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Introduction The aim of the study is the regulatory effect of MicroRNA-210 (MiR- 210) on cigarette smoke extract (CSE)-induced mouse lung epithelial type II cells (MLE-12) apoptosis and determine whether the MiR-210 is involved in cigarette smoke extract-induced apoptosis of MLE-12 via Shh signaling pathway. Methods Expression of MiR-210 in CSE-induced MLE-12 was assessed by qRTPCR. The emphysema mouse model and MiR-210 knockdown mice were each established by inhaling cigarette smoke or intratracheal lentiviral vector instillation. The Sonic hedgehog (Shh), Ptch1, Gli1, B-cell lymphoma-2 (Bcl-2), and Caspase 3 protein expressions were detected by Western blotting. mRNA expressions of MiR-210, Shh, Ptch1, and Gli1 were measured using quantitative real-time polymerase chain reaction (qRT-PCR). Apoptotic ratios in mice and CSE-induced HPVEC were assessed using TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling) assays and flow cytometry. Results Our results showed that MiR-210 mRNA levels were significantly downregulated in the CSE-induced MLE 12. MLE 12 apoptosis with down-regulated Shh, Ptch1, Gli1, and Bcl-2 expression, increased Caspase 3 expression in the emphysema mouse model and CSE-induced MLE 12. Knockdown MiR-210 can facilitate cell apoptosis and emphysema via the Shh signaling pathway in mice. In vitro , MiR-210 can attenuate the apoptosis of CSE-exposed MLE 12. Moreover, MiR-210 regulated the Shh pathway and promoted its expression. Conclusions MiRNA-210 is involved in cigarette smoke extract-induced apoptosis of MLE-12 via the Shh signaling pathway. The present study reveals that MiRNA-210 may be a key regulator of cellular apoptosis and could be explored as a potential therapeutic target in the future.

Abstract Background Coronary artery disease (CAD) is a common comorbidity of chronic obstructive pulmonary disease (COPD). However, data related to the impact of CAD on outcomes of acute exacerbation of COPD (AECOPD) are limited and whether the relationship depends on sex remains unknown. Our aim was to determine the impact of comorbid CAD on clinical outcomes among men and women with AECOPD. Methods We used data from the acute exacerbation of chronic obstructive pulmonary disease inpatient registry (ACURE) study, which is a nationwide observational real-world study conducted between September 2017 and February 2020 at 163 centers in patients admitted with AECOPD as their primary diagnosis. Patients were stratified according to the presence or absence of CAD in men and women. The primary outcomes were the length of hospital stay and economic burden during hospitalization. Results Among 3906 patients included in our study, the prevalence of CAD was 17.0%, and it was higher in women than in men (19.5% vs. 16.3%; P = 0.034). Age and other cardiovascular diseases were common factors associated with comorbid CAD in men and women, while body-mass index, cerebrovascular disease, and diabetes were determinants in men and pre-admission use of long-acting beta-adrenoceptor agonist and home oxygen therapy were protective factors in women. Only in men, patients with CAD had a longer length of hospital stay (median 10.0 vs. 9.0 days, P

Abstract Background The clinical value of blood eosinophils and their stability in chronic obstructive pulmonary disease (COPD) remains controversial. There are limited studies on association between the stability of blood eosinophils in acute exacerbation of COPD (AECOPD) and clinical outcomes. This study aimed to evaluate the stability of blood eosinophils in hospitalized AECOPD and its relationship to clinical outcomes. Methods This prospective observational study recruited patients hospitalized with AECOPD from November 2016 to July 2020. The eligible patients were divided into four groups according to their blood eosinophil counts at admission and discharge: persistently

Abstract To explore the status of diagnostic delay and to clarify its potentially influencing factors in patients with chronic obstructive pulmonary disease (COPD). A cross-sectional study was conducted in a Chinese tertiary hospital between July 2019 and February 2020. A total of 408 eligible outpatients with COPD were recruited, and relevant data were collected in the form of questionnaires. Diagnostic delay was compared among different characteristics using the Wilcoxon test and Kruskal–Wallis H test. Multivariable linear regression analysis was performed to determine the factors related to diagnostic delay. The median (interquartile range [IQR]) duration of diagnostic delay was 230 (50–720) days. The proportions of COPD patients who chose tertiary, secondary, and first-level hospitals for the first visit were 53.7%, 29.9%, and 16.4%, respectively. Additionally, the proportions of patients who underwent pulmonary function tests for the first visit in tertiary, secondary, and first-level hospitals were 74.0%, 24.6%, and 1.5% (p

Abstract Obstructive sleep apnea syndrome (OSAS), a state of sleep disorder, is characterized by repetitive apnea, chronic hypoxia, oxygen desaturation, and hypercapnia. Previous studies have revealed that intermittent hypoxia (IH) conditions in OSAS patients elicited neuron injury (especially in the hippocampus and cortex), leading to cognitive dysfunction, a significant and extraordinary complication of OSAS patients. The repeated courses of airway collapse and obstruction in OSAS patients resulted in apnea and arousal during sleep, leading to IH and excessive daytime sleepiness (EDS) and subsequently contributing to the development of inflammation. IH-mediated inflammation could further trigger various types of cognitive dysfunction. Many researchers have found that, besides continuous positive airway pressure (CPAP) treatment and surgery, anti-inflammatory substances might alleviate IH-induced neurocognitive dysfunction. Clarifying the role of inflammation in IH-mediated cognitive impairment is crucial for potentially valuable therapies and future research in the related domain. The objective of this article was to critically review the relationship between inflammation and cognitive deficits in OSAS.

Background: Although medical guidelines discourage the use of methylxanthines in patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD), they are still widely used in clinical practice. This study investigated the real-world use of methylxanthines in the management of AECOPD.Methods: Patient data from the Acute exacerbation of Chronic obstructive pulmonary disease Using REgistry data (ACURE, NCT02657525) study database were screened. Enrolled patients were divided into treatment and control groups. Propensity score (PS) matching and Cox regression analyses were used to minimize confounding factors and determine the association between methylxanthine treatment and the length of stay (LOS).Results: Among the 2088 eligible patients, 1,563 (74.9%) were in the methylxanthine treatment group. Patients treated with methylxanthines had more severe respiratory symptoms and worse lung function than those in the control group. Doxophylline was the most commonly used methylxanthine in both secondary and tertiary hospitals. After PS matching, 966 patients were equally divided into two groups. The LOS of patients in the two groups was similar [median: 8 days, interquartile range (IQR): 7–11 days, p = 0.730]. Patients in the treatment group (median: 8, IQR: 4–12) had a more significant decrease in the COPD Assessment Test score from admission to discharge than those in the control group (median: 6, IQR: 2–10, p < 0.001). Among all matched patients, the LOS was not significantly associated with methylxanthine treatment [adjusted hazard ratio (HR): 1.02, 95% confidence intervals (CIs): 0.89–1.16]. However, in the subgroup analysis, methylxanthines were significantly associated with a short LOS in patients with blood eosinophil count >4% (adjusted HR: 1.56, 95% CIs: 1.12–2.17).Conclusion: This study revealed that methylxanthines, especially doxophylline, are widely used in China. Methylxanthines were effective in improving symptoms in AECOPD patients. Higher blood eosinophil count may be associated with a better efficacy of methylxanthine treatment.

Background and Objective: Elevated eosinophils in chronic obstructive pulmonary disease (COPD) are recognized as a biomarker to guide inhaled corticosteroids use, but the value of blood eosinophils in hospitalized exacerbations of COPD remains controversial. This study aimed to evaluate the accuracy of eosinophils in predicting clinical outcomes in acute exacerbation of COPD (AECOPD).Methods: We analyzed data from the acute exacerbation of chronic obstructive pulmonary disease inpatient registry (ACURE) study, which is an ongoing nationwide multicenter, observational real-world study in patients admitted for AECOPD. Data collected between January 2018 and December 2019 in 163 centers were first reviewed. The eligible patients were divided into eosinophilic and non-eosinophilic groups, according to blood eosinophil with 2% of the total leukocyte count as the threshold. Propensity score (PS) matching was performed to adjust for confounders.Results: A total of 1,566 patients (median age: 69 years; 80.3% male) were included and 42.7% had an eosinophilic AECOPD. Eosinophil count

Background: The evidence for real-world antibiotic use in treating acute exacerbations of chronic obstructive pulmonary disease (AECOPD) is insufficient. This study aimed to investigate real-world antibiotic use in the management of AECOPD in China.Methods: All hospitalized AECOPD patients from the acute exacerbation of chronic obstructive pulmonary disease inpatient registry (ACURE) study conducted at 163 sites between January 2018 and December 2019 were screened according to the eligible criteria. The eligible study population was divided into secondary and tertiary hospital groups. Patients’ baseline characteristics, antibiotic use, and bacterial pathogen characteristics were retrieved and analyzed using SPSS 23.0.Results: A total of 1663 patients were included in the study, including 194 patients from secondary hospitals and 1469 patients from tertiary hospitals. Among the 1663 AECOPD patients enrolled, 1434 (86.2%) received antibiotic treatment, comprising approximately 85.6% and 86.3% of patients in the secondary and tertiary hospital groups, respectively. The median antibiotic therapy duration was 9.0 (interquartile range [IQR]: 7.0 - 11.0)°days. Regarding the routes of antibiotic use, 1400 (97.6%) patients received intravenous antibiotics, 18 (1.3%) patients received oral antibiotics, 15 (1.0%) patients received both intravenous and oral antibiotics, and one (0.1%) patient received both oral and nebulized antibiotic treatment. In addition, cephalosporin, penicillin, and quinolone were the most commonly prescribed antibiotics (43.6%, 37.0%, and 34.2%, respectively). In total, 990 (56.5%) patients underwent pathogen examinations; the proportion of patients receiving pathogen examinations in the second hospital group was significantly lower than that in the tertiary hospital group (46.4% vs 61.3%, p < 0.001).Conclusion: This study demonstrates that an antibiotic overuse may exist in the treatment of AECOPD in China. Measures should be taken to prevent the overuse of antibiotics and potential antimicrobial resistance (AMR) in Chinese AECOPD patients.

BackgroundCoronavirus disease 2019 (COVID-19) has developed into a worldwide pandemic. This study aimed to retrospectively describe the use of corticosteroids in treating COVID-19.MethodsFor this multicenter retrospective study, medical records from 488 symptomatic COVID-19 patients were reviewed. Patients were divided into severe and nonsevere groups. Baseline characteristics, signs and symptoms, laboratory findings, treatments, and disease outcomes were compared. Specific data for corticosteroid treatment were further analyzed.ResultsFour hundred fifty COVID-19 patients were included in this study, including 82 severe patients and 368 nonsevere cases. Out of the 450 patients, 126 (28.0%) received corticosteroid treatment. In the 126 patients treated with corticosteroids, the median daily dose of corticosteroid therapy was 56.6 [interquartile range (IQR): 40.0–78.4] mg and median corticosteroid therapy duration was 5.0 (IQR: 3.0–7.0) days. Among nonsevere cases, patients treated with corticosteroids were significantly older in comparison with patients who did not receive corticosteroid treatment (p0.05).ConclusionOur study indicates that corticosteroids are regarded as one of treatments in the general clinical practice of COVID-19. However, corticosteroid use may be accompanied by increased use of antibiotics, longer hospitalization, and prolonged viral shedding.

Objective To evaluate the feasibility of mean platelet volume (MPV) as a biomarker for chronic obstructive pulmonary disease (COPD). Methods A systematic search for studies published up to March 2019 was performed in the PubMed and Web of Science databases. Three independent investigators screened the titles and abstracts of including studies according to eligibility criteria. The Newcastle–Ottawa Scale was used to assess the quality of eligible studies, and statistical analyses were performed using Review Manager version 5.3. Results A total of eight studies with 1230 COPD patients and 443 healthy controls were included in our meta-analysis. No significant differences in MPV level were identified in pairwise comparisons of the acute exacerbations of COPD (AECOPD), stable COPD, and control groups. Furthermore, no significant correlation was observed between MPV level and systemic inflammatory biomarkers. Conclusions MPV does not appear to represent a suitable biomarker of disease phase or inflammatory burden in COPD. However, future large-scale studies should be performed to further investigate the relationship between MPV and COPD.

Biosafety hazards can trigger a host immune response after infection, invasion, or contact with the host. Whether infection with a microorganism results in disease or biosafety concerns depends to a large extent on the immune status of the population. Therefore, it is essential to investigate the immunological characteristics of the host and the mechanisms of biological threats and agents to protect the host more effectively. Emerging and re-emerging infectious diseases, such as the current coronavirus disease 2019 (COVID-19) pandemic, have raised concerns regarding both biosafety and immunology worldwide. Interdisciplinary studies involved in biosafety and immunology are relevant in many fields, including the development of vaccines and other immune interventions such as monoclonal antibodies and T-cells, herd immunity (or population-level barrier immunity), immunopathology, and multispecies immunity, i.e., animals and even plants. Meanwhile, advances in immunological science and technology are occurring rapidly, resulting in important research achievements that may contribute to the recognition of emerging biosafety hazards, as well as early warning, prevention, and defense systems. This review provides an overview of the interdisciplinary field of biosafety and immunology. Close collaboration and innovative application of immunology in the field of biosafety is becoming essential for human health.

Abstract Background Palatal expansion is a common way of treating maxillary transverse deficiency. Under mechanical force, the midpalatal suture is expanded, causing local immune responses. This study aimed to determine whether macrophages participate in bone remodeling of the midpalatal suture during palatal expansion and the effects on bone remodeling. Methods Palatal expansion model and macrophage depletion model were established. Micro-CT, histological staining, and immunohistochemical staining were used to investigate the changes in the number and phenotype of macrophages during palatal expansion as well as the effects on bone remodeling of the midpalatal suture. Additionally, the effect of mechanically induced M2 macrophages on palatal osteoblasts was also elucidated in vitro. Results The number of macrophages increased significantly and polarized toward M2 phenotype with the increase of the expansion time, which was consistent with the trend of bone remodeling. After macrophage depletion, the function of osteoblasts and bone formation at the midpalatal suture were impaired during palatal expansion. In vitro, conditioned medium derived from M2 macrophages facilitated osteogenic differentiation of osteoblasts and decreased the RANKL/OPG ratio. Conclusions Macrophages through polarizing toward M2 phenotype participated in midpalatal suture bone remodeling during palatal expansion, which may provide a new idea for promoting bone remodeling from the perspective of regulating macrophage polarization.

Abstract Background The mechanotransduction mechanisms by which cells regulate tissue remodeling are not fully deciphered. Circular RNAs (circRNAs) are crucial to various physiological processes, including cell cycle, differentiation, and polarization. However, the effects of mechanical force on circRNAs and the role of circRNAs in the mechanobiology of differentiation and remodeling in stretched periodontal ligament stem cells (PDLSCs) remain unclear. This article aims to explore the osteogenic function of mechanically sensitive circular RNA protein kinase D3 (circPRKD3) and elucidate its underlying mechanotransduction mechanism. Materials and methods PDLSCs were elongated with 8% stretch at 0.5 Hz for 24 h using the Flexcell® FX-6000™ Tension System. CircPRKD3 was knockdown or overexpressed with lentiviral constructs or plasmids. The downstream molecules of circPRKD3 were predicted by bioinformatics analysis. The osteogenic effect of related molecules was evaluated by quantitative real-time PCR (qRT‐PCR) and western blot. Results Mechanical force enhanced the osteogenesis of PDLSCs and increased the expression of circPRKD3. Knockdown of circPRKD3 hindered PDLSCs from osteogenesis under mechanical force, while overexpression of circPRKD3 promoted the early osteogenesis process of PDLSCs. With bioinformatics analysis and multiple software predictions, we identified hsa-miR-6783-3p could act as the sponge of circPRKD3 to indirectly regulate osteogenic differentiation of mechanically stimulated PDLSCs. Conclusions Our results first suggested that both circPRKD3 and hsa-miR-6783-3p could enhance osteogenesis of stretched PDLSCs. Furthermore, hsa-miR-6783-3p could sponge circPRKD3 to indirectly regulate RUNX2 during the periodontal tissue remodeling process in orthodontic treatment.

Global aging is a tendency of the world, as is the increasing prevalence of diabetes, and the two are closely linked. In our early research, Enteromorpha prolifera oligosaccharide (EPO) possesses the excellent ability of anti-oxidative, anti-inflammatory, and anti-diabetic. We aim to further explore the deeper mechanism of how EPO delays aging and regulates glycometabolism. EPO effectively impacts crotonylation procession to enhance glucose metabolism and reduce cell senescence in aging diabetic rats. Crotonylation modification of XPO1 influences the expression of critical genes, including p53, CDK1, and CCNB1, which affect cell cycle regulation and aging. Additionally, EPO improves glucose metabolism by inhibiting the crotonylation modification of HSPA8-K126 and activating the AKT pathway. EPO promotes crotonylation of histones in intestinal cells, influencing the aging process by increasing the butyric acid-producing bacteria Ruminococcaceae. The observed enhancement in pyrimidine metabolism underscores EPO’s potential role in regulating intestinal health, presenting a promising avenue for delaying aging. In summary, our findings affirm EPO as a naturally bioactive ingredient with significant potential for anti-aging and antidiabetic interventions.

Abstract The geographical variation and domestication of tree species are an important part of the theory of forest introduction, and the tracing of the germplasm is the theoretical basis for the establishment of high‐quality plantations. Chinese pine (Pinus tabuliformis Carr.) is an important native timber tree species widely distributed in northern China, but it is unclear exactly where germplasm of the main Chinese pine plantation populations originated. Here, using two mtDNA markers, we analyzed 796 individuals representing 35 populations (matR marker), and 873 individuals representing 38 populations (nad5‐1 marker) of the major natural and artificial populations in northern China, respectively (Shanxi, Hebei and Liaoning provinces). The results confirmed that the core position of natural SX* populations (“*” means natural population) in the Chinese pine populations of northern China, the genetic diversity of HB and LN plantations was higher than that of natural SX* populations, and there was a large difference in genetic background within the groups of SX* and LN, HB showed the opposite. More importantly, we completed the “point by point” tracing of the HB and LN plantings. The results indicated that almost all HB populations originated from SX* (GDS*, ZTS*, GCS*, and THS*), which resulted in homogeneity of the genetic background of HB populations. Most of germplasm of the LN plantations originated from LN* (ZJS* and WF*), and the other part originated from GDS* (SX*), resulting in the large differences in the genetic background within the LN group. Our results provided a reliable theoretical basis for the scientific allocation, management, and utilization of Chinese pine populations in northern China, and for promoting the high‐quality establishment of Chinese pine plantations.

Older adults have a high prevalence of falls due to a decline in physiological functions and various chronic diseases. This study aimed to investigate the prevalence of and risk factors for falls among older individuals in the Chinese Longitudinal Healthy Longevity Survey (CLHLS). We collected information from 9737 older individuals (average age=84.26 years) from the CLHLS and used binary logistic regression analysis to explore the independent risk factors and protective factors for falls. The logistic regression analysis results are reported as adjusted odds ratios (aORs) and 95% confidence intervals (95%CIs). The prevalence of falls among older adults in China was 21.6%, with women (24.6%) having a higher prevalence than men (18.1%). Logistic regression analysis revealed that never (or rarely) eating fresh fruit, difficulty with hearing, cataracts, and arthritis were the common independent risk factors for falls in older Chinese men and women. Among men, age ≥80 years (aOR=1.86), never doing housework (aOR=1.36), and dyslipidemia (aOR=1.47) were risk factors, while eating milk products once a week was a protective factor. Alcohol consumption (aOR=1.40), physical labor (aOR=1.28), and heart disease (aOR=1.21) were risk factors for falls in women, while a daily sleep duration of 6-12 h and garlic consumption once a week were protective factors. The prevalence of falls among older adults in China is 21.6% and is greater in women than in men. These risk and protective factors can be used to formulate reasonable recommendations for living habits, diet, and chronic disease control strategies.

A growing number of viruses pose significant threats to human health, impact agricultural production and compromise food safety. Minimizing the impact of viral infections demands for effective technologies that can deliver sensitive viral detection under various settings. Functional nucleic acids (FNAs) – natural or synthetic nucleic acid molecules with catalytic and/or binding properties – have been increasingly explored as key components for setting up diagnostic tests for viral detection. FNA-based viral biosensors offer distinct advantages, such as the ability to achieve sensitive viral detection in complex biological samples, ease of use, scalability, and cost-effectiveness. This mini-review will be dedicated to appraising progress made in recent years in FNA-based biosensors for diagnosing diverse human and animal viruses. We will first describe virus structures and potential biomarkers that can be utilized as the targets for FNA probe engineering. This is followed by reviewing the latest advances in two classes of FNAs - DNAzyme and DNA aptamers, with focuses on DNAzyme- and DNA aptamer-based biosensors that employ diverse signal transduction mechanisms to achieve sensitive viral detections. Finally, we will discuss current challenges in the field and suggest future research directions that can address these challenges.

Abstract Background The preference for glucose oxidative mode has crucial impacts on various physiological activities, including determining stem cell fate. External mechanical factors can play a decisive role in regulating critical metabolic enzymes and pathways of stem cells. Periodontal ligament stem cells (PDLSCs) are momentous effector cells that transform mechanical force into biological signals during the reconstruction of alveolar bone. However, mechanical stimuli-induced alteration of oxidative characteristics in PDLSCs and the underlying mechanisms have not been fully elucidated. Methods Herein, we examined the expression of LDH and COX4 by qRT-PCR, western blot, immunohistochemistry and immunofluorescence. We detected metabolites of lactic acid and reactive oxygen species for functional tests. We used tetramethylrhodamine methyl ester (TMRM) staining and a transmission electron microscope to clarify the mitochondrial status. After using western blot and immunofluorescence to clarify the change of DRP1, we further examined MFF, PINK1, and PARKIN by western blot. We used cyclosporin A (CsA) to confirm the regulation of mitophagy and ceased the stretching as a rescue experiment. Results Herein, we ascertained that mechanical force could increase the level of LDH and decrease the expression of COX4 in PDLSCs. Simultaneously, the yield of reactive oxygen species (ROS) in PDLSC reduced after stretching, while lactate acid augmented significantly. Furthermore, mitochondrial function in PDLSCs was negatively affected by impaired mitochondrial membrane potential (MMP) under mechanical force, and the augment of mitochondrial fission further induced PRKN-dependent mitophagy, which was confirmed by the rescue experiments via blocking mitophagy. As a reversible physiological stimulation, the anaerobic preference of PDLSCs altered by mechanical force could restore after the cessation of force stimulation. Conclusions Altogether, our study demonstrates that PDLSCs under mechanical force preferred anaerobic oxidation induced by the affected mitochondrial dynamics, especially mitophagy. Our findings support an association between mechanical stimulation and the oxidative profile of stem cells, which may shed light on the mechanical guidance of stem cell maintenance and commitment, and lay a molecular foundation for periodontal tissue regeneration. Graphical Abstract

Background: This study aimed to evaluate the C-reactive protein to serum albumin ratio (CAR) to predict prognosis in COPD patients with acute exacerbations (AECOPD). Methods: A retrospective cohort study of AECOPD patients, admitted to a large tertiary hospital between January 2017 and June 2018, was conducted. Univariate and multivariate logistic regression models were built to assess the relationship between variables and different clinical outcomes in one-year follow up. In addition, Kaplan-Meier method was used to estimate the relationship between CAR and the time to first rehospitalization due to acute exacerbation of COPD. Results: A total of 167 AECOPD patients were included in this study, with an overall age of 68.5 ± 9.4 years. Both univariate and multivariate logistic regression analysis demonstrated that CAR at admission was significantly associated with rehospitalization and frequent exacerbations in COPD patients (p < 0.05). Kaplan-Meier curve showed that the rehospitalization event-free rate was significantly higher in the low CAR group than the high CAR group (p < 0.01). Conclusions: As an easily available parameter, CAR at admission can be an independent predictor for rehospitalization and frequent exacerbations in COPD patients with acute exacerbations. [ABSTRACT FROM AUTHOR]

Single-stage compression loading experiments were carried out on concrete specimens of various strengths to explore the characteristic parameters of the acoustic emission signal and its damage evolution law in the concrete damage process. These specimens were monitored in real time with acoustic emission and DIC instruments during the loading process, and internal pores and slices were scanned with CT scanning instruments after compression. The acoustic emission phenomenon was expressed using the energy activity coefficient, and the law relating to the phenomenon was summarized. The results show that when the peak and mean values in the first adjacent time domain grow rapidly, the specimen produces a large crack and enters the stage of rapid crack development, which can be taken as an indication of the impending damage to the specimen. The energy activity coefficient reflects the damage development intensity as follows: the smaller the energy activity coefficient, the more the cracks developed; the faster the speed, the larger the deformation. With an increase in the load level, the energy activity coefficient gradually tends to stabilize, and the specimen enters the stage of rapid crack development. However, when the energy activity coefficient suddenly increases again, the specimen is destabilized and destroyed. Therefore, the energy activity coefficient responds to the degree of congenital defects in the specimen. As the load increases, the energy activity coefficient is more stable, and the defects are smaller; in contrast, the energy activity coefficient drastically oscillating indicates that the material is very defective.

High-quality, chromosome-scale genomes are essential for genomic analyses. Analyses, including 3D genomics, epigenetics, and comparative genomics rely on a high-quality genome assembly, which is often accomplished with the assistance of Hi-C data. Curation of genomes reveal that current Hi-C-assisted scaffolding algorithms either generate ordering and orientation errors or fail to assemble high-quality chromosome-level scaffolds. Here, we offer the software Puzzle Hi-C, which uses Hi-C reads to accurately assign contigs or scaffolds to chromosomes. Puzzle Hi-C uses the triangle region instead of the square region to count interactions in a Hi-C heatmap. This strategy dramatically diminishes scaffolding interference caused by long-range interactions. This software also introduces a dynamic, triangle window strategy during assembly. Initially small, the window expands with interactions to produce more effective clustering. Puzzle Hi-C outperforms available scaffolding tools.

Li et al. evaluate the immunogenicity and safety of the CoronaVac inactivated COVID-19 vaccine in elderly patients with underlying medical conditions in China. Most patients show comparable neutralizing antibody and SARS-CoV-2-specific T cell responses to healthy controls, and no serious adverse effects are seen.

As a multifunctional tree species, Cyclocarya paliurus leaves are rich in bioactive substances with precious healthy values. To meet the huge requirement of C. paliurus leaf production, sites with some environmental stresses would be potential land for developing its plantations due to the limitation of land resources in China. Nitric oxide (NO) and hydrogen sulfide (H2S) are common gas messengers used to alleviate abiotic stress damage, whereas the mechanism of these messengers in regulating salt resistance of C. paliurus still remains unclear. We performed a comprehensive study to reveal the physiological response and molecular regulatory mechanism of C. paliurus seedlings to the application of exogenous NO and H2S under salt stress. The results showed that the application of sodium hydrosulfide (NaHS) and sodium nitroprusside (SNP) not only maintained the photosynthetic capacity and reduced the loss of leaf biomass, but also promoted endogenous NO synthesis and reduced oxidative damage by activating antioxidant enzyme activity and increasing the content of soluble protein and flavonoids. Moreover, transcriptome and metabolome analysis indicated the expression of genes encoding phenylalanine ammonia lyase (PAL), cytochromeP450 (CYP), chalcone synthase (CHS), dihydroflavonol 4-reductase (DFR) and flavonol synthase (FLS) in flavonoid biosynthesis pathway was all up-regulated by the application of NO and H2S. Meanwhile, 15 transcriptional factors (TFs) such as WRKY, ERF, bHLH and HY5 induced by NO were found to regulated the activities of several key enzymes in flavonoid biosynthesis pathway under salt stress, via the constructed co-expression network. Our findings revealed the underlying mechanism of NO and H2S to alleviate salt stress and regulate flavonoid biosynthesis, which provides a theoretical basis for establishing C. paliurus plantations in the salt stress areas.

In light of recent advancements in synchrotron radiation technology and nano-technology, there has been a marked increase in the need for ultra-precision nano-positioning mechanisms. This paper presents a method that integrates physical models with multi-objective optimization for developing an optical angle nano-positioning mechanism. We begin by examining the actual motion law of the mechanism, based on kinematic principles. The outcomes from this kinematic analysis facilitate a static analysis of the flexible hinge, identified as a critical component of the mechanism. Subsequently, we establish a dynamic model for the entire mechanism. By employing the physical model as a base and combining it with the optimization algorithm, we identify the optimal design parameters for the mechanism. The design achieves a resolution of 50 nrad and meets the specified requirements. The first-order inherent frequency of the mechanism is approximately 43.75 Hz. There is a discrepancy of 2.63% from the finite element modal analysis results and a 3.33% difference from the theoretical analysis results, validating the reliability of the design method proposed in this study.

Objectives: Neutrophil gelatinase-associated lipocalin (NGAL) in synovial fluid (SF) may have potential diagnostic value for prosthetic joint infection (PJI). This study aimed to study (i) the diagnostic performance of SF-NGAL levels for diagnosing PJI and (ii) the impact of previous antibiotic use on the SF-NGAL levels. Methods: Consecutive patients who needed hip or knee revision surgery were included prospectively from January 2017 to September 2018. The patients were divided into the PJI group and the aseptic failure group. An enzyme-linked immunosorbent assay was used to determine the SF-NGAL level. Results: A total of 50 of 78 included patients were diagnosed with PJI. The median SF-NGAL level was 3633 ng/ml (interquartile range [IQR], 1332-10,737) in the PJI group and 26.8 ng/ml (IQR, 12.4-52.5) in the aseptic failure group (P

As a highly valued and multiple function tree species, the leaves of Cyclocarya paliurus are enriched in diverse bioactive substances with healthy function. To meet the requirement for its leaf production and medical use, the land with salt stress would be a potential resource for developing C. paliurus plantations due to the limitation of land resources in China. The basic helix-loop-helix (bHLH) transcription factor protein family, the second largest protein family in plants, has been found to play essential roles in the response to multiple abiotic stresses, especially salt stress. However, the bHLH gene family in C.paliurus has not been investigated. In this study, 159 CpbHLH genes were successfully identified from the whole-genome sequence data, and were classified into 26 subfamilies. Meanwhile, the 159 members were also analyzed from the aspects of protein sequences alignment, evolution, motif prediction, promoter cis-acting elements analysis and DNA binding ability. Based on transcriptome profiling under a hydroponic experiment with four salt concentrations (0%, 0.15%, 0.3%, and 0.45% NaCl), 9 significantly up- or down-regulated genes were screened, while 3 genes associated with salt response were selected in term of the GO annotation results. Totally 12 candidate genes were selected in response to salt stress. Moreover, based on expression analysis of the 12 candidate genes sampled from a pot experiment with three salt concentrations (0%, 0.2% and 0.4% NaCl), CpbHLH36/68/146 were further verified to be involved in the regulation of salt tolerance genes, which is also confirmed by protein interaction network analysis. This study was the first analysis of the transcription factor family at the genome-wide level of C. paliurus, and our findings would not only provide insight into the function of the CpbHLH gene family members involved in salt stress but also drive progress in genetic improvement for the salt tolerance of C. paliurus.

Vegetative propagation is an important method of reproduction and rejuvenation in forestry. The growth and development of asexually propagated trees are influenced by the age and position of the propagule on the plant, effects referred to as cyclophysis and topophysis, respectively. Due to the long lifespans and large body sizes of woody trees, the selection of propagules is critically important. Here, we used three vegetative propagation methods (shoot cutting, root sprouting, and root cutting) to study the effect of different regeneration methods on juvenility of the resulting black locust plants, with seed-derived seedlings used as a control. Most characteristics of plantlets generated by root-sprouting were similar to those of seed-derived seedlings, including leaf traits and leaf anatomical structure. However, there were significant differences between the plantlets derived from shoot-cuttings and seedlings from seeds. Furthermore, the data showed that some of these age-related small RNAs and genes differed in expression among propagation methods and between plantlets/seedlings and mature trees. These age-related small RNAs, genes, and transcription factors may be used as molecular markers of juvenility and phase transitions in black locust. Our results provide useful information for the optimal propagation of woody trees and for further research into the mechanisms of root regeneration.

Many treatments have been used for glucose metabolism diseases such as type 2 diabetes, and all of those treatments have several advantages as well as limitations. This review introduces a 3D co-culture intestinal organoid system developed from stem cells, which has the special function of simulating human tissues. Recent studies have revealed that the gut is an important site for exploring the interactions among glucose metabolism, gut microbial metabolism, and gut microbiota. Therefore, 3D intestinal organoid systems can be used to imitate the congenital errors of human gut development, drug screening, food transportation and toxicity analysis. The intestinal organoid system construction methods and their progress as compared with traditional 2D culture methods have also been summarised in the manuscript. This paper discusses the research progress in terms of intestinal organoids applicable to glucose metabolism and provides new ideas for developing anti-diabetic drugs with high efficiency and low toxicity.

Summary: Background: More effective vaccine candidates against variants of concern as a booster dose are needed in people primed with two-dose inactivated COVID-19 vaccines. Methods: This randomised, double-blinded, investigator-initiated phase 2 trial aims to evaluate immunogenicity, durability, and safety of an mRNA vaccine candidate (RQ3013) and three other platform vaccines (an adenovirus-vectored vaccine candidate [ChAdTS-S], a recombinant protein vaccine candidate [ZR202-CoV], and an inactivated vaccine [CoronaVac]) as a booster. 250 eligible volunteers, who had received a prime two-dose CoronaVac (3 to 5 weeks apart) vaccination 100-270 days before, were randomly assigned in a 1:1:1:1:1 ratio to receive a third dose of RQ3013 (30 μg mRNA per 0.15 mL), ChAdTS-S (5×1010 viral particles per 0.5 mL), ZR202-CoV (25 μg prefusion-stabilized Spike ectodomain trimer per 0.5 mL), CoronaVac (3 μg inactivated CN02 strain of SARS-CoV-2 per 0.5 mL) or placebo (0.5 mL of 0.9% sodium chloride solution) via intramuscular injection into the upper arm at a single clinical site in Kunming, China. Participants, investigators, and immunogenicity laboratory were masked to group assignment. The primary immunogenicity outcomes were geometric mean titres (GMTs) of neutralising antibodies against live SARS-CoV-2 (wild-type, delta and omicron) virus at day 0 (before vaccination), day 7, day 14 and day 28 after vaccination, as analysed in a modified intention-to-treat (mITT) population (all participants who completed their booster doses and had at least one post-dose immunogenicity data). Secondary outcomes include T cell responses against the wild-type and omicron SARS-CoV-2 Spike protein. The primary safety outcome was incidence of adverse events within 14 days after the booster vaccination. This trial is registered with ChiCTR.org.cn, ChiCTR2200057758. Findings: Between January 1, 2022, and February 28, 2022, 235 eligible participants were enrolled and vaccinated, and the primary analysis included 234 participants. At baseline, neutralising antibodies against wild-type virus, the delta, or omicron variants were low or undetectable in all groups. After the booster vaccination, GMTs of neutralising antibodies ranged from 75.4 (95% confidence interval [CI] 61.4-92.5) in CoronaVac to 950.1 (95% CI 785.4-1149.3) in RQ3013 against live wild-type SARS-CoV-2, and from 8.1 (95% CI: 6.1-10.7) in CoronaVac to 247.0 (95% CI 194.1-314.3) in RQ3013 against the omicron variant at day 14. Immunogenicities of all heterologous regimens were superior to that of homologous regimen in neutralisation against all tested SARS-CoV-2 strains, with RQ3013 showing the highest geometric mean ratios (GMRs) of 12.6, 14.7, and 31.3 against the wild-type, the delta variant and the omicron variant compared to CoronaVac at day 14 post-vaccination, respectively. Durability analysis at day 90 showed that >90% of participants in RQ3013 and ZR202-CoV were seropositive for the omicron variant while ZR202-CoV with adjuvants containing CpG showed a slightly better durability than RQ3013. T cell responses specific to the omicron variant were similar to that of the wild-type, with RQ3013 showing the highest boosting effect. Any solicited injection site or systemic adverse events reported within 14 days after vaccination were most commonly observed in RQ3013 (47/47, 100%), followed by ZR202-CoV (46/47, 97.9%) and ChAdTS-S (43/48, 89.6%), and then CoronaVac (37/46, 80.4%) and placebo (21/47, 44.7%). More than 90% of the adverse events were grade 1 (mild) or 2 (moderate) with a typical resolution time of 3 days. No grade 4 adverse events or serious adverse events were reported by study vaccines. Interpretation: Although all study vaccines boosted neutralising antibodies with no safety concerns, RQ3013 showed much stronger cross-neutralisation and cellular responses, adding more effective vaccine candidates against the omicron variant. Funding: Yunnan Provincial Science and Technology Department China (202102AA100051 and 202003AC100010), the Double First-class University funding to Yunnan University, National Natural Science Foundation of China (81960116, 82060368 and 82170711), Yunnan Natural Science Foundation (202001AT070085), High-level Health Technical Personnel Project of Yunnan Province (H-2018102) and Spring City Plan: The High-level Talent Promotion and Training Project of Kunming.

Pancreatic cystic neoplasms (PCNs) are a group of heterogeneous diseases with distinct prognosis. Existing differential diagnosis methods require invasive biopsy or prolonged monitoring. We sought to develop an inexpensive, non-invasive differential diagnosis system for PCNs based on radiomics features and clinical characteristics for a higher total PCN screening rate. We retrospectively analyzed computed tomography images and clinical data from 129 patients with PCN, including 47 patients with intraductal papillary mucinous neoplasms (IPMNs), 49 patients with serous cystadenomas (SCNs), and 33 patients with mucinous cystic neoplasms (MCNs). Six clinical characteristics and 944 radiomics features were tested, and nine features were finally selected for model construction using DXScore algorithm. A five-fold cross-validation algorithm and a test group were applied to verify the results. In the five-fold cross-validation section, the AUC value of our model was 0.8687, and the total accuracy rate was 74.23%, wherein the accuracy rates of IPMNs, SCNs, and MCNs were 74.26%, 78.37%, and 68.00%, respectively. In the test group, the AUC value was 0.8462 and the total accuracy rate was 73.61%. In conclusion, our research constructed an end-to-end powerful PCN differential diagnosis system based on radiomics method, which could assist decision-making in clinical practice.

Abstract TEFM (transcription elongation factor of mitochondria) has been identified as a novel nuclear-encoded transcription elongation factor in the transcription of mitochondrial genome. Our bioinformatics analysis of TCGA data revealed an aberrant over-expression of TEFM in hepatocellular carcinoma (HCC). We analyzed its biological effects and clinical significance in this malignancy. TEFM expression was analyzed by quantitative real-time PCR, western blot, and immunohistochemistry analysis in HCC tissues and cell lines. The effects of TEFM on HCC cell growth and metastasis were determined by cell proliferation, colony formation, flow cytometric cell cycle and apoptosis, migration, and invasion assays. TEFM expression was significantly increased in HCC tissues mainly caused by down-regulation of miR-194-5p. Its increased expression is correlated with poor prognosis of HCC patients. TEFM promoted HCC growth and metastasis both in vitro and in vivo by promoting G1–S cell transition, epithelial-to-mesenchymal transition (EMT), and suppressing cell apoptosis. Mechanistically, TEFM exerts its tumor growth and metastasis promoting effects at least partly through increasing ROS production and subsequently by activation of ERK signaling. Our study suggests that TEFM functions as a vital oncogene in promoting growth and metastasis in HCC and may contribute to the targeted therapy of HCC.

Abstract Background Hepatolithiasis often leads to atrophy–hypertrophy complex due to bile duct obstruction, inflammation or infection in the affected liver segments and compensatory response in the normal segments. In severe bilateral diffuse cases, main liver can all be atrophic, leaving the caudate lobe to be extremely hypertrophic. Subtotal (segment II–VIII) hepatectomy can be an option in selected patients under such circumstances. Since rare cases have been reported, our study aims to highlight the preoperative evaluation and key points of this procedure. Case presentation Two patients with primary and secondary bilateral diffuse hepatolithiasis, respectively, were enrolled in this case series. The atrophy of the left and right liver with an exceeding hypertrophy of the caudate lobe were observed. Since the liver anatomy had completely been changed, contrast computed tomography, magnetic resonance imaging combined with 3D liver reconstruction were employed for comprehensive evaluation and pre-operational planning. The patients underwent standard subtotal (segment II–VIII) hepatectomy. During operation, the hepatoduodenal ligament around porta hepatis was dissected firstly to expose the hepatic artery, portal vein, bile duct and their branches successively. And then the vessels and bile duct to caudate lobe were preserved safely through cutting off the left and right hepatic artery, portal vein and bile duct at a safe point distal to the origin of the branches to caudate lobe. Operation time was 300 min and 360 min, respectively. Blood loss was 200 ml and 300 ml. No evidence of liver dysfunction, hepatolithiasis relapse or cholangitis was observed during the follow-up of 12 and 26 months. Conclusions Subtotal (segment II–VIII) hepatectomy may be one of several treatments possible in selected patients with compensatory caudate lobe hypertrophy caused by bilateral diffuse hepatolithiasis.

Objectives: Pathogen identification is crucial for the diagnosis and management of periprosthetic joint infection (PJI). Although culturing methods are the foundation of pathogen detection in PJI, false-negative results often occur. Oxford nanopore sequencing (ONS) is a promising alternative for detecting pathogens and providing information on their antimicrobial resistance (AMR) profiles, without culturing. Methods: To evaluate the capability of metagenomic ONS (mONS) in detecting pathogens from PJI samples, both metagenomic next-generation sequencing (mNGS) and mONS were performed in 15 osteoarticular samples from nine consecutive PJI patients according to the modified Musculoskeletal Infection Society (MSIS) criteria. The sequencing data generated from both platforms were then analyzed for pathogen identification and AMR detection using an in-house-developed bioinformatics pipeline. Results: Our results showed that mONS could be applied to detect the causative pathogen and characterize its AMR features in fresh PJI samples. By real-time sequencing and analysis, pathogen identification and AMR detection from the initiation of sequencing were accelerated. Conclusion: We showed proof of concept that mONS can function as a rapid, accurate tool in PJI diagnostic microbiology. Despite efforts to reduce host DNA, the high proportion of host DNA was still a limitation of this method that prevented full genome analysis.

Abstract Background Periodontal ligament stem cells (PDLSCs) have many applications in the field of cytotherapy, tissue engineering, and regenerative medicine. However, the effect of age on the biological and immunological characteristics of PDLSCs remains unclear. Methods In this study, we compared PDLSCs isolated from young and adult individuals. PDLSC proliferation was analyzed by Cell Counting Kit-8 (CCK-8) and 5-ethynyl-2′-deoxyuridine (EdU) staining, and apoptosis level was detected by Annexin V-PE/7-ADD staining. PDLSC osteogenic/adipogenic/chondrogenic differentiation potentials were assessed by alkaline phosphatase (ALP), Alizarin Red, Oil Red O, Alcian Blue staining, and related quantitative analysis. PDLSC immunosuppressive capacity was determined by EdU and Annexin V-PE/7-ADD staining. To explore its underlying mechanism, microarray, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR), and western blot analyses were performed to detect differentially expressed genes and proteins in PDLSCs. Results Our results demonstrated that with aging, the proliferation and osteogenic/adipogenic/chondrogenic differentiation potential of PDLSCs decreased, whereas apoptosis of PDLSCs increased. Moreover, the immunosuppressive ability of PDLSCs decreased with aging. Compared with PDLSCs from young subjects, analysis of mRNA expression revealed an upregulation of CCND3 and RC3H2, and a downregulation of Runx2, ALP, COL1A1, PPARγ2, CXCL12, FKBP1A, FKBP1B, NCSTN, P2RX7, PPP3CB, RIPK2, SLC11A1, and TP53 in those from adult individuals. Furthermore, protein expression levels of Runx2, ALP, COL1A1, and PPARγ2 in the adult group were decreased, whereas that of CCND3 increased. Conclusions Taken together, aging influences the biological and immunological characteristics of PDLSCs, and thus, it is more appropriate to utilize PDLSCs from young individuals for tissue regeneration, post-aging treatment, and allotransplantation.

Red-heart Chinese fir (Cunninghamia lanceolata) has the advantages of high density and attractive color, making it popular in the market. To date, most studies about stems of woody plants have only been reported at the cytological level because of few living cells. In this study, the xylem was successfully partitioned into three effective sampling areas: sapwood, transition zone, and heartwood. Secondary metabolites, cell survival, and differentially expressed genes in the three sampling areas were, respectively, investigated. First, we identified the phenylpropanoid and flavonoid pathways closely related to color. Based on the chemical structure of secondary metabolites in pathways, two notable directions had been found. Luteolin’s glycosylation products might be the key substances that regulated the color of heartwood in red-heart Chinese fir because of the 1,000-fold difference between red-heart and white-heart. We also found pinocembrin and pinobanksin in Chinese fir, which were rarely reported before. At the cytological level, we believed that the transition zone of red-heart Chinese fir was a critical region for color production because of the fewer living ray parenchyma cells. In addition, transcriptome and quantitative reverse transcription PCR (qRT-PCR) proved that genes regulating the entire phenylpropanoid pathway, upstream of the flavonoid pathway, and some glycosyltransferases were significantly upregulated in the transition zone of red-heart and then colored the heartwood by increasing metabolites. This is the first report on the color-related secondary metabolites regulated by differential genes in red-heart Chinese fir. This study will broaden our knowledge on the effects of metabolites on coloring woody plant xylems.

The preparation of novel antioxidant peptides from food raw materials is one of the research focuses, but there are fewer studies on the preparation of antioxidant peptides from walnut meal, a by-product of processing walnuts. This study analyzed the antioxidant properties and protective effects of walnut protein hydrolyzed by alkaline protease and trypsin on the oxidative stress of HT22 cells. The peptides were identified by UPLC-MS/MS, and the anti-oxidative peptides were screened based on virtual computer tools. The potential anti-oxidative stress mechanism of the walnut polypeptide on HT22 cells was explored by molecular docking. The results revealed that walnut protein hydrolysates (WPH) with molecular weights of less than 1 kDa had good antioxidant properties and inhibited oxidative damage of HT22 cells by regulating the levels of reactive oxygen species (ROS) and antioxidant enzyme catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px). Six of the ninety identified new peptides showed good solubility, non-toxicity, and bioactivity. The molecular docking results showed that the six peptides could dock with Keap1 successfully, and EYWNR and FQLPR (single-letter forms of peptide writing) could interact with the binding site of Nrf2 in the Keap1-Kelch structural domain through hydrogen bonds with strong binding forces. The results of this study provided important information on the antioxidant molecular mechanism of the walnut polypeptide and provided a basis for further development of walnut antioxidant polypeptide products.

Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in humans. A well-known challenge in the development of a live attenuated RSV vaccine is that interferon (IFN)-mediated antiviral responses are strongly suppressed by RSV nonstructural proteins which, in turn, dampens the subsequent adaptive immune responses. Here, we discovered a novel strategy to enhance innate and adaptive immunity to RSV infection. Specifically, we found that recombinant RSVs deficient in viral RNA N6-methyladenosine (m6A) and RSV grown in m6A methyltransferase (METTL3)-knockdown cells induce higher expression of RIG-I, bind more efficiently to RIG-I, and enhance RIG-I ubiquitination and IRF3 phosphorylation compared to wild-type virion RNA, leading to enhanced type I IFN production. Importantly, these m6A-deficient RSV mutants also induce a stronger IFN response in vivo, are significantly attenuated, induce higher neutralizing antibody and T cell immune responses in mice and provide complete protection against RSV challenge in cotton rats. Collectively, our results demonstrate that inhibition of RSV RNA m6A methylation enhances innate immune responses which in turn promote adaptive immunity.

Orthodontic tooth movement (OTM) relies on mechanical force-induced bone remodeling. As a metabolic intermediate of glycolysis, lactate has recently been discovered to participate in bone remodeling by serving as a signaling molecule. However, whether lactate could respond to mechanical stimulus during OTM, as well as whether lactate has an impact on the alveolar bone remodeling during orthodontics, remain to be further elucidated. In the current study, we observed physiologically elevated production of lactate along with increased osteogenic differentiation, proliferation, and migration of alveolar bone marrow mesenchymal cells (ABMMCs) under mechanical force. Inhibition of lactate, induced by cyclic mechanical stretch by GNE-140, remarkably suppressed the osteogenic differentiation, proliferation, and migration, yet enhanced apoptosis of ABMMCs. Mechanistically, these regulatory effects of lactate were mediated by histone lactylation. Taken together, our results suggest that force-induced lactate is involved in controlling bone remodeling-related cellular activities in ABMMCs and plays a vital role in the alveolar bone remodeling during OTM. Our findings indicate that lactate might be a critical modulator for alveolar bone remodeling during OTM, providing a novel therapeutic target for the purpose of more effectively controlling tooth movement and improving the stability of orthodontic results.

Abstract Epitranscriptome profiling using MeRIP-seq is a powerful technique for in vivo functional studies of reversible RNA modifications. We develop RADAR, a comprehensive analytical tool for detecting differentially methylated loci in MeRIP-seq data. RADAR enables accurate identification of altered methylation sites by accommodating variability of pre-immunoprecipitation expression level and post-immunoprecipitation count using different strategies. In addition, it is compatible with complex study design when covariates need to be incorporated in the analysis. Through simulation and real dataset analyses, we show that RADAR leads to more accurate and reproducible differential methylation analysis results than alternatives, which is available at https://github.com/scottzijiezhang/RADAR.

Here, Xue et al. identify N 6-methyladenosine (m6A) modification sites in RNAs of respiratory syncytial virus (RSV) and show that these sites, particularly sites in the transcript encoding for the viral glycoprotein, affect virus replication in primary human cells and cotton rats.

Objectives The effect of age on the response of peripheral blood mononuclear cells (PBMCs) to immunosuppression induced by human periodontal ligament stem cells (hPDLSCs) is unclear. The identity of the cytokines most effective in inducing the PBMC immune response remains unknown. This study investigated the effects of age on immunophenotype, proliferation, activation, and cytokine secretion capacities of PBMCs following co-culture with hPDLSCs. Methods PBMCs were collected from younger (16–19 years) and older (45–55 years) donors, then co-cultured with confirmed hPDLSCs for various lengths of time. T lymphocyte proliferation and cell surface marker expression were analyzed by flow cytometry. Cytokine expression levels were measured by quantitative polymerase chain reaction assays and enzyme-linked immunosorbent assays. Results CD28 expression by T lymphocytes decreased with age, indicating reduced proliferation; CD95 expression increased with age, indicating enhanced apoptosis. Moreover, hPDLSCs inhibited T lymphocyte proliferation in both age groups; this inhibition was stronger in cells from older donors than in cells from younger donors. Age reduced the secretion of interleukin-2 and interferon-γ, whereas it increased the secretion of tumor necrosis factor-β by PBMCs cultured with hPDLSCs. Conclusions Aging may have a robust effect on the response of PBMCs towards hPDLSC-induced immunosuppression.

Abstract Background N 6-methyldeoxyadenosine (6mA or m6dA) was shown more than 40 years ago in simple eukaryotes. Recent studies revealed the presence of 6mA in more prevalent eukaryotes, even in vertebrates. However, functional characterizations have been limited. Results We use Tetrahymena thermophila as a model organism to examine the effects of 6mA on nucleosome positioning. Independent methods reveal the enrichment of 6mA near and after transcription start sites with a periodic pattern and anti-correlation relationship with the positions of nucleosomes. The distribution pattern can be recapitulated by in vitro nucleosome assembly on native Tetrahymena genomic DNA but not on DNA without 6mA. Model DNA containing artificially installed 6mA resists nucleosome assembling compared to unmodified DNA in vitro. Computational simulation indicates that 6mA increases dsDNA rigidity, which disfavors nucleosome wrapping. Knockout of a potential 6mA methyltransferase leads to a transcriptome-wide change of gene expression. Conclusions These findings uncover a mechanism by which DNA 6mA assists to shape the nucleosome positioning and potentially affects gene expression.

The crystal structure of the title compound, [Ni(C25H28N4)(C8H12)]·C4H8O or (MesNHC2Me)Ni(COD), which contains a bidentate N-heterocyclic carbene (NHC) ligand with mesityl aryl groups is reported. The complex at 100 K has monoclinic (P21/c) symmetry and a distorted tetrahedral geometry around the nickel center, with the cyclooctadiene ligand coordinated in a κ2,η2 fashion. The bidentate NHC ligand is not planar, with a C(carbene)—Ni—C(carbene) angle of 91.51 (12)°, resulting in the mesityl groups being on the same side of the cyclooctadiene (COD) ligand. One molecule of tetrahydrofuran (THF) is co-crystallized with the nickel complex and has positional disorder.