A review of Ribosome profiling and tools used in Ribo-seq data analysis.

Translational regulation plays the most critical role in gene expression. Ribosome profiling sequencing (Ribo-Seq) is one of the methods to study translation and its regulation. It is a high throughput technology based on deep sequencing, which targets ribosome protected mRNA fragments to produce a 'global snapshot' of translatome. There has been an annual increase in the number of publications incorporating Ribo-seq technology. Because of its importance, we used PubMed database to conduct a comprehensive bibliometric analysis on Ribo-seq. We identified 2744 published articles that utilized the term 'Ribo-seq' between 2009 and Jan 2024, and 684 articles that contained both Ribo-seq and RNA-seq terms. Based on keywords correlation analysis, we discovered that the primary focus of Ribo-seq articles lies in the areas of translation, transcriptome, and ribosome in the past few years and other topics such as single-cell ribo-seq and crispr within two years, reflecting current areas of interests in Ribo-seq research. The Ribo-seq data analysis applications were also explored and summarized, providing a guide for researchers to choose corresponding tools for different types of analysis. Overall, we highlighted the advances made by Ribo-seq technologies, and the possibilities of utilizing machine learning models to unravel information from multi-omics data. The integration of Ribo-seq with other omics data, such as RNA-seq, is essential to understand the gene expression in complex biological systems.

RUNX1-BMP2 promotes vasculogenic mimicry in laryngeal squamous cell carcinoma via activation of the PI3K-AKT signaling pathway.

BACKGROUND: Laryngeal squamous cell carcinoma (LSCC) is one of the most common malignant tumors of the head and neck. Vasculogenic mimicry (VM) is crucial for tumor growth and metastasis and refers to the formation of fluid channels by invasive tumor cells rather than endothelial cells. However, the regulatory mechanisms underlying VM during the malignant progression of LSCC remain largely unknown. METHODS: Gene expression and clinical data for LSCC were obtained from the TCGA and Gene GEO (GSE27020) databases. A risk prediction model associated with VM was established using LASSO and Cox regression analyses. Based on their risk scores, patients with LSCC were categorized into high- and low-risk groups. The disparities in immune infiltration, tumor mutational burden (TMB), and functional enrichment between these two groups were examined. The core genes in LSCC were identified using the machine learning (SVM-RFE) and WGCNA algorithms. Subsequently, the involvement of bone morphogenetic protein 2 (BMP2) in VM and metastasis was investigated both in vitro and in vivo. To elucidate the downstream signaling pathways regulated by BMP2, western blotting was performed. Additionally, ChIP experiments were employed to identify the key transcription factors responsible for modulating the expression of BMP2. RESULTS: We established a new precise prognostic model for LSCC related to VM based on three genes: BMP2, EPO, and AGPS. The ROC curves from both TCGA and GSE27020 validation cohorts demonstrated precision survival prediction capabilities, with the nomogram showing some net clinical benefit. Multiple algorithm analyses indicated BMP2 as a potential core gene. Further experiments suggested that BMP2 promotes VM and metastasis in LSCC. The malignant progression of LSCC is promoted by BMP2 via the activation of the PI3K-AKT signaling pathway, with the high expression of BMP2 in LSCC resulting from its transcriptional activation by runt-related transcription factor 1 (RUNX1). CONCLUSION: BMP2 predicts poor prognosis in LSCC, promotes LSCC VM and metastasis through the PI3K-AKT signaling pathway, and is transcriptionally regulated by RUNX1. BMP2 may be a novel, precise, diagnostic, and therapeutic biomarker of LSCC.

Gender associations between phthalate exposure and biomarkers of oxidative stress: A prospective cohort study.

Previous epidemiologic research has shown that phthalate exposure in pregnant women is related to adverse birth outcomes in a sex-specific manner. However, the biological mechanism of phthalate exposure that causes these birth outcomes remains poorly defined. In this research, we investigated the association between phthalate exposure and placental oxidative stress in a large population-based cohort study, aiming to initially explore the relationship between phthalate exposure and gene expression in placental oxidative stress in a sex-specific manner. Quantitative PCR was performed to measure the expression of placental inflammatory mRNAs (HO-1, HIF1α, and GRP78) in 2469 placentae. The multiple linear regression models were used to investigate the associations between mRNA and urinary phthalate monoesters. Phthalate metabolites monomethyl phthalate (MMP) and mono-n-butyl phthalate (MBP) were positively correlated with higher HIF1α expression in placentae of male fetuses (p < .05). Mono-benzyl phthalate (MBzP) increased the expression of HO-1, HIF1α, and GRP78 in placentae of male fetuses, and mono-(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP) up-regulated the expression of HIF1α and GRP78. Additionally, mono-(2-ethyl-5-oxohexyl) phthalate (MEOHP) was negatively correlated with HO-1, HIF1α, and GRP78 in placentae of female fetuses. Maternal phthalate exposure was associated with oxidative stress variations in placental tissues. The associations were closer in the placentas of male fetuses than in that of female ones. The placenta oxidative stress is worth further investigation as a potential mediator of maternal exposure-induced disease risk in children.

Z-scheme heterojunction photocatalyst formed by MOF-derived C-TiO2 and Bi2WO6 for enhancing degradation of oxytetracycline: Mechanistic insights and toxicity evaluation in the presence of a single active species.

In the work, Bi2WO6/C-TiO2 photocatalyst was successfully synthesized for the first time by loading narrow bandgap semiconductor Bi2WO6 on MOF-derived carboxyl modified TiO2. The phase structure, morphology, photoelectric properties, surface chemical states and photocatalytic performance of the prepared photocatalysts were systematically investigated using various characterization tools. The degradation efficiency of oxytetracycline by 6BT Z-scheme heterojunction photocatalyst under visible light could reach 93.6 % within 100 min, which was related to the high light harvesting and effective separation and transfer of photo-generated carriers. Furthermore, the effects of various environmental factors in actual wastewater were further investigated, and the results showed that 6BT exhibited good adaptability, durability and resistance to interference. Unlike most works, the degradation system with a different single active species were designed and constructed based on their formation mechanism. In addition, for the first time, a positive study was conducted on the priority attack sites, intermediate products, and degradation pathways for the photocatalytic degradation of oxytetracycline by a single active species through HPLC-MS and Fukui index calculations. The toxicity changes of intermediate products produced in three different single active species oxidation systems were evaluated using toxicity assessment software tools (T.E.S.T.), Escherichia coli growth experiments, and wheat growth experiments. Among them, the intermediate products formed through O2- oxidation had the lowest toxicity and the main active sites it attacked were the 20C, 38O, 18C, 41O, and 55O atoms with high f+ values in the oxytetracycline molecular structure. This work provided the insight into the role of each active species in the degradation of antibiotics and offered new ideas for the design and synthesis of efficient and eco-friendly photocatalysts.

Global, regional and national burden of retinopathy of prematurity among childhood and adolescent: a spatiotemporal analysis based on the Global Burden of Disease Study 2019.

BACKGROUND: This study aimed to provide a comprehensive assessment of burden estimates and the secular trend of vision loss due to retinopathy of prematurity (ROP) among people younger than 20 years, at the global, regional and national levels. METHODS: Data were obtained from the Global Burden of Disease Study 2019 database. The average annual percentage change (AAPC) was calculated to quantify the temporal trends in the measures of vision loss. RESULTS: In 2019, the global age-standardised rates (ASRs) of prevalence per 100 000 population was 86.4 for vision loss, specifically, 35 for moderate vision loss, 19.9 for severe vision loss, 31.6 for blindness due to ROP among people younger than 20 years. Moreover, the ASR of years lived with disability per 100 000 was 10.6 for vision loss, specifically, 1.1 for moderate vision loss, 3.6 for severe vision loss, 5.9 for blindness, respectively. From 1990 to 2019, the ASR of prevalence of blindness and vision loss due to ROP significantly increased, while its burden slightly decreased. Males showed higher ASR of prevalence than females in 2019, whereas females have larger increasing trend than males from 1990 to 2019. The global highest ASR of disease burden was observed in South Asia and Southern sub-Saharan Africa, as well as low sociodemographic index (SDI) regions in 2019. CONCLUSIONS: Globally, although the burden decreased, the prevalence of childhood and adulthood vision loss due to ROP continues to increase. Reasonable resource allocation and advanced intervention are recommended to prevent and control the vision loss due to ROP.

Distribution characteristics, risk assessment, and relevance with surrounding soil of heavy metals in coking solid wastes from coking plants in Shanxi, China.

Heavy metal concentrations represent important pollution evaluation indices, and it is necessary to assess the potential environmental and health risks from heavy metals associated with coking wastes from coking plants. In this study, coking sludge (CS), tar residue (TR), coke powder (CP), and sulfur paste (SP) from three coking plants (Plant A, Plant B, and Plant C) in central, western, and southern Shanxi Province and from soils surrounding Plant A were selected as the research objects, and the distributions of Cu, Ni, Pb, Zn, Mn, Cd, and Cr were determined. The results showed that Cd in the four solid wastes far exceeded the soil background value by a factor of 16~195, and the contents of Pb in TR (three plants) and CS (Plant C) exceeded the soil background values 19.70-, 23.57-, 14.46-, and 12.56-fold, respectively. Similarly, the concentrations of Cu, Ni, Pb, Zn, and Cd in soils were higher than the background values by factors of 31.18, 8.35, 34.79, 29.48, and 3.43, respectively. In addition, the Cu, Ni, Pb, and Cr in the four solid wastes and soils mainly existed in the residual state. As depth increased, the overall Ni, Pb, Mn, and Cd concentrations in soils increased. The high ecological risks associated with the four solid wastes were mainly due to the enrichment of Cd. Workers in coking plants face certain Cr health risks. This study provides theoretical support for the coking industry with respect to the treatment, disposal, and management of solid wastes.

Associations of 10 trace element levels in the whole blood with risk of three types of obesity in the elderly.

BACKGROUND: Currently, over 2 billion people worldwide suffer from obesity, which poses a serious health risk. More and more attention is being given to the effects of trace elements on obesity in recent years. Synergistic or antagonistic interactions among these elements can adversely or positively impact human health. However, epidemiological evidence on the relationship between trace element exposure levels and obesity has been inconclusive. METHODS: Baseline data of 994 participants from the Cohort of Elderly Health and Environment Controllable Factors were used in the present study. ICP-MS was used to measure the concentrations of 10 trace elements in the whole blood of the older population. Binary logistic regression, restricted cubic splines (RCS) models, and Bayesian kernel machine regression (BKMR) models were employed to assess single, nonlinear, and mixed relationships between 10 trace element levels and three types of obesity based on body mass index (BMI), waist circumference (WC), and body fat percentage (BFP) in the elderly. RESULTS: Based on BMI, WC and BFP, 51.8% of the included old population were defined as general overweight/obesity, 67.1% as abdominal obesity, and 36.2% as having slightly high/high BFP. After multivariable adjustment, compared with the lowest tertile, the highest tertile of blood selenium (Se) concentration was associated with an increased risk of all three types of obesity. Additionally, compared with the lowest tertile, higher tertiles of strontium (Sr) concentrations were associated with a lower risk of general overweight/obesity and having slightly high/high BFP, and the highest tertile of barium (Ba) was associated with a lower risk of having slightly high BFP, while higher tertiles of arsenic (As) concentrations were associated with an increased risk of having slightly high/high BFP, and the highest tertile of manganese (Mn) was associated with a higher risk of abdominal obesity. BKMR analyses showed a strong linear positive association between Se and three types of obesity. Higher blood levels of trace element mixture were associated with increased obesity risks in a dose-response pattern, with Se having the highest value of the posterior inclusion probability (PIP) within the mixture. CONCLUSIONS: In this study, we found higher Se levels were associated with an elevated risk of obesity and high levels of Ba, Pb and Cr were associated with a decreased risk of obesity. Studies with larger samples are needed to confirm these findings.

Lifestyle behaviors and stress are risk factors for overweight and obesity in healthcare workers: a cross-sectional survey.

BACKGROUND: Overweight and obesity have become major public health concerns worldwide. Persistent stress can activate the human hypothalamic‒pituitary‒adrenal axis (HPA) and increase the intake of "self-rewarding food", thereby raising the incidence of obesity. Health care workers (HCWs) experience higher workloads and mental stress than workers in many other industries, which may put them at increased risk for overweight/obesity. However, few studies have been carried out on overweight and obesity among HCWs in China, and the overall scenario and behind-the-scenes factors of their overweight and obesity are unknown. The aim of this study is to understand the epidemic of overweight and obesity and risk factors among Chinese HCWs. METHODS: Based on a cross-sectional web survey design, 23,234 HCWs from 100 health institutions in 5 provinces/autonomous regions/municipalities across China were sampled to answer a self-administered questionnaire that was purposely developed using a multi-staged clustered random-sampling method. Chi-square test and ANOVA were performed to compare variables between two or more groups. Univariate analyses were conducted to identify the influence of self-reported persistent stress and/or recurrent anxiety/depressed mood on lifestyle behaviors. A multivariate binary logistic regression model was used to analyse the risk factors of overweight/obesity. RESULTS: Among the respondents, 34.26% were overweight, and 11.22% were obese. Most of the respondents had regular exercise habits (68.17%), had habitually stayed-up late (65.06%) and had been affected by persistent stress and/or recurrent anxiety/depressed mood (62.04%). A higher proportion of those with persistent stress and/or recurrent anxiety/depressed mood than those without habitually staying-up late (76.18%); consumed take-out food (54.92%), fried food (49.93%), snacks or desserts (50.51%); drank sugary drinks (46.57%); smoked (14.27%); and drank alcohol (23.34%). Gender (Female) (OR: 0.314, 95%CI: 0.292-0.336), age (OR: 1.742-2.334, 95%CI: 1.544-2.858), education (OR: 0.620-0.728, 95%CI: 0.445-0.973), living and working area (OR: 1.271, 95%CI: 1.192-1.355), breakfast (OR: 0.898, 95%CI: 0.839-0.960), fried food (OR: 1.133, 95%CI: 1.048-1.224), and alcohol consumption (OR: 1.111, 95%CI: 1.017-1.214) were factors for overweight/obesity. All of the aforementioned results were significant (P < 0.05). CONCLUSIONS: The overweight/obesity rate of Chinese HCWs is rather high, which might be directly associated with lifestyle behaviors. However, these behaviors fundamentally originated from persistent stress and/or recurrent anxiety/depression, mediated by lifestyle behaviors. Substantial measures should be taken for stress reduction and mental health promotion for overweight/obesity prevention and control among HCWs.

Development and validation of an improved QuEChERS method for the extraction of semi-volatile organic compounds (SVOCs) from complex soils.

In order to achieve rapid, sensitive, and high-throughput determination of typical semi-volatile organic compounds (SVOCs) in soil samples, a method for the rapid determination of 63 SVOCs in soil was developed by optimizing and improving the QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) extraction technique in conjunction with gas chromatography-mass spectrometry (GC-MS) analysis. A small amount of soil sample (5.0 g) was vortexed with 10 mL of a mixture of acetone and n-hexane (V/V = 1 : 1) for 2 min, followed by rapid vortex purification and centrifugation using a mixture of copper powder and octadecylsilane (C18) dispersant. The resulting supernatant was then purified through a 0.22 µm filter membrane. The results showed that the 63 SVOCs exhibited good linear relationships within the concentration range of 100-5000 µg L-1, with correlation coefficients (R2) above 0.99. The method detection limit (MDL = 3.3 Sy/m) was lower than 0.050 mg kg-1. At a spike concentration of 1 mg kg-1, the recovery rates of the 63 SVOCs were almost above 70% (n = 7). Compared with the rapid solvent extraction (ASE) method specified in US EPA 3545 standard, this method reduced the organic solvent usage by 14 times and significantly shortened the operation time. Furthermore, this method did not involve any transfer or concentration steps of the extractant during the experimental process, reducing the exposure time of toxic compounds and providing support for the principles of green analytical chemistry. Moreover, in the detection of most compounds in the same batch of contaminated soil, the extraction results obtained by QuEChERS were superior to those obtained by the ASE method, providing evidence for the practical application of this method. This method is rapid, simple, accurate, requires a small sample volume, and causes minimal environmental pollution. It provides a high-throughput detection method for the rapid screening of SVOCs in soil.

The associations of non-essential metal mixture with fasting plasma glucose among Chinese older adults without diabetes.

The evidence about the effect of non-essential metal mixture on fasting plasma glucose (FPG) levels among older adults without diabetes is limited. This study aims to estimate the individual and joint relationship between five non-essential metals and FPG levels in Chinese older adults without diabetes. This study included 2362 older adults without diabetes. Urinary concentrations of five non-essential metals, i.e., cesium (Cs), aluminum (Al), thallium (Tl), cadmium (Cd), and arsenic (As), were detected by inductively coupled plasma mass spectrometry (ICP-MS). The associations of single metals and the metal mixture with FPG levels were assessed using linear regression and Bayesian kernel machine regression (BKMR) models, respectively. Adjusted single-metal linear regression models showed positive associations of urinary Al (ß = 0.016, 95%CI: 0.001-0.030) and Cs (ß = 0.018, 95%CI: 0.006-0.031) with FPG levels. When comparing the 2th, 3th, and 4th quartiles of urine Cs to its 1th quartile, the significant associations between Cs and FPG levels were found and presented as an "inverted U" trend (ßQ2 vs. Q1: 0.034; ßQ3 vs. Q1:0.054; ßQ4 vs. Q1: 0.040; all P<0.05). BKMR analyses showed urinary level of Cs exhibited an "inverted U" shape association with FPG levels. Moreover, the FPG levels increased linearly with the raised levels of the non-essential metal mixture, and the posterior inclusion probability (PIP) of Cs was the highest (0.92). Potential positive interaction of As and Cs on FPG levels was found in BKMR model. Stratified analysis displayed significant interactions of hyperlipidemia and urine Cs or Tl on FPG levels. An inverse U-shaped association between Cs and FPG was found, individually and as mixture. The FPG levels increased with the raised levels of the non-essential metal mixture, and Cs was the most contributor to FPG levels. Further research is required to confirm the correlation between non-essential metals and FPG levels and to clarify the underlying mechanisms.

The association between the essential metal mixture and fasting plasma glucose in Chinese community-dwelling elderly people.

BACKGROUND: Epidemiological studies about the effect of essential metal mixture on fasting plasma glucose (FPG) levels among elderly people are sparse. The object of this study was to examine the associations of single essential metals and essential metal mixture with FPG levels in Chinese community-dwelling elderly people. METHODS: The study recruited 2348 community-dwelling elderly people in total. Inductively coupled plasma-mass spectrometry was adopted to detect the levels of vanadium (V), selenium (Se), magnesium (Mg), cobalt (Co), calcium (Ca), and molybdenum (Mo) in urine. The relationships between single essential metals and essential metal mixture and FPG levels were evaluated by linear regression and Bayesian kernel machine regression (BKMR) models, respectively. RESULTS: In multiple-metal linear regression models, urine V and Mg were negatively related to the FPG levels (ß = - 0.016, 95 % CI: - 0.030 to - 0.003 for V; ß = - 0.021, 95 % CI: - 0.033 to - 0.009 for Mg), and urine Se was positively related to the FPG levels (ß = 0.024, 95 % CI: 0.014-0.034). In BKMR model, the significant relationships of Se and Mg with the FPG levels were also found. The essential metal mixture was negatively associated with FPG levels in a dose-response pattern, and Mg had the maximum posterior inclusion probability (PIP) value (PIP = 1.0000), followed by Se (PIP = 0.9968). Besides, Co showed a significant association with decreased FPG levels in older adults without hyperlipemia and in women. CONCLUSIONS: Both Mg and Se were associated with FPG levels, individually and as a mixture. The essential metal mixture displayed a linear dose-response relationship with reduced FPG levels, with Mg having the largest contribution to FPG levels, followed by Se. Further prospective investigations are necessary to validate these exploratory findings.

Denitrification performance and in-situ fermentation mechanism of the wastepaper-flora slow-release carbon source.

Using wastepaper as external carbon sources is an optional way to achieve total nitrogen removal faced with low carbon to nitrogen ratio municipal sewage. Most of studies have primarily focused on using cellulose-rich wastes establishing the separate denitrification units to achieve in-situ fermentation, which can cause blockages and prolong the process chain. In response, a novel in-situ fermentation wastepaper-flora slow-release carbon source (IF-WF) was proposed using in the original denitrification unit. IF-WF could be efficiently utilized in situ and the denitrification rate increased with the increase of nitrate nitrogen. The fermentation products were highly available, but internal acidification of IF-WF inhibited fermentation. Moreover, IF-WF limited the growth of polysaccharides in the extracellular polymeric substances of denitrified sludge. IF-WF finally formed the structure dominated by nitrate-reduction bacteria outside and cellulose-degrading bacteria inside. These results provide guidance for understanding the mechanism of IF-WF for in-situ fermentation to promote nitrogen removal.

Enhanced nitrate reduction by metal deposited g-C3N4/rGO/TiO2 Z-schematic photocatalysts: Performance and mechanism comparison of Pd-Cu and Ag.

Deposition of bimetals on Z-scheme photocatalysts has been reported to improve the nitrate nitrogen (NO3-) reduction properties. However, it is not clear whether bimetal deposition possesses advantage over single metal deposition and what is the different reaction mechanisms. In this work, the g-C3N4(Pd-Cu)/rGO/TiO2 and g-C3N4(Ag)/rGO/TiO2 composites with bimetallic Pd-Cu and single metal Ag deposited on the graphitic carbon nitride/reduced graphene oxide/titanium dioxide (g-C3N4/rGO/TiO2) Z-scheme photocatalyst were prepared, and their photocatalytic NO3- reduction properties and the mechanisms under visible light irradiation were studied. The results showed that the NO3- and total nitrogen (TN) removal efficiencies of g-C3N4(Pd-Cu)/rGO/TiO2 were 57.78% and 20.1%, respectively, 1.15 and 1.72 times higher than those of g-C3N4(Ag)/rGO/TiO2. This can be ascribed to that Pd-Cu enriched more electrons and absorbed more NO3- molecules due to the different charge densities, and the NO3- reduction process were enhanced by the staged NO3-→NO2- and NO2-→N2/NH4+ processes on Cu and Pd. The effects of reductive species were demonstrated to be photogenerated electrons > ·OH (·CO2-) > ·O2- in g-C3N4(Ag)/rGO/TiO2, while it was photogenerated electrons > ·O2- > ·OH (·CO2-) in g-C3N4(Pd-Cu)/rGO/TiO2, which may be caused by the better O2 reduction property of the latter. Finally, the cyclic experiment proved the good stability of both materials. This work provided some reference for design of metal deposited Z-scheme photocatalysts for various reduction reactions.

Efficient elimination of nonylphenol and 4-tert-octylphenol by weak electrical stimulated anaerobic microbial processes.

The investigation into the degradation of alkylphenol pollutants (APs) has become a hotspot due to their harmful effects on the environment and human health. In this study, microbial electrolysis cells (MECs) were used to degrade nonylphenol (NP) and 4-tert-octylphenol (4-tert-OP). The study found that the degradation rates of NP and 4-tert-OP for a 6-day period were 83.6% and 96.3%, respectively, which were 30.53% and 26.7% higher than those of the group without applied voltage. The double layer area in the degradation of 4-tert-OP was larger than that of NP, and the resistance exhibited by 4-tert-OP (87.47 Ω) in MEC was lower than that of NP (99.42 Ω). Meanwhile, NP had a greater effect on the bioenzyme activity than 4-tert-OP. GC-MS analysis showed that the degradation pathways of both pollutants mainly included oxidation and hydroxylation reactions. Furthermore, the microbial community analysis indicated that the main functional bacteria in NP degradation were Citrobacter, Desulfovibrio and Advenella, and those in 4-tert-OP degradation were Stenotrophomonas, Chryseobacterium, Dokdonella, and the key microbiomes underlying the cooperative relationship. The biotoxicity test indicated that the toxicity of residual substances was significantly reduced. Therefore, the MEC system is efficient and environmentally friendly and has broad application prospects in phenol refractory organics.

Transcriptome analysis reveals the differential inflammatory effects between propofol and sevoflurane during lung cancer resection: a randomized pilot study.

BACKGROUND: Propofol and sevoflurane are two commonly used perioperative anesthetics. Some studies have found that these anesthetic drugs affect tumorigenesis. Previous studies have mostly focused on in vitro experiments, and the specimens collected were mainly peripheral body fluids, lacking direct evidence of the impact of anesthetic drugs on human tissues. This study aimed to elucidate the effects of propofol and sevoflurane on lung cancer using next-generation sequencing through an in vivo experiment. METHODS: Patients were randomly assigned to a group receiving either propofol or sevoflurane during surgery. Then, the patients' tumor and paired normal samples were collected and sequenced by next-generation sequencing. Differentially expressed genes (DEG) were analyzed by two statistical models, followed by cluster analysis, PCA, Gene Ontology, and KEGG pathway analysis. Candidate genes were confirmed by qRT-PCR. RESULTS: The demographic data of the two study groups were not statistically significant. Through single-factor model analysis, 810 DEG in the propofol group and 508 DEG in the sevoflurane group were obtained. To better reflect the differential effects between propofol and sevoflurane while reducing the false-positive DEG, we used multifactor model analysis, which resulted in 124 DEG. In PCA and cluster analysis, four groups (propofol cancer group, propofol normal group, sevoflurane cancer group, sevoflurane normal group) were separated adequately, indicating the accuracy of the analysis. We chose seven significant pathways (cellular response to interleukin-1, chemokine-mediated signaling pathway, chemokine signaling pathway, cytokine-cytokine receptor interaction, inflammatory response, immune response, and TNF signaling pathway) for downstream analysis. Based on the pathway analysis, three candidate genes (CXCR1, CXCL8, and TNFAIP3) were chosen, and their qRT-PCR results were consistent with the sequencing results. CONCLUSIONS: Through RNA-seq analysis, the effects of propofol and sevoflurane during lung cancer resection were different, mainly in inflammatory-related pathways, which might be possibly by targeting CXCL8. TRIAL REGISTRATION: Trial registry number was ChiCTR1900026213 .

Urinary antibiotic exposure and low grip strength risk in community-dwelling elderly Chinese by gender and age.

Emerging studies have shown that environmental contaminants were related to decreased handgrip strength. Nevertheless, no prior research has investigated the relationship of exposure to environmental antibiotics with grip strength. Thus, we explored the relationship between urinary antibiotic burden and grip strength among the elderly in China. This study consisted of 451 men and 539 women from the baseline survey of a cohort study. Commonly used antibiotics for humans and animals were detected in 990 urine samples through a biomonitoring method. Grip strength was measured by an electronic dynamometer. We examined the associations of antibiotic exposure with low grip strength (LGS), grip strength, and grip strength index, respectively. Results suggested that 34.9% of participants developed LGS, and 93.0% of individuals were exposed to 1-10 antibiotics. Among women, oxytetracycline (Quartile 2: odds ratio: 2.97, 95% confidence interval: 1.36-6.50), florfenicol (Quartile 3: 2.60 [1.28-5.27]), fluoroquinolones (Quartile 4: 1.88 [1.07-3.30]), and chloramphenicols (Quartile 3: 2.73 [1.35-5.51]) could enhance LGS risk. Among men, ofloxacin (Quartile 2: 3.32 [1.45-7.59]) increased LGS risk, whereas tetracycline (Quartile 2: 0.31 [0.11-0.88]) was implicated in reduced LGS risk. In participants < 70 years, ofloxacin (Quartile 2: 3.00 [1.40-6.42]) could increase LGS risk. For participants who were 70 years of age or older, veterinary antibiotics (Quartile 3: 1.73 [1.02-2.94]) were linked to a 73% increased risk of LGS. Our findings suggested that antibiotics mainly pertained to LGS, and there were gender and age disparities in associations between antibiotic exposure and muscle strength indicators in the elderly Chinese population.

ATAC-DEA: A Web-Based ATAC-Seq Data Differential Peak and Annotation Analysis Application.

Assay for transposase-accessible chromatin sequencing (ATAC-seq) has become one of the most widely used sequencing methods in studies of gene regulation, aiming to identify open chromatin sites and decipher how chromatin accessibility regulates gene expression. However, due to a lack of programming experience or minimal bioinformatics training, it is difficult for biologists to fully explore and interpret ATAC-seq results. Despite several available programs or websites that allow researchers to analyze and visualize ATAC-seq data, several limitations exist. ATAC-seq data differential expression analysis (ATAC-DEA), a web application that facilitates the exploration and visualization of differential peak analysis and annotation from ATAC-seq data, was developed (www.atac-dea.xyz:3838/ATAC-DEA). ATAC-DEA uses DiffBind and ChIPpeakAnno to process differential peak and annotation analysis results. ATAC-DEA has five features: (1) runs on a web server; (2) processes three files into one small file, which is used as the input for ATAC-DEA; (3) availability of various downloadable plots; (4) multifactor analysis and customized contrast model; and (5) annotates individual, overlapped, and differential peaks. It provides an easy-to-use user interface (UI) design for users to explore the data and modify the parameters interactively based on experimental purposes. ATAC-DEA allows biologists to generate user-friendly visual results from ATAC-seq downstream analysis.

Selenium attenuates the association of co-exposure to arsenic, cadmium, and lead with cognitive function among Chinese community-dwelling older adults.

The effects of interactions between the toxic and essential metal mixtures on cognitive function are poorly understood. This study aims to identify the joint association of arsenic (As), cadmium (Cd), and lead (Pb) with cognitive function in older adults and the moderating role of selenium (Se), zinc (Zn), and copper (Cu) in this association. This study included 1000 community-dwelling older adults. Cognitive function was assessed by the Mini-Mental State Examination (MMSE). Blood concentrations of As, Cd, Pb, Se, Zn, and Cu were measured using inductively coupled plasma mass spectrometry. Linear regression and Bayesian kernel machine regression (BKMR) models were applied to assess the individual and joint associations of As, Cd, and Pb with cognitive function and to examine whether Se, Zn, and Cu (individually and as a mixture) modified these associations. In the adjusted single-metal models, both Cd (ß = - 0.37, 95% CI: - 0.73 to - 0.01) and Pb (ß = - 0.44, 95% CI: - 0.86 to - 0.02) were associated with MMSE scores, while Se (ß = 0.71, 95% CI: 0.30 to 1.13) exhibited a positive relationship with MMSE scores. Univariate exposure-response functions from BKMR models showed similar results. Moreover, the toxic metal mixture (As, Cd, and Pb) exhibited a significant negative association with MMSE scores in a dose-response pattern, with Pb being the greatest contributor within the mixture. The negative association of Pb alone or the toxic metal mixture with MMSE scores became weaker at higher concentrations of Se within its normal range, especially when Se levels were greater than the median (89.18 µg/L). Our findings support that Se can attenuate the negative associations of exposure to single Pb or the As, Cd, and Pb mixtures with cognitive function. Future prospective studies are needed to replicate our findings.

Association Between the Ratios of Selenium to Several Elements and Mild Cognitive Impairment in the Elderly.

To investigate the relationship between the correlation ratios of selenium (Se) and other elements and mild cognitive impairment (MCI) among older adults. A total of 1000 individuals participated in our research analysis. The concentrations of elements in whole blood were determined using inductively coupled plasma mass spectrometry to reflect their exposure levels. Participants' cognitive function was assessed using the Mini-Mental State Examination. Logistic regression analysis was used to evaluate the relationship between elemental ratios and MCI. Se concentration was positively correlated with red blood cell count (r = 0.219, p < 0.001), haemoglobin level (r = 0.355, p < 0.001), haematocrit (r = 0.215, p < 0.001), mean corpuscular haemoglobin (r = 0.294, p < 0.001) and mean corpuscular haemoglobin concentration (r = 0.428, p < 0.001) and negatively correlated with red cell volume distribution width-standard deviation (r = -0.232, p < 0.001) and platelet distribution width (r = -0.382, p < 0.001). Compared with the normal group, the ratios of Se/vanadium (V), Se/lead (Pb) and Se/cadmium (Cd) in the whole blood of the MCI group were significantly lower (all p < 0.001), while the ratios of manganese (Mn)/Se and iron (Fe)/Se were higher (all p < 0.001). The increase in the ratios of Se/V, Se/Pb and Se/Cd is related to a decreased risk of MCI among older adults; contrarily, an increase in the ratios of Mn/Se and Fe/Se may be a risk factor for MCI.

Fabrication of WPI-EGCG covalent conjugates/gellangum double network emulsion gels by duo-induction of GDL and CaCl2 for colon-controlled Lactobacillus Plantarum delivery.

In this study, we demonstrated the role of whey protein isolate (WPI)/(-)-epigallocatechin-3-gallate (EGCG) covalent conjugates/gellangum double network emulsion gels by duo-induction of glucono-δ-lactone (GDL) and CaCl2 on the digestion viability of Lactobacillus Plantarum powders. We employed a novel one-step continuous cold gelation strategy to product double network emulsion gels. The gellan gum in continuous phase was first induced by CaCl2 to form a gel in a short time. Besides, the GDL was improved covalent cross-linking between WPI-EGCG covalent conjugate Pickering particles or particle-coated oil droplets because of the slowly pH reduction. The first cross-linked gellan gum gels could be more closely integrated into the GDL-induced second gel networks with synergistic role, which promoted the formation of compact and homogeneous networks through hydrophobic interactions and disulfide bonds. Thus, the results provide a promising strategy for probiotic powders encapsulation of double network emulsion gels in oral applications of gel type foods.