A novel statistical framework for meta-analysis of total mediation effect with high dimensional omics mediators in large-scale genomic consortia.

Meta-analysis is used to aggregate the effects of interest across multiple studies, while its methodology is largely underexplored in mediation analysis, particularly in estimating the total mediation effect of high-dimensional omics mediators. Large-scale genomic consortia, such as the Trans-Omics for Precision Medicine (TOPMed) program, comprise multiple cohorts with diverse technologies to elucidate the genetic architecture and biological mechanisms underlying complex human traits and diseases. Leveraging the recent established asymptotic standard error of the R-squared-based mediation effect estimation for high-dimensional omics mediators, we have developed a novel meta-analysis framework requiring only summary statistics and allowing inter-study heterogeneity. Whereas the proposed meta-analysis can uniquely evaluate and account for potential effect heterogeneity across studies due to, for example, varying genomic profiling platforms, our extensive simulations showed that the developed method was more computationally efficient and yielded satisfactory operating characteristics comparable to analysis of the pooled individual-level data when there was no inter-study heterogeneity. We applied the developed method to 8 TOPMed studies with over 5800 participants to estimate the mediation effects of gene expression on age-related variation in systolic blood pressure and sex-related variation in high-density lipoprotein (HDL) cholesterol. The proposed method is available in R package MetaR2M on GitHub.

Tumor-repopulating cells evade ferroptosis via PCK2-dependent phospholipid remodeling.

Whether stem-cell-like cancer cells avert ferroptosis to mediate therapy resistance remains unclear. In this study, using a soft fibrin gel culture system, we found that tumor-repopulating cells (TRCs) with stem-cell-like cancer cell characteristics resist chemotherapy and radiotherapy by decreasing ferroptosis sensitivity. Mechanistically, through quantitative mass spectrometry and lipidomic analysis, we determined that mitochondria metabolic kinase PCK2 phosphorylates and activates ACSL4 to drive ferroptosis-associated phospholipid remodeling. TRCs downregulate the PCK2 expression to confer themselves on a structural ferroptosis-resistant state. Notably, in addition to confirming the role of PCK2-pACSL4(T679) in multiple preclinical models, we discovered that higher PCK2 and pACSL4(T679) levels are correlated with better response to chemotherapy and radiotherapy as well as lower distant metastasis in nasopharyngeal carcinoma cohorts.

Boosting Upconversion Efficiency in Optically Inert Shelled Structures with Electroactive Membrane through Electron Donation.

This study innovatively addresses challenges in enhancing upconversion efficiency in lanthanide-based nanoparticles (UCNPs) by exploiting Shewanella oneidensis MR-1, a microorganism capable of extracellular electron transfer. Electroactive membranes, rich in c-type cytochromes, are extracted from bacteria and integrated into membrane-integrated liposomes (MILs), encapsulating core-shelled UCNPs with an optically inactive shell, forming UCNP@MIL constructs. The electroactive membrane, tailored to donate electrons through the inert shell, independently boosts upconversion emission under near-infrared excitation (980 nm or 1550 nm), bypassing ligand-sensitized UCNPs. The optically inactive shell restricts energy migration, emphasizing electroactive membrane electron donation. Density functional theory calculations elucidate efficient electron transfer due to the electroactive membrane hemes' highest occupied molecular orbital being higher than the valence band maximum of the optically inactive shell, crucial for enhancing energy transfer to emitter ions. The introduction of a SiO2 insulator coating diminishes light enhancement, underscoring the importance of unimpeded electron transfer. Luminescence enhancement remains resilient to variations in emitter or sensitizing ions, highlighting the robustness of the electron transfer-induced phenomenon. However, altering the inert shell material diminishes enhancement, emphasizing the role of electron transfer. This methodology holds significant promise for diverse biological applications. UCNP@MIL offers an advantage in cellular uptake, which proves beneficial for cell imaging. This article is protected by copyright. All rights reserved.

A Compact Handheld Sensor Package with Sensor Fusion for Comprehensive and Robust 3D Mapping.

This paper introduces an innovative approach to 3D environmental mapping through the integration of a compact, handheld sensor package with a two-stage sensor fusion pipeline. The sensor package, incorporating LiDAR, IMU, RGB, and thermal cameras, enables comprehensive and robust 3D mapping of various environments. By leveraging Simultaneous Localization and Mapping (SLAM) and thermal imaging, our solution offers good performance in conditions where global positioning is unavailable and in visually degraded environments. The sensor package runs a real-time LiDAR-Inertial SLAM algorithm, generating a dense point cloud map that accurately reconstructs the geometric features of the environment. Following the acquisition of that point cloud, we post-process these data by fusing them with images from the RGB and thermal cameras and produce a detailed, color-enriched 3D map that is useful and adaptable to different mission requirements. We demonstrated our system in a variety of scenarios, from indoor to outdoor conditions, and the results showcased the effectiveness and applicability of our sensor package and fusion pipeline. This system can be applied in a wide range of applications, ranging from autonomous navigation to smart agriculture, and has the potential to make a substantial benefit across diverse fields.

Appropriate induction of TOC1 ensures optimal MYB44 expression in ABA signaling and stress response in Arabidopsis.

Plants possess the remarkable ability to integrate the circadian clock with various signalling pathways, enabling them to quickly detect and react to both external and internal stress signals. However, the interplay between the circadian clock and biological processes in orchestrating responses to environmental stresses remains poorly understood. TOC1, a core component of the plant circadian clock, plays a vital role in maintaining circadian rhythmicity and participating in plant defences. Here, our study reveals a direct interaction between TOC1 and the promoter region of MYB44, a key gene involved in plant defence. TOC1 rhythmically represses MYB44 expression, thereby ensuring elevated MYB44 expression at dawn to help the plant in coping with lowest temperatures during diurnal cycles. Additionally, both TOC1 and MYB44 can be induced by cold stress in an Abscisic acid (ABA)-dependent and independent manner. TOC1 demonstrates a rapid induction in response to lower temperatures compared to ABA treatment, suggesting timely flexible regulation of TOC1-MYB44 regulatory module by the circadian clock in ensuring a proper response to diverse stresses and maintaining a balance between normal physiological processes and energy-consuming stress responses. Our study elucidates the role of TOC1 in effectively modulating expression of MYB44, providing insights into the regulatory network connecting the circadian clock, ABA signalling, and stress-responsive genes.

Loss of LPAR6 and CAB39L dysregulates the basal-to-luminal urothelial differentiation program, contributing to bladder carcinogenesis.

We describe a strategy that combines histologic and molecular mapping that permits interrogation of the chronology of changes associated with cancer development on a whole-organ scale. Using this approach, we present the sequence of alterations around RB1 in the development of bladder cancer. We show that RB1 is not involved in initial expansion of the preneoplastic clone. Instead, we found a set of contiguous genes that we term "forerunner" genes whose silencing is associated with the development of plaque-like field effects initiating carcinogenesis. Specifically, we identified five candidate forerunner genes (ITM2B, LPAR6, MLNR, CAB39L, and ARL11) mapping near RB1. Two of these genes, LPAR6 and CAB39L, are preferentially downregulated in the luminal and basal subtypes of bladder cancer, respectively. Their loss of function dysregulates urothelial differentiation, sensitizing the urothelium to N-butyl-N-(4-hydroxybutyl)nitrosamine-induced cancers, which recapitulate the luminal and basal subtypes of human bladder cancer.

Identification of Pancreatic Cancer Germline Risk Variants With Effects That Are Modified by Smoking.

PURPOSE: Pancreatic cancer (PC) is a deadly disease most often diagnosed in late stages. Identification of high-risk subjects could both contribute to preventative measures and help diagnose the disease at earlier timepoints. However, known risk factors, assessed independently, are currently insufficient for accurately stratifying patients. We use large-scale data from the UK Biobank (UKB) to identify genetic variant-smoking interaction effects and show their importance in risk assessment. METHODS: We draw data from 15,086,830 genetic variants and 315,512 individuals in the UKB. There are 765 cases of PC. Crucially, robust resampling corrections are used to overcome well-known challenges in hypothesis testing for interactions. Replication analysis is conducted in two independent cohorts totaling 793 cases and 570 controls. Integration of functional annotation data and construction of polygenic risk scores (PRS) demonstrate the additional insight provided by interaction effects. RESULTS: We identify the genome-wide significant variant rs77196339 on chromosome 2 (per minor allele odds ratio in never-smokers, 2.31 [95% CI, 1.69 to 3.15]; per minor allele odds ratio in ever-smokers, 0.53 [95% CI, 0.30 to 0.91]; P = 3.54 × 10-8) as well as eight other loci with suggestive evidence of interaction effects (P < 5 × 10-6). The rs77196339 region association is validated (P < .05) in the replication sample. PRS incorporating interaction effects show improved discriminatory ability over PRS of main effects alone. CONCLUSION: This study of genome-wide germline variants identified smoking to modify the effect of rs77196339 on PC risk. Interactions between known risk factors can provide critical information for identifying high-risk subjects, given the relative inadequacy of models considering only main effects, as demonstrated in PRS. Further studies are necessary to advance toward comprehensive risk prediction approaches for PC.

Catalytic Nanoparticles in Biomedical Applications: Exploiting Advanced Nanozymes for Therapeutics and Diagnostics.

Catalytic nanoparticles (CNPs) as heterogeneous catalyst reveals superior activity due to their physio-chemical features, such as high surface-to-volume ratio and unique optical, electric, and magnetic properties. The CNPs, based on their physio-chemical nature, can either increase the reactive oxygen species (ROS) level for tumor and antibacterial therapy or eliminate the ROS for cytoprotection, anti-inflammation, and anti-aging. In addition, the catalytic activity of nanozymes could specifically trigger a specific reaction accompanied by the optical feature change, presenting the feasibility of biosensor and bioimaging applications. Undoubtedly, CNPs play a pivotal role in pushing the evolution of technologies in medical and clinical fields, and advanced strategies and nanomaterials rely on the input of chemical experts to develop. Herein, we present a systematic and comprehensive review of the challenges and recent development of catalytic NPs for biomedical applications from the viewpoint of advanced nanomaterial with unique catalytic activity and additional functions. Furthermore, we critically discuss the biosafety issue of applying biodegradable and non-biodegradable nanozymes and future perspectives to guide a promising direction in developing span-new nanozymes and more intelligent strategies for overcoming the current clinical limitations. This article is protected by copyright. All rights reserved.

Inferring Bladder Cancer Evolution from Mucosal field Effects by Whole-Organ Spatial Mutational, Proteomic, and Metabolomic Mapping.

Multi-platform mutational, proteomic, and metabolomic spatial mapping was used on the whole-organ scale to identify the molecular evolution of bladder cancer from mucosal field effects. We identified complex proteomic and metabolomic dysregulations in microscopically normal areas of bladder mucosa adjacent to dysplasia and carcinoma in situ. The mutational landscape developed in a background of complex defects of protein homeostasis which included dysregulated nucleocytoplasmic transport, splicesome, ribosome biogenesis, and peroxisome. These changes were combined with altered urothelial differentiation which involved lipid metabolism and protein degradations controlled by PPAR. The complex alterations of proteome were accompanied by dysregulation of gluco-lipid energy-related metabolism. The analysis of mutational landscape identified three types of mutations based on their geographic distribution and variant allele frequencies. The most common were low frequency α mutations restricted to individual mucosal samples. The two other groups of mutations were associated with clonal expansion. The first of this group referred to as ß mutations occurred at low frequencies across the mucosa. The second of this group called γ mutations increased in frequency with disease progression. Modeling of the mutations revealed that carcinogenesis may span nearly 30 years and can be divided into dormant and progressive phases. The α mutations developed gradually in the dormant phase. The progressive phase lasted approximately five years and was signified by the advent of ß mutations, but it was driven by γ mutations which developed during the last 2-3 years of disease progression to invasive cancer. Our study indicates that the understanding of complex alterations involving mucosal microenvironment initiating bladder carcinogenesis can be inferred from the multi-platform whole-organ mapping.

Enhancing Efficiency and Stability in Carbon-Based Perovskite Solar Cells by Double Passivation with Ultralow-Cost Coal-Derived Graphene and Its Derivatives.

Coal-derived carbon nanomaterials possess numerous superior features compared to other classic carbon, such as readily accessible surfaces, tunable pore structure, and facile and precise surface functionalization. Therefore, the controllable preparation of coal-derived carbon nanomaterials is anticipated to be of great significance for the performance improvement and commercialization process of carbon-based perovskite solar cells (C-PSCs). In this study, we successfully synthesized highly stable and commercially valuable graphene oxide (GO) and reduced graphene oxide (rGO) utilizing coal. Compared to traditional methods and commercial graphene, the chemical oxidation and pyrolysis process used in this study is mild and simple, offering the advantages of controlled composition and the absence of other impurities. GO or rGO was incorporated into the top of the SnO2 electron transport layer (ETL) of C-PSCs. Under optimized conditions and ultraviolet-ozone (UVO) irradiation, the ultimate power conversion efficiency (PCE) increased from the unmodified 12.4 to 14.04% (based on rGO) and 15.18% (based on GO), representing improvements of 22 and 31%, respectively. The improved photovoltaic performance is mainly owing to enhanced charge transport capabilities, denser interfacial contacts, improved carrier separation properties, increased conductivity, and abundance of hydrophilic functional groups in GO, which can form more stable hydrogen bonds with SnO2. After being stored at room temperature and ambient humidity for 30 days, the modified, unpacked devices retained 87% of the highest power conversion efficiency (PCE). This study introduces a practical and manageable method to enhance the performance of C-PSCs by using functional carbon nanomaterials derived from coal.

Internal Pressure-Temperature Coupling Analysis Method for Thermal Decomposition of GFRP Composites Based on the Overlapping Elements Method.

A method of internal pressure-temperature coupling analysis for the thermal decomposition of GFRP composites under high-temperature conditions was established, which incorporates coupled calculations of heat transfer equations, the Arrhenius equation, Darcy's law, and the ideal gas state equation. Using the overlapping mesh method, the coupling calculation of temperature and internal pressure is realized based on the UMATHT and USDFLD user subroutines developed. Specifically, two user subroutines, UMATHT-1 and UMATHT-2, are used to define the heat transfer equation and gas diffusion equation separately. Numerical simulations are conducted to simulate the polymers' thermal decomposition in high-temperature environments. For glass fiber/vinyl ester composites and glass fiber/phenolic composites, the predicted temperature and pressure values are in good agreement with experimental measurements, and porosity and permeability are then analyzed. Due to the accumulation of thermal decomposition gases, inter-pressure within the material surged and reached a peak value. After that, it began to decrease, but the factors affecting the pressure decrease vary at different positions. Specifically, the pressure closest to the heating surface is influenced by the combined effects of decomposition rate, permeability, and porosity, while the pressure far away from the heating surface is only affected by the initial permeability. The pressure in the intermediate region may be influenced by both increased porosity and initial permeability.

Drug resistance­related gene targets and molecular mechanisms in the A2780/Taxol­resistant epithelial ovarian cancer cell line.

Epithelial ovarian cancer (EOC) is a fatal gynecological malignant tumor with a low 5-year survival rate. The use of the first-line chemotherapeutic drug, paclitaxel, for the treatment of EOC is associated with resistance, often leading to treatment failure. The present study investigated the gene targets in an A2780 paclitaxel-resistant EOC cell line (A2780/Taxol), and the potential underlying mechanisms using transcriptome sequencing technology and bioinformatics analysis. The transcriptome of the A2780/Taxol cell line was sequenced, and 498 differentially expressed genes were obtained contained in the Gene Expression Omnibus dataset. Further bioinformatics analysis revealed that matrix metalloproteinase 1 (MMP1), zyxin (ZYX) and Unc-5 netrin receptor C (UNC5C) may be gene targets related to paclitaxel resistance. Moreover, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that a potential mechanism associated with paclitaxel resistance was related to cell migration. Furthermore, the expression levels of MMP1, ZYX and UNC5C were verified using western blotting, immunofluorescence and immunohistochemistry in vitro. The results revealed that the expression levels of MMP1 and ZYX were significantly increased in A2780/Taxol cells, while UNC5C expression was significantly decreased, which was consistent with the results of the transcriptome sequencing. The present study demonstrated that MMP1, ZYX and UNC5C may be the gene targets associated with paclitaxel resistance in EOC. These genes have potential to be used as molecular markers for EOC drug therapy, targeted elimination of drug resistance, and evaluation of treatment efficacy and patient prognosis.

Dual-layer conduit containing VEGF-A - Transfected Schwann cells promotes peripheral nerve regeneration via angiogenesis.

Peripheral nerve injuries (PNIs) can cause neuropathies and significantly affect the patient's quality of life. Autograft transplantation is the gold standard for conventional treatment; however, its application is limited by nerve unavailability, size mismatch, and local tissue adhesion. Tissue engineering, such as nerve guidance conduits, is an alternative and promising strategy to guide nerve regeneration for peripheral nerve repair; however, only a few conduits could reach the high repair efficiency of autografts. The healing process of PNI is frequently accompanied by not only axonal and myelination regeneration but also angiogenesis, which initializes nerve regeneration through vascular endothelial growth factor A (VEGF-A). In this study, a composite nerve conduit with a poly (lactic-co-glycolic acid) (PLGA) hollow tube as the outer layer and gelatin methacryloyl (GelMA) encapsulated with VEGF-A transfected Schwann cells (SCs) as the inner layer was established to evaluate its promising ability for peripheral nerve repair. A rat model of peripheral nerve defect was used to examine the efficiency of PLGA/GelMA-SC (VA) conduits, whereas autograft, PLGA, PLGA/GelMA, and PLGA/GelMA-SC (NC) were used as controls. VEGF-A-transfected SCs can provide a stable source for VEGF-A secretion. Furthermore, encapsulation in GelMA cannot only promote proliferation and tube formation of human umbilical vein endothelial cells but also enhance dorsal root ganglia and neuronal cell extension. Previous animal studies have demonstrated that the regenerative effects of PLGA/GelMA-SC (VA) nerve conduit were similar to those of autografts and much better than those of other conduits. These findings indicate that combination of VEGF-A-overexpressing SCs and PLGA/GelMA conduit-guided peripheral nerve repair provides a promising method that enhances angiogenesis and regeneration during nerve repair. STATEMENT OF SIGNIFICANCE: Nerve guidance conduits shows promise for peripheral nerve repair, while achieving the repair efficiency of autografts remains a challenge. In this study, a composite nerve conduit with a PLGA hollow tube as the outer layer and gelatin methacryloyl (GelMA) encapsulated with vascular endothelial growth factor A (VEGF-A)-transfected Schwann cells (SCs) as the inner layer was established to evaluate its potential ability for peripheral nerve repair. This approach preserves growth factor bioactivity and enhances material properties. GelMA insertion promotes Schwann cell proliferation and morphology extension. Moreover, transfected SCs serve as a stable VEGF-A source and fostering angiogenesis. This study offers a method preserving growth factor efficacy and safeguarding SCs, providing a comprehensive solution for enhanced angiogenesis and nerve regeneration.

Antioxidant and anti-aging activities of Longan crude and purified polysaccharide (LP-A) in nematode Caenorhabditis elegans.

Oxidative damage is an important cause of aging. The antioxidant and anti-aging activities of Longan polysaccharides, especially purified Longan polysaccharides, have not been thoroughly investigated. Therefore, this study aimed to investigate the antioxidant and anti-aging activities and mechanisms of crude polysaccharides and purified polysaccharides from Longan. A purified acidic Longan polysaccharide LP-A was separated from Longan crude polysaccharide LP. Subsequently, its structural characterization, anti-aging activity and mechanism were studied. The results showed that LP-A was an acidic heteropolysaccharide with an average molecular weight (Mw) of 4.606 × 104 Da which was composed of nine monosaccharides. The scavenging rate of ABTS free radical in vitro reached 99 %. In the nematode life experiment, 0.3 mg/mL LP group and LP-A group could prolong the average lifespan of nematodes by 9.31 % and 25.80 %, respectively. Under oxidative stress stimulation, LP-A group could prolong the survival time of nematodes by 69.57 %. In terms of mechanism, Longan polysaccharide can regulate insulin / insulin-like growth factor (IIS) signaling pathway, increase the activity of antioxidant enzymes, reduce lipid peroxidation, enhance the body's resistance to stress damage, and effectively prolong the lifespan of nematodes. In conclusion, LP-A has better anti-aging activity than crude polysaccharide LP, which has great potential for developing as an anti-aging drug.

Tenuifolin improves learning and memory by regulating long-term potentiation and dendritic structure of hippocampal CA1 area in healthy female mice but not male mice.

Polygala tenuifolia Wild is an ancient traditional Chinese medicine. Its main component, tenuifolin (TEN), has been proven to improve cognitive impairment caused by neurodegenerative diseases and ovariectomy. However, there was hardly any pharmacological research about TEN and its potential gender differences. Considering the reduction of TEN on learning and memory dysfunction in ovariectomized animals, therefore, we focused on the impact of TEN in different mice genders in the current study. Spontaneous alternation behavior (SAB), light-dark discrimination, and Morris water maze (MWM) tests were used to evaluate the mice's learning and memory abilities. The field excitatory postsynaptic potential (fEPSP) of the hippocampal CA1 region was recorded using an electrophysiological method, and the morphology of the dendritic structure was examined using Golgi staining. In the behavioral experiments, TEN improved the correct rate in female mice in the SAB test, the correct rate in the light-dark discrimination test, and the number of crossing platforms in the MWM test. Additionally, TEN reduced the latency of female mice rather than male mice in light-dark discrimination and MWM tests. Moreover, TEN could significantly increase the slope of fEPSP in hippocampal Schaffer-CA1 and enhance the total length and the number of intersections of dendrites in the hippocampal CA1 area in female mice but not in male mice. Collectively, the results of the current study showed that TEN improved learning and memory by regulating long-term potentiation (LTP) and dendritic structure of hippocampal CA1 area in female mice but not in males. These findings would help to explore the improvement mechanism of TEN on cognition and expand the knowledge of the potential therapeutic value of TEN in the treatment of cognitive impairment.