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Abstract Skull-base chordoma is a rare, aggressive bone cancer with a high recurrence rate. Despite advances in genomic studies, its molecular characteristics and effective therapies remain unknown. Here, we conduct integrative genomics, transcriptomics, proteomics, and phosphoproteomics analyses of 187 skull-base chordoma tumors. In our study, chromosome instability is identified as a prognostic predictor and potential therapeutic target. Multi-omics data reveals downstream effects of chromosome instability, with RPRD1B as a putative target for radiotherapy-resistant patients. Chromosome 1q gain, associated with chromosome instability and upregulated mitochondrial functions, lead to poorer clinical outcomes. Immune subtyping identify an immune cold subtype linked to chromosome 9p/10q loss and immune evasion. Proteomics-based classification reveals subtypes (P-II and P-III) with high chromosome instability and immune cold features, with P-II tumors showing increased invasiveness. These findings, confirmed in 17 paired samples, provide insights into the biology and treatment of skull-base chordoma.

Abstract EMT dysfunction is a dominant mechanisms of hypospadias. Thus, identification of EMT‐related lncRNAs based on transcriptome sequencing data of hypospadias might provide novel molecular markers and therapeutic targets for hypospadias. First, the microarray data related to hypospadias were downloaded from Gene Expression Omnibus (GEO). Besides, the differentially expressed lncRNAs and messenger RNAs (mRNAs) related to EMT were screened to construct lncRNA‐mRNA co‐expression interaction pairs. In addition, the microRNA (miRNA) prediction analysis was performed through bioinformatics methods to construct a ceRNA network. Moreover, function prediction and function enrichment and pathway analyses were also performed. Finally, the core EMT‐related lncRNAs were verified based on mRNA expression changes and cell functions. A total of 6 EMT‐related lncRNAs were identified and 123 mRNA‐lncRNA co‐expression interaction pairs were screened in this study. Additionally, a ceRNA regulatory network comprising 17 mRNAs, 4 lncRNAs, and 28 miRNAs was constructed based on the prediction of hypospadias‐related miRNAs. The validation results of the dataset GSE121712 revealed that only BEX1 was positively correlated with the expression of the lncRNA GNAS‐AS1 (r = 0.874, P < 0.01), both of which had high expression. The cell experiment results demonstrated that interfering with the expression of GNAS‐AS1 significantly promoted the proliferation, migration, and EMT of cells. Importantly, it was confirmed that GNAS‐AS1 can serve as a ceRNA and play an important role in the EMT of hypospadias. Hence, it may be considered as a potential target in the treatment of this disease.

Abstract Pecan (Carya illinoinensis) is an economically important nut crop known for its genetic diversity and adaptability to various climates. Understanding the growth variability, phenological traits, and population structure of pecan populations is crucial for breeding programs and conservation. In this study, plant growth and phenological traits were evaluated over three consecutive seasons (2015–2017) for 550 genotypes from 26 provenances. Significant variations in plant height, stem diameter, and budbreak were observed among provenances, with Southern provenances exhibiting faster growth and earlier budbreak compared to Northern provenances. Population structure analysis using SNP markers revealed eight distinct subpopulations, reflecting genetic differentiation among provenances. Notably, Southern Mexico collections formed two separate clusters, while Western collections, such as 'Allen 3', 'Allen 4', and 'Riverside', were distinguished from others. 'Burkett' and 'Apache' were grouped together due to their shared maternal parentage. Principal component analysis and phylogenetic tree analysis further supported subpopulation differentiation. Genetic differentiation among the 26 populations was evident, with six clusters highly in agreement with the subpopulations identified by STRUCTURE and fastSTRUCTURE. Principal components analysis (PCA) revealed distinct groups, corresponding to subpopulations identified by genetic analysis. Discriminant analysis of PCA (DAPC) based on provenance origin further supported the genetic structure, with clear separation of provenances into distinct clusters. These findings provide valuable insights into the genetic diversity and growth patterns of pecan populations. Understanding the genetic basis of phenological traits and population structure is essential for selecting superior cultivars adapted to diverse environments. The identified subpopulations can guide breeding efforts to develop resilient rootstocks and contribute to the sustainable management of pecan genetic resources. Overall, this study enhances our understanding of pecan genetic diversity and informs conservation and breeding strategies for the long-term viability of pecan cultivation.

Purpose Three‐level hybrid surgery (HS) consisting of cervical disc arthroplasty (CDA) and anterior cervical discectomy and fusion (ACDF) has been partly used for the treatment of multi‐level cervical degenerative disc disease (CDDD). The complications related to the implants and the collapse of the surgical vertebral bodies had been reported in multi‐level anterior cervical spine surgery. Thus, this study aimed to explore the biomechanical effects on the prostheses and vertebrae in three‐level HS. Methods A FE model of cervical spine (C0‐T1) was constructed. Five surgical models were developed. They were FAF model (ACDF‐CDA‐ACDF), AFA model (CDA‐ACDF‐CDA), FFF model (three‐level ACDF), SF model (single‐level ACDF), and SA model (single‐level CDA). A 75‐N follower load and 1.0‐N·m moment was applied to produce flexion, extension, lateral bending, and axial rotation. Results Compared with the intact model, the range of motion (ROM) of total cervical spine in FAF model decreased by 34.54%, 54.48%, 31.76%, and 27.14%, respectively, in flexion, extension, lateral bending, and axial rotation, which were lower than those in FFF model and higher than those in AFA model. The ROMs of CDA segments in FAF and AFA models were similar to the intact model and SA model. Compared with the intact model, the ROMs at C3/4 segment in FFF model increased from 5.71% to 7.85%, and increased from 5.31% to 6.81% at C7/T1 segment, following by FAF model, then the FAF model. The maximum interface pressures of the Prestige‐LP in FAF model were similar to SA model, however the corresponding values were increased in AFA model. The maximum interface pressures of the Zero‐P were increased in FAF and AFA model compared with those in SF and FFF models. The stress was mainly distributed on the screws. In AFA model, the maximum pressures of the ball and trough articulation in superior and inferior Prestige‐LP were all increased compared with those in SA and FAF model. In FFF model, the maximum pressures of the vertebrae were higher than those in other models. The stress was mainly distributed on the anterior area of the vertebral bodies. Conclusions HS seemed to be more suitable than ACDF for the surgical treatment of three‐level CDDD in consideration of the biomechanical effects, especially for the two‐level CDA and one‐level ACDF construct. But a more appropriate CDA prosthesis should be explored in the future.

This qualitative study explored the perceptions of EFL students at a Chinese university regarding collocation learning. The participating students were provided with a collocation instruction and practice component over ten weeks within a regular one-semester EFL course. The participants were 15 Chinese first-year non-English major students. The data consisted of semi-structured interviews conducted after the students had completed the intervention component (week 12). Analysis of the transcripts of audio-recorded interviews revealed that the students showed a generally positive attitude towards learning collocations. Also, the collocation component helped the participants raise their awareness of learning collocations, become less dependent on their first language in interpreting and using collocations, and highly value the importance of collocations in writing and translation. The students also expressed some concerns in learning and using collocations. Pedagogical implications are discussed.

Abstract Objective To investigate (1) lateral atlantoaxial articulation (LAA) morphology in patients with basilar invagination (BI) with atlantoaxial dislocation (AAD) and healthy individuals and its relationship with the severity of dislocation and (2) the effect of the LAA morphology on reduction degree (RD) after surgery. Methods In this retrospective propensity score matching case-control study, imaging and baseline data of 62 patients with BI and AAD from 2011 to 2022 were collected. Six hundred thirteen participants without occipitocervical junctional deformity served as controls. Logistic regression and receiver operating characteristic (ROC) curve were used for analysis. Results The age, BMI and sex did not differ significantly between the two groups after propensity score matching. Sagittal slope angle (SSA) and coronal slope angle (CSA) was lower and greater, respectively, in the patient group than in the control group. A negative SSA value usually indicates anteverted LAA. Regression analysis revealed a significant negative correlation between SSA and severity of dislocation. However, no relationship was found between CSA and the severity of dislocation. The multivariate logistic regression analysis revealed that minimum-SSA emerged as an independent predictor of satisfactory reduction (RD ≥ 90%). The ROC curve demonstrated an area under the curve of 0.844, with a cut-off value set at -40.2. Conclusion SSA in patients group was significantly smaller and more asymmetric than that in the control group. Dislocation severity was related to SSA but not to CSA. Minimum-SSA can be used as a predictor of horizontal RD after surgery.

Abstract Melanoma is one of the most prevalent skin cancers, with high metastatic rates and poor prognosis. Understanding its molecular pathogenesis is crucial for improving its diagnosis and treatment. Integrated analysis of multi-omics data from 207 treatment-naïve melanomas (primary-cutaneous-melanomas (CM, n = 28), primary-acral-melanomas (AM, n = 81), primary-mucosal-melanomas (MM, n = 28), metastatic-melanomas (n = 27), and nevi (n = 43)) provides insights into melanoma biology. Multivariate analysis reveals that PRKDC amplification is a prognostic molecule for melanomas. Further proteogenomic analysis combined with functional experiments reveals that the cis-effect of PRKDC amplification may lead to tumor proliferation through the activation of DNA repair and folate metabolism pathways. Proteome-based stratification of primary melanomas defines three prognosis-related subtypes, namely, the ECM subtype, angiogenesis subtype (with a high metastasis rate), and cell proliferation subtype, which provides an essential framework for the utilization of specific targeted therapies for particular melanoma subtypes. The immune classification identifies three immune subtypes. Further analysis combined with an independent anti-PD-1 treatment cohort reveals that upregulation of the MAPK7-NFKB signaling pathway may facilitate T-cell recruitment and increase the sensitivity of patients to immunotherapy. In contrast, PRKDC may reduce the sensitivity of melanoma patients to immunotherapy by promoting DNA repair in melanoma cells. These results emphasize the clinical value of multi-omics data and have the potential to improve the understanding of melanoma treatment.

Objective Modic change (MC) is defined as abnormalities observed in the intervertebral disc subchondral and adjacent vertebral endplate subchondral bone changes. Most studies on MC were reported in the lumbar spine and associated with lower back pain. However, MC has been rarely reported in the cervical spine, let alone in those who underwent cervical disc replacement (CDR). This study aimed to focus on MC in the cervical spine and reveal clinical and radiological parameters, especially heterotopic ossification (HO), for patients who underwent CDR. Furthermore, we illustrated the association between MC and HO. Methods We retrospectively reviewed patients who underwent CDA from January 2008 to December 2019. The Japanese Orthopaedic Association (JOA), Neck Disability Index (NDI), and Visual Analog Scale (VAS) scores were used to evaluate the clinical outcomes. Radiological evaluations were used to conclude the cervical alignment (CL) and range of motion (ROM) of C2‐7, functional spinal unit angle (FSUA), shell angle (SA), FSU height, and HO. Univariate and multivariate logistic regressions were performed to identify the risk factors for HO. The Kaplan–Meier (K‐M) method was used to analyze potential risk factors, and multivariate Cox regression was used to identify independent risk factors. Results A total of 139 patients were evaluated, with a mean follow‐up time of 46.53 ± 26.60 months. Forty‐nine patients were assigned to the MC group and 90 to the non‐MC group. The incidence of MC was 35.3%, with type 2 being the most common. Clinical outcomes (JOA, NDI, VAS) showed no significant difference between the two groups. The differences in C2‐7 ROM between the two groups were not significant, while the differences in SA ROM and FSUA ROM were significantly higher in the non‐MC than in the MC group (p

Abstract The identification of effective therapeutic targets plays a pivotal role in advancing cancer treatment outcomes. We employed a comprehensive pan-cancer analysis, complemented by experimental validation, to explore the potential of Nicotinamide N-methyltransferase (NNMT) as a promising therapeutic strategy for human cancers. By analyzing large-scale transcriptomic datasets across various cancer types, we consistently observed upregulated expression of NNMT. Furthermore, elevated NNMT expression correlated with inferior overall survival in multiple cancer cohorts, underscoring its significance as a prognostic biomarker. Additionally, we investigated the relationship between NNMT expression and the tumor immune microenvironment, which plays a crucial role in regulating anti-tumor immune responses. To confirm the malignant functions of NNMT in tumor cells, we conducted a series of cell-based experiments, revealing that NNMT promotes cancer cell proliferation and invasion, indicative of its oncogenic properties. The integration of computational analysis and experimental validation in our study firmly establishes NNMT as a potential therapeutic target for human cancers. Specifically, targeting NNMT holds promise for the development of innovative and effective cancer treatments. Further investigations into NNMT's role in cancer pathogenesis could potentially pave the way for groundbreaking advancements in cancer treatment.

Abstract Dual blocker therapy (DBT) has the enhanced antitumor benefits than the monotherapy. Yet, few effective biomarkers are developed to monitor the therapy response. Herein, we investigate the DBT longitudinal plasma proteome profiling including 113 longitudinal samples from 22 patients who received anti-PD1 and anti-CTLA4 DBT therapy. The results show the immune response and cholesterol metabolism are upregulated after the first DBT cycle. Notably, the cholesterol metabolism is activated in the disease non-progressive group (DNP) during the therapy. Correspondingly, the clinical indicator prealbumin (PA), free triiodothyronine (FT3) and triiodothyronine (T3) show significantly positive association with the cholesterol metabolism. Furthermore, by integrating proteome and radiology approach, we observe the high-density lipoprotein partial remodeling are activated in DNP group and identify a candidate biomarker APOC3 that can reflect DBT response. Above, we establish a machine learning model to predict the DBT response and the model performance is validated by an independent cohort with balanced accuracy is 0.96. Thus, the plasma proteome profiling strategy evaluates the alteration of cholesterol metabolism and identifies a panel of biomarkers in DBT.

ABSTRACT Cryptococcus neoformans is a life-threatening fungal pathogen that is a causative agent for pulmonary infection and meningoencephalitis in both immunocompetent and immunodeficient individuals. Recent studies have elucidated the important function of the target of rapamycin (TOR) signaling pathway in the modulation of C. neoformans virulence factor production and pathogenicity in animal infection models. Herein, we discovered that Ypk1, a critical component of the TOR signaling pathway, acts as a critical modulator in fungal pathogenicity through post-translational modifications (PTMs). Mass spectrometry analysis revealed that Ypk1 is subject to protein acetylation at lysines 315 and 502, and both sites are located within kinase functional domains. Inhibition of the C. neoformans TOR pathway by rapamycin activates the deacetylation process for Ypk1. The YPK1Q strain, a hyper-acetylation of Ypk1, exhibited increased sensitivity to rapamycin, decreased capsule formation ability, reduced starvation tolerance, and diminished fungal pathogenicity, indicating that deacetylation of Ypk1 is crucial for responding to stress. Deacetylase inhibition assays have shown that sirtuin family proteins are critical to the Ypk1 deacetylation mechanism. After screening deacetylase mutants, we found that Dac1 and Dac7 directly interact with Ypk1 to facilitate the deacetylation modification process via a protein–protein interaction. These findings provide new insights into the molecular basis for regulating the TORC–Ypk1 axis and demonstrate an important function of protein acetylation in modulating fungal pathogenicity.IMPORTANCECryptococcus neoformans is an important opportunistic fungal pathogen in humans. While there are currently few effective antifungal treatments, the absence of novel molecular targets in fungal pathogenicity hinders the development of new drugs. There is increasing evidence that protein post-translational modifications (PTMs) can modulate the pathogenicity of fungi. In this study, we discovered that the pathogenicity of C. neoformans was significantly impacted by the dynamic acetylation changes of Ypk1, the immediate downstream target of the TOR complex. We discovered that Ypk1 is acetylated at lysines 315 and 502, both of which are within kinase functional domains. Deacetylation of Ypk1 is necessary for formation of the capsule structure, the response to the TOR pathway inhibitor rapamycin, nutrient utilization, and host infection. We also demonstrate that the sirtuin protein family is involved in the Ypk1 deacetylation mechanism. We anticipate that the sirtuin–Ypk1 regulation axis could be used as a potential target for the development of antifungal medications.

ABSTRACT The underlying mechanism of thermotolerance, which is a key virulence factor essential for pathogenic fungi such as Cryptococcus neoformans, is largely unexplored. In this study, our findings suggest that Set302, a homolog of Set3 and a subunit of histone deacetylase complex Set3C, contributes to thermotolerance in C. neoformans. Specifically, the deletion of the predicted Set3C core subunit, Set302, resulted in further reduction in the growth of C. neoformans at 39°C, and survival of transient incubation at 50°C. Transcriptomics analysis revealed that the expression levels of numerous heat stress-responsive genes altered at both 30°C and 39°C due to the lack of Set302. Notably, at 39°C, the absence of Set302 led to the downregulation of gene expression related to the ubiquitin-proteasome system (UPS). Based on the GFP-α-synuclein overexpression model to characterize misfolded proteins, we observed a pronounced accumulation of misfolded GFP-α-synuclein at 39°C, consequently inhibiting C. neoformans thermotolerance. Furthermore, the loss of Set302 exacerbated the accumulation of misfolded GFP-α-synuclein during heat stress. Interestingly, the set302∆ strain exhibited a similar phenotype under proteasome stress as it did at 39°C. Moreover, the absence of Set302 led to reduced production of capsule and melanin. set302∆ strain also displayed significantly reduced pathogenicity and colonization ability compared to the wild-type strain in the murine infection model. Collectively, our findings suggest that Set302 modulates thermotolerance by affecting the degradation of misfolded proteins and multiple virulence factors to mediate the pathogenicity of C. neoformans.IMPORTANCECryptococcus neoformans is a pathogenic fungus that poses a potential and significant threat to public health. Thermotolerance plays a crucial role in the wide distribution in natural environments and host colonization of this fungus. Herein, Set302, a critical core subunit for the integrity of histone deacetylase complex Set3C and widely distributed in various fungi and mammals, governs thermotolerance and affects survival at extreme temperatures as well as the formation of capsule and melanin in C. neoformans. Additionally, Set302 participates in regulating the expression of multiple genes associated with the ubiquitin-proteasome system (UPS). By eliminating misfolded proteins under heat stress, Set302 significantly contributes to the thermotolerance of C. neoformans. Moreover, Set302 regulates the pathogenicity and colonization ability of C. neoformans in a murine model. Overall, this study provides new insight into the mechanism of thermotolerance in C. neoformans.

Abstract Objective This study aims to screen the differentially expressed long non-coding RNAs (DELncRNAs) related to the regulation of epithelial-mesenchymal transition (EMT) in hypospadias in mesenchymal stem cell-derived exosomes (MSC-Exons) and explore the potential mechanism of these lncRNAs for the EMT in hypospadias. Methods In this study, the microarray data related to MSC-Exos and hypospadias were downloaded from Gene Expression Omnibus (GEO). Besides, the lncRNAs highly expressed in MSC-Exos and the differentially expressed mRNAs and lncRNAs in children with hypospadias were screened, respectively. In addition, the lncRNAs enriched in MSC-Exos and differentially expressed lncRNAs in hypospadias were intersected to obtain the final DElncRNAs. Moreover, the co-expression interaction pairs of differentially expressed lncRNAs and mRNAs were analyzed to construct a Competing Endogenous RNA (ceRNA) network. Finally, the candidate lncRNAs in exosomes were subjected to in vitro cell function verification. Results In this study, a total of 4 lncRNAs were obtained from the microarray data analysis. Further, a ceRNA regulatory network of MSC-Exo-derived lncRNAs related to the regulation of EMT in hypospadias was constructed, including 4 lncRNAs, 2 mRNAs, and 6 miRNAs. The cell function verification results indicated that the exosomes secreted by MSCs may transport HLA complex group 18 (HCG18) into target cells, which promoted the proliferation, migration, and EMT of these cells. Conclusion MSC-Exo-derived lncRNA HCG18 can enter target cells, and it may be involved in the regulation of EMT in hypospadias through the ceRNA network.

In order to solve the contradiction between large aperture elements and high-resolution images, in this study, we propose an improved image-resolution method based on generative adversarial network (GAN). First, we analyze the imaging principle of the optical synthetic aperture. Further, we improve a super-resolution GAN; especially, this network uses a multi-scale convolutional cascade to obtain global features of the image, and a multi-scale receptive field block and residual in residual dense block are built to obtain image details. In addition, this study uses the Mish function as the activation function of the discriminator to solve the problems of neuron extreme, gradient explosion, and poor generalization ability of the model. Through simulation, the results show that the proposed method can achieve a peak signal-to-noise ratio (PSNR) of 30 dB compared with traditional image super-resolution reconstruction methods for synthetic aperture image. The method proposed has an improvement of 2 dB in the PSNR and 0.016 in structure similarity index measure compared with the original super-resolution GAN. Therefore, this method can effectively reduce the image distortion and improve the quality of image reconstruction.

Abstract Wilms tumor (WT) is the most common malignancy of the genitourinary system in children. Currently, the Integration of single-cell RNA sequencing (scRNA-Seq) and Bulk RNA sequencing (RNA-Seq) analysis of heterogeneity between different cell types in pediatric WT tissues could more accurately find prognostic markers, but this is lacking. RNA-Seq and clinical data related to WT were downloaded from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Small nucleolar RNA host gene 15 (SNHG15) was identified as a risk signature from the TARGET dataset by using weighted gene co-expression network analysis, differentially expressed analysis and univariate Cox analysis. After that, the functional mechanisms, immunological and molecular characterization of SNHG15 were investigated at the scRNA-seq, pan-cancer, and RNA-seq levels using Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), ESTIMATE, and CIBERSORT. Based on scRNA-seq data, we identified 20 clusters in WT and annotated 10 cell types. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing M2 macrophages as hubs for intercellular communication. In addition, in vitro cellular experiments showed that siRNAs interfering with SNHG15 significantly inhibited the proliferation and migration of G401 cells and promoted the apoptosis of G401 cells compared with the control group. The effect of siRNAs interfering with SNHG15 on EMT-related protein expression was verified by Western blotting assay. Thus, our findings will improve our current understanding of the pathogenesis of WT, and they are potentially valuable in providing novel prognosis markers for the treatment of WT.

Abstract Layered rock slope exists widely. Because of its special slope structure, it is prone to bending deformation and toppling failure, which is a serious threat to engineering construction and safety operation. At present, the research of layered rock slope still has great innovation potential. During the construction of Wudongde Hydropower Station on Jinsha River, safety and stability problems such as slope geological structure development, face rock unloading and relaxation, and even slip and large deformation were encountered. Through field exploration, it is found that the rock and soil stratification of the slope on both sides of Wudongde Hydropower Station is highly obvious. At present, there is a lack of research on-site long-term displacement monitoring of layered rock high-steep slope, especially for layered slope in complex hydrogeology and construction environment. In order to strengthen the research on the deformation and stability of layered rock slope, this paper analyzes the measured displacement data of Wudongde hydropower station slope, and establishes three-dimensional geological finite element model with the help of numerical simulation software. The stability of the slope is calculated by combining the finite difference method and the strength reduction method. Finally, the evolution mechanism of the deformation of the layered rock slope is explained according to the geological structure characteristics. The main conclusions of this paper are as follows: the layered slope in the dam reservoir area is prone to deformation under the combined action of long-term construction disturbance and fissure water seepage, and the construction disturbance has a strong influence on the artificial excavation area below 1070 m, and the maximum rock mass deformation and surface displacement in the artificial excavation area of the slope reach 92.2 mm and 312.5 mm, respectively. However, the influence of construction disturbance on the natural mountain above 1070 m is limited, the valley deformation of the natural mountain on the left bank of the reservoir area is higher than that on the right bank, and the cumulative deformation is still less than 20 mm. The influence of seepage on the displacement of the area with higher elevation at the top of the slope is more obvious, and the influence of excavation and other disturbances on the displacement of the artificial excavation area with lower elevation is more obvious. The deformation of the river valley in the water cushion pond behind the dam increases slowly, and the change trend of the field deformation data is mostly consistent with that of the numerical calculation. The horizontal shrinkage of the mountains on both sides shows a contraction trend on the whole, and the maximum horizontal shrinkage calculated by numerical simulation is close to 20 mm, which is located at the elevation of 990 m.