still quite limited, and much remains unclear about their structural chirality and electronic properties. Here we report an optical second-harmonic generation (SHG) study on multiwalled WS2 nanotubes on a single-tube level. As it is highly sensitive to the crystallographic symmetry, SHG microscopy unveiled multiple structural domains within a single WS2 nanotube, which are otherwise hidden under conventional white-light optical microscopy. Moreover, the polarization-resolved SHG anisotropy patterns revealed that different domains on the same tube can be of different chirality. In addition, we observed the excitonic states of individual WS2 nanotubes via SHG excitation spectroscopy, which were otherwise difficult to acquire due to the indirect band gap of the material.

One-step duplex RT-droplet digital PCR assay for the detection of norovirus GI and GII in lettuce and strawberry.

The study was designed to develop a sensitive one-step duplex reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) to detect norovirus genogroup I and II (NoV GI and GII) in lettuce and strawberry. The specificity, sensitivity, repeatability and robustness of the assay was compared with RT-qPCR. The lowest concentration detected by RT-ddPCR for NoV GI and NoV GII were 4.68 and 8.47 copies/µL respectively, much lower than that of RT-qPCR with a number of 46.8 and 84.7 copies/µL, respectively. Lettuce and strawberry samples were artificially contaminated with NoV GI and GII suspensions, with inoculum size of 3.00 × 106 to 1.70 × 108 copies and 4.80 × 105 to 2.50 × 107 copies, respectively. Strawberry spiked with low inoculum size revealed positive results by RT-ddPCR, while recorded negative by RT-qPCR. Meanwhile, RT-ddPCR also showed a higher average recovery rate for NoV in lettuce and strawberry than RT-qPCR.The limit of detection (LoDs) of RT-ddPCR for NoVs in lettuce was 2.32 × 104 copies/25g (NoV GI) and 2.36 × 104 ciopies/25g (NoV GII), and that in strawberry was 2.56 × 104 copies/25g (NoV GI) and 2.64 × 104 ciopies/25g (NoV GII), which were 10 folds lower than that of RT-qPCR. The developed duplex RT-ddPCR assay exhibited stability and increased capacity to resist inhibitors in food samples with low concentration of NoV, making it a reliable method to avoid false negative result as opposed to RT-qPCR. In conclusion, one-step RT-ddPCR method developed in this study is pertinent in detecting foodborne virus such as NoV.

Hybrid nanostructured plasmonic electrodes for flexible organic light-emitting diodes.

Improved performance in flexible organic light-emitting diodes (OLEDs) is demonstrated by using a hybrid nanostructured plasmonic electrode consisting of silver nanowires (AgNWs) decorated with silver nanoparticles (AgNPs) and covered by exfoliated graphene sheets. Such all-solution processed electrodes show high optical transparency and electrical conductivity. When integrated in an OLED with super yellow polyphenylene vinylene as the emissive layer, the plasmon coupling of the NW-NP hybrid plasmonic system is found to significantly enhance the fluorescence, demonstrated by both simulations and photoluminescence measurements, leading to a current efficiency of 11.61 cd A-1 and a maximum luminance of 20 008 cd m-2 in OLEDs. Stress studies reveal a superior mechanical flexibility to the commercial indium-tin-oxide (ITO) counterparts, due to the incorporation of exfoliated graphene sheets. Our results show that these hybrid nanostructured plasmonic electrodes can be applied as an effective alternative to ITO for use in high-performance flexible OLEDs.

Tuning the optical nonlinearity of graphene.

Tuning of nonlinear optical responses is the essence to many photonics and optoelectronics applications. Due to the low-dimensionality and dispersion of massless Dirac Fermions, the nonlinear optical susceptibilities of graphene can be readily controlled via electrical gating. Based on the quantum interference between multi-photon transition pathways, the tuning mechanism of graphene nonlinearity is intrinsically different from most other systems. The phenomenon enables investigations into some nonlinear optical processes from fundamental regards. It also exhibits appealing features contrasting conventional materials, which can be desirable for novel device applications.

Hexagonal Boron Nitride Growth on Cu-Si Alloy: Morphologies and Large Domains.

Controllable synthesis of high-quality hexagonal boron nitride (h-BN) is desired toward the industrial application of 2D devices based on van der Waals heterostructures. Substantial efforts are devoted to synthesize h-BN on copper through chemical vapor deposition, which has been successfully applied to grow graphene. However, the progress in synthesizing h-BN has been significantly retarded, and it is still challenging to realize millimeter-scale domains and control their morphologies reliably. Here, the nucleation density of h-BN on Cu is successfully reduced by over two orders of magnitude by simply introducing a small amount of silicon, giving rise to large triangular domains with maximum 0.25 mm lateral size. Moreover, the domain morphologies can be modified from needles, tree patterns, and leaf darts to triangles through controlling the growth temperature. The presence of silicon alters the growth mechanism from attachment-limited mode to diffusion-limited mode, leading to dendrite domains that are rarely observed on pure Cu. A phase-field model is utilized to reveal the growing dynamics regarding B-N diffusion, desorption, flux, and reactivity variables, and explain the morphology evolution. The work sheds lights on the h-BN growth toward large single crystals and morphology probabilities.

Chiral selection rules for multi-photon processes in two-dimensional honeycomb materials.

We examine the chirality-dependent optical selection rules in two-dimensional monolayer materials with honeycomb lattices, and, based on symmetry argument, we generalize these rules to multi-photon transitions of arbitrary orders. We also present the phase relations between incident and outgoing photons in such processes. The results agree nicely with our experimental observations of second- and third-harmonic generation. In particular, we demonstrate that the phase relation of chiral second-harmonic generation can serve as a handy tool for imaging domains and domain boundaries of these monolayers. Our results can benefit future studies on chirality-related optical phenomena and opto-electronic applications of such materials.

Doping-Induced Second-Harmonic Generation in Centrosymmetric Graphene from Quadrupole Response.

For centrosymmetric materials such as monolayer graphene, no optical second-harmonic generation (SHG) is generally expected, because it is forbidden under the electric-dipole approximation. Yet we observe a strong, doping-induced SHG from graphene, with its highest strength comparable to the electric-dipole-allowed SHG in noncentrosymmetric 2D materials. This novel SHG has the nature of an electric-quadrupole response, arising from the effective breaking of inversion symmetry by optical dressing with an in-plane photon wave vector. More remarkably, the SHG is widely tuned by carrier doping or chemical potential, being sharply enhanced at Fermi-edge resonances but vanishing at the charge neutral point that manifests the electron-hole symmetry of massless Dirac fermions. This striking behavior in graphene, which should also arise in graphenelike Dirac materials, expands the scope of nonlinear optics and holds the promise of novel optoelectronic and photonic applications.

A phosphorescent probe for cephalexin consisting of mesoporous thioglycolic acid-modified Mn:ZnS quantum dots coated with a molecularly imprinted polymer.

The authors have synthesized a phosphorescent probe of type SiO2-QD-MIP, where QD stands for Mn:ZnS quantum dots and MIP is a polymer coating that was molecularly imprinted with cephalexin. The nanoprobe with high specificity was prepared via sol-gel polymerization using thioglycolic acid (TGA)-modified QDs as luminescent materials, cephalexin as the template, 3-aminopropyltriethoxysilane as the functional monomer, and tetraethoxysilane as the crosslinking agent. The SiO2-QD-MIPs were characterized by X-ray powder diffraction, transmission electron microscopy, scanning electron microscopy, and Fourier transform infrared spectrometry. The orange emission of the probe, with excitation/emission maxima at 295/590 nm, decreases linearly in the 2.5-50 µg·L-1 cephalexin concentration range with a limit of detection (LOD) of 0.81 µg·L-1. The nanoprobe was successfully applied to the determination of cephalexin in (spiked) raw milk and milk powder. The recoveries ranged from 91.7 to 103.7%.

Probing Phonon Dynamics in Individual Single-Walled Carbon Nanotubes.

Interactions between elementary excitations, such as carriers, phonons, and plasmons, are critical for understanding the optical and electronic properties of materials. The significance of these interactions is more prominent in low-dimensional materials and can dominate their physical properties due to the enhanced interactions between these excitations. One-dimensional single-walled carbon nanotubes provide an ideal system for studying such interactions due to their perfect physical structures and rich electronic properties. Here we investigated G-mode phonon dynamics in individual suspended chirality-resolved single-walled carbon nanotubes by time-resolved anti-Stokes Raman spectroscopy. The improved technique allowed us to probe the intrinsic phonon information on a single-tube level and exclude the influences of tube-tube and tube-substrate interactions. We found that the G-mode phonon lifetime ranges from 0.75-2.25 ps and critically depends on whether the tube is metallic or semiconducting. In comparison with the phonon lifetimes in graphene and graphite, we revealed structure-dependent carrier-phonon and phonon-phonon interactions in nanotubes. Our results provide new information for optimizing the design of nanotube electronic/optoelectronic devices by better understanding and utilizing their phonon decay channels.

Gate Switching of Ultrafast Photoluminescence in Graphene.

The control of optical properties by electric means is the key to optoelectronic applications. For atomically thin two-dimensional (2D) materials, the natural advantage lies in that the carrier doping could be readily controlled through the electric gating effect, possibly affecting the optical properties. Exploiting this advantage, here we report the gate switching of the ultrafast upconverted photoluminescence from monolayer graphene. The luminescence can be completely switched off by the Pauli-blocking of one-photon interband transition in graphene with an on/off ratio exceeding 100, which is remarkable compared to other 2D semiconductors and 3D bulk counterparts. The chemical potential and pump fluence dependences of the luminescence are nicely described by a two-temperature model, including both the hot carrier dynamics and carrier-optical phonon interaction. This gate switchable and background-free photoluminescence can open up new opportunities for graphene-based ultrafast optoelectronic applications.

High-Performance Wafer-Scale MoS2 Transistors toward Practical Application.

Atomic thin transition-metal dichalcogenides (TMDs) are considered as an emerging platform to build next-generation semiconductor devices. However, to date most devices are still based on exfoliated TMD sheets on a micrometer scale. Here, a novel chemical vapor deposition synthesis strategy by introducing multilayer (ML) MoS2 islands to improve device performance is proposed. A four-probe method is applied to confirm that the contact resistance decreases by one order of magnitude, which can be attributed to a conformal contact by the extra amount of exposed edges from the ML-MoS2 islands. Based on such continuous MoS2 films synthesized on a 2 in. insulating substrate, a top-gated field effect transistor (FET) array is fabricated to explore key metrics such as threshold voltage (V T ) and field effect mobility (µFE ) for hundreds of MoS2 FETs. The statistical results exhibit a surprisingly low variability of these parameters. An average effective µFE of 70 cm2 V-1 s-1 and subthreshold swing of about 150 mV dec-1 are extracted from these MoS2 FETs, which are comparable to the best top-gated MoS2 FETs achieved by mechanical exfoliation. The result is a key step toward scaling 2D-TMDs into functional systems and paves the way for the future development of 2D-TMDs integrated circuits.