Publications by authors named "Xin Chen"

3,951 Publications

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Novel Long Non-coding RNA Expression Profile of Peripheral Blood Mononuclear Cells Reveals Potential Biomarkers and Regulatory Mechanisms in Systemic Lupus Erythematosus.

Front Cell Dev Biol 2021 2;9:639321. Epub 2021 Jun 2.

Department of Rheumatology, School of Medicine, The Second Affiliated Hospital, Zhejiang University, Hangzhou, China.

Objective: The multisystem involvement and high heterogeneity of systemic lupus erythematosus (SLE) lead to great challenges in its diagnosis and treatment. The purpose of this study was to find new lncRNAs in peripheral blood mononuclear cells of SLE patients by transcriptome sequencing and explore their potential as biomarkers and their correlation with clinical features.

Materials And Methods: Transcriptome sequencing was used to screen differentially expressed lncRNAs (DELs) and mRNAs (DEMs). The expression of these selected lncRNAs and mRNAs in SLE patients and healthy controls was verified by qPCR. DAVID and WebGestalt were used to perform enrichment analysis. Cytoscape was used to construct a protein-protein network, a coexpression network, and a competitive endogenous RNA network to reveal the regulatory mechanisms of lncRNAs at the transcriptome level.

Results: A total of 1737 DELs and 4078 DEMs were identified between SLE patients and healthy controls. Ten lncRNAs and eight genes were verified by qPCR in a larger sample set. The lncRNA was significantly downregulated in SLE patients and was also significantly related to the activity and severity of disease. The upregulated genes were enriched in defense and the immune response, while the downregulated genes were mainly enriched in SLE-related pathways. Topology network analysis revealed that the lncRNAs were involved in regulation at the transcriptome level, including acting directly on mRNA or indirectly affecting gene expression by acting on miRNA.

Conclusion: In this work, we identified many mRNAs and novel lncRNAs by transcriptome sequencing. The functions and regulatory mechanisms of these lncRNAs were analyzed by bioinformatic methods. The novel lncRNA is significantly downregulated in SLE patients and is significantly related to the activity and severity of disease. Additionally, we propose that may enhance the signal transduction of β2-AR by cis regulating , inducing NK cells to produce high levels of IFN-γ and thereby exacerbating SLE.
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http://dx.doi.org/10.3389/fcell.2021.639321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8208038PMC
June 2021

Untargeted Global Metabolomic Analysis Reveals the Mechanism of Tripropylamine-Enhanced Lycopene Accumulation in .

Front Bioeng Biotechnol 2021 2;9:673225. Epub 2021 Jun 2.

Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China.

We previously determined that the cyclase inhibitor tripropylamine (TPA) significantly enhances lycopene accumulation in . To elucidate the mechanism of TPA-enhanced lycopene accumulation, the untargeted metabolome of treated with TPA was analyzed by UHPLC-Q-TOF/MS. Forty-two differential metabolites were identified, of which 15 significantly differential metabolites meeting the following parameters were screened: variable importance for the projection > 1, < 0.05, and fold change > 1.5. The down-regulated metabolites were mainly cyclic dipeptides, bacteriostatic compounds, and lipids, while the up-regulated metabolites were mainly unsaturated fatty acid. Furthermore, the bacteriostatic ability was poor, the extracellular and intracellular pH levels were high, and hyphae with vesicles were swollen locally in after treatment with TPA. Our data suggest that the TPA enhances lycopene accumulation not only by inhibiting the cyclization of β-carotene but also by down-regulating cyclic dipeptides for quorum sensing; up-regulating unsaturated fatty acids, 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine, and 4-hydroxybenzoate and down-regulating choline, resulting in locally swelling mycelium with vacuoles; and down-regulating bacteriostatic metabolites for metabolic flux redistribution.
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http://dx.doi.org/10.3389/fbioe.2021.673225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8207141PMC
June 2021

Anti-Tumor Effects of in Acute Myeloid Leukemia.

Front Oncol 2021 4;11:694594. Epub 2021 Jun 4.

Department of Pharmacology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.

Dysregulation of ketone metabolism has been reported in various types of cancer. In order to find out its role in acute myeloid leukemia (AML) pathogenesis, we first analyzed the expression levels of 10 key genes involved in ketone metabolism in AML blasts and CD34 hematopoietic stem cells (HSCs) from healthy donors. We found that the expression level of was significantly lower in AML than in normal HSCs. The downregulation of gene expression in AML cell lines as compared with normal HSCs was further confirmed with real-time RT-PCR. Analysis of TCGA and other database revealed that the downregulation of was associated with worse prognosis in AML patients. In addition, we showed that overexpression of inhibited the viability and proliferation of AML cells. In contrast, knock-down promoted AML cell growth. Collectively, our results suggest the previously unappreciated anti-tumor role of in AML, and low expression predicts poor survival.
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http://dx.doi.org/10.3389/fonc.2021.694594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8213090PMC
June 2021

BiOBr anchored on TiC MXene with ohmic heterojunction in photocatalytic NH production: Insights from combined experimental and theoretical calculations.

J Colloid Interface Sci 2021 Jun 11;602:553-562. Epub 2021 Jun 11.

Shaanxi Key Laboratory of Chemical Reaction Engineering, Yan'an University, Yanan 716000, PR China.

Nitrogen-to-ammonia conversion under mild conditions offers a tremendous prospect as a sustainable technology for synthesizing ammonia (NH) in the future. In this study, we elaborately designed BiOBr/TiC heterojunction combined with electrostatic adsorption with in-situ growth to form a photocatalyst with a 2D/2D structure. This unique structure substantially improved the exposure of active edge sites for photocatalytic dinitrogen reduction reaction. Notably, TiC MXene acted as an efficient cocatalyst for the conversion of N to NH of BiOBr/TiC with a yield of 277.74 μmol gh without the use of a sacrificial agent; this yield was five times higher than that of BiOBr. Density functional theory calculations demonstrated that the ohmic contact was at the BiOBr/TiC interface. The ohmic heterojunction could expedite the separation of spatial carriers and extraction of photoexcited charge carriers, which had outstanding reducibility to cleavage the N≡N bond. This work provides a novel strategy for designing highly efficient BiOBr-based photocatalysts through the integration of multifunctional materials. This work also offers guidance for implementing high-performance nitrogen-to-ammonia conversion by introducing interfacial modifiers.
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http://dx.doi.org/10.1016/j.jcis.2021.06.049DOI Listing
June 2021

On-demand manipulation of tumorigenic microenvironments by nano-modulator for synergistic tumor therapy.

Biomaterials 2021 Jun 12;275:120956. Epub 2021 Jun 12.

State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China.

Proper manipulation of tumorigenic microenvironments has been considered as one of the most effective approaches for tumor therapy, which is still a challenge to be well performed. Herein, a nano-modulator was fabricated to manipulate the hypoxia, glucose, radicals and local temperature in tumor tissue as needed, which consists of hemoglobin (Hb) and ferric ion (Fe) co-conjugated polydopamine (PDA) as core, glucose oxidase (GOD) as shell, and folic acid (FA) modified polyethylene glycol (PEG) as corona. The PEG-FA corona not only protected Hb and GOD against protease in blood circulation, but serve as tumor targeting agent for tumor specific accumulation of the nano-modulator. The Hb is in charge of oxygen supply to reverse the hypoxic environment of tumor tissue, which promotes the function of GOD to achieve rapid glucose consumption and hydrogen peroxide generation. The polydopamine was employed to raise local temperature under NIR irradiation, meanwhile to continuously reduce Fe to produce ferrous ions (Fe), which further catalyze hydrogen peroxide to cytotoxic hydroxyl radicals via Fenton reaction. Both in vitro and in vivo results showed excellent tumor inhibition and high survival rate of tumor-bearing mice after treatment by our nano-modulator, indicating this synergistic therapy via on-demand manipulation of various tumorigenic microenvironments could be a green approach for tumor treatment with high efficiency and minimum side effects.
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http://dx.doi.org/10.1016/j.biomaterials.2021.120956DOI Listing
June 2021

Exosomal miR-2276-5p in Plasma Is a Potential Diagnostic and Prognostic Biomarker in Glioma.

Front Cell Dev Biol 2021 1;9:671202. Epub 2021 Jun 1.

Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.

Introduction: Exosomal microRNAs (miRNAs) play an essential role in near and distant intercellular communication and are potential diagnostic and prognostic biomarkers for various cancers. This study focused on evaluation of exosomal miR-2276-5p in plasma as a diagnostic and prognostic biomarker for glioma.

Methods: Plasma exosomes from 124 patients with glioma and 36 non-tumor controls were collected and subjected to quantitative real-time polymerase chain reaction (qRT-PCR) analysis for the exosomal miR-2276-5p expression. Bioinformatic analyses were performed to identify a gene target, and CGGA and TCGA databases were checked for evaluation of prognostic relevance.

Results: The exosomal miR-2276-5p in glioma patients had a significantly decreased expression, compared with non-glioma patients ( < 0.01). Receiver operating characteristics (ROC) curve analyses were observed to regulate the diagnostic sensitivity and specificity of miR-2276-5p in glioma; the area under the curve (AUC) for miR-2276-5p was 0.8107. The lower expression of exosomal miR-2276-5p in patients with glioma correlated with poorer survival rates. RAB13 was identified as the target of miR-2276-5p which was high in glioma patients, especially those with higher tumor grades and correlated with poor survival.

Conclusion: The circulating exosomal miR-2276-5p is significantly reduced in the plasma of glioma patients, and thus, it could be a potential biomarker for patients with glioma for diagnostic and/or prognostic purposes.
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http://dx.doi.org/10.3389/fcell.2021.671202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8204016PMC
June 2021

Epitaxial Lift-Off of Flexible GaN-Based HEMT Arrays with Performances Optimization by the Piezotronic Effect.

Nanomicro Lett 2021 Feb 10;13(1):67. Epub 2021 Feb 10.

Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 100083, People's Republic of China.

High-electron-mobility transistors (HEMTs) are a promising device in the field of radio frequency and wireless communication. However, to unlock the full potential of HEMTs, the fabrication of large-size flexible HEMTs is required. Herein, a large-sized (> 2 cm) of AlGaN/AlN/GaN heterostructure-based HEMTs were successfully stripped from sapphire substrate to a flexible polyethylene terephthalate substrate by an electrochemical lift-off technique. The piezotronic effect was then induced to optimize the electron transport performance by modulating/tuning the physical properties of two-dimensional electron gas (2DEG) and phonons. The saturation current of the flexible HEMT is enhanced by 3.15% under the 0.547% tensile condition, and the thermal degradation of the HEMT was also obviously suppressed under compressive straining. The corresponding electrical performance changes and energy diagrams systematically illustrate the intrinsic mechanism. This work not only provides in-depth understanding of the piezotronic effect in tuning 2DEG and phonon properties in GaN HEMTs, but also demonstrates a low-cost method to optimize its electronic and thermal properties.
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http://dx.doi.org/10.1007/s40820-021-00589-4DOI Listing
February 2021

Polysaccharide from attenuates markers of metabolic syndrome by modulating the gut microbiota and lipid metabolism in high fat diet-fed mice.

Food Funct 2021 Jun 17. Epub 2021 Jun 17.

College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.

Natural biological macromolecules with putative functions of gut microbiota regulation possess the advantage of improving metabolic syndrome (MS). In this research, we aimed to determine the effects of Flammulina velutipes polysaccharide (FVP) (Expt. 1) and fecal microbiota transplantation (FMT) (Expt. 2) on MS-related disorders, gut microbiota structure changes and their underlying mechanisms in a murine model fed with high-fat diet (HFD). In Expt. 1, six-week-old male C57BL/6J mice were fed with a control diet (10% calories from fat) or a high fat diet (45% calories from fat), administered with saline or FVP (0.4 mg per g b.w.) by gavage over a 12-week period. In Expt. 2, mice were fed with a HFD, administered with fecal supernatants from healthy and FVP-fed donor mice for 12 weeks simultaneously. The body mass, blood lipid levels and blood glucose homeostasis of mice were analyzed, and total RNA from mouse liver and adipose tissue were extracted by TRIzol and the lipid metabolism-related gene expressions were calculated by qRT-PCR. Gut microbiota changes were evaluated by high-throughput sequencing. Results indicated that FVP and FMT supplementations showed an attenuation effect on mouse obesity, hyperlipidemia and insulin resistance. Up-regulated expressions of Ampkα1 and Ppara were found both in FVP and FMT treatment groups. Different changes were found in the gut microbiota caused by FVP and FMT, respectively. PICRUSt analysis indicated that compared with FVP supplementation, FMT showed a significant effect on regulating lipid metabolism in HFD-fed mice. The findings from this study indicated that oral administrations of FVP or FMT could significantly attenuate MS-related obesity, hyperlipidemia and insulin resistance in HFD-fed mice, and the beneficial effects may be mediated through lipid metabolism and gut microbiota regulation in different ways. These results improve the understanding of the functional activity of FVP as prebiotics.
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http://dx.doi.org/10.1039/d1fo00534kDOI Listing
June 2021

Boron Dopant Induced Electron-Rich Bismuth for Electrochemical CO Reduction with High Solar Energy Conversion Efficiency.

Small 2021 Jun 16:e2101128. Epub 2021 Jun 16.

TJU-NIMS International Collaboration Laboratory, Key Lab of Advanced Ceramics and Machining Technology (Ministry of Education) and Tianjin Key Laboratory of Composite and Functional Materials, School of Material Science and Engineering, Tianjin University, 92 Weijin Road, Tianjin, 300072, P. R. China.

Electrochemical CO reduction to formate offers a mild and feasible pathway for the utilization of CO , and bismuth is a promising metal for its unique hydrogen evolution reaction inhibition. Reported works of Bi-based electrodes generally exhibit high selectivity while suffering from relatively narrow working potential range. From the perspective of electronic modification engineering, B-doped Bi is prepared by a facile chemical reduction method in this work. With B dopant, above 90% Faradaic efficiency for formate over a broad window of working potential of -0.6 to -1.2 V (vs. reversible hydrogen electrode) is achieved. In situ Raman spectroscopy, X-ray adsorption spectroscopy, and computational analysis demonstrate that the B dopant induces the formation of electron-rich bismuth, which is in favor of the formation of formate by fine-tuning the adsorption energy of *OCHO. Moreover, full-cell electrolysis system coupled with photovoltaic device is constructed and achieves the solar-to-formate conversion efficiency as high as 11.8%.
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http://dx.doi.org/10.1002/smll.202101128DOI Listing
June 2021

YAP Accelerates NOTCH Driven Cholangiocarcinogenesis via mTORC1 in Mice.

Am J Pathol 2021 Jun 12. Epub 2021 Jun 12.

School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States. Electronic address:

Intrahepatic cholangiocarcinoma (iCCA) is a lethal malignancy with limited therapeutic options. Previously, we demonstrated that Notch1 overexpression alone suffices to induce iCCA in the mouse, albeit after long latency. Here, we show that activation of the Yap protooncogene occurs during Notch1 driven iCCA progression. After co-expressing activated Notch1 (Nicd) and Yap (YapS127A) in the mouse liver, rapid iCCA formation and progression occurred in Nicd/Yap mice. Mechanistically, an increased expression of amino acid transporters and activation of the mTORC1 signaling pathway was detected in Nicd/Yap mouse liver tumors. Significantly, the genetic deletion of Raptor, the major mTORC1 component, completely suppressed iCCA development in Nicd/Yap mice. Elevated expression of NOTCH1, YAP, amino acid transporters, and members of the mTORC1 pathway was also detected ubiquitously in a collection of human iCCA specimens. Their levels were associated with a poor patient outcome. Altogether, our study demonstrates that NOTCH and YAP concomitant activation is frequent in human cholangiocarcinogenesis. NOTCH and YAP synergize to promote iCCA formation by activating the mTORC1 pathway.
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http://dx.doi.org/10.1016/j.ajpath.2021.05.017DOI Listing
June 2021

Effects of seated lumbar rotation manipulation in treating degenerative lumbar instability: a protocol for a randomized controlled trial.

Trials 2021 Jun 14;22(1):398. Epub 2021 Jun 14.

Department of Spine, Wangjing Hospital of China Academy of Chinese Medical Sciences, Beijing, 100102, China.

Background: Degenerative lumbar instability (DLI) is a common disease that causes low back pain (LBP) in clinic. It is difficult to completely recover from DLI, and it occurs repeatedly, which seriously affects the quality of life of patients. The epidemiological survey showed that 20-30% of low back pain was related to lumbar instability. Increasing evidence shows that seated lumbar rotation manipulation can effectively improve the clinical symptoms of patients with low back pain. The primary aim of this clinical trial is to observe the intervention effect of seated lumbar rotation manipulation on DLI patients.

Method/design: A total of 60 participants with DLI will be recruited and randomly allocated into the seated lumbar rotation manipulation group (the intervention group) or lumbar traction in supine position group (the control group) in this prospective, outcome assessor-blind, two-arm randomized controlled clinical trial. The treatment of the two groups lasted for 3 weeks, and the manipulation of the intervention group would be carried out once every other day, three times a week, a total of 9 times; the control group would be given lumbar traction once a day, five times a week, a total of 15 times. JOA (Japanese Orthopaedic Association) and VAS (Visual Analogue Scales) scores will be recorded as the primary outcomes before the treatment and at the 1st, 3rd, 5th, 8th, 10th, 12th, 15th, 17th, and 19th days after treatment and follow-up visit at the first, third, and sixth months. JOA efficacy evaluation standard will be used to evaluate the overall efficacy as the secondary outcomes.

Discussion: The results of this prospective, randomized controlled trial will provide a clinical evidence for the treatment of DLI with seated lumbar rotation manipulation.

Trial Registration: Chinese Clinical Trial Registry ChiCTR2000032017 . Registered on 18 April 2020, Prospective registration.
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http://dx.doi.org/10.1186/s13063-021-05350-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8204577PMC
June 2021

Identifying Mitochondrial-Related Genes NDUFA10 and NDUFV2 as Prognostic Markers for Prostate Cancer through Biclustering.

Biomed Res Int 2021 22;2021:5512624. Epub 2021 May 22.

Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou 510006, China.

Prostate cancer is currently associated with higher morbidity and mortality in men in the United States and Western Europe, so it is important to identify genes that regulate prostate cancer. The high-dimension gene expression profile impedes the discovery of biclusters which are of great significance to the identification of the basic cellular processes controlled by multiple genes and the identification of large-scale unknown effects hidden in the data. We applied the biclustering method MCbiclust to explore large biclusters in the TCGA cohort through a large number of iterations. Two biclusters were found with the highest silhouette coefficient value. The expression patterns of one bicluster are highly similar to those found by the gene expression profile of the known androgen-regulated genes. Further gene set enrichment revealed that mitochondrial function-related genes were negatively correlated with AR regulation-related genes. Then, we performed differential analysis, AR binding site analysis, and survival analysis on the core genes with high phenotypic contribution. Among the core genes, NDUFA10 showed a low expression value in cancer patients across different expression profiles, while NDUFV2 showed a high expression value in cancer patients. Survival analysis of NDUFA10 and NDUFV2 demonstrated that both genes were unfavorable prognostic markers.
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http://dx.doi.org/10.1155/2021/5512624DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8168472PMC
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

Design and system evaluation of a dual-panel portable PET (DP-PET).

EJNMMI Phys 2021 Jun 12;8(1):47. Epub 2021 Jun 12.

Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.

Background: Integrated whole-body PET/MR technology continues to mature and is now extensively used in clinical settings. However, due to the special design architecture, integrated whole-body PET/MR comes with a few inherent limitations. Firstly, whole-body PET/MR lacks sensitivity and resolution for focused organs. Secondly, broader clinical access of integrated PET/MR has been significantly restricted due to its prohibitively high cost. The MR-compatible PET insert is an independent and removable PET scanner which can be placed within an MRI bore. However, the mobility and configurability of all existing MR-compatible PET insert prototypes remain limited.

Methods: An MR-compatible portable PET insert prototype, dual-panel portable PET (DP-PET), has been developed for simultaneous PET/MR imaging. Using SiPM, digital readout electronics, novel carbon fiber shielding, phase-change cooling, and MRI compatible battery power, DP-PET was designed to achieve high-sensitivity and high-resolution with compatibility with a clinical 3-T MRI scanner. A GPU-based reconstruction method with resolution modeling (RM) has been developed for the DP-PET reconstruction. We evaluated the system performance on PET resolution, sensitivity, image quality, and the PET/MR interference.

Results: The initial results reveal that the DP-PET prototype worked as expected in the MRI bore and caused minimal compromise to the MRI image quality. The PET performance was measured to show a spatial resolution ≤ 2.5 mm (parallel to the detector panels), maximum sensitivity = 3.6% at the center of FOV, and energy resolution = 12.43%. MR pulsing introduces less than 2% variation to the PET performance measurement results.

Conclusions: We developed a MR-compatible PET insert prototype and performed several studies to begin to characterize the performance of the proposed DP-PET. The results showed that the proposed DP-PET performed well in the MRI bore and would cause little influence on the MRI images. The Derenzo phantom test showed that the proposed reconstruction method could obtain high-quality images using DP-PET.
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http://dx.doi.org/10.1186/s40658-021-00392-5DOI Listing
June 2021

Algebraic graph-assisted bidirectional transformers for molecular property prediction.

Nat Commun 2021 06 10;12(1):3521. Epub 2021 Jun 10.

School of Advanced Materials, Peking University, Shenzhen Graduate School, Shenzhen, China.

The ability of molecular property prediction is of great significance to drug discovery, human health, and environmental protection. Despite considerable efforts, quantitative prediction of various molecular properties remains a challenge. Although some machine learning models, such as bidirectional encoder from transformer, can incorporate massive unlabeled molecular data into molecular representations via a self-supervised learning strategy, it neglects three-dimensional (3D) stereochemical information. Algebraic graph, specifically, element-specific multiscale weighted colored algebraic graph, embeds complementary 3D molecular information into graph invariants. We propose an algebraic graph-assisted bidirectional transformer (AGBT) framework by fusing representations generated by algebraic graph and bidirectional transformer, as well as a variety of machine learning algorithms, including decision trees, multitask learning, and deep neural networks. We validate the proposed AGBT framework on eight molecular datasets, involving quantitative toxicity, physical chemistry, and physiology datasets. Extensive numerical experiments have shown that AGBT is a state-of-the-art framework for molecular property prediction.
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http://dx.doi.org/10.1038/s41467-021-23720-wDOI Listing
June 2021

CT-Based Radiomics Signature With Machine Learning Predicts MYCN Amplification in Pediatric Abdominal Neuroblastoma.

Front Oncol 2021 24;11:687884. Epub 2021 May 24.

Department of Radiology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China.

Purpose: MYCN amplification plays a critical role in defining high-risk subgroup of patients with neuroblastoma. We aimed to develop and validate the CT-based machine learning models for predicting MYCN amplification in pediatric abdominal neuroblastoma.

Methods: A total of 172 patients with MYCN amplified (n = 47) and non-amplified (n = 125) were enrolled. The cohort was randomly stratified sampling into training and testing groups. Clinicopathological parameters and radiographic features were selected to construct the clinical predictive model. The regions of interest (ROIs) were segmented on three-phrase CT images to extract first-, second- and higher-order radiomics features. The ICCs, mRMR and LASSO methods were used for dimensionality reduction. The selected features from the training group were used to establish radiomics models using Logistic regression, Support Vector Machine (SVM), Bayes and Random Forest methods. The performance of four different radiomics models was evaluated according to the area under the receiver operator characteristic (ROC) curve (AUC), and then compared by Delong test. The nomogram incorporated of clinicopathological parameters, radiographic features and radiomics signature was developed through multivariate logistic regression. Finally, the predictive performance of the clinical model, radiomics models, and nomogram was evaluated in both training and testing groups.

Results: In total, 1,218 radiomics features were extracted from the ROIs on three-phrase CT images, and then 14 optimal features, including one original first-order feature and eight wavelet-transformed features and five LoG-transformed features, were identified and selected to construct the radiomics models. In the training group, the AUC of the Logistic, SVM, Bayes and Random Forest model was 0.940, 0.940, 0.780 and 0.927, respectively, and the corresponding AUC in the testing group was 0.909, 0.909, 0.729, 0.851, respectively. There was no significant difference among the Logistic, SVM and Random Forest model, but all better than the Bayes model (p <0.005). The predictive performance of the Logistic radiomics model based on three-phrase is similar to nomogram, but both better than the clinical model and radiomics model based on single venous phase.

Conclusion: The CT-based radiomics signature is able to predict MYCN amplification of pediatric abdominal NB with high accuracy based on SVM, Logistic and Random Forest classifiers, while Bayes classifier yields lower predictive performance. When combined with clinical and radiographic qualitative features, the clinics-radiomics nomogram can improve the performance of predicting MYCN amplification.
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http://dx.doi.org/10.3389/fonc.2021.687884DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8181422PMC
May 2021

Discovery of as a Potent and Orally Bioavailable Inhibitor of the WDR5-Mixed Lineage Leukemia 1 Protein-Protein Interaction for the Treatment of MLL Fusion Leukemia.

J Med Chem 2021 Jun 9. Epub 2021 Jun 9.

Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.

WD repeat-containing protein 5 (WDR5) is essential for the stability and methyltransferase activity of the mixed lineage leukemia 1 (MLL1) complex. Dysregulation of the gene is associated with human acute leukemias, and the direct disruption of the WDR5-MLL1 protein-protein interaction (PPI) is emerging as an alternative strategy for MLL-rearranged cancers. Here, we represent a new aniline pyrimidine scaffold for WDR5-MLL1 inhibitors. A comprehensive structure-activity analysis identified a potent inhibitor (), with an IC of 29 nM in a competitive fluorescence polarization assay and a value of 72.9 nM for the WDR5 protein. Compound selectively inhibited MLL histone methyltransferase activity and the proliferation of MLL translocation-harboring cells. Furthermore, displayed good pharmacokinetic properties and suppressed the growth of MV4-11 xenograft tumors in mice after oral administration, first verifying the efficacy of targeting the WDR5-MLL1 PPI by small molecules.
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http://dx.doi.org/10.1021/acs.jmedchem.1c00091DOI Listing
June 2021

The complete chloroplast genome of (Acanthaceae).

Mitochondrial DNA B Resour 2021 May 19;6(6):1668-1669. Epub 2021 May 19.

Key Laboratory of Plant Resources Conservation & Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China.

is a plietesial species endemic to China. The complete chloroplast genome (cp genome) of was sequenced for the first time. The cp genome of is 144,012 bp in length. It consists of a large single copy (LSC) region (91,628 bp) and a small single copy (SSC) region (17,666 bp), which are separated by two inverted repeats (IRs, 34,718 bp). It contains 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The overall GC content is 38.2%. Phylogenetic analysis of 13 species has been conducted. This newly sequenced cp genome will be useful to further genetic diversity, phylogeny, and genomic studies of the genus .
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http://dx.doi.org/10.1080/23802359.2021.1927868DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8143611PMC
May 2021

New type of borneol-based fluorine-free superhydrophobic antibacterial polymeric coating.

Des Monomers Polym 2021 May 7;24(1):145-155. Epub 2021 May 7.

Key Laboratory of Science and Technology of EcoTextile, Donghua University, Ministry of Education, Shanghai, China.

A new type of superhydrophobic borneol-based polymeric coating has been prepared. The chemical composition of the polymer particles was analyzed by Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy, which showed that the polymer did not contain fluorine, which can effectively avoid the cytotoxic risk of fluorine. By dynamic light scattering, scanning electron microscopy, and static contact angle measurement, the contact angle of the prepared coating gradually increased with increasing diameter of the polymer particles, and a superhydrophobic coating surface was finally obtained. Interestingly, after dissolving the superhydrophobic sample with tetrahydrofuran and making it a normal hydrophobic sample, the antiadhesion performance for was greatly reduced, and it could not effectively prevent adhesion. In addition, a long-term antiadhesion study of bacteria was performed. The superhydrophobic borneol-based polymer coating showed long-term resistance to adhesion. Therefore, the excellent antibacterial properties and cell compatibility mean that this series of polymer materials has great potential in the field of biomedicine.
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http://dx.doi.org/10.1080/15685551.2021.1924959DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8118525PMC
May 2021

Associations of TCF7L2 rs11196218 (A/G) and GLP-1R rs761386 (C/T) Gene Polymorphisms with Obesity in Chinese Population.

Diabetes Metab Syndr Obes 2021 1;14:2465-2472. Epub 2021 Jun 1.

Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, People's Republic of China.

Introduction: This study aimed to investigate the genetic polymorphism associations with obesity of the transcription factor 7-like 2 () gene rs11196218 (A/G) and glucagon-like peptide 1 receptor () gene rs761386 (C/T) in the Chinese population.

Patients And Methods: This was a case-control pilot study involving 60 patients with obesity and 69 non-obesity Chinese adults, and the two groups were sex and age matched. Anthropometric indices of obesity, fasting blood glucose, blood pressure, and blood lipids were assessed. Both polymorphisms were genotyped using matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF).

Results: There were significant differences in the allelic frequencies of the rs11196218 and rs761386 between obesity and non-obesity groups (P = 0.003, OR = 2.32, 95% CI [1.31~4.09]; P = 0.034, OR = 1.94, 95% CI [1.05~3.60], respectively). In allele model, the genotypic frequencies of rs11196218 and rs761386 also differed between obesity and non-obesity groups (P = 0.014 and 0.033, respectively). In dominant model, the rs11196218 A-carrier (AA/AG) had a higher risk of obesity than GG genotype (P = 0.014, OR = 2.54, 95% CI [1.21~5.35]). Comparison of clinical and biochemical parameters between genotypes showed no significant difference.

Conclusion: These findings suggest that the rs11196218 (A/G) polymorphism of the gene and the rs761386 (C/T) polymorphism of the gene were associated with obesity in the Chinese population.
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http://dx.doi.org/10.2147/DMSO.S310069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8179745PMC
June 2021

Association between sleep disturbance and multidimensional frailty assessed by Frailty Index in hospitalized cirrhosis.

Eur J Gastroenterol Hepatol 2021 Jun 7. Epub 2021 Jun 7.

Department of Gastroenterology and Hepatology Tianjin Institute of Digestive Disease Department of Neurology, Tianjin Medical University General Hospital Department of Nutriology, Tianjin Third Central Hospital Department of Internal Medicine, Tianjin Hexi Hospital, Tianjin, China.

Objectives: Both sleep disturbance and frailty are common in patients with cirrhosis, but their correlation remains elusive. We aimed to investigate whether dysregulated sleep [as estimated by Pittsburgh Sleep Quality Index (PSQI)] is independently associated with frailty and their relationship in distinct subgroups.

Methods: In total 105 adult cirrhotic patients were recruited. The frailty phenotype was identified by a self-reported scale (Frailty Index) which demonstrates good validity and moderate performance based on our previous publication. Patients were categorized into frailty and nonfrailty groups according to a cut-point of 0.38 by Frailty Index. Multiple linear regression was performed to determine independent factors associated with frailty.

Results: The median PSQI was 6.0 in the entire cohort and sleep disturbance was observed in 61 patients with cirrhosis (58.1%). Poor sleepers had a significantly higher Frailty Index than that in good sleepers (0.11 vs. 0.08; P = 0.025). In univariate analysis, PSQI score was markedly associated with the Frailty Index (β = 0.012; 95% CI, 0.006-0.018; P < 0.001), and remained significantly associated with frailty phenotype in multivariate adjustment (β = 0.010; 95% CI, 0.004-0.015; P = 0.001). The escalating PSQI scores were more prominent in frail patients, with female gender or aged 65 years and over.

Conclusions: Poor sleep quality is strongly associated with frailty in patients with cirrhosis. Given that sleep disturbance is modifiable, our data suggest that efficient interventions to mitigate frailty should incorporate strategies by reversing sleep dysfunction in cirrhotics with poor sleep quality.
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http://dx.doi.org/10.1097/MEG.0000000000002231DOI Listing
June 2021

Insight into the role of multiple signaling pathways in regulating cancer stem cells of gynecologic cancers.

Semin Cancer Biol 2021 Jun 9. Epub 2021 Jun 9.

Center of Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China. Electronic address:

Mounting evidence has demonstrated that a myriad of developmental signaling pathways, such as the Wnt, Notch, Hedgehog and Hippo, are frequently deregulated and play a critical role in regulating cancer stem cell (CSC) activity in human cancers, including gynecologic malignancies. In this review article, we describe an overview of various signaling pathways in human cancers. We further discuss the developmental roles how these pathways regulate CSCs from experimental evidences in gynecologic cancers. Moreover, we mention several compounds targeting CSCs in gynecologic cancers to enhance the treatment outcomes. Therefore, these signaling pathways might be the potential targets for developing targeted therapy in gynecologic cancers.
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http://dx.doi.org/10.1016/j.semcancer.2021.06.001DOI Listing
June 2021

A human antibody of potent efficacy against SARS-CoV-2 in rhesus macaques showed strong blocking activity to B.1.351.

MAbs 2021 Jan-Dec;13(1):1930636

Shanghai Jemincare Pharmaceuticals Co., Ltd., Shanghai, People's Republic of China.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which causes coronavirus disease-2019 (COVID-19), interacts with the host cell receptor angiotensin-converting enzyme 2 (hACE2) via its spike 1 protein during infection. After the virus sequence was published, we identified two potent antibodies against the SARS-CoV-2 receptor binding domain (RBD) from antibody libraries using a phage-to-yeast (PtY) display platform in only 10 days. Our lead antibody JMB2002, now in a Phase 1 clinical trial (ChiCTR2100042150), showed broad-spectrum blocking activity against hACE2 binding to the RBD of multiple SARS-CoV-2 variants, including B.1.351 that was reportedly much more resistant to neutralization by convalescent plasma, vaccine sera and some clinical-stage neutralizing antibodies. Furthermore, JMB2002 has demonstrated complete prophylactic and potent therapeutic efficacy in a rhesus macaque disease model. Prophylactic and therapeutic countermeasure intervention of SARS-CoV-2 using JMB2002 would likely slow down the transmission of currently emerged SARS-CoV-2 variants and result in more efficient control of the COVID-19 pandemic.
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http://dx.doi.org/10.1080/19420862.2021.1930636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8189090PMC
June 2021

Essential Oils from cv. Shatangju Peel: Optimization of Hydrodistillation Extraction by Response Surface Methodology and Evaluation of Their Specific Adhesive Effect to Polystyrene.

ACS Omega 2021 Jun 19;6(21):13695-13703. Epub 2021 May 19.

College of Biology & Food Engineering, Jilin Institute of Chemical Technology, 45 Chengde Street, Longtan District, Jilin City 132002, China.

Essential oil (Eo) from the peel has been widely used, and its adhesive effect on polystyrene (PS) was found accidentally. To analyze the essential oils of cv. Shatangju (CrspEos), the extraction of these oils by steam distillation was optimized using the response surface method. The chemical composition of CrspEos was analyzed by gas chromatography-mass spectrometry. Then, the adhesive effect of these essential oils on PS was evaluated. The adhesion area, the influence of adhesion on the thickness of the essential oil on the materials, the effect of adhesion on the transmittance of PS, the strength of adhesion point, and specificity of adhesion were determined. The optimum extraction conditions resulting in the extraction yield of 47.37 μL g were a ratio of liquid-to-solid of 8.94:1, a soaking time of 199.45 min, and an extraction time of 138.71 min. The major component in the essential oils was d-limonene (56.66%), followed by myrcene (6.62%). CrspEos presented a specific adherence effect on PS without influencing the thickness and transmittance of PS but with stronger tenacity than the parent material. CrspEos can be used as an environmentally friendly specific adhesive for PS.
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http://dx.doi.org/10.1021/acsomega.1c00895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8173550PMC
June 2021

Gaussian Process Autoregression for Joint Angle Prediction Based on sEMG Signals.

Front Public Health 2021 21;9:685596. Epub 2021 May 21.

College of Electrical Engineering and Automation, Fuzhou University, Fuzhou, China.

There is uncertainty in the neuromusculoskeletal system, and deterministic models cannot describe this significant presence of uncertainty, affecting the accuracy of model predictions. In this paper, a knee joint angle prediction model based on surface electromyography (sEMG) signals is proposed. To address the instability of EMG signals and the uncertainty of the neuromusculoskeletal system, a non-parametric probabilistic model is developed using a Gaussian process model combined with the physiological properties of muscle activation. Since the neuromusculoskeletal system is a dynamic system, the Gaussian process model is further combined with a non-linear autoregressive with eXogenous inputs (NARX) model to create a Gaussian process autoregression model. In this paper, the normalized root mean square error (NRMSE) and the correlation coefficient (CC) are compared between the joint angle prediction results of the Gaussian process autoregressive model prediction and the actual joint angle under three test scenarios: speed-dependent, multi-speed and speed-independent. The mean of NRMSE and the mean of CC for all test scenarios in the healthy subjects dataset and the hemiplegic patients dataset outperform the results of the Gaussian process model, with significant differences ( < 0.05 and < 0.05, < 0.05 and < 0.05). From the perspective of uncertainty, a non-parametric probabilistic model for joint angle prediction is established by using Gaussian process autoregressive model to achieve accurate prediction of human movement.
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http://dx.doi.org/10.3389/fpubh.2021.685596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8175857PMC
June 2021

Improvement in Midline Shift Is a Positive Prognostic Predictor for Malignant Middle Cerebral Artery Infarction Patients Undergoing Decompressive Craniectomy.

Front Neurol 2021 20;12:652827. Epub 2021 May 20.

Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.

The aim of this retrospective study is to evaluate the risk factors of malignant middle cerebral artery infarction (MMCAI) patients and explore an applicable prognostic predictor for MMCAI patients undergoing decompressive craniectomy (DC). Clinical data from the period 2012-2017 were retrospectively evaluated. Forty-three consecutive MMCAI patients undergoing DC were enrolled in this study. The 30-day mortality was assessed, and age, location, hypertension, pupil dilation, onset to operation duration, midline shift, and Glasgow Coma Scale (GCS) score were identified by univariate analysis and binary logistic regression. In this retrospective study for DC patients, the 30-day mortality was 44.2%. In the univariate analysis, advanced age (≥60 years), right hemispheric location, hypertension, pupil dilation, shorter onset to operation duration (<48 h), improved midline shift ( = 4.214, < 0.01), and lower pre-operation GCS score were significant predictors of death within 30 days. In binary logistic regression analysis, age [odds ratio (OR) = 1.141, 95% CI 1.011-1.287], the improvement of the midline shift (OR = 0.764, 95% CI 0.59-0.988), and pupillary dilation (OR = 15.10, 95% CI 1.374-165.954) were independent influencing factors. For the receiver operating characteristic (ROC) analysis of the relationship between post-operation outcomes and midline shift improvement, the area under the curve (AUC) was 0.844, and the cutoff point of midline shift improvement was 0.83 cm. Improved midline shift was a significant predictor of 30-day mortality. The improved midline shift of >0.83 cm indicated survival at 30 days.
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http://dx.doi.org/10.3389/fneur.2021.652827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8176305PMC
May 2021

The Influence of Personality Traits on School Bullying: A Moderated Mediation Model.

Front Psychol 2021 21;12:650070. Epub 2021 May 21.

Key Laboratory of Applied Psychology, Chongqing Normal University, Chongqing, China.

We recruited 1,631 middle and high school students to explore the relationship between personality traits and school bullying, and the moderated and mediating roles of self-concept and loneliness on this relationship. Results showed that (1) neuroticism had a significant positive predictive effect on being bullied, extroversion had a significant negative predictive effect on being bullied, and agreeableness had a significant negative predictive effect on bullying/being bullied; (2) loneliness played a mediating role between neuroticism and bullied behaviors, extroversion and bullying behaviors, and agreeableness and bullying/bullied behaviors; (3) self-concept played a moderating role on the mediation pathway of loneliness on neuroticism, extraversion, agreeableness and bullying behaviors. Therefore, to reduce the frequency of school bullying among adolescents, we should not only reduce their levels of loneliness but also improve their levels of self-concept.
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http://dx.doi.org/10.3389/fpsyg.2021.650070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8177084PMC
May 2021

Circular RNA circDUS2 Is a Potential Biomarker for Intracranial Aneurysm.

Front Aging Neurosci 2021 19;13:632448. Epub 2021 May 19.

Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.

CircRNAs have been found to play a crucial role in the pathological process of various kinds of diseases. However, the role of circRNAs in the formation and rupture of intracranial aneurysm is still unknown. Differentially expressed circRNAs profiles between superficial temporal arteries ( = 5) and intracranial aneurysms ( = 5) were analyzed using the Arraystar human circRNAs microarray. Quantitative real-time PCR was utilized to validate the differential expression of circDUS2. Fluorescence hybridization (FISH) was meant for the location of circDUS2 in human brain vascular smooth muscle cell (HBVSMC). Structural analysis was used to speculate on the function of circDUS2. Five hundred forty-three upregulated and 397 downregulated significantly in intracranial aneurysm as compared to superficial temporal arteries. Quantitative real-time PCR verified the elevated expression of the upregulated circDUS2. The FISH test revealed that circDUS2 is located in the cytoplasm of brain vascular smooth muscle cells. This study showed differential expression data of circRNAs between superficial temporal artery and intracranial aneurysm and revealed that circDUS2 is a potential molecular marker for intracranial aneurysm.
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http://dx.doi.org/10.3389/fnagi.2021.632448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8171118PMC
May 2021