Genomic and phenotypic analyses reveal Paenibacillus polymyxa PJH16 is a potential biocontrol agent against cucumber fusarium wilt.

In recent years, bacterial-based biocontrol agents (BCA) have become a new trend for the control of fungal diseases such as fusarium wilt that seriously threaten the yield and quality of cucumber, which are transmitted through infested soil and water. This study was set out with the aim of figuring the mechanism of the isolated rhizobacterial strain Paenibacillus polymyxa PJH16 in preventing Fusarium oxysporum f. sp. cucumerinum (Foc). Biocontrol and growth-promoting experiments revealed that bacterial strain causes effective inhibition of the fungal disease through a significant growth-promoting ability of plants, and had activities of ß-1,3-glucanase, cellulase, amylase and protease. It could produce siderophore and indole-3-acetic acid, too. Using the high-throughput sequencing tool PacBio Sequel II system and the database annotation, the bacterial strain was identified as P. polymyxa PJH16 and contained genes encoding for presence of biofilm formation, antimicrobial peptides, siderophores and hydrolyases. From comparing data between the whole genome of P. polymyxa PJH16 with four closely related P. polymyxa strains, findings revealed markedly the subtle differences in their genome sequences and proposed new antifungal substances present in P. polymyxa PJH16. Therefore, P. polymyxa PJH16 could be utilized in bioengineering a microbial formulation for application as biocontrol agent and bio-stimulant, in the future.

Effects of biodiversity on functional stability of freshwater wetlands: a systematic review.

Freshwater wetlands are the wetland ecosystems surrounded by freshwater, which are at the interface of terrestrial and freshwater ecosystems, and are rich in ecological composition and function. Biodiversity in freshwater wetlands plays a key role in maintaining the stability of their habitat functions. Due to anthropogenic interference and global change, the biodiversity of freshwater wetlands decreases, which in turn destroys the habitat function of freshwater wetlands and leads to serious degradation of wetlands. An in-depth understanding of the effects of biodiversity on the stability of habitat function and its regulation in freshwater wetlands is crucial for wetland conservation. Therefore, this paper reviews the environmental drivers of habitat function stability in freshwater wetlands, explores the effects of plant diversity and microbial diversity on habitat function stability, reveals the impacts and mechanisms of habitat changes on biodiversity, and further proposes an outlook for freshwater wetland research. This paper provides an important reference for freshwater wetland conservation and its habitat function enhancement.

Genomics Analysis Reveals the Potential Biocontrol Mechanism of Pseudomonas aeruginosa QY43 against Fusarium pseudograminearum.

Fusarium crown rot (FCR) in wheat is a prevalent soil-borne disease worldwide and poses a significant threat to the production of wheat (Triticum aestivum) in China, with F. pseudograminearum being the dominant pathogen. Currently, there is a shortage of biocontrol resources to control FCR induced by F. pseudograminearum, along with biocontrol mechanisms. In this study, we have identified 37 strains of biocontrol bacteria displaying antagonistic effects against F. pseudograminearum from over 8000 single colonies isolated from soil samples with a high incidence of FCR. Among them, QY43 exhibited remarkable efficacy in controlling FCR. Further analysis identified the isolate QY43 as Pseudomonas aeruginosa, based on its colony morphology and molecular biology. In vitro, QY43 significantly inhibited the growth, conidial germination, and the pathogenicity of F. pseudograminearum. In addition, QY43 exhibited a broad spectrum of antagonistic activities against several plant pathogens. The genomics analysis revealed that there are genes encoding potential biocontrol factors in the genome of QY43. The experimental results confirmed that QY43 secretes biocontrol factor siderophores and pyocyanin. In summary, QY43 exhibits a broad spectrum of antagonistic activities and the capacity to produce diverse biocontrol factors, thereby showing substantial potential for biocontrol applications to plant disease.

The Use of E-Learning in Peyton's 4-Step Approach: Evaluation of Facial Computed Tomography Scans.

Imparting procedural skills is challenging. Peyton's approach is an effective face-to-face teaching technique increasingly used in complex skills training. Institutions are beginning to incorporate online training as part of their procedural curriculum. We developed E-Peyton's to employ Peyton's approach through an electronic learning platform. The efficacy of E-Peyton's approach in teaching the interpretation of facial computed tomography (CT) scans is evaluated in this study. Naïve learners (n=41) were randomized into 2 groups based on teaching techniques employed: E-Peyton's (n=20) and Peyton's (n=21) approaches. The distance between the infraorbital margin and the posterior ledge was measured using a 3-part standardized measuring protocol on OsiriX. Twenty measurements were assessed for accuracy against the benchmark (±2 mm) at week 0 and week 1. Training durations were compared. Questionnaires were administered before and after the study to identify learners' acceptance of teaching techniques and their confidence in interpreting facial CT scans. Learners in both teaching techniques had comparable skills retention. Gap scores indicate significant improvement in learner's confidence levels regardless of teaching technique (P<0.05). Both teaching techniques were well-accepted by learners. E-Peyton's and Peyton's approaches required a similar training duration. The COVID-19 pandemic highlights the importance of effective remote learning platforms. E-Peyton's approach is comparable to that of Peyton's in all areas of assessment. E-Peyton's approach effectively automates Peyton's approach, allowing for standardized, high-quality procedural skills training while reducing manpower burden.

The hyphal-specific toxin candidalysin promotes fungal gut commensalism.

The fungus Candida albicans frequently colonizes the human gastrointestinal tract, from which it can disseminate to cause systemic disease. This polymorphic species can transition between growing as single-celled yeast and as multicellular hyphae to adapt to its environment. The current dogma of C. albicans commensalism is that the yeast form is optimal for gut colonization, whereas hyphal cells are detrimental to colonization but critical for virulence1-3. Here, we reveal that this paradigm does not apply to multi-kingdom communities in which a complex interplay between fungal morphology and bacteria dictates C. albicans fitness. Thus, whereas yeast-locked cells outcompete wild-type cells when gut bacteria are absent or depleted by antibiotics, hyphae-competent wild-type cells outcompete yeast-locked cells in hosts with replete bacterial populations. This increased fitness of wild-type cells involves the production of hyphal-specific factors including the toxin candidalysin4,5, which promotes the establishment of colonization. At later time points, adaptive immunity is engaged, and intestinal immunoglobulin A preferentially selects against hyphal cells1,6. Hyphal morphotypes are thus under both positive and negative selective pressures in the gut. Our study further shows that candidalysin has a direct inhibitory effect on bacterial species, including limiting their metabolic output. We therefore propose that C. albicans has evolved hyphal-specific factors, including candidalysin, to better compete with bacterial species in the intestinal niche.

Deep groundwater irrigation altered microbial community and increased anammox and methane oxidation in paddy wetlands of Sanjiang Plain, China.

The over-utilizing of nitrogen fertilizers in paddy wetlands potentially threatens to the surrounding waterbody, and a deep understanding of the community and function of microorganisms is crucial for paddy non-point source pollution control. In this study, top soil samples (0-15 cm) of paddy wetlands under groundwater's irrigation at different depths (H1: 6.8 m, H2: 13.7 m, H3: 14.8 m, H4: 15.6 m, H5: 17.0 m, and H6: 17.8 m) were collected to investigate microbial community and function differences and their interrelation with soil properties. Results suggested some soil factor differences for groundwater's irrigation at different depths. Deep-groundwater's irrigation (H2-H6) was beneficial to the accumulation of various electron acceptors. Nitrifying-bacteria Ellin6067 had high abundance under deep groundwater irrigation, which was consistent with its diverse metabolic capacity. Meanwhile, denitrifying bacteria had diverse distribution patterns. Iron-reducing bacteria Geobacter was abundant in H1, and Anaeromyxobacter was abundant under deep groundwater irrigation; both species could participate in Fe-anammox. Furthermore, Geobacter could perform dissimilatory nitrate reduction to ammonia using divalent iron and provide substrate supply for anammox. Intrasporangium and norank_f_Gemmatimonadacea had good chromium- and vanadium-reducting potentials and could promote the occurrence of anammox. Low abundances of methanotrophs Methylocystis and norank_f_Methyloligellaceae were associated with the relatively anoxic environment of paddy wetlands, and the presence of aerobic methane oxidation was favorable for in-situ methane abatement. Moisture, pH, and TP had crucial effects on microbial community under phylum- and genus-levels. Microorganisms under shallow groundwater irrigation were highly sensitive to environmental changes, and Fe-anammox, nitrification, and methane oxidation were favorable under deep groundwater irrigation. This study highlights the importance of comprehensively revealing the microbial community and function of paddy wetlands under groundwater's irrigation and reveals the underlying function of indigenous microorganisms in agricultural non-point pollution control and greenhouse gas abatement.

Platelet TLR7 is essential for the formation of platelet-neutrophil complexes and low-density neutrophils in lupus nephritis.

OBJECTIVES: Platelets and low-density neutrophils (LDNs) are major players in the immunopathogenesis of SLE. Despite evidence showing the importance of platelet-neutrophil complexes (PNCs) in inflammation, little is known about the relationship between LDNs and platelets in SLE. We sought to characterize the role of LDNs and Toll-like receptor 7 (TLR7) in clinical disease. METHODS: Flow cytometry was used to immunophenotype LDNs from SLE patients and controls. The association of LDNs with organ damage was investigated in a cohort of 290 SLE patients. TLR7 mRNA expression was assessed in LDNs and high-density neutrophils (HDNs) using publicly available mRNA sequencing datasets and our own cohort using RT-PCR. The role of TLR7 in platelet binding was evaluated in platelet-HDN mixing studies using TLR7-deficient mice and Klinefelter syndrome patients. RESULTS: SLE patients with active disease have more LDNs, which are heterogeneous and more immature in patients with evidence of kidney dysfunction. LDNs are platelet bound, in contrast to HDNs. LDNs settle in the peripheral blood mononuclear cell (PBMC) layer due to the increased buoyancy and neutrophil degranulation from platelet binding. Mixing studies demonstrated that this PNC formation was dependent on platelet-TLR7 and that the association results in increased NETosis. The neutrophil:platelet ratio is a useful clinical correlate for LDNs, and a higher NPR is associated with past and current flares of LN. CONCLUSIONS: LDNs sediment in the upper PBMC fraction due to PNC formation, which is dependent on the expression of TLR7 in platelets. Collectively, our results reveal a novel TLR7-dependent crosstalk between platelets and neutrophils that may be an important therapeutic opportunity for LN.

Three-dimensional instrument polarization analysis and optimization of liquid-crystal-based Stokes polarimeter.

The Stokes polarimeter based on liquid crystal variable retarders (LCVRs) is a space polarization measurement technology widely used. However, due to the tilt of the optic axis of the LCVR with the driving voltage in the direction of light propagation and the interference in LCVR, the LCVRs-based Stokes polarimeter produces a large instrument polarization, which affects the accurate polarization measurement. In this paper, we combine polarization ray tracing with multi-beam interference, and establish a general three-dimensional polarization analysis model of the LCVRs-based Stokes polarimeter. The simulation results of adjusting the LCVR voltage to reduce the instrument polarization are analyzed, and the variation of polarization measurement accuracy with the field of view before and after optimization of the LCVRs-based Stokes polarimeter is simulated and analyzed. A LCVR structure with additional films for matching the refractive index is proposed. According to the simulation results, this structure can significantly reduce the interference effects and reduce the impact of variations in liquid crystal layer thickness on the interference effects.

Genome sequencing and analysis of Bacillus velezensis VJH504 reveal biocontrol mechanism against cucumber Fusarium wilt.

One major issue in reducing cucumber yield is the destructive disease Cucumber (Cucumis sativus L.) wilt disease caused by Fusarium oxysporum f. sp. cucumerinum (Foc). When using the isolate VJH504 isolated from cucumber rhizosphere soil and identified as Bacillus velezensis, the growth of Foc in the double culture experiment was effectively inhibited. Phenotypic, phylogenetic, and genomic analyses were conducted to enhance understanding of its biocontrol mechanism. According to the result of the phenotype analysis, B. velezensis VJH504 could inhibit cucumber fusarium wilt disease both in vitro and in vivo, and significantly promote cucumber seed germination and seedling growth. Additionally, the tests of growth-promoting and biocontrol characteristics revealed the secretion of proteases, amylases, ß-1,3-glucanases, cellulases, as well as siderophores and indole-3-acetic acid by B. velezensis VJH504. Using the PacBio Sequel II system, we applied the complete genome sequencing for B. velezensis VJH504 and obtained a single circular chromosome with a size of 3.79 Mb. A phylogenetic tree was constructed based on the 16S rRNA gene sequences of B. velezensis VJH504 and 13 other Bacillus species, and Average Nucleotide Identity (ANI) analysis was performed using their whole-genome sequences, confirming isolateVJH504 as B. velezensis. Following this, based on the complete genome sequence od B. velezensis VJH504, specific functional analysis, Carbohydrate-Active Enzymes (CAZymes) analysis, and secondary metabolite analysis were carried out, predicting organism's abilities for biofilm formation, production of antifungal CAZymes, and synthesis of antagonistic secondary metabolites against pathogens. Afterwards, a comparative genomic analysis was performed between B. velezensis VJH504 and three other B. velezensis strains, revealing subtle differences in their genomic sequences and suggesting the potential for the discovery of novel antimicrobial substances in B. velezensis VJH504. In conclusion, the mechanism of B. velezensis VJH504 in controlling cucumber fusarium wilt was predicted to appear that B. velezensis VJH504is a promising biocontrol agent, showcasing excellent application potential in agricultural production.

Effects of chromate on nitrogen removal and microbial community in two-stage vertical-flow constructed wetlands.

Nitrogen and chromium (Cr(VI)) pollution in waterbodies pose great threats to human health, and a cost-effective alternative with Cr(VI) and nitrogen simultaneous removal is still needed. This study investigated the influence of Cr(VI) on nitrogen removal in the two-stage vertical-flow constructed wetlands (TS-VFCWs) along with iron ore and woodchip, and explored relationship between Cr(VI) and nitrogen removal. The results showed that efficient Cr(VI) and nitrogen removal were simultaneously achieved in TS-VFCWs together with iron-ore and woodchip under 2 mg/L-Cr(VI), whereas 10 mg/L-Cr(VI) gave significant and recoverable inhibition of nitrogen removal. Cr(VI) supplementation promoted the beneficiation of Cr(VI)-reducing/resistant bacteria IMCC26207 and Bryobacter on iron-ore. Woodchip enriched Cr(VI)-reducing bacteria Streptomyces and Thiobacillus. XRD and XPS showed that abundant bound-Cr existed in the surface of iron ore and woodchip, and Cr(III) precipitation/oxide was the major product. High abundances of nitrifying and autotrophic/heterotrophic denitrifying bacteria ensured good nitrogen removal at Cr(VI) stress.

The Candida albicans reference strain SC5314 contains a rare, dominant allele of the transcription factor Rob1 that modulates filamentation, biofilm formation, and oral commensalism.

IMPORTANCE: Candida albicans is a commensal fungus that colonizes the human oral cavity and gastrointestinal tract but also causes mucosal as well as invasive disease. The expression of virulence traits in C. albicans clinical isolates is heterogeneous and the genetic basis of this heterogeneity is of high interest. The C. albicans reference strain SC5314 is highly invasive and expresses robust filamentation and biofilm formation relative to many other clinical isolates. Here, we show that SC5314 derivatives are heterozygous for the transcription factor Rob1 and contain an allele with a rare gain-of-function SNP that drives filamentation, biofilm formation, and virulence in a model of oropharyngeal candidiasis. These findings explain, in part, the outlier phenotype of the reference strain and highlight the role heterozygosity plays in the strain-to-strain variation of diploid fungal pathogens.

Co-metabolic biodegradation of chlorinated ethene in an oxygen- and ethane-based membrane biofilm reactor.

Groundwater contamination by chlorinated ethenes is an urgent concern worldwide. One approach for detoxifying chlorinated ethenes is aerobic co-metabilims using ethane (C2H6) as the primary substrate. This study evaluated long-term continuous biodegradation of three chlorinated alkenes in a membrane biofilm reactor (MBfR) that delivered C2H6 and O2 via gas-transfer membranes. During 133 days of continuous operation, removals of dichloroethane (DCE), trichloroethene (TCE), and tetrachloroethene (PCE) were as high as 94 % and with effluent concentrations below 5 µM. In situ batch tests showed that the co-metabolic kinetics were faster with more chlorination. C2H6-oxidizing Comamonadaceae and "others," such as Methylococcaceae, oxidized C2H6 via monooxyenation reactions. The abundant non-ethane monooxygenases, particularly propane monooxygenase, appears to have been responsible for C2H6 aerobic metabolism and co-metabolism of chlorinated ethenes. This work proves that the C2H6 + O2 MBfR is a platform for ex-situ bioremediation of chlorinated ethenes, and the generalized action of the monooxygenases may make it applicable for other chlorinated organic contaminants.

The Candida albicans reference strain SC5314 contains a rare, dominant allele of the transcription factor Rob1 that modulates biofilm formation and oral commensalism.

Candida albicans is a diploid human fungal pathogen that displays significant genomic and phenotypic heterogeneity over a range of virulence traits and in the context of a variety of environmental niches. Here, we show that the effects of Rob1 on biofilm and filamentation virulence traits is dependent on both the specific environmental condition and the clinical strain of C. albicans . The C. albicans reference strain SC5314 is a ROB1 heterozygote with two alleles that differ by a single nucleotide polymorphism at position 946 resulting in a serine or proline containing isoform. An analysis of 224 sequenced C. albicans genomes indicates that SC5314 is the only ROB1 heterozygote documented to date and that the dominant allele contains a proline at position 946. Remarkably, the ROB1 alleles are functionally distinct and the rare ROB1 946S allele supports increased filamentation in vitro and increased biofilm formation in vitro and in vivo, suggesting it is a phenotypic gain-of-function allele. SC5314 is amongst the most highly filamentous and invasive strains characterized to date. Introduction of the ROB1 946S allele into a poorly filamenting clinical isolate increases filamentation and conversion of an SC5314 laboratory strain to a ROB1 946S homozygote increases in vitro filamentation and biofilm formation. In a mouse model of oropharyngeal infection, the predominant ROB1 946P allele establishes a commensal state while the ROB1 946S phenocopies the parent strain and invades into the mucosae. These observations provide an explanation for the distinct phenotypes of SC5314 and highlight the role of heterozygosity as a driver of C. albicans phenotypic heterogeneity. Importance: Candida albicans is a commensal fungus that colonizes human oral cavity and gastrointestinal tracts but also causes mucosal as well as invasive disease. The expression of virulence traits in C. albicans clinical isolates is heterogenous and the genetic basis of this heterogeneity is of high interest. The C. albicans reference strain SC5314 is highly invasive and expresses robust filamentation and biofilm formation relative to many other clinical isolates. Here, we show that SC5314 derivatives are heterozygous for the transcription factor Rob1 and contain an allele with a rare gain-of-function SNP that drives filamentation, biofilm formation, and virulence in a model of oropharyngeal candidiasis. These finding explain, in part, the outlier phenotype of the reference strain and highlight the role of heterozygosity plays in the strain-to-strain variation of diploid fungal pathogens.

Unipedicular-Screw Index Vertebra Manipulation Technique for Minimally Invasive Short-Segment Thoracolumbar Fracture Fixation.

BACKGROUND: Minimally invasive spine surgery (MIS) has revolutionized fixation of thoracolumbar fractures with burst elements. Recent studies have proven that percutaneous pedicle screw instrumentation is as effective as open instrumentation but with reduced intraoperative blood loss and operative duration. Techniques such as short-segment pedicle screw fixation including the fractured vertebra have shown satisfactory radiological correction and functional outcomes, avoiding the need for extensile posterior constructs. OBJECTIVE: In the present study, the authors our technique utilizing unipedicular index vertebra fixation and manipulation in MIS for thoracolumbar fractures with burst elements. To our knowledge, this technique is not well described in literature as open approaches are often adopted for the above. The authors sought to highlight the 2-year radiological and functional outcomes of 20 consecutive patients who underwent this technique. METHODS: A retrospective review of prospectively collected data was conducted on 20 patients with thoracolumbar fractures with burst elements who underwent fixation using our technique. Patient data collected included demographic characteristics, mechanism of injury, associated injuries, neurological deficit at the time of admission, pre- and postoperative neurological evaluation, and length of hospital stay. Radiological investigations included plain radiographs, computed tomography of the spine with reconstruction, and magnetic resonance imaging of the spine, which provided data for radiological fracture classifications such as AO Spine and derivation of Thoracolumbar Injury Classification and Severity Score, as well as preoperative planning. Radiological investigations in the postoperative period were carried out by standing radiographs or EOS whole spine at each postoperative follow-up for up to 2 years. Radiological parameters-vertebral wedge angle, regional kyphosis angle, coronal Cobb angle, and anterior and posterior vertebral body heights-were recorded at preoperative, intraoperative, postoperative, and up to 2-year follow-up. Clinical outcome scores (visual analog score [VAS] and Oswestry Disability Index [ODI]) were also recorded at similar timepoints. RESULTS: Radiological outcomes reflect significant lordotic corrections of the vertebral wedge angles up to 2-year follow-up when compared with preoperative values (intraoperative: P = 0.06; postoperative: P = 0.001; 3 months: P = 0.002; 6 months: P = 0.004; 1 year: P = 0.011; 2 years: P = 0.016). Additionally, significant lordotic corrections of regional kyphosis angles (intraoperative: P = 0.00; postoperative: P = 0.00; 3 months: P = 0.031; 6 months: P = 0.039) and increases in anterior vertebral body heights (postoperative: P = 0.001; 3 months: P = 0.010; 6 months: P = 0.020) at up to 6-month follow-up were found. Preoperatively, median VAS of 85 (range 30-100) and ODI of 90 (range 40-98) were recorded. Statistically significant improvements in VAS and ODI were found across all timepoints when compared with preoperative values, with a mean VAS of 11.5 (SD 4.8) and ODI of 9.9 (SD 4.5) at 2-year follow-up. CONCLUSION: Surgical management of thoracolumbar fractures with or without neurological deficit has a role in reducing nursing requirements and postoperative morbidity in patients with polytrauma and other associated injuries. Our approach in treating thoracolumbar fractures with burst elements using MIS short-segment fixation and unipedicular screw manipulation technique shows satisfactory radiological correction and high rates of fracture union while reducing approach-related morbidity and improving functional outcomes.

Single-Level Cervical Artificial Disc Replacement Compared with Cage Screw Implants: 2-Year Clinical and Radiological Outcomes Especially Adjacent Level Ossification.

STUDY DESIGN: Retrospective single-center, single-surgeon cohort study. PURPOSE: Our goal was to compare the 2-year clinical and radiological results of artificial disc replacement (ADR) and cage screw (CS) implants in patients with cervical degenerative disc disease (DDD). OVERVIEW OF LITERATURE: Anterior cervical discectomy and fusion with CS implants are an acceptable alternative to traditional cageplate construct due to perceived decreased complications of dysphagia. However, patients may experience adjacent segment disease because of increased motion and intradiscal pressure. ADR is an alternative to restore the physiological kinematics of the operated disc. Few studies directly compare ADR and CS construct for their efficacy. METHODS: Patients who received single-level ADR or CS between January 2008 and December 2018 were included. Data collected was preoperatively, intraoperatively, and postoperatively (6, 12, 24 months). Demographic information, surgical information, complications, follow-up surgery, and outcome ratings (Japanese Orthopaedic Association [JOA], Neck Disability Index [NDI], Visual Analog Scale [VAS] neck and arm, 36-item Short Form Health Survey [SF-36], EuroQoL-5 Dimension [EQ-5D]) were gathered. The radiological assessment included motion segment height, adjacent disc height, lordosis, cervical lordosis, T1 slope, the sagittal vertical axis C2-7, and adjacent level ossification development (ALOD). RESULTS: Fifty-eight patients were included (ADR: 37 and CS: 21). At 6 months, both groups' JOA, VAS, NDI, SF-36, and EQ-5D scores significantly improved, and the positive trends persisted at 2 years. Noted no significant difference in the enhancement of clinical scores except for the VAS arm (ADR: 5.95 vs. CS: 3.43, p =0.001). Radiological parameters were comparable except for the progression of ALOD of the subjacent disc (ADR: 29.7% vs. CS: 66.9%, p =0.02). No significant difference in adverse events or severe complications seen. CONCLUSIONS: ADR and CS obtain good clinical results for symptomatic single-level cervical DDD. ADR demonstrated a significant advantage over CS in the improvement of VAS arm and reduced progression of ALOD of the adjacent lower disc. No statistically significant difference of dysphonia or dysphagia between the two groups were seen, attributed to their comparable zero profile.

EEG Signal Epilepsy Detection With a Weighted Neighbor Graph Representation and Two-Stream Graph-Based Framework.

Epilepsy is one of the most common neurological diseases. Clinically, epileptic seizure detection is usually performed by analyzing electroencephalography (EEG) signals. At present, deep learning models have been widely used for single-channel EEG signal epilepsy detection, but this method is difficult to explain the classification results. Researchers have attempted to solve interpretive problems by combining graph representation of EEG signals with graph neural network models. Recently, the combination of graph representations and graph neural network (GNN) models has been increasingly applied to single-channel epilepsy detection. By this methodology, the raw EEG signal is transformed to its graph representation, and a GNN model is used to learn latent features and classify whether the data indicates an epileptic seizure episode. However, existing methods are faced with two major challenges. First, existing graph representations tend to have high time complexity as they generally require each vertex to traverse all other vertices to construct a graph structure. Some of them also have high space complexity for being dense. Second, while separate graph representations can be derived from a single-channel EEG signal in both time and frequency domains, existing GNN models for epilepsy detection can learn from a single graph representation, which makes it hard to let the information from the two domains complement each other. For addressing these challenges, we propose a Weighted Neighbour Graph (WNG) representation for EEG signals. Reducing the redundant edges of the existing graph, WNG can be both time and space-efficient, and as informative as its less efficient counterparts. We then propose a two-stream graph-based framework to simultaneously learn features from WNG in both time and frequency domain. Extensive experiments demonstrate the effectiveness and efficiency of the proposed methods.

Microorganisms in coastal wetland sediments: a review on microbial community structure, functional gene, and environmental potential.

Coastal wetlands (CW) are the junction of the terrestrial and marine ecosystems and have special ecological compositions and functions, which are important for maintaining biogeochemical cycles. Microorganisms inhabiting in sediments play key roles in the material cycle of CW. Due to the variable environment of CW and the fact that most CW are affected by human activities and climate change, CW are severely degraded. In-depth understanding of the community structure, function, and environmental potential of microorganisms in CW sediments is essential for wetland restoration and function enhancement. Therefore, this paper summarizes microbial community structure and its influencing factors, discusses the change patterns of microbial functional genes, reveals the potential environmental functions of microorganisms, and further proposes future prospects about CW studies. These results provide some important references for promoting the application of microorganisms in material cycling and pollution remediation of CW.

Establishment and validation of a prognostic risk classification for patients with stage T1-3N0M0 esophageal squamous cell carcinoma.

INTRODUCTION: At present, clinical factors and hematological indicators have been proved to have great potential in predicting the prognosis of cancer patients, and no one has combined these two valuable indicators to establish a prognostic model for esophageal squamous cell carcinoma (ESCC) patients with stage T1-3N0M0 after R0 resection. To verify, we aimed to combine these potential indicators to establish a prognostic model. METHODS: Stage T1-3N0M0 ESCC patients from two cancer centers (including training cohort: N = 819, and an external validation cohort: N = 177)-who had undergone esophagectomy in 1995-2015 were included. We integrated significant risk factors for death events by multivariable logistic regression methods and applied them to the training cohort to build Esorisk. The parsimonious aggregate Esorisk score was calculated for each patient; the training set was divided into three prognostic risk classes according to the 33rd and 66th percentiles of the Esorisk score. The association of Esorisk with cancer-specific survival (CSS) was assessed using Cox regression analyses. RESULTS: The Esorisk model was: [10 + 0.023 × age + 0.517 × drinking history - 0.012 × hemoglobin-0.042 × albumin - 0.032 × lymph nodes]. Patients were grouped into three classes-Class A (5.14-7.26, low risk), Class B (7.27-7.70, middle risk), and Class C (7.71-9.29, high risk). In the training group, five-year CSS decreased across the categories (A: 63%; B: 52%; C: 30%, Log-rank P < 0.001). Similar findings were observed in the validation group. Additionally, Cox regression analysis showed that Esorisk aggregate score remained significantly associated with CSS in the training cohort and validation cohort after adjusting for other confounders. CONCLUSIONS: We combined the data of two large clinical centers, and comprehensively considered their valuable clinical factors and hematological indicators, established and verified a new prognostic risk classification that can predict CSS of stage T1-3N0M0 ESCC patients.

Effects of Rhizosphere Microbial Communities on Cucumber Fusarium wilt Disease Suppression.

Cucumber Fusarium wilt is a worldwide soil-borne disease that seriously restricts the yield and quality of cucumber. The rhizosphere soil microbiome, as the first line of defense against pathogens invading plant roots, plays a key role in rhizosphere immune formation and function. The purpose of this study was to reveal the key microecological factors and dominant microbial flora affecting cucumber resistance and susceptibility to Fusarium wilt by analyzing the physical and chemical properties and microbial flora of rhizosphere soil with different degrees of susceptibility and resistance to cucumber Fusarium wilt, thereby laying a foundation to establish cucumber resistance to the Fusarium wilt rhizosphere core microbiome. Firstly, Illumina Miseq sequencing technology was used to evaluate the physical and chemical properties and microbial groups of cucumber rhizosphere soil at different health levels, and the key environmental factors and microbial factors related to cucumber Fusarium wilt were screened out. Subsequently, PICRUSt2 and FUNGuild were used to predict the functions of rhizosphere bacteria and fungi. Combined with functional analysis, the possible interactions among soil physical and chemical properties, cucumber rhizosphere microorganisms, and Fusarium wilt were summarized. The results showed that the available potassium content in the rhizosphere soil of healthy cucumber decreased by 10.37% and 0.56%, respectively, compared with the rhizosphere soil of severely susceptible cucumber and mildly susceptible cucumber. Exchangeable calcium content increased by 25.55% and 5.39%; the α diversity Chao1 index of bacteria and fungi in the rhizosphere soil of healthy cucumber was significantly lower than that in the rhizosphere soil of seriously infected cucumber, and the MBC content of its physical and chemical properties was also significantly lower than that in the rhizosphere soil of seriously infected cucumber. There was no significant difference in the Shannon and Simpson diversity indexes between healthy cucumber rhizosphere soil and seriously infected cucumber rhizosphere soil. The results of the ß diversity analysis showed that the bacterial and fungal community structure of healthy cucumber rhizosphere soil was significantly different from that of severely and mildly infected cucumber rhizosphere soil. At the genus level, through statistical analysis, LEfSe analysis, and RDA analysis, the key bacterial and fungal genera with potential biomarker values were screened out as SHA_26, Subgroup_22, MND1, Aeromicrobium, TM7a, Pseudorhodoplanes, Kocuria, Chaetomium, Fusarium, Olpidium, and Scopulariopsis, respectively. The bacteria SHA_26, Subgroup_22, and MND1 related to cucumber Fusarium wilt inhibition belong to Chloroflexi, Acidobacteriota, and Proteobacteria, respectively. Chaetomiacea belongs to Sordariomycates. The results of functional prediction showed that changes to the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway in the bacterial microbiota were concentrated in tetracycline biosynthesis, selenocompound metabolism, lipopolysaccharide biosynthesis, etc., which were mainly involved in the metabolism of terpenoids and polyketides, energy metabolism, metabolism of other amino acids, glycan biosynthesis and metabolism, lipid metabolism, cell growth and death, transcription, metabolism of cofactors and vitamins, and biosynthesis of other secondary metabolites. The difference in fungi was mainly dung saprotroph-ectomycorrhizal-soil saprotroph-wood saprotroph. Through the correlation analysis and functional predictions of the key environmental factors, microbial flora, and cucumber health index in cucumber rhizosphere soil, we determined that the inhibition of cucumber Fusarium wilt was a synergistic effect of environmental factors and microbial flora, and a model diagram was drawn to briefly explain its mechanism. This work will provide a basis for the biological control of cucumber Fusarium wilt in the future.

Reconsidering N component of cancer staging for T1-2N0-2M0 small-cell lung cancer: a retrospective study based on multicenter cohort.

BACKGROUND: The current nodal (pN) classification still has limitations in stratifying the prognosis of small cell lung cancer (SCLC) patients with pathological classifications T1-2N0-2M0. Thus. This study aimed to develop and validate a modified nodal classification based on a multicenter cohort. MATERIALS AND METHODS: We collected 1156 SCLC patients with pathological classifications T1-2N0-2M0 from the Surveillance, Epidemiology, and End Results database and a multicenter database in China. The X-tile software was conducted to determine the optimal cutoff points of the number of examined lymph nodes (ELNs) and lymph node ratio (LNR). The Kaplan-Meier method, the Log-rank test, and the Cox regression method were used in this study. We classified patients into three pathological N modification categories, new pN#1 (pN0-#ELNs > 3), new pN#2 (pN0-#ELNs ≤ 3 or pN1-2-#LNR ≤ 0.14), and new pN#3 (N1-2-#LNR > 0.14). The Akaike information criterion (AIC), Bayesian Information Criterion, and Concordance index (C-index) were used to compare the prognostic, predictive ability between the current pN classification and the new pN component. RESULTS: The new pN classification had a satisfactory effect on survival curves (Log-rank P < 0.001). After adjusting for other confounders, the new pN classification could be an independent prognostic indicator. Besides, the new pN component had a much more accurate predictive ability in the prognostic assessment for SCLC patients of pathological classifications T1-2N0-2M0 compared with the current pN classification in the SEER database (AIC: 4705.544 vs. 4731.775; C-index: 0.654 vs. 0.617, P < 0.001). Those results were validated in the MCDB from China. CONCLUSIONS: The multicenter cohort developed and validated a modified nodal classification for SCLC patients with pathological category T1-2N0-2M0 after surgery. Besides, we propose that an adequate lymph node dissection is essential; surgeons should perform and consider the situation of ELNs and LNR when they evaluate postoperative prognoses of SCLC patients.