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To address the issue of accurately recognizing and locating picking points for tea-picking robots in unstructured environments, a visual positioning method based on RGB-D information fusion is proposed. First, an improved T-YOLOv8n model is proposed, which improves detection and segmentation performance across multi-scale scenes through network architecture and loss function optimizations. In the far-view test set, the detection accuracy of tea buds reached 80.8%; for the near-view test set, the mAP 0.5 values for tea stem detection in bounding boxes and masks reached 93.6% and 93.7%, respectively, showing improvements of 9.1% and 14.1% over the baseline model. Secondly, a layered visual servoing strategy for near and far views was designed, integrating the RealSense depth sensor with robotic arm cooperation. This strategy identifies the region of interest (ROI) of the tea bud in the far view and fuses the stem mask information with depth data to calculate the three-dimensional coordinates of the picking point. The experiments show that this method achieved a picking point localization success rate of 86.4%, with a mean depth measurement error of 1.43 mm. The proposed method improves the accuracy of picking point recognition and reduces depth information fluctuations, providing technical support for the intelligent and rapid picking of premium tea.

Aim: As a major efflux pump system in Gram-negative bacteria, AcrAB-TolC plays a key role in the transport of multiple drug substrates and is considered a potential target for the development of novel antimicrobials. Our previous study found that TolC inactivation compromised the resistance to different antimicrobials in porcine extraintestinal pathogenic Escherichia coli (ExPEC) strain PPECC042 (WT). This study was designed to investigate the functional substitution of TolC by other outer membrane proteins (OMPs) with similar β-barrel structures in pumping out different antimicrobials., Methods and Results: In this study, we found that over-expression of several OMPs with similar β-barrel structures, OmpX, OmpC, OmpN, OmpW, and PhoE, in the ΔtolC strain restored the resistance to macrolides, quinolones, or tetracyclines to the level of WT strain. However, the introduction of any one of the five OMPs did not affect the resistance of the strains ΔacrA, ΔacrB, and ΔacrAΔtolC. Further study revealed that the efflux activity was significantly reduced in the ΔtolC strain, but not in the WT strain and the ΔtolC strains over-expressing various OMPs. Additionally, Nile red dye test and ciprofloxacin accumulation test confirmed that the lost efflux activity and drug accumulation in bacterial periplasm by TolC inactivation was restored by the over-expression of each OMP, depending on the presence of genes acrA and acrB., Conclusion: All five OMPs can replace the TolC protein to play the efflux role in pumping out the drugs from the periplasm to the extracellular space with the help of proteins AcrA and AcrB., (© The Author(s) 2024. Published by Oxford University Press on behalf of Applied Microbiology International.)

To improve detection efficiency and reduce cost consumption in fishery surveys, target detection methods based on computer vision have become a new method for fishery resource surveys. However, the specialty and complexity of underwater photography result in low detection accuracy, limiting its use in fishery resource surveys. To solve these problems, this study proposed an accurate method named BSSFISH-YOLOv8 for fish detection in natural underwater environments. First, replacing the original convolutional module with the SPD-Conv module allows the model to lose less fine-grained information. Next, the backbone network is supplemented with a dynamic sparse attention technique, BiFormer, which enhances the model's attention to crucial information in the input features while also optimizing detection efficiency. Finally, adding a 160 × 160 small target detection layer (STDL) improves sensitivity for smaller targets. The model scored 88.3% and 58.3% in the two indicators of mAP@50 and mAP@50:95, respectively, which is 2.0% and 3.3% higher than the YOLOv8n model. The results of this research can be applied to fishery resource surveys, reducing measurement costs, improving detection efficiency, and bringing environmental and economic benefits.

It is worthwhile to calculate the execution cost of a manipulator for selecting a planning algorithm to generate trajectories, especially for an agricultural robot. Although there are various off-the-shelf trajectory planning methods, such as pursuing the shortest stroke or the smallest time cost, they often do not consider factors synthetically. This paper uses the state-of-the-art Python version of the Robotics Toolbox for manipulator trajectory planning instead of the traditional D-H method. We propose a cost function with mass, iteration, and residual to assess the effort of a manipulator. We realized three inverse kinematics methods (NR, GN, and LM with variants) and verified our cost function's feasibility and effectiveness. Furthermore, we compared it with state-of-the-art methods such as Double A* and MoveIt. Results show that our method is valid and stable. Moreover, we applied LM (Chan λ = 0.1) in mobile operation on our agricultural robot platform.

With the development of agricultural information technology, the Internet of Things and blockchain have become important in the traceability of agricultural products. Sensors collect real-time data in agricultural production and a blockchain provides a secure and transparent storage medium for these data, which improves the transparency and credibility of agricultural product traceability. However, existing agricultural product traceability solutions are limited by the immutability of the blockchain, making it difficult to delete erroneous data and modify the scope of data sharing. This damages the credibility of traceability data and is not conducive to the exchange and sharing of information among enterprises. In this article, we propose an agricultural product traceability data management scheme based on a redactable blockchain. This scheme allows agricultural enterprises to encrypt data to protect privacy. In order to facilitate the maintenance and sharing of data, we introduce a chameleon hash function to provide data modification capabilities. Enterprises can fix erroneous data and update the access permissions of the data. To improve the efficiency of block editing, our scheme adopts a distributed block editing method. This method supports threshold editing operations, avoiding single-point-of-failure issues. We save records of data modifications on the blockchain and establish accountability mechanisms to identify malicious entities. Finally, in this paper we provide a security analysis of our proposed solution and verify its effectiveness through experiments. Compared with the existing scheme, the block generating speed is improved by 42% and the block editing speed is improved by 29.3% at 125 nodes.

Listeria monocytogenes is a ubiquitous foodborne pathogen causing human and animal listeriosis with high mortality. Neurological and maternal-neonatal listeriosis outbreaks in Europe and the United States were frequently associated with clonal complexes CC1, CC2 and CC6 harboring Listeria Pathogenicity Island-1 (LIPI-1), as well as CC4 carrying both LIPI-1 and LIPI-4. However, human listeriosis in China was predominantly linked to CC87 and CC619 from serotype 1/2b. To understand the genetic evolution and distribution patterns of CC619, we characterized the epidemic history, population structure, and transmission feature of CC619 strains through analysis of 49,421 L. monocytogenes genomes globally. We found that CC619 was uniquely distributed in China, and closely related with perinatal infection. As CC619 strains were being mainly isolated from livestock and poultry products, we hypothesized that pigs and live chicken were the reservoirs of CC619. Importantly, all CC619 strains not only harbored the intact LIPI-1 and LIPI-4, but these also carried LIPI-3 that could facilitate host colonization and invasion. The deficiency of LIPI-3 or LIPI-4 markedly decreased L. monocytogenes colonization capacity in a model of intragastric infection in the mouse. Altogether, our findings suggest that the hypervirulent CC619 harboring three pathogenicity islands LIPI-1, LIPI-3 and LIPI-4 is a putatively persistent population in various foods, environment, and human population, warranting the further research for deciphering its pathogenicity and strengthening epidemiological surveillance., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Staphylococcus aureus stands as one of the most pervasive pathogens given its morbidity and mortality worldwide due to its roles as an infectious agent that causes a wide variety of diseases ranging from moderately severe skin infections to fatal pneumonia and sepsis. S. aureus produces a variety of exotoxins that serve as important virulence factors in S. aureus -related infectious diseases and food poisoning in both humans and animals. For example, staphylococcal enterotoxins (SEs) produced by S. aureus induce staphylococcal foodborne poisoning; toxic shock syndrome toxin-1 (TSST-1), as a typical superantigen, induces toxic shock syndrome; hemolysins induce cell damage in erythrocytes and leukocytes; and exfoliative toxin induces staphylococcal skin scalded syndrome. Recently, Panton-Valentine leucocidin, a cytotoxin produced by community-associated methicillin-resistant S. aureus (CA-MRSA), has been reported, and new types of SEs and staphylococcal enterotoxin-like toxins (SEls) were discovered and reported successively. This review addresses the progress of and novel insights into the molecular structure, biological activities, and pathogenicity of both the classic and the newly identified exotoxins produced by S. aureus .

Appropriate histone modifications emerge as essential cell fate regulators of neuronal identities across neocortical areas and layers. Here we showed that NSD1, the methyltransferase for di-methylated lysine 36 of histone H3 (H3K36me2), controls both area and layer identities of the neocortex. Nsd1-ablated neocortex showed an area shift of all four primary functional regions and aberrant wiring of cortico-thalamic-cortical projections. Nsd1 conditional knockout mice displayed defects in spatial memory, motor learning, and coordination, resembling patients with the Sotos syndrome carrying NSD1 mutations. On Nsd1 loss, superficial-layer pyramidal neurons (PNs) progressively mis-expressed markers for deep-layer PNs, and PNs remained immature both morphologically and electrophysiologically. Loss of Nsd1 in postmitotic PNs causes genome-wide loss of H3K36me2 and re-distribution of DNA methylation, which accounts for diminished expression of neocortical layer specifiers but ectopic expression of non-neural genes. Together, H3K36me2 mediated by NSD1 is required for the establishment and maintenance of region- and layer-specific neocortical identities., Competing Interests: Declaration of interests The authors declare no conflict of interest., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Extraintestinal pathogenic Escherichia coli (ExPEC) is an important zoonotic pathogen. Recently, ExPEC has been reported to be an emerging problem in pig farming. However, the mechanism of pathogenicity of porcine ExPEC remains to be revealed. In this study, we constructed a transposon (Tn) mutagenesis library covering Tn insertion in over 72% of the chromosome-encoded genes of a virulent and multi-drug resistant porcine ExPEC strain PCN033. By using a mouse infection model, a transposon-directed insertion site sequencing (TraDIS) assay was performed to identify in vivo fitness factors. By comparing the Tn insertion frequencies between the input Tn library and the recovered library from different organs, 64 genes were identified to be involved in fitness during systemic infection. 15 genes were selected and individual gene deletion mutants were constructed. The in vivo fitness was evaluated by using a competitive infection assay. Among them, Δ fimG was significantly outcompeted by the WT strain in vivo and showed defective adhesion to host cells. rfa which was involved in lipopolysaccharide biosynthesis was shown to be critical for in vivo fitness which may have resulted from its role in the resistance to serum killing. In addition, several metabolic genes including fepB , sdhC , fepG , gltS , dcuA , ccmH , ddpD , narU , glpD , malM , and yabL and two regulatory genes metJ and baeS were shown as important determinants of in vivo fitness of porcine ExPEC. Collectively, this study performed a genome-wide screening for in vivo fitness factors which will be important for understanding the pathogenicity of porcine ExPEC.

The scalable development of an environmentally adaptive and homogeneous Li + supplementary route remains a formidable challenge for the existing prelithiation technologies, restricting the full potential of high-capacity anodes. In this study, we present a moisture-tolerant interfacial prelithiation approach through casting a hydrophobic poly(vinylidene- co -hexafluoropropylene) membrane blended with a deep-lithiated alloy (Li 22 Si 5 @ C/PVDF-HFP) onto Si based anodes. This strategy could not only extend to various high-capacity anode systems (SiO x @C, hard carbon) but also align with industrial roll-to-roll assembly processes. By carefully adjusting the thickness of the prelithiation layer, the densely packed Si@C electrode (4.5 mAh cm -2 ) exhibits significantly improved initial Coulombic efficiency until a close-to-unit value, as well as extreme moisture tolerance (60% relative humidity). Furthermore, it achieves more than 10-fold enhancement of ionic conductivity across the electrode. As pairing the prelithiated Si@C anode with the LiNi 0.8 Co 0.1 Mn 0.1 O 2 cathode, the 2 Ah pouch-format prototype balances an energy density of ∼371 Wh kg -1 as well as 83.8% capacity retention for 1000 cycles. The combined operando phase tracking and spatial arrangement analysis of the intermediate alloy elucidate that the enhanced Li utilization derives from the gradient stress dissipation model upon a spontaneous Li -1 as well as 83.8% capacity retention for 1000 cycles. The combined operando phase tracking and spatial arrangement analysis of the intermediate alloy elucidate that the enhanced Li utilization derives from the gradient stress dissipation model upon a spontaneous Li + redistribution process.

Li-containing alloys and metallic deposits offer substantial Li + storage capacities as alternative anodes to commercial graphite. However, the thermodynamically in sequence, yet kinetically competitive mechanism between Li solubility in the solid solution and intermediate alloy-induced Li deposition remains debated, particularly across the multiple scales. The elucidation of the mechanism is rather challenging due to the dynamic alloy evolution upon the non-equilibrium, transient lithiation processes under coupled physical fields. Here, influential factors governing Li solubility in the Li-Zn alloy are comprehensively investigated as a demonstrative model, spanning from the bulk electrolyte solution to the ion diffusion within the electrode. Through real-time phase tracking and spatial distribution analysis of intermediate alloy/Li metallic species at varied temperatures, current densities and particle sizes, the driving force of Li solubility and metallic plating along the Li migration pathway are probed in-depth. This study investigates the correlation between kinetics (pronounced concentration polarization, miscibility gap in lattice grains) and rate-limiting interfacial charge transfer thermodynamics in dedicating the Li diffusion into the solid solution. Additionally, the lithiophilic alloy sites with the balanced diffusion barrier and Li adsorption energy are explored to favor the homogeneous metal plating, which provides new insights for the rational innovation of high-capacity alloy/metallic anodes., (© 2023 Wiley-VCH GmbH.)

Aim: This study aims to investigate the prevalence of intestinal pathogenic Escherichia coli (InPEC) in healthy pig-related samples and evaluate the potential virulence of the InPEC strains., Methods and Results: A multiplex PCR method was established to identify different pathotypes of InPEC. A total of 800 rectal swab samples and 296 pork samples were collected from pig farms and slaughterhouses in Hubei province, China. From these samples, a total of 21 InPEC strains were isolated, including 19 enteropathogenic E. coli (EPEC) and 2 shiga toxin-producing E. coli (STEC) strains. By whole-genome sequencing and in silico typing, it was shown that the sequence types and serotypes were diverse among the strains. Antimicrobial susceptibility assays showed that 90.48% of the strains were multi-drug resistant. The virulence of the strains was first evaluated using the Galleria mellonella larvae model, which showed that most of the strains possessed medium to high pathogenicity. A moderately virulent EPEC isolate was further selected to characterize its pathogenicity using a mouse model, which suggested that it could cause significant diarrhea. Bioluminescence imaging (BLI) was then used to investigate the colonization dynamics of this EPEC isolate, which showed that the EPEC strain could colonize the mouse cecum for up to 5 days., (© The Author(s) 2023. Published by Oxford University Press on behalf of Applied Microbiology International.)

The dissemination of Staphylococcus aureus in the pork production chain is a major food safety concern. Abattoirs can serve both as disruptor and transmitter for S. aureus . In this study, we conducted a systematic genomic epidemiology research on the prevalence, heterogeneity, and transmission of S. aureus in 3,638 samples collected from four pig abattoirs in Hubei province, China. Our findings revealed substantial heterogeneity between S. aureus recovered from samples collected at upstream (from stunning step to head-removal step) and downstream (from splitting step to chilling step) locations within the slaughter process. Overall, 966 (26.6%) samples were positive for S. aureus , with significantly higher overall prevalence for upstream samples (29.0%, 488/1,681) compared to downstream samples (24.4%, 478/1,957). Antimicrobial susceptibility testing demonstrated that the isolates from the upstream exhibited significantly higher resistance proportions to different antimicrobials than those from the downstream. Whole-genome sequencing of 126 isolates revealed that ST398 (32.9%, 23/70) and ST9 (22.9%, 16/70) were more common among upstream isolates, while ST7 (35.7%, 20/56) and ST97 (28.6%, 16/56) were most frequently observed among downstream isolates. Additionally, molecular characterization analysis demonstrated that upstream isolates possessed significantly higher enterotoxigenic potential, more antimicrobial resistance genes, and S. aureus pathogenicity islands than downstream isolates. Notably, we discovered that enterotoxigenic S. aureus could be transmitted across different slaughter stages, with knives, water, and air serving as vectors. Although slaughtering processes had a substantial effect on reducing the food safety risk posed by enterotoxigenic S. aureus , the possibility of its widespread transmission should not be disregarded. IMPORTANCE Staphylococcus aureus ( S. aureus ) is one of the most important foodborne pathogens, and can cause foodborne poisoning by producing enterotoxins. Pork is a preferable reservoir and its contamination often occurs during the slaughter process. Our findings revealed significant differences in the prevalence, antimicrobial resistance, and enterotoxigenic potential between the upstream and downstream isolates within the slaughter process. Also, it is imperative not to overlook enterotoxigenic S. aureus transmitted across all stages of the slaughter process, with notable vectors being knives, water, and air. These findings hold significant implications for policy-makers to reassess their surveillance projects, and underscore the importance of implementing effective control measures to minimize the risk of S. aureus contamination in pork production. Moreover, we provide a more compelling method of characterizing pathogen transmission based on core-SNPs of bacterial genomes.

This paper discusses a semantic segmentation framework and shows its application in agricultural intelligence, such as providing environmental awareness for agricultural robots to work autonomously and efficiently. We propose an ensemble framework based on the bagging strategy and the UNet network, using RGB and HSV color spaces. We evaluated the framework on our self-built dataset (Maize) and a public dataset (Sugar Beets). Then, we compared it with UNet-based methods (single RGB and single HSV), DeepLab V3+, and SegNet. Experimental results show that our ensemble framework can synthesize the advantages of each color space and obtain the best IoUs (0.8276 and 0.6972) on the datasets (Maize and Sugar Beets), respectively. In addition, including our framework, the UNet-based methods have faster speed and a smaller parameter space than DeepLab V3+ and SegNet, which are more suitable for deployment in resource-constrained environments such as mobile robots.

Hard carbons (HCs) are extensively investigated as the potential anodes for commercialization of sodium-ion batteries (SIBs). However, the practical deployment of HC anode suffers from the retarded Na + diffusion at the high-rate or low-temperature operation scenarios. Herein, a multiscale modification strategy by tuning HC microstructure on the particle level as well as replenishing extra Na + reservoir for the electrode through a homogeneous presodiation therapy is presented. Consequently, the coulombic efficiency of HC anode can be precisely controlled till the close-to-unit value. Detailed kinetics analysis observes that the Na + diffusivity can be drastically enhanced by two orders of magnitude at the low potential region (< 0.1 V vs. Na + /Na), which accelerates the rate-limiting step. As pairing the presodiated HC anode (≈5.0 ± 0.2 mg cm -2 ) with the NaVPO 4 F cathode (≈10.3 mg cm -2 ) in the 200 mAh pouch cell, the optimal balance of the cyclability (83% over 1000 cycles), low-temperature behavior till -40 °C as well as the maximized power output of 1500 W kg -1 can be simultaneously achieved. This synergistic modification strategy opens a new avenue to exploit the reversible, ultrafast Na + storage kinetics of HC anodes, which thus constitutes a quantum leap forward toward high-rate SIB prototyping., (© 2023 Wiley-VCH GmbH.)

Glioblastoma multiforme (GBM), a highly malignant and heterogeneous brain tumor, contains various types of tumor and non-tumor cells. Whether GBM cells can trans-differentiate into non-neural cell types, including mural cells or endothelial cells (ECs), to support tumor growth and invasion remains controversial. Here we generated two genetic GBM models de novo in immunocompetent mouse brains, mimicking essential pathological and molecular features of human GBMs. Lineage-tracing and transplantation studies demonstrated that, although blood vessels in GBM brains underwent drastic remodeling, evidence of trans-differentiation of GBM cells into vascular cells was barely detected. Intriguingly, GBM cells could promiscuously express markers for mural cells during gliomagenesis. Furthermore, single-cell RNA sequencing showed that patterns of copy number variations (CNVs) of mural cells and ECs were distinct from those of GBM cells, indicating discrete origins of GBM cells and vascular components. Importantly, single-cell CNV analysis of human GBM specimens also suggested that GBM cells and vascular cells are likely separate lineages. Rather than expansion owing to trans-differentiation, vascular cell expanded by proliferation during tumorigenesis. Therefore, cross-lineage trans-differentiation of GBM cells is very unlikely to occur during gliomagenesis. Our findings advance understanding of cell lineage dynamics during gliomagenesis, and have implications for targeted treatment of GBMs., (©The Author(s) 2022. Published by Oxford University Press on behalf of Higher Education Press.)

Aims: To assess the co-transmission risk of phenotypic and genetic resistance to cephalosporins, colistin, and fosfomycin in Salmonella strains collected along the whole pork production chain., Methods and Results: From a total of 107 Salmonella isolates from samples collected in pig slaughterhouses and markets, 15 ESBL-producing Salmonella strains resistant to cefotaxime were identified by broth microdilution method and clavulanic acid inhibition test, including 14 monophasic Salmonella Typhimurium strains and one Salmonella Derby strain. Whole genome sequence analysis showed that nine monophasic S. Typhimurium strains coresistant to colistin and fosfomycin carried the resistance genes blaCTX-M-14, mcr-1, and fosA3. Conjugational transfer tests demonstrated that the phenotypic and genetic resistance to cephalosporins, colistin, and fosfomycin could cotransfer back and forth between Salmonella and Escherichia coli via an IncHI2/pSH16G4928-like plasmid., Conclusions: This study reports the cotransmission of phenotypic and genetic resistance to cephalosporins, colistin, and fosfomycin via an IncHI2/pSH16G4928-like plasmid in Salmonella strains of animal origin, giving an alarm for the prevention of the development and spread of bacterial multidrug resistance., (© The Author(s) 2022. Published by Oxford University Press on behalf of Applied Microbiology International.)

Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex 398 (CC398) is the dominant livestock-associated (LA) MRSA lineage in European livestock and an increasing cause of difficult-to-treat human disease. LA-CC398 MRSA evolved from a diverse human-associated methicillin-sensitive population, and this transition from humans to livestock was associated with three mobile genetic elements (MGEs). In this study, we apply transposon-directed insertion site sequencing (TraDIS), a high-throughput transposon mutagenesis approach, to investigate genetic signatures that contribute to LA-CC398 causing disease in humans. We identified 26 genes associated with LA-CC398 survival in human blood and 47 genes in porcine blood. We carried out phylogenetic reconstruction on 1,180 CC398 isolates to investigate the genetic context of all identified genes. We found that all genes associated with survival in human blood were part of the CC398 core genome, while 2/47 genes essential for survival in porcine blood were located on MGEs. Gene SAPIG0966 was located on the previously identified Tn 916 transposon carrying a tetracycline resistance gene, which has been shown to be stably inherited within LA-CC398. Gene SAPIG1525 was carried on a phage element, which in part, matched phiSa2wa&#95;st1, a previously identified bacteriophage carrying the Panton-Valentine leucocidin (PVL) virulence factor. Gene deletion mutants constructed in two LA-CC398 strains confirmed that the SAPIG0966 carrying Tn 916 and SAPIG1525 were important for CC398 survival in porcine blood. Our study shows that MGEs that carry antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for host adaptation. IMPORTANCE CC398 is the dominant type of methicillin-resistant Staphylococcus aureus (MRSA) in European livestock and a growing cause of human infections. Previous studies have suggested MRSA CC398 evolved from human-associated methicillin-sensitive Staphylococcus aureus and is capable of rapidly readapting to human hosts while maintaining antibiotic resistance. Using high-throughput transposon mutagenesis, our study identified 26 and 47 genes important for MRSA CC398 survival in human and porcine blood, respectively. Two of the genes important for MRSA CC398 survival in porcine blood were located on mobile genetic elements (MGEs) carrying resistance or virulence genes. Our study shows that these MGEs carrying antimicrobial resistance and virulence genes could have a secondary function in bacterial survival in blood and may be important for blood infection and host adaptation.

Fusarium head blight (FHB) is considered one of the most serious fungal diseases of wheat. Fusarium resulted in yield losses and contamination of harvested grains with mycotoxins. Therefore, diagnosing Fusarium head blight in early asymptomatic wheat is vital. To detect early FHB, a micro-near-infrared spectrometer was used to collect the spectrum of wheat grains, and FHB infection of wheat was detected by combining chemometrics in the 900-1700 nm near-infrared spectral region. First, the obtained spectra were analysed accordingly, and the pre-processed data were compared. The modelling analysis was then performed using the support vector machine (SVM), random forest (RF), extreme gradient descent (XGBoost), Autokeras, and Autogluon (with SVM) algorithms. The results showed that SG smoothing with standard normal variate (SG + SNV) was the best pre-treatment method. In addition, after SG + SNV was combined with the Autogluon (with SVM) model, the optimal classification results were obtained, with an accuracy of 73.33 % and an F1 value of 72.86 %. Autogluon (with SVM) could prevent overfitting and optimize generalization. Then, this manuscript discusses the performance of the Autogluon (with SVM) model with different stacking layers. The results show that one stacking layer can obtain a classification model with excellent performance. These results indicated that the near infrared spectrum (NIR) has the potential for early detection of Fusarium head blight with asymptomatic early statements., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Development of cefotaxime-resistance and biofilm formation increase the difficulty to prevent and control the infection and contamination of Salmonella, one of the most important foodborne and zoonotic bacterial pathogen. Our previous study observed that 1/8 minimum inhibitory concentration (MIC) of cefotaxime induced the enhancement of biofilm formation and filamentous morphological change by a monophasic Salmonella Typhimurium strain SH16SP46. This study was designed to explore the role of three penicillin-binding proteins (PBPs) in mediating the induction effect of cefotaxime. Three deletion mutants of the genes mrcA, mrcB, and ftsI, encoding the proteins PBP1a, PBP1b, and PBP3, respectively, were constructed using the parental Salmonella strain SH16SP46. Gram staining and scanning electron microscopy showed that these mutants showed normal morphology comparable to the parental strain without cefotaxime treatment. However, under the stress of 1/8 MIC of cefotaxime, the strains WT, ΔmrcA, and ΔftsI, rather than ΔmrcB, exhibited filamentous morphological change. Moreover, cefotaxime treatment significantly enhanced biofilm formation by the strains WT, ΔmrcA, and ΔftsI, but not by the ΔmrcB strain. The complement of mrcB gene in the ΔmrcB strain recovered the enhanced biofilm formation and filamentous morphological change induced by cefotaxime. Our results suggest that PBP1b encoded by mrcB gene may be a binding target of cefotaxime for initiating the effect on Salmonella morphology and biofilm formation. The study will contribute to further understanding of the regulatory mechanism of cefotaxime on Salmonella biofilm formation., (© The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.)

Purpose: Surface-based image-to-patient registration in current surgical navigation is mainly achieved by a 3D scanner, which has several limitations in clinical practice such as uncontrollable scanning range, complicated operation, and even high failure rate. An accurate, robust, and easy-to-perform image-to-patient registration method is urgently required., Methods: An incremental point cloud registration method was proposed for surface-based image-to-patient registration. The point cloud in image space was extracted from the computed tomography (CT) image, and a template matching method was applied to remove the redundant points. The corresponding point cloud in patient space was incrementally collected by an optically tracked pointer, while the nearest point distance (NPD) constraint was applied to ensure the uniformity of the collected points. A coarse-to-fine registration method under the constraints of coverage ratio (CR) and outliers ratio (OR) was then proposed to obtain the optimal rigid transformation from image to patient space. The proposed method was integrated in the recently developed endoscopic navigation system, and phantom study and clinical trials were conducted to evaluate the performance of the proposed method., Results: The results of the phantom study revealed that the proposed constraints greatly improved the accuracy and robustness of registration. The comparative experimental results revealed that the proposed registration method significantly outperform the scanner-based method, and achieved comparable accuracy to the fiducial-based method. In the clinical trials, the average registration duration was 1.24 ± 0.43 min, the target registration error (TRE) of 294 marker points (59 patients) was 1.25 ± 0.40 mm, and the lower 97.5% confidence limit of the success rate of positioning marker points exceeds the expected value (97.56% vs. 95.00%), revealed that the accuracy of the proposed method significantly met the clinical requirements (TRE ⩽ 2 mm, p < 0.05)., Conclusions: The proposed method has both the advantages of high accuracy and convenience, which were absent in the scanner-based method and the fiducial-based method. Our findings will help improve the quality of endoscopic sinus and skull base surgery., (© 2022 American Association of Physicists in Medicine.)

Staphylococcus aureus is one of the major foodborne pathogens and can cause serious foodborne illness in humans by foods contaminated with S. aureus enterotoxins. In recent years, livestock-associated S. aureus has been a major public health concern for humans and has emerged in various countries globally. China is one of the largest producers of pigs and pork in the world. However, there are few studies on the detailed genotypic and pathogenic characterization of pork-associated S. aureus in China. In this study, the prevalence, antimicrobial resistance, and genotypic characteristics of S. aureus in raw pork in Wuhan, China, were investigated through multilocus sequence typing (MLST), staphylococcal protein A gene ( spa ) typing, and whole-genome sequencing analysis. A total of 518 S. aureus isolates (16.9%) were isolated from 3067 retail and wholesale pork samples. The prevalence of S. aureus in retail pork (22.7%) was significantly higher than in wholesale pork (15.1%), while the proportion of multidrug-resistant (MDR) isolates in wholesale pork (12.9%) was significantly higher than in retail pork (6.2%). Among the isolates, 10.8% were resistant to three or more antibiotics, with higher rates of resistance to penicillin (88.8%) and erythromycin (58.1%). A total of 28 sequence types (STs) were identified in the 518 isolates, and the predominant type was ST7 (57.5%), followed by ST5 (9.1%). In addition, based on the whole-genome sequences of 39 representative strains, 17 spa types were identified among the isolates, of which t899, t091, and t437 were the most common. Furthermore, 19 staphylococcal enterotoxin (SE) and SE-like (SEl) toxin genes were detected in the isolates, of which selw was the most common type (100%), followed by sei , sem , seo , seu , and selv (46.2%); sey (35.9%); and sea , seg , and sen (33.3%). This study found for the first time that ST7-t091- selw and ST9-t899-SCCmecXII- selw were the predominant genotypes of S. aureus in pork in China, which indicated the spreading of S. aureus with multiple virulence factors, especially with new SE/SEl types in pigs and pork, is a serious new challenge for food safety. Good hygiene and good production practices to prevent interspecies transmission and cross-contamination of S. aureus in the pig-pork chain are of great significance to public health.

It is well known that crop classification is essential for genetic resources and phenotype development. Compared with traditional methods, convolutional neural networks can be utilized to identify features automatically. Nevertheless, crops and scenarios are quite complex, which makes it challenging to develop a universal classification method. Furthermore, manual design demands professional knowledge and is time-consuming and labor-intensive. In contrast, auto-search can create network architectures when faced with new species. Using rapeseed images for experiments, we collected eight types to build datasets (rapeseed dataset (RSDS)). In addition, we proposed a novel target-dependent search method based on VGGNet (target-dependent neural architecture search (TD-NAS)). The result shows that test accuracy does not differ significantly between small and large samples. Therefore, the influence of the dataset size on generalization is limited. Moreover, we used two additional open datasets (Pl@ntNet and ICL-Leaf) to test and prove the effectiveness of our method due to three notable features: (a) small sample sizes, (b) stable generalization, and (c) free of unpromising detections., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Fu, Li, Rao, Liang, Teng and He.)

Trace element deficiency diagnosis plays a critical role in pear cultivation. However, high-quality diagnostic models are challenging to investigate, making it difficult to collect samples. Therefore, this manuscript developed a novel transfer learning method, named Tran&#95;NAS, with a fine-tuning neural network that uses a neural architecture search (NAS) to transfer learning from nitrogen (N) and phosphorus (P) to iron (Fe) and magnesium (Mg) to diagnose pear leaf element deficiencies. The best accuracy of the transferred NAS model is 89.12%, which is 11% more than that of the model without the transfer of trace element-deficient samples. Meanwhile, Tran&#95;NAS also has better performance on source datasets after comparing with different proportions of training sets. Finally, this manuscript summarizes the transfer model coincident characteristics, including the methods of batch normalization (BN) and dropout layers, which make the model more generalizable. This manuscript applies a symmetric homogeneous feature-based transfer learning method on NAS that is designed explicitly for near-infrared (NIR) data collected from nutrient-deficient pear leaves. The novel transfer learning method would be more effective for the micro-NIR spectrum of the nondestructive diagnosis., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

Salmonella is one of the most important foodborne and zoonotic pathogens, and monophasic S. Typhimurium is ranked among the top-five Salmonella serovars causing animal and human infections worldwide. Resistance to the third- and higher-generation cephalosporins in Salmonella has attracted great attention. Bacteria are frequently exposed to sub-minimal inhibitory concentrations (sub-MICs) of antimicrobials that can trigger diverse adaptive responses such as biofilm formation. Biofilms can promote bacterial defense to external and internal harsh conditions. This study aimed to investigate the effect of sub-MICs of cefotaxime, one of the third-generation cephalosporins, on biofilm formation by non-clinical S. enterica strains. Crystal violet staining demonstrated that cefotaxime at 1/8 MIC enhanced biofilm formation by two monophasic S. Typhimurium strains. Confocal laser scanning microscopy and enzymatic treatment assay revealed that cellulose was the most dominant extracellular matrix component contributing to Salmonella biofilm formation. Scanning electron microscopy demonstrated that cefotaxime treatment led to bacterial incomplete cell division and filamentous morphology during the whole process of biofilm formation. Our study is the first to report the enhancement effect of cefotaxime on non-clinical, monophasic S. Typhimurium by affecting bacterial morphology. The results will contribute to conducting risk assessments of Salmonella in the pork production chain and guiding the rational use of antimicrobial agents to reduce the risk of biofilm formation., (© The Author(s) 2022. Published by Oxford University Press on behalf of FEMS.)

There is evidence that non-coding RNAs play significant roles in the regulation of nutrient homeostasis, development, and stress responses in plants. Accurate identification of ncRNAs is the first step in determining their function. While a number of machine learning tools have been developed for ncRNA identification, no dedicated tool has been developed for ncRNA identification in plants. Here, an automated machine learning tool, PINC is presented to identify ncRNAs in plants using RNA sequences. First, we extracted 91 features from the sequence. Second, we combined the F-test and variance threshold for feature selection to find 10 features. The AutoGluon framework was used to train models for robust identification of non-coding RNAs from datasets constructed for four plant species. Last, these processes were combined into a tool, called PINC, for the identification of plant ncRNAs, which was validated on nine independent test sets, and the accuracy of PINC ranged from 92.74% to 96.42%. As compared with CPC2, CPAT, CPPred, and CNIT, PINC outperformed the other tools in at least five of the eight evaluation indicators. PINC is expected to contribute to identifying and annotating novel ncRNAs in plants.

The trace element boron (Boron, B) is an important factor in crops' development, pollination, and fertilization. Available boron (AB) in soil is the main source of boron nutrient absorption for crops. Rapid detection of AB is of great significance for crop nutrition diagnosis, soil testing and fertilization, precision agriculture development, scientific production management, and guarantee of stable yield and high quality. In this study, we propose a new method to predict soil available boron content using handheld nonimaging hyperspectroscopy in the visible-near-infrared range (350-1655 nm). As boron content is one of the fewest soil chemical elements, a rapid and accurate method has yet to be developed to detect and quantify the soil available boron. Visible-near-infrared ray (VIS-NIR) spectroscopy is widely utilized in the detection and quantification of soil available nutrients. There is, however, scant research on the detection of soil boron based on NIR data, and the performance of current regression model is still far from satisfactory. Our soil samples were collected from southern Anhui, China, with their NIR spectroscopy examined and the NIR data pretreated by 29 transformations and modeled with 10 regression algorithms. Of all the tested methods, SVM&#95;RBF, BPNN, and PLS&#95;RBF algorithms demonstrated the best performance and gave 0.80∼0.82 coefficient of determination value. At the same time, Random Forest algorithm (RFA), Successive Projection Algorithm (SPA), and Variable Importance in Projection (VIP) were used to extract the spectral characteristic wavelength data of soil available boron, and then the characteristic wavelength data were modeled with three regression algorithms: SVM&#95;RBF, PLS&#95;RBF, and BPNN. A comparative analysis of the prediction performance ( R 2 , RPD, RMSE, and RPIQ) of the models established at the full band showed that the RFA-MSC/BPNN model achieved the best performance. Compared with the best full-wavelength model DT/SVM&#95;RBF, the test set achieved a 3.06% increase in R 2 , a 7.12% drop in RMSE, a 7.71% gain in RPD, and a 7.78% increase in RPIQ. Our work sheds lights on how to achieve rapid quantification of the soil available boron concentration., Competing Interests: The authors declare that there are no conflicts of interest regarding the publication of this paper., (Copyright © 2022 Juanjuan Zhu et al.)

Background: Medical education accreditation in China has been conducted by the Working Committee for the Accreditation of Medical Education (WCAME) and 129 medical schools have completed accreditation by December 2021. Despite studies on the standards, process and effectiveness of accreditation, the actual information transparency of accredited medical schools in China has not been examined. The study investigated the status of publicly available information from WCAME-accredited medical schools in China, and whether public availability of information had significant differences among different types of universities., Methods: The 129 medical schools' official websites were reviewed for the 21 criteria of the WFME Global Standards for Quality Improvement: Basic Medical Education. Dichotomous method was used to record information as presence or absence. SPSS was utilized for descriptive and ANOVA analyses., Results: The mean of the publicly available information on the 21 criteria was 13.77 ± 3.57, and only 5 (3.9%) accredited medical schools had all relevant information available. Publicly available information on Governance (100%) and Administration (100%) was the most, whereas information on Assessment in support of learning (16.3%) was the least. Public availability of information differed significantly among schools accredited with higher (18.15 ± 2.16), medium (13.69 ± 3.41) and lower results (12.79 ± 3.19) (F = 14.71, p < 0.05). Medical universities and comprehensive universities did not show significant differences in their overall information availability (F = 0.25, p > 0.05). Central government funded universities had a remarkably larger amount of publicly available information than local government funded universities (17.86 ± 1.98 vs. 12.75 ± 2.93, p < 0.05)., Conclusion: Public availability of information from the accredited medical schools in China needs to be improved to promote transparency and continuous quality improvement, especially with regard to information on curriculum, assessment and quality assurance. Explicit information availability requirements need to be considered to include in medical education standards, and further studies are warranted to explore which information elements should be made publicly available., (© 2022. The Author(s).)

Background: Orphan gene play an important role in the environmental stresses of many species and their identification is a critical step to understand biological functions. Moso bamboo has high ecological, economic and cultural value. Studies have shown that the growth of moso bamboo is influenced by various stresses. Several traditional methods are time-consuming and inefficient. Hence, the development of efficient and high-accuracy computational methods for predicting orphan genes is of great significance., Results: In this paper, we propose a novel deep learning model (CNN + Transformer) for identifying orphan genes in moso bamboo. It uses a convolutional neural network in combination with a transformer neural network to capture k-mer amino acids and features between k-mer amino acids in protein sequences. The experimental results show that the average balance accuracy value of CNN + Transformer on moso bamboo dataset can reach 0.875, and the average Matthews Correlation Coefficient (MCC) value can reach 0.471. For the same testing set, the Balance Accuracy (BA), Geometric Mean (GM), Bookmaker Informedness (BM), and MCC values of the recurrent neural network, long short-term memory, gated recurrent unit, and transformer models are all lower than those of CNN + Transformer, which indicated that the model has the extensive ability for OG identification in moso bamboo., Conclusions: CNN + Transformer model is feasible and obtains the credible predictive results. It may also provide valuable references for other related research. As our knowledge, this is the first model to adopt the deep learning techniques for identifying orphan genes in plants., (© 2022. The Author(s).)

Flagellum-mediated bacterial motility is important for bacteria to take up nutrients, adapt to environmental changes, and establish infection. The twin-arginine translocation system (Tat) is an important protein export system, playing a critical role in bacterial physiology and pathogenesis. It has been observed for a long time that the Tat system is critical for bacterial motility. However, the underlying mechanism remains unrevealed. In this study, a comparative transcriptomics analysis was performed with extraintestinal pathogenic Escherichia coli (ExPEC), which identified a considerable number of genes differentially expressed when the Tat system was disrupted. Among them, a large proportion of flagellar biosynthesis genes showed downregulation, indicating that transcription regulation plays an important role in mediating the motility defects. We further identified three Tat substrate proteins, MdoD, AmiA, and AmiC, that were responsible for the nonmotile phenotype. The Rcs system was deleted in the Δ tat , the Δ mdoD , and the Δ amiA Δ amiC strains, which restored the motility of Δ mdoD and partially restored the motility of Δ tat and Δ amiA Δ amiC . The flagella were also observed in all of the Δ tat Δ rcsDB , Δ mdoD Δ rcsDB , and Δ amiA Δ amiC Δ rcsDB strains, but not in the Δ tat , Δ mdoD , and Δ amiA Δ amiC strains, by using transmission electron microscopy. Quantitative reverse transcription-PCR data revealed that the regulons of the Rcs system displayed differential expression in the tat mutant, indicating that the Rcs signaling was activated. Our results suggest that the Rcs system plays an important role in mediating the motility defects of the tat mutant of ExPEC. IMPORTANCE The Tat system is an important protein export system critical for bacterial physiology and pathogenesis. It has been observed for a long time that the Tat system is critical for bacterial motility. However, the underlying mechanism remains unrevealed. In this study, we combine transcriptomics analysis and bacterial genetics, which reveal that transcription regulation plays an important role in mediating the motility defects of the tat mutant of extraintestinal pathogenic Escherichia coli. The Tat substrate proteins responsible for the motility defects are identified. We further show that the Rcs system contributes to the motility suppression. We for the first time reveal the link between the Tat system and bacterial motility, which is important for understanding the physiological functions of the Tat system.

The pulse duration of the near quarter-acoustic period (τ a ) is demonstrated in transient stimulated Brillouin scattering (SBS) pulse compression by the suppressing Stokes trailing-edge broadening at high intensities. A theoretical analysis reveals that the difficulty in attaining the transient compression limit is caused by the broadening of the Stokes trailing edge owing to insufficient pump depletion, and this undesirable phenomenon can be significantly suppressed by a high SBS gain coefficient. An average pulse duration of ∼1.05 τ a was experimentally achieved in transient compression with a high-energy efficiency of over 30%. Benefiting from energy back conversion, compression below the transient SBS limit (< τ a ) also occurred when the pump peak power was increased to 150 MW.

Live bacterial vector vaccines are one of the most promising vaccine types and have the advantages of low cost, flexibility, and good safety. Meanwhile, protein secretion systems have been reported as useful tools to facilitate the release of heterologous antigen proteins from bacterial vectors. The twin-arginine translocation (Tat) system is an important protein export system that transports fully folded proteins in a signal peptide-dependent manner. In this study, we constructed a live vector vaccine using an engineered commensal Escherichia coli strain in which amiA and amiC genes were deleted, resulting in a leaky outer membrane that allows the release of periplasmic proteins to the extracellular environment. The protective antigen proteins SLY, enolase, and Sbp against Streptococcus suis were targeted to the Tat pathway by fusing a Tat signal peptide. Our results showed that by exploiting the Tat pathway and the outer membrane-defective E. coli strain, the antigen proteins were successfully secreted. The strains secreting the antigen proteins were used to vaccinate mice. After S. suis challenge, the vaccinated group showed significantly higher survival and milder clinical symptoms compared with the vector group. Further analysis showed that the mice in the vaccinated group had lower burdens of bacteria load and slighter pathological changes. Our study reports a novel live bacterial vector vaccine that uses the Tat system and provides a new alternative for developing S. suis vaccine.

Light/ultrasound/magnetic-responsive nanomaterials exhibit excellent performance in imaging and therapy and play an important role in precision theranostics of tumors. In contrast to deep organs, urinary organs (such as bladder and prostate) can easily be studied via intervention mode, which has greatly brought promising applications of stimuli-responsive nanoprobes in visualized theranostics of urinary tumors. Therefore, it has been very critical to develop stimuli-responsive nanoprobes with high safety, stability, and reliability against urinary tumors. In this review, recent advances in light/ultrasound/magnetic-responsive nanoprobes in visualized theranostics of urinary tumors are summarized, including magnetic resonance/fluorescence/ultrasound/photoacoustic imaging and multimodal imaging, photothermal/photodynamic/sonodynamic therapy and combination therapy, and single-modal/multimodal-imaging-guided visualized theranostics. Finally, the future perspectives of light/ultrasound/magnetic-responsive nanoprobes against urinary tumors are also prospected.

There has been increasing concern that the overuse of antibiotics in livestock farming is contributing to the burden of antimicrobial resistance in people. Farmed animals in Europe and North America, particularly pigs, provide a reservoir for livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA ST398 lineage) found in people. This study is designed to investigate the contribution of MRSA from Chinese pig farms to human infection. A collection of 483 MRSA are isolated from 55 farms and 4 hospitals in central China, a high pig farming density area. CC9 MRSA accounts for 97.2% of all farm isolates, but is not present in hospital isolates. ST398 isolates are found on farms and hospitals, but none of them formed part of the "LA-MRSA ST398 lineage" present in Europe and North America. The hospital ST398 MRSA isolate form a clade that is clearly separate from the farm ST398 isolates. Despite the presence of high levels of MRSA found on Chinese pig farms, the authors find no evidence of them spilling over to the human population. Nevertheless, the ST398 MRSA obtained from hospitals appear to be part of a widely distributed lineage in China. The new animal-adapted ST398 lineage that has emerged in China is of concern., (© 2021 The Authors. Advanced Science published by Wiley-VCH GmbH.)

Basic leucine zipper (bZIP) is a conserved transcription factor (TF) widely present in eukaryotes, and it plays an important role in regulating plant growth and stress responses. To better understand the white pear bZIP gene family, comprehensive bioinformatics analysis of the pear genome was performed. A total of 84 PbbZIP genes were identified, which were divided into 13 subfamilies by phylogenetic analysis. The 84 PbbZIP genes were all located in the nucleus, and 77 of those genes were unevenly distributed across the 17 chromosomes of white pear. The other 7 PbbZIP genes were located on the scaffold. Subsequent expression profile analysis showed that PbbZIP genes in exocarp were significantly upregulated or downregulated in 'Huangguan' pear with brown spot (BS) compared with healthy pear and in response to hormonal treatment with gibberellin A3 (GA3). These results provide helpful insights into the characteristics of PbbZIP genes and their responses to BS in 'Huangguan' pear.

Background: Augmented reality (AR) based fusion imaging in endoscopic surgeries rely on the quality of image-to-patient registration and camera calibration, and these two offline steps are usually performed independently to get the target transformation separately. The optimal solution can be obtained under independent conditions but may not be globally optimal. All residual errors will be accumulated and eventually lead to inaccurate AR fusion., Methods: After a careful analysis of the principle of AR imaging, a robust online calibration framework was proposed for an endoscopic camera to enable accurate AR fusion. A 2D checkerboard-based homography estimation algorithm was proposed to estimate the local pose of the endoscopic camera, and the least square method was used to calculate the compensation matrix in combination with the optical tracking system., Results: In comparison with conventional methods, the proposed compensation method improved the performance of AR fusion, which reduced physical error by up to 82%, reduced pixel error by up to 83%, and improved target coverage by up to 6%. Experimental results of simulating mechanical noise revealed that the proposed compensation method effectively corrected the fusion errors caused by the rotation of the endoscopic tube without recalibrating the camera. Furthermore, the simulation results revealed the robustness of the proposed compensation method to noises., Conclusions: Overall, the experiment results proved the effectiveness of the proposed compensation method and online calibration framework, and revealed a considerable potential in clinical practice., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Pig is usually the carrier of Salmonella and Staphylococcus aureus , and can transmit the bacteria along the pork production chain to cause severe public health problems. In this study, we investigated the prevalence of Salmonella and S. aureus in fattening pigs in Hubei Province, China. The overall prevalence of Salmonella in rectal swab among 896 samples from 22 farms was 17.30%, and that of S. aureus in nasal swab among 814 samples from 20 farms was 28.26%. Antimicrobial resistance (AMR) analysis showed that 95.33% of the Salmonella strains exhibited resistance to more than three classes of antimicrobial agents tested. The highest resistance proportions were for chloramphenicol (100%), sulfamethoxazole/trimethoprim (SXT) (100%), and tetracycline (TET) (93.46%), while the lowest proportions were for cefotaxime (37.38%), gentamicin (GEN) (34.58%), and ciprofloxacin (24.30%). On the other hand, 98.42% of the S. aureus strains were resistant to more than three classes of antimicrobial agents tested. The most common resistance among the S. aureus strains was against SXT (100.00%), followed by TET (98.43%), erythromycin (91.34%), and clindamycin (91.34%), while the lowest frequent resistances were against GEN (34.65%) and oxacillin (16.54%). The prevalence and AMR of Salmonella and S. aureus exhibited an obvious diversity among different pig farms. Our results provided the epidemiological data for risk analysis of foodborne bacteria and AMR in pig farms.

In this study, we performed a bioinformatics analysis to identify immune checkpoint genes (ICGs) associated with prognosis and the immunotherapeutic response in endometrial carcinoma (EC) patients. We classified 47 ICGs into high, medium, and low expression groups by performing RNA-sequencing data analysis of EC patient samples from The Cancer Genome Atlas ( n = 521) and GSE77688 ( n = 88) datasets. Univariate Cox regression analysis showed that seven ICGs ( VTCN1, TNFRSF18, TNFRSF14, TNFRSF4, CD40LG, TMIGD2, and BTLA ) were associated with prognosis in EC patients. Spearman correlation analysis showed that prognosis-related ICGs correlated positively with immunotherapy response factors, including tumor mutation burden (TMB), mismatch repair gene mutations, neoantigens, clinical stages, and adaptive immune resistance pathway genes. We identified a prognostic gene signature of four ICGs ( IDO1, CD274, CTLA4, and TNFRSF14 ) that accurately predicted survival outcomes of EC patients. TIMER database and Kaplan-Meier survival analysis showed that OS among EC patients with low TNFRSF14 expression was significantly shorter than among those with high TNFRSF14 expression. In vitro experiments showed that TNFRSF14 silencing increased the migration and invasiveness of EC cells by promoting epithelial-mesenchymal transition (EMT). Collectively, these findings reveal an immune checkpoint gene signature that accurately predicts survival outcomes and immunotherapeutic responses in EC patients.

Three-dimensional scanners have been widely applied in image-guided surgery (IGS) given its potential to solve the image-to-patient registration problem. How to perform a reliable calibration between a 3D scanner and an external tracker is especially important for these applications. This study proposes a novel method for calibrating the extrinsic parameters of a 3D scanner in the coordinate system of an optical tracker. We bound an optical marker to a 3D scanner and designed a specified 3D benchmark for calibration. We then proposed a two-step calibration method based on the pointset registration technique and nonlinear optimization algorithm to obtain the extrinsic matrix of the 3D scanner. We applied repeat scan registration error (RSRE) as the cost function in the optimization process. Subsequently, we evaluated the performance of the proposed method on a recaptured verification dataset through RSRE and Chamfer distance (CD). In comparison with the calibration method based on 2D checkerboard, the proposed method achieved a lower RSRE (1.73 mm vs. 2.10, 1.94, and 1.83 mm) and CD (2.83 mm vs. 3.98, 3.46, and 3.17 mm). We also constructed a surgical navigation system to further explore the application of the tracked 3D scanner in image-to-patient registration. We conducted a phantom study to verify the accuracy of the proposed method and analyze the relationship between the calibration accuracy and the target registration error (TRE). The proposed scanner-based image-to-patient registration method was also compared with the fiducial-based method, and TRE and operation time (OT) were used to evaluate the registration results. The proposed registration method achieved an improved registration efficiency (50.72 ± 6.04 vs. 212.97 ± 15.91 s in the head phantom study). Although the TRE of the proposed registration method met the clinical requirements, its accuracy was lower than that of the fiducial-based registration method (1.79 ± 0.17 mm vs. 0.92 ± 0.16 mm in the head phantom study). We summarized and analyzed the limitations of the scanner-based image-to-patient registration method and discussed its possible development., Competing Interests: ZT was employed by company Ariemedi Medical Technology (Beijing) CO., LTD. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Li, Fan, Li, Tian, Zheng, Ai, Song and Yang.)

Listeria monocytogenes is a ubiquitous bacteria and causative agent of zoonotic listeriosis with high mortality. The consumption of contaminated animal-derived foods has been linked with both epidemic and sporadic listeriosis. In this work, a total of 64 L. monocytogenes isolates from 259 pork samples sold in 11 supermarket chains were identified and characterized by comparative whole-genome analysis. All isolates were delineated into eight clonal complexes (CCs), namely CC2, CC8, CC9, CC11, CC155, CC121, CC204, and CC619, spanning two lineages (I and II) and carrying 3-5 antibiotic-resistant genes ( fosX , lnu , mprF , tetM , and dhfR ). It is noted that Listeria pathogenicity island (LIPI)-1, LIPI-3, and LIPI-4 were distributed in all ST619 isolates from two supermarket chains that were closely related with clinical isolates (<40 SNP). Some of the isolates from different supermarket chains with 0 SNP difference indicated a common pork supply source. Notably, 57.81% of the strains carried types IB, IIA, or IIIB CRISPR-Cas system, CC121 isolates carried both types IB and IIA CRISPR-Cas systems, Cas proteins of CC155 isolates located between two CRISPR loci, each CC has unique organization of Cas proteins as well as CRISPR loci. CRISPR-Cas system-based subtyping improved discrimination of pork-derived L. monocytogenes isolates. Comparisons at the genome level contributed to understand the genetic diversities and variations among the isolates and provided insights into the genetic makeup and relatedness of these pathogens., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Wang, Ji, Li and Liu.)

The discovery and clinical use of multitarget monotherapeutic antibiotics is regarded as a promising approach to reduce the development of antibiotic resistance. Platencin (PTN), a potent natural antibiotic initially isolated from a soil actinomycete, targets both FabH and FabF, the initiation and elongation condensing enzymes for bacterial fatty acid biosynthesis. However, its further clinical development has been hampered by poor pharmacokinetics. Herein we report the semisynthesis and biological evaluation of platencin derivatives 1 - 15 with potent antibacterial activity against methicillin-resistant Staphylococcus aureus in vitro. Some of these PTN analogues showed similar yet distinct interactions with FabH and FabF, as shown by molecular docking, differential scanning fluorometry, and isothermal titration calorimetry. Compounds 3 , 8 , 10 , and 14 were further evaluated in a mouse peritonitis model, among which 8 showed in vivo antibacterial activity comparable to that of PTN. Our results suggest that semisynthetic modification of PTN is a rapid route to obtain active PTN derivatives that might be further developed as promising antibiotics against drug-resistant major pathogens., Competing Interests: The authors declare no competing financial interest., (© 2021 American Chemical Society.)

Background: Cancer resistance to chemotherapy is closely associated with changes in transporter systems. In this study, we investigated the possible regulation of 1 copper ion transporter (ATP7A; ATPase copper transporting alpha) by microRNA miR-495 and its implications in cisplatin resistance and angiogenesis in esophageal cancer. Methods: MiR-495 and ATP7A mRNA expression in clinical tissue samples and 2 cancer cell lines (Eca-109 and TE1) were detected by quantitative real-time polymerase chain reaction. The levels of miR-495 and ATP7A expression in Eca-109 and TE1 cells were increased by transfection with miR-495 mimics and ATP7A-overexpression vectors. Cell proliferation, apoptosis, and angiogenesis were assessed by CCK-8, flow cytometry, and tube formation assays, respectively. The levels of TNF-α and VEGF in cell culture supernatants were detected by enzyme linked immunosorbent assay, and in situ expression of NLRP3 was measured by immunofluorescence. The binding of miR-495 to ATP7A sequences was verified by dual luciferase reporter assays. Results: ATP7A expression was significantly increased, while miR-495 expression was decreased in the cancer tissues of esophageal cancer patients. MiR-495 mimics decreased the proliferation and promoted the apoptosis of cisplatin-resistant Eca-109 and TE1 cells. Furthermore, tube formation by human umbilical vein endothelial cells, TNF-α and VEGF secretion, and the levels of MRP1, ABCG1, ABCA1, and NLRP3 expression in cisplatin-resistant Eca-109 and TE1 cells were all reduced by miR-495 mimics. MiR-495 was shown to directly bind to ATP7A gene sequences to repress ATP7A expression in Eca-109 and TE1 cells. ATP7A overexpression substantially abrogated the changes in proliferation, apoptosis, angiogenesis, and above-mentioned gene expression in cisplatin-resistant Eca-109 and TE1 cells. Conclusions: MiR-495 suppressed cisplatin resistance and angiogenesis in esophageal cancer cells by targeting ATP7A gene expression.

The twin-arginine translocation (Tat) system is involved in a variety of important bacterial physiological processes. Conserved among bacteria and crucial for virulence, the Tat system is deemed as a promising anti-microbial drug target. However, the mechanism of how the Tat system functions in bacterial pathogenesis has not been fully understood. In this study, we showed that the Tat system was critical for the virulence of an extra-intestinal pathogenic E. coli (ExPEC) strain PCN033. A total of 20 Tat-related mutant strains were constructed, and competitive infection assays were performed to evaluate the relative virulence of these mutants. The results demonstrated that several Tat substrate mutants, including the Δ sufI , Δ amiA Δ amiC double mutant as well as each single mutant, Δ yahJ , Δ cueO , and Δ napG , were significantly outcompeted by the WT strain, among which the Δ sufI and Δ amiA Δ amiC strains showed the lowest competitive index (CI) value. Results of individual mouse infection assay, in vitro cell adhesion assay, whole blood bactericidal assay, and serum bactericidal assay further confirmed the virulence attenuation phenotype of the Δ sufI and Δ amiA Δ amiC strains. Moreover, the two mutants displayed chained morphology in the log phase resembling the Δ tat and were defective in stress response. Our results suggest that the Tat system and its dependent cell division proteins SufI, AmiA, and AmiC play critical roles during ExPEC pathogenesis.

Orphan genes are associated with regulatory patterns, but experimental methods for identifying orphan genes are both time-consuming and expensive. Designing an accurate and robust classification model to detect orphan and non-orphan genes in unbalanced distribution datasets poses a particularly huge challenge. Synthetic minority over-sampling algorithms (SMOTE) are selected in a preliminary step to deal with unbalanced gene datasets. To identify orphan genes in balanced and unbalanced Arabidopsis thaliana gene datasets, SMOTE algorithms were then combined with traditional and advanced ensemble classified algorithms respectively, using Support Vector Machine, Random Forest (RF), AdaBoost (adaptive boosting), GBDT (gradient boosting decision tree), and XGBoost (extreme gradient boosting). After comparing the performance of these ensemble models, SMOTE algorithms with XGBoost achieved an F1 score of 0.94 with the balanced A. thaliana gene datasets, but a lower score with the unbalanced datasets. The proposed ensemble method combines different balanced data algorithms including Borderline SMOTE (BSMOTE), Adaptive Synthetic Sampling (ADSYN), SMOTE-Tomek, and SMOTE-ENN with the XGBoost model separately. The performances of the SMOTE-ENN-XGBoost model, which combined over-sampling and under-sampling algorithms with XGBoost, achieved higher predictive accuracy than the other balanced algorithms with XGBoost models. Thus, SMOTE-ENN-XGBoost provides a theoretical basis for developing evaluation criteria for identifying orphan genes in unbalanced and biological datasets., (Copyright © 2020 Gao, Jin, Xia, Wu, Gu, Yan, Xia and Li.)

This study was designed to investigate the prevalence and characteristics of Salmonella in three Chinese pig abattoirs (A, B, and C) in Wuhan city in 2016. Four types of pig samples were collected and cultured for Salmonella . Salmonella was detected from 329 samples among the 1440 tested (22.9%). There was no significant difference in the overall prevalence between the first visit and the second visit and among the three abattoirs. Rectal swabs (RS) exhibited a significantly higher prevalence than carcass swabs and pork. A total of 177 isolates were characterized by multilocus sequence typing, serotyping, and antimicrobial susceptibility testing. Among 17 sequence types (STs) and 13 serotypes detected, ST40, ST469, and ST34, corresponding to serovars Derby, Rissen, and Typhimurium, respectively, were predominant. The isolates from different abattoirs exhibited diverse ST distribution. The minimum inhibitory concentrations were determined using the microdilution broth method. Resistance to at least one of the antimicrobials was observed for 96.6% of the strains (171/177), and multidrug resistant (MDR) isolates accounted for 75.7% of the strains (134/177). The highest resistance proportion was for tetracycline (92.7%), and the lowest was for cefotaxime (14.1%). The isolates from abattoir A exhibited a significantly lower MDR proportion than those from other abattoirs ( p  < 0.05). The isolates recovered from RS and pork samples exhibited significantly higher MDR proportions than those recovered from carcass swab samples. Notably, among three predominant STs of isolates, the ST34 isolates showed the highest MDR proportion. In view of the high Salmonella prevalence and antimicrobial resistance, great attention must be paid to the monitoring and controlling of Salmonella in a full pork production chain.

Transmissible gastroenteritis virus (TGEV) is a porcine intestinal coronavirus that causes fatal severe watery diarrhea in piglets. The neonatal Fc receptor (FcRn) is the only IgG transport receptor, its expression on mucosal surfaces is triggered upon viral stimulation, which significantly enhances mucosal immunity. We utilized TGEV as a model pathogen to explore the role of FcRn in resisting viral invasion in overall intestinal mucosal immunity. TGEV induced FcRn expression by activating NF-κB signaling in porcine small intestinal epithelial (IPEC-J2) cells, however, the underlying mechanisms are unclear. First, using small interfering RNAs, we found that TGEV up-regulated FcRn expression via TLR3, TLR9 and RIG-I. Moreover, TGEV induced IL-1β, IL-6, IL-8, TGF-β, and TNF-α production. TGF-β-stimulated IPEC-J2 cells highly up-regulated FcRn expression, while treatment with a JNK-specific inhibitor down-regulated the expression. TGEV nucleocapsid (N) protein also enhanced FcRn promoter activity via the NF-κB signaling pathway and its central region (aa 128-252) was essential for FcRn activation. Additionally, N protein-mediated FcRn up-regulation promotes IgG transcytosis. Thus, TGEV N protein and TGF-β up-regulated FcRn expression, further clarifying the molecular mechanism of up-regulation of FcRn expression by TGEV., (Copyright © 2020 Qian, Gao, Cao, Yang, Cui, Li, Meng, He and Li.)

Rearing systems play an important role in animal welfare, health and the composition of the gut microbiome. Therefore, the purpose of this study was to investigate the effects of different rearing systems on the composition and function of cecal microbiota in chickens. The 120-day-old Lohmann hens of cage rearing systems (CRS) and free-range systems (FRS) were studied. The cecal bacterial populations of hens were surveyed by high-throughput sequencing (HTS) of the bacterial 16S rRNA hypervariable region V3-V4 combined with metagenomic sequencing analysis. The 16S rRNA sequencing analysis showed that the cecal microbiota differed between the FRS and CRS. The three most abundant bacteria phyla in the two systems were the Bacteroidetes (> 48%), Firmicutes (> 37%), and Proteobacteria (> 6%), the Deferribacteres (> 2.4%) were found in FRS and almost absent in CRS (< 0.01%). The three most abundant genera were the Bacteroides , Rikenellaceae&#95;RC9 , and Faecalibacterium , and we found relative abundance of the Parabacteroides ( P  < 0.05), Prevotellaceae &#95;Ga6A1 ( P  < 0.01), unclassified Proteobacteria ( P  < 0.05), and unclassified Spirochaetaceae ( P  < 0.01) was greater in FRS, whereas abundance of Faecalibacterium , Ruminococcaceae , and Helicobacter was greater in CRS ( P  < 0.05). Functional gene classification of metagenomic sequencing suggested that energy production and conversion, carbohydrate transport and metabolism, as well as amino acid transport and metabolism were significantly more abundant in FRS, and we identified a range of antibiotic resistance categories in gut microbes of hens reared under both systems. We confirmed differences in microbe gut composition and function in hens reared using two contrasting systems, and ARGs were also identified in the microbiota of these hens. This work has produced new data for laying hens in different production systems and increased the understanding of intestinal microorganisms in laying hens., Competing Interests: Conflict of interestThe authors declare that they have no conflicts of interest., (© King Abdulaziz City for Science and Technology 2019.)

During the operation of lithium metal batteries, the direct observation of the evolving characteristics of the deposited lithium is rather challenging in consideration of the requirements for the fast-tracking and high spatial resolution of the signals within native organic electrolytes. However, the weak scattering of electrons and X-rays with low-atomic-number lithium deteriorates the spectral resolution of the signals. Therefore, this mini-review compares various influencing factors that determine the lithium nucleation process based on electrochemical performance evaluations, including the artificial protective layer, electrolyte formulation, lithiophilic sites and hierarchies of the substrate; additionally, the possibility of the dynamic observations of chemical, electronic, and geometric changes during the operation of metallic batteries is exhibited. For each category of the technique, a brief account of the advancements of the characterizing equipment is followed with novel cell designs. Finally, the prospects that advance the precise description of the lithium nucleation process are summarized. This mini-review highlights the mitigating strategies of lithium dendrites at molecular, electrode, and device levels and summarizes the state-of-the-art in operando techniques, thereby promoting the future design of metallic battery systems.

Riemerellosis, a Riemerella anatipestifer infection, can cause meningitis, pericarditis, parahepatitis, and airsacculitis in ducks, leading to serious economic losses in the duck meat industry. However, the molecular mechanism of the pathogenesis and virulence factors of this infection are poorly understood. In the present study, we created a mutant strain RA-YMΔCas9 using trans-conjugation. Bacterial virulence tests indicated that the median lethal dose (LD 50 ) of RA-YMΔCas9 was 5.01 × 10 7  CFU, significantly lower than that of the RA-YM strain, which was 1.58 × 10 5  CFU. The distribution and blood bacterial load from the infection groups showed no significant difference in the brain between the RA-YMΔCas9 mutant and the wild-type RA-YM strains, however, the number of mutant strains were significantly reduced in the liver, heart, and blood. Animal immunization experiments demonstrated that the intranasal administration of RA-YMΔCas9 in ducklings provided 80% protection after challenge with the wild-type strain, showing potential use as a live mucosal vaccine. RNAseq analysis indicated that Cas9 protein played a regulatory role in gene expression. This study is the first to report on the involvement of Cas9 in the regulation and pathogenesis of R. anatipestifer, and provides a theoretical basis for the development of relevant genetic engineering vaccines., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Riemerella anatipestifer is a Gram-negative, pathogenic bacterium, which is harmful to poultry. However, the genomic islands (GIs) in R. anatipestifer are not well-studied. In this study, a 10K genomic island was predicted by the bioinformatics analysis of R. anatipestifer ATCC 11845, which is widely found in other R. anatipestifer genomes. We had first reported the genomic island integration and excision function in R. anatipestifer . We successfully constructed the integration plasmid by using the integrase and 53 bp attP elements. The 10K GI was found integrated at the 53 bp attB located in the Arg-tRNA of the R. anatipestifer RA-YM chromosome. We identified an integrase that helped in the precise integration and excision in R. anatipestifer and elucidated the molecular mechanism of the 10K genomic island integration and excision. Furthermore, we provided a new method for the gene expression and construction of complementary strain., (Copyright © 2019 Wang, Zhang, Cui, Sun, Zhou, Hu, Li, Liu, Meng, Xiao, Shi, Bi and Li.)