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Mutations in the Cockayne Syndrome group B (CSB) gene cause cancer in mice, but premature aging and severe neurodevelopmental defects in humans. CSB, a member of the SWI/SNF family of chromatin remodelers, plays diverse roles in regulating gene expression and transcription-coupled nucleotide excision repair (TC-NER); however, these functions do not explain the distinct phenotypic differences observed between CSB-deficient mice and humans. During investigating Cockayne Syndrome-associated genome instability, we uncover an intrinsic mechanism that involves elongating RNA polymerase II (RNAPII) undergoing transient pauses at internal T-runs where CSB is required to propel RNAPII forward. Consequently, CSB deficiency retards RNAPII elongation in these regions, and when coupled with G-rich sequences upstream, exacerbates genome instability by promoting R-loop formation. These R-loop prone motifs are notably abundant in relatively long genes related to neuronal functions in the human genome, but less prevalent in the mouse genome. These findings provide mechanistic insights into differential impacts of CSB deficiency on mice versus humans and suggest that the manifestation of the Cockayne Syndrome phenotype in humans results from the progressive evolution of mammalian genomes.

Abstract The role of neoadjuvant chemotherapy and its benefits in patients with triple-negative breast cancer (TNBC) and small tumors are unclear. This study aims to compare survival differences between clinical T1 TNBC receiving neoadjuvant chemotherapy (NAC) and adjuvant chemotherapy (AC). Data for patients with clinical T1 TNBC were extracted from the Surveillance, Epidemiology, and End Results (SEER) database. Patients were categorized according to whether they received chemotherapy before or after surgery. Propensity Score Matching (PSM) was used to minimize the influence of confounding factors. OS and BCSS were compared between the two treatment sequences using Kaplan–Meier and univariate and multivariable Cox proportional hazards regression analyses. The study included 6249 women with T1 TNBC. In multivariate analysis, compared with that in the AC group, the hazard ratio for death in the NAC group was 1.54 (95% confidence interval 1.26–1.89, p

BackgroundReactor core computational fluid dynamics (CFD) plays a crucial role in identifying core vulnerabilities, optimizing feature structures, and improving safety and economic in nuclear reactors. However, conventional pressurized water reactor fuel assemblies often feature a multitude of spacer grids with mixing vanes, leading to challenges in mesh generation and numerical solution instability, excessive computational resource requirements. The current momentum source model established on the basis of the mechanism of fluid-structure interaction has not considered the effect of the low-pressure region on the fluid downstream of the mixing vanes, leading to significant errors in predicting the axial flow distribution downstream of the mixing vanes. Furthermore, it is challenging to identify the solid domain of the mixing vanes and to add momentum source terms.PurposeThis study aims to present a joint simulation scheme based on detailed porous media and momentum source modeling to simulate coolant flow in 5×5 rod bundle channels with mixing vanes, hence to reduce cells, lower mesh generation difficulty, and enhance numerical stability during the CFD solving process.MethodsThis scheme employed a detailed porous media approach in the spacer zone, while adopting Global Momentum Source Model in the vane zone. Simultaneously, a domain identification scheme was developed to determine the placement of momentum sources and detailed porous media models. The position of mixing vanes within the fluid domain was accurately located by this approach and established detailed porous media and momentum source models based on the fluid-structure interactions in the grid spacer zone and leeward side and windward side of mixing vanes. To simulate the flow field distribution within the spacer zone, a detailed porous media model was employed to enhance local flow resistance, thereby achieving an accurate simulation of the flow field distribution in the spacer zone. Finally, validation against experimental and body-fitted mesh simulations was performed to examine the effectiveness of this scheme in simulating flow blockage, fluid flow, mixing, and vortex shedding.ResultsThis scheme, compared to the momentum source scheme, exhibits stronger numerical stability. In the vane zone, the established momentum source model simultaneously considers the effects of the leeward side and the windward side of mixing vanes, leading to a more accurate prediction of axial flow velocity and heat transfer downstream of the mixing vanes. This approach allows for modeling without needing to consider the structure of the spacer grids with mixing vanes, thus greatly simplifying mesh generation. It achieves complete structured mesh modeling, significantly reducing the number of cells, and enhancing computational efficiency. Validation confirm the effectiveness of this scheme and results in a 90% reduction in cells and a 60% decrease in computational time for modeling and simulation of a 5×5 rod bundle channel with mixing vanes.ConclusionsThis scheme offers simplicity in modeling, reduces CFD computation time, insensitivity to mesh, and superior robustness. Furthermore, when identifying larger-scale components, the approach involves identifying the multi-span fuel components, since the mixing vanes form a regular array in both axial and transverse directions. Therefore, domain identification at a larger scale can be achieved by modifying coordinates, applying momentum source model developed in this paper.

Abstract Purpose To assess the efficacy of neoadjuvant endocrine therapy in female HR‐positive/HER2‐negative breast cancer patients. Data and Methods We identified female patients aged ≥18 years with cT1‐4N0‐XM0, HR(+), and HER2(−) breast cancer from the National Cancer Database. The patients who underwent surgery first were categorized as “surgery‐first,” while those who received NET before surgery were classified as “NET.” Propensity score‐matching, Cox proportional‐hazard model, variance inflation factors, and interaction analysis were employed to estimate the correlation between NET and survival outcomes. Results Among 432,387 cases, 2914 NET patients and 2914 surgery‐first patients were matched. Compared with the surgery‐first group, the NET group received less adjuvant chemotherapy (p

Abstract The role of m6A modification in the regulation of the immune microenvironment (IME) of ischemic stroke (IS) is barely known. Thus, we aim to investigate the impact of m6A modification on the IME of IS and its diagnostic value in IS. We comprehensively assessed the m6A modification patterns, the relationship between these modification patterns and the characteristics of the IME. The m6A modification patterns of individual IS sample were quantified by m6Ascore. The performance of m6A phenotype-related genes as potential biomarkers was evaluated by the area under the receiver operating characteristic curve. Experimental validation was also performed by qRT-PCR. Six dysregulated m6A regulators were identified and a classification model consisting of four key m6A regulators (METLL3, RBMX, RBM15B, YTDHF3) could distinguish IS and healthy control samples well. METTL3 and YTHDF3 are closely related to circulating neutrophil abundance. Two distinct m6A modification patterns were determined which differed in immunocyte abundance. We also identified six m6A phenotype-related genes (APOBEC3A, PTMA, FCGR3A, LOC440926, LOC649946, and FTH1L11), and further explored their biological function. Among them, APOBEC3A, FCGR3A, and FTH1L11 were positively associated with neutrophil abundance. APOBEC3A and FCGR3A were stable diagnostic m6A-associated genes in both the discovery and validation cohorts. This study reveals that m6A modification plays a non-negligible role in the formation of a diversified and complex IME in IS. The m6A phenotype-related genes could be diagnostic biomarkers of IS.

Abstract Phosphorylation proteomics is the basis for the study of abnormally activated kinase signaling pathways in breast cancer, which facilitates the discovery of new oncogenic agents and drives the discovery of potential targets for early diagnosis and therapy of breast cancer. In this study, we have explored the aberrantly active kinases in breast cancer development and to elucidate the role of PRKCD_pY313 in triple negative breast cancer (TNBC) progression. We collected 47 pairs of breast cancer and paired far-cancer normal tissues and analyzed phosphorylated tyrosine (pY) peptides by Superbinder resin and further enriched the phosphorylated serine/threonine (pS/pT) peptides using TiO2 columns. We mapped the kinases activity of different subtypes of breast cancer and identified PRKCD_pY313 was upregulated in TNBC cell lines. Gain-of-function assay revealed that PRKCD_pY313 facilitated the proliferation, enhanced invasion, accelerated metastasis, increased the mitochondrial membrane potential and reduced ROS level of TNBC cell lines, while Y313F mutation and low PRKCD_pY313 reversed these effects. Furthermore, PRKCD_pY313 significantly upregulated Src_pY419 and p38_pT180/pY182, while low PRKCD_pY313 and PRKCD_Y313F had opposite effects. Dasatinib significantly inhibited the growth of PRKCD_pY313 overexpression cells, and this effect could be enhanced by Adezmapimod. In nude mice xenograft model, PRKCD_pY313 significantly promoted tumor progression, accompanied by increased levels of Ki-67, Bcl-xl and Vimentin, and decreased levels of Bad, cleaved caspase 3 and ZO1, which was opposite to the trend of Y313F group. Collectively, the heterogeneity of phosphorylation exists in different molecular subtypes of breast cancer. PRKCD_pY313 activates Src and accelerates TNBC progression, which could be inhibited by Dasatinib.

Abstract Pelvic organ prolapse (POP) markedly affects the quality of life of women, including significant financial burden. Using single-cell RNA sequencing, we constructed a transcriptional profile of 30,452 single cells of the uterosacral ligament in POP and control samples, which has never been constructed before. We identified 10 major cell types, including smooth muscle cells, endothelial cells, fibroblasts, neutrophils, macrophages, monocytes, mast cells, T cells, B cells, and dendritic cells. We performed subpopulation analysis and pseudo-time analysis of POP primary cells, and explored differentially expressed genes. We verified previous cell clusters of human neutrophils of uterosacral ligaments. We found a significant reduction in receptor-ligand pairs related to ECM and cell adhesion between fibroblasts and endothelial cells in POP. The transcription factors related to the extracellular matrix, development, and immunity were identified in USL. Here we provide insight into the molecular mechanisms of POP and valuable information for future research directions.

Abstract Purification of ethylene (C2H4) as the most extensive and output chemical, from complex multi-components is of great significance but highly challenging. Herein we demonstrate that precise pore structure tuning by controlling the network hydrogen bonds in two highly-related porous coordination networks can shift the efficient C2H4 separation function from C2H2/C2H4/C2H6 ternary mixture to CO2/C2H2/C2H4/C2H6 quaternary mixture system. Single-crystal X-ray diffraction revealed that the different amino groups on the triazolate ligands resulted in the change of the hydrogen bonding in the host network, which led to changes in the pore shape and pore chemistry. Gas adsorption isotherms, adsorption kinetics and gas-loaded crystal structure analysis indicated that the coordination network Zn-fa-atz (2) weakened the affinity for three C2 hydrocarbons synchronously including C2H4 but enhanced the CO2 adsorption due to the optimized CO2-host interaction and the faster CO2 diffusion, leading to effective C2H4 production from the CO2/C2H2/C2H4/C2H6 mixture in one step based on the experimental and simulated breakthrough data. Moreover, it can be shaped into spherical pellets with maintained porosity and separation performance.

Electrochemical reaction is a continuous dynamic process, accompanied by electron transfer and generation of short-lived intermediates. The mechanism investigation of electrochemical interfaces is pivotal for the progression of energy storage, electro-organic synthesis, electrocatalysis, and electroanalysis. The valuable insights for optimizing performance, improving efficiency, and developing novel methodologies can be attained by elucidating the complicated pathways involved in the electrochemical processes. Thus, how to monitor transient intermediates formed at the solid-liquid interface becomes the critical point in unraveling these intricate processes. To this end, a series of in-situ analytical methods such as in-situ electron paramagnetic resonance spectroscopy (in-situ EPR), in-situ Raman spectroscopy, in-situ infrared spectroscopy (in-situ IR) and in-situ electrochemical mass spectrometry (in-situ EC-MS) have been exploited to probe the chemical transformations at the electrode/electrolyte interface. Among them, due to the superior specificity for interpreting molecular information, EC-MS has progressively gained extensive attention as a powerful and reliable tool for capturing intermediates and revealing the mechanisms in electrochemical reactions. In this review, the research progresses in the recent advancements in the detection of transient reaction intermediates through electrochemical mass spectrometry were presented. The discussion centered on elucidating the principle and configuration of the devices employed in EC-MS, with a specific focus on electrospray ionization mass spectrometry (ESI-MS), atmospheric pressure ionization mass spectrometry (AIMS) and time-of-flight secondary ion mass spectrometry (TOF-SIMS). In addition, the review delved into the wide-ranging applications of EC-MS in monitoring electrochemical processes in electro-organic synthesis, electrocatalysis, lithium-ion batteries, electrochemiluminescence, and bioelectrochemical reactions. Despite the remarkable progress has made, the challenges in the field of EC-MS are prospected. There is still an urgent need for further improvement of the experimental apparatus to enhance the sampling efficiency and time resolution to capture short-lived and low-concentration reaction intermediates. In the future, we anticipate that EC-MS will be combined with other in situ analytical techniques, such as in situ infrared or Raman spectroscopy, enabling multi-dimensional characterization and monitoring of electrochemical reaction intermediates.

Abstract Lung cancer is the leading cause of cancer-related death. Lysosomes are key degradative compartments that maintain protein homeostasis. In current study, we aimed to construct a lysosomes-related genes signature to predict the overall survival (OS) of patients with Lung Adenocarcinoma (LUAD). Differentially expressed lysosomes-related genes (DELYs) were analyzed using The Cancer Genome Atlas (TCGA-LUAD cohort) database. The prognostic risk signature was identified by Least Absolute Shrinkage and Selection Operator (LASSO)-penalized Cox proportional hazards regression and multivariate Cox analysis. The predictive performance of the signature was assessed by Kaplan–Meier curves and Time-dependent receiver operating characteristic (ROC) curves. Gene set variant analysis (GSVA) was performed to explore the potential molecular biological function and signaling pathways. ESTIMATE and single sample gene set enrichment analysis (ssGSEA) were applied to estimate the difference of tumor microenvironment (TME) between the different risk subtypes. An eight prognostic genes (ACAP3, ATP8B3, BTK, CAV2, CDK5R1, GRIA1, PCSK9, and PLA2G3) signature was identified and divided patients into high-risk and low-risk groups. The prognostic signature was an independent prognostic factor for OS (HR > 1, p

Summary: Glandular trichomes (GTs) play a crucial role in plant defenses and the synthesis of secondary metabolites. Understanding the developmental trajectory of GTs is essential for unraveling their functional significance and potential applications. Here we established a comprehensive single-cell atlas of Nicotiana tabacum leaves, a model plant for GT studies. The atlas included a total of 40,433 cells and successfully captured both long GTs (LGTs) and short GTs (SGTs) from Nicotiana leaves. The developmental trajectories of these trichomes were delineated, revealing potential disparities in epidermal development. Comparative analysis of Arabidopsis and Nicotiana trichome development indicated limited similarity between Arabidopsis epidermal non-glandular trichomes and Nicotiana LGTs and SGTs, implying the essentiality of studying the genes directly involved in the development of Nicotiana GTs for a proper and comprehensive understanding of GT biology. Overall, our results provide profound insights into the developmental intricacies of the specialized GTs.

BackgroundThis study aimed to employ plasma proteomics to investigate the molecular changes, pathway alterations, and potential novel biochemical markers associated with balloon pulmonary angioplasty (BPA) in patients with chronic thromboembolic pulmonary hypertension (CTEPH).MethodsPre- and post-BPA plasma samples from five CTEPH patients in the PRACTICE study were analyzed to identify differentially expressed proteins. Proteomic and bioinformatics analyses were conducted, and the identified proteins were further validated using ELISA assays in a separate cohort of the same study. Correlation and multivariate regression analyses were performed to investigate the associations between these differentially expressed proteins and clinical parameters.ResultsSignificantly higher serum levels of asialoglycoprotein receptor 2 (ASGR2) were detected in 5 CTEPH patients compared to those in healthy individuals but decreased significantly after successful BPA procedures. The decrease in serum levels of ASGR2 after the completion of BPA procedures was further validated in a separate cohort of 48 patients with CTEPH [0.70 (0.51, 1.11) ng/mL vs. 0.38 (0.27, 0.59) ng/mL, P < 0.001]. Significant associations were found between the pre-BPA ASGR2 level and clinical parameters, including neutrophil percentage (R = 0.285, P < 0.05), platelet (PLT) count (R = 0.386, P < 0.05), and high-density lipoprotein cholesterol (HDL-C) before BPA (R = -0.285, P < 0.05). Significant associations were detected between post-BPA serum ASGR2 levels and lymphocyte percentage (LYM%) (R = 0.306, P < 0.05), neutrophil-to-lymphocyte ratio (R = -0.294, P < 0.05), and pulmonary vascular resistance after BPA (R = -0.35, P < 0.05). Multivariate stepwise regression analysis revealed that pre-BPA ASGR2 levels were associated with HDL-C and PLT count (both P < 0.001), while post-BPA ASGR2 levels were associated with LYM% (P < 0.05).ConclusionSerum levels of ASGR2 may be a biomarker for the effectiveness of BPA treatment in CTEPH patients. The pre-BPA serum level of ASGR2 in CTEPH patients was associated with HDL-C and the PLT count. The post-BPA serum level of ASGR2 was correlated with the LYM%, which may reflect aspects of immune and inflammatory status.

Pesticide residues in cowpeas have raised worldwide concern. However, only a few studies have focused on pesticide accumulation and distribution in greenhouse and open-field cowpeas. Field trial results suggest that difenoconazole, dimethomorph, thifluzamide and pyraclostrobin dissipated faster in open fields (mean half-lives, 1.72–1.99 days) than in greenhouses (2.09–3.55 days); moreover, fungicide residues in greenhouse cowpeas were 0.84–8.19 times higher than those in the open-field cowpeas. All fungicides accumulated in the greenhouse and open-field cowpeas after repeated spraying. Fungicide residues in old cowpeas were higher than those in tender cowpeas, and residues in the upper halves of cowpea pods were higher than those in the lower halves. In addition, cowpeas distributed in the lower halves of the plants had higher fungicide residues. Our findings suggest that greenhouse cultivation contributed to the pesticide residues in cowpeas after repeated spraying, although the levels of dietary health risks remained acceptable under both cultivation scenarios.

Flavor profiles of various Pyrus spp. cultivars exhibit significant variations, yet the underlying flavor-contributing factors remain elusive. In this investigation, a comprehensive approach encompassing metabolomics analysis, volatile fingerprint analysis, and descriptive sensory analysis was employed to elucidate the flavor disparities among Nanguoli, Korla fragrant pear, and Qiuyueli cultivars and uncover potential flavor contributor. The study comprehensively characterized the categories and concentrations of nonvolatile and volatile metabolites, and 925 metabolites were identified. Flavonoids and esters dominated the highest cumulative response, respectively. Utilizing weighted correlation network analysis (WGCNA), seven highly correlated modules were identified, yielding 407 pivotal metabolites. Further correlation analysis of the differential substances provided potential flavor constituents strongly associated with various sensory attributes; taste factors had a certain association with olfactory characteristics. Our findings demonstrated the manifestation of flavor was a result of the synergistic effect of various compounds; evaluation olfactory flavor necessitated a comprehensive consideration of taste substances.

In broad sense, beverages made from nuts and plant fruits/pulp, as well as other plant-derived materials including proteins etc. are collectively known as plant-based milk. Plant-based milk has multiple advantages such as lactose free, cholesterol free, hormone free, low saturated fat, antibiotics free, special sensory flavor, as well as unique nutritional functions, which fit with the diversified needs of consumers. The market size of plant-based milk in China is huge, which also has great development potential. However, there are still many unsolved problems, such as backward processing technology, insufficient raw material development, unsatisfied sensory properties, vague nutritional and digestive characteristics, and incomplete academic discipline etc. From this, the processing problems of plant-based milk, new processing technology and equipment, innovative technology development trend, industrialization policy comprehensively are described and discussed in this paper. This paper will contribute to the industrial development of domestic plant-based milk, and further satisfying people's growing demand for nutrition and health.