Anoikis-related gene signatures predict prognosis of lung adenocarcinoma patients and reveal immune infiltration.

Background: Lung adenocarcinoma (LUAD), a type of lung cancer, is one of the most aggressive and deadly malignancies worldwide. Malignant tumor cells exhibit strong anti-anoikis properties to achieve distant metastasis through the circulatory system. However, more research is needed to understand how anoikis is involved in the progression, metastasis and especially the prognosis of LUAD. Methods: We obtained anoikis-related genes (ARGs) from two websites, Harmonizome and Genecards, and integrated them to select and model the genes associated with LUAD prognosis. In addition, we investigated differences in the immune cell microenvironment and pathways of enrichment analysis between subtypes. We finally constructed a nomogram based on ARGs and used decision curve analysis (DCA) to demonstrate that this model could help clinicians make clinical decisions. Results: Sixty-four differentially expressed genes (DEGs) were found to be associated with survival, and of these, six were chosen to build a prognostic model. The time-dependent receiver operating characteristic (ROC) curves showed that the model had a satisfactory predictive ability. Enrichment analysis and immune microenvironment analysis revealed that the immune status and drug sensitivity of populations at high and low risk were different. We integrated the clinicopathological features of LUAD with the risk score to build the nomogram. The nomogram was shown to be a good predictor of short- and long-term survival in LUAD patients through DCA analysis. Conclusions: This new model based on six ARGs and nomograms in our study could help patients with LUAD develop personalized treatment plans.

Development and Validation of a Machine Learning Prognostic Model of m5C Related immune Genes in Lung Adenocarcinoma.

BACKGROUND: The aim of this retrospective research was to develop an immune-related genes significantly associated with m5C methylation methylation (m5C-IRGs)-related signature associated with lung adenocarainoma (LUAD). METHODS: We introduced transcriptome data to screen out m5C-IRGs in The Cancer Genome Atlas (TCGA)-LUAD dataset. Subsequently, the m5C-IRGs associated with survival were certificated by Kaplan Meier (K-M) analysis. The univariate Cox, least absolute shrinkage and selection operator (LASSO) regression, and xgboost.surv tool were adopted to build a LUAD prognostic signature. We further conducted gene functional enrichment, immune microenvironment and immunotherapy analysis between 2 risk subgroups. Finally, we verified m5C-IRGs-related prognostic gene expression in transcription level. RESULTS: A total of 76 m5C-IRGs were identified in TCGA-LUAD dataset. Furthermore, 27 m5C-IRGs associated with survival were retained. Then, a m5C-IRGs prognostic signature was build based on the 3 prognostic genes (HLA-DMB, PPIA, and GPI). Independent prognostic analysis suggested that stage and RiskScore could be used as independent prognostic factors. We found that 4104 differentially expressed genes (DEGs) between the 2 risk subgroups were mainly concerned in immune receptor pathways. We found certain distinction in LUAD immune microenvironment between the 2 risk subgroups. Then, immunotherapy analysis and chemotherapeutic drug sensitivity results indicated that the m5C-IRGs-related gene signature might be applied as a therapy predictor. Finally, we found significant higher expression of PPIA and GPI in LUAD group compared to the normal group. CONCLUSIONS: The prognostic signature comprised of HLA-DMB, PPIA, and GPI based on m5C-IRGs was established, which might provide theoretical basis and reference value for the research of LUAD. PUBLIC DATASETS ANALYZED IN THE STUDY: TCGA-LUAD dataset was collected from the TCGA (https://portal.gdc.cancer.gov/) database, GSE31210 (validation set) was retrieved from GEO (https://www.ncbi.nlm.nih.gov/geo/) database.

Head-to-head comparison of 18F-FDG PET/CT and 18F-FDG PET/MRI for lymph node metastasis staging in non-small cell lung cancer: a meta-analysis.

PURPOSE: The current meta-analysis aimed to compare the diagnostic performance of 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) with 18F-FDG PET/magnetic resonance imaging (MRI) in non-small cell lung cancer (NSCLC) lymph node metastasis staging. METHODS: We searched the PubMed, Web of Science, and Embase databases for relevant articles between November 1992 and September 2022. Studies evaluating the head-to-head comparison of 18F-FDG PET/CT and 18F-FDG PET/MRI for lymph node metastasis in patients with NSCLC were included. The quality of each study was assessed using the Quality Assessment of Diagnostic Performance Studies-2 tool. RESULTS: The analysis includes six studies with a total of 434 patients. The pooled sensitivity of 18F-FDG PET/CT and 18F-FDG PET/MRI was 0.78 [95% confidence interval (CI): 0.59-0.90] and 0.84 (95% CI: 0.68-0.93), and the pooled specificity was 0.87 (95% CI: 0.72-0.94) and 0.87 (95% CI: 0.80-0.92), respectively. The accuracy of 18F-FDG PET/CT and 18F-FDG PET/MRI was 0.81 (95% CI: 0.71-0.90) and 0.84 (95% CI: 0.75-0.92), respectively. When the pre-test probability was set at 50%, the post-test probability for 18F-FDG PET/CT could increase to 85%, and the post-test probability for 18F-FDG PET/MRI could increase to 87%. CONCLUSION: 18F-FDG PET/CT and 18F-FDG PET/MRI have similar diagnostic performance in detecting lymph node metastasis in NSCLC. However, the results of this study were from a small sample study, and further studies with larger sample sizes are needed.

Diagnostic potential of [18F]FDG PET/MRI in non-small cell lung cancer lymph node metastasis: a meta-analysis.

PURPOSE: This meta-analysis evaluated the diagnostic accuracy and diagnostic value of [18F]FDG PET/MRI for mediastinal lymph node staging of NSCLC. METHODS: Relevant articles in PubMed, Embase, Web of Science, and the Cochrane Library were searched until January 2023. Research evaluating [18F]FDG PET/MRI for mediastinal lymph node staging of NSCLC was included. Pooled estimates of sensitivity, specificity, PLR, and NLR were calculated by the "Stata" software. RESULTS: Nine researches were included, containing 618 patients. The pooled sensitivity of [18F]FDG PET/MRI for detecting mediastinal lymph node staging of NSCLC was 0.82 (0.70-0.90), and the pooled specificity was 0.88 (0.82-0.93). PLR and NLR were 7.38 (4.73-11.52) and 0.20 (0.11-0.36), respectively. The AUC value of this imaging modality was 0.92 (0.90-0.94). The post-test probability for [18F]FDG PET/MRI might rise to 88% when the pre-test probability was set at 50%. CONCLUSIONS: We considered [18F]FDG PET/MRI as an effective imaging tool with relatively high specificity and sensitivity. It has great potential to be used in the clinical management of patients in NSCLC who are amenable to early surgery. More studies with large sample sizes in the same direction are needed in future to obtain more reliable evidence-based support.

An Uncertainty-Guided Deep Learning Method Facilitates Rapid Screening of CYP3A4 Inhibitors.

Cytochrome P450 3A4 (CYP3A4), a prominent member of the P450 enzyme superfamily, plays a crucial role in metabolizing various xenobiotics, including over 50% of clinically significant drugs. Evaluating CYP3A4 inhibition before drug approval is essential to avoiding potentially harmful pharmacokinetic drug-drug interactions (DDIs) and adverse drug reactions (ADRs). Despite the development of several CYP inhibitor prediction models, the primary approach for screening CYP inhibitors still relies on experimental methods. This might stem from the limitations of existing models, which only provide deterministic classification outcomes instead of precise inhibition intensity (e.g., IC50) and often suffer from inadequate prediction reliability. To address this challenge, we propose an uncertainty-guided regression model to accurately predict the IC50 values of anti-CYP3A4 activities. First, a comprehensive data set of CYP3A4 inhibitors was compiled, consisting of 27,045 compounds with classification labels, including 4395 compounds with explicit IC50 values. Second, by integrating the predictions of the classification model trained on a larger data set and introducing an evidential uncertainty method to rank prediction confidence, we obtained a high-precision and reliable regression model. Finally, we use the evidential uncertainty values as a trustworthy indicator to perform a virtual screening of an in-house compound set. The in vitro experiment results revealed that this new indicator significantly improved the hit ratio and reduced false positives among the top-ranked compounds. Specifically, among the top 20 compounds ranked with uncertainty, 15 compounds were identified as novel CYP3A4 inhibitors, and three of them exhibited activities less than 1 µM. In summary, our findings highlight the effectiveness of incorporating uncertainty in compound screening, providing a promising strategy for drug discovery and development.

Functional Group Modulation in Carbon Quantum Dots for Accelerating Photocatalytic CO2 Reduction.

This study investigates the mechanism behind the enhanced photocatalytic performance of carbon quantum dot (CQD)-induced photocatalysts. Red luminescent CQDs (R-CQDs) were synthesized using a microwave ultrafast synthesis strategy, exhibiting similar optical and structural properties but varying in surface functional group sites. Model photocatalysts were synthesized by combining R-CQDs with graphitic carbon nitride (CN) using a facile coupling technique, and the effects of different functionalized R-CQDs on CO2 reduction were investigated. This coupling technique narrowed the band gap of R1-CQDs/CN, made the conduction band potentials more negative, and made photogenerated electrons and holes less likely to recombine. These improvements greatly enhanced the deoxygenation ability of the photoinduced carriers, increased light absorption of solar energy, and raised the carrier concentration, resulting in excellent stability and remarkable CO production. R1-CQDs/CN demonstrated the highest photocatalytic activity, with CO production up to 77 µmol g-1 within 4 h, which is approximately 5.26 times higher than that of pure CN. Our results suggest that the superior photocatalytic performance of R1-CQDs/CN arises from its strong internal electric field and high Lewis acidity and alkalinity, attributed to the abundant pyrrolic-N and oxygen-containing surface groups, respectively. These findings offer a promising strategy for producing efficient and sustainable CQD-based photocatalysts to address global energy and environmental problems.

High-Capacity and Long-Life Zinc Electrodeposition Enabled by a Self-Healable and Desolvation Shield for Aqueous Zinc-Ion Batteries.

Artificial interfaces can alleviate the side reactions and the formation of the metallic (e.g., Li, Na, and Zn) dendrites. However, the traditional ones always breakdown during the repeated plating/stripping and fail to regulate the electrodeposition behaviors of the electrodes. Herein, a self-healable ion regulator (SIR) is designed as a desolvation shield to protect the Zn electrodes and guide the Zn electrodeposition. Benefiting from the intermolecular hydrogen bonds, SIR shows a superb capability to in situ repair the plating/stripping-induced cracks. Besides, the results of theoretical calculations and electrochemical characterizations show that the coating reduces water molecules in the solvated sheath of hydrated Zn2+ and restrains the random Zn2+ diffusion on the Zn surface. Even with a coating layer of only 360 nm, the SIR-modified Zn electrode exhibits excellent long-term stability for >3500 h at 2 mAh cm-2 and >950 h at an ultrahigh areal capacity of 20 mAh cm-2 .

Investigation into the effects of leukemia inhibitory factor on the bone repair capacity of BMSCs-loaded BCP scaffolds in the mouse calvarial bone defect model.

Leukemia inhibitory factor (LIF) is known to play a major role in bone physiology. In the present study, we examined the in vitro effects of LIF on osteoblast differentiation of bone marrow stem cells (BMSCs) and explored in vivo effects of LIF on the bone repair capacity of BMSCs-loaded biphasic calcium phosphate (BCP) scaffolds in mouse calvarial bone defect model. The mRNA and protein expression levels in the BMSCs were determined by quantitative real-time PCR and western blot, respectively; the in vitro osteoblast differentiation of the BMSCs was evaluated by using Alizarin Red S staining. The bone volume and bone density in the repaired calvarial bone defect were determined by Micro-CT. Bone regeneration was also histologically evaluated by hematoxylin and eosin staining and Masson's trichrome staining. Hypoxia treatment induced the up-regulation of Lif mRNA and LIF protein in the BMSCs. Lif overexpression up-regulated the mRNA expression levels of osteopontin and Runt-related transcription factor 2, and increased intensity of Alizarin Red S staining in the BMSCs; while Lif silence exerted the opposite effects. The in vivo studies showed that implantation of Lif-overexpressing BMSCs-loaded BCP scaffolds significantly increased the bone volume and bone density at 4 and 8 weeks after transplantation, and promoted the regeneration of bone tissues in the mouse calvarial bone defect at 8 weeks after transplantation when compared to the BMSCs-loaded BCP scaffolds group; while Lif-silencing BMSCs-loaded BCP scaffolds had the opposite effects. The present study for the first time demonstrated that LIF promoted the in vitro osteoblast differentiation of hypoxia-treated BMSCs; and further studies revealed that LIF exerted enhanced effects on the bone repair capacity of BMSCs-load BCP scaffolds in mouse calvarial bone defect model. However, future studies are warranted to determine the detailed mechanisms of LIF in the large-scale bone defect repair.

An effective digitization method for CTG paper report with binary background grids taken by smartphone.

BACKGROUND AND OBJECTIVE: Cardiotocography (CTG) is the most popular prenatal diagnostic examination, which includes continuous monitoring of foetal heart rate (FHR, bpm) and uterine contraction (UC, mmHg) signals. Compared with CTG paper reports, digitized reports have better storage, transmission and retrieval capabilities, in addition to being able to assess foetal health. However, most of the existing digitization methods extract signals from paper reports with colour background grids, and they cannot extract signals completely from paper reports with binary background grids, which are widely used in clinical CTG monitoring. Moreover, the existing digitization algorithms often neglect the image distortion caused by the imaging equipment. METHODS: To overcome the above drawbacks, a digitization method for CTG paper reports with binary background grids taken by smartphones is proposed in this paper. In the stage of removing the grid background, a region merger based on super-pixels and an improved binary line mask removal are designed. Then, signal extraction is performed separately according to the different states of the image column. Through a projection map used to synchronize the signal, the distortion effect of the mobile phone is removed. RESULTS: The experimental results show that the average correlation coefficient (ρ) between the recovery signal obtained by the proposed method and the reference signal is 0.9855±0.0108 for FHR and 0.9866 ± 0.1020 for UC, and the root mean square errors (RMSE) of FHR and UC processed by the proposed method are 1.0366 ± 0.4953 and 2.0355 ± 1.0246, and the mean absolute errors (MAE) of FHR and UC processed by the proposed method are 0.8735 ± 0.0684 and 1.4991 ± 0.2837, which are higher than those of the existing digitization methods. Compared with clinical signals, no significant difference is found in the feature of digitization CTG. CONCLUSION: The proposed digitization method is a promising useful tool to realize the electronization of CTG signal.

Necklace-like ferroferric oxide (Fe3O4) nanoparticle/carbon nanofibril aerogels with enhanced lithium storage by carbonization of ferric alginate.

Theoretically, transition metal oxide/carbon nanofibril aerogels are promising candidates for lithium-ion battery anode materials as they combine the high stability and electrical conductivity of the carbon matrix and the high theoretical specific capacity of transition metal oxide (TMO). However, challenges still exist to embed TMO nanoparticles into thin carbon nanofibril absolutely and tightly, limiting further improvements in electrochemical performances of the composites. Herein, necklace-like Fe3O4/carbon nanofibril aerogel (Fe3O4/CNF) was constructed by crosslinking alginate with Fe3+, followed by carbonization of the obtained ferric alginate aerogel. Based on an "egg-box" helical structure resulting from strong coordination between the Fe3+ and the carboxylate groups of alginate, three-dimensional interconnected carbon aerogel was facilely fabricated with Fe3O4 nanoparticles (~11 nm in diameter) firmly embedded in ultrafine carbon nanofibrils (~18 nm in diameter), exhibiting a special necklace-like structure. Consequently, the composite exhibits a high reversible capacity and stability of 1176 mAh g-1 over 200 cycles at 1 A g-1 and a high rate performance of 615 mAh g-1 at 4 A g-1. These Fe3O4/CNF aerogels may have potential applications for enhanced lithium storage of electrochemical devices.

Keratinocyte growth factor (KGF) induces podosome formation via integrin-Erk1/2 signaling in human immortalized oral epithelial cells.

Recent study established the role of integrins in keratinocyte growth factor (KGF)-induced oral epithelial adhesion and rete peg elongation. However, how extracellular matrix (ECM) remodeling cooperates with the increased epithelial adhesion during rete peg elongation has yet to be determined. Podosomes are cell-matrix contact structures that combine several abilities, including adhesion and matrix degradation. In the present study, we identified podosome formation at the ventral side of human immortalized oral epithelial cells (HIOECs) upon KGF treatment. Moreover, podosomal components including integrin α6，ß4，α3，ß1 and MMP14 colocalized with the F-actin-cortactin complex and matrix degradation assays demonstrated the ability of the F-actin-cortactin complex to degrade matrix. Inhibition both of integrin subunits ß4 and ß1 with specific blocking antibodies and inhibition of Erk1/2 abrogated the KGF-induced podosome formation. Notably, knockdown of integrin subunits ß4 and ß1 with specific small interfering RNA (siRNA) downregulated the phosphorylation levels of Erk1/2. In contrast, inhibition of both Erk1/2 could upregulate the expression of integrin subunits ß4 and ß1. These results demonstrate that KGF induces podosome formation via integrin-Erk1/2 signaling in HIOECs, suggesting a novel mechanism by which integrins enhance oral epithelial adhesion and rete peg elongation.

A ß-carotene-binding protein carrying a red pigment regulates body-color transition between green and black in locusts.

Changes of body color have important effects for animals in adapting to variable environments. The migratory locust exhibits body color polyphenism between solitary and gregarious individuals, with the former displaying a uniform green coloration and the latter having a prominent pattern of black dorsal and brown ventral surface. However, the molecular mechanism underlying the density-dependent body color changes of conspecific locusts remain largely unknown. Here, we found that upregulation of ß-carotene-binding protein promotes the accumulation of red pigment, which added to the green color palette present in solitary locusts changes it from green to black, and that downregulation of this protein led to the reverse, changing the color of gregarious locusts from black to green. Our results provide insight that color changes of locusts are dependent on variation in the red ß-carotene pigment binding to ßCBP. This finding of animal coloration corresponds with trichromatic theory of color vision.

The Arabidopsis nucleoporin NUP1 is essential for megasporogenesis and early stages of pollen development.

KEY MESSAGE: Loss-of-function of nucleoporin NUP1 in Arabidopsis causes defect in both male and female gametogenesis. Its ovules are arrested during meiosis, and its pollen grains are aborted at mitosis I. Nuclear pore complex (NPC) plays crucial roles in nucleocytoplasmic trafficking of proteins and RNAs. The NPC contains approximately 30 different proteins termed nucleoporins (NUPs). So far, only a few of plant NUPs have been characterized. The Arabidopsis NUP1 was identified as an ortholog of the yeast NUP1 and animal NUP153. Loss-of-function of NUP1 in Arabidopsis caused fertility defect; however, the molecular mechanism of this defect remains unknown. Here, we found that both male and female gametogenesis of the nup1 mutants were defective. nup1 ovules were arrested from the meiosis stage onward; only approximately 6.7% and 3% ovules of the nup1-1 and nup1-4 mutants developed up to the FG7 stage, respectively. Pollen development of the nup1 mutants was arrested during the first mitotic division. In addition, enlarged pollen grains with increased DNA content were observed in the nup1 mutant. RNA-sequencing showed that expression levels of genes involved in pollen development or regulation of cell size were reduced dramatically in nup1 compared with wild type. These results suggest that NUP1 plays an important role in gametogenesis.