Diagnostic Role of Metagenomic Next-Generation Sequencing in Tubercular Orthopedic Implant-Associated Infection.

Objective: The diagnosis of tubercular orthopedic implant-associated infection (TB-IAI) is challenging. This study evaluated the value of metagenomic next-generation sequencing (mNGS) for the diagnosis of TB-IAI and developed a standardized diagnostic procedure for TB-IAI. Methods: The records of all patients with TB-IAI diagnosed and treated at our institution between December 2018 and September 2022 were retrospectively reviewed. Patient demographic characteristics, medical history, laboratory test, microbial culture, histopathology, and mNGS results, and time to diagnosis were recorded. The diagnostic efficiency of mNGS for TB-IAI was assessed by comparing the results and diagnostic time with that of other diagnostic modalities. Results: Ten patients were included in the analysis, including eight with prosthetic joint infections and two with fracture-related infections. The mNGS positivity rate was 100% (10/10), which was higher than that of TB-antibody (11%, 1/9), real-time quantitative polymerase chain reaction (22%, 2/9), T-SPOT.TB (25%, 2/8), purified protein derivative (50%, 4/8), microbial culture (50%, 5/10), and histopathology (20%, 2/10). mNGS shortened the time to diagnosis of TB-IAI. A standardized diagnostic procedure for TB-IAI was developed based on the findings. Conclusion: mNGS is useful for the diagnosis of TB-IAI. mNGS is recommended in cases where it is difficult to identify a pathogen using routine diagnostic tests. The standardized diagnostic procedure might improve TB-IAI diagnosis. Importance: TB-IAI is a rare infection, which occurs after orthopedic surgery and hard to diagnose microbiologically. mNGS is a new detection technique not yet discussed in current literature as a means for TB-IAI diagnostics. Here we describe a cohort of patients with TB-IAI diagnosed by mNGS show high efficiency of mNGS for detection of this pathology and present a clinical algorithm supplementing conventional methods for TB-IAI assessment.

The mediating role of synovitis in meniscus pathology and knee osteoarthritis radiographic progression.

Meniscus pathologies (damage, extrusion) and synovitis are associated with knee osteoarthritis (KOA); however, whether synovitis mediates the relationship between meniscus pathologies and KOA radiographic progression remains unclear. We conducted an observational study in the Osteoarthritis Initiative (OAI) cohort, with a 48-month follow-up. Meniscus pathology and synovitis were measured by MRI osteoarthritis knee score (MOAKS) at baseline and 24 months, and a comprehensive synovitis score was calculated using effusion and Hoffa synovitis scores. The knee osteoarthritis radiographic progression was considered that Kellgren-Lawrence (KL) grade and joint space narrowing (JSN) grade at 48 months were increased compared to those at baseline. This study included a total of 589 participants, with KL grades mainly being KL1 (26.5%), KL2 (34.1%), and KL3 (30.2%) at baseline, while JSN grades were mostly 0 at baseline. A logistic regression model was used to analyze the relationship between meniscus pathology, synovitis, and KOA progression. Mediation analysis was used to evaluate the mediation effect of synovitis. The average age of the participants was 61 years old, 62% of which were female. The medial meniscus extrusion was longitudinally correlated with the progression of KL (odds ratio [OR]: 2.271, 95% confidence interval [CI]: 1.412-3.694) and medial JSN (OR: 3.211, 95% CI: 2.040-5.054). Additionally, the longitudinal correlation between medial meniscus damage and progression of KOA (OR: 1.853, 95% CI: 1.177-2.941) and medial JSN (OR: 1.655, 95% CI: 1.053-2.602) was significant. Synovitis was found to mediate the relationship between medial meniscus extrusion and KL and medial JSN progression at baseline (ß: 0.029, 95% CI: 0.010-0.053; ß: 0.022, 95% CI: 0.005-0.046) and beyond 24 months (ß: 0.039, 95% CI: 0.016-0.068; ß: 0.047, 95% CI: 0.020-0.078). However, we did not find evidence of synovitis mediating the relationship between meniscal damage and KOA progression. Synovitis mediates the relationship between medial meniscus extrusion (rather than meniscus damage) and KOA progression.

Use of 1.5-Stage Functional Articulating Hip Spacers for Two-Stage Treatment of Hip Infection.

BACKGROUND: A two-stage treatment is commonly used for chronic hip infections. This study compared the clinical efficacy and complications associated with 1.5-stage functional articulating hip spacers (FAHS) and handmade spacers utilized during two-stage treatment. METHODS: This retrospective study included 50 patients who had hip infections, of which 41 were periprosthetic joint infections, 3 were internal fixation infections, and 6 had septic arthritis. They were divided into two groups according to the spacer type: 23 patients treated with handmade spacers comprising 1 to 2 Kirschner wires as an endoskeleton (group A) and 27 patients treated with 1.5-stage FAHS comprising a cemented femoral stem, metal femoral head, and polyethylene acetabular liner or cemented acetabular cup (group B). Clinical characteristics, surgical data, infection control rate, spacer complications, modified Harris hip, visual analog scale, and 36-item short-form physical functioning scale scores were compared between the groups. All patients were followed up for at least 24 months after the last surgical procedure. RESULTS: No significant differences were noted in the infection eradication rate between the two groups (100 versus 96.30%, P = 1.0). The incidence of mechanical complications, especially spacer fracture, was significantly lower in group B than in group A (P = .044). Hip function and quality of life were significantly better in group B during the interim period. Group B patients had a longer interval time (median 7.40 versus 4.30 months, P = .004) and a lower reimplantation rate than group A patients (42.31 versus 82.61%, P = .004). CONCLUSIONS: The 1.5-stage FAHS surgical technique is feasible for the treatment of hip infection, with a lower mechanical complication rate, better hip function, and better quality of life during the interim period compared to that of handmade spacers. The 1.5-stage FAHS with maintained function could delay or negate the need for second-stage revision.

Targeted Light-Induced Immunomodulatory Strategy for Implant-Associated Infections via Reversing Biofilm-Mediated Immunosuppression.

The clinical treatment efficacy for implant-associated infections (IAIs), particularly those caused by Methicillin-resistant Staphylococcus aureus (MRSA), remains unsatisfactory, primarily due to the formation of biofilm barriers and the resulting immunosuppressive microenvironment, leading to the chronicity and recurrence of IAIs. To address this challenge, we propose a light-induced immune enhancement strategy, synthesizing BSA@MnO2@Ce6@Van (BMCV). The BMCV exhibits precise targeting and adhesion to the S. aureus biofilm-infected region, coupled with its capacity to catalyze oxygen generation from H2O2 in the hypoxic and acidic biofilm microenvironment (BME), promoting oxygen-dependent photodynamic therapy efficacy while ensuring continuous release of manganese ions. Notably, targeted BMCV can penetrate biofilms, producing ROS that degrade extracellular DNA, disrupting the biofilm structure and impairing its barrier function, making it vulnerable to infiltration and elimination by the immune system. Furthermore, light-induced reactive oxygen species (ROS) around the biofilm can lyse S. aureus, triggering bacterium-like immunogenic cell death (ICD), releasing abundant immune costimulatory factors, facilitating the recognition and maturation of antigen-presenting cells (APCs), and activating adaptive immunity. Additionally, manganese ions in the BME act as immunoadjuvants, further amplifying macrophage-mediated innate and adaptive immune responses and reversing the immunologically cold BME to an immunologically hot BME. We prove that our synthesized BMCV elicits a robust adaptive immune response in vivo, effectively clearing primary IAIs and inducing long-term immune memory to prevent recurrence. Our study introduces a potent light-induced immunomodulatory nanoplatform capable of reversing the biofilm-induced immunosuppressive microenvironment and disrupting biofilm-mediated protective barriers, offering a promising immunotherapeutic strategy for addressing challenging S. aureus IAIs.

Neutrophil Function Conversion Driven by Immune Switchpoint Regulator against Diabetes-Related Biofilm Infections.

Reinforced biofilm structures and dysfunctional neutrophils induced by excessive oxidative stress contribute to the refractoriness of diabetes-related biofilm infections (DRBIs). Herein, in contrast to traditional antibacterial therapies, an immune switchpoint-driven neutrophil immune function conversion strategy based on a deoxyribonuclease I loaded vanadium carbide MXene (DNase-I@V2 C) nanoregulator is proposed to treat DRBIs via biofilm lysis and redirecting neutrophil functions from NETosis to phagocytosis in diabetes. Owing to its intrinsic superoxide dismutase/catalase-like activities, DNase-I@V2 C effectively scavenges reactive oxygen species (ROS) in a high oxidative stress microenvironment to maintain the biological activity of DNase-I. By increasing the depth of biofilm penetration of DNase-I, DNase-I@V2 C thoroughly degrades extracellular DNA and neutrophil extracellular traps (NETs) in extracellular polymeric substances, thus breaking the physical barrier of biofilms. More importantly, as an immune switchpoint regulator, DNase-I@V2 C can skew neutrophil functions from NETosis toward phagocytosis by intercepting ROS-NE/MPO-PAD4 and activating ROS-PI3K-AKT-mTOR pathways in diabetic microenvironment, thereby eliminating biofilm infections. Biofilm lysis and synergistic neutrophil function conversion exert favorable therapeutic effects on biofilm infections in vitro and in vivo. This study serves as a proof-of-principle demonstration of effectively achieving DRBIs with high therapeutic efficacy by regulating immune switchpoint to reverse neutrophil functions.

Methylation of AcGST1 Is Associated with Anthocyanin Accumulation in the Kiwifruit Outer Pericarp.

Most red-fleshed kiwifruit cultivars, such as Hongyang, only accumulate anthocyanins in the inner pericarp; the trait of full red flesh becomes the goal pursued by breeders. In this study, we identified a mutant "H-16" showing a red color in both the inner and outer pericarps, and the underlying mechanism was explored. Through transcriptome analysis, a key differentially expressed gene AcGST1 was screened out, which was positively correlated with anthocyanin accumulation in the outer pericarp. The result of McrBC-PCR and bisulfite sequencing revealed that the SG3 region (-292 to -597 bp) of AcGST1 promoter in "H-16" had a significantly lower CHH cytosine methylation level than that in Hongyang, accompanied by low expression of methyltransferase genes (MET1 and CMT2) and high expression of demethylase genes (ROS1 and DML1). Transient calli transformation confirmed that demethylase gene DML1 can activate transcription of AcGST1 to enhance its expression. Overexpression of AcGST1 enhanced the anthocyanin accumulation in the fruit flesh and leaves of the transgenic lines. These results suggested that a decrease in the methylation level of the AcGST1 promoter may contribute to accumulation of anthocyanin in the outer pericarp of "H-16".

ITGB1 alleviates osteoarthritis by inhibiting cartilage inflammation and apoptosis via activating cAMP pathway.

OBJECTIVE: We aimed to screen novel biomarkers for osteoarthritis (OA) using bioinformatic methods and explore its regulatory mechanism in OA development. METHODS: Differentially expressed genes were screened out from GSE98918 and GSE82107 datasets. Protein-protein interaction network and enrichment analysis were employed to search for hub gene and regulatory pathway. Hematoxylin-eosin, Safranin O-Fast green staining, and immunohistochemistry were performed to assess pathological damage. TNF-α, IL-1ß, and IL-6 concentrations were determined by enzyme-linked immunosorbent assay. Real-time quantitative PCR was applied to verify expression of hub genes in OA model. The expression of key protein and pathway proteins was determined by western blot. Furthermore, Cell Counting Kit-8 and flow cytometry were conducted to explore the role of hub gene in chondrocytes. RESULTS: We identified 6 hub genes of OA, including ITGB1, COL5A1, COL1A1, THBS2, LAMA1, and COL12A1, with high prediction value. ITGB1 was screened as a pivotal regulator of OA and cAMP pathway was selected as the key regulatory pathway. ITGB1 was down-regulated in OA model. ITGB1 overexpression attenuated pathological damage and apoptosis in OA rats with the reduced levels of TNF-α, IL-1ß and IL-6. ITGB1 overexpression activated cAMP pathway in vivo and vitro models. In vitro model, ITGB1 overexpression promoted cell viability, while inhibited apoptosis. ITGB1 overexpression also caused a decrease of TNF-α, IL-1ß, and IL-6 concentrations. cAMP pathway inhibitor reversed the positive effect of ITGB1 on OA cell model. CONCLUSION: ITGB1 is a novel biomarker for OA, which inhibits OA development by activating the cAMP pathway.

Trends in microbiological epidemiology of orthopedic infections: a large retrospective study from 2008 to 2021.

BACKGROUND: This study assessed the distribution characteristics of pathogens isolated from cases of orthopedic infections and focused on the antimicrobial susceptibility of the main pathogens. METHODS: This retrospective study involved patients with orthopedic infection in a tertiary medical center located in Shanghai, China, from 2008 to 2021.Pathogen information and the basic information of patients were identified from clinical microbiology laboratory data and the institutional medical record system. RESULTS: In total, the pathogen information of 2821 patients were enrolled in the study. S. aureus (37.71%) was the main causative pathogen responsible for orthopedic infection. Gender, pathogens distribution and polymicrobial infection rates were significantly different (P < 0.05) among patients with different orthopedic infection diseases.The trends in the distribution of pathogens in the total cohort, implant-related infection group (Group A), non-implant-related infection group (Group B), and the sub-group of cases with arthroplasty showed significant linear changes over time. And the polymicrobial infection rates of the total cohort (from 17.17% to 11.00%), Group B(from 24.35% to 14.47%), and the sub-group of cases with internal fixation (from 10.58% to 4.87%) decreased significantly. The antimicrobial susceptibility showed changing trends with time for some main pathogens, especially for S.aureus and Enterobacter spp. CONCLUSIONS: Our research indicated that the pathogen distribution and antimicrobial susceptibility in orthopedic infections changed over time. And the distribution of pathogens varied significantly among different types of orthopedic infectious diseases. These findings may serve as a reference for prophylaxis and empirical treatment strategies of orthopedic infection.

Identification of Staphylococcus aureus virulence-modulating RNA from transcriptomics data with machine learning.

The virulence factors of Staphylococcus aureus are tightly controlled by two-component systems (TCSs) and small RNA (sRNA). TCSs have been well studied over the past several decades, but our understanding of sRNA functions lags far behind that of TCS functions. Here, we studied the biological role of sRNA from 506 S. aureus RNA-seq datasets using independent component analysis (ICA). We found that a previously neglected sRNA, Sau-41, functions in the Agr system. Sau-41 is located within the PSMα operon and controlled by the Agr system. It was predicted to share 22-base complementarity with RNAIII, a major regulator of S. aureus virulence. The EMSA results demonstrated that Sau-41 directly binds to RNAIII. Furthermore, our results found that Sau-41 is capable of repressing S. aureus haemolysin activity by downregulating α-haemolysin and δ-toxin. The repression of α-haemolysin was attributed to the competition between the 5' UTR of hla and Sau-41 for binding RNAIII. We observed that Sau-41 mitigated S. aureus virulence in an orthopaedic implant infection mouse model and alleviated osteolysis. Together, our results indicate that Sau-41 is a virulence-regulating RNA and suggest that Sau-41 might be involved in a negative feedback mechanism to control the Agr system. This work is a demonstration of using ICA in sRNA identification by mining high-throughput data and could be extended to other organisms as well.

Evaluation of the prognostic value of the anatomical characteristics of the bony structures in the shoulder in bursal-sided partial-thickness rotator cuff tears.

Background: In recent studies, individual scapular anatomy has been found to be related to degenerative full-thickness rotator cuff tears. However, research on the relationship between the anatomical characteristics of shoulder radiographs and bursal-sided partial-thickness rotator cuff tears (PTRCTs) is limited, and the risk factors for this pathology still need to be determined. Methods: The bursal-sided PTRCTs group included 102 patients without a history of shoulder trauma who underwent arthroscopy between January 2021 and October 2022. A total of 102 demographically matched outpatients with intact rotator cuffs were selected as the control group. Radiographs were used to measure the lateral acromial angle (LAA), critical shoulder angle (CSA), greater tuberosity angle (GTA), ß-angle, acromion index (AI), acromiohumeral distance (AHD), acromial tilt (AT), acromial slope (AS), acromial type, and acromial spur by two independent observers. Multivariate analyses of these data were used to identify potential risk factors for bursal-sided PTRCTs. Receiver operating characteristic (ROC) analysis was performed to assess the sensitivity and specificity of CSA, GTA, and AI for this type of pathology. Result: The ß-angle, AHD, AS and acromion type showed no difference between bursal-sided PTRCTs and controls (p = 0.009, 0.200, 0.747 and 0.078, respectively). CSA, GTA and AI were significantly higher in bursal-sided PTRCTs (p < 0.001). LAA, ß-angle and AT were significantly lower in bursal-sided PTRCTs. Multivariate logistic regression analysis demonstrated significant correlations between the acromial spur (p = 0.024), GTA (p = 0.004), CSA (p = 0.003) and AI (p = 0.048) and bursal-sided PTRCTs. The areas under the ROC curves for AI, CSA, and GTA were 0.655 (95% CI 0.580-0.729), 0.714 (95% CI 0.644-0.784), and 0.695 (95% CI 0.622-0.767), respectively. Conclusion: Acromial spur, GTA, CSA, and AI were independent risk factors for bursal-sided PTRCTs. Furthermore, CSA was the most powerful predictor of bursal-sided PTRCTs compared to GTA and AI.

Interactions between Macrophages and Biofilm during Staphylococcus aureus-Associated Implant Infection: Difficulties and Solutions.

Staphylococcus aureus (S. aureus) biofilm is the major cause of failure of implant infection treatment that results in heavy social and economic burden on individuals, families, and communities. Planktonic S. aureus attaches to medical implant surfaces where it proliferates and is wrapped by extracellular polymeric substances, forming a solid and complex biofilm. This provides a stable environment for bacterial growth, infection maintenance, and diffusion and protects the bacteria from antimicrobial agents and the immune system of the host. Macrophages are an important component of the innate immune system and resist pathogen invasion and infection through phagocytosis, antigen presentation, and cytokine secretion. The persistence, spread, or clearance of infection is determined by interplay between macrophages and S. aureus in the implant infection microenvironment. In this review, we discuss the interactions between S. aureus biofilm and macrophages, including the effects of biofilm-related bacteria on the macrophage immune response, roles of myeloid-derived suppressor cells during biofilm infection, regulation of immune cell metabolic patterns by the biofilm environment, and immune evasion strategies adopted by the biofilm against macrophages. Finally, we summarize the current methods that support macrophage-mediated removal of biofilms and emphasize the importance of considering multi-dimensions and factors related to implant-associated infection such as immunity, metabolism, the host, and the pathogen when developing new treatments.

Flexible Radiative Cooling Textiles Based on Composite Nanoporous Fibers for Personal Thermal Management.

Passive radiative cooling textiles can reflect sunlight and dissipate heat directly to the outside space without any energy input. However, radiative cooling textiles with high performance, large scalability, cost effectiveness, and high biodegradability are still uncommon. Herein, we exploit a porous fiber-based radiative cooling textile (PRCT) via nonsolvent-induced phase separation and scalable roll-to-roll electrospinning technology. Nanopores are introduced into single fibers, and the pore size can be accurately optimized by managing the relative humidity of the spinning environment. The anti-ultraviolet radiation and superhydrophobicity of textiles were improved by the introduction of core-shell silica microspheres. An optimized PRCT yields a strong solar reflectivity of 98.8% and atmospheric window emissivity of 97%, which results in a sub-ambient temperature drop of 4.5 °C, with the solar intensity over 960 W·m-2 and 5.5 °C at night. For personal thermal management, it is demonstrated that the PRCT can obtain a temperature drop of 7.1 °C compared to the bare skin under direct sunlight. Given the excellent optical and cooling properties, flexibility, and self-cleaning property, PRCT was demonstrated to be a potential candidate for commercial applications in multifarious complex scenarios to afford a style for global decarbonization.

Single-cell transcriptome reveals Staphylococcus aureus modulating fibroblast differentiation in the bone-implant interface.

BACKGROUND: This study aimed to delineate the cell heterogeneity in the bone-implant interface and investigate the fibroblast responses to implant-associated S. aureus infection. METHODS: Single-cell RNA sequencing of human periprosthetic tissues from patients with periprosthetic joint infection (PJI, n = 3) and patients with aseptic loosening (AL, n = 2) was performed. Cell type identities and gene expression profiles were analyzed to depict the single-cell landscape in the periprosthetic environment. In addition, 11 publicly available human scRNA-seq datasets were downloaded from GSE datasets and integrated with the in-house sequencing data to identify disease-specific fibroblast subtypes. Furthermore, fibroblast pseudotime trajectory analysis and Single-cell regulatory network inference and clustering (SCENIC) analysis were combined to identify transcription regulators responsible for fibroblast differentiation. Immunofluorescence was performed on the sequenced samples to validate the protein expression of the differentially expressed transcription regulators. RESULTS: Eight major cell types were identified in the human bone-implant interface by analyzing 36,466 cells. Meta-analysis of fibroblasts scRNA-seq data found fibroblasts in the bone-implant interface express a high level of CTHRC1. We also found fibroblasts could differentiate into pro-inflammatory and matrix-producing phenotypes, each primarily presented in the PJI and AL groups, respectively. Furthermore, NPAS2 and TFEC which are activated in PJI samples were suggested to induce pro-inflammatory polarization in fibroblasts, whereas HMX1, SOX5, SOX9, ZIC1, ETS2, and FOXO1 are matrix-producing regulators. Meanwhile, we conducted a CMap analysis and identified forskolin as a potential regulator for fibroblast differentiation toward matrix-producing phenotypes. CONCLUSIONS: In this study, we discovered the existence of CTHRC1+ fibroblast in the bone-implant interface. Moreover, we revealed a bipolar mode of fibroblast differentiation and put forward the hypothesis that infection could modulate fibroblast toward a pro-inflammatory phenotype through NPAS2 and TFEC.

A comprehensive metabolic map reveals major quality regulations in red-flesh kiwifruit (Actinidia chinensis).

Kiwifruit (Actinidia chinensis) is one of the popular fruits world-wide, and its quality is mainly determined by key metabolites (sugars, flavonoids, and vitamins). Previous works on kiwifruit are mostly done via a single omics approach or involve only limited metabolites. Consequently, the dynamic metabolomes during kiwifruit development and ripening and the underlying regulatory mechanisms are poorly understood. In this study, using high-resolution metabolomic and transcriptomic analyses, we investigated kiwifruit metabolic landscapes at 11 different developmental and ripening stages and revealed a parallel classification of 515 metabolites and their co-expressed genes into 10 distinct metabolic vs gene modules (MM vs GM). Through integrative bioinformatics coupled with functional genomic assays, we constructed a global map and uncovered essential transcriptomic and transcriptional regulatory networks for all major metabolic changes that occurred throughout the kiwifruit growth cycle. Apart from known MM vs GM for metabolites such as soluble sugars, we identified novel transcription factors that regulate the accumulation of procyanidins, vitamin C, and other important metabolites. Our findings thus shed light on the kiwifruit metabolic regulatory network and provide a valuable resource for the designed improvement of kiwifruit quality.

Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa).

The most commercialized kiwifruit, Actinidia chinensis var. deliciosa (Acd), is an allohexaploid (2n = 6x = 174), making high-quality assemblage genome challenging. We previously discovered a rare naturally occurring diploid Acd plant. Here, chromosome-level de novo genome assembly for this diploid Acd was reported, reaching approximately 621.98 Mb in length with contig and scaffold N50 values of 10.08 and 21.09 Mb, respectively, 99.66% of the bases anchored to 29 pseudochromosomes, and 38,990 protein-coding genes and 42.29% repetitive elements annotated. The divergence time of A. chinensis cv. 'Red5' and 'Hongyang' (11.1-27.7 mya) was more recent compared with the divergence time of them and Acd (19.9-41.2 mya), with the divergence time of A. eriantha cv. 'White' being the earliest (22.9-45.7 mya) among that of the four Actinidia species. The 4DTv distance distribution highlighted three recent whole-genome duplication events in Acd. This is the first high-quality diploid Acd genome, which lays an important foundation for not only kiwifruit functional genomics studies but also further elucidating genome evolution of allohexaploid Acd.

Integrative Analysis of Metabolome and Transcriptome Reveals the Mechanism of Color Formation in Yellow-Fleshed Kiwifruit.

During the development of yellow-fleshed kiwifruit (Actinidia chinensis), the flesh appeared light pink at the initial stage, the pink faded at the fastest growth stage, and gradually changed into green. At the maturity stage, it showed bright yellow. In order to analyze the mechanism of flesh color change at the metabolic and gene transcription level, the relationship between color and changes of metabolites and key enzyme genes was studied. In this study, five time points (20 d, 58 d, 97 d, 136 d, and 175 d) of yellow-fleshed kiwifruit were used for flavonoid metabolites detection and transcriptome, and four time points (20 d, 97 d, 136 d, and 175 d) were used for targeted detection of carotenoids. Through the analysis of the content changes of flavonoid metabolites, it was found that the accumulation of pelargonidin and cyanidin and their respective anthocyanin derivatives was related to the pink flesh of young fruit, but not to delphinidin and its derivative anthocyanins. A total of 140 flavonoid compounds were detected in the flesh, among which anthocyanin and 76% of the flavonoid compounds had the highest content at 20 d, and began to decrease significantly at 58 d until 175 d, resulting in the pale-pink fading of the flesh. At the mature stage of fruit development (175 d), the degradation of chlorophyll and the increase of carotenoids jointly led to the change of flesh color from green to yellow, in addition to chlorophyll degradation. In kiwifruit flesh, 10 carotenoids were detected, with none of them being linear carotenoids. During the whole development process of kiwifruit, the content of ß-carotene was always higher than that of α-carotene. In addition, ß-cryptoxanthin was the most-accumulated pigment in the kiwifruit at 175 d. Through transcriptome analysis of kiwifruit flesh, seven key transcription factors for flavonoid biosynthesis and ten key transcription factors for carotenoid synthesis were screened. This study was the first to analyze the effect of flavonoid accumulation on the pink color of yellow-fleshed kiwifruit. The high proportion of ß-cryptoxanthin in yellow-fleshed kiwifruit was preliminarily found. This provides information on metabolite accumulation for further revealing the pink color of yellow-fleshed kiwifruit, and also provides a new direction for the study of carotenoid biosynthesis and regulation in yellow-fleshed kiwifruit.

A novel method to detect the early warning signal of COVID-19 transmission.

BACKGROUND: Infectious illness outbreaks, particularly the corona-virus disease 2019 (COVID-19) pandemics in recent years, have wreaked havoc on human society, and the growing number of infected patients has put a strain on medical facilities. It's necessary to forecast early warning signals of potential outbreaks of COVID-19, which would facilitate the health ministry to take some suitable control measures timely to prevent or slow the spread of COVID-19. However, since the intricacy of COVID-19 transmission, which connects biological and social systems, it is a difficult task to predict outbreaks of COVID-19 epidemics timely. RESULTS: In this work, we developed a new model-free approach, called, the landscape network entropy based on Auto-Reservoir Neural Network (ARNN-LNE), for quantitative analysis of COVID-19 propagation, by mining dynamic information from regional networks and short-term high-dimensional time-series data. Through this approach, we successfully identified the early warning signals in six nations or areas based on historical data of COVID-19 infections. CONCLUSION: Based on the newly published data on new COVID-19 disease, the ARNN-LNE method can give early warning signals for the outbreak of COVID-19. It's worth noting that ARNN-LNE only relies on small samples data. Thus, it has great application potential for monitoring outbreaks of infectious diseases.

Integrative analyses of metabolome and genome-wide transcriptome reveal the regulatory network governing flavor formation in kiwifruit (Actinidia chinensis).

Soluble sugars, organic acids and volatiles are important components that determine unique fruit flavor and consumer preferences. However, the metabolic dynamics and underlying regulatory networks that modulate overall flavor formation during fruit development and ripening remain largely unknown for most fruit species. In this study, by integrating flavor-associated metabolism and transcriptome data from 12 fruit developmental and ripening stages of Actinidia chinensis cv Hongyang, we generated a global map of changes in the flavor-related metabolites throughout development and ripening of kiwifruit. Using this dataset, we constructed complex regulatory networks allowing to identify key structural genes and transcription factors that regulate the metabolism of soluble sugars, organic acids and important volatiles in kiwifruit. Moreover, our study revealed the regulatory mechanism involving key transcription factors regulating flavor metabolism. The modulation of flavor metabolism by the identified key transcription factors was confirmed in different kiwifruit species providing the proof of concept that our dataset provides a suitable tool for clarification of the regulatory factors controlling flavor biosynthetic pathways that have not been previously illuminated. Overall, in addition to providing new insight into the metabolic regulation of flavor during fruit development and ripening, the outcome of our study establishes a foundation for flavor improvement in kiwifruit.

Multicenter analysis of gastrointestinal stromal tumors in inner Mongolia of China: A study of 804 cases.

INTRODUCTION: To analyze the clinicopathological characteristics, immunohistochemistry, genotyping and prognosis of patients in the multicenter GIST data in Inner Mongolia, China. METHODS: Retrospective analysis was performed on GIST data from January 2013 to January 2018 in Inner Mongolia. Descriptive statistics were used to analyze the clinical characteristics of GIST patients. The Chi-square test was performed on the modified NIH criteria by age distribution, and Kaplan-Merie method was used for survival analysis. RESULTS: A total of 804 patients were included in the GIST database in Inner Mongolia, with a male to female ratio of 1.1102:1. The most common location was the gastric (465). Mitotic count ≤5/50HPFs was found in 67.3 % patients. There were 276 patients with tumor diameter of 2-5 cm and 354 patients with tumor diameter of 5.1-10 cm.The modified NIH criteria was mainly of intermediate risk (210) and high risk (342). The recurrence and metastasis of patients were related to the tumor location, mitotic index, tumor size, and modified NIH criteria. All patients were followed up for 1-10 years, in which 63.1 % of them were followed up for at least three years. The 3-year survival rates of patients with modified NIH criteria of very low risk, low risk, intermediate risk, and high risk were 100 %, 100 %, 100 %, and 96.3 %, respectively. CONCLUSIONS: The incidence of GIST in middle-aged and elder people in Inner Mongolia is high, and the long-term prognosis of patients after surgical treatment is good, which can objectively reflect the incidence, diagnosis and treatment of GIST in Inner Mongolia.