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N6-Methyladenine (6mA) is a naturally occurring DNA modification in both prokaryotes and eukaryotes. Herein, we developed a deaminase-mediated sequencing (DM-seq) method for genome-wide mapping of 6mA at single-nucleotide resolution. The method capitalizes on the selective deamination of adenine, but not 6mA, in DNA mediated by an evolved adenine deaminase, ABE8e. By employing this method, we achieved genome-wide mapping of 6mA in Escherichia coli and in mammalian mitochondrial DNA (mtDNA) at single-nucleotide resolution. We found that the 6mA sites are mainly located in the GATC motif in the E. coli genome. We also identified 17 6mA sites in mtDNA of HepG2 cells, where all of the 6mA sites are distributed in the heavy strand of mtDNA. We envision that DM-seq will be a valuable tool for uncovering new functions of 6mA in DNA and for exploring its potential roles in mitochondria-related human diseases.

Abstract Background Retroperitoneal liposarcoma (RLPS) constitutes the majority of retroperitoneal sarcomas. While surgical resection remains the sole curative approach, determining the optimal surgical strategy for RLPS remains elusive. This study addresses the ongoing debate surrounding the optimal surgical strategy for RLPS. Methods We recruited 77 patients with RLPS who underwent aggressive surgical policies. Patients were categorized into three surgical subtypes: suprapancreatic RLPS, pancreatic RLPS, and subpancreatic RLPS. Our standardized surgical strategy involved resecting macroscopically uninvolved adjacent organs according to surgical subtypes. We collected clinical, pathological and prognostic data for analyses. Results The median follow-up was 45.5 months. Overall survival (OS) and recurrence-free survival (RFS) were significantly correlated with multifocal RLPS, pathological subtype, recurrent RLPS and histological grade (P for OS = 0.011, 0.004, 0.010, and

Background: Hypoxic pulmonary hypertension (HPH) is the main pathological change in vascular remodeling, a complex cardiopulmonary disease caused by hypoxia. Some research results have shown that ginsenoside Rg1 (Rg1) can improve vascular remodeling, but the effect and mechanism of Rg1 on hypoxia-induced pulmonary hypertension are not clear. The purpose of this study was to discuss the potential mechanism of action of Rg1 on HPH. Methods: C57BL/6 mice, calpain-1 knockout mice and Pulmonary artery smooth muscle cells (PASMCs) were exposed to a low oxygen environment with or without different treatments. The effect of Rg1 and calpain-1 silencing on inflammation, fibrosis, proliferation and the protein expression levels of calpain-1, STAT3 and p-STAT3 were determined at the animal and cellular levels. Results: At the mouse and cellular levels, hypoxia promotes inflammation, fibrosis, and cell proliferation, and the expression of calpain-1 and p-STAT3 is also increased. Ginsenoside Rg1 administration and calpain-1 knockdown, MDL-28170, and HY-13818 treatment showed protective effects on hypoxia-induced inflammation, fibrosis, and cell proliferation, which may be associated with the downregulation of calpain-1 and p-STAT3 expression in mice and cells. In addition, overexpression of calpain 1 increased p-STAT3 expression, accelerating the onset of inflammation, fibrosis and cell proliferation in hypoxic PASMCs. Conclusion: Ginsenoside Rg1 may ameliorate hypoxia-induced pulmonary vascular remodeling by suppressing the calpain-1/STAT3 signaling pathway.

Abstract Background Oral cavity squamous cell carcinoma (OCSCC) is the most common pathological type in oral tumors. This study intends to construct a novel prognostic nomogram model based on China populations for these resectable OCSCC patients, and then validate these nomograms. Methods A total of 607 postoperative patients with OCSCC diagnosed between June 2012 and June 2018 were obtained from two tertiary medical institutions in Xinxiang and Zhengzhou. Then, 70% of all the cases were randomly assigned to the training group and the rest to the validation group. The endpoint time was defined as overall survival (OS) and disease-free survival (DFS). The nomograms for predicting the 3-, and 5-year OS and DFS in postoperative OCSCC patients were established based on the independent prognostic factors, which were identified by the univariate analysis and multivariate analysis. A series of indexes were utilized to assess the performance and net benefit of these two newly constructed nomograms. Finally, the discrimination capability of OS and DFS was compared between the new risk stratification and the American Joint Committee on Cancer (AJCC) stage by Kaplan-Meier curves. Results 607 postoperative patients with OCSCC were selected and randomly assigned to the training cohort (n = 425) and validation cohort (n = 182). The nomograms for predicting OS and DFS in postoperative OCSCC patients had been established based on the independent prognostic factors. Moreover, dynamic nomograms were also established for more convenient clinical application. The C-index for predicting OS and DFS were 0.691, 0.674 in the training group, and 0.722, 0.680 in the validation group, respectively. Besides, the calibration curve displayed good consistency between the predicted survival probability and actual observations. Finally, the excellent performance of these two nomograms was verified by the NRI, IDI, and DCA curves in comparison to the AJCC stage system. Conclusion The newly established and validated nomograms for predicting OS and DFS in postoperative patients with OCSCC perform well, which can be helpful for clinicians and contribute to clinical decision-making.

Abstract Background Despite the advances of therapies, multiple myeloma (MM) remains an incurable hematological cancer that most patients experience relapse. Tumor angiogenesis is strongly correlated with cancer relapse. Human leukocyte antigen G (HLA-G) has been known as a molecule to suppress angiogenesis. We aimed to investigate whether soluble HLA-G (sHLA-G) was involved in the relapse of MM. Methods We first investigated the dynamics of serum sHLA-G, vascular endothelial growth factor (VEGF) and interleukin 6 (IL-6) in 57 successfully treated MM patients undergoing remission and relapse. The interactions among these angiogenesis-related targets (sHLA-G, VEGF and IL-6) were examined in vitro. Their expression at different oxygen concentrations was investigated using a xenograft animal model by intra-bone marrow and skin grafts with myeloma cells. Results We found that HLA-G protein degradation augmented angiogenesis. Soluble HLA-G directly inhibited vasculature formation in vitro. Mechanistically, HLA-G expression was regulated by hypoxia-inducible factor-1α (HIF-1α) in MM cells under hypoxia. We thus developed two mouse models of myeloma xenografts in intra-bone marrow (BM) and underneath the skin, and found a strong correlation between HLA-G and HIF-1α expressions in hypoxic BM, but not in oxygenated tissues. Yet when stimulated with IL-6, both HLA-G and HIF-1α could be targeted to ubiquitin-mediated degradation via PARKIN. Conclusion These results highlight the importance of sHLA-G in angiogenesis at different phases of multiple myeloma. The experimental evidence that sHLA-G as an angiogenesis suppressor in MM may be useful for future development of novel therapies to prevent relapse.

Abstract Background Clinical evidence for the rapidity and effectiveness of fentanyl buccal soluble film (FBSF) in reducing pain intensity of breakthrough cancer pain (BTcP) remains inadequate. This study aimed to evaluate the efficacy of FBSF proportional to the around-the‐clock (ATC) opioid regimens in rapidly relieving the intensity of BTcP episodes by determining the percentage of patients requiring further dose titration. Methods The study procedure included a dose-finding period followed by a 14-day observation period. Pain intensity was recorded with a Numeric Rating Scale (NRS) at onset and 5, 10, 15, and 30 min after FBSF self-administration. Meaningful pain relief was defined as the final NRS score ≤ 3. Satisfaction survey was conducted for each patient after treatment using the Global Satisfaction Scale. Results A total of 63 BTcP episodes occurred in 30 cancer patients. Only one patient required rescue medication at first BTcP episode and then achieved meaningful pain relief after titrating FBSF by 200 µg. Most BTcP episodes relieved within 10 min. Of 63 BTcP episodes, 30 (47.6%), 46 (73.0%), and 53 (84.1%) relieved within 5, 10, and 15 min after FBSF administration. Only grade 1/2 adverse events were reported, including somnolence, malaise, and dizziness. Of the 63 BTcP episodes, 82.6% were rated as excellent/good satisfaction with FBSF. Conclusion FBSF can be administrated “on demand” by cancer patients at the onset of BTcP, providing rapid analgesia by achieving meaningful pain relief within 10 min. Trial registration This study was retrospectively registered 24 December, 2021 at Clinicaltrial.gov (NCT05209906): https://clinicaltrials.gov/study/NCT05209906 .

Abstract The current practice of restoring the anatomical structure in the treatment of pelvic floor dysfunction includes implantation of synthetic sling, which carries potential complications. This study aimed to develop biological substitutes to improve tissue function using scaffolds as a support to the host cells, through formation of new tissue. Human amniotic fluid stem cells (hAFSCs) were seeded on synthetic mesh-scaffold of AlloDerm Regenerative Tissue Matrix (RTM), Poly-DL-lactico-glycolic acid (PLGA) mesh (VICRYL) and Polydioxanone (PDS) meshes. In vitro study evaluates the metabolic activity of hAFSCs seeded mesh-scaffolds. In vivo study involving Sprague–Dawley rats was performed by assigning into 7 groups of sham control with fascia operation, AlloDerm implant, PDS implant, PLGA implant, AlloDerm harvest with hAFSC (AlloDerm-SC), PDS harvest with hAFSC(PDS-SC) and PLGS harvest with hAFSC (PGLA-SC). In vitro study reveals cell viability and proliferation of hAFSC on mesh scaffolds varies between meshes, with AlloDerm growing the fastest. The biomechanical properties of tissue-mesh-complex tension strength declined over time, showing highest tension strength on week-1, deteriorated similar to control group on week-12. All hAFSC-seeded mesh provides higher tension strength, compared to without. This study shed the potential of synthetic mesh as a scaffold for hAFSC for the surgical treatment of pelvic floor dysfunction.

Abstract Underwater explosions (UNDEX) generate shock waves that interact with the air–water interface and structures, leading to the occurrence of rarefaction waves and inducing cavitation phenomena. In deep-water explosions, complex coupling relationships exist between shock wave propagation, bubble motion, and cavitation evolution. The shock wave initiates the formation of cavitation, and their growth and collapse are influenced by the pressure field. The collapsing bubbles generate additional shock waves and fluid motion, affecting subsequent shock wave propagation and bubble behavior. This intricate interaction significantly impacts the hydrodynamic characteristics of deep-water explosions, including pressure distribution, density, and phase changes in the surrounding fluid. In this paper, we utilize a two-fluid phase transition model to capture the evolution of cavitation in deep-water explosions. Our numerical results demonstrate that the introduction of a two-phase vapor–liquid phase change model is necessary to accurately capture scenarios involving prominent evaporation or condensation phenomena. Furthermore, we find that the cavitation produced by the same charge under different explosion depths exhibits significant differences, as does the peak value of cavitation collapse pressure. Similarly, the cavitation produced by different charge quantities under the same explosion depth varies, and the relationship between cavitation volume and charge quantity is not a simple linear increase. The research methods and results presented in this paper provide an important reference for studying the dynamic characteristics of deep-water explosions.

Abstract Communications between immune cells are essential to ensure appropriate coordination of their activities. Here, we observed the infiltration of activated macrophages into the joint-footpads of chikungunya virus (CHIKV)-infected animals. Large numbers of CD64+MHCII+ and CD64+MHCII- macrophages were present in the joint-footpad, preceded by the recruitment of their CD11b+Ly6C+ inflammatory monocyte precursors. Recruitment and differentiation of these myeloid subsets were dependent on CD4+ T cells and GM-CSF. Transcriptomic and gene ontology analyses of CD64+MHCII+ and CD64+MHCII- macrophages revealed 89 differentially expressed genes, including genes involved in T cell proliferation and differentiation pathways. Depletion of phagocytes, including CD64+MHCII+ macrophages, from CHIKV-infected mice reduced disease pathology, demonstrating that these cells play a pro-inflammatory role in CHIKV infection. Together, these results highlight the synergistic dynamics of immune cell crosstalk in driving CHIKV immunopathogenesis. This study provides new insights in the disease mechanism and offers opportunities for development of novel anti-CHIKV therapeutics.

Abstract Autism spectrum disorder (ASD) is a neurodevelopmental disorder, characterized by social communication disability and stereotypic behavior. This study aims to investigate the impact of prenatal exposure to 1‐nitropyrene (1‐NP), a key component of motor vehicle exhaust, on autism‐like behaviors in a mouse model. Three‐chamber test finds that prenatal 1‐NP exposure causes autism‐like behaviors during the weaning period. Patch clamp shows that inhibitory synaptic transmission is reduced in medial prefrontal cortex of 1‐NP‐exposed weaning pups. Immunofluorescence finds that prenatal 1‐NP exposure reduces the number of prefrontal glutamate decarboxylase 67 (GAD67) positive interneurons in fetuses and weaning pups. Moreover, prenatal 1‐NP exposure retards tangential migration of GAD67‐positive interneurons and downregulates interneuron migration‐related genes, such as Nrg1, Erbb4, and Sema3F, in fetal forebrain. Mechanistically, prenatal 1‐NP exposure reduces hydroxymethylation of interneuron migration‐related genes through inhibiting ten‐eleven translocation (TET) activity in fetal forebrain. Supplement with alpha‐ketoglutarate (α‐KG), a cofactor of TET enzyme, reverses 1‐NP‐induced hypohydroxymethylation at specific sites of interneuron migration‐related genes. Moreover, α‐KG supplement alleviates 1‐NP‐induced migration retardation of interneurons in fetal forebrain. Finally, maternal α‐KG supplement improves 1‐NP‐induced autism‐like behaviors in weaning offspring. In conclusion, prenatal 1‐NP exposure causes autism‐like behavior partially by altering DNA hydroxymethylation of interneuron migration‐related genes in developing brain.

Increasing evidences demonstrate that environmental stressors are important inducers of acute kidney injury (AKI). This study aimed to investigate the impact of exposure to Cd, an environmental stressor, on renal cell ferroptosis. Transcriptomics analyses showed that arachidonic acid (ARA) metabolic pathway was disrupted in Cd-exposed mouse kidneys. Targeted metabolomics showed that renal oxidized ARA metabolites were increased in Cd-exposed mice. Renal 4-HNE, MDA, and ACSL4, were upregulated in Cd-exposed mouse kidneys. Consistent with animal experiments, the in vitro experiments showed that mitochondrial oxidized lipids were elevated in Cd-exposed HK-2 cells. Ultrastructure showed mitochondrial membrane rupture in Cd-exposed mouse kidneys. Mitochondrial cristae were accordingly reduced in Cd-exposed mouse kidneys. Mitochondrial SIRT3, an NAD+-dependent deacetylase that regulates mitochondrial protein stability, was reduced in Cd-exposed mouse kidneys. Subsequently, mitochondrial GPX4 acetylation was elevated and mitochondrial GPX4 protein was reduced in Cd-exposed mouse kidneys. Interestingly, Cd-induced mitochondrial GPX4 acetylation and renal cell ferroptosis were exacerbated in Sirt3−/− mice. Conversely, Cd-induced mitochondrial oxidized lipids were attenuated in nicotinamide mononucleotide (NMN)-pretreated HK-2 cells. Moreover, Cd-evoked mitochondrial GPX4 acetylation and renal cell ferroptosis were alleviated in NMN-pretreated mouse kidneys. These results suggest that mitochondrial GPX4 acetylation, probably caused by SIRT3 downregulation, is involved in Cd-evoked renal cell ferroptosis.

Most sugarcane cultivation areas in China have undergone over 30 years of continuous monocropping, and long-term chemical fertilizer application has led to severe soil degradation. Arbuscular mycorrhizal fungi (AMF) play a crucial role in promoting plant nutrient uptake, enhancing plant stress tolerance, and improving soil quality and restoration. However, in agroecosystems, AMF are susceptible to the effects of cultivation, fertilization, and other factors. The goal of this study was to investigate the influence of chemical fertilization on the AMF community in the rhizosphere soil of plant crop of sugarcane. In this study, sugarcane varieties GT58 and GT29 were selected for experiment. Four different chemical fertilization rates were established using controlled-release compound chemical fertilizer (N: P: K = 17:7:17): T1 (0.0 kg/ha), T2 (562.5 kg/ha), T3 (1,125.0 kg/ha), and T4 (2,250.0 kg/ha). The results showed that different fertilization rates significantly affected the cane yield in GT58. T3 and T4 increased the cane yield by 12.67% and 11.11%, respectively, compared to the control T1 (P < 0.05). The impact on the cane yield in GT29 was not significant. The diversity indices of root-associated AMF in GT58 (Chao index and Shannon index) varied significantly in different fertilization rates. T3 had the highest diversity, showing no significant difference from T1 and T2 but significantly higher than T4. For GT29, there were no significant differences in the diversity indices of root-associated AMF among different fertilization rates. Analyzing the differential species in root-associated soil with different fertilization rates in GT58 at the OTU level revealed that T3 had significantly higher abundances for 5 OTUs compared to the other treatments, and all the differentially abundant species belonged to Glomus. The Mantel analysis revealed that the genus Acaulospora was significantly and positively correlated with millable stalks (P < 0.001), and significantly and positively correlated with tiller number (P < 0.05). The genus Scutellospora showed a significant positive correlation with sprouting rate (P < 0.05). However, the other AMF genera did not show significant correlations with the agronomic traits of sugarcane. In summary, different chemical fertilization rates significantly affected the cane yield in GT58 and the AMF community in the rhizosphere soil, but not in GT29, which suggests that sugarcane chemical fertilization should consider different sugarcane varieties and the diversity of AMF communities in soil.

Experimental test campaigns have begun to demonstrate the potential of methanol as an alternative fuel for heavy-duty spark-ignited engines. However, there is no consensus yet on the scope of this solution in terms of maximum power and engine size. A zero-dimensional combustion model is therefore being developed outside the scope of this work. Its main objective will be to predict key performance parameters such as power and efficiency as function of engine size. Due to the high loads typically encountered in heavy-duty engines, knock will be the main constraint to maximize the engine's potential. This work therefore aims to find an accurate knock model that can be implemented in the modelling framework. The Livengood–Wu knock integral model is being considered as a good candidate, as it is computationally inexpensive and thus allows for a large number of engine configurations to be modelled within a reasonable time. Due to a lack of autoignition delay times of methanol at conditions relevant to heavy-duty engines, a large database was created using chemical kinetics calculations. A neural network model was trained with the tabulated data for fast data retrieval. To validate whether the knock integral approach is robust enough to be applied to a wide range of engine sizes, a calibration constant was added to match the knock predictions to experimental data. Its value was calculated for three different engines, a light and heavy-duty SI engine and a large-bore dual-fuel engine. They highlight a remarkable difference in calibration constant across the different engines investigated.

This study investigates the impact of neighboring buildings on diaphragm wall deformation during deep excavation for building foundations. Prior numerical analyses predominantly utilized surface loading models, overlooking the influence of neighboring basements. Employing the finite-element method with PLAXIS 3D AE software, we assess the effects of neighboring structures on deep excavation. Our simulation adopts the top-down construction method, employing plate elements to represent diaphragm walls Temporary retaining support measures are implemented using H-shaped steel assemblies with preloaded anchors to simulate realistic excavation conditions. Neighboring building structures are accurately modeled using plate elements. Our findings reveal that the lateral displacement of the diaphragm wall varies with the depth of neighboring basements. At depths approximately half that of the excavation depth, the displacement significantly increases, reaching approximately 1.7 times the excavation depth and stabilizing thereafter. When neighboring buildings are about twice the excavation depth away, the deformation curve of the wall converges to that of ''no loading,'' suggesting negligible influence on diaphragm wall deformation beyond this distance. Additionally, within one excavation depth, the maximum lateral displacement depth tends to be closer to the surface as the distance to the diaphragm wall decreases. Beyond a distance of one excavation depth from the diaphragm wall, the maximum lateral displacement position is approximately at the excavation face. This study significantly contributes to the comprehension of neighboring structures' influence on diaphragm walls during deep excavation, providing crucial insights for enhancing safety measures.

Abstract Avermectins (AVEs), a family of macrocyclic polyketides produced by Streptomyces avermitilis, have eight components, among which B1a is noted for its strong insecticidal activity. Biosynthesis of AVE “a” components requires 2‐methylbutyryl‐CoA (MBCoA) as starter unit, and malonyl‐CoA (MalCoA) and methylmalonyl‐CoA (MMCoA) as extender units. We describe here a novel strategy for increasing B1a production by enhancing acyl‐CoA precursor supply. First, we engineered meilingmycin (MEI) polyketide synthase (PKS) for increasing MBCoA precursor supply. The loading module (using acetyl‐CoA as substrate), extension module 7 (using MMCoA as substrate) and TE domain of MEI PKS were assembled to produce 2‐methylbutyrate, providing the starter unit for B1a production. Heterologous expression of the newly designed PKS (termed Mei‐PKS) in S. avermitilis wild‐type (WT) strain increased MBCoA level, leading to B1a titer 262.2 μg/mL – 4.36‐fold higher than WT value (48.9 μg/mL). Next, we separately inhibited three key nodes in essential pathways using CRISPRi to increase MalCoA and MMCoA levels in WT. The resulting strains all showed increased B1a titer. Combined inhibition of these key nodes in Mei‐PKS expression strain increased B1a titer to 341.9 μg/mL. Overexpression of fatty acid β‐oxidation pathway genes in the strain further increased B1a titer to 452.8 μg/mL – 8.25‐fold higher than WT value. Finally, we applied our precursor supply strategies to high‐yield industrial strain A229. The strategies, in combination, led to B1a titer 8836.4 μg/mL – 37.8% higher than parental A229 value. These findings provide an effective combination strategy for increasing AVE B1a production in WT and industrial S. avermitilis strains, and our precursor supply strategies can be readily adapted for overproduction of other polyketides.

BackgroundAccurate and rapid discrimination between benign and malignant ovarian masses is crucial for optimal patient management. This study aimed to establish an ultrasound image-based nomogram combining clinical, radiomics, and deep transfer learning features to automatically classify the ovarian masses into low risk and intermediate-high risk of malignancy lesions according to the Ovarian- Adnexal Reporting and Data System (O-RADS).MethodsThe ultrasound images of 1,080 patients with 1,080 ovarian masses were included. The training cohort consisting of 683 patients was collected at the South China Hospital of Shenzhen University, and the test cohort consisting of 397 patients was collected at the Shenzhen University General Hospital. The workflow included image segmentation, feature extraction, feature selection, and model construction.ResultsThe pre-trained Resnet-101 model achieved the best performance. Among the different mono-modal features and fusion feature models, nomogram achieved the highest level of diagnostic performance (AUC: 0.930, accuracy: 84.9%, sensitivity: 93.5%, specificity: 81.7%, PPV: 65.4%, NPV: 97.1%, precision: 65.4%). The diagnostic indices of the nomogram were higher than those of junior radiologists, and the diagnostic indices of junior radiologists significantly improved with the assistance of the model. The calibration curves showed good agreement between the prediction of nomogram and actual classification of ovarian masses. The decision curve analysis showed that the nomogram was clinically useful.ConclusionThis model exhibited a satisfactory diagnostic performance compared to junior radiologists. It has the potential to improve the level of expertise of junior radiologists and provide a fast and effective method for ovarian cancer screening.