Publications by authors named "Jie Ren"

948 Publications

Induction and modulation of the unfolded protein response during porcine deltacoronavirus infection.

Vet Microbiol 2022 Jun 14;271:109494. Epub 2022 Jun 14.

State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China. Electronic address:

Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus that has the potential for cross-species infection. Many viruses have been reported to induce endoplasmic reticulum stress (ERS) and activate the unfolded protein response (UPR). To date, little is known about whether and, if so, how the UPR is activated by PDCoV infection. Here, we investigated the activation state of UPR pathways and their effects on viral replication during PDCoV infection. We found that PDCoV infection induced ERS and activated all three known UPR pathways (inositol-requiring enzyme 1 [IRE1], activating transcription factor 6 [ATF6], and PKR-like ER kinase [PERK]), as demonstrated by IRE1-mediated XBP1 mRNA cleavage and increased mRNA expression of XBP1s, ATF4, CHOP, GADD34, GRP78, and GRP94, as well as phosphorylated eIF2α expression. Through pharmacologic treatment, RNA interference, and overexpression experiments, we confirmed the negative role of the PERK-eIF2α pathway and the positive regulatory role of the ATF6 pathway, but found no obvious effect of IRE1 pathway, on PDCoV replication. Taken together, our results characterize, for the first time, the state of the ERS response during PDCoV infection and identify the PERK and ATF6 pathways as potential antiviral targets.
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http://dx.doi.org/10.1016/j.vetmic.2022.109494DOI Listing
June 2022

Transcriptome and Metabolome Profiling to Explore the Causes of Purple Leaves Formation in Non-Heading Chinese Cabbage ( L. ssp. Makino var. Hort.).

Foods 2022 Jun 17;11(12). Epub 2022 Jun 17.

Horticulture College, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang 110866, China.

Purple non-heading Chinese cabbage is one of the most popular vegetables, and is rich in various health-beneficial anthocyanins. Research related to genes associated with anthocyanin biosynthesis in non-heading Chinese cabbage is important. This study performed integrative transcriptome and metabolome analysis in the purple non-heading Chinese cabbage wild type (WT) and its green mutant to elucidate the formation of purple leaves. The anthocyanin level was higher in purple than in green plants, while the contents of chlorophyll and carotenoid were higher in the green mutant than in the purple WT. Twenty-five anthocyanins were identified in purple and green cultivars; eleven anthocyanin metabolites were identified specifically in the purple plants. RNA-seq analysis indicated that 27 anthocyanin biosynthetic genes and 83 transcription factors were significantly differentially expressed between the WT and its mutant, most of them with higher expression in the purple than green non-heading Chinese cabbage. Transcriptome and metabolome analyses showed that UGT75C1 catalyzing the formation of pelargonidin-3,5--diglucoside and cyanidin-3,5--diglucoside may play a critical role in purple leaf formation in non-heading Chinese cabbage. Therefore, these results provide crucial information for elucidating the formation of purple leaves in non-heading Chinese cabbage.
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http://dx.doi.org/10.3390/foods11121787DOI Listing
June 2022

Machine learning shows that the Covid-19 pandemic is impacting U.S. public companies unequally by changing risk structures.

Authors:
Likun Cao Jie Ren

PLoS One 2022 22;17(6):e0269582. Epub 2022 Jun 22.

School of Economics and Management, University of Science and Technology Beijing, Beijing, China.

Covid-19 has impacted the U.S. economy and business organizations in multiple ways, yet its influence on company fundamentals and risk structures have not been fully elucidated. In this paper, we apply LDA, a mainstream topic model, to analyze the risk factor section from SEC filings (10-K and 10-Q), and describe risk structure change over the past two years. The results show that Covid-19 has transformed the risk structures U.S. companies face in the short run, exerting excessive stress on international interactions, operations, and supply chains. However, this shock has been waning since the second quarter of 2020. Our model shows that risk structure change (measured by topic distribution) from Covid-19 is a significant predictor of lower performance, but smaller companies tend to be stricken harder.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0269582PLOS
June 2022

Correction to: Melatonin prevents chronic intermittent hypoxia-induced injury by inducing sirtuin 1-mediated autophagy in steatotic liver of mice.

Sleep Breath 2022 Jun 22. Epub 2022 Jun 22.

Department of Respiratory and Critical Care Medicine, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.

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http://dx.doi.org/10.1007/s11325-022-02656-5DOI Listing
June 2022

CLP1 is a Prognosis-Related Biomarker and Correlates With Immune Infiltrates in Rheumatoid Arthritis.

Front Pharmacol 2022 1;13:827215. Epub 2022 Jun 1.

Department of Orthopaedics, The First Affiliated Hospital, Jinan University, Guangzhou, China.

Rheumatoid arthritis (RA) is a chronic, heterogeneous autoimmune disease with a high disability rate that seriously affects society and individuals. However, there is a lack of effective and reliable diagnostic markers and therapeutic targets. In this study, we identified diagnostic markers of RA based on RNA modification and explored its role as well as degree of immune cell infiltration. We used the gene expression profile data of three synovial tissues (GSE55235, GSE55457, GSE77298) from the Gene Expression Omnibus (GEO) database and the gene of 5 RNA modification genes (including m6A, m1A, m5C, APA, A-1), combined with cluster analysis, identified four RNA modifiers closely related to RA (YTHDC1, LRPPRC, NOP2, and CLP1) and five immune cells namely T cell CD8, CD4 memory resting, T cells regulatory (Tregs) Macrophages M0, and Neutrophils. Based on the LASSO regression algorithm, hub genes and immune cell prediction models were established respectively in RA and a nomogram based on the immune cell model was built. Around 4 key RNA modification regulator genes, miRNA-mRNA, mRNA-TF networks have been established, and GSEA-GO, KEGG-GSEA enrichment analysis has been carried out. Finally, CLP1 was established as an effective RA diagnostic marker, and was highly positively correlated with T cells follicular helper (Tfh) infiltration. On the other hand, highly negatively correlated with the expression of mast cells. In short, CLP1 may play a non-negligible role in the onset and development of RA by altering immune cell infiltration, and it is predicted to represent a novel target for RA clinical diagnosis and therapy.
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http://dx.doi.org/10.3389/fphar.2022.827215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9201986PMC
June 2022

Phenotype Identification of HeLa Cells Knockout CDK6 Gene Based on Label-Free Raman Imaging.

Anal Chem 2022 Jun 15. Epub 2022 Jun 15.

Institute of Drug Development & Chemical Biology, College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, Zhejiang 313200, People's Republic of China.

Identifying cell phenotypes is essential for understanding the function of biological macromolecules and molecular biology. We developed a noninvasive, label-free, single-cell Raman imaging analysis platform to distinguish between the cell phenotypes of the HeLa cell wild type (WT) and cyclin-dependent kinase 6 (CDK6) gene knockout (KO) type. Via large-scale Raman spectral and imaging analysis, two phenotypes of the HeLa cells were distinguished by their intrinsic biochemical profiles. A significant difference was found between the two cell lines: large lipid droplets formed in the knockout HeLa cells but were not observed in the WT cells, which was confirmed by Oil Red O staining. The band ratio of the Raman spectrum of saturated/unsaturated fatty acids was identified as the Raman spectral marker for HeLa cell WT or gene knockout type differentiation. The interaction between organelles involved in lipid metabolism was revealed by Raman imaging and Lorentz fitting, where the distribution intensity of the mitochondria and the endoplasmic reticulum membrane decreased. At the same time, lysosomes increased after the CDK6 gene knockout. The parameters obtained from Raman spectroscopy are based on hierarchical cluster analysis and one-way ANOVA, enabling highly accurate cell classification.
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http://dx.doi.org/10.1021/acs.analchem.2c00188DOI Listing
June 2022

Expression and hormone regulation of UCP2 in goat uterus.

Anim Reprod Sci 2022 Jun 6;243:107015. Epub 2022 Jun 6.

The Laboratory of Cell and Developmental Biology, Northeast Agricultural University, Harbin 150030, China. Electronic address:

Pregnancy success is closely related to the molecular mechanisms that control energy metabolism balance. However, the mechanisms have not been fully understood. Uncoupling protein 2 (UCP2) plays a physiological role by regulating energy metabolism in numerous tissues. In this study, we determined the expression and hormone regulation of UCP2 in goat uterus. UCP2 is expressed in the luminal and glandular epithelia of goat uterus during early pregnancy, as revealed by in situ hybridization and immunohistochemistry conducted on pregnant goats. The signals were detected from day 0 (D0) to D30 of pregnancy, though weak on D16 (the adhesion period). The low levels of UCP2 on D16 were confirmed by RT-qPCR and western blot. In goat uterus and endometrial epithelial cells (EECs), UCP2 was up-regulated by progesterone and estrogen. In addition, after goat EECs were treated with genipin (an inhibitor of UCP2), not only UCP2 expression but also cell proliferation was inhibited. Collectively, UCP2 is dynamically expressed in goat uterus and can affect EEC proliferation, suggesting that it may participate in regulating the energy metabolism balance of goat uterus during early pregnancy.
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http://dx.doi.org/10.1016/j.anireprosci.2022.107015DOI Listing
June 2022

Preclinical Pharmacokinetics and Bioavailability of Oxypeucedanin in Rats after Single Intravenous and Oral Administration.

Molecules 2022 Jun 2;27(11). Epub 2022 Jun 2.

School of Pharmacy, Nantong University, Nantong 226001, China.

Oxypeucedanin, a furanocoumarin extracted from many traditional Chinese herbal medicines, has a variety of pharmacological effects. However, the independent pharmacokinetic characteristics and bioavailability of this compound remains elusive. In this study, a rapid, sensitive, and selective method using ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC/MS/MS) was developed for evaluating the intravenous and oral pharmacokinetics of oxypeucedanin. After intravenous administration of oxypeucedanin (2.5, 5, and 10 mg/kg), and intragastric administration of oxypeucedanin (20 mg/kg), blood samples were collected periodically from the tail vein. The plasma concentration-time curves were plotted, and the pharmacokinetic parameters were calculated using a non-compartmental model analysis. After intravenous administration of oxypeucedanin (single dosing at 2.5, 5, and 10 mg/kg) to rats, the pharmacokinetics fit the linear kinetics characteristics, which showed that some parameters including average elimination half-life (T of 0.61~0.66 h), mean residence time (MRT of 0.62~0.80 h), apparent volume of distribution (V of 4.98~7.50 L/kg), and systemic clearance (CL of 5.64~8.55 L/kg/h) are dose-independent and the area under concentration-time curve (AUC) increased in a dose-proportional manner. Single oral administration of oxypeucedanin (20 mg/kg) showed poor and slow absorption with the mean time to reach the peak concentration (T) of 3.38 h, MRT of 5.86 h, T of 2.94 h, and a mean absolute bioavailability of 10.26% in rats. These results provide critical information for a better understanding of the pharmacological effect of oxypeucedanin, which will facilitate its research and development.
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http://dx.doi.org/10.3390/molecules27113570DOI Listing
June 2022

Molecular Mechanisms for Anti-aging of Low-Vacuum Cold Plasma Pretreatment in Caenorhabditis elegans.

Appl Biochem Biotechnol 2022 Jun 6. Epub 2022 Jun 6.

National-Local Joint Engineering Research Center of Biomass Refining and High-Quality Utilization, Changzhou, 213164, Jiangsu, China.

Cold plasma pretreatment has the potential of anti-aging. However, its molecular mechanism is still not clear. Here, cold plasma pretreatment was firstly used to investigate the anti-aging effects of Caenorhabditis elegans using transcriptomic technique. It showed that the optimal parameters of discharge power, processing time, and working pressure for cold plasma pretreatment were separately 100 W, 15 s, and 135 Pa. The released 0.32 mJ/cm of the moderate apparent energy density was possibly beneficial to the strong positive interaction between plasma and C. elegans. The longest lifespan (13.67 ± 0.50 for 30 days) was obviously longer than the control (10.37 ± 0.46 for 23 days). Furthermore, compared with the control, frequencies of head thrashes with an increase of 26.01% and 37.31% and those of body bends with an increase of 33.37% and 34.51% on the fourth and eighth day, respectively, indicated movement behavior was improved. In addition, the variation of the enzyme activity of superoxide dismutase (SOD), catalase (CAT), and malondialdehyde (MDA) hinted that the cold plasma pretreatment contributed to the enhanced anti-aging effects in nematodes. Transcriptomics analysis revealed that cold plasma pretreatment resulted in specific gene expression. Anatomical structure morphogenesis, response to stress, regulation of biological quality, phosphate-containing compound metabolic process, and phosphorus metabolic process were the most enriched biological process for GO analysis. Cellular response to heat stress and HSF1-dependent transactivation were the two most enriched KEGG pathways. This work would provide the methodological basis using cold plasma pretreatment and the potential gene modification targets for anti-aging study.
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http://dx.doi.org/10.1007/s12010-022-03989-3DOI Listing
June 2022

5-HT2B-mediated serotonin activation in enterocytes suppresses colitis-associated cancer initiation and promotes cancer progression.

Theranostics 2022 9;12(8):3928-3945. Epub 2022 May 9.

Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.

Serotonin (5-hydroxytryptamine, 5-HT) is generally considered to be involved in colitis-associated cancer (CAC), but previous research has yielded inconsistent results regarding the effect of 5-HT on CAC. 5-HT2B is one of the receptors of 5-HT, and the receptor is expressed in intestinal epithelial cells (IECs). However, the functions of 5-HT2B in CAC remain unclear. Our work demonstrates the variable functions of 5-HT/5-HT2B signaling in the initiation and progression of CAC in mice. We constructed two types of mutant mice homozygous knockout of , the gene encoding 5-HT2B, in IECs ( and ) to study the role of 5-HT2B in AOM/DSS-induced CAC model. Inflammation was measured using the body weight, colon length, and colitis severity score, and by histologic analysis of colon tissues. Tumor severity was assessed by tumor quantity, load, and histologic analysis of colon tumor tissues. In mice, AOM/DSS induced an enhancement of colitis and tumor severity. This process was due to the inhibition of TGF-β/SMAD signaling pathway and activation of IL-6/STAT3 signaling pathway. IL-6 antibody treatment reversed the stimulating effect of deletion on tumorigenesis. However, tumor severity decreased in mice injected with tamoxifen on day 48 of AOM/DSS treatment. Knockout Akt1 eliminated the function of 5-HT in promoting tumor cells. Our work elucidates 5-HT/5-HT2B/TGF-β signaling as a critical tumor suppressing axis during CAC initiation but as a promoter of cancer progression in the late-stage of CAC. Our findings provide a new understanding of the role of 5-HT in the initiation and progression of CAC, offering a new perspective on the long-standing debate on whether the 5-HT signal promotes or inhibits tumors.
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http://dx.doi.org/10.7150/thno.70762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9131283PMC
June 2022

DeepSCP: utilizing deep learning to boost single-cell proteome coverage.

Brief Bioinform 2022 Jun 2. Epub 2022 Jun 2.

Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.

Multiplexed single-cell proteomes (SCPs) quantification by mass spectrometry greatly improves the SCP coverage. However, it still suffers from a low number of protein identifications and there is much room to boost proteins identification by computational methods. In this study, we present a novel framework DeepSCP, utilizing deep learning to boost SCP coverage. DeepSCP constructs a series of features of peptide-spectrum matches (PSMs) by predicting the retention time based on the multiple SCP sample sets and fragment ion intensities based on deep learning, and predicts PSM labels with an optimized-ensemble learning model. Evaluation of DeepSCP on public and in-house SCP datasets showed superior performances compared with other state-of-the-art methods. DeepSCP identified more confident peptides and proteins by controlling q-value at 0.01 using target-decoy competition method. As a convenient and low-cost computing framework, DeepSCP will help boost single-cell proteome identification and facilitate the future development and application of single-cell proteomics.
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http://dx.doi.org/10.1093/bib/bbac214DOI Listing
June 2022

The Double-Faceted Role of Leucine-Rich Repeat Kinase 2 in the Immunopathogenesis of Parkinson's Disease.

Front Aging Neurosci 2022 11;14:909303. Epub 2022 May 11.

Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.

() is one of the most common causative genes in Parkinson's disease (PD). The complex structure of this multiple domains' protein determines its versatile functions in multiple physiological processes, including migration, autophagy, phagocytosis, and mitochondrial function, among others. Mounting studies have also demonstrated the role of LRRK2 in mediating neuroinflammation, the prominent hallmark of PD, and intricate functions in immune cells, such as microglia, macrophages, and astrocytes. Of those, microglia were extensively studied in PD, which serves as the resident immune cell of the central nervous system that is rapidly activated upon neuronal injury and pathogenic insult. Moreover, the activation and function of immune cells can be achieved by modulating their intracellular metabolic profiles, in which LRRK2 plays an emerging role. Here, we provide an updated review focusing on the double-faceted role of LRRK2 in regulating various cellular physiology and immune functions especially in microglia. Moreover, we will summarize the latest discovery of the three-dimensional structure of LRRK2, as well as the function and dysfunction of LRRK2 in immune cell-related pathways.
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http://dx.doi.org/10.3389/fnagi.2022.909303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9131027PMC
May 2022

Impact of Emulsifier Structure and Concentration on Lipolysis Dynamics and Curcumin Bioaccessibility in the Nanoemulsions Stabilized by Polyglycerol Fatty Acid Esters.

Food Biophys 2022 May 24:1-11. Epub 2022 May 24.

Innovation Center of Bioactive Molecule Development and Application, South China Institute of Collaborative Innovation, Dongguan, 221116 China.

Polyglycerol fatty acid esters (PGFEs), a type of nonionic surfactants, have been widely used in food industry. However, the effects of the aliphatic chain lengths in PGFEs and the concentrations of PGFEs on digestive profiles in emulsion-based systems are poorly understood. The present study has investigated the physicochemical stability, lipolysis dynamics and curcumin bioaccessibility in the nanoemulsions stabilized by synthesized PGFEs with different aliphatic chains (C-C) at various concentrations using an in vitro gastrointestinal tract (GIT) model. Shorter aliphatic chain or higher concentrations of PGFEs resulted in smaller droplets in the emulsions before and during digestion. PGFEs concentration had different impacts on lipolysis dynamics of nanoemulsions depending on the aliphatic chain lengths of PGFEs. Furthermore, long aliphatic chain of PGFEs contributed to a greater rate and extent of lipolysis, but a lower bioaccessibility of curcumin compared with medium ones, which was attributed to the formation of insoluble calcium soaps induced by calcium ions. These results are expected to facilitate the application of PGFEs for developing optimized nanoemulsions in encapsulating poorly water-soluble nutraceuticals in functional food industry.

Supplementary Information: The online version contains supplementary material available at 10.1007/s11483-021-09681-z.
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http://dx.doi.org/10.1007/s11483-021-09681-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9128773PMC
May 2022

Dynamic DNA 5-hydroxylmethylcytosine and RNA 5-methycytosine reprogramming during early human development.

Genomics Proteomics Bioinformatics 2022 May 26. Epub 2022 May 26.

Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China. Electronic address:

After implantation, complex and highly specialized molecular events render functionally distinct organ formation, whereas how the epigenome shapes organ-specific development remains to be fully elucidated. Here, nano-hmC-Seal, RNA bisulfite sequencing (RNA-BisSeq), and RNA sequencing (RNA-Seq) were performed, and the first multilayer landscapes of DNA 5-hydroxymethylcytosine (5hmC) and RNA 5-methylcytosine (mC) epigenome were obtained in the heart, kidney, liver, and lung of the human foetuses at 13-28 weeks with 123 samples in total. We identified 70,091 and 503 organ-stage-specific differentially hydroxymethylated regions (DhMRs) and mC-modified mRNAs, respectively. The key transcription factors (TFs), T-box transcription factor 20 (TBX20), paired box protein pax-8 (PAX8), krueppel-like factor 1 (KLF1), transcription factor 21 (TCF21), and CCAAT enhancer binding protein beta (CEBPB), specifically contribute to the formation of distinct organs at different stages. Additionally, 5hmC-enriched Alu elements may participate in the regulation of expression of TF-targeted genes. Our integrated studies revealed a putative essential link between DNA modification and RNA methylation, and illustrate the epigenetic maps during human foetal organogenesis, which provide a foundation for understanding the in-depth epigenetic mechanisms for early development and birth defects.
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http://dx.doi.org/10.1016/j.gpb.2022.05.005DOI Listing
May 2022

The outcome of intravenous and inhalation anesthesia after pancreatic cancer resection: a retrospective study.

BMC Anesthesiol 2022 May 30;22(1):169. Epub 2022 May 30.

Department of Anesthesiology, Harbin Medical University Cancer Hospital, No.150 Haping Rd., Nangang District, Harbin, 150081, China.

Background: Different types of anesthesia may affect cancer patient's outcomes, we compared the overall survival (OS) and disease-free survival (DFS) of patients with pancreatic cancer under total intravenous and inhalation anesthesia.

Methods: The authors collected the electronic medical records of patients who had accepted at a pancreatectomy from January 1, 2010 to December 31, 2016. Patients respectively received total intravenous anesthesia (TIVA) or inhalational anesthesia (INHA). Stabilized inverse probability of treatment weighting (SIPTW)was used to minimize differences. Kaplan-Meier survival was established to analyze the influence of sort of anesthesia on disease-free and overall survival. We compare the effects of each sort of anesthesia on cancer recurrence or metastasis and all-cause mortality.

Results: A total of 463 patients who had undergone pancreatic cancer resection were collected in this study, of which 421 patients were available (TIVA group, n = 114 INHA group, n = 307). After SIPTW there were no significant differences between the two groups in disease-free survival (hazard ratio, 1.01, 95%CI, 0.78 to 1.29, P = 0.959) or overall survival (hazard ratio, 1.11, 95%CI, 0.87 to 1.42, P = 0.405).

Conclusions: In conclusion, the present study showed no significant difference in overall survival and disease-free survival between total intravenous anesthesia and volatile anesthesia.
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http://dx.doi.org/10.1186/s12871-022-01703-8DOI Listing
May 2022

A new evaluation model of a water conveyance channel based on Bayesian theory by integrating monitoring and detection information.

Sci Rep 2022 May 26;12(1):8914. Epub 2022 May 26.

College of Civil and Transportation Engineering, Hohai University, Nanjing, 210098, China.

Channels are commonly used in long-distance water transfer projects, where landslides, collapses, or erosion may occur in its course of operation; thus, safety evaluation is conducted through monitoring and detection in its key and potentially hazardous areas. However, monitoring and detection information cannot comprehensively reflect the prominent problems of the safety state of the channel in terms of time and space. Therefore, studying how to realize the integration of monitoring and detection information is an important task for the safety evaluations of channels. In this paper, a method of integrating monitoring and detection information based on Bayesian theory is presented. The research shows that the fusion method of gathering monitoring and detection information based on Bayesian theory successfully captures the safety state of high-filling channels, and it can quantify and reduce uncertainty compared with fuzzy theory and the GA-BP neural network. By studying the influence of monitoring information on the safety of the channel, it is found that the horizontal displacement has a greater impact on the safety of the channel than the vertical displacement. A comparison of the results of fusing seven different monitoring points shows that the comprehensive utilization of horizontal and vertical displacement can improve the accuracy of the evaluation results. Compared to the safety coefficient calculated by the actual exploration, the error rate of the GA-BP neural network is 42.7%, and the fusion method based on Bayesian theory is 2.9%. The proposed method based on Bayesian theory can better use the detection information to recognize and understand the rock and soil in advance; hence, the evaluation results are more reliable and consistent with the actual engineering state.
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http://dx.doi.org/10.1038/s41598-022-12997-6DOI Listing
May 2022

Heterochronic parabiosis induces stem cell revitalization and systemic rejuvenation across aged tissues.

Cell Stem Cell 2022 Jun 24;29(6):990-1005.e10. Epub 2022 May 24.

State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China. Electronic address:

The young circulatory milieu capable of delaying aging in individual tissues is of interest as rejuvenation strategies, but how it achieves cellular- and systemic-level effects has remained unclear. Here, we constructed a single-cell transcriptomic atlas across aged tissues/organs and their rejuvenation in heterochronic parabiosis (HP), a classical model to study systemic aging. In general, HP rejuvenated adult stem cells and their niches across tissues. In particular, we identified hematopoietic stem and progenitor cells (HSPCs) as one of the most responsive cell types to young blood exposure, from which a continuum of cell state changes across the hematopoietic and immune system emanated, through the restoration of a youthful transcriptional regulatory program and cytokine-mediated cell-cell communications in HSPCs. Moreover, the reintroduction of the identified rejuvenating factors alleviated age-associated lymphopoiesis decline. Overall, we provide comprehensive frameworks to explore aging and rejuvenating trajectories at single-cell resolution and revealed cellular and molecular programs that instruct systemic revitalization by blood-borne factors.
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http://dx.doi.org/10.1016/j.stem.2022.04.017DOI Listing
June 2022

Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging.

Dev Cell 2022 Jun 24;57(11):1347-1368.e12. Epub 2022 May 24.

State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China. Electronic address:

Nuclear deformation, a hallmark frequently observed in senescent cells, is presumed to be associated with the erosion of chromatin organization at the nuclear periphery. However, how such gradual changes in higher-order genome organization impinge on local epigenetic modifications to drive cellular mechanisms of aging has remained enigmatic. Here, through large-scale epigenomic analyses of isogenic young, senescent, and progeroid human mesenchymal progenitor cells (hMPCs), we delineate a hierarchy of integrated structural state changes that manifest as heterochromatin loss in repressive compartments, euchromatin weakening in active compartments, switching in interfacing topological compartments, and increasing epigenetic entropy. We found that the epigenetic de-repression unlocks the expression of pregnancy-specific beta-1 glycoprotein (PSG) genes that exacerbate hMPC aging and serve as potential aging biomarkers. Our analyses provide a rich resource for uncovering the principles of epigenomic landscape organization and its changes in cellular aging and for identifying aging drivers and intervention targets with a genome-topology-based mechanism.
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http://dx.doi.org/10.1016/j.devcel.2022.05.004DOI Listing
June 2022

Studies in the antiviral molecular mechanisms of 25-hydroxycholesterol: Disturbing cholesterol homeostasis and post-translational modification of proteins.

Eur J Pharmacol 2022 Jul 19;926:175033. Epub 2022 May 19.

College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Huzhou, 313200, Zhejiang, PR China. Electronic address:

Efficient antiviral drug discovery has been a pressing issue of global public health concern since the outbreak of coronavirus disease 2019. In recent years, numerous in vitro and in vivo studies have shown that 25-hydroxycholesterol (25HC), a reactive oxysterol catalyzed by cholesterol-25-hydroxylase, exerts broad-spectrum antiviral activity with high efficiency and low toxicity. 25HC restricts viral internalization and disturbs the maturity of viral proteins using multiple mechanisms. First, 25HC reduces lipid rafts and cholesterol in the cytomembrane by inhibiting sterol-regulatory element binding proteins-2, stimulating liver X receptor, and activating Acyl-coenzyme A: cholesterol acyl-transferase. Second, 25HC impairs endosomal pathways by restricting the function of oxysterol-binding protein or Niemann-pick protein C1, causing the virus to fail to release nucleic acid. Third, 25HC disturbs the prenylation of viral proteins by suppressing the sterol-regulatory element binding protein pathway and glycosylation by increasing the sensitivity of glycans to endoglycosidase. This paper reviews previous studies on the antiviral activity of 25HC in order to fully understand its role in innate immunity and how it may contribute to the development of urgently needed broad-spectrum antiviral drugs.
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http://dx.doi.org/10.1016/j.ejphar.2022.175033DOI Listing
July 2022

Research Progress of Raman Spectroscopy and Raman Imaging in Pharmaceutical Analysis.

Curr Pharm Des 2022 May 18. Epub 2022 May 18.

College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, People\'s Republic of China.

The analytical investigation of the pharmaceutical process monitors the critical process parameters of the drug, beginning from its development until marketing and postmarketing, and appropriate corrective action can be taken to change the pharmaceutical design at any stage of the process. Advanced analytical methods, such as Raman spectroscopy, are particularly suitable for use in the field of drug analysis, especially for qualitative and quantitative work, due to the advantages of simple sample preparation, fast, nondestructive analysis speed, and effective avoidance of moisture interference. Advanced Raman imaging techniques have gradually become a powerful alternative method for monitoring changes in polymorph distribution and active pharmaceutical ingredient distribution in drug processing and pharmacokinetics. Surface-enhanced Raman spectroscopy (SERS) has also solved the inherent insensitivity and fluorescence problems of Raman, which has made good progress in the field of illegal drug analysis. This review summarizes the application of Raman spectroscopy and imaging technology, which are used in the qualitative and quantitative analysis of solid tablets, quality control of the production process, drug crystal analysis, illegal drug analysis, and monitoring of drug dissolution and release in the field of drug analysis in recent years.
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http://dx.doi.org/10.2174/1381612828666220518145635DOI Listing
May 2022

Research on the Optimization of Basketball Teaching Content of Physical Education Major in Artificial Intelligence Colleges and Universities.

Appl Bionics Biomech 2022 9;2022:6938911. Epub 2022 May 9.

Basic Department, Shanxi Medical University Jinci College, Taiyuan, China.

The article uses the literature material law, expert interview method, mathematical statistics, the author of Suzhou University, Chengdu research, education of Guangdong Institute of Education, Guangdong teachers college education schools such as the current sports education professional study, and the similarities and differences in teaching outline of education of Guangdong province basketball specialty to conduct a comprehensive study and analysis and comparison on the current situation of education of Guangdong teachers college basketball in the system. This paper expounds the Guangdong education normal study and the Guangdong education status of school physical education professional basketball specialty courses, for Guangdong teachers college education reform of physical education professional basketball specializing in research, and the Guangdong education for theory reference.
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http://dx.doi.org/10.1155/2022/6938911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9110232PMC
May 2022

Biomedical Argument Mining Based on Sequential Multi-Task Learning.

IEEE/ACM Trans Comput Biol Bioinform 2022 May 16;PP. Epub 2022 May 16.

Biomedical argument mining aims to automatically identify and extract the argumentative structure in biomedical text. It helps to determine not only what positions people adopt, but also why they hold such opinions, which provides valuable insights into medical decision making. Generally, biomedical argument mining consists of three subtasks: argument component identification, argument component classification and relation identification. Current approaches employ conventional multi-task learning framework for jointly addressing the latter two subtasks, and achieve some successes. However, explicit sequential dependency between these two subtasks is ignored, which is crucial for accurate biomedical argument mining. Moreover, relation identification is conducted solely based on the argument component pair without considering its potentially valuable context. Therefore, in this paper, a novel sequential multi-task learning approach is proposed for biomedical argument mining. Specifically, to model explicit sequential dependency between argument component classification and relation identification, an information transfer strategy is employed to capture the information of argument component types that is transferred to relation identification. Furthermore, graph convolutional network is employed to model dependency relation among the related argument component pairs. The proposed method has been evaluated on a benchmark dataset and the experimental results show that the proposed method outperforms the state-of-the-art methods.
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http://dx.doi.org/10.1109/TCBB.2022.3173447DOI Listing
May 2022

Urolithin A protects human dermal fibroblasts from UVA-induced photoaging through NRF2 activation and mitophagy.

J Photochem Photobiol B 2022 Jul 11;232:112462. Epub 2022 May 11.

Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, PR China. Electronic address:

Photoaging, caused by exposure to sunlight and especially UVA, has been identified as one of the culprits for age-related skin deterioration. Here, we initially demonstrated that urolithin A (UroA), a metabolite derived from intestine microflora, possessed sufficient photoprotective capacity and attenuated UVA-induced senescent phenotypes in human fibroblasts, such as growth inhibition, senescence-associated β-galactosidase activity, breakdown of extracellular matrix, synthesis of senescence-associated secretory phenotypes and cell cycle arrest. Furthermore, UroA lessened the accumulation of intracellular reactive oxygen species, which promoted the phosphorylation and afterwards nuclear translocation of NRF2, subsequently driving the activation of downstream antioxidative enzymes. In parallel, we proved that UroA restored mitochondrial function by induction of mitophagy, which was regulated by the SIRT3-FOXO3-PINK1-PARKIN network. Taken together, our results showed that UroA protected dermal fibroblast from UVA damage through NRF2/ARE activation and mitophagy process, thus supporting UroA as a potential therapeutic agent for photoaging.
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http://dx.doi.org/10.1016/j.jphotobiol.2022.112462DOI Listing
July 2022

Identification of a biomass unaffected pale green mutant gene in Chinese cabbage (Brassica rapa L. ssp. pekinensis).

Sci Rep 2022 May 11;12(1):7731. Epub 2022 May 11.

College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.

Chlorophyll (Chl) is an essential component of the photosynthetic apparatus and pigments in plant greening. Leaf color is an important agronomic and commercial trait of Chinese cabbage. In this study, we identified a pale green mutant pgm created by ethyl methane sulfonate (EMS) mutagenesis in Chinese cabbage. Compared with wild-type (FT), pgm had a lower Chl content with a higher Chl a/b ratio, imperfect chloroplast structure, and lower non-photochemical quenching. However, its net photosynthetic rate and biomass showed no significant differences. Genetic analysis revealed that the pale green phenotype of pgm was controlled by a recessive nuclear gene, designated as Brpgm. We applied BSR-Seq, linkage analysis, and whole-genome resequencing to map Brpgm and predicted that the target gene was BraA10g007770.3C (BrCAO), which encodes chlorophyllide a oxygenase (CAO). Brcao sequencing results showed that the last nucleotide of its first intron changed from G to A, causing the deletion of the first nucleotide in its second CDS and termination of the protein translation. The expression of BrCAO in pgm was upregulated, and the enzyme activity of CAO in pgm was significantly decreased. These results provide an approach to explore the function of BrCAO and create a pale green variation in Chinese cabbage.
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http://dx.doi.org/10.1038/s41598-022-11825-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9095832PMC
May 2022

Evaluation of inactivated COVID-19 vaccine on semen parameters in reproductive-age males: a retrospective cohort study.

Asian J Androl 2022 May 3. Epub 2022 May 3.

Department of Andrology, Shanghai Ji Ai Genetics and IVF institute China-USA Center, Shanghai 200011, China.

During the coronavirus disease (COVID-19) epidemic, there have been concerns about the impact of vaccines on people's fertility, including the fertility of those who are currently preparing for pregnancy and those who might become pregnant in future. However, there is still a lack of research on the effect of the COVID-19 vaccine on male fertility, and it is not surprising that couples and donors have concerns regarding vaccination. In this study, a retrospective cohort study was conducted to examine semen quality before and after receipt of the inactivated COVID-19 vaccine. There were no statistically significant changes in semen parameters (volume, sperm concentration, progressive motility, and total progressive motile count) after two doses of vaccine (all P > 0.05). In summary, our study updates the most recent studies on the effects of the COVID-19 vaccine on male fertility, and the information from this study could be used to guide fertility recommendations for assisted reproductive technology (ART) patients and donors.
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http://dx.doi.org/10.4103/aja202225DOI Listing
May 2022

The interplay between language acquisition and cognitive development.

Infant Behav Dev 2022 05 4;67:101718. Epub 2022 May 4.

Department Linguistik, Universität Potsdam, Germany.

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http://dx.doi.org/10.1016/j.infbeh.2022.101718DOI Listing
May 2022

Analysis of the association of ANO3/MUC15, COL4A4, RRBP1, and KLK1 polymorphisms with COPD susceptibility in the Kashi population.

BMC Pulm Med 2022 May 5;22(1):178. Epub 2022 May 5.

Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashi, Kashi, 844000, Xinjiang, People's Republic of China.

Objective: Chronic obstructive pulmonary disease (COPD) is a complex, multifactorial, polygenic disease. The rate of occurrence of COPD in the Kashi population (Uyghur) is significantly higher than that observed nationwide. The identification of COPD-related genes in the Chinese Uyghur population could provide useful insights that could help us understand this phenomenon. Our previous whole-exome sequencing study of three Uyghur families with COPD demonstrated that 72 mutations in 55 genes might be associated with COPD; these included rs15783G > A in the anoctamin 3 (ANO3) gene/mucin 15 (MUC15) gene, rs1800517G > A in the collagen type IV alpha 4 chain (COL4A4) gene, rs11960G > A in the ribosome binding protein 1 (RRBP1) gene, and rs5516C > G in the kallikrein 1 (KLK1) gene. This case-control study aimed to further validate the association of the four mutations with COPD in the Chinese Uyghur population.

Methods: Sanger sequencing was used for the genotyping of four polymorphisms (ANO3/MUC15 rs15783, COL4A4 rs1800517, RRBP1 rs11960, and KLK1 rs5516) in 541 unrelated Uyghur COPD patients and 534 Uyghur healthy controls. We then conducted stratified analyses based on the smoking status and airflow limitation severity, to explore the correlation between selected gene polymorphisms and COPD.

Results: ANO3/MUC15 rs15783 and KLK1 rs5516 polymorphisms could significantly reduce COPD risk (p < 0.05), but COL4A4 rs1800517 and RRBP1 rs11960 polymorphisms were not correlated with COPD in the entire population. In a stratified analysis of smoking status, non-smokers with the ANO3/MUC15 rs15783G/G genotype (OR = 0.63, p = 0.032) or COL4A4 rs1800517 allele G (OR = 0.80, p = 0.023) had a reduced risk of COPD. Smokers with the RRBP1 rs11960A/G genotype had a lower risk of COPD (OR = 0.41, p = 0.025). The KLK1 rs5516G > C polymorphism was associated with a decreased risk of COPD (OR < 1, p < 0.05), irrespective of the smoking status of individuals. No significant association with COPD severity was observed in individuals with these four polymorphisms (p > 0.05).

Conclusion: We identified four previously unreported mutations (ANO3/MUC15 rs15783, COL4A4 rs1800517, RRBP1 rs11960, and KLK1 rs5516) that might decrease the COPD risk in individuals with different smoking statuses in the Chinese Uyghur population. Our findings provide new light for the genetic risk factors associated with the occurrence of COPD.
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http://dx.doi.org/10.1186/s12890-022-01975-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9074245PMC
May 2022

Liver Fibrosis Assessment by Viewing Sinusoidal Capillarization: US Molecular Imaging versus Two-dimensional Shear-Wave Elastography in Rats.

Radiology 2022 May 3:212325. Epub 2022 May 3.

From the Department of Ultrasound, Laboratory of Novel Optoacoustic (Ultrasonic) Imaging, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China.

Background US elastography is a first-line assessment of liver fibrosis severity; however, its application is limited by its insufficient sensitivity in early-stage fibrosis detection and its measurements are affected by inflammation. Purpose To assess the sensitivity of US molecular imaging (USMI) in early-stage liver fibrosis detection and to determine whether USMI can specifically distinguish fibrosis regardless of inflammation when compared with two-dimensional (2D) shear-wave elastography (SWE). Materials and methods USMI and 2D SWE were performed prospectively (January to June 2021) in 120 male Sprague-Dawley rats with varying degrees of liver fibrosis and acute hepatitis and control rats. Liver sinusoidal capillarization was viewed at CD34-targeted USMI and quantitatively analyzed by the normalized intensity difference (NID). Data were compared by using a two-sided Student test or one-way analysis of variance. Linear correlation analyses were used to evaluate the relationships between collagen proportionate area values and NID and liver stiffness measurement (LSM) values. Receiver operating characteristic curves were used to assess the diagnostic performance in detecting liver fibrosis. Results Both NID and LSM values showed good linear correlation with collagen proportionate area values ( = 0.91 and 0.87, respectively). No difference was observed between the areas under the receiver operating characteristic curve in detecting stage F0-F1 between USMI and 2D SWE (0.97 vs 0.91, respectively; = .20). USMI depicted liver fibrosis at an early stage more accurately than 2D SWE (area under the curve, 0.97 vs 0.82, respectively; = .01). Rats with hepatitis had higher liver stiffness values than control rats (9.83 kPa ± 0.79 vs 6.55 kPa ± 0.38, respectively; < .001), with no difference in the NID values between control rats and rats with hepatitis (6.75% ± 1.43 vs 6.74% ± 0.86, respectively; = .98). Conclusion Sinusoidal capillarization viewed at US molecular imaging helped to detect early-stage liver fibrosis more accurately than two-dimensional shear-wave elastography and helped assess fibrosis regardless of inflammation. © RSNA, 2022 . See also the editorial by Barr in this issue.
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http://dx.doi.org/10.1148/radiol.212325DOI Listing
May 2022

Contrast-enhanced ultrasound improves the potency of fine-needle aspiration in thyroid nodules with high inadequate risk.

BMC Med Imaging 2022 05 2;22(1):83. Epub 2022 May 2.

Department of Medical Ultrasonic, Laboratory of Novel Optoacoustic (Ultrasonic) Imaging, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.

Background: This study aims to determine the clinical value of contrast enhanced ultrasound (CEUS) for fine-needle aspiration (FNA) of high inadequate risky thyroid nodules.

Methods: During April 2018 and April 2021, consecutive 3748 thyroid nodules underwent FNA were retrospectively analyzed. CEUS guided FNA (CEUS-FNA) was applied in 115 nodules with high inadequate risk in Lingnan Campus. Ten nodules underwent CEUS-FNA presented non-enhancing, and would be further analyzed independently. Other 105 partial or total enhancing nodules were included as CEUS-FNA group, and 210 nodules with high inadequate risk in Tianhe Campus were match as the US-FNA control group. FNA specimens were collected for liquid-based preparation. Cytological results were classified following the Bethesda System for Reporting Thyroid Cytopathology.

Results: The overall FNA specimen inadequate rate in our center was 6.6%. All of the ten non-enhancing nodules under CEUS have an inadequate result in cytopathological analyzes. The subsequent postoperative pathology and follow-up ultrasonography showed the non-enhancing nodules were benign or stable without further malignant features. Total specimen inadequate rate of high inadequate risk thyroid nodules in CEUS-FNA group was significantly lower than US-FNA group (6.7% vs. 16.7%, P = 0.014). Further stratified analyzed shown that FNA under US guidance, the inadequate rates in cystic, predominantly cystic, predominantly solid and solid sub-groups were 28.1%, 17.1%, 10.0% and 9.2% (P = 0.019). In contrast, the inadequate rates in cystic, predominantly cystic, predominantly solid and solid sub-groups were 7.4%, 6.7%, 5.6% and 6.7% (P = 0.996) in CEUS-FNA group.

Conclusions: CEUS can improve the specimen adequacy of FNA in high inadequate risk thyroid nodules by avoiding unnecessary FNAs of the non-enhancing nodules, and accurately locating the viable tissue and precise guidance in real-time. CEUS is a recommend modality for FNA guidance of high inadequate risk thyroid nodules.
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http://dx.doi.org/10.1186/s12880-022-00805-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9063232PMC
May 2022

Insight into the Fischer-Tropsch mechanism on hcp-FeC (211) by density functional theory: the roles of surface carbon and vacancies.

RSC Adv 2021 Oct 25;11(55):34533-34543. Epub 2021 Oct 25.

Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical Technology, Tianjin University Tianjin 300072 P. R. China,

Iron carbide phases discovered in the spent iron catalysts have proved to be active in the Fischer-Tropsch process. The surface carbon of the iron carbide played a key role in the Fischer-Tropsch mechanism. Since there are two surface carbons, C1 and C2, on the hcp-FeC (211), which are close to each other, their reaction mechanisms would be significant. Hence, the DFT calculations were performed to investigate the Fischer-Tropsch mechanism involving the surface carbon. It was found that the HC + C pathway was the major C-C coupling reaction pathway with an effective energy barrier of 0.97 eV. Ethane would be the major C product from the HCC2 species through the stepwise hydrogenation pathway due to the high adsorption energy of ethylene (1.67 eV). After the desorption process of ethane, the carbon vacancy would form. The carbon vacancy was found to be the CO activation site through the CO direct dissociation pathway and the carbon vacancy would recover. It was concluded that the defect-hcp-FeC (211) is the high active facet of the Fischer-Tropsch synthesis, the carbon vacancy sites are the CO activation sites and the surface carbon sites are the C-C coupling sites. The surface carbons not only act as the chain initiation sites but also act as the chain growth sites in the Fischer-Tropsch mechanism on hcp-FeC (211).
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http://dx.doi.org/10.1039/d1ra06396kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9042690PMC
October 2021
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