Publications by authors named "Chen X"

71,286 Publications

Immunological Significance of Prognostic DNA Methylation Sites in Hepatocellular Carcinoma.

Front Mol Biosci 2021 26;8:683240. Epub 2021 May 26.

The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.

Hepatocellular carcinoma (HCC) is a tumor with high morbidity and high mortality worldwide. DNA methylation, one of the most common epigenetic changes, might serve a vital regulatory role in cancer. To identify categories based on DNA methylation data, consensus clustering was employed. The risk signature was yielded by systematic bioinformatics analyses based on the remarkably methylated CpG sites of cluster 1. Kaplan-Meier analysis, variable regression analysis, and ROC curve analysis were further conducted to validate the prognosis predictive ability of risk signature. Gene set enrichment analysis (GSEA) was performed for functional annotation. To uncover the context of tumor immune microenvironment (TIME) of HCC, we employed the ssGSEA algorithm and CIBERSORT method and performed TIMER database exploration and single-cell RNA sequencing analysis. Additionally, quantitative real-time polymerase chain reaction was employed to determine the LRRC41 expression and preliminarily explore the latent role of LRRC41 in prognostic prediction. Finally, mutation data were analyzed by employing the "maftools" package to delineate the tumor mutation burden (TMB). HCC samples were assigned into seven subtypes with different overall survival and methylation levels based on 5'-cytosine-phosphate-guanine-3' (CpG) sites. The risk prognostic signature including two candidate genes (LRRC41 and KIAA1429) exhibited robust prognostic predictive accuracy, which was validated in the external testing cohort. Then, the risk score was significantly correlated with the TIME and immune checkpoint blockade (ICB)-related genes. Besides, a prognostic nomogram based on the risk score and clinical stage presented powerful prognostic ability. Additionally, LRRC41 with prognostic value was corroborated to be closely associated with TIME characterization in both expression and methylation levels. Subsequently, the correlation regulatory network uncovered the potential targets of LRRC41 and KIAA1429. Finally, the methylation level of KIAA1429 was correlated with gene mutation status. In summary, this is the first to identify HCC samples into distinct clusters according to DNA methylation and yield the CpG-based prognostic signature and quantitative nomogram to precisely predict prognosis. And the pivotal player of DNA methylation of genes in the TIME and TMB status was explored, contributing to clinical decision-making and personalized prognosis monitoring of HCC.
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http://dx.doi.org/10.3389/fmolb.2021.683240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8187884PMC
May 2021

Exogenous Biological Renal Support Improves Kidney Function in Mice With Rhabdomyolysis-Induced Acute Kidney Injury.

Front Med (Lausanne) 2021 28;8:655787. Epub 2021 May 28.

State Key Laboratory of Kidney Diseases, Department of Nephrology, National Clinical Research Center for Kidney Diseases, Chinese People's Liberation Army (PLA) Institute of Nephrology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China.

Rhabdomyolysis (RM) is a clinical syndrome characterized by breakdown of skeletal muscle fibers and release of their contents into the circulation. Myoglobin-induced acute kidney injury (AKI) is one of the most severe complications of RM. Based on our previous research, exogenous biological renal support alleviates renal ischemia-reperfusion injury in elderly mice. This study aimed to determine whether exogenous biological renal support promotes renal recovery from RM-induced AKI and to preliminarily explore the mechanisms involved. A parabiosis animal model was established to investigate the effects of exogenous biological renal support on RM-induced AKI. Mice were divided into three groups: the control group (in which mice were injected with sterile saline), the RM group (in which mice were injected with 8 mL/kg glycerol), and the parabiosis + RM group (in which recipient mice were injected with glycerol 3 weeks after parabiosis model establishment). Blood samples and kidney tissue were collected for further processing 48 h after RM induction. Bioinformatics analysis was conducted via Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, functional enrichment analysis, and clustering analysis. No mice died within 48 h after the procedure. Exogenous biological renal support attenuated the histological and functional deterioration in mice with RM-induced AKI. Bioinformatics analysis identified key pathways and proteins involved in this process. We further demonstrated that exogenous biological renal support ameliorated AKI through multiple mechanisms, including by suppressing the complement system; attenuating oxidative stress, inflammation, and cell death; and increasing proliferation. Exogenous biological renal support provided by parabiosis can improve renal function in RM-induced AKI by suppressing the complement system; decreasing oxidative stress, inflammation, and cell death; and promoting tubular cell proliferation. Our study provides basic research evidence for the use of bioartificial kidneys to treat RM-induced AKI.
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http://dx.doi.org/10.3389/fmed.2021.655787DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8193099PMC
May 2021

Optimizing Safe Dental Practice During the COVID-19 Pandemic: Recommendations Based on a Guide Developed for Dental Practices in China.

Front Med (Lausanne) 2021 26;8:619357. Epub 2021 May 26.

Department of Periodontology and Oral Implantology, Stomatological Hospital, Southern Medical University, Guangzhou, China.

The current global coronavirus disease 2019 (COVID-19) outbreak is still exerting severe global implications, and its development in various regions is complex and variable. The high risk of cross-infection poses a great challenge to the dental practice environment; it is therefore urgent to develop a set of pandemic prevention measures to ensure dental practice safety during the COVID-19 outbreak. Therefore, we combined the epidemiological characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), public emergency measures for COVID-19, characteristics of dental practice, and relevant literature reports to develop a set of dynamic practice measures for dental practices in high-, medium-, and low-risk areas affected by COVID-19. This will help dental practices to achieve standard prevention and ensure their safe and smooth operation during the pandemic. It is hoped that these measures will provide a reference basis for dental hospitals and dental clinics in their care and pandemic prevention work.
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http://dx.doi.org/10.3389/fmed.2021.619357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8187590PMC
May 2021

Identifying Periampullary Regions in MRI Images Using Deep Learning.

Front Oncol 2021 28;11:674579. Epub 2021 May 28.

Department of General Surgery (Hepatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou, China.

Background: Development and validation of a deep learning method to automatically segment the peri-ampullary (PA) region in magnetic resonance imaging (MRI) images.

Methods: A group of patients with or without periampullary carcinoma (PAC) was included. The PA regions were manually annotated in MRI images by experts. Patients were randomly divided into one training set, one validation set, and one test set. Deep learning methods were developed to automatically segment the PA region in MRI images. The segmentation performance of the methods was compared in the validation set. The model with the highest intersection over union (IoU) was evaluated in the test set.

Results: The deep learning algorithm achieved optimal accuracies in the segmentation of the PA regions in both T1 and T2 MRI images. The value of the IoU was 0.68, 0.68, and 0.64 for T1, T2, and combination of T1 and T2 images, respectively.

Conclusions: Deep learning algorithm is promising with accuracies of concordance with manual human assessment in segmentation of the PA region in MRI images. This automated non-invasive method helps clinicians to identify and locate the PA region using preoperative MRI scanning.
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http://dx.doi.org/10.3389/fonc.2021.674579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8193851PMC
May 2021

Comprehensive Analysis of GLUT1 Immune Infiltrates and ceRNA Network in Human Esophageal Carcinoma.

Front Oncol 2021 28;11:665388. Epub 2021 May 28.

Department of Nuclear Medicine and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of Medicine, Shiyan, China.

Background: Glucose transporter 1 (GLUT1) is encoded by the solute carrier family 2A1 (SLC2A1) gene and is one of the glucose transporters with the greatest affinity for glucose. Abnormal expression of GLUT1 is associated with a variety of cancers. However, the biological role of GLUT1 in esophageal carcinoma (ESCA) remains to be determined.

Methods: We analyzed the expression of GLUT1 in pan-cancer and ESCA as well as clinicopathological analysis through multiple databases. Use R and STRING to perform GO/KEGG function enrichment and PPI analysis for GLUT1 co-expression. TIMER and CIBERSORT were used to analyze the relationship between GLUT1 expression and immune infiltration in ESCA. The TCGA ESCA cohort was used to analyze the relationship between GLUT1 expression and m6A modification in ESCA, and to construct a regulatory network in line with the ceRNA hypothesis.

Results: GLUT1 is highly expressed in a variety of tumors including ESCA, and is closely related to histological types and histological grade. GO/KEGG functional enrichment analysis revealed that GLUT1 is closely related to structural constituent of cytoskeleton, intermediate filament binding, cell-cell adheres junction, epidermis development, and P53 signaling pathway. PPI shows that GLUT1 is closely related to TP53, GIPC1 and INS, and these three proteins all play an important role in tumor proliferation. CIBERSORT analysis showed that GLUT1 expression is related to the infiltration of multiple immune cells. When GLUT1 is highly expressed, the number of memory B cells decreases. ESCA cohort analysis found that GLUT1 expression was related to 7 m6A modifier genes. Six possible crRNA networks in ESCA were constructed by correlation analysis, and all these ceRNA networks contained GLUT1.

Conclusion: GLUT1 can be used as a biomarker for the diagnosis and treatment of ESCA, and is related to tumor immune infiltration, m6A modification and ceRNA network.
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http://dx.doi.org/10.3389/fonc.2021.665388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8195627PMC
May 2021

Paeoniflorin improves functional recovery through repressing neuroinflammation and facilitating neurogenesis in rat stroke model.

PeerJ 2021 28;9:e10921. Epub 2021 May 28.

Anesthesiology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China.

Background: Microglia, neuron, and vascular cells constitute a dynamic functional neurovascular unit, which exerts the crucial role in functional recovery after ischemic stroke. Paeoniflorin, the principal active component of Paeoniae Radix, has been verified to exhibit neuroprotective roles in cerebralischemic injury. However, the mechanisms underlying the regulatory function of Paeoniflorin on neurovascular unit after cerebral ischemia are still unclear.

Methods: In this study, adult male rats were treated with Paeoniflorin following transient middle cerebral artery occlusion (tMCAO), and then the functional behavioral tests (Foot-fault test and modified improved neurological function score, mNSS), microglial activation, neurogenesis and vasculogenesis were assessed.

Results: The current study showed that Paeoniflorin treatment exhibited a sensorimotor functional recovery as suggested via the Foot-fault test and the enhancement of spatial learning as suggested by the mNSS in rat stroke model. Paeoniflorin treatment repressed microglial cell proliferation and thus resulted in a significant decrease in proinflammatory cytokines IL-1, IL-6 and TNF-. Compared with control, Paeoniflorin administration facilitated von Willebrand factor (an endothelia cell marker) and doublecortin (a neuroblasts marker) expression, indicating that Paeoniflorin contributed to neurogenesis and vasculogenesis in rat stroke model. Mechanistically, we verified that Paeoniflorin repressed JNK and NF-B signaling activation.

Conclusions: These results demonstrate that Paeoniflorin represses neuroinflammation and facilitates neurogenesis in rat stroke model and might be a potential drug for the therapy of ischemic stroke.
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http://dx.doi.org/10.7717/peerj.10921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8166241PMC
May 2021

Deep learning provides high accuracy in automated chondrocyte viability assessment in articular cartilage using nonlinear optical microscopy.

Biomed Opt Express 2021 May 16;12(5):2759-2772. Epub 2021 Apr 16.

Department of Bioengineering, Clemson University, Clemson, SC 29634, USA.

Chondrocyte viability is a crucial factor in evaluating cartilage health. Most cell viability assays rely on dyes and are not applicable for or longitudinal studies. We previously demonstrated that two-photon excited autofluorescence and second harmonic generation microscopy provided high-resolution images of cells and collagen structure; those images allowed us to distinguish live from dead chondrocytes by visual assessment or by the normalized autofluorescence ratio. However, both methods require human involvement and have low throughputs. Methods for automated cell-based image processing can improve throughput. Conventional image processing algorithms do not perform well on autofluorescence images acquired by nonlinear microscopes due to low image contrast. In this study, we compared conventional, machine learning, and deep learning methods in chondrocyte segmentation and classification. We demonstrated that deep learning significantly improved the outcome of the chondrocyte segmentation and classification. With appropriate training, the deep learning method can achieve 90% accuracy in chondrocyte viability measurement. The significance of this work is that automated imaging analysis is possible and should not become a major hurdle for the use of nonlinear optical imaging methods in biological or clinical studies.
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http://dx.doi.org/10.1364/BOE.417478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8176803PMC
May 2021

First-generation species-selective chemical probes for fluorescence imaging of human senescence-associated β-galactosidase.

Chem Sci 2020 Jun 17;11(28):7292-7301. Epub 2020 Jun 17.

State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology Shanghai 200237 China

Human senescence-associated β-galactosidase (SA-β-gal), the most widely used biomarker of aging, is a valuable tool for assessing the extent of cell 'healthy aging' and potentially predicting the health life span of an individual. Human SA-β-gal is an endogenous lysosomal enzyme expressed from , the catalytic domain of which is very different from that of β-gal, a bacterial enzyme encoded by . However, existing chemical probes for this marker still lack the ability to distinguish human SA-β-gal from β-gal of other species, such as bacterial β-gal, which can yield false positive signals. Here, we show a molecular design strategy to construct fluorescent probes with the above ability with the aid of structure-based steric hindrance adjustment catering to different enzyme pockets. The resulting probes normally work as traditional SA-β-gal probes, but they are unique in their powerful ability to distinguish human SA-β-gal from β-gal, thus achieving species-selective visualization of human SA-β-gal for the first time. NIR-emitting fluorescent probe as their representative further displays excellent species-selective recognition performance in biological systems, which has been herein verified by testing in senescent cells, in -transfected cells and in -β-gal-contaminated tissue sections of mice. Because of our probes, it was also discovered that SA-β-gal content in mice increased gradually with age and SA-β-gal accumulated most in the kidneys among the main organs of naturally aging mice, suggesting that the kidneys are the organs with the most severe aging during natural aging.
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http://dx.doi.org/10.1039/d0sc01234cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8159415PMC
June 2020

A Series of N-of-1 Trials for Traditional Chinese Medicine Using a Bayesian Method: Study Rationale and Protocol.

Evid Based Complement Alternat Med 2021 17;2021:9976770. Epub 2021 Apr 17.

Department of Respiratory Disease and Department of Pharmacy, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China.

. Our previous studies showed that N-of-1 trials could reflect the individualized characteristics of traditional Chinese medicine (TCM) syndrome differentiation with good feasibility, but the sensitivity was low. Therefore, this study will use hierarchical Bayesian statistical method to improve the sensitivity and applicability of N-of-1 trials of TCM. . This is a randomized, double-blind, placebo-controlled, three-pair crossover trial for a single subject, including 4-8 weeks of run-in period and 24 weeks of formal trial. In this study, we will recruit a total of 30 participants who are in the stable stage of bronchiectasis. The trial will be divided into three pairs (cycles), and one cycle contains two observation periods. The medications will be taken for three weeks and stopped for one week in the last week of each observation period. The order of syndrome differentiation decoction and placebo will be randomly determined. Patient self-reported symptom score (on a 7-point Likert scale) is the primary outcome. . Some confounding variables (such as TCM syndrome type and potential carryover effect of TCM) will be introduced into hierarchical Bayesian statistical method to improve the sensitivity and applicability of N-of-1 trials of TCM, and the use of prior available information (e.g., "borrowing from strength" of previous trial results) within the analysis may improve the sensitivity of the results of a series of N-of-1 trials, from both the individual and population level to study the efficacy of TCM syndrome differentiation. It is the exploration of improving the objective evaluation method of the clinical efficacy of TCM and may provide reference value for clinical trials of TCM in other chronic diseases. This trial is registered with ClinicalTrials.gov (ID: NCT04601792).
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http://dx.doi.org/10.1155/2021/9976770DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8189794PMC
April 2021

Interleukin-20 Acts as a Promotor of Osteoclastogenesis and Orthodontic Tooth Movement.

Stem Cells Int 2021 26;2021:5539962. Epub 2021 May 26.

Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China.

Objectives: Bones constitute organs that are engaged in constant self-remodelling. Osteoblast and osteoclast homeostasis during remodelling contribute to overall skeletal status. Orthodontics is a clinical discipline that involves the investigation and implementation of moving teeth through the bone. The application of mechanical force to the teeth causes an imbalance between osteogenesis and osteogenesis in alveolar bone, leading to tooth movement. Osteoimmunology comprises the crosstalk between the immune and skeletal systems that regulate osteoclast-osteoblast homeostasis. Interleukin- (IL-) 20, an IL-10 family member, is regarded as a proinflammatory factor for autoimmune diseases and has been implicated in bone loss disease. However, the mechanism by which IL-20 regulates osteoclast differentiation and osteoclastogenesis activation remains unclear. This study investigated the effects of IL-20 on osteoclast differentiation in a rat model; it explored the underlying molecular mechanism in vitro and the specific effects on orthodontic tooth movement in vivo.

Methods: For in vitro analyses, primary rat bone marrow-derived macrophages (BMMs) were prepared from Sprague-Dawley rats for osteoclast induction. After BMMs had been treated with combinations of recombinant IL-20 protein, siRNA, and plasmids, the expression levels of osteoclast-specific factors and signalling pathway proteins were detected through real-time polymerase chain reaction, western blotting, and immunofluorescence staining. For in vivo analyses, IL-20 was injected into the rat intraperitoneal cavity after the establishment of a rat orthodontic tooth movement (OTM) model. OTM distance was detected by Micro-CT and HE staining; the expression levels of protein were detected through immunofluorescence staining.

Results: In vitro analyses showed that a low concentration of IL-20 promoted preosteoclast proliferation and osteoclastogenesis. However, a high concentration of IL-20 inhibited BMM proliferation and osteoclastogenesis. IL-20 knockdown decreased the expression of osteoclast specific-markers, while IL-20 overexpression increased the expression of osteoclast specific-markers. Furthermore, IL-20 regulated osteoclast differentiation through the OPG/RANKL/RANK pathway. Overexpression of IL-20 could significantly upregulate RANKL-mediated osteoclast differentiation and osteoclast specific-marker expression; moreover, RANKL/NF-B/NFATc1 acted as downstream signalling molecule for IL-20. In vivo analysis showed that OTM speed was significantly increased after intraperitoneal injection of IL-20; additionally, mechanical stress sensing proteins were markedly activated.

Conclusions: IL-20 augments osteoclastogenesis and osteoclast-mediated bone erosion through the RANKL/NF-B/NFATc1 signalling pathway. IL-20 inhibition can effectively reduce osteoclast differentiation and diminish bone resorption. Furthermore, IL-20 can accelerate orthodontic tooth movement and activate mechanical stress sensing proteins.
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http://dx.doi.org/10.1155/2021/5539962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8172288PMC
May 2021

The Central Roles of Noncoding RNA in Estrogen-Dependent Female Reproductive System Tumors.

Int J Endocrinol 2021 24;2021:5572063. Epub 2021 May 24.

Department of Gynecology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China.

The pathogenesis of ovarian and endometrial cancers is closely associated with estrogen-related pathways. These estrogen-dependent tumors seriously threaten the health and quality of life in women. Noncoding RNAs (ncRNAs) are defined as RNAs that do not encode proteins, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), both of which have been reported in estrogen-dependent female reproductive system tumors. This review systematically summarizes the role of ncRNAs in estrogen-dependent tumors and common patterns of regulatory mechanisms to explore their future research directions in tumor diagnosis, treatment, and prognosis. This may provide new ideas for the potential application of ncRNAs in estrogen-dependent female reproductive system tumors.
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http://dx.doi.org/10.1155/2021/5572063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8169271PMC
May 2021

Corrigendum: Bovine Pre-adipocyte Adipogenesis Is Regulated by bta-miR-150 Through mTOR Signaling.

Front Genet 2021 26;12:688741. Epub 2021 May 26.

College of Animal Science and Technology, Northwest A&F University, Xianyang, China.

[This corrects the article DOI: 10.3389/fgene.2021.636550.].
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http://dx.doi.org/10.3389/fgene.2021.688741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8189425PMC
May 2021

Transcriptional Start Site Coverage Analysis in Plasma Cell-Free DNA Reveals Disease Severity and Tissue Specificity of COVID-19 Patients.

Front Genet 2021 28;12:663098. Epub 2021 May 28.

BGI-Shenzhen, Shenzhen, China.

Symptoms of coronavirus disease 2019 (COVID-19) range from asymptomatic to severe pneumonia and death. A deep understanding of the variation of biological characteristics in severe COVID-19 patients is crucial for the detection of individuals at high risk of critical condition for the clinical management of the disease. Herein, by profiling the gene expression spectrum deduced from DNA coverage in regions surrounding transcriptional start site in plasma cell-free DNA (cfDNA) of COVID-19 patients, we deciphered the altered biological processes in the severe cases and demonstrated the feasibility of cfDNA in measuring the COVID-19 progression. The up- and downregulated genes in the plasma of severe patient were found to be closely related to the biological processes and functions affected by COVID-19 progression. More importantly, with the analysis of transcriptome data of blood cells and lung cells from control group and cases with severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection, we revealed that the upregulated genes were predominantly involved in the viral and antiviral activity in blood cells, reflecting the intense viral replication and the active reaction of immune system in the severe patients. Pathway analysis of downregulated genes in plasma DNA and lung cells also demonstrated the diminished adenosine triphosphate synthesis function in lung cells, which was evidenced to correlate with the severe COVID-19 symptoms, such as a cytokine storm and acute respiratory distress. Overall, this study revealed tissue involvement, provided insights into the mechanism of COVID-19 progression, and highlighted the utility of cfDNA as a noninvasive biomarker for disease severity inspections.
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http://dx.doi.org/10.3389/fgene.2021.663098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8194351PMC
May 2021

Effects of Hydrological Regime on Foliar Decomposition and Nutrient Release in the Riparian Zone of the Three Gorges Reservoir, China.

Front Plant Sci 2021 26;12:661865. Epub 2021 May 26.

Key Laboratory of Eco-Environments in the Three Gorges Reservoir Region (Ministry of Education), State Cultivation Base of Eco-Agriculture for Southwest Mountainous Land, College of Life Sciences, Southwest University, Chongqing, China.

Foliar decomposition has significant effects on nutrient cycling and the productivity of riparian ecosystems, but studies on the impact of related hydrological dynamics have been lacking. Here, the litterbag method was carried out to compare decomposition and nutrient release characteristics , including three foliage types [two single-species treatments using (L.) Rich., Koidz., or a mixture with equal proportions of leaf mass], three flooding depths (unflooded, shallow flooding, and deep flooding), two hydrodynamic processes (continuous flooding and flooded-to-unflooded hydrological processes), and one hydrological cycle (1 year) in the riparian zone of the Three Gorges Reservoir. The results showed that both hydrological processes significantly promoted foliage decomposition, and all foliage types decomposed the fastest in a shallow flooding environment ( < 0.05). The mixed-species samples decomposed most quickly in the flooded hydrological process in the first half of the year and the unflooded hydrological process in the second half of the year. Flooding also significantly promoted the release of nutrients ( < 0.05). Mixed-species samples had the fastest release rates of carbon and nutrients in the flooded hydrological process in the first half of the year and the unflooded hydrological process in the second half of the year. Foliage decomposition was also closely related to environmental factors, such as water depth, temperature, and hydrological processes. Our research clarified the material cycling and energy flow process of the riparian ecosystem in the Three Gorges Reservoir area. It also provided a new reference for further understanding of foliage decomposition and nutrient release under different hydrological environments.
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http://dx.doi.org/10.3389/fpls.2021.661865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8187854PMC
May 2021

Community Trait Responses of Three Dominant Macrophytes to Variations in Flooding During 2011-2019 in a Yangtze River-Connected Floodplain Wetland (Dongting Lake, China).

Front Plant Sci 2021 28;12:604677. Epub 2021 May 28.

Key Laboratory of Agro-ecological Processes in Subtropical Region, The Chinese Academy of Sciences, Changsha, China.

In lacustrine wetlands connected to rivers, the changes in flood regimes caused by hydrological projects lead to changes in the community traits of dominant macrophytes and, consequently, influence the structure and function of wetland vegetation. However, community trait responses of macrophytes to the timing and duration of flood disturbance have been rarely quantified. In 2011-2019, we investigated plant species diversity, density, and biomass in three dominant macrophyte communities ( C.B. Clarke, (Maxim.) Hackel, and L.) through monthly field surveys in Dongting Lake wetlands. Partial least squares regressions were used to analyze how the variations in hydrological regimes affected plant community traits. Apparent inter-annual fluctuations in plant community traits were detected during 2011-2019. The species richness and Shannon index of diversity of and communities increased, whereas the Shannon index of diversity of community decreased. Variation in flooding had a greater effect on and community traits than on community traits. Flooding disturbed all plant communities, especially when the duration and timing varied. Shorter inundation periods caused the biomass of community to decline, and that of and communities to increase. Earlier flood recession caused the species richness and Shannon index of diversity of and community to increase, and those of community to decrease. These findings imply that shorter inundation durations and earlier flood recession generated by the operation of the Three Gorges Dam have changed the macrophyte growth pattern.
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http://dx.doi.org/10.3389/fpls.2021.604677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8193728PMC
May 2021

The Diagnostic and Prognostic Potential of the B-Cell Repertoire in Membranous Nephropathy.

Front Immunol 2021 27;12:635326. Epub 2021 May 27.

Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China.

Membranous nephropathy (MN), an autoimmune glomerular disease, is one of the most common causes of nephrotic syndrome in adults. In current clinical practice, the diagnosis is dependent on renal tissue biopsy. A new method for diagnosis and prognosis surveillance is urgently needed for patients. In the present study, we recruited 66 MN patients before any treatment and 11 healthy control (HC) and analyzed multiple aspects of the immunoglobulin heavy chain (IGH) repertoire of these samples using high-throughput sequencing. We found that the abnormalities of CDR-H3 length, hydrophobicity, somatic hypermutation (SHM), and germ line index were progressively more prominent in patients with MN, and the frequency of in post-therapy patients was significantly lower than that in pre-therapy patients. Moreover, we found that the gene was significantly related to PLA2R, which is the most commonly used biomarker. The most important discovery was that several , transcripts, CDR-H3 length, and SHM rate in pre-therapy patients had the potential to predict the therapeutic effect. Our study further demonstrated that the IGH repertoire could be a potential biomarker for prognosis prediction of MN. The landscape of circulating B-lymphocyte repertoires sheds new light on the detection and surveillance of MN.
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http://dx.doi.org/10.3389/fimmu.2021.635326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190383PMC
May 2021

Effect of COVID-19 on Male Reproductive System - A Systematic Review.

Front Endocrinol (Lausanne) 2021 27;12:677701. Epub 2021 May 27.

Scientific Research and Training Office, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China.

Background: Angiotensin-converting enzyme II (ACE2), a receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to enter host cells, is widely expressed in testes and prostate tissues. The testis and prostate produce semen. At present, there are contradictory reports about whether SARS-CoV-2 can exist in the semen of infected men.

Objective: To provide a comprehensive overview of the topic of whether COVID-19 can impact on male reproductive system.

Methods: We reviewed the relevant publications on the possible impact of Coronavirus Disease 2019 (COVID-19) on male reproductive system and summarized the latest and most important research results so far. Literature published in English from December 2019 to January 31, 2021 regarding the existence of SARS-CoV-2 in semen, testis, and prostatic fluid and the effects of COVID-19 on male reproductive were included.

Results: We identified 28 related studies, only one of which reported the presence of SARS-CoV-2 in semen. The study found that the semen quality of patients with moderate infection was lower than that of patients with mild infection and healthy controls. The impaired semen quality may be related to fever and inflammation. Pathological analysis of the testis/epididymis showed that SARS-CoV-2 viral particles were positive in 10 testicular samples, and the spermatogenic function of the testis was impaired. All 94 expressed prostatic secretion (EPS) samples were negative for SARS-CoV-2 RNA.

Conclusion: The likelihood of SARS-CoV-2 in the semen of COVID-19 patients is very small, and semen should rarely be regarded as a carrier of SARS-CoV-2 genetic material. However, COVID-19 may cause testicular spermatogenic dysfunction immune or inflammatory reactions. Long-term follow-up is needed for COVID-19 male patients and fetuses conceived during the father's infection period.
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http://dx.doi.org/10.3389/fendo.2021.677701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190708PMC
May 2021

Current and Future Roles of Circular RNAs in Normal and Pathological Endometrium.

Front Endocrinol (Lausanne) 2021 26;12:668073. Epub 2021 May 26.

Department of Gynecology, Shenzhen Second People's Hospital/The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China.

The uterine endometrium, which lines the mammalian uterus, is essential for embryo implantation. This lining undergoes significant changes during sexual and menstrual cycles. The endometrium is also associated with hormone-related diseases such as endometriosis and endometrial cancer. Circular RNAs (circRNAs) play a role in various biological processes. Recent studies have determined that circRNAs function in both normal and pathological endometrial environments. Here, we review high-throughput studies pertaining to circRNAs as well as individual circRNAs active in the endometrium, in order to explore the myriad functions of circRNAs in the endometrium and mechanisms underlying these functions, from panoramic and individual perspectives. Owing to their abundant expression, stability, and small size, circRNAs have displayed potential usefulness as diagnostic markers and treatment targets for endometrial-related diseases. Therefore, the specific role of circRNAs in the endometrium warrants systematic investigation in the future.
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http://dx.doi.org/10.3389/fendo.2021.668073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8187767PMC
May 2021

Pyrethroids Toxicity to Male Reproductive System and Offspring as a Function of Oxidative Stress Induction: Rodent Studies.

Front Endocrinol (Lausanne) 2021 27;12:656106. Epub 2021 May 27.

The State Key Lab of Reproductive, Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.

Pyrethroids may be related to male reproductive system damage. However, the results of many previous studies are contradictory and uncertain. Therefore, a systematic review and a meta-analysis were performed to assess the relationship between pyrethroid exposure and male reproductive system damage. A total of 72 articles were identified, among which 57 were selected for meta-analysis, and 15 were selected for qualitative analysis. Pyrethroid exposure affected sperm count (SMD= -2.0424; 95% CI, -2.4699 to -1.6149), sperm motility (SMD=-3.606; 95% CI, -4.5172 to -2.6948), sperm morphology (SMD=2.686; 95% CI, 1.9744 to 3.3976), testis weight (SMD=-1.1591; 95% CI, -1.6145 to -0.7038), epididymal weight (SMD=-1.1576; 95% CI, -1.7455 to -0.5697), and serum testosterone level (SMD=-1.9194; 95% CI, -2.4589 to -1.3798) in the studies of rats. We found that gestational and lactational exposure to pyrethroids can reduce sperm count (SMD=1.8469; 95% CI, -2.9010 to -0.7927), sperm motility (SMD=-2.7151; 95% CI, -3.9574 to -1.4728), testis weight (SMD=-1.4361; 95% CI, -1.8873 to -0.9848), and epididymal weight (SMD=-0.6639; 95% CI, -0.9544 to -0.3733) of F1 offspring. Exposure to pyrethroids can increase malondialdehyde (SMD=3.3451; 95% CI 1.9914 to 4.6988) oxide in testes and can reduce the activities of glutathione (SMD=-2.075; 95% CI -3.0651 to -1.0848), superoxide dismutase (SMD=-2.4856; 95% CI -3.9612 to -1.0100), and catalase (SMD=-2.7564; 95% CI -3.9788 to -1.5340). Pyrethroid exposure and oxidative stress could damage male sperm quality. Gestational and lactational pyrethroid exposure affects the reproductive system of F1 offspring.
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http://dx.doi.org/10.3389/fendo.2021.656106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190395PMC
May 2021

Negative Emotion Arousal and Altruism Promoting of Online Public Stigmatization on COVID-19 Pandemic.

Front Psychol 2021 26;12:652140. Epub 2021 May 26.

School of Business Administration and Tourism Management, Yunnan University, Kunming, China.

The outbreak of COVID-19 is a public health crisis that has had a profound impact on society. Stigma is a common phenomenon in the prevalence and spread of infectious diseases. In the crisis caused by the pandemic, widespread public stigma has influenced social groups. This study explores the negative emotions arousal effect from online public stigmatization during the COVID-19 pandemic and the impact on social cooperation. We constructed a model based on the literature and tested it on a sample of 313 participants from the group being stigmatized. The results demonstrate: (1) relevance and stigma perception promote negative emotions, including anxiety, anger, and grief; (2) the arousal of anger and grief leads to a rise in the altruistic tendency within the stigmatized group; and (3) stigmatization-induced negative emotions have a complete mediating effect between perceived relevance and altruistic tendency, as well as perceived stigma and altruistic tendency. For a country and nation, external stigma will promote the group becoming more united and mutual help. One wish to pass the buck but end up helping others unintentionally. We should not simply blame others, including countries, regions, and groups under the outbreak of COVID-19, and everyone should be cautious with the words and actions in the Internet public sphere.
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http://dx.doi.org/10.3389/fpsyg.2021.652140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8187574PMC
May 2021

Combination of AZD3463 and DZNep Prevents Bone Metastasis of Breast Cancer by Suppressing Akt Signaling.

Front Pharmacol 2021 28;12:652071. Epub 2021 May 28.

Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Osteolysis resulting from osteoclast overactivation is one of the severe complications of breast cancer metastasis to the bone. Previous studies reported that the anti-cancer agent DZNep induces cancer cell apoptosis by activating Akt signaling. However, the effect of DZNep on breast cancer bone metastasis is unknown. We previously found that DZNep enhances osteoclast differentiation by activating Akt. Therefore, we explored the use of the anti-cancer agent AZD3463 (an Akt inhibitor) along with DZNep, as AZD3463 can act as an anti-cancer agent and can also potentially ameliorate bone erosion. We evaluated osteoclast and breast cancer cell phenotypes and Akt signaling by treating cells with DZNep and AZD3463. Furthermore, we developed a breast cancer bone metastasis animal model in mouse tibiae to further determine their combined effects . Treatment of osteoclast precursor cells with DZNep alone increased osteoclast differentiation, bone resorption, and expression of osteoclast-specific genes. These effects were ameliorated by AZD3463. The combination of DZNep and AZD3463 inhibited breast cancer cell proliferation, colony formation, migration, and invasion. Finally, intraperitoneal injection of DZNep and AZD3463 ameliorated tumor progression and protected against bone loss. In summary, DZNep combined with AZD3463 prevented skeletal complications and inhibited breast cancer progression by suppressing Akt signaling.
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http://dx.doi.org/10.3389/fphar.2021.652071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8193724PMC
May 2021

The Optimal Adjuvant Strategy of Aidi Injection With Gemcitabine and Cisplatin in Advanced Non-small Cell Lung Cancer: A Meta-analysis of 70 Randomized Controlled Trials.

Front Pharmacol 2021 28;12:582447. Epub 2021 May 28.

Department of General Practice, Affiliated Hospital of Zunyi Medical University, Zunyi, China.

Aidi injection (Aidi) is composed of cantharidin, astragaloside, ginsenoside, and elentheroside E. As an important adjuvant therapy, Aidi in combination with gemcitabine and cisplatin (GP) is often used in the treatment of non-small cell lung cancer (NSCLC). We performed a new evaluation to demonstrate the clinical efficacy and safety of the Aidi and GP combination and further explored an optimal strategy for achieving an ideal response and safety level in advanced NSCLC. We collected all the related trials from Chinese and English-language databases, analyzed their methodological bias risk using the Cochrane evaluation Handbook for Systematic Reviews of Interventions Version 5.1.0, extracted all the data using a predefined data extraction form, pooled the data using a series of meta-analyses, and finally summarized the quality of evidence using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. We included 70 trials with 5,509 patients. Compared with GP alone, the Aidi and GP combination showed a significant improvement in the objective response rate (ORR) [1.82 (1.62-2.04)], disease control rate (DCR) [2.29 (1.97-2.67)], and quality of life (QOL) [3.03 (2.55-3.60)] and a low incidence of hematotoxicity and gastrointestinal and hepatorenal toxicity. Aidi might be more suitable for patients who are first-treated, elderly, or patients with a Karnofsky Performance Status (KPS) score ≥ 60 or anticipated survival time (AST) ≥3 months. An Aidi (50 ml/day, 7-14 days/cycle for one to two cycles), gemcitabine (1000 mg/m), and cisplatin (20-30 mg/m, 40-50 mg/m, or 60-80 mg/m) might be an optimal regimen for realizing an ideal response and safety level. Most results were robust and of moderate quality. Current evidence indicates that Aidi's value in adjuvant chemotherapy may be broad-spectrum, not just for some regimens. The Aidi and GP combination may show a good short-term response, antitumor immunity, and safety level in patients with NSCLC. Aidi (50 ml/day, 7-14 days/cycle for one and two cycles) with GEM (1000 mg/m) and DDP (20-30 mg/m or 40-50 mg/m) may be an optimal regimen for realizing an ideal goal in patients who are first-treatment, elderly, or have a KPS score ≥ 60 or AST≥3 months.
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http://dx.doi.org/10.3389/fphar.2021.582447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8194277PMC
May 2021

In Vitro and In Vivo Comparative Evaluation of a Shellac-Ammonium Paclitaxel-Coated Balloon versus a Benchmark Device.

J Interv Cardiol 2021 25;2021:9962313. Epub 2021 May 25.

Department of Medical Affair, Cardionovum Co, Ltd, Wuhan, China.

Objectives: The present study was designed to compare the characteristics and performance regarding drug delivery of a novel drug-coated balloon (DCB) to a benchmark device (Restore® versus SeQuent® Please) in an in vitro and in vivo model.

Background: Although Restore® and SeQuent® are both paclitaxel-coated, they use different coating excipient, shellac-ammonium salt and iopromide, respectively. Preclinical study comparing these two different commercial DCBs regarding their characteristics and effects on early vascular response is sparse.

Methods: Restore® and SeQuent® DCBs were scanned with electron microscopy for surface characteristic assessment. Both DCBs were transported in an in vitro vessel model for the evaluation of drug wash-off rate and particulate formation. Eighteen coronary angioplasties with either Restore® or SeQuent® DCBs were conducted in 6 swine (three coronary vessels each). Histopathological images of each vessel were evaluated for vessel injury.

Results: The surface of Restore® DCB was smooth and evenly distributed with hardly visible crystal, while SeQuent® DCB showed a rougher surface with relatively larger apparent crystals. Restore® DCB had a lower drug wash-off rate and fewer large visible particles, compared to the SeQuent® DCB. No significant difference in mean injure score was found between Restore® and SeQuent® group.

Conclusion: Our results suggest that Restore® is better in preclinical performance regarding less release of particles and lower drug wash-off rate as compared to SeQuent® Please. The Restore® DCB, using stable amorphous coating and shellac-ammonium salt as an excipient, appears to provide an advantage in drug delivery efficacy; however, further clinical studies are warranted.
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http://dx.doi.org/10.1155/2021/9962313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8172300PMC
May 2021

Poly(vinyl alcohol) Hydrogels with Integrated Toughness, Conductivity, and Freezing Tolerance Based on Ionic Liquid/Water Binary Solvent Systems.

ACS Appl Mater Interfaces 2021 Jun 13. Epub 2021 Jun 13.

State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Shanghai Stomatological Hospital, Laboratory of Advanced Materials, Fudan University, 220 Handan Road, Shanghai 200433, People's Republic of China.

In recent years, ionic conductive hydrogels have shown great potential for application in flexible sensors, energy storage devices, and actuators. However, developing facile and effective methods for fabricating such hydrogels remains a great challenge, especially for hydrogels that retain their properties in extreme environmental conditions, such as at subzero temperatures or storage in open-air conditions. Herein, a water-miscible ionic liquid (IL), such as 1-ethyl-3-methylimidazolium acetate (EMImAc), was introduced to form an IL/water binary solvent system for poly(vinyl alcohol) (PVA) to create ionic conductive PVA hydrogels. The physically crosslinked PVA/EMImAc/HO hydrogels showed better mechanical properties and transparency than the traditional PVA hydrogel prepared by the freeze-thaw method due to the formation of homogeneous and small PVA microcrystals in the EMImAc/HO binary solvent system. More importantly, the PVA/EMImAc/HO hydrogel exhibited significant anti-freezing and water-retaining properties because of the presence of the IL. The hydrogels remained flexible and conductive at temperatures as low as -50 °C and retained more than 90% of their weight after storage in open-air conditions for 2 weeks. In addition, the thermal stability of the hydrogel could be increased to 95 °C through the addition of Mg(II) ions. A multimodal sensor based on the PVA/EMImAc/HO/Mg(II) hydrogel showed high sensitivity and a quick response to changes in pressure, strain, and temperature, with both long-term stability and a wide working temperature range. This study may open a new route for the fabrication of functional PVA-based hydrogel electrolytes and provide a practical pathway for their use in multifunctional electronic and sensory device applications.
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http://dx.doi.org/10.1021/acsami.1c09006DOI Listing
June 2021

RANKL from bone marrow adipose lineage cells promotes osteoclast formation and bone loss.

EMBO Rep 2021 Jun 13:e52481. Epub 2021 Jun 13.

Institute of Translational Medicine, Shanghai University, Shanghai, China.

Receptor activator of NF-κB ligand (RANKL) is essential for osteoclast formation and bone remodeling. Nevertheless, the cellular source of RANKL for osteoclastogenesis has not been fully uncovered. Different from peripheral adipose tissue, bone marrow (BM) adipose lineage cells originate from bone marrow mesenchymal stromal cells (BMSCs). Here, we demonstrate that adiponectin promoter-driven Cre expression (Adipoq ) can target bone marrow adipose lineage cells. We cross the Adipoq mice with rankl mice to conditionally delete RANKL from BM adipose lineage cells. Conditional deletion of RANKL increases cancellous bone mass of long bones in mice by reducing the formation of trabecular osteoclasts and inhibiting bone resorption but does not affect cortical bone thickness or resorption of calcified cartilage. Adipoq ; rankl mice exhibit resistance to estrogen deficiency and rosiglitazone (ROS)-induced trabecular bone loss but show bone loss induced by unloading. BM adipose lineage cells therefore represent an essential source of RANKL for the formation of trabecula osteoclasts and resorption of cancellous bone during remodeling under physiological and pathological conditions. Targeting bone marrow adiposity is a promising way of preventing pathological bone loss.
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http://dx.doi.org/10.15252/embr.202152481DOI Listing
June 2021

Race/Ethnicity, Nativity Status, and Patient Portal Access and Use.

J Health Care Poor Underserved 2021 ;32(2):700-711

We examined whether patient portal (online medical records) access and use differed between groups of various races/ethnicities and nativity status. We used data from the nationally representative Health Information National Trends Survey (N=3,191). We used logistic regression to examine associations between nativity status and the following three binary outcomes: (1) being offered access to patient portals by health care providers/insurers, (2) being encouraged to use one by their health care providers, and (3) having used one within the past 12 months. We also investigated whether race/ethnicity moderated the relation between nativity status and these three outcomes. Among Asians, the likelihood of being offered access to a patient portal depended on nativity status. U.S.-born Asians had the highest rate of being offered access to a portal (66%) and foreign-born Asians had the lowest rate (38%). There were no differences as a function of nativity status for other racial/ethnic groups.
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http://dx.doi.org/10.1353/hpu.2021.0099DOI Listing
January 2021

Effect of CAD-CAM ceramic materials on the color match of veneer restorations.

J Prosthet Dent 2021 Jun 11. Epub 2021 Jun 11.

Professor, Department of Prosthodontics, Dalian Stomatological Hospital, Dalian, PR China. Electronic address:

Statement Of Problem: With the different translucency levels and types of computer-aided design and computer-aided manufacturing (CAD-CAM) ceramic materials, choosing the most appropriate CAD-CAM ceramic materials to better reproduce the color appearance of natural teeth can be challenging.

Purpose: The purpose of this in vitro study was to analyze the color differences between natural teeth and milled veneers fabricated with the different types of CAD-CAM ceramic materials.

Material And Methods: Ten extracted maxillary central incisor teeth with the A2 shade in the body region were prepared for ceramic veneers. The veneer restorations were designed by using the duplicating method and fabricated from 9 milling blocks (IPS e.max CAD HT/LT, Lava Ultimate CAD HT/LT, VITA SUPRINITY HT/T, IPS Empress CAD HT/LT/Multi) in a dental milling unit (n=10). The bonding surface of the abutment tooth was coated with a thin layer of a separating agent, and the veneer specimen with resin cement was then bonded to the corresponding abutment tooth. A clinical spectrophotometer was used to measure the Commission Internationale de l'Eclairage Lab values of natural teeth, abutment teeth, and milled veneers in the cervical, body, and incisal regions. Color differences between the natural tooth and A2 shade tab (ΔE) and between the milled veneer and natural tooth (ΔE) were calculated. The ΔE values were compared with the perceptibility threshold (ΔE=2.6) and acceptability threshold (ΔE=5.5). The paired-samples t test, 1-way analysis of covariance, and 2-way ANOVA were used to analyze data (α=.05).

Results: The results of 1-way analysis of covariance showed that ceramic materials significantly affected the a∗ and b∗ values of the milled veneers (P<.001) but did not affect the L∗ values of the milled veneers (P>.05). The results of 2-way ANOVA indicated that the ΔE values were not significantly affected by different CAD-CAM ceramic materials (F=1.560, P=.138), while statistically significant differences were found in the veneer regions (F=6.588, P=.002). The ΔE values ranged from 2.41 to 5.36, less than the clinically acceptable color threshold of 5.5.

Conclusions: The color parameters of milled veneers were affected by the different types of CAD-CAM ceramic materials. The color of the veneer restoration was able to match that of the natural tooth.
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http://dx.doi.org/10.1016/j.prosdent.2021.04.029DOI Listing
June 2021

Activated Th9 cells in diabetic coronary heart disease.

J Biol Regul Homeost Agents 2021 Jun 14;35(3). Epub 2021 Jun 14.

Department of Endocrinology, Changzheng Hospital, Naval Medical University, Shanghai, China.

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http://dx.doi.org/10.23812/20-703-LDOI Listing
June 2021

Functional examination of lncRNAs in allotetraploid Gossypium hirsutum.

BMC Genomics 2021 Jun 13;22(1):443. Epub 2021 Jun 13.

College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China.

Background: An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown.

Results: We employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. LncRNA expression was preferentially associated with that of the flanking PCGs. Selected highly-expressed lncRNA candidates (n = 111) were subjected to a functional screening pilot test in which virus-induced gene silencing was integrated with abiotic stress treatment. From this low-throughput screen, we obtained candidate lncRNAs relating to plant height and tolerance to drought and other abiotic stresses.

Conclusions: Low-throughput screen is an effective method to find functional lncRNA for further study. LncRNAs were more active in abiotic stresses than PCG expression, especially temperature stress. LncRNA XLOC107738 may take a cis-regulatory role in response to environmental stimuli. The degree to which lncRNAs are constitutively expressed may impact expression patterns and functions on the individual gene level rather than in genome-wide aggregate.
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http://dx.doi.org/10.1186/s12864-021-07771-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201905PMC
June 2021

NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes.

BMC Bioinformatics 2021 Jun 13;22(1):321. Epub 2021 Jun 13.

Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China.

Background: Nucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organization in mammalian genomes are very limited mainly due to the lack of comprehensive data quality control (QC) assessment and uneven data quality of public data sets.

Results: The NUCOME is a database focused on filtering qualified nucleosome organization referenced landscapes covering various cell types in human and mouse based on QC metrics. The filtering strategy guarantees the quality of nucleosome organization referenced landscapes and exempts users from redundant data set selection and processing. The NUCOME database provides standardized, qualified data source and informative nucleosome organization features at a whole-genome scale and on the level of individual loci.

Conclusions: The NUCOME provides valuable data resources for integrative analyses focus on nucleosome organization. The NUCOME is freely available at http://compbio-zhanglab.org/NUCOME .
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http://dx.doi.org/10.1186/s12859-021-04239-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201709PMC
June 2021