Arbitrarily Configurable Nonlinear Topological Modes.

Topological modes (TMs) are typically localized at boundaries, interfaces and dislocations, and exponentially decay into the bulk of a large enough lattice. Recently, the non-Hermitian skin effect has been leveraged to delocalize the wave functions of TMs from the boundary and thus to increase the capacity of TMs dramatically. Here, we explore the capability of nonlinearity in designing and configuring the wave functions of TMs. With growing intensity, wave functions of these in-gap nonlinear TMs undergo an initial deviation from exponential decay, gradually merge into arbitrarily designable plateaus, then encompass the entire nonlinear domain, and eventually concentrate at the nonlinear boundary. Intriguingly, such extended nonlinear TMs are still robust against defects and disorders, and stable in dynamics under external excitation. Advancing the conceptual understanding of the nonlinear TMs, our results open new avenues for increasing the capacity of TMs and developing compact and configurable topological devices.

[Establishment and optimization of Agrobacterium tumefaciens-mediated genetic transformation system for Polyporus umbellatus].

The unstable quality of Polyporus umbellatus sclerotia during cultivation is the key factor affecting the quality and yield of P. umbellatus sclerotia. In order to provide technical support for obtaining superior P. umbellatus by molecular breeding, the genetic transformation system mediated by Agrobacterium tumefaciens was studied in this paper. A. tumefaciens-mediated method was used to investigate the effects of antibiotic concentration, strain type, A. tumefaciens concentration, receptor material, infection time, co-culture time, and screening conditions on the genetic transformation efficiency of P. umbellatus. The transformants were screened and detected by hygromycin resistance marker genes, polymerase chain reaction(PCR) of specific primers, and fluorescence detection methods. The results showed that the A. tumefaciens GV3101 strain could genetically transfer P. umbellatus mycelium cells, and the optimal conditions for infection were as follows: the A. tumefaciens concentration A_(600 nm)= 0.6, P. umbellatus mycelium cells as receptor material, infection time of 30 min, and co-culture time of 3 days. The two-step screening method involving hygromycin of 9 and 13 µg·mL~(-1 )was the best screening condition. The results of hygromycin resistance screening, PCR detection of specific primers, and fluorescence detection showed that the exogenous gene eGFP had been transferred into the P. umbellatus mycelium cells, integrated into the genome, and successfully expressed. Under optimal conditions, the conversion efficiency could be increased to 2.3%, and the genetic transformation period was shortened from more than 90 days to less than 60 days. This study established and optimized the genetic transformation system of P. umbellatus mycelium cells mediated by A. tumefaciens, laying a foundation for the analysis of the molecular mechanism of P. umbellatus during growth and molecular breeding.

[Effects of soil relative water content on growth characteristics of Armillaria spp. and seedling production of Gastrodia elata f. glauca].

The seedling survival rate, yield, and individual weight of Gastrodia elata is closely related to the soil relative water content(RWC) and the growth characteristics of the associated fungi Armillaria spp. This study explored the effects of the soil RWC on the growth characteristics of Armillaria spp. and the seedling production of G. elata f. glauca, aiming to provide guidance for breeding G. elata f. glauca and selecting elite strains of Armillaria. According to the growth characteristics on the medium for activation, thirty strains of Armillaria were classified into 4 clusters. Two strains with good growth indicators were selected from each cluster and cultiva-ted with immature tuber(Mima) and the branches of the broad-leaved trees in a water-controlled box. The results showed that the Armillaria clusters with uniaxial branches of rhizoid cords, such as clusters Ⅲ and Ⅳ, were excellent clusters in symbiosis with G. elata f. glauca. The soil RWC had significant effects on the growth characteristics of Armillaria strains and the seedling survival rate, yield, and individual weight of G. elata f. glauca. The growth characteristics of Armillaria strains and the seedling survival rate, yield, and individual weight of G. elata f. glauca in the case of the soil RWC being 75% were significantly better than those in the case of other soil RWC. Cultivating Mima with elite strains of Armillaria, together with branches of broad-leaved trees, in the greenhouses with the artificial control of the soil RWC, can achieve efficient seedling production and Mima utilization of G. elata f. glauca.

Observation of Nonlinear Exceptional Points with a Complete Basis in Dynamics.

The exotic physics associated with exceptional points (EPs) is always under the scrutiny of theoretical and experimental science. Recently, considerable effort has been invested in the combination of nonlinearity and non-Hermiticity. The concept of nonlinear EPs (NEPs) has been introduced, which can avoid the loss of completeness of the eigenbasis in dynamics while retaining the key features of linear EPs. Here, we present the first direct experimental demonstration of a NEP based on two non-Hermition coupled circuit resonators combined with a nonlinear saturable gain. At the NEP, the response of the eigenfrequency to perturbations demonstrates a third-order root law and the eigenbasis of the Hamiltonian governing the system dynamics is still complete. Our results bring this counterintuitive aspect of the NEP to light and possibly open new avenues for applications.

Nonlinear Exceptional Points with a Complete Basis in Dynamics.

Exceptional points (EPs) are special spectral singularities at which two or more eigenvalues, and their corresponding eigenvectors, coalesce and become identical. In conventional wisdom, the coalescence of eigenvectors inevitably leads to the loss of completeness of the eigenbasis. Here, we show that this scenario breaks down in general at nonlinear EPs (NEPs). As an example, we realize a fifth-order NEP (NEP_{5}) within only three coupled resonators with both a theoretical model and simulations in circuits. One stable and another four auxiliary steady eigenstates of the nonlinear Hamiltonian coalesce at the NEP_{5}, and the response of eigenfrequency to perturbations demonstrates a fifth-order root law. Intriguingly, the biorthogonal eigenbasis of the Hamiltonian governing the system dynamics is still complete, and this fact is corroborated by a finite Petermann factor instead of a divergent one at conventional EPs. Consequently, the amplification of noise, which diverges at other EPs, converges at our NEP_{5}. Our finding transforms the understanding of EPs and shows potential for miniaturizing various key applications operating near EPs.

[Cloning and gene function of dicarboxylate-tricarboxylate carrier protein in Gastrodia elata].

The gene GeDTC encoding the dicarboxylate-tricarboxylate carrier protein in Gastrodia elata was cloned by specific primers which were designed based on the transcriptome data of G. elata. Bioinformatics analysis on GeDTC gene was carried out by using ExPASY, ClustalW, MEGA, etc. Positive transgenic plants and potato minituber were obtained by virtue of the potato genetic transformation system. Agronomic characters, such as size, weight, organic acid content, and starch content, of potato minituber were tested and analyzed and GeDTC gene function was preliminarily investigated. The results showed that the open reading frame of GeDTC gene was 981 bp in length and 326 amino acid residues were encoded, with a relative molecular weight of 35.01 kDa. It was predicted that the theoretical isoelectric point of GeDTC protein was 9.83, the instability coefficient was 27.88, and the average index of hydrophilicity was 0.104, which was indicative of a stable hydrophilic protein. GeDTC protein had a transmembrane structure and no signal peptide and was located in the inner membrane of mitochondria. The phylogenetic tree showed that GeDTC was highly homologous with DTC proteins of other plant species, among which GeDTC had the highest homology with DcDTC(XP＿020675804.1) in Dendrobium candidum, reaching 85.89%. GeDTC overexpression vector pCambia1300-35Spro-GeDTC was constructed by double digests, and transgenic potato plants were obtained by Agrobacterium-mediated gene transformation. Compared with the wild-type plants, transgenic potato minituber harvested by transplanting had smaller size, lighter weight, lower organic acid content, and no significant difference in starch content. It is preliminarily induced that GeDTC is the efflux channel of tricarboxylate and related to the tuber development, which lays a foundation for further elucidating the molecular mechanism of G. elata tuber development.

[Application of strigolactone analogs in storage of Gastrodia elata].

This study explored the preservation effect of strigolactone analogs on Gastrodia elata tubers and screened out the suitable preservation measures of G. elata to provide a safer and more effective method for its storage and preservation. Fresh G. elata tubers were treated with 7FGR24, 2,4-D isooctyl ester, and maleic hydrazide, respectively. The growth of flower buds, the activities of CAT, and MDA, and the content of gastrodin and p-hydroxybenzyl alcohol were measured to compare the effects of different compounds on the storage and preservation of G. elata. The effects of different storage temperatures on the preservation of 7FGR24 were compared and analyzed. The gibberellin signal transduction receptor gene GeGID1 was cloned, and the effect of 7FGR24 on the expression level of GeGID1 was analyzed by quantitative polymerase chain reaction(qPCR). The toxicity of the G. elata preservative 7FGR24 was analyzed by intragastric administration in mice to evaluate its safety. The results showed that compared with 2,4-D isooctyl ester and maleic hydrazide, 7FGR24 treatment had a significant inhibitory effect on the growth of G. elata flower buds, and the CAT enzyme activity of G. elata was the highest, indicating that its preservation effect was stronger. Different storage temperatures had different effects on the preservation of G. elata, and the preservation effect was the strongest at 5 ℃. The open reading frame(ORF) of GeGID1 gene was 936 bp in length, and its expression level was significantly down-regulated after 7FGR24 treatment, indicating that 7FGR24 may inhibit the growth of flower buds by inhibiting the gibberellin signal of G. elata, thereby exerting a fresh-keeping effect. Feeding preservative 7FGR24 had no significant effect on the behavior and physiology of mice, indicating that it had no obvious toxicity. This study explored the application of the strigolactone analog 7FGR24 in the storage and preservation of G. elata and preliminarily established a method for the storage and preservation of G. elata, laying a foundation for the molecular mechanism of 7FGR24 in the storage and preservation of G. elata.

Nonlinearity-enabled higher-order exceptional singularities with ultra-enhanced signal-to-noise ratio.

Higher-order exceptional points (HOEPs) with extraordinary responsivity are expected to exhibit a vastly improved performance in detection-related applications. However, over the past few years, such an approach has been questioned due to several potential drawbacks, including the stringent parameter requirements, fundamental resolution limits and noise. Here, exploring the consequence of nonlinear gain saturation in exceptional singularities of non-Hermitian systems, we offer a feasible scheme to overcome all the above difficulties. We provide a simple and intuitive example by demonstrating with both theory and circuit experiments an 'exceptional nexus' ('EX'), a HOEP with an ultra-enhanced signal-to-noise ratio (SNR), in only two coupled resonators with the aid of nonlinear gain. The tedious parameter tuning in a six-dimensional hyper-dimensional space is reduced to two dimensions. The feedback mechanism of nonlinear saturable gain can give a solution to the ongoing debate on the SNR of EPs in other linear systems. Our findings advance the fundamental understanding of the peculiar topology of nonlinear non-Hermitian systems, significantly reduce the practical difficulty in EP sensing and possibly open new avenues for applications.

[Screening of an Armillaria gallica strain for Gastrodia elata cultivation].

This study aims to screen a strain from Armillaria for the cultivation of Gastrodia elata. Specifically, Armillaria strains were isolated from different producing areas of G. elata and identified. Based on the growth characteristics of the strains and the experiment on the cultivation of G. elata, an optimal A. gallica strain was screened out. The specific process is as follows. The fungus-gro-wing materials of G. elata were collected from four producing areas and the Armillaria strains were isolated(G,Y,S,H). The strains were then identified based on morphological observation and phylogeny analysis and the commonly used strains were determined. The sucrase genotypes of the strains were identified according to our previous research findings, and the growth characteristics of the strains, such as growth rate, diameter, dry weight, and polysaccharide content of the rhizomorphs, were measured. According to the biological characteristics and sucrase genotypes, two strains were selected for the cultivation of G. elata. The tuber yield and the content of gastrodin and p-hydroxybenzyl alcohol in the tuber of G. elata were measured to select the optimal strain. The results showed that the four strains were all A. gallica. The rhizomorphs of strains G and H of the same sucrase genotype had larger/higher length, growth rate, diameter, branch number, dry weight, and polysaccharide content than those of strains S and Y of the same sucrase genotype. The tuber yield and the total content of gastrodin and p-hydroxybenzyl alcohol in tuber of G. elata cultivated with strain H were 6.528 kg·m~(-2) and 0.566%, respectively, which were 4.58 and 1.30 folds those of G. elata cultivated with strain S. Strains H and S were screened out from four strains of A. gallica based on the growth characteristics and sucrase genotype. According to the tuber yield and content of total gastrodin and p-hydroxybenzyl alcohol in the tuber of G. elata, strain H was identified as the optimal one. The findings in this study are expected to lay a basis for cultivating G. elata with high yield and quality of tubers.

PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment.

With advances in synthetic biology and genome engineering comes a heightened awareness of potential misuse related to biosafety concerns. A recent study employed machine learning to identify the lab-of-origin of DNA sequences to help mitigate some of these concerns. Despite their promising results, this deep learning based approach had limited accuracy, was computationally expensive to train, and wasn't able to provide the precise features that were used in its predictions. To address these shortcomings, we developed PlasmidHawk for lab-of-origin prediction. Compared to a machine learning approach, PlasmidHawk has higher prediction accuracy; PlasmidHawk can successfully predict unknown sequences' depositing labs 76% of the time and 85% of the time the correct lab is in the top 10 candidates. In addition, PlasmidHawk can precisely single out the signature sub-sequences that are responsible for the lab-of-origin detection. In summary, PlasmidHawk represents an explainable and accurate tool for lab-of-origin prediction of synthetic plasmid sequences. PlasmidHawk is available at https://gitlab.com/treangenlab/plasmidhawk.git .

[Identification of four Armillaria strains and their effects on quality and yield of Gastrodia elata f. glauca].

In order to improve the quality and yield of Gastrodia elata f. glauca,determine the suitable Armillaria strains for the accompanying experiment in Xiaocaoba,Yiliang,four Armillaria strains were selected. They were used for G. elata cultivation,and the gene sequence,r DNA-ITS,ß-tubulin and EF1-α of four Armillaria strains,were compared and analyzed. The yield was mesured in November which was based on previous laboratory research. The tubers were washed and steamed,then dried and powdered. The content of gastrodin and p-hydroxybenzyl alcohol was determined by UPLC,the polysaccharide was determined by phenol-concentrated sulfuric acid method. The results showed that the strains M1,M2,M3 and M4 were Armillaria gallica group but there were differences in the yield and active ingredient content when they were cultivated with the same G. elata. The yield of G. elata( Jian Ma) was the lowest when cultivated with Armillaria strain M3,but it was not the same when used M1,0. 981 kg·m-2,the highest yield in the four stains.The content of gastrodin was 0. 581%,the total content of gastrodin and p-hydroxybenzyl alcohol was 0. 595%,when accompanied with M1 strains. It was higher than other strains. The content of G. elata polysaccharide was 2. 132%,which was similar to the content of M3 strain,higher than that of M2 and M4 strain. Selecting phylogenesis of Armillaria strians,the content of active ingredient,and the yield as indicators,it was concluded concerned that the M1 strain was the best of four strains. The results will provide a theoretical basis and guidance for higher yield and quality in cultivation of G. elata in Yiliang.

Fast image interpolation via random forests.

This paper proposes a two-stage framework for fast image interpolation via random forests (FIRF). The proposed FIRF method gives high accuracy, as well as requires low computation. The underlying idea of this proposed work is to apply random forests to classify the natural image patch space into numerous subspaces and learn a linear regression model for each subspace to map the low-resolution image patch to high-resolution image patch. The FIRF framework consists of two stages. Stage 1 of the framework removes most of the ringing and aliasing artifacts in the initial bicubic interpolated image, while Stage 2 further refines the Stage 1 interpolated image. By varying the number of decision trees in the random forests and the number of stages applied, the proposed FIRF method can realize computationally scalable image interpolation. Extensive experimental results show that the proposed FIRF(3, 2) method achieves more than 0.3 dB improvement in peak signal-to-noise ratio over the state-of-the-art nonlocal autoregressive modeling (NARM) method. Moreover, the proposed FIRF(1, 1) obtains similar or better results as NARM while only takes its 0.3% computational time.