A Lateral Flow-Recombinase Polymerase Amplification Method for Colletotrichum gloeosporioides Detection.

The greater yam (Dioscorea alata), a widely cultivated and nutritious food crop, suffers from widespread yield reduction due to anthracnose caused by Colletotrichum gloeosporioides. Latent infection often occurs before anthracnose phenotypes can be detected, making early prevention difficult and causing significant harm to agricultural production. Through comparative genomic analysis of 60 genomes of 38 species from the Colletotrichum genus, this study identified 17 orthologous gene groups (orthogroups) that were shared by all investigated C. gloeosporioides strains but absent from all other Colletotrichum species. Four of the 17 C. gloeosporioides-specific orthogroups were used as molecular markers for PCR primer designation and C. gloeosporioides detection. All of them can specifically detect C. gloeosporioides out of microbes within and beyond the Colletotrichum genus with different sensitivities. To establish a rapid, portable, and operable anthracnose diagnostic method suitable for field use, specific recombinase polymerase amplification (RPA) primer probe combinations were designed, and a lateral flow (LF)-RPA detection kit for C. gloeosporioides was developed, with the sensitivity reaching the picogram (pg) level. In conclusion, this study identified C. gloeosporioides-specific molecular markers and developed an efficient method for C. gloeosporioides detection, which can be applied to the prevention and control of yam anthracnose as well as anthracnose caused by C. gloeosporioides in other crops. The strategy adopted by this study also serves as a reference for the identification of molecular markers and diagnosis of other plant pathogens.

Sticky Links: Encoding Quantitative Data of Graph Edges.

Visually encoding quantitative information associated with graph links is an important problem in graph visualization. A conventional approach is to vary the thickness of lines to encode the strength of connections in node-link diagrams. In this paper, we present Sticky Links, a novel visual encoding method that draws graph links with stickiness. Taking the metaphor of links with glues, sticky links represent connection strength using spiky shapes, ranging from two broken spikes for weak connections to connected lines for strong connections. We conducted a controlled user study to compare the efficiency and aesthetic appeal of stickiness with conventional thickness encoding. Our results show that stickiness enables more effective and expressive quantitative encoding while maintaining the perception of node connectivity. Participants also found sticky links to be more aesthetic and less visually cluttering than conventional thickness encoding. Overall, our findings suggest that sticky links offer a promising alternative to conventional methods for encoding quantitative information in graphs.

Puerarin attenuates remifentanil­induced postoperative hyperalgesia via targeting PAX6 to regulate the transcription of TRPV1.

Remifentanil­induced hyperalgesia (RIH) is characterized by the emergence of stimulation­induced pain, including phenomena such as allodynia and thermal hyperalgesia following remifentanil infusion. As a sequence­specific DNA binding transcription factor, PAX6 positively and negatively regulates transcription and is expressed in multiple cell types in the developing and adult central nervous system. It was hypothesized that puerarin could relieve RIH via targeting PAX6 to regulate transcription of transient receptor potential cation channel subfamily V Member 1 (TRPV1). A total of 32 rats were randomly divided into five groups, namely control group, RI group, RI + 10 mg/kg puerarin group (RI + puerarin10), RI + 20 mg/kg puerarin group (RI + puerarin20), and RI + 40 mg/kg puerarin group (RI + puerarin40). Mechanical and thermal hyperalgesia were tested at ­24, 2, 6, 24 and 48 h after remifentanil infusion. Following the sacrifice of rats after the last behavioral test, western blot was used to detect the expression levels of TRPV1 in the tissues; Immunofluorescence staining and western blotting were used to detect the expression of PAX6 in the spinal cord. PharmMapper and JASPAR were used to predict the binding sites of puerarin/PAX6/TRPV1. Chromatin immunoprecipitation­PCR and dual luciferase reporter assay were used to verify the targeting relationship between PAX6 and TRPV1. Immunofluorescence was used to detect the expression levels of TRPV1 and p­NR2B. The results revealed that puerarin (10, 20, 40 mg/kg) dose­dependently reduced thermal and mechanical hyperalgesia from 2 to 48 h after remifentanil infusion. Remifentanil infusion remarkably stimulated the expression of phosphorylated (p­)NR2B. Nevertheless, the increased amount of p­NR2B by RIH was dose­dependently suppressed by puerarin in rats. In conclusion, puerarin was revealed to attenuate postoperative RIH via targeting PAX6 to regulate the transcription of TRPV1.

Low-coverage whole genome sequencing of diverse Dioscorea bulbifera accessions for plastome resource development, polymorphic nuclear SSR identification, and phylogenetic analyses.

Dioscorea bulbifera (Dioscoreaceae), a versatile herbaceous climber native to Africa and Asia, holds significant nutritional and medicinal value. Despite extensive characterization and genetic variability analyses of African accessions, studies on the genetic variation of this species in China are limited. To address this gap, we conducted low-coverage whole genome sequencing on D. bulbifera accessions from diverse regions across mainland China and Taiwan island. Our initial investigation encompassed comprehensive comparative plastome analyses of these D. bulbifera accessions, and developing plastome resources (including plastome-derived repetitive sequences, SSRs, and divergent hotspots). We also explored polymorphic nuclear SSRs and elucidated the intraspecific phylogeny of these accessions. Comparative plastome analyses revealed that D. bulbifera plastomes exhibited a conserved quadripartite structure with minimal size variation mainly attributed to intergenic spacer regions, reinforcing prior observations of a high degree of conservation within a species. We identified 46 to 52 dispersed repeats and 151 to 163 plastome-derived SSRs, as well as highlighted eight key divergent hotspots in these D. bulbifera accessions. Furthermore, we developed 2731 high-quality candidate polymorphic nuclear SSRs for D. bulbifera. Intraspecific phylogenetic analysis revealed three distinct clades, where accessions from Southeast China formed a sister group to those from South China and Taiwan island, and collectively, these two clades formed a sister group to the remaining accessions, indicating potential regional genetic divergence. These findings not only contributed to the understanding of the genetic variation of D. bulbifera, but also offered valuable resources for future research, breeding efforts, and utilization of this economically important plant species.

Unraveling the Molecular Basis of Color Variation in Dioscorea alata Tubers: Integrated Transcriptome and Metabolomics Analysis.

Dioscorea alata L. (Dioscoreaceae) is a widely cultivated tuber crop with variations in tuber color, offering potential value as health-promoting foods. This study focused on the comparison of D. alata tubers possessing two distinct colors, white and purple, to explore the underlying mechanisms of color variation. Flavonoids, a group of polyphenols known to influence plant color and exhibit antioxidant properties, were of particular interest. The total phenol and total flavonoid analyses revealed that purple tubers (PTs) have a significantly higher content of these metabolites than white tubers (WTs) and a higher antioxidant activity than WTs, suggesting potential health benefits of PT D. alata. The transcriptome analysis identified 108 differentially expressed genes associated with the flavonoid synthesis pathway, with 57 genes up-regulated in PTs, including CHS, CHI, DFR, FLS, F3H, F3'5'H, LAR, ANS, and ANR. The metabolomics analysis demonstrated that 424 metabolites, including 104 flavonoids and 8 tannins, accumulated differentially in PTs and WTs. Notably, five of the top ten up-regulated metabolites were flavonoids, including 6-hydroxykaempferol-7-O-glucoside, pinocembrin-7-O-(6″-O-malonyl)glucoside, 6-hydroxykaempferol-3,7,6-O-triglycoside, 6-hydroxykaempferol-7-O-triglycoside, and cyanidin-3-O-(6″-O-feruloyl)sophoroside-5-O-glucoside, with the latter being a precursor to anthocyanin synthesis. Integrating transcriptome and metabolomics data revealed that the 57 genes regulated 20 metabolites within the flavonoid synthesis pathway, potentially influencing the tubers' color variation. The high polyphenol content and antioxidant activity of PTs indicate their suitability as nutritious and health-promoting food sources. Taken together, the findings of this study provide insights into the molecular basis of tuber color variation in D. alata and underscore the potential applications of purple tubers in the food industry and human health promotion. The findings contribute to the understanding of flavonoid biosynthesis and pigment accumulation in D. alata tubers, opening avenues for future research on enhancing the nutritional quality of D. alata cultivars.

Effects of temperature-related changes on charred bone in soil: From P release to microbial community.

Phosphorus (P) is one of the most common limited nutrients in terrestrial ecosystems. Animal bones, with abundant bioapatite, are considerable P sources in terrestrial ecosystems. Heating significantly promotes P release from bone bioapatite, which may alleviate P limitation in soil. This study aimed to explore P release from charred bone (CB) under heating at various temperatures (based on common natural heating). It showed that heating at ∼300 °C significantly increased the P release (up to ∼30 mg/kg) from CB compared with other heating temperatures. Then, the subsequent changes of available P and pH induced evident alternation of soil microbial community composition. For instance, CB heated at ∼300 °C caused elevation of phosphate-solubilizing fungi (PSF) abundance. This further stimulated P mobility in the soil. Meanwhile, the fungal community assembly process was shifted from stochastic to deterministic, whereas the bacterial community was relatively stable. This indicated that the bacterial community showed fewer sensitive responses to the CB addition. This study hence elucidated the significant contribution of heated bone materials on P supply. Moreover, functional fungi might assist CB treated by natural heating (e.g., fire) to construct P "Hot Spots".

Features of MR signals of retroplacental basal decidual space and its diagnostic significance.

BACKGROUND: With more pregnant women undergoing cesarean section, the number of women with scarring in the uterus undergoing uterine magnetic resonance (MR) examination in the second and third trimesters following a subsequent pregnancy, has increased. OBJECTIVE: To investigate features of MR signals in retroplacental basal decidual space. METHODS: The MR imaging data of patients with clinically and pathologically confirmed placenta implantation and complete placental abruption were retrospectively analyzed. RESULTS: Patients with high-intensity signals in T2-weighted images (T2WI) of the retroplacental basal decidual space did not suffer placenta implantation after delivery, while high-intensity signals in T2WI of the retroplacental basal decidual space was not observed in patients with different degrees of placenta implantation. CONCLUSION: As the retroplacental basal decidual space is the barrier between the placenta and myometrium, high-intensity signals in T2WI can improve the confidence of MR exclusion diagnostics of placenta implantation, and can be used as exclusion criteria for MR diagnosis of placenta implantation.

Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data.

Dioscorea nipponica Makino, a perennial twining herb with medicinal importance, has a disjunctive distribution in the Sino-Japanese Floristic Region. It has a long history in traditional Chinese medicine, with demonstrated efficacy against various health conditions. However, the limited genomic data and knowledge of genetic variation have hindered its comprehensive exploration, utilization and conservation. In this study, we undertook low-coverage whole genome sequencing of diverse D. nipponica accessions to develop both plastome (including whole plastome sequences, plastome-derived SSRs and plastome-divergent hotspots) and nuclear genomic resources (including polymorphic nuclear SSRs and single-copy nuclear genes), as well as elucidate the intraspecific phylogeny of this species. Our research revealed 639 plastome-derived SSRs and highlighted six key mutational hotspots (namely CDS ycf1, IGS trnL-rpl32, IGS trnE-trnT, IGS rps16-trnQ, Intron 1 of clpP, and Intron trnG) within these accessions. Besides, three IGS regions (i.e., ndhD-cssA, trnL-rpl32, trnD-trnY), and the intron rps16 were identified as potential markers for distinguishing D. nipponica from its closely related species. In parallel, we successfully developed 988 high-quality candidate polymorphic nuclear SSRs and identified 17 single-copy nuclear genes for D. nipponica, all of which empower us to conduct in-depth investigations into phylogenetics and population genetics of this species. Although our phylogenetic analyses, based on plastome sequences and single-copy nuclear genes revealed cytonuclear discordance within D. nipponica, both findings challenged the current subspecies classification. In summary, this study developed a wealth of genomic resources for D. nipponica and enhanced our understanding of the intraspecific phylogeny of this species, offering valuable insights that can be instrumental in the conservation and strategic utilization of this economically significant plant.

Predictive model for epileptogenic tubers from all tubers in patients with tuberous sclerosis complex based on 18F-FDG PET: an 8-year single-centre study.

BACKGROUND: More than half of patients with tuberous sclerosis complex (TSC) suffer from drug-resistant epilepsy (DRE), and resection surgery is the most effective way to control intractable epilepsy. Precise preoperative localization of epileptogenic tubers among all cortical tubers determines the surgical outcomes and patient prognosis. Models for preoperatively predicting epileptogenic tubers using 18F-FDG PET images are still lacking, however. We developed noninvasive predictive models for clinicians to predict the epileptogenic tubers and the outcome (seizure freedom or no seizure freedom) of cortical tubers based on 18F-FDG PET images. METHODS: Forty-three consecutive TSC patients with DRE were enrolled, and 235 cortical tubers were selected as the training set. Quantitative indices of cortical tubers on 18F-FDG PET were extracted, and logistic regression analysis was performed to select those with the most important predictive capacity. Machine learning models, including logistic regression (LR), linear discriminant analysis (LDA), and artificial neural network (ANN) models, were established based on the selected predictive indices to identify epileptogenic tubers from multiple cortical tubers. A discriminating nomogram was constructed and found to be clinically practical according to decision curve analysis (DCA) and clinical impact curve (CIC). Furthermore, testing sets were created based on new PET images of 32 tubers from 7 patients, and follow-up outcome data from the cortical tubers were collected 1, 3, and 5 years after the operation to verify the reliability of the predictive model. The predictive performance was determined by using receiver operating characteristic (ROC) analysis. RESULTS: PET quantitative indices including SUVmean, SUVmax, volume, total lesion glycolysis (TLG), third quartile, upper adjacent and standard added metabolism activity (SAM) were associated with the epileptogenic tubers. The SUVmean, SUVmax, volume and TLG values were different between epileptogenic and non-epileptogenic tubers and were associated with the clinical characteristics of epileptogenic tubers. The LR model achieved the better performance in predicting epileptogenic tubers (AUC = 0.7706; 95% CI 0.70-0.83) than the LDA (AUC = 0.7506; 95% CI 0.68-0.82) and ANN models (AUC = 0.7425; 95% CI 0.67-0.82) and also demonstrated good calibration (Hosmer‒Lemeshow goodness-of-fit p value = 0.7). In addition, DCA and CIC confirmed the clinical utility of the nomogram constructed to predict epileptogenic tubers based on quantitative indices. Intriguingly, the LR model exhibited good performance in predicting epileptogenic tubers in the testing set (AUC = 0.8502; 95% CI 0.71-0.99) and the long-term outcomes of cortical tubers (1-year outcomes: AUC = 0.7805, 95% CI 0.71-0.85; 3-year outcomes: AUC = 0.8066, 95% CI 0.74-0.87; 5-year outcomes: AUC = 0.8172, 95% CI 0.75-0.87). CONCLUSIONS: The 18F-FDG PET image-based LR model can be used to noninvasively identify epileptogenic tubers and predict the long-term outcomes of cortical tubers in TSC patients.

The effect of gender on the clinical outcome of PD-1/PD-L1 inhibitor in advanced lung cancer patients.

BACKGROUND: Programmed death protein-1/ligand-1 (PD-1/L1) inhibitors have widely used in the treatment of lung cancer. Some literatures indicated that different gender might not have equal immune response, but no agreement have reached on the issue. Hence, we performed a systematic review and meta-analysis that examine the effect of gender on the clinical outcome of PD-1/PD-L1 inhibitor in advanced lung cancer patients. METHODS: Related database and conferences were searched. Studies that reported the relationship between gender and the overall survival (OS) or progression-free survival (PFS) of PD-1/L1 inhibitor were included. Meta-analysis was conducted to obtain pooled hazard ratios (HRs) with 95% CI. RESULTS: We included 34 studies with 11,883 lung cancer patients. Meta-analysis showed that PD-1/PD-L1 inhibitors significantly prolonged the OS (males: HR 0.71, 95%CI 0.66-0.77; females: HR 0.72, 95%CI 0.63-0.82) and PFS (males: HR 0.60, 95%CI 0.55-0.66; females: HR 0.72, 95%CI 0.62-0.84) versus chemotherapy. The clinical benefit (OS HR: 0.99; PFS HR: 0.83) was not statistically significant between males and females. In patients treated with cemiplimab, male patients had a better OS (0.53, 95%CI 0.42-0.66) and PFS (OS 1.51, 95%CI 0.80-2.82) compared with female patients, but the small number of female patients precludes us from drawing any firm conclusions in female subpopulations. CONCLUSION: The clinical benefit of PD-1/PD-L1 inhibitors was not statistically significant between males and females during the treatment of lung cancer. In the future, researchers who are designing new immunotherapy studies should ensure a larger inclusion of women in trials, to avoid erroneously extending to women results that are obtained mainly in male patients.

Low-coverage whole genome sequencing of eleven species/subspecies in Dioscorea sect. Stenophora (Dioscoreaceae): comparative plastome analyses, molecular markers development and phylogenetic inference.

Dioscorea sect. Stenophora (Dioscoreaceae) comprises about 30 species that are distributed in the temperate and subtropical regions of the Northern Hemisphere. Despite being evolutionarily "primitive" and medically valuable, genomic resources and molecular studies of this section are still scarce. Here, we conducted low-coverage whole genome sequencing of 11 Stenophora species/subspecies to retrieve their plastome information (whole plastome characteristics, plastome-divergent hotspots, plastome-derived SSRs, etc.) and polymorphic nuclear SSRs, as well as performed comparative plastome and phylogenetic analyses within this section. The plastomes of Stenophora species/subspecies ranged from 153,691 bp (D. zingiberensis) to 154,149 bp (D. biformifolia) in length, and they all contained the same 114 unique genes. All these plastomes were highly conserved in gene structure, gene order and GC content, although variations at the IR/SC borders contributed to the whole length differences among them. The number of plastome-derived SSRs among Stenophora species/subspecies varied from 74 (D. futschauensis) to 93 (D. zingiberensis), with A/T found to be the most frequent one. Seven highly variable regions and 12 polymorphic nuclear SSRs were identified in this section, thereby providing important information for further taxonomical, phylogenetic and population genetic studies. Phylogenomic analyses based on whole plastome sequences and 80 common protein coding genes strongly supported D. biformifolia and D. banzhuana constituted the successive sister species to the remaining sampled species, which could be furtherly divided into three clades. Overall, this study provided a new perspective for plastome evolution of Stenophora, and proved the role of plastome phylogenomic in improving the phylogenetic resolution in this section. These results also provided an important reference for the protection and utilization of this economically important section.

Copy number alteration features in pan-cancer homologous recombination deficiency prediction and biology.

Homologous recombination deficiency (HRD) renders cancer cells vulnerable to unrepaired double-strand breaks and is an important therapeutic target as exemplified by the clinical efficacy of poly ADP-ribose polymerase (PARP) inhibitors as well as the platinum chemotherapy drugs applied to HRD patients. However, it remains a challenge to predict HRD status precisely and economically. Copy number alteration (CNA), as a pervasive trait of human cancers, can be extracted from a variety of data sources, including whole genome sequencing (WGS), SNP array, and panel sequencing, and thus can be easily applied clinically. Here we systematically evaluate the predictive performance of various CNA features and signatures in HRD prediction and build a gradient boosting machine model (HRDCNA) for pan-cancer HRD prediction based on these CNA features. CNA features BP10MB[1] (The number of breakpoints per 10MB of DNA is 1) and SS[ > 7 & <=8] (The log10-based size of segments is greater than 7 and less than or equal to 8) are identified as the most important features in HRD prediction. HRDCNA suggests the biallelic inactivation of BRCA1, BRCA2, PALB2, RAD51C, RAD51D, and BARD1 as the major genetic basis for human HRD, and may also be applied to effectively validate the pathogenicity of BRCA1/2 variants of uncertain significance (VUS). Together, this study provides a robust tool for cost-effective HRD prediction and also demonstrates the applicability of CNA features and signatures in cancer precision medicine.

TLimmuno2: predicting MHC class II antigen immunogenicity through transfer learning.

Major histocompatibility complex (MHC) class II molecules play a pivotal role in antigen presentation and CD4+ T cell response. Accurate prediction of the immunogenicity of MHC class II-associated antigens is critical for vaccine design and cancer immunotherapies. However, current computational methods are limited by insufficient training data and algorithmic constraints, and the rules that govern which peptides are truly recognized by existing T cell receptors remain poorly understood. Here, we build a transfer learning-based, long short-term memory model named 'TLimmuno2' to predict whether epitope-MHC class II complex can elicit T cell response. Through leveraging binding affinity data, TLimmuno2 shows superior performance compared with existing models on independent validation datasets. TLimmuno2 can find real immunogenic neoantigen in real-world cancer immunotherapy data. The identification of significant MHC class II neoantigen-mediated immunoediting signal in the cancer genome atlas pan-cancer dataset further suggests the robustness of TLimmuno2 in identifying really immunogenic neoantigens that are undergoing negative selection during cancer evolution. Overall, TLimmuno2 is a powerful tool for the immunogenicity prediction of MHC class II presented epitopes and could promote the development of personalized immunotherapies.

Tetrahedral-Framework Nucleic Acid Loaded with MicroRNA-155 Enhances Immunocompetence in Cyclophosphamide-Induced Immunosuppressed Mice by Modulating Dendritic Cells and Macrophages.

Nanomaterials are often used as immunomodulators because they can be tailored by a controllable process. In this work, a complex based on a tetrahedral framework nucleic acid delivery system and MicroRNA-155, known as T-155, is synthesized for the modulation of immunosuppression. In vivo, T-155 ameliorated spleen and thymus damage and hematopoiesis suppression in cyclophosphamide-induced immunosuppressed mice by promoting T-cell proliferation to resist oxidative stress. In vitro, T-155 induced immature dendritic cells (DCs) to differentiate into mature DCs by the ERK1/2 pathway and converted M0 macrophages (Mφ) into the M1 type by the NF-κB pathway to enhance the surveillance capabilities of antigen-presenting cells. The experimental results suggest that T-155 has therapeutic potential as an immunomodulator for immunosuppression.

Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses.

Dioscorea alata L. (Dioscoreaceae), commonly known as greater yam, water yam, or winged yam, is a popular tuber vegetable/food crop worldwide, with nutritional, health, and economical importance. China is an important domestication center of D. alata, and hundreds of cultivars (accessions) have been established. However, genetic variations among Chinese accessions remain ambiguous, and genomic resources currently available for the molecular breeding of this species in China are very scarce. In this study, we generated the first pan-plastome of D. alata, based on 44 Chinese accessions and 8 African accessions, and investigated the genetic variations, plastome evolution, and phylogenetic relationships within D. alata and among members of the section Enantiophyllum. The D. alata pan-plastome encoded 113 unique genes and ranged in size from 153,114 to 153,161 bp. A total of four whole-plastome haplotypes (Haps I-IV) were identified in the Chinese accessions, showing no geographical differentiation, while all eight African accessions shared the same whole-plastome haplotype (Hap I). Comparative genomic analyses revealed that all four whole plastome haplotypes harbored identical GC content, gene content, gene order, and IR/SC boundary structures, which were also highly congruent with other species of Enantiophyllum. In addition, four highly divergent regions, i.e., trnC-petN, trnL-rpl32, ndhD-ccsA, and exon 3 of clpP, were identified as potential DNA barcodes. Phylogenetic analyses clearly separated all the D. alata accessions into four distinct clades corresponding to the four haplotypes, and strongly supported that D. alata was more closely related to D. brevipetiolata and D. glabra than D. cirrhosa, D. japonica, and D. polystachya. Overall, these results not only revealed the genetic variations among Chinese D. alata accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species.

A self-circulating electro-fenton-like process over Fe3O4-CaO2 cathode for highly efficient degradation of levofloxacin.

Electro-Fenton reaction was limited by the generation of H2O2 and the circulation of Fe(Ⅱ)/Fe(Ⅲ). Herein, an efficient electro-Fenton-like process was constructed based on Fe3O4-CaO2 cathode promoted by peroxymonosulfate (PMS). Levofloxacin (LEV) could be efficiently degraded (92.1%) and mineralized with the TOC removal of 74.5% in this self-circulating process. More importantly, the Fe3O4-CaO2 exhibited good stability in the recycles due that CaO2 was covered by Fe3O4, which inhibited the rapid release of H2O2. Mechanism analysis indicated that CaO2 could not only replace H2O2 to accelerate the oxidation of Fe(Ⅱ) to Fe(Ⅲ), but also could form complexes with Fe(Ⅲ) and PMS to transfer electrons from ligands to metals, thereby enhancing the reduction of Fe(Ⅲ) to Fe(Ⅱ). As a result, the electrical consumption was significantly reduced, which was only 5.0% of the Fe3O4 in electro-Fenton reaction. Meanwhile, the hydrolyzed product of Ca(OH)2 reacted with Fe(Ⅲ) in the presence of H2O2 and converted into CaO2. Thus, the self-circulation of CaO2/Ca(OH)2 and Fe(Ⅲ)/Fe(Ⅱ) was realized, which accelerated the generation of active species, such as, ·OH, O2·- and 1O2. This work first proposed a self-circulating electro-Fenton-like system and demonstrated the potential application of Fe3O4-CaO2 in the treatment of wastewater.

Application of biochar and polyacrylamide to revitalize coastal saline soil quality to improve rice growth.

Poor soil quality is affected by salinity, which limits land productivity and sustainable agricultural development in coastal China. Hence, it is essential to choose suitable and efficient approaches to revitalize coastal saline soil quality and improve agricultural productivity. Biochar and polyacrylamide (PAM) have been widely applied as soil amendments to enhance soil structure, but the interactive effects of biochar and PAM on rice growth are unclear. The experiment described in this study was conducted over five consecutive growing seasons (from 2016 to 2020) with biochar (at 0, 32, and 79 t/hm2) and PAM (at 0, 0.6, and 1.6 t/hm2) applications to study the effects of amendments on soil properties, rice photosynthesis, and rice yield in coastal saline land. The soil property results showed that wheat straw biochar and PAM lowered soil total salt and bulk density, but increased the soil organic matter (SOM), mean weight diameter of water-stable aggregates (MWD), and macroaggregate (> 0.25 mm) content. The application of either biochar or PAM increased the rice net photosynthetic rate, transpiration rate, and stomatal conductance. The combined application of 32 t/hm2 biochar + 0.6 t/hm2 PAM increased the net photosynthetic rate by 26.0% and the transpiration rate by 24.8% relative to the control. The application of 32 t/hm2 biochar and 1.6 t/hm2 PAM significantly increased the rice grain yield. The path analysis model showed that spikelets per panicle and canopy gross photosynthesis had strong and significant positive effects on grain yield, whereas soil total salt had a negative effect on grain yield. The combined application of 32 t/hm2 biochar + 0.6 t/hm2 PAM was identified as the most effective for rice growth. Biochar and PAM amendments at an optimal level may enhance soil properties by reducing salinity. These findings indicate that biochar and PAM have the potential to remediate coastal saline soil quality and the environment, which would simultaneously increase the sustainable use of coastal land resources and food production to preserve the ecological environment.

Genome Sequence Resource for Colletotrichum gloeosporioides, an Important Pathogenic Fungus Causing Anthracnose of Dioscorea alata.

Anthracnose disease is one of the most important diseases of Dioscorea alata and many other food yams, which is caused by Colletotrichum gloeosporioides fungus from the Glomerellaceae family of the Sordariomycetes class. In the present study, a C. gloeosporioides starin named CgDa01 was isolated from D. alata, and its genome was sequenced based on Oxford Nanopore technology (ONT) and the Illumina sequencing platform. The high-quality genome of CgDa01 was assembled with a 62.78 Mb genome size and 15,845 predicted protein-coding genes. The proteins of predicted genes were annotated using multiple public databases, including the nonredundant protein database, the InterProScan databases, and Kyoto Encyclopedia of Genes and Genomes. Among the annotated protein-coding genes, 55 were predicted as potential virulence genes by the fungal virulence factor database. The C. gloeosporioides CgDa01 genome assembly described in this study can serve as a resource for better understanding the pathogenic mechanism of C. gloeosporioides on yam hosts.

The Effectiveness Assessment of Agricultural Subsidy Policies on Food Security: Evidence from China's Poverty-Stricken Villages.

This paper builds a theoretical model based on a representative peasant household in the neoclassical model, comprehensively considers three types of farmer households in China, and evaluates the effects of the agricultural subsidy policy under equilibrium conditions. Based on the two bottom lines of guaranteeing China's grain security and ensuring no large-scale return to poverty, this paper uses 2010, 2012, and 2014 tracking survey data from the Mutual Aid Fund for Poverty-Stricken Villages in China to construct an econometric model to evaluate agricultural subsidy effectiveness from the three aspects of farmers' total sown area, total grain output, and total income. The research draws the following conclusions: (1) Agricultural subsidies can significantly increase the sown area, grain production, and total income of farmers in poverty-stricken areas, which is conducive to improving the farmers' comprehensive capacity for grain production as well as income, and this conclusion remains valid after performing a series of robustness tests and solving endogeneity problems. (2) The effects of the agricultural subsidy policy are affected by natural conditions, economic development levels, and functional orientation of grain production in different regions, and they have divergent influences on farmers' total sown area, total output, and total income. (3) Agricultural subsidies boost farmers' willingness to cultivate grain, reduce land abandonment, and increase the total sown area, total output, and total grain income. The willingness to cultivate grain is an important mechanism that affects the effectiveness of the agricultural subsidy policy.

Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction.

Neoantigens derived from somatic DNA alterations are ideal cancer-specific targets. In recent years, the combination therapy of PD-1/PD-L1 blockers and neoantigen vaccines has shown clinical efficacy in original PD-1/PD-L1 blocker non-responders. However, not all somatic DNA mutations result in immunogenicity among cancer cells and efficient tools to predict the immunogenicity of neoepitopes are still urgently needed. Here, we present the Seq2Neo pipeline, which provides a one-stop solution for neoepitope feature prediction using raw sequencing data. Neoantigens derived from different types of genome DNA alterations, including point mutations, insertion deletions and gene fusions, are all supported. Importantly, a convolutional neural network (CNN)-based model was trained to predict the immunogenicity of neoepitopes and this model showed an improved performance compared to the currently available tools in immunogenicity prediction using independent datasets. We anticipate that the Seq2Neo pipeline could become a useful tool in the prediction of neoantigen immunogenicity and cancer immunotherapy. Seq2Neo is open-source software under an academic free license (AFL) v3.0 and is freely available at Github.