Construction of a prognostic model for lung adenocarcinoma based on m6A/m5C/m1A genes.

BACKGROUND: Developing a prognostic model for lung adenocarcinoma (LUAD) that utilizes m6A/m5C/m1A genes holds immense importance in providing precise prognosis predictions for individuals. METHODS: This study mined m6A/m5C/m1A-related differential genes in LUAD based on public databases, identified LUAD tumor subtypes based on these genes, and further built a risk prognostic model grounded in differential genes between subtypes. The immune status between high- and low-risk groups was investigated, and the distribution of feature genes in tumor immune cells was analyzed using single-cell analysis. Based on the expression levels of feature genes, a projection of chemotherapeutic and targeted drugs was made for individuals identified as high-risk. Ultimately, cell experiments were further verified. RESULTS: The 6-gene risk prognosis model based on differential genes between tumor subtypes had good predictive performance. Individuals classified as low-risk exhibited a higher (P < 0.05) abundance of infiltrating immune cells. Feature genes were mainly distributed in tumor immune cells like CD4+T cells, CD8+T cells, and regulatory T cells. Four drugs with relatively low IC50 values were found in the high-risk group: Elesclomol, Pyrimethamine, Saracatinib, and Temsirolimus. In addition, four drugs with significant positive correlation (P < 0.001) between IC50 values and feature gene expression were found, including Alectinib, Estramustine, Brigatinib, and Elesclomol. The low expression of key gene NTSR1 reduced the IC50 value of irinotecan. CONCLUSION: Based on the m6A/m5C/m1A-related genes in LUAD, LUAD patients were divided into 2 subtypes, and a m6A/m5C/m1A-related LUAD prognostic model was constructed to provide a reference for the prognosis prediction of LUAD.

Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies.

Phages can specifically recognize and kill bacteria, which lead to important application value of bacteriophage in bacterial identification and typing, livestock aquaculture and treatment of human bacterial infection. Considering the variety of human-infected bacteria and the continuous discovery of numerous pathogenic bacteria, screening suitable therapeutic phages that are capable of infecting pathogens from massive phage databases has been a principal step in phage therapy design. Experimental methods to identify phage-host interaction (PHI) are time-consuming and expensive; high-throughput computational method to predict PHI is therefore a potential substitute. Here, we systemically review bioinformatic methods for predicting PHI, introduce reference databases and in silico models applied in these methods and highlight the strengths and challenges of current tools. Finally, we discuss the application scope and future research direction of computational prediction methods, which contribute to the performance improvement of prediction models and the development of personalized phage therapy.

PB-LKS: a python package for predicting phage-bacteria interaction through local K-mer strategy.

Bacteriophages can help the treatment of bacterial infections yet require in-silico models to deal with the great genetic diversity between phages and bacteria. Despite the tolerable prediction performance, the application scope of current approaches is limited to the prediction at the species level, which cannot accurately predict the relationship of phages across strain mutants. This has hindered the development of phage therapeutics based on the prediction of phage-bacteria relationships. In this paper, we present, PB-LKS, to predict the phage-bacteria interaction based on local K-mer strategy with higher performance and wider applicability. The utility of PB-LKS is rigorously validated through (i) large-scale historical screening, (ii) case study at the class level and (iii) in vitro simulation of bacterial antiphage resistance at the strain mutant level. The PB-LKS approach could outperform the current state-of-the-art methods and illustrate potential clinical utility in pre-optimized phage therapy design.

Voxel-based texture similarity networks reveal individual variability and correlate with biological ontologies.

The human brain is organized as a complex, hierarchical network. However, the structural covariance patterns among brain regions and the underlying biological substrates of such covariance networks remain to be clarified. The present study proposed a novel individualized structural covariance network termed voxel-based texture similarity networks (vTSNs) based on 76 refined voxel-based textural features derived from structural magnetic resonance images. Validated in three independent longitudinal healthy cohorts (40, 23, and 60 healthy participants, respectively) with two common brain atlases, we found that the vTSN could robustly resolve inter-subject variability with high test-retest reliability. In contrast to the regional-based texture similarity networks (rTSNs) that calculate radiomic features based on region-of-interest information, vTSNs had higher inter- and intra-subject variability ratios and test-retest reliability in connectivity strength and network topological properties. Moreover, the Spearman correlation indicated a stronger association of the gene expression similarity network (GESN) with vTSNs than with rTSNs (vTSN: r = 0.600, rTSN: r = 0.433, z = 39.784, P < 0.001). Hierarchical clustering identified 3 vTSN subnets with differential association patterns with 13 coexpression modules, 16 neurotransmitters, 7 electrophysiology, 4 metabolism, and 2 large-scale structural and 4 functional organization maps. Moreover, these subnets had unique biological hierarchical organization from the subcortex-limbic system to the ventral neocortex and then to the dorsal neocortex. Based on 424 unrelated, qualified healthy subjects from the Human Connectome Project, we found that vTSNs could sensitively represent sex differences, especially for connections in the subcortex-limbic system and between the subcortex-limbic system and the ventral neocortex. Moreover, a multivariate variance component model revealed that vTSNs could explain a significant proportion of inter-subject behavioral variance in cognition (80.0 %) and motor functions (63.4 %). Finally, using 494 healthy adults (aged 19-80 years old) from the Southwest University Adult Lifespan Dataset, the Spearman correlation identified a significant association between aging and vTSN strength, especially within the subcortex-limbic system and between the subcortex-limbic system and the dorsal neocortex. In summary, our proposed vTSN is robust in uncovering individual variability and neurobiological brain processes, which can serve as biologically plausible measures for linking biological processes and human behavior.

Stimulus-Induced Dynamic Behavior Regulation of Flexible Crystals through the Tuning of Module Rigidity.

Introducing dynamic behavior into periodic frameworks has borne fruit in the form of flexible porous crystals. The detailed molecular design of frameworks in order to control their collective dynamics is of particular interest, for example, to achieve stimulus-induced behavior. Herein, by varying the degree of rigidity of ditopic pillar linkers, two isostructural flexible metal-organic frameworks (MOFs) with common rigid supermolecular building bilayers were constructed. The subtle substitution of single (in bibenzyl-4,4'-dicarboxylic acid; H2BBDC) with double (in 4,4'-stilbenedicarboxylic acid; H2SDC) C-C bonds in pillared linkers led to markedly different flexible behavior of these two MOFs. Upon the removal of guest molecules, both frameworks clearly show reversible single-crystal-to-single-crystal transformations involving the cis-trans conformation change and a resulting swing of the corresponding pillar linkers, which gives rise to Flex-Cd-MOF-1a and Flex-Cd-MOF-2a, respectively. Strikingly, a more favorable gas-induced dynamic behavior in Flex-Cd-MOF-2a was verified in detail by stepwise C3H6/C3H8 sorption isotherms and the corresponding in situ powder X-ray diffraction experiments. These insights are strongly supported by molecular modeling studies on the sorption mechanism that explores the sorption landscape. Furthermore, a consistency between the macroscopic elasticity and microscopic flexibility of Flex-Cd-MOF-2 was observed. This work fuels a growing interest in developing MOFs with desired chemomechanical functions and presents detailed insights into the origins of flexible MOFs.

Heteroatoms-Doped Mesoporous Carbon Nanosheets with Dual Diffusion Pathways for Highly Efficient Potassium Ion Storage.

The high potassization/depotassization energy barriers and lack of efficient ion diffusion pathways are two serious obstacles for carbon-based materials to achieve satisfactory potassium ion storage performance. Herein, a facile and controllable one-step exfoliation-doping-etching strategy is proposed to construct heteroatoms (N, O, and S)-doped mesoporous few-layer carbon nanosheets (NOS-C). The mixed molten salts of KCl/K2SO4 are innovatively used as the exfoliators, dopants, and etching agents, which enable NOS-C with expanded interlayer spacing and uniformly distributed mesopores with the adjusted electronic structure of surrounding carbon atoms, contributing efficient dual (vertical and horizontal) K-ion diffusion pathways, low potassization/depotassization energy barriers and abundant active sites. Thus, the NOS anodes achieve a high reversible capacity of 516.8 mAh g-1 at 0.05 A g-1, superior rate capability of 202.8 mAh g-1 at 5 A g-1 and excellent long-term cyclic stability, and their practical application potential is demonstrated by the assembled potassium-ion full batteries. Moreover, a surface-interlayer synergetic K+ storage mechanism is revealed by a combined theoretical and experimental approach including in situ EIS, in situ Raman, ex situ XPS, and SEM analysis. The proposed K+ storage mechanism and unique structural engineering provide a new pathway for potassium-ion storage devices and even beyond.

Modulating Surface Architecture and Electronic Conductivity of Li-rich Manganese-Based Cathode.

Li-rich manganese-based cathode (LRMC) has attracted intense attention to developing advanced lithium-ion batteries with high energy density. However, LRMC is still plagued by poor cyclic stability, undesired rate capacity, and irreversible oxygen release. To address these issues, herein, a feasible polyvinylidene fluoride (PVDF)-assisted interface modification strategy is proposed for modulating the surface architecture and electronic conductivity of LRMC by intruding the F-doped carbon coating, spinel structure, and oxygen vacancy on the LRMC, which can greatly enhance the cyclic stability and rate capacity, and restrain the oxygen release for LRMC. As a result, the modified material delivers satisfactory cyclic performance with a capacity retention of 90.22% after 200 cycles at 1 C, an enhanced rate capacity of 153.58 mAh g-1 at 5 C and 126.32 mAh g-1 at 10 C, and an elevated initial Coulombic efficiency of 85.63%. Moreover, the thermal stability, electronic conductivity, and structure stability of LRMC are also significantly improved by the PVDF-assisted interface modification strategy. Therefore, the strategy of simultaneously modulating the surface architecture and the electronic conductivity of LRMC provides a valuable idea to improve the comprehensive electrochemical performance of LRMC, which offers a promising reference for designing LRMC with high electrochemical performance.

A diagnostic model for Parkinson's disease based on circadian rhythm-related genes.

BACKGROUND: Circadian rhythm (CR) disturbance is intricately associated with Parkinson's disease (PD). However, the involvement of CR-related mechanisms in the pathogenesis and progression of PD remains elusive. METHODS: A total of 141 PD patients and 113 healthy participants completed CR-related clinical examinations in this study. To further investigate the CR-related mechanisms in PD, we obtained datasets (GSE7621, GSE20141, GSE20292) from the Gene Expression Omnibus database to identify differentially expressed genes between PD patients and healthy controls and further selected CR-related genes (CRRGs). Subsequently, the least absolute shrinkage and selection operator (LASSO) followed by logistic algorithms were employed to identify the hub genes and construct a diagnostic model. The predictive performance was evaluated by area under the curve (AUC), calibration curve, and decision curve analyses in the training set and external validation sets. Finally, RT‒qPCR and Western blotting were conducted to verify the expression of these hub genes in blood samples. In addition, Pearson correlation analysis was utilized to validate the association between expression of hub genes and circadian rhythm function. RESULTS: Our clinical observational study revealed that even early-stage PD patients exhibited a higher likelihood of experiencing sleep disturbances, nocturnal hypertension, reverse-dipper blood pressure, and reduced heart rate variability compared to healthy controls. Furthermore, 4 CR-related hub genes (AGTR1, CALR, BRM14, and XPA) were identified and subsequently incorporated as candidate biomarkers to construct a diagnostic model. The model showed satisfactory diagnostic performance in the training set (AUC = 0.941), an external validation set GSE20295 (AUC = 0.842), and our clinical centre set (AUC = 0.805). Additionally, the up-regulation of CALR, BRM14 and the down-regulation of AGTR1, XPA were associated with circadian rhythm disruption. CONCLUSION: CR disturbance seems to occur in the early stage of PD. The diagnostic model based on CR-related genes demonstrated robust diagnostic efficacy, offering novel insights for future clinical diagnosis of PD and providing a foundation for further exploration into the role of CR-related mechanisms in the progression of PD.

Nondestructive measurement of terahertz optical thin films by machine learning based on physical consistency.

Optical scattering measurement is one of the most commonly used methods for non-contact online measurement of film properties in industrial film manufacturing. Terahertz photons have low energy and are non-ionizing when measuring objects, so combining these two methods can enable online nondestructive testing of thin films. In the visible light band, some materials are transparent, and their thickness and material properties cannot be measured. Therefore, a method based on physical consistency modeling and machine learning is proposed in this paper, which realizes the method of obtaining high-precision thin film parameters through single-frequency terahertz wave measurement, and shows good performance. Through the experimental measurement of organic material thin films, it is proved that the proposed method is an effective terahertz online detection technology with high precision and high throughput.

Re-emergent Tremor in Parkinson's Disease: Evidence of Pathologic ß and Prokinetic γ Activity.

BACKGROUND: Re-emergent tremor is characterized as a continuation of resting tremor and is often highly therapy refractory. This study examines variations in brain activity and oscillatory responses between resting and re-emergent tremors in Parkinson's disease. METHODS: Forty patients with Parkinson's disease (25 males, mean age, 66.78 ± 5.03 years) and 40 age- and sex-matched healthy controls were included in the study. Electroencephalogram and electromyography signals were simultaneously recorded during resting and re-emergent tremors in levodopa on and off states for patients and mimicked by healthy controls. Brain activity was localized using the beamforming technique, and information flow between sources was estimated using effective connectivity. Cross-frequency coupling was used to assess neuronal oscillations between tremor frequency and canonical frequency oscillations. RESULTS: During levodopa on, differences in brain activity were observed in the premotor cortex and cerebellum in both the patient and control groups. However, Parkinson's disease patients also exhibited additional activity in the primary sensorimotor cortex. On withdrawal of levodopa, different source patterns were observed in the supplementary motor area and basal ganglia area. Additionally, levodopa was found to suppress the strength of connectivity (P < 0.001) between the identified sources and influence the tremor frequency-related coupling, leading to a decrease in ß (P < 0.001) and an increase in γ frequency coupling (P < 0.001). CONCLUSIONS: Distinct variations in cortical-subcortical brain activity are evident in tremor phenotypes. The primary sensorimotor cortex plays a crucial role in the generation of re-emergent tremor. Moreover, oscillatory neuronal responses in pathological ß and prokinetic γ activity are specific to tremor phenotypes. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Circ_0001361/miR-490-5p/IGF2 Axis Regulates the Viability and Apoptosis of Neuroblastoma Cells.

BACKGROUND: Circular RNAs (circRNAs) are involved in the neuroblastoma (NB) development. Objectie: The study aimed to determine the biological behaviors of circ_0001361 and explore its underlying mechanism in NB. METHODS: The circ_0001361, miR-490-5p, and IGF2 levels were measured using quantitative real-time polymerase chain reaction. Cellular processes were analyzed using MTT assay or fluorescence-activated cell sorting (FACS). Phosphorylated (p)-PI3K, p-AKT, Bax, and caspase-3 were tested by western blot. Dual-luciferase reporter analysis together with RNA pull-down analysis were utilized to evaluate the correlation of miR-490-5p and circ_0001361 or IGF2. RESULTS: The results in this study illustrated that an elevation of circ_0001361 levels was observed in NB. Depletion of circ_0001361 suppressed the viability but facilitated apoptosis of NB cells. Circ_0001361 sponged miR-490-5p, which targeted to regulate IGF2. Inhibition of miR-490-5p rescued the effect induced by circ_0001361 knockdown, while deletion of IGF2 rescued the effect induced by the miR-490-5p inhibitor. CONCLUSIONS: In summary, a loss of circ_0001361 inhibited NB progression via targeting the miR-490-5p/IGF2 axis, suggesting that circ_0001361 may be a novel therapeutical target of NB.

Observation of anodic electrochemiluminescence from silicon quantum dots for the detection of hydrogen peroxide.

Silicon quantum dots (QDs) with stable positively charged intermediates are prepared using chemical etching to generate strong anodic electrochemiluminescence (ECL) under a positive potential. Their surfaces could be passivated in the presence of strong oxidants, leading to enhanced ECL and offering the ability to carry out analysis for hydrogen peroxide.

The excitability of ipsilateral motor evoked potentials is not task-specific and spatially distinct from the contralateral motor hotspot.

OBJECTIVE: The role of ipsilateral descending motor pathways in voluntary movement of humans is still a matter of debate, with partly contradictory results. The aim of our study therefore was to examine the excitability of ipsilateral motor evoked potentials (iMEPs) regarding site and the specificity for unilateral and bilateral elbow flexion extension tasks. METHODS: MR-navigated transcranial magnetic stimulation mapping of the dominant hemisphere was performed in twenty healthy participants during tonic unilateral (iBB), bilateral homologous (bBB) or bilateral antagonistic elbow flexion-extension (iBB-cAE), the map center of gravity (CoG) and iMEP area from BB were obtained. RESULTS: The map CoG of the ipsilateral BB was located more anterior-laterally than the hotspot of the contralateral BB within the primary motor cortex, with a significant difference in CoG in iBB and iBB-cAE, but not bBB compared to the hotspot for the contralateral BB (each p < 0.05). However, different tasks had no effect on the size of the iMEPs. CONCLUSION: Our data demonstrated that excitability of ipsilateral and contralateral MEP differ spatially in a task-specific manner suggesting the involvement of different motor networks within the motor cortex.

Saturation effects of the relationship between physical exercise and systemic immune inflammation index in the short-sleep population: a cross-sectional study.

BACKGROUND: Short sleep can lead to an increase in inflammation and regular exercise has been shown to have a mitigation effect. However, the association between physical exercise (PE) and inflammation in the short sleep population is an unknown and intriguing issue. METHODS: NHANES dataset spanning the years 2007 to 2018 were analyzed. To investigate the relationship mentioned above, we carried out multivariate linear regression models controlling for sociodemographic and lifestyles factors. The systemic immune inflammation index (SII) served as a reflection of inflammatory potential, calculated as the product of platelet count, neutrophil count, and divided by the lymphocyte count. Self-reported questionnaires were used to collect sleep and exercise information. RESULTS: A total of 14,664 participants were included for final analysis. Across the three models, PE showed significant negative associations with SII as a continuous variable [Crude Model, ß (95% CI): -1.261(-1.600, -0.922), p < 0.001; Model 1, ß (95% CI): -1.005(-1.344, -0.666), p < 0.001; Model 2, ß (95% CI): -0.470(-0.827, -0.112), p = 0.011]. The consistent nature of the findings persisted when investigating physical exercise (PE) as a categorized variable. By two-piecewise linear regression model, we calculated a saturation effect of PE with the inflection point as 2400 MET-minutes/week. CONCLUSION: This study suggested that performing no more than 2400 MET-minutes/week of PE was associated with lower SII levels in the short sleep population, while more PE might not bring additional benefits.

Analyzing the dynamic effect of energy endowment-demand distortion on sustainable development: Insights from China's regional disparity.

The distribution of China's energy resources is concentrated in the central and western regions, whereas the energy demand is predominantly centered in the eastern regions. Under the ambitious "carbon neutrality" goal, how to effectively quantify and respond to the impact of this energy "endowment-demand" distortion (EEDD) on economy and environment has become a key issue. We introduce an EEDD index that quantifies the distortion characteristics of China's energy endowment and demand. Based on the EEDD index, a panel vector auto regression-generalized method of moments (PVAR-GMM) model is adopted to assess the interactive effects between regional EEDD and sustainable development variables. The obtained results indicate that the energy endowment-demand distortions are progressively worsening across most provinces. Interestingly, we discover that the EEDD has significant beneficial effects on regional sustainable development. Moreover, the EEDD is found to be significantly influenced by the sustainability-related variables. These impacts between EEDD and sustainable development variables demonstrate significant regional heterogeneity. This study provides crucial empirical evidence for advancing the comprehensive and sustainable development of regional energy, environment, and economy.

Selective Adsorption of Sr(II) from Aqueous Solution by Na3FePO4CO3: Experimental and DFT Studies.

The efficient segregation of radioactive nuclides from low-level radioactive liquid waste (LLRW) is paramount for nuclear emergency protocols and waste minimization. Here, we synthesized Na3FePO4CO3 (NFPC) via a one-pot hydrothermal method and applied it for the first time to the selective separation of Sr2+ from simulated LLRW. Static adsorption experimental results indicated that the distribution coefficient Kd remained above 5000 mL·g-1, even when the concentration of interfering ions was more than 40 times that of Sr2+. Furthermore, the removal efficiency of Sr2+ showed no significant change within the pH range of 4 to 9. The adsorption of Sr2+ fitted the pseudo-second-order kinetic model and the Langmuir isotherm model, with an equilibrium time of 36 min and a maximum adsorption capacity of 99.6 mg·g-1. Notably, the adsorption capacity was observed to increment marginally with an elevation in temperature. Characterization analyses and density functional theory (DFT) calculations elucidated the adsorption mechanism, demonstrating that Sr2+ initially engaged in an ion exchange reaction with Na+. Subsequently, Sr2+ coordinated with four oxygen atoms on the NFPC (100) facet, establishing a robust Sr-O bond via orbital hybridization.

Fucoxanthin Induces Ferroptosis in Cancer Cells via Downregulation of the Nrf2/HO-1/GPX4 Pathway.

This study investigated the mechanism by which fucoxanthin acts as a novel ferroptosis inducer to inhibit tongue cancer. The MTT assay was used to detect the inhibitory effects of fucoxanthin on SCC-25 human tongue squamous carcinoma cells. The levels of reactive oxygen species (ROS), mitochondrial membrane potential (MMP), glutathione (GSH), superoxide dismutase (SOD), malondialdehyde (MDA), and total iron were measured. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and Western blotting were used to assess glutathione peroxidase 4 (GPX4), nuclear factor erythroid 2-related factor 2 (Nrf2), Keap1, solute carrier family 7 member 11 (SLC7A11), transferrin receptor protein 1 (TFR1), p53, and heme oxygenase 1 (HO-1) expression. Molecular docking was performed to validate interactions. Compared with the control group, the activity of fucoxanthin-treated SCC-25 cells significantly decreased in a dose- and time-dependent manner. The levels of MMP, GSH, and SOD significantly decreased in fucoxanthin-treated SCC-25 cells; the levels of ROS, MDA, and total iron significantly increased. mRNA and protein expression levels of Keap1, GPX4, Nrf2, and HO-1 in fucoxanthin-treated cells were significantly decreased, whereas levels of TFR1 and p53 were significantly increased, in a concentration-dependent manner. Molecular docking analysis revealed that binding free energies of fucoxanthin with p53, SLC7A11, GPX4, Nrf2, Keap1, HO-1, and TFR1 were below -5 kcal/mol, primarily based on active site hydrogen bonding. Our findings suggest that fucoxanthin can induce ferroptosis in SCC-25 cells, highlighting its potential as a treatment for tongue cancer.

Fucoxanthin Inhibits the Proliferation and Metastasis of Human Pharyngeal Squamous Cell Carcinoma by Regulating the PI3K/Akt/mTOR Signaling Pathway.

Human pharyngeal squamous cell carcinoma (HPSCC) is the most common malignancy in the head and neck region, characterized by high mortality and a propensity for metastasis. Fucoxanthin, a carotenoid isolated from brown algae, exhibits pharmacological properties associated with the suppression of tumor proliferation and metastasis. Nevertheless, its potential to inhibit HPSCC proliferation and metastasis has not been fully elucidated. This study represents the first exploration of the inhibitory effects of fucoxanthin on two human pharyngeal squamous carcinoma cell lines (FaDu and Detroit 562), as well as the mechanisms underlying those effects. The results showed dose-dependent decreases in the proliferation, migration, and invasion of HPSCC cells after fucoxanthin treatment. Further studies indicated that fucoxanthin caused a significant reduction in the expression levels of proteins in the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mechanistic target of rapamycin (mTOR) pathway, as well as the downstream proteins matrix metalloproteinase (MMP)-2 and MMP-9. Specific activators of PI3K/AKT reversed the effects of fucoxanthin on these proteins, as well as on cell proliferation and metastasis, in FaDu and Detroit 562 cells. Molecular docking assays confirmed that fucoxanthin strongly interacted with PI3K, AKT, mTOR, MMP-2, and MMP-9. Overall, fucoxanthin, a functional food component, is a potential therapeutic agent for HPSCC.