bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive Experimental Assessment of Unsteady Pressure and Heat Flux in a Small-Core Turbine Over-Tip Shroud
Authors: Sauca Antonio Castillo , Bhatnagar Lakshya , Inhestern Lukas Benjamin , Paniagua Perez Guillermo
Published: October 2024

For novel high-speed small core turbines, with tip clearance below 0.5 mm, even small blade-to-blade tip clearance variation is significant. The assessment of these complex flows is pertinent to the design of the next generation of small-core turbines. This paper provides a thorough experimental analysis of the shroud's unsteady heat flux and static pressure in a small-core squealer-tip blade turbine. Atomic layer thermopile sensors (ALTPs) and fast response pressure transducers were used to perform high-frequency acquisition at 2 MHz around the 51% axial blade chord on the shroud. Measurements were taken at engine-representative conditions at several operational conditions and tip clearances. The signals were phase-locked averaged (PLA) over the revolution period and synchronized to identify individual blade and row signature. The linear relationship between the rotational tip Reynolds and the static pressure ratio across the blade tip reveals the transition point to reverse over-tip flows. Total heat flux is decomposed into the different steady and unsteady heat flux contributions. It is demonstrated that the adiabatic wall temperature governs the unsteady heat flux and contributes to one-third of the total surface heat flux. A linear trend was observed between the unsteady heat flux and the tip clearance measured at the pressure and suction side rims. Similar trends were observed between the local heat flux and the pressure ratio across the tip. A comparison with computational fluid dynamics (CFD) predictions highlights some limitations on resolving the detached and secondary flows, evidencing the necessity of complementary experimental data.
Modeling and Experimental Validation of a Cable-Driven Robot for Three-Dimensional Printing Construction
Authors: Qian Sen , Li Changqi , Zhao Zeyao , Zi Bin
Published: October 2024

Cable-driven robots are characterized by a large workspace, high speed, and load-to-weight ratio, providing a new technology approach for large-scale autonomous 3D construction of lunar surface shelters. A novel deployable cable-driven construction 3D printer (CDCP) is developed in this study. Guiding pulleys are considered and modeled to improve the accuracy of the system. A fuzzy adaptive differential evolution PID (FDEPID) control is proposed to reduce end-effector motion errors in Cartesian space and thus improve printing quality and stability. Concentric and zigzag infill strategies are compared to optimize printing efficiency and infill effectiveness in path planning. The simulations focus on evaluating the effects of pulley kinematics on trajectory tracking, evaluating system dynamics under low-gravity conditions, and examining the effectiveness of motion control and path planning methods. Finally, experiments are carried out to validate the proposed FDEPID control and path planning strategies which demonstrate the great potential of the developed cable-driven printer in the construction of lunar architecture.
Multidisciplinary Optimization of a Mixed-Flow Impeller With 140 Parameters and Its Shapley Additive Explanations
Authors: Xi Guang , Zhang Yong , Ji Cheng , Zhang Chenqing
Published: October 2024

In recent years, we have made several improvements to the geometric parameterization method, the surrogate model method, and the sampling method, with the goal of making the traditional surrogate model-based optimization method applicable to aerodynamic optimization of hundreds of parameters with reasonable computational cost. However, increasing the number of control parameters raises two additional issues. First, the impeller geometry becomes too complex to ensure the required mechanical performance. Second, the optimization mechanism becomes difficult to understand with too many parameters. To address the first issue, this paper builds a multidisciplinary optimization platform to achieve the optimization of a large flow coefficient mixed-flow impeller under 140 control parameters, resulting in a significant improvement in both aerodynamic and mechanical performance. To address the latter, a novel machine learning interpretation tool, Shapley additive explanations (SHAP), is introduced in this paper. Using this methodology, the contribution of all 140 parameter values in the final optimal impeller to each aspect of the performance improvement is presented in this paper, providing the first in-depth understanding of the intricate mechanisms involved in the multidisciplinary optimization of hundreds of control parameters.
Introduction of Axisymmetric Grooves as a Tip Seal Treatment for Small-Core Turbines
Authors: Wiese Connor J. , Berdanier Reid A. , Thole Karen A.
Published: October 2024

The aerodynamic penalties associated with the tip gap flow in axial turbines remain a challenging problem for turbine manufacturers. As modern gas turbines with small-core architectures are brought online, the influence of the tip gap continues to grow. While technologies to reduce the losses associated with the tip gap flow have been implemented into the blades themselves, little attention has been paid to the stationary tip seal, or casing, around the rotor wheel. In this study, an introduction to the use of axisymmetric groove enhancements for the casing of the rotor tip is examined computationally. These studies use the National Experimental Turbine (NExT) geometry, an engine-representative high-pressure turbine blade.

Steady, Reynolds-averaged Navier–Stokes simulations are used to assess the basic characteristics of axisymmetric grooves, such as depth, location, and arrangement. The objective of this introductory study was to determine the feasibility of impacting the tip leakage vortex formation and the associated losses in rotor efficiency. Furthermore, analyses were done with different tip gap heights along with both flat- and squealer-tipped blades. Tip seals with a single groove are demonstrated to improve rotor aerodynamic efficiency relative to ungrooved seals by up to 0.4 points when applied to flat-tipped rotor blades and up to 0.15 points with squealer tips. Alternating arrays of grooves show improvements for flat-tipped blade performance by up to 0.76 points while having a little additional aerodynamic effect on the squealer tip compared to the best single-groove designs. Finally, grooved tip seals appear to exert greater influence on the aerodynamic performance of the turbine rotor when at larger tip gaps, indicating that grooved tip seals alter the sensitivity of rotor performance to the tip gap.
A Dual-Iterative Meshing Stiffness Model and Vibration Analysis for an Angular Misaligned Helical Gear Pair Considering Misalignment-Induced Contact Line Variation
Authors: Wang Liming , Zhang Hao , Duan Lintao , Zou Desheng , Yu Wennian , Xiao Huifang , Chen Zaigang
Published: October 2024

Angular misalignment is a common error in gear transmission systems, significantly altering the contact and dynamic behaviors of the gear system. Conventionally, the time-varying mesh stiffness (TVMS) of helical gear pairs with angular misalignment is estimated under the assumption of a uniform load distribution along a fixed contact line. However, this simplification neglects the variations in contact line length and load distribution due to angular misalignment, thereby compromising the accuracy of TVMS predictions. To address this limitation, we propose a novel dual-iterative model for TVMS calculation in helical gears, accounting for the angular misalignment-induced contact line variation. This model combines traditional iterative calculations for gear slices with an additional iterative loop for the misalignment-induced contact line changes. Furthermore, it considers both axial and tangential meshing stiffnesses. The proposed dual-iterative TVMS model is verified by using the finite element (FE) method. Moreover, a six degree-of-freedom (DOF) dynamic model for misaligned helical gears is established to investigate the effects of misalignments on the vibration characteristics of the gear pair. An experimental setup utilizing a back-to-back helical gear test rig with adjustable angular misalignment is constructed to validate the proposed model. The experimental results exhibit a close alignment with the simulation predictions. It is concluded that the proposed model is suitable for estimating the TVMS and dynamic analysis of helical gear pairs with angular misalignment errors.
Maturity-Associated Longitudinal Variations in Exercise-Induced Acute Hormonal Responses in Adolescent Male Athletes
Authors: Sekine Yuta
Published: October 2024

Purpose: To examine longitudinal changes in exercise-induced hormonal responses in adolescent male basketball players. Methods: Fifteen adolescent males were assigned to prepeak height velocity (pre-PHV) and post-PHV groups according to the predicted age at PHV. Salivary testosterone, cortisol levels, and the testosterone-to-cortisol ratio were evaluated before (PRE), immediately after (POST), and 15 minutes after a bodyweight resistance training session, which was repeated after 1 year to analyze longitudinal changes in testosterone and cortisol levels. Results: Resting testosterone levels and acute testosterone responses after bodyweight resistance training increased in both groups after 1 year at all measurement points. The POST testosterone levels at initial measurement and PRE and 15-minute postexercise levels at 1 year in the post-PHV group were significantly higher than those in the pre-PHV group. Cortisol levels significantly decreased in the post-PHV group at baseline and 1 year later. In the post-PHV, the testosterone-to-cortisol ratio after bodyweight resistance training was significantly increased at baseline and 1 year later. Conclusions: Although testosterone levels increase with age, no acute response to bodyweight resistance training was observed after 1 year. The change in anabolic status indicated by the testosterone-to-cortisol ratio was due to a decrease in cortisol levels.
The de novo purine synthesis enzyme Adssl1 promotes cardiomyocyte proliferation and cardiac regeneration
Authors: Li Zhigang , Dong Xiaxi , Zhuang Lingfang , Jia Kangni , Cheng Haomai , Sun Hang , Cui Yuke , Ma Wenqi , Wei Keying , Zhang Pupu , Xie Hongyang , Yi Lei , Chen Zhiyong , Lu Lin , Li Tao , Zhang Ruiyan , Yan Xiaoxiang
Published: October 2024

There is a short window during which the neonatal heart has the proliferative capacity to completely repair damage, an ability that is lost in adulthood. Inducing proliferation in adult cardiomyocytes by reactivating cell cycle reentry after myocardial infarction (MI) improves cardiac function. De novo purine synthesis is a critical source of nucleotides for cell proliferation. Here, using loss- and gain-of-function genetic approaches, we explored the role of the muscle-specific de novo purine synthesis enzyme Adssl1 in cardiac regeneration. Deletion of Adssl1 in mouse neonatal hearts reduced cardiomyocyte proliferation and attenuated heart regeneration after apical resection. Conversely, cardiomyocyte-specific Adssl1 overexpression extended the postnatal regenerative window and induced robust cell cycle reentry after MI, which decreased fibrotic scar size and improved cardiac function. RNA sequencing analysis suggested that Adssl1 overexpression induced strong dedifferentiation and cell cycle entry. Moreover, LC-MS/MS analysis showed that Adssl1 overexpression was associated with increased amounts of purine metabolites, including inosine, which is in clinical use. Administration of exogenous inosine promoted cardiac repair after MI in adult mice. At a molecular level, the increase in purine metabolite production mediated by Adssl1 enhanced the activity of the proliferation-promoting mTORC1 pathway. Our study identifies a role for Adssl1 in supporting cardiomyocyte proliferation and cardiac regeneration.
Intranasal liposomal angiotensin-(1-7) administration reduces inflammation and viral load in the lungs during SARS-CoV-2 infection in K18-hACE2 transgenic mice
Authors: Mendes Sabrina , Guimarães Lays Cordeiro , Costa Pedro Augusto Carvalho , Fernandez Clara Couto , Figueiredo Maria Marta , Teixeira Mauro Martins , dos Santos Robson Augusto Souza , Guimarães Pedro Pires Goulart , Frézard Frédéric
Published: October 2024

To effectively reduce the health impact of coronavirus disease (COVID-19), it is essential to adopt comprehensive strategies to protect individuals from severe acute respiratory syndrome. In that sense, much effort has been devoted to the discovery and repurposing of effective antiviral and anti-inflammatory molecules. The endogenous peptide angiotensin-(1-7) [Ang-(1-7)] has been recently proposed as a promising anti-inflammatory agent to control respiratory infections. Liposomes also emerged as a safe and effective drug carrier system for local drug delivery to the lungs. In this context, the aim of this study was to develop a liposomal formulation of Ang-(1-7) [LAng (1-7)] and investigate its impact on animal survival as well as its antiviral and anti-inflammatory efficacies after intranasal administration in transgenic K18-hACE2 mice infected with SARS-CoV-2. The liposomal formulation was prepared by the ethanol injection method, exhibiting a mean diameter of 100 nm and a polydispersity index of 0.1. Following treatment of infected mice every 12 hours for 5 days, LAng (1-7) extended animal survival compared to the control groups that received either empty liposomes, free Ang-(1-7), or phosphate-buffered saline. Furthermore, the treatment with LAng (1-7) significantly decreased the viral load, as well as IL-6 and tumor necrosis factor levels in the lungs. Conventional treatment with remdesivir by parenteral route used as a positive control promoted similar effects, leading to improved survival rates and reduced viral load in the lungs without significant effects on IL-6 level. In conclusion, liposomal Ang-(1-7) emerges as a promising formulation to improve the treatment and decrease the severity of respiratory infections, such as COVID-19.
Novel plasmid-mediated CMY variant (CMY-192) conferring ceftazidime-avibactam resistance in multidrug-resistant
Escherichia coli
Authors: Xu Tingting , Wu Weiyuan , Huang Lili , Liu Bin , Zhang Qiaodong , Song Jingjie , Liu Jialong , Li Bing , Li Zhao , Zhou Kai
Published: October 2024

The rapid rise of multidrug resistance (MDR) among Gram-negative bacteria has accelerated the development of novel therapies. Ceftazidime-avibactam (CZA) is a novel β-lactam/β-lactamase inhibitor recently approved for the treatment of limited infectious diseases. Here, we describe a novel CMY variant, CMY-192, that confers high-level resistance to CZA. This gene was detected in a clinical MDR
Escherichia coli
strain (Ec73552) isolated from an outpatient with a community-acquired urinary tract infection who had not received prior CZA treatment. Ec73552 was typed as O101:H9-ST10, a high-risk clone associated with human and animal diseases. Ec73552 was able to colonize the bladder in a mouse model, suggesting that this strain was uropathogenic. CMY-192 shared the highest amino acid identity (98.95%) with CMY-172 and conferred at least a 32-fold increase in CZA MIC (from ≤0.125/4 to 8/4 mg/L) when cloned into a CZA-susceptible
E. coli
DH5α strain. Knockout of CMY-192 in Ec73552 resulted in a 256-fold reduction in CZA MIC (from 64/4 to 0.25/4 mg/L). CMY-192 was encoded on an IncB/O/K/Z-type plasmid (pCMY192). Conjugation assays confirmed that pCMY192 was self-transmissible, resulting in a 256-fold increase in the CZA MIC of the recipient. Notably, pCMY192 cured in Ec73552 did not confer a growth advantage, while the conjugant exhibited reduced biomass and growth rate, indicating that fitness costs imposed by pCMY192 may have been compensated in Ec73552. Our findings highlight the importance of continuous monitoring of CZA susceptibility to prevent the spread of resistance in clinical settings.
Effects of different carbapenemase and siderophore production on cefiderocol susceptibility in
Klebsiella pneumoniae
Authors: Yang Chengcheng , Wang Liang , Lv Jingnan , Wen Yicheng , Gao Qizhao , Qian Feinan , Tian Xiangxiang , Zhu Jie , Zhu Zhichen , Chen Liang , Du Hong
Published: October 2024

The resistance mechanism of Gram-negative bacteria to the siderophore antibiotic cefiderocol is primarily attributed to carbapenemase and siderophore uptake pathways; however, specific factors and their relationships remain to be fully elucidated. Here, we constructed cefiderocol-resistant
Klebsiella pneumoniae
(CRKP) strains carrying different carbapenemases and knocked out siderophore genes to investigate the roles of various carbapenemases and siderophores in the development of cefiderocol resistance. Antimicrobial susceptibility testing revealed that both
bla
NDM
and
bla
KPC
significantly increased the minimum inhibitory concentration (MIC) of
Klebsiella pneumoniae
(KP) to cefiderocol, while
bla
OXA-48
showed a modest increase. Notably, KP expressing NDM exhibited a higher cefiderocol MIC compared to KP expressing KPC, although expression of NDM alone did not induce cefiderocol resistance. Laboratory evolutionary experiments demonstrated that combining pNDM with mutations in the siderophore uptake receptor gene
cirA
and pKPC with a mutation in the two-component system gene
envZ
led to KP reaching a high level of cefiderocol resistance. Although combining pOXA with mutations in the two-component system gene
baeS
did not induce cefiderocol resistance, it significantly reduced susceptibility. Moreover, siderophores could influence the development of cefiderocol resistance. Strains deficient in enterobactin exhibited increased susceptibility to cefiderocol, while deficiencies in yersiniabactin and salmochelin showed no significant alterations. In conclusion, carbapenemase gene expression facilitates cefiderocol resistance, but its presence alone is insufficient. Cefiderocol resistance in CRKP typically involves abnormal expression of certain genes and other factors, such as mutations in siderophore uptake receptor genes and two-component system genes. The enterobactin siderophore synthesis gene
entB
may also contribute to resistance.
Multidrug tolerance conferred by loss-of-function mutations in anti-sigma factor RshA of
Mycobacterium abscessus
Authors: Aragaw Wassihun Wedajo , Gebresilase Tewodros T. , Negatu Dereje A. , Dartois Véronique , Dick Thomas
Published: October 2024

Low-level drug resistance in noncanonical pathways can constitute steppingstones toward acquisition of high-level on-target resistance mutations in the clinic. To capture these intermediate steps in
Mycobacterium abscessus
(Mab), we performed classic mutant selection experiments with moxifloxacin at twofold its minimum inhibitory concentration (MIC) on solid medium. We found that low-level resistance emerged reproducibly as loss-of-function mutations in RshA (MAB_3542c), an anti-sigma factor that negatively regulates activity of SigH, which orchestrates a response to oxidative stress in mycobacteria. Since oxidative stress is generated in response to many antibiotics, we went on to show that deletion of
rshA
confers low to moderate resistance—by measure of MIC—to a dozen agents recommended or evaluated for the treatment of Mab pulmonary infections. Interestingly, this moderate resistance was associated with a wide range of drug tolerance, up to 1,000-fold increased survival of a Δ
rshA
Mab mutant upon exposure to several β-lactams and DNA gyrase inhibitors. Consistent with the putative involvement of the SigH regulon, we showed that addition of the transcription inhibitor rifabutin (RBT) abrogated the high-tolerance phenotype of Δ
rshA
to representatives of the β-lactam and DNA gyrase inhibitor classes. In a survey of 10,000 whole Mab genome sequences, we identified several loss-of-function mutations in
rshA
as well as non-synonymous polymorphisms in two cysteine residues critical for interactions with SigH. Thus, the multidrug multiform resistance phenotype we have uncovered may not only constitute a step toward canonical resistance acquisition during treatment but also contribute directly to treatment failure.
Multigeographic clinical assessment of a molecular diagnostic assay for detection of key codons to predict decreased susceptibility or resistance to cephalosporins in
Neisseria gonorrhoeae
Authors: Wang Liqin , Li Yamei , Xiu Leshan , Hu Lihua , Huang Jia , Yong Gang , Wang Youwei , Cao Wenling , Yang Yang , Wang Feng , Gu Weiming , Peng Junping
Published: October 2024

Cephalosporin resistance in
Neisseria gonorrhoeae
has severely compromised the efficacy of World Health Organization (WHO)-recommended therapies. This study aimed to methodologically evaluate the optimized Six-Codon
Plus
assay, and additionally conducted a multicenter evaluation to assess its clinical application, especially for predicting antimicrobial resistance (AMR). For methodological evaluation, 397 sequence-known
N. gonorrhoeae
isolates were evaluated for specificity, 17 nongonococcal isolates were assessed for cross-reactivity, 159 uncultured urogenital swabs and urine samples were evaluated for sensitivity at the clinical level. For multicenter evaluation, 773 isolates with confirmed phenotypic data and 718 clinical urogenital swabs collected from four geographical cities were, respectively, utilized for the evaluation of AMR-prediction strategies and the clinical application of the assay. The assay accurately identified specific single-nucleotide polymorphisms in resistance-associated genes, the detection limits dropped to 10 copies/reaction for individual targets. The specificity reached 100% and no cross-reactivity occurred with double-target confirmation. The assay could be directly applied to clinical samples containing over 20 copies/reaction. Multicenter evaluation formulated two optimal strategies for decreased susceptibility prediction in specific scenarios, and one tactic for prediction of resistance and identification of FC428-like strains. High sensitivity of 86.84% (95% CI, 71.11–95.05) and specificity of 99.59% (95% CI, 98.71–99.89) for resistance prediction were demonstrated for ceftriaxone (CRO). Regarding
N. gonorrhoeae
identification among multicenter swabs, specificity reached 97.53% (95% CI, 95.49–98.69), and sensitivity reached 93.77% (95% CI, 90.04–96.22). The Six-Codon
Plus
assay exhibited excellent detection performance and formulated optimal AMR-related prediction strategy with regional adaptability, providing critical information for population screening and clinical treatment.
Helicase protein DDX11 as a novel antiviral factor promoting RIG-I-MAVS-mediated signaling pathway
Authors: Zhang Jiyu , Zhang Liaoyuan , Liu Dakai , Shi Hongyan , Zhang Xin , Chen Jianfei , Yang Xiaoman , Zeng Miaomiao , Zhang Jialin , Feng Tingshuai , Zhu Xiaoyuan , Jing Zhaoyang , Ji Zhaoyang , Shi Da , Feng Li
Published: October 2024

Type Ι interferon (IFN) production mediated by retinoic acid-inducible gene 1 (RIG-I) and mitochondrial antiviral signaling protein (MAVS) is essential for antiviral innate immune responses. Here, we report the identification of a novel co-sensor for cytosolic nucleic acids: DEAD/H-box helicase 11 (DDX11), a member of the DExD/H (Asp-Glu-x-Asp/His)-box helicase family. Knockdown or knockout of DDX11 attenuated the ability of cells to increase IFN-β, IFN-stimulated gene 56, and C-X-C motif chemokine ligand 10 in response to SeV and poly (I:C) by blocking the activation of TANK-binding kinase 1 and IFN regulatory factor 3. Nucleic acid sensing by DDX11 was independent of the stimulator of IFN genes but was dependent on RIG-I and MAVS. DDX11 regulated RIG-I-MAVS-mediated IFN signaling by specifically interacting with nucleic acid, RIG-I, and MAVS to enhance RIG-I-double-strand RNA and RIG-I-MAVS binding affinity. Overall, our results identified a critical role for DDX11 in the innate immune response and provided molecular insights into the mechanisms by which DDX11 recognized cytosolic nucleic acid and interacted with RIG-Ι and MAVS for potent IFN signaling and antiviral immunity.

IMPORTANCE

Innate immunity is the first and most rapid host defense against virus infection. Recognition of viral RNA by the retinoic acid-inducible gene 1 (RIG-I)-like receptors (RLRs) initiates innate antiviral immune responses. How the binding of viral RNA to and activation of the RLRs are regulated remains enigmatic. In this study, we identified DEAD/H-box helicase 11 (DDX11) as a positive regulator of the RIG-I-mitochondrial antiviral signaling protein (MAVS)-mediated signaling pathways. Mechanistically, we demonstrated that DDX11 bound to viral RNA, interacted with RIG-I, and promoted their binding to viral RNA. DDX11 also promoted the interaction between RIG-I and MAVS and activation of RIG-I-MAVS signaling. Overall, our results elucidate the role of DDX11 in RIG-I-MAVS-dependent signaling pathways and may shed light on innate immune gene regulation.
S-palmitoylation of MAP kinase is essential for fungal virulence
Authors: Duan Yuhang , Li Pingping , Zhang Deyao , Wang Lili , Fang Yuan , Hu Hong , Mao Qiulu , Zhou Xiaolan , Zhao Panpan , Li Xuechun , Wei Jinfeng , Tang Jintian , Pan Li , Liu Hao , Chen Xiaolin , Chen Xiaoyang , Hsiang Tom , Huang Junbin , Zheng Lu
Published: October 2024

S-palmitoylation is an important reversible protein post-translational modification in organisms. However, its role in fungi is uncertain. Here, we found the treatment of the rice false fungus
Ustilaginoidea virens
with S-palmitoylation inhibitor 2 BP resulted in a significant decrease in fungal virulence. Comprehensive identification of S-palmitoylation sites and proteins in
U. virens
revealed a total of 4,089 S-palmitoylation sites identified among 2,192 proteins and that S-palmitoylated proteins were involved in diverse biological processes. Among the five palmitoyltransferases, UvPfa3 and UvPfa4 were found to regulate the pathogenicity of
U. virens
. We then performed quantitative proteomic analysis of ∆
UvPfa3
and ∆
UvPfa4
mutants. Interestingly, S-palmitoylated proteins were significantly enriched in the mitogen-activated protein kinase and autophagy pathways, and MAP kinase UvSlt2 was confirmed to be an S-palmitoylated protein which was palmitoylated by UvPfa4. Mutations of S-palmitoylation sites in
UvSlt2
resulted in significantly reduced fungal virulence and decreased kinase enzymatic activity and phosphorylation levels. Simulations of molecular dynamics demonstrated mutation of S-palmitoylation sites in
UvSlt2
causing decreased hydrophobic solvent-accessible surface area, thereby weakening the bonding force with its substrate UvRlm1. Taken together, S-palmitoylation promotes
U. virens
virulence through palmitoylation of MAP kinase UvSlt2 by palmitoyltransferase UvPfa4. This enhances the enzymatic phosphorylation activity of the kinase, thereby increasing hydrophobic solvent-accessible surface area and binding activity between the UvSlt2 enzyme and its substrate UvRlm1. Our studies provide a framework for dissecting the biological functions of S-palmitoylation and reveal an important role for S-palmitoylation in regulating the virulence of the pathogen.

IMPORTANCE

S-palmitoylation is an important post-translational lipid modification of proteins. However, its role in fungi is uncertain. In this study, we found that S-palmitoylation promotes virulence of rice false smut fungus
U. virens
through palmitoylation of MAP kinase UvSlt2 by palmitoyltransferase UvPfa4. This enhances the enzymatic phosphorylation activity of the kinase, thereby increasing hydrophobic solvent-accessible surface area and binding activity between the UvSlt2 enzyme and its substrate UvRlm1. Our studies provide a framework for dissecting the biological functions of S-palmitoylation and reveal an important role for S-palmitoylation in regulating the virulence of the pathogen. This is the first functional study to reveal the role of S-palmitoylation in fungal virulence.
Complete genome sequence of
Bulleidia
sp. 10714-15 isolated from human colon cancer patients
Authors: Ikeda Haruto , Oshibuchi Kota , Yang Jiayue , Fukuda Shinji , Arakawa Kazuharu
Published: October 2024

Bulleidia
sp. is a non-spore-forming, obligatory anaerobic, Gram-positive bacterium isolated from the stool samples of human colon cancer patients. We report the complete genome sequence of
Bulleidia
sp. 10714-15, comprising a single linear chromosome of 2,218,984 bp with a G + C content of 36.6%.
Surfactin from
Bacillus subtilis
enhances immune response and contributes to the maintenance of intestinal microbial homeostasis
Authors: Jia Junpeng , Fu Mei , Ji Wenxin , Xiong Ningna , Chen Peng , Lin Jian , Yang Qian
Published: October 2024

Surfactin, a lipopeptide biosurfactant produced by
Bacillus
spp., has emerged as a promising bioactive compound due to its potent inhibitory effects on bacterial and viral pathogens. This showcases its potential as a non-antibiotic strategy for managing infectious diseases. Our investigation reveals that surfactin administration significantly promotes weight gain and improves immune organ indices in mice, reflecting enhanced immunity and gut health. Surfactin augments phagocytic function in peritoneal macrophages and boosts proliferative responses in splenic lymphocytes post-chicken red blood cell immunization. Furthermore, it increases intestinal villi height, indicative of superior nutrient absorption. It elevates mucin secretion and expression of intestinal mucosal proteins, such as secretory IgA, Muc1, and Muc2, and tight junction proteins claudin-1, occludin, and Zo-1 in the jejunum and colon. Crucially, surfactin modifies the gut microbiota composition by reducing
Escherichia coli
populations and ameliorating cyclophosphamide-induced gut dysbiosis. Our data suggest that oral surfactin could be a valuable therapeutic modality to alleviate immune suppression and gut damage, proposing a new pathway for immunomodulatory treatment.

IMPORTANCE

The potential of surfactin as a microbial surfactant extends beyond its surfactant properties, impacting immune regulation and gut health. As the need for alternatives to traditional antibiotics continues to grow, surfactin’s ability to enhance host defense mechanisms against common pathogens without directly targeting them with antibiotics offers a strategic advantage. Understanding how surfactin shapes the immune landscape and the gut microbiome can inform innovative interventions against immunosuppression and intestinal impairment, particularly in contexts such as cyclophosphamide-induced toxicity.
Characterization of cross-reactive, non-neutralizing monoclonal antibodies against a pandemic GII.4 norovirus variant
Authors: Ford-Siltz Lauren A. , Tohma Kentaro , Kihn Kyle , Kendra Joseph A. , Deredge Daniel , Wintrode Patrick , Gao Yamei , Parra Gabriel I.
Published: October 2024

Antibodies are thought to play a major role in protection against human norovirus infection. Mouse humoral responses closely mimic those of humans; thus, mouse models are used to characterize norovirus epitopes on the major viral capsid protein, VP1. We have developed a panel of mouse monoclonal antibodies (mAbs) produced against the last pandemic variant to emerge, Sydney 2012. While most mAbs (25/44) were mapped to variable antigenic sites on VP1, 19 of the mAbs were cross-reactive against multiple genotypes or GII.4 variants. Most (12/19) of the cross-reactive mAbs bound to the Shell domain and were cross-reactive with different GII noroviruses. Interestingly, mAb 30A11 exhibited cross-reactivity against all tested norovirus genotypes (GI, GII, GIV, and GIX). This mAb was mapped to a highly conserved region of the Shell domain (
51
PIDPWII
57
) using peptide ELISA and immunofluorescence. Of those mapping to the Protruding (P) domain, two (19C10 and 14B11) showed cross-reactivity with GII noroviruses. Using hydrogen-deuterium exchange mass spectrometry, we mapped 19C10 to a conserved region of the P domain near the P/Shell interface, which explains its cross-reactivity with different GII noroviruses and lack of histo-blood group antigen-blocking activity. Binding and mutational analyses showed that residues 518, 519, and 525 are important for 19C10 and 14B11 epitope recognition. While the antibodies described here are mostly non-neutralizing, they can be useful tools for research and diagnostics of noroviruses. The role of non-neutralizing, cross-reactive antibodies targeting different areas of the viral capsid merits further research to facilitate our understanding of immunity to norovirus infection and disease.

IMPORTANCE

To gain insights into the overall immune responses to human norovirus, we characterized non-neutralizing, cross-reactive monoclonal antibodies (mAbs) developed against a pandemic GII.4 norovirus. We determined the binding epitope of an antibody that exhibited cross-reactivity against all tested noroviruses, which makes it a useful tool for research and diagnostics. The epitope of two additional non-neutralizing mAbs was mapped to a less conserved region on the viral capsid protein, explaining their cross-reactivity patterns. Often overlooked, the role of non-neutralizing, cross-reactive mAbs merits further research to facilitate our understanding of immunity to norovirus infection and disease.
Biofilm-mediated antibiotic tolerance in
Staphylococcus aureus
from spinal cord stimulation device-related infections
Authors: Sivori Francesca , Cavallo Ilaria , Truglio Mauro , Pelagalli Lorella , Mariani Valerio , Fabrizio Giorgia , Abril Elva , Santino Iolanda , Fradiani Piera Assunta , Solmone Mariacarmela , Pimpinelli Fulvia , Toma Luigi , Arcioni Roberto , De Blasi Roberto Alberto , Di Domenico Enea Gino
Published: October 2024

Staphylococcus aureus
is a predominant cause of infections in individuals with spinal cord stimulation (SCS) devices. Biofilm formation complicates these infections, commonly requiring both surgical and antibiotic treatments. This study explored the biofilm matrix composition and antimicrobial susceptibility of planktonic and biofilm-growing
S. aureus
isolates from individuals with SCS-related infections. Whole-genome sequencing (WGS) examined genotypes, virulome, resistome, and the pan-genome structure. The study also analyzed biofilm matrix composition, early surface adhesion, hemolytic activity, and antibiotic-susceptibility testing. WGS revealed genetic diversity among isolates. One isolate, though oxacillin susceptible, contained the
mec
A gene. The median number of virulence factor genes per isolate was 58. All isolates harbored the biofilm-related
ica
A/D genes. When assessing phenotypic characteristics, all strains demonstrated the ability to form biofilms
in vitro
. The antimicrobial susceptibility profile indicated that oxacillin, rifampin, and teicoplanin showed the highest efficacy against
S. aureus
biofilm. Conversely, high biofilm tolerance was observed for vancomycin, trimethoprim/sulfamethoxazole, and levofloxacin. These findings suggest that
S. aureus
isolates are highly virulent and produce robust biofilms. In cases of suspected biofilm infections caused by
S. aureus
, vancomycin should not be the primary choice due to its low activity against biofilm. Instead, oxacillin, rifampin, and teicoplanin appear to be more effective options to manage SCS infections.

IMPORTANCE

SCS devices are increasingly used to manage chronic pain, but infections associated with these devices, particularly those caused by
Staphylococcus aureus
, present significant clinical challenges. These infections are often complicated by biofilm formation, which protects bacteria from immune responses and antibiotic treatments, making them difficult to eradicate. Understanding the genetic diversity, virulence, and biofilm characteristics of
S. aureus
isolates from SCS infections is critical to improving treatment strategies. Our study highlights the need to reconsider commonly used antibiotics like vancomycin, which shows reduced activity against biofilm-growing cells. Identifying more effective alternatives, such as oxacillin, rifampin, and teicoplanin, provides valuable insight for clinicians when managing biofilm-related
S. aureus
infections in patients with SCS implants. This research contributes to the growing evidence that biofilm formation is crucial in treating device-related infections, emphasizing the importance of tailoring antimicrobial strategies to the biofilm phenotype.
Integrated multi-omics analysis of the microbial profile characteristics associated with pulmonary arterial hypertension in congenital heart disease
Authors: Xie Jiahui , Zhang Xiaoyu , Cheng Liming , Deng Yao , Ren Haobo , Mu Minghua , Zhao Liang , Mu Chunjie , Chen Jiaxiang , Liu Kai , Ma Runwei
Published: October 2024

Dysregulation of immune and inflammatory cells around blood vessels and metabolic dysfunction are key mechanisms in the development of pulmonary arterial hypertension (PAH). The homeostasis of the human microbiome plays a crucial role in regulating immune responses and the progression of diseases. For pulmonary arterial hypertension associated with congenital heart disease involving body-lung shunt (PAH-CHD), the potential impact of the microbiome on the “gut-lung axis” remains underexplored. This study recruited 15 healthy individuals and 15 patients with pulmonary arterial hypertension due to congenital heart disease from Fuwai Yunnan Hospital, Chinese Academy of Medical Sciences, and Kunming Children's Hospital. We performed differential analyses of metabolites and microbiota from both the gut and lower respiratory tract for these two groups. The goal was to investigate the “gut-lung axis” microbiome and metabolome profiles in children with PAH-CHD and to analyze the interrelationships between these profiles. Ultimately, we aim to propose the potential value of these profiles in aiding diagnosis. The results indicated that the gut and pulmonary microbiota of children with PAH-CHD are characterized by an increased abundance of beneficial symbionts, which are closely linked to changes in the metabolome. Metabolite functional enrichment analysis revealed energy metabolism reprogramming in the PAH-CHD group, with active metabolic pathways associated with bile acid secretion and carnitine homeostasis. Moreover, the differential expression of metabolites was correlated with right heart function and growth development.

IMPORTANCE

Previous studies have primarily focused on the relationship between the gut microbiome and PAH. However, the impact of microbial homeostasis on the progression of PAH-CHD from the perspective of the gut-lung axis has not been adequately elucidated. Our study utilizes an integrated multi-omics approach to report on the differential characteristics of gut and lung microbiota between children with PAH-CHD and reference subjects. We found that microbiota influence the pathological changes and disease manifestations of PAH-CHD through their metabolic activity. Additionally, alterations in metabolites impact the microbial ecological structure. Our findings suggest that modulating the microbiome composition may have positive implications for maintaining and regulating the immune environment and pathological progression of PAH-CHD.
Real-time plasmid transmission detection pipeline
Authors: Scherff Natalie , Rothgänger Jörg , Weniger Thomas , Mellmann Alexander , Harmsen Dag
Published: October 2024

The spread of antimicrobial resistance among bacteria by horizontal plasmid transmissions poses a major challenge for clinical microbiology. Here, we evaluate a new real-time plasmid transmission detection pipeline implemented in the SeqSphere
+
(Ridom GmbH, Münster, Germany) software. Within the pipeline, a local Mash plasmid database is created, and Mash searches with a distance threshold of 0.001 are used to trigger plasmid transmission early warning alerts (EWAs). Clonal transmissions are detected using core-genome multi-locus sequence typing allelic differences. The tools MOB-suite, NCBI AMRFinderPlus, CGE MobileElementFinder, pyGenomeViz, and MUMmer, integrated in SeqSphere+, are used to characterize plasmids and for visual pairwise plasmid comparisons, respectively. We evaluated the pipeline using published hybrid assemblies (Oxford Nanopore Technology/Illumina) of a surveillance and outbreak data set with plasmid transmissions. To emulate prospective usage, samples were imported in chronological order of sampling date. Different combinations of the user-adjustable parameters sketch size (1,000 vs 10,000) and plasmid size correction were tested, and discrepancies between resulting clusters were analyzed with Quast. When using a sketch size of 1,000 with size correction turned on, the SeqSphere
+
pipeline agreed with the published data and produced the same clonal and carbapenemase-carrying plasmid clusters. EWAs were in the correct chronological order. In summary, the developed pipeline presented here is suitable for integration into clinical microbiology settings with limited bioinformatics knowledge due to its automated analyses and alert system, which are combined with the GUI-based SeqSphere
+
platform. Thus, with its integrated sample database, (near) real-time plasmid transmission detection is within reach in bacterial routine-diagnostic settings when long-read sequencing is employed.

IMPORTANCE

Plasmid-mediated spread of antimicrobial resistance is a major challenge for clinical microbiology, and monitoring of potential plasmid transmissions is essential to combat further dissemination. Whole-genome sequencing is often used to surveil nosocomial transmissions but usually limited to the detection of clonal transmissions (based on chromosomal markers). Recent advances in long-read sequencing technologies enable full reconstruction of plasmids and the detection of very similar plasmids, but so far, easy-to-use bioinformatic tools for this purpose have been missing. Here, we present an evaluation of an innovative real-time plasmid transmission detection pipeline. It is integrated into the GUI-based SeqSphere
+
software, which already offers core-genome multi-locus sequence typing-based pathogen outbreak detection. It requires very limited bioinformatics knowledge, and its database, automated analyses, and alert system make it well suited for prospective clinical application.
Supplemental Material: Volcanic activity driving rapid organic carbon burial during the Ordovician–Silurian transition
Authors: Liang Chao , Wu Jing , al. et
Published: October 2024

Tables S1–S3: Location information on wells and sections in Figures 1, 3, 5–7, and 9, and global black shale sequestration of organic carbon during the OST. Supplemental Data S1 and S2: Data related to changes in the sedimentary environment at the meter-scale samples and at the centimeter-scale samples.
Making medical education great again: analysing trainee feedback to identify key drivers of trainee satisfaction and improve experience
Authors: Ferin Katheryn , Hufflett Tony , Rance Thomas , Round Jonathan
Published: October 2024

Objectives

The London School of Paediatrics (LSP) surveys trainees annually regarding their training placements. There is a wide variation in satisfaction. We explored the last 5 years of data to identify trends and determine predictors of overall trainee satisfaction.

Methods

The survey is distributed annually to all London paediatric trainees with response rates of 86–90%. It explores overall placement satisfaction, followed by key questions covering staffing, supervision, teaching, facilities and other facets. The survey blends both quantitative and qualitative feedback.

Satisfaction levels were analysed using time series trend analysis. Overall levels were compared using t-tests. Associations between satisfaction and components of the survey were identified using a convergence of multiple regression and other multivariate analyses.

Results

Overall trainee satisfaction increased steadily until 2020. There was a considerable variation across sites, some having consistently higher or lower scores than the median, while others showed an upward or downward trend, or very variable pattern.

By training levels, ST3 trainees consistently rated their placement below average and ST7 trainees above average. There was also a considerable variation in responses by training level with regard to perceived staffing levels and teaching.

To understand the influences on overall satisfaction, regression coefficients were derived between specific metrics and overall satisfaction using multiple regression and then normalised to 100%. The explanatory power of this list to explain satisfaction overall is high at 82% R2.

Trainee satisfaction was most strongly correlated with workplace atmosphere and consultant support. Staffing, educational supervision, facilities and wider MDT (Multidisciplinary Team) support are associated with overall satisfaction, but to a lesser degree.

Conclusions

Trainee satisfaction is crucial, affecting patient safety, retention and trainee mental health. Our analysis identified significant associations with satisfaction including modifiable elements such as consultant engagement and team morale. Staffing levels were less related to satisfaction than expected.

Experimental data exploring the components of clinical training in real-world situations are lacking. These data use the natural experiment of placing trainees in different training locations to explore the factors that relate to their overall experience.
Peroxisome inter-organelle cooperation in Drosophila
Authors: Cheng Andy Y. , Simmonds Andrew J.
Published: October 2024

Many cellular functions are compartmentalized within the optimized environments of organelles. However, processing or storage of metabolites from the same pathway can occur in multiple organelles. Thus, spatially separated organelles need to cooperate functionally. Coordination between organelles in different specialized cells is also needed, with shared metabolites passed via circulation. Peroxisomes are membrane-bounded organelles responsible for cellular redox and lipid metabolism in eukaryotic cells. Peroxisomes coordinate with other organelles including mitochondria, endoplasmic reticulum, lysosomes, and lipid droplets. This functional coordination requires, or is at least enhanced by, direct contact between peroxisomes and other organelles. Peroxisome dysfunction in humans leads to multiorgan effects including neurological, metabolic, developmental, and age-related diseases. Thus, increased understanding of peroxisome coordination with other organelles, especially cells in various organs is essential. Drosophila melanogaster (fruit fly) has emerged recently as an effective animal model for understanding peroxisomes. Here we review current knowledge of pathways regulating coordination between peroxisomes with other organelles in flies, speculating about analogous roles for conserved Drosophila genes encoding proteins with known organelle coordinating roles in other species.