Genomic divergence and demographic history of Quercus aliena populations.

BACKGROUND: Quercus aliena is a major montane tree species of subtropical and temperate forests in China, with important ecological and economic value. In order to reveal the species' population dynamics, genetic diversity, genetic structure, and association with mountain habitats during the evolutionary process, we re-sequenced the genomes of 72 Q. aliena individuals. RESULTS: The whole chloroplast and nuclear genomes were used for this study. Phylogenetic analysis using the chloroplast genome dataset supported four clades of Q. aliena, while the nuclear dataset supported three major clades. Sex-biased dispersal had a critical role in causing discordance between the chloroplast and nuclear genomes. Population structure analysis showed two groups in Q. aliena. The effective population size sharply declined 1 Mya, coinciding with the Poyang Glaciation in Eastern China. Using genotype-climate association analyses, we found a positive correlation between allele frequency variation in SNPs and temperature, suggesting the species has the capacity to adapt to changing temperatures. CONCLUSION: Overall, this study illustrates the genetic divergence, genomic variation, and evolutionary processes behind the demographic history of Q. aliena.

Mechanically strained osteocyte-derived exosomes contained miR-3110-5p and miR-3058-3p and promoted osteoblastic differentiation.

BACKGROUND: Osteocytes are critical mechanosensory cells in bone, and mechanically stimulated osteocytes produce exosomes that can induce osteogenesis. MicroRNAs (miRNAs) are important constituents of exosomes, and some miRNAs in osteocytes regulate osteogenic differentiation; previous studies have indicated that some differentially expressed miRNAs in mechanically strained osteocytes likely influence osteoblastic differentiation. Therefore, screening and selection of miRNAs that regulate osteogenic differentiation in exosomes of mechanically stimulated osteocytes are important. RESULTS: A mechanical tensile strain of 2500 µÎµ at 0.5 Hz 1 h per day for 3 days, elevated prostaglandin E2 (PGE2) and insulin-like growth factor-1 (IGF-1) levels and nitric oxide synthase (NOS) activity of MLO-Y4 osteocytes, and promoted osteogenic differentiation of MC3T3-E1 osteoblasts. Fourteen miRNAs differentially expressed only in MLO-Y4 osteocytes which were stimulated with mechanical tensile strain, were screened, and the miRNAs related to osteogenesis were identified. Four differentially expressed miRNAs (miR-1930-3p, miR-3110-5p, miR-3090-3p, and miR-3058-3p) were found only in mechanically strained osteocytes, and the four miRNAs, eight targeted mRNAs which were differentially expressed only in mechanically strained osteoblasts, were also identified. In addition, the mechanically strained osteocyte-derived exosomes promoted the osteoblastic differentiation of MC3T3-E1 cells in vitro, the exosomes were internalized by osteoblasts, and the up-regulated miR-3110-5p and miR-3058-3p in mechanically strained osteocytes, were both increased in the exosomes, which was verified via reverse transcription quantitative polymerase chain reaction (RT-qPCR). CONCLUSIONS: In osteocytes, a mechanical tensile strain of 2500 µÎµ at 0.5 Hz induced the fourteen differentially expressed miRNAs which probably were in exosomes of osteocytes and involved in osteogenesis. The mechanically strained osteocyte-derived exosomes which contained increased miR-3110-5p and miR-3058-3p (two of the 14 miRNAs), promoted osteoblastic differentiation.

Cryopreservation-enhanced differentiation capacity of embryogenic cultures of Castanea mollissima.

A cryopreservation protocol has been developed for embryogenic cultures (ECs) of Castanea mollissima, an important economic species of the Castanea genus in China. We achieved 100 % regrowth when ECs were treated with Plant Vitrification Solution 2 (PVS2) for 30, 60 and 90 min on ice. Optimal PVS2 treatment for cryopreservation was determined to be 30 min on ice based on the highest biomass regrowth after thawing. Fluorescein diacetate (FDA) staining could rapidly and reliably determine post-thaw cell viability and its use facilitated the optimization of the cryopreservation protocols. Although the proliferation rate of the re-established ECs remained largely unchanged compared to non-cryopreserved ECs, the capacity of the re-established ECs to differentiate (on two media) into somatic embryos nearly doubled to approximately 2200-2300 globular somatic embryos per 1 g of re-established ECs. Based on cell cluster size analysis, this enhanced growth is primarily attributed to the presence of significantly greater cell clusters with a diameter of 100-200 µm, which have the highest level of differentiation ability. In order to understand the increased embryogenic potential following cryopreservation, we analyzed the expression of key genes related to somatic embryogenesis. Genes CmWUS and CmABP1 were downregulated while CmLEC1, CmAGL15, CmGRF2, and CmFUS3 were upregulated in re-established ECs when compared to non-cryopreserved ECs.

Diet and risk for hernia: a Mendelian randomization analysis.

Background: The relationship between dietary factors and hernias is currently unclear. Methods: The UK Biobank was used to extract dietary factors that were used as exposures, including intake of alcohol, non-oily fish, beef, fresh fruit, oily fish, salad/raw vegetables, dried fruit, coffee, cereal, salt, tea, water, cooked vegetables, cheese, Lamb/mutton, pork, poultry, processed meat, and bread. The FinnGen biobank was used to obtain GWAS data on hernias as outcomes. The main analysis of this study was performed using the weighted median, MR-Egger, and IVW methods. Cochran's Q test was utilized to assess heterogeneity. To find potential outliers, the MR-PRESSO method was used. Leave-one-out analysis was employed to assess the IVW method's robustness. Results: Alcoholic consumption per week (OR: 0.614; p = 0.00614) reduced the risk of inguinal hernia. Alcohol intake frequency (OR: 1.309; p = 0.0477) increased the risk of ventral hernia (mainly including incisional hernia and parastomal hernia). The intake of non-oily fish (OR: 2.945; p = 0.0214) increased the risk of inguinal hernia. Salt added to food (OR: 1.841; p = 0.00267) increased the risk of umbilical hernia. Cheese intake (OR: 0.434; p = 0.000536) and dried fruit intake (OR: 0.322; p = 0.00716) decreased the risk of ventral hernia, while cooked vegetable intake (OR: 4.475; p = 0.0380) increased the risk of ventral hernia. No causal relationships were found with hernias from other dietary factors. Conclusion: Inguinal, umbilical, and ventral hernias are all related to dietary factors.

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.

The mechanical regulatory role of ATP13a3 in osteogenic differentiation of pre-osteoblasts.

PURPOSE: The process of osteogenic differentiation hinges upon the pivotal role of mechanical signals. Previous studies found that mechanical tensile strain of 2500 microstrain (µÎµ) at a frequency of 0.5 â€‹Hz promoted osteogenesis in vitro. However, the mechanism of the mechanical strain influencing osteogenesis at the cellular and molecular levels are not yet fully understood. This study aimed to explore the mechanism of mechanical strain on osteogenic differentiation of MC3T3-E1 cells. MATERIALS AND METHODS: Proteomics analysis was conducted to explore the mechanical strain that significantly impacted the protein expression. Bioinformatics identified important mechanosensitive proteins and the expression of genes was investigated using real-time PCR. The dual-luciferase assay revealed the relationship between the miRNA and its target gene. Overexpression and downexpression of the gene, to explore its role in mechanically induced osteogenic differentiation and transcriptomics, revealed further mechanisms in this process. RESULTS: Proteomics and bioinformatics identified an important mechanosensitive lowexpression protein ATP13A3, and the expression of Atp13a3 gene was also reduced. The dual-luciferase assay revealed that microRNA-3070-3p (miR-3070-3p) targeted the Atp13a3 gene. Furthermore, the downexpression of Atp13a3 promoted the expression levels of osteogenic differentiation-related genes and proteins, and this process was probably mediated by the tumor necrosis factor (TNF) signaling pathway. CONCLUSION: Atp13a3 responded to mechanical tensile strain to regulate osteogenic differentiation, and the TNF signaling pathway regulated by Atp13a3 was probably involved in this process. These novel insights suggested that Atp13a3 was probably a potential osteogenesis and bone formation regulator.

Dietary factors and hypertension: A Mendelian randomization analysis.

This research explores the causal link between dietary habits and hypertension through Mendelian randomization, providing distinct perspectives on the role of diet in addressing this worldwide health issue. Utilizing instrumental variables, we applied advanced statistical methods, including the weighted median, inverse variance weighted, and MR-Egger, to evaluate the impact of 17 dietary elements on hypertension. These elements ranged across various food groups, such as fruits, meats, vegetables, and beverages, both alcoholic and nonalcoholic. Our results identified a significant positive association of hypertension with weekly alcohol consumption (OR 1.340 [95%CI 1.0001 to 1.794], p = .0499) and poultry intake (OR 2.569 [95%CI 1.305 to 5.057], p = .00631). Conversely, a negative association was observed with lamb/mutton (OR 0.550 [95%CI 0.343 to 0.881], p = .0129), cheese (OR 0.650 [95%CI 0.519 to 0.813], p = .000159), tea (OR 0.797 [95%CI 0.640 to 0.993], p = .0433), cereal (OR 0.684 [95%CI 0.494 to 0.948], p = .0227), and dried fruit consumption (OR 0.492 [95%CI 0.343 to 0.707], p = .000127). These findings suggest that dietary modifications, such as increasing consumption of specific foods like cheese, lamb/mutton, tea, cereals, and dried fruits, could potentially reduce hypertension risk while reducing intake of alcoholic beverages and poultry might mitigate its increase. No direct causal relationships were established between other dietary factors and hypertension. The study highlights the importance of specific dietary modifications for the prevention and control of hypertension, making a substantial contribution to public health tactics and recommendations.

How to assess the accuracy of volume conduction models? A validation study with stereotactic EEG data.

Introduction: Volume conduction models of the human head are used in various neuroscience fields, such as for source reconstruction in EEG and MEG, and for modeling the effects of brain stimulation. Numerous studies have quantified the accuracy and sensitivity of volume conduction models by analyzing the effects of the geometrical and electrical features of the head model, the sensor model, the source model, and the numerical method. Most studies are based on simulations as it is hard to obtain sufficiently detailed measurements to compare to models. The recording of stereotactic EEG during electric stimulation mapping provides an opportunity for such empirical validation. Methods: In the study presented here, we used the potential distribution of volume-conducted artifacts that are due to cortical stimulation to evaluate the accuracy of finite element method (FEM) volume conduction models. We adopted a widely used strategy for numerical comparison, i.e., we fixed the geometrical description of the head model and the mathematical method to perform simulations, and we gradually altered the head models, by increasing the level of detail of the conductivity profile. We compared the simulated potentials at different levels of refinement with the measured potentials in three epilepsy patients. Results: Our results show that increasing the level of detail of the volume conduction head model only marginally improves the accuracy of the simulated potentials when compared to in-vivo sEEG measurements. The mismatch between measured and simulated potentials is, throughout all patients and models, maximally 40 microvolts (i.e., 10% relative error) in 80% of the stimulation-recording combination pairs and it is modulated by the distance between recording and stimulating electrodes. Discussion: Our study suggests that commonly used strategies used to validate volume conduction models based solely on simulations might give an overly optimistic idea about volume conduction model accuracy. We recommend more empirical validations to be performed to identify those factors in volume conduction models that have the highest impact on the accuracy of simulated potentials. We share the dataset to allow researchers to further investigate the mismatch between measurements and FEM models and to contribute to improving volume conduction models.

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.

Nomogram for predicting prognosis and identifying chemotherapy beneficiaries for completely resected stage I invasive mucinous lung adenocarcinoma.

Background: At present, there is a lack of studies in invasive mucinous adenocarcinoma (IMA) that combine clinicopathological and imaging features to stratify risk and select optimal treatment regimen. We aimed to develop and validate a nomogram for predicting recurrence-free survival (RFS) and identifying adjuvant chemotherapy (ACT) beneficiaries for completely resected stage I primary IMA. Methods: This retrospective study included 750 patients from three hospitals. Patients from two hospitals were divided into training (n=424) and validating cohort (n=185), and patients from the remaining other one hospital constituted external test cohort (n=141) and preoperative computed tomography (CT) image features of each patient were consecutively evaluated. The nomogram was developed by integrating significant prognostic factors of RFS identified in the multivariate analysis. The risk score (RS) based on nomogram was calculated in the entire cohort and the optimal cut-off point for risk stratification was obtained by X-tile software. The Kaplan-Meier method, log-rank test and interaction were used to evaluate the difference in RFS and overall survival (OS) between different risk and treatment groups. Results: Visceral pleural invasion (VPI, P<0.001), lymph-vascular invasion (LVI, P<0.001), tumor size (P<0.001), smoking history (P<0.001), lobulation (P<0.001) were identified as independent prognostic factors for RFS. The concordance index (C-index) of the nomogram was higher than that of tumor-node-metastasis (TNM) staging system (validation cohort: 0.73±0.09 vs. 0.62±0.08, P<0.001; external test cohort: 0.74±0.10 vs. 0.70±0.09, P=0.035). The patients with higher RS were associated with worse RFS [hazard ratios (HRs) ≥4.76] and OS (HRs ≥2.55) in all included cohorts. Chemotherapy benefits in terms of RFS and OS were observed for patients in higher RS group in both stage IB (interaction P=0.012 for RFS and P=0.037 for OS) and stage I IMA (interaction P<0.001 for both RFS and OS). Conclusions: The nomogram based on CT image and clinicopathologic features showed superior performance in predicting RFS for stage I IMA and might identify ACT candidates for personalized patient treatment.

Exploration of the mechanism of levofloxacin removal by N-doped-induced interfacial micro-electric field-activated persulfate.

The defects formed by N doping always coexist with pyrrole nitrogen (Po) and pyridine nitrogen (Pd), and the synergistic mechanisms of H2O2 production and PMS activation between the different Po: Pd are unknown. This paper synthesized MOF-derived carbon materials with different nitrogen-type ratios as cathode materials in an electro-Fenton system using precursors with different nitrogen-containing functional groups. Several catalysts with different Po: Pd ratios (0:4, 1:3, 2:2, 3:1, 4:0) were prepared, and the best catalyst for LEV degradation was FC-CN (Po: Pd=3:1). X-ray Photoelectron Spectroscopy (XPS) and density-functional theory (DFT) calculations show that the introduction of nitrogen creates an interfacial micro-electric field (IMEF) in the carbon layer and the metal, accelerates the electron transfer from the carbon layer to the Co atoms, and promotes cycling between the Fe3+/Co2+ redox pairs, with the electron transfer reaching a maximum at Po: Pd = 3:1. FC-CN (Po: Pd=3:1) achieved more than 95 % LEV degradation in 90 min at pH = 3-9, with a lower energy consumption of 0.11 kWh m-3 order-1. and the energy consumption of the catalyst for LEV degradation is lower than that of those catalysts reported. In addition, the degradation pathway of LEV was proposed based on UPLC-MS and Fukui function. This study offers some valuable information for the application of MOF derivatives.

Mechanistic insights into tris(2-chloroisopropyl) phosphate biomineralization coupled with lead (II) biostabilization driven by denitrifying bacteria.

The ubiquity and persistence of organophosphate esters (OPEs) and heavy metal (HMs) pose global environmental risks. This study explored tris(2-chloroisopropyl)phosphate (TCPP) biomineralization coupled to lead (Pb2+) biostabilization driven by denitrifying bacteria (DNB). The domesticated DNB achieved synergistic bioremoval of TCPP and Pb2+ in the batch bioreactor (efficiency: 98 %).TCPP mineralized into PO43- and Cl-, and Pb2+ precipitated with PO43-. The TCPP-degrading/Pb2+-resistant DNB: Achromobacter, Pseudomonas, Citrobacter, and Stenotrophomonas, dominated the bacterial community, and synergized TCPP biomineralization and Pb2+ biostabilization. Metagenomics and metaproteomics revealed TCPP underwent dechlorination, hydrolysis, the TCA cycle-based dissimilation, and assimilation; Pb2+ was detoxified via bioprecipitation, bacterial membrane biosorption, EPS biocomplexation, and efflux out of cells. TCPP, as an initial donor, along with NO3-, as the terminal acceptor, formed a respiratory redox as the primary energy metabolism. Both TCPP and Pb2+ can stimulate phosphatase expression, which established the mutual enhancements between their bioconversions by catalyzing TCPP dephosphorylation and facilitating Pb2+ bioprecipitation. TCPP may alleviate the Pb2+-induced oxidative stress by aiding protein phosphorylation. 80 % of Pb2+ converted into crystalized pyromorphite. These results provide the mechanistic foundations and help develop greener strategies for synergistic bioremediation of OPEs and HMs.