Publications by authors named "Siyu Xia"

26 Publications

  • Page 1 of 1

Modulation of genes expression in aged rat liver, brain, and kidney by caloric restriction analyzed via single-nucleus/cell RNA sequencing.

Autophagy 2022 Jun 23:1-10. Epub 2022 Jun 23.

Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University; the First Affiliated Hospital of Southern University of Science and Technology), Shenzhen, Guangdong, China.

Dysregulation of macroautophagy/autophagy has been closely implicated in aging. Caloric restriction (CR) is an effective intervention of aging partially via activation of autophagy. Recently, a high-throughput single-cell RNA-seq technique has been employed to detect the comprehensive transcriptomes of individual cells. However, the transcriptional networks of (autophagy related) genes in the aging process and the modulation of genes expression by CR at the single-cell level have not been elucidated. Here, by performing data analysis of single nucleus/cells RNA sequencing in rats undergoing aging and the modulation by CR, we demonstrate that the transcription patterns of genes in different cell types of rat liver, brain, and kidney are highly heterogeneous. Importantly, CR reversed aging-induced changes of multiple genes across different cell types in the brain, liver, and kidney. In summary, our results, for the first time, provide comprehensive information on gene expression in specific cell types of different organs in a mammal during aging and give novel insight into the protective role of autophagy and CR in aging at the single-cell resolution. genes: autophagy-related genes; : autophagy related 5; : autophagy related 7; CR: caloric restriction; DEATG: differentially expressed autophagy-related; NAFLD: nonalcoholic fatty liver disease; ScRNA-seq: single-cell RNA sequencing.
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http://dx.doi.org/10.1080/15548627.2022.2091903DOI Listing
June 2022

Multi-scale attention network for segmentation of electron dense deposits in glomerular microscopic images.

Microsc Res Tech 2022 Jun 20. Epub 2022 Jun 20.

School of Automation, Southeast University, Nanjing, China.

Electron dense deposit on the epithelial side of the glomerular capillary basement membrane is one of the pathological changes of membranous nephropathy. Automatic segmentation of deposits can relieve clinicians from the tedious and manual effort of identifying and localizing region of interest (ROI) in medical images and also assist to diagnose membranous nephropathy. Electron dense deposits are characterized by different sizes, irregular shapes, and low contrast to surrounding tissue structures in glomerular electron microscopy images. Considering the characteristics of dense deposits, we propose a multi-scale attention network for automatic segmentation of electron dense deposits of glomeruli in electron microscope images. Our method is built on the fully convolutional network but also takes advantages of the multi-scale skip connections and attention mechanism. Specifically, the multi-scale skip connection combines feature maps of different scales, makes the segmentation field larger, and integrates the shallow features of the image and high-level semantic information, which is more conducive to distinguishing dense deposits. At the same time, attention mechanism can focus on salient structures that normally produces a distinguishable feature representation. To evaluate the segmentation performance of the proposed method, we also collected a dataset of electron microscope images of membranous nephropathy. To the best of our knowledge, this is the largest image dataset for segmentation of glomerular basement membrane dense deposits. Experimental result shows that our model can accurately segment ordinary-sized dense deposits. Compared with state-of-the-art methods, our proposed method lower both false positive and false negative segmentation of small-sized protein sediments.
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http://dx.doi.org/10.1002/jemt.24182DOI Listing
June 2022

Treating intrauterine adhesion using conditionally reprogrammed physiological endometrial epithelial cells.

Stem Cell Res Ther 2022 05 3;13(1):178. Epub 2022 May 3.

School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China.

Background: There is unmet need for effective therapies of intrauterine adhesions (IUAs) that are common cause of menstrual disturbance and infertility, since current clinical procedures do not improve prognosis for patients with moderate to severe IUA, with a recurrence rate of 23-50%. Stem cell-based therapy has emerged as a therapeutic option with unsolved issues for IUA patients in the past few years. Primary endometrial epithelial cells for cell therapy are largely hampered with the extremely limited proliferation capacity of uterine epithelial cells. This study was to evaluate whether IUA is curable with conditionally reprogrammed (CR) endometrial epithelial cells.

Methods: Mouse endometrial epithelial cells (MEECs) were isolated from C57BL female mice, and long-term cultures of MEECs were established and maintained with conditional reprogramming (CR) method. DNA damage response analysis, soft agar assay, and matrigel 3D culture were carried out to determine the normal biological characteristics of CR-MEECs. The tissue-specific differentiation potential of MEECs was analyzed with air-liquid interface (ALI) 3D culture, hematoxylin and eosin (H&E) staining, Masson's trichrome and DAB staining, immunofluorescence assay. IUA mice were constructed and transplanted with CR-MEECs. Repair and mechanisms of MEECs transplantation in IUA mice were measured with qRT-PCR, Masson's trichrome, and DAB staining.

Results: We first successfully established long-term cultures of MEECs using CR approach. CR-MEECs maintained a rapid and stable proliferation in this co-culture system. Our data confirmed that CR-MEECs retained normal biological characteristics and endometrium tissue-specific differentiation potential. CR-MEECs also expressed estrogen and progesterone receptors and maintained the exquisite sensitivity to sex hormones in vitro. Most importantly, allogeneic transplantation of CR-MEECs successfully repaired the injured endometrium and significantly improved the pregnancy rate of IUA mice.

Conclusions: Conditionally reprogrammed physiological endometrial epithelial cells provide a novel strategy in IUA clinics in a personalized or generalized manner and also serve as a physiological model to explore biology of endometrial epithelial cells and mechanisms of IUA.
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http://dx.doi.org/10.1186/s13287-022-02860-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9066886PMC
May 2022

Mask removal : Face inpainting via attributes.

Multimed Tools Appl 2022 Apr 5:1-13. Epub 2022 Apr 5.

Key Laboratory of Measurement and Control of Complex Systems of Engineering, Ministry of Education, Southeast University, Nanjing, 210096 People's Republic of China.

Due to the outbreak of the COVID-19 pandemic, wearing masks in public areas has become an effective way to slow the spread of disease. However, it also brings some challenges to applications in daily life as half of the face is occluded. Therefore, the idea of removing masks by face inpainting appeared. Face inpainting has achieved promising performance but always fails to guarantee high-fidelity. In this paper, we present a novel mask removal inpainting network based on face attributes known in advance including nose, chubby, makeup, gender, mouth, beard and young, aiming to ensure the repaired face image is closer to ground truth. To achieve this, a dual pipeline network based on GANs has been proposed, one of which is a reconstructive path used in training that utilizes missing regions in ground truth to get prior distribution, while the other is a generative path for predicting information in the masked region. To establish the process of mask removal, we build a synthetic facial occlusion that mimics the real mask. Experiments show that our method not only generates faces more similarly aligned with real attributes, but also ensures semantic and structural rationality compared with state-of-the-art methods.
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http://dx.doi.org/10.1007/s11042-022-12912-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982301PMC
April 2022

A single-cell atlas of bisphenol A (BPA)-induced testicular injury in mice.

Clin Transl Med 2022 03;12(3):e789

Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China.

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http://dx.doi.org/10.1002/ctm2.789DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8958349PMC
March 2022

Effective removal of Hg(II) and MeHg from aqueous environment by ball milling aided thiol-modification of biochars: Effect of different pyrolysis temperatures.

Chemosphere 2022 May 29;294:133820. Epub 2022 Jan 29.

Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China. Electronic address:

In order to synthesize biochar with the enhanced adsorption of inorganic mercury (Hg(II)) and organic mercury (Methylmercury, MeHg), biochars pyrolyzed at different pyrolysis temperatures (300, 500, and 700 °C) were ball milled with 3-trimethoxysilylpropanethiol (3-MPTS). Characterization results showed that 3-MPTS acted as an activator which further enlarged pores in biochars and ball-milling increased surface area of biochars. During ball milling, oxygen-containing functional groups increased which facilitated the loading of -SH group. The maximum adsorption capacities for Hg(II) adsorption in ball mill sulfhydryl modified biochars of 300, 500, and 700 °C were 401.8, 379.6 and 270.6 mg/g, respectively; simultaneously, the maximum adsorption capacity of MeHg was 108.16, 85.27 and 39.14 mg/g, respectively, which showed preferential increasing of 5.54 times on MeHg compared to the non-thiol modified biochar at low pyrolysis temperature of 300 °C. Results of kinetic adsorption experiments suggested that sorption data fitted well with Pseudo-second-order kinetic model, which proved that the mainly rate-limiting adsorption step was surface diffusion. Langmuir isotherm model fitting result showed that ligand exchange, surface complexation, surface adsorption and electrostatic attraction are dominant removal mechanisms. The 3-MPTS content and ball milling time are crucial during ball milling, and 2% 3-MPTS and 30 h of ball milling were found to be the most suitable conditions for both Hg(II) and MeHg adsorption. The result suggests that ball milling aided thiol-modification has great potential in synthesis of -SH modified biochar with prioritized MeHg adsorption.
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http://dx.doi.org/10.1016/j.chemosphere.2022.133820DOI Listing
May 2022

Embryonic exposure to phenanthrene caused developmental defects of craniofacial cartilage in F1 larvae.

Aquat Toxicol 2022 Feb 15;243:106080. Epub 2022 Jan 15.

State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, PR China. Electronic address:

As a representative polycyclic aromatic hydrocarbon with low ring numbers, phenanthrene (Phe) is ubiquitously present in the environment. In this study, zebrafish embryos were exposed to Phe at 0.05, 0.5, 5 and 50 nmol/L for 96 h, and then cultured to adulthood in clean water, the developmental defects of craniofacial cartilage were observed in F1 larvae produced by adult males and females mated with untreated fish. Delayed development of craniofacial cartilage, including a shorter and wider Meckel's cartilage and mandibular arch were observed in F1 larvae from adult fish of both sexes. Maternal F1 larvae showed a greater impact on the lower jaw than paternal F1 larvae, this may be connected with greater downregulation of the transcription of genes related to the development of craniofacial cartilage such as runt-related transcription factor 2 (runx2), fibroblast growth factor 8 (fgf8), sonic hedgehog (shh), Indian hedgehog (ihh). Further results indicated that the modification DNA methylation levels in the promotors of gene runx2 and shh in maternal and paternal F1 larvae were inherited from embryonic F0 larvae, and might be linked with the toxicity of craniofacial cartilage in F1 larvae. This study illustrated that embryonic exposure to Phe could induce adverse effects on craniofacial development in F1 offspring, emphasizing the importance of transgenerational toxicology studies in risk assessment.
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http://dx.doi.org/10.1016/j.aquatox.2022.106080DOI Listing
February 2022

Immune inactivation by APOBEC3B enrichment predicts response to chemotherapy and survival in gastric cancer.

Oncoimmunology 2021 15;10(1):1975386. Epub 2021 Sep 15.

Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China.

Apolipoprotein B mRNA editing enzyme catalytic polypeptide 3B (APOBEC3B) plays an important role in tumor mutagenesis. However, its clinical significance in gastric cancer (GC) remains largely unknown. We enrolled a total of 482 GC patients from Zhongshan Hospital, Fudan University for immunohistochemistry (IHC) staining to evaluate the prognostic and predictive values of APOBEC3B. Genomic and phenotypic datasets from the Cancer Genome Atlas (TCGA) and Asian Cancer Research Group (ACRG) cohort were downloaded for external validation and complementary bioinformatic analysis. Fresh specimens of additional 60 patients from Zhongshan Hospital, Fudan University were collected to detect CD8 T cell phenotype with flow cytometry (FCM). The high expression of APOBEC3B indicated inferior overall survival (OS, < .001 and = .003) and disease-free survival (DFS, < .001 and < .001), yet superior therapeutic responsiveness to fluorouracil-based adjuvant chemotherapy (ACT) in TNM stage II patients. The tumor microenvironment (TME) of APOBEC3B-enriched tumors was characterized by reduced infiltration of tumor reactive CD8 T cells expressing both effector molecules and immune checkpoints. APOBEC3B CD8 T cell GC patients were most likely to benefit from ACT and PD-1 blockade. Our study demonstrates that APOBEC3B was an independent prognostic and predictive factor in GC. The potential interplay between APOBEC3B and CD8 T cells merited further investigations.
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http://dx.doi.org/10.1080/2162402X.2021.1975386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8451457PMC
October 2021

Removal notice to "VitSeg: Weakly supervised vitiligo segmentation in skin image" [Comput. Med. Imag. Graph. 85 (2020) 101779].

Comput Med Imaging Graph 2021 07 30;91:101954. Epub 2021 Jun 30.

Dept. of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA.

This article has been removed: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been removed at the request of the Authors and Editor-in-Chief because complete consent was not obtained by the authors in accordance with journal policy prior to publication. The authors and the journal sincerely apologize for this oversight.
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http://dx.doi.org/10.1016/j.compmedimag.2021.101954DOI Listing
July 2021

Developmental neurotoxicity of antimony (Sb) in the early life stages of zebrafish.

Ecotoxicol Environ Saf 2021 May 8;218:112308. Epub 2021 May 8.

Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400030, China. Electronic address:

Accumulating studies have revealed the toxicity of antimony (Sb) to soil-dwelling and aquatic organisms at the individual level. However, little is known about the neurotoxic effects of antimony and its underlying mechanisms. To assess this issue, we investigated the neurotoxicity of antimony (0, 200, 400, 600 and 800 mg/L) in zebrafish embryos. After exposure, zebrafish embryos showed abnormal phenotypes such as a shortened body length, morphological malformations, and weakened heart function. Behavioral experiments indicated that antimony caused neurotoxicity in zebrafish embryos, manifested in a decreased spontaneous movement frequency, delayed response to touch, and reduced movement distance. We also showed that antimony caused a decrease in acetylcholinesterase (AChE) levels in zebrafish embryos, along with decreased expression of neurofunctional markers such as gfap, nestin, mbp, and shha. Additionally, antimony significantly increased reactive oxygen species levels and significantly reduced glutathione (GSH) and superoxide dismutase (SOD) activity. In summary, our findings indicated that antimony can induce developmental toxicity and neurotoxicity in zebrafish embryos by affecting neurotransmitter systems and oxidative stress, thus altering behavior. These outcomes will advance our understanding of antimony-induced neurotoxicity, environmental problems, and health hazards.
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http://dx.doi.org/10.1016/j.ecoenv.2021.112308DOI Listing
May 2021

Removed: VitSeg: Weakly supervised vitiligo segmentation in skin image.

Comput Med Imaging Graph 2020 10 26;85:101779. Epub 2020 Aug 26.

Dept. of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA. Electronic address:

This article has been removed: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been removed at the request of the Authors and Editor-in-Chief because complete consent was not obtained by the authors in accordance with journal policy prior to publication. The authors and the journal sincerely apologize for this oversight.
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http://dx.doi.org/10.1016/j.compmedimag.2020.101779DOI Listing
October 2020

Coupled CRC 2D and ALI 3D Cultures Express Receptors of Emerging Viruses and Are More Suitable for the Study of Viral Infections Compared to Conventional Cell Lines.

Stem Cells Int 2020 9;2020:2421689. Epub 2020 Jul 9.

State Key Laboratory of Virology/Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China.

Infections of emerging and reemerging viruses (SARS-CoVs, influenza H1N1, etc.) largely and globally affect human health. Animal models often fail to reflect a physiological status because of species tropism of virus infection. Conventional cell lines are usually genetically and phenotypically different from primary cells. Developing an physiological model to study the infection of emerging viruses will facilitate our understanding of virus-host cell interactions, thereby benefiting antiviral drug discovery. In the current work, we first established normal airway epithelial cells (upper and lower airway track) in 2D and 3D culture systems using conditional reprogramming (CR) and air-liquid interface (ALI) techniques. These long-term cultures maintained differentiation potential. More importantly, these cells express two types of influenza virus receptors, 2-6-Gal- and 2-3-Gal-linked sialic acids, and angiotensin-converting enzyme 2 (ACE2), a receptor for SARS-CoVs as well. These cells were permissive to the infection of pandemic influenza H1N1 (H1N1pdm). In contrast, the lung cancer cell line A549 and immortalized airway epithelial cells (16HBE) were not susceptible to H1N1 infection. A virus-induced cytopathic effect (CPE) on 2D CRC cultures developed in a time-dependent manner. The pathological effects were also readily observed spreading from the apical layer to the basal layer of the 3D ALI culture. This integrated 2D CRC and 3D ALI cultures provide a physiological and personalized model to study the infection of emerging viruses. This novel model can be used for studying virus biology and host response to viral infection and for antiviral drug discovery.
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http://dx.doi.org/10.1155/2020/2421689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368225PMC
July 2020

Long Term Culture of Human Kidney Proximal Tubule Epithelial Cells Maintains Lineage Functions and Serves as an Ex vivo Model for Coronavirus Associated Kidney Injury.

Virol Sin 2020 Jun 29;35(3):311-320. Epub 2020 Jun 29.

State Key Laboratory of Virology/Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.

The mechanism of how SARS-CoV-2 causes severe multi-organ failure is largely unknown. Acute kidney injury (AKI) is one of the frequent organ damage in severe COVID-19 patients. Previous studies have shown that human renal tubule cells could be the potential host cells targeted by SARS-CoV-2. Traditional cancer cell lines or immortalized cell lines are genetically and phenotypically different from host cells. Animal models are widely used, but often fail to reflect a physiological and pathogenic status because of species tropisms. There is an unmet need for normal human epithelial cells for disease modeling. In this study, we successfully established long term cultures of normal human kidney proximal tubule epithelial cells (KPTECs) in 2D and 3D culture systems using conditional reprogramming (CR) and organoids techniques. These cells had the ability to differentiate and repair DNA damage, and showed no transforming property. Importantly, the CR KPTECs maintained lineage function with expression of specific transporters (SLC34A3 and cubilin). They also expressed angiotensin-converting enzyme 2 (ACE2), a receptor for SARS-CoV and SARS-CoV-2. In contrast, cancer cell line did not express endogenous SLC34A3, cubilin and ACE2. Very interestingly, ACE2 expression was around twofold higher in 3D organoids culture compared to that in 2D CR culture condition. Pseudovirion assays demonstrated that SARS-CoV spike (S) protein was able to enter CR cells with luciferase reporter. This integrated 2D CR and 3D organoid cultures provide a physiological ex vivo model to study kidney functions, innate immune response of kidney cells to viruses, and a novel platform for drug discovery and safety evaluation.
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http://dx.doi.org/10.1007/s12250-020-00253-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7322379PMC
June 2020

A High-matched Melamine Sensor Using Core/shell Nano Particles of [email protected] and Ionic Liquid as Imprinted Polymeric Monomers.

Anal Sci 2020 Jun 17;36(6):745-751. Epub 2020 Jan 17.

School of Chemical Biology and Materials Engineering, Suzhou University of Science and Technology.

We describe here a magnetic molecular imprinted polymeric ionic liquid (MMIPIL) film by using a functionalized ionic liquid (3-vinyl-4-amino-5-imidazole carboxamide chloride, IL) and [email protected] as a functional monomer and supporting materials. The change in the direction of the charge density in the structure of MMIPIL polymer resulted in a red shift of about 100 nm for the characteristic group of -C=O. Polyrutin containing an electron-rich benzene ring and multiple hydroxyl groups not only prevented the aggregation of FeO, but also benefitted to immobilize template molecules. More symmetric amino groups in the template molecules generated more hydrogen bonds and other synergistic effects between MEL and the functional monomers, which resulted in a highly-matched and highly stable MMIPIL sensor. The proposed magnetic sensor lowered the matching potential, and enhanced the signal for the detection of melamine (MEL) in milk powder. Under the optimum conditions, the MEL template molecule showed a significant linear relationship between 5.0 × 10 and 0.8 μg/L with a detection limit (S/N = 3) of 1.5 × 10 μg/L. The MMIPIL sensor showed wonderful selectivity and exhibited facile, fast and efficient results in the monitoring MEL with recoveries of between 96.5 and 108.3%.
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http://dx.doi.org/10.2116/analsci.19P371DOI Listing
June 2020

Thiol-modified biochar synthesized by a facile ball-milling method for enhanced sorption of inorganic Hg and organic CHHg

J Hazard Mater 2020 02 30;384:121357. Epub 2019 Sep 30.

Tianjin Key Laboratory of Clean Energy and pollution control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China. Electronic address:

Modification of thiol on biochar often demands complex synthetic procedures and chemicals. In this work, a simple and environment friendly thiol-modified biochar (BMS-biochar) was successfully synthesized by ball milling pristine biochar with 3-mercaptopropyltrimethoxysilane (3-MPTS). The resultant BMS-biochar was characterized and tested for aqueous inorganic Hg and organic CHHg removal. Characterization results showed that 3-MPTS was loaded on the surface of biochar through oxygen-containing functional groups (i.e., OH and CO) and π-π bond. Ball milling method improved the properties of BMS-biochar, namely, more efficient SH load, a larger surface area, more functional groups, more negatively charged surface, which resulted in higher removal efficiency of Hg and CHHg (320.1 mg/g for Hg and 104.9 mg/g for CHHg) compared to the pristine biochar (105.7 mg/g for Hg and 8.21 mg/g for CHHg) and thiol-modified biochar through chemical impregnation (CIS-biochar) (175.6 mg/g for Hg and 58.0 mg/g for CHHg). Ball milling increased the sorption capacities of Hg and CHHg through surface adsorption, electrostatic attraction, ligand exchange, and surface complexation. Modeling results suggested that the surface diffusion was the rate-limiting adsorption step for BMS-biochar. This work gave prominence to the potential of ball milling for the preparation of thiol-modified biochar to remove mercury especially organic CHHg by adsorption.
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http://dx.doi.org/10.1016/j.jhazmat.2019.121357DOI Listing
February 2020

Arc-support Line Segments Revisited: An Efficient High-quality Ellipse Detection.

IEEE Trans Image Process 2019 Aug 15. Epub 2019 Aug 15.

Over the years many ellipse detection algorithms spring up and are studied broadly, while the critical issue of detecting ellipses accurately and efficiently in real-world images remains a challenge. In this paper, we propose a valuable industry-oriented ellipse detector by arc-support line segments, which simultaneously reaches high detection accuracy and efficiency. To simplify the complicated curves in an image while retaining the general properties including convexity and polarity, the arc-support line segments are extracted, which grounds the successful detection of ellipses. The arc-support groups are formed by iteratively and robustly linking the arc-support line segments that latently belong to a common ellipse. Afterward, two complementary approaches, namely, locally selecting the arc-support group with higher saliency and globally searching all the valid paired groups, are adopted to fit the initial ellipses in a fast way. Then, the ellipse candidate set can be formulated by hierarchical clustering of 5D parameter space of initial ellipses. Finally, the salient ellipse candidates are selected and refined as detections subject to the stringent and effective verification. Extensive experiments on three public datasets are implemented and our method achieves the best F-measure scores compared to the state-of-the-art methods. The source code is available at https://github.com/AlanLuSun/High-quality-ellipse-detection.
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http://dx.doi.org/10.1109/TIP.2019.2934352DOI Listing
August 2019

Preparation of various thiol-functionalized carbon-based materials for enhanced removal of mercury from aqueous solution.

Environ Sci Pollut Res Int 2019 Mar 1;26(9):8709-8720. Epub 2019 Feb 1.

Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.

In this work, biochar (BC), activated carbon (AC), and graphene oxide (GO) were thiol-functionalized using 3-mercaptopropyltrimethoxysilane (3-MPTS) (named as BCS, ACS, and GOS, respectively). BCS, ACS, and GOS were synthesized mainly via the interaction between hydrolyzed 3-MPTS and surface oxygen-containing functional groups (e.g., -OH, O-C=O, and C=O) and π-π interaction. The materials before and after modification were characterized and tested for mercury removal, including sorption kinetics and isotherms, the effects of adsorbent dosage, initial pH, and ionic strength. Pseudo-second-order sorption kinetic model (R = 0.992~1.000) and Langmuir sorption isotherm model (R = 0.964~0.998) fitted well with the sorption data of mercury. GOS had the most -SH groups with the largest adsorption capacity for Hg and CHHg (449.6 and 127.5 mg/g), followed by ACS (235.7 and 86.7 mg/g) and BCS (175.6 and 30.3 mg/g), which were much larger than GO (96.7 and 4.9 mg/g), AC (81.1 and 24.6 mg/g), and BC (95.6 and 9.4 mg/g). GOS and ACS showed stable mercury adsorption properties at a wide pH range (2~9) and ionic strength (0.01~0.1 mol/L). Mercury maybe removed by ligand exchange, surface complexation, and electrostatic attraction.
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http://dx.doi.org/10.1007/s11356-019-04320-0DOI Listing
March 2019

Effective removal of inorganic mercury and methylmercury from aqueous solution using novel thiol-functionalized graphene oxide/Fe-Mn composite.

J Hazard Mater 2019 03 18;366:130-139. Epub 2018 Nov 18.

College of Environmental Science and Engineering, Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, Nankai University, Tianjin 300350, China.

A novel thiol-functionalized graphene oxide/Fe-Mn (SGO/Fe-Mn) was investigated for aqueous Hg and CHHg removal. Mercury were removed mainly through ligand exchange and surface complexation with surface active sites (i.e., -SH, OH, OCO, CC, SiO, and ππ bond). SH had the strongest binding ability with mercury, forming sulfur-containing organic matter or polymers with Hg, and sulfur-containing organometallic compounds or thiolate-like species with CHHg. The BET sorption isotherm model well simulated the sorption isotherm data of Hg (R=0.995, q=233.17 mg/g) and CHHg (R=0.997, q=36.69 mg/g), indicating a multilayer adsorption process. The mercury uptake was promoted with the increase of 3-MPTS content, adsorbent dosage, and pH (<5.5), whereas the uptake was inhibited by high pH (>5.5) and high concentrations of humic acid and electrolytes. SGO/Fe-Mn demonstrated high mercury uptake in simulated surface water/groundwater and in the presence of Pb, Cu, Ni, Sb, Cd and Zn. The mercury-laden SGO/Fe-Mn can be successfully regenerated and reused for three times with 98.1% and 67.0% of original Hg and CHHg sorption capacity when 5% thiourea + 2 M KI was used as the desorbing agent. This study demonstrates potential and viability of SGO/Fe-Mn for mercury remediation.
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http://dx.doi.org/10.1016/j.jhazmat.2018.11.074DOI Listing
March 2019

E6 Protein Expressed by High-Risk HPV Activates Super-Enhancers of the and Oncogenes by Destabilizing the Histone Demethylase KDM5C.

Cancer Res 2018 03 16;78(6):1418-1430. Epub 2018 Jan 16.

Department of Medical Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan, China.

The high-risk (HR) human papillomaviruses (HPV) are causative agents of anogenital tract dysplasia and cancers and a fraction of head and neck cancers. The HR HPV E6 oncoprotein possesses canonical oncogenic functions, such as p53 degradation and telomerase activation. It is also capable of stimulating expression of several oncogenes, but the molecular mechanism underlying these events is poorly understood. Here, we provide evidence that HPV16 E6 physically interacts with histone H3K4 demethylase KDM5C, resulting in its degradation in an E3 ligase E6AP- and proteasome-dependent manner. Moreover, we found that HPV16-positive cancer cell lines exhibited lower KDM5C protein levels than HPV-negative cancer cell lines. Restoration of KDM5C significantly suppressed the tumorigenicity of CaSki cells, an HPV16-positive cervical cancer cell line. Whole genome ChIP-seq and RNA-seq results revealed that CaSki cells contained super-enhancers in the proto-oncogenes and Ectopic KDM5C dampened these super-enhancers and reduced the expression of proto-oncogenes. This effect was likely mediated by modulating H3K4me3/H3K4me1 dynamics and decreasing bidirectional enhancer RNA transcription. Depletion of KDM5C or HPV16 E6 expression activated these two super-enhancers. These results illuminate a pivotal relationship between the oncogenic E6 proteins expressed by HR HPV isotypes and epigenetic activation of super-enhancers in the genome that drive expression of key oncogenes like and This study suggests a novel explanation for why infections with certain HPV isotypes are associated with elevated cancer risk by identifying an epigenetic mechanism through which E6 proteins expressed by those isotypes can drive expression of key oncogenes. .
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http://dx.doi.org/10.1158/0008-5472.CAN-17-2118DOI Listing
March 2018

CircView: a visualization and exploration tool for circular RNAs.

Brief Bioinform 2018 11;19(6):1310-1316

Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School.

Circular RNAs (circRNAs) are novel rising stars of noncoding RNAs, which are highly abundant and evolutionarily conserved across species. Number of publications related to circRNAs increased sharply in recent years, representing emerging focuses in the field. Therefore, tools, pipelines and databases have been developed to identify and store circRNAs. However, there is no existing tool to visualize and explore circRNAs. Therefore, we introduce CircView, a user-friendly visualization tool for circRNAs detected from existing tools. CircView enables users to visualize circRNAs and to quantify number of samples with detected circRNAs. CircView allows users to explore circRNAs detected by unique or multiple tools. Furthermore, CircView allows users to view the regulatory elements, such as microRNA response elements and RNA-binding protein binding sites. CircView is a unique tool to visualize and explore circRNAs, which helps users to better understand potential functions of circRNAs and design the functional experiments.
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http://dx.doi.org/10.1093/bib/bbx070DOI Listing
November 2018

CSCD: a database for cancer-specific circular RNAs.

Nucleic Acids Res 2018 01;46(D1):D925-D929

School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China.

Circular RNA (circRNA) is a large group of RNA family extensively existed in cells and tissues. High-throughput sequencing provides a way to view circRNAs across different samples, especially in various diseases. However, there is still no comprehensive database for exploring the cancer-specific circRNAs. We collected 228 total RNA or polyA(-) RNA-seq samples from both cancer and normal cell lines, and identified 272 152 cancer-specific circRNAs. A total of 950 962 circRNAs were identified in normal samples only, and 170 909 circRNAs were identified in both tumor and normal samples, which could be further used as non-tumor background. We constructed a cancer-specific circRNA database (CSCD, http://gb.whu.edu.cn/CSCD). To understand the functional effects of circRNAs, we predicted the microRNA response element sites and RNA binding protein sites for each circRNA. We further predicted potential open reading frames to highlight translatable circRNAs. To understand the association between the linear splicing and the back-splicing, we also predicted the splicing events in linear transcripts of each circRNA. As the first comprehensive cancer-specific circRNA database, we believe CSCD could significantly contribute to the research for the function and regulation of cancer-associated circRNAs.
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http://dx.doi.org/10.1093/nar/gkx863DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753219PMC
January 2018

Genome-wide characterization of lncRNAs in acute myeloid leukemia.

Brief Bioinform 2018 07;19(4):627-635

School of Basic Medical Sciences, Wuhan University, Wuhan, China.

Long noncoding RNAs (lncRNAs) are a large family of noncoding RNAs that play a critical role in various normal bioprocesses as well as tumorigenesis. However, the expression patterns and biological functions of lncRNAs in acute leukemia have not been well studied. Here, we performed transcriptome-wide lncRNA expression profiling of acute myeloid leukemia (AML) patient samples, along with non-leukemia control hematopoietic samples. We found that lncRNAs were differentially expressed in AML samples relative to control samples. Notably, we identified that lncRNAs upregulated in AML (relative to the control samples) are associated with a lower degree of DNA methylation and a higher ratio of being bound by transcription factors such as SP1, STAT4, ATF-2 and ELK-1 compared with those downregulated in AML. Moreover, an enrichment of H3K4me3 and a depletion of H3K27me3 were observed in upregulated lncRNAs in AML. Expression patterns of three types of lncRNAs (antisense, enhancer and intergenic lncRNAs) have previously been characterized. Of the identified lncRNAs, we found that high expression level lncRNA LOC285758 is associated with the poor prognosis in AML patients. Furthermore, we found that LOC285758 regulates proliferation of AML cell lines by enhancing the expression of HDAC2, a key factor in carcinogenesis. Collectively, our study depicts a landscape of important lncRNAs in AML and provides novel potential therapeutic targets and prognostic markers for AML treatment.
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http://dx.doi.org/10.1093/bib/bbx007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355113PMC
July 2018

Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes.

Brief Bioinform 2017 Nov;18(6):984-992

Circular RNA (circRNA) is a group of RNA family generated by RNA circularization, which was discovered ubiquitously across different species and tissues. However, there is no global view of tissue specificity for circRNAs to date. Here we performed the comprehensive analysis to characterize the features of human and mouse tissue-specific (TS) circRNAs. We identified in total 302 853 TS circRNAs in the human and mouse genome, and showed that the brain has the highest abundance of TS circRNAs. We further confirmed the existence of circRNAs by reverse transcription polymerase chain reaction (RT-PCR). We also characterized the genomic location and conservation of these TS circRNAs and showed that the majority of TS circRNAs are generated from exonic regions. To further understand the potential functions of TS circRNAs, we identified microRNAs and RNA binding protein, which might bind to TS circRNAs. This process suggested their involvement in development and organ differentiation. Finally, we constructed an integrated database TSCD (Tissue-Specific CircRNA Database: http://gb.whu.edu.cn/TSCD) to deposit the features of TS circRNAs. This study is the first comprehensive view of TS circRNAs in human and mouse, which shed light on circRNA functions in organ development and disorders.
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http://dx.doi.org/10.1093/bib/bbw081DOI Listing
November 2017

Systematic Characterization of Long Noncoding RNAs Reveals the Contrasting Coordination of Cis- and Trans-Molecular Regulation in Human Fetal and Adult Hearts.

Circ Cardiovasc Genet 2016 Apr 19;9(2):110-8. Epub 2016 Feb 19.

From the Stanford Cardiovascular Institute (C.H., K.D.W., H.W., J.C., J.C.W.), Division of Cardiology, Department of Medicine (C.H., H.W., J.C., J.C.W.), Department of Pathology (K.D.W.), and Program in Epithelial Biology (K.Q., H.Y.C.), Stanford University, CA; and School of Basic Medical Science (C.H., H.H., S.X.) and International School of Software (J.F.), Wuhan University, Wuhan, China.

Background: The molecular regulation of heart development is regulated by cis- and trans-factors acting on the genome and epigenome. As a class of important regulatory RNAs, the role of long noncoding RNAs (lncRNAs) in human heart development is still poorly understood. Furthermore, factors that interact with lncRNAs in this process are not well characterized.

Methods And Results: Using RNA sequencing, we systematically define the contrasting lncRNA expression patterns between fetal and adult hearts. We report that lncRNAs upregulated in adult versus fetal heart have different sequence features and distributions. For example, the adult heart expresses more sense lncRNAs compared with fetal heart. We also report the coexpression of lncRNAs and neighboring coding genes that have important functions in heart development. Importantly, the regulation of lncRNA expression during fetal to adult heart development seems to be due, in part, to the coordination of specific developmental epigenetic modifications, such as H3K4me1 and H3k4me3. The expression of promoter-associated lncRNAs in adult and fetal hearts also seems to be related to these epigenetic states. Finally, transcription factor-binding analysis suggests that lncRNAs are directly regulating cardiac gene expression during development.

Conclusions: We provide a systematic analysis of lncRNA control of heart development that gives clues to the roles that specific lncRNAs play in fetal and adult hearts.
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http://dx.doi.org/10.1161/CIRCGENETICS.115.001264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862831PMC
April 2016

Luminescence and energy transfer of the color-tunable phosphor Li₆Gd(BO₃)₃:Tb³⁺/Bi³⁺, Eu³⁺.

Appl Radiat Isot 2016 Feb 17;108:148-153. Epub 2015 Dec 17.

School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China. Electronic address:

Bi(3+)/Tb(3+), Eu(3+) co-doped Li6Gd(BO3)3 (LGBO) phosphors were synthesized via a traditional solid-state method. Phase purity was investigated using X-ray diffraction, absorption strength of the phosphors were investigated by UV-vis absorption spectra, and the photoluminescence properties of the phosphors were studied systematically. Results showed that the emission intensity of Bi(3+), Eu(3+) co-doped LBOG was 2.76 times higher than that of Eu(3+)-doped LGBO irradiated at 275 nm, thereby implying the possibility of energy transfer from Bi(3+) to Eu(3+). The excitation spectra of Tb(3+), Eu(3+) co-doped LGBO phosphors are broader in comparison with single-doped phosphors and show tunable colors from green to yellow to orange-red when the ratio of Tb(3+) to Eu(3+) is adjusted These results demonstrate that LGBO:Tb(3+), Eu(3+) phosphors have potential use in light-emitting diodes.
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http://dx.doi.org/10.1016/j.apradiso.2015.12.042DOI Listing
February 2016

Luminescence and energy transfer of color-tunable Li6Gd(BO3)3:Ce(3+), Tb(3+) phosphor.

Spectrochim Acta A Mol Biomol Spectrosc 2015 Oct 11;149:682-6. Epub 2015 May 11.

School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China. Electronic address:

A series of novel color-tunable phosphors of Ce(3+), Tb(3+)-codoped Li6Gd(BO3)3 was synthesized through a classic solid-state reaction. The color of these phosphors changes from blue to green by adjusting the ratio of Ce(3+) to Tb(3+). The photoluminescence properties of the synthesized phosphors were investigated, and several major emission bands that belong to Ce(3+) and Tb(3+) ions were irradiated with near ultraviolet light. Moreover, the energy transfer mechanism between Ce(3+) and Tb(3+) in Li6Gd(BO3)3 was explored. The photoluminescence decay curves were performed to validate the energy transfer. The analysis demonstrated that the energy transfer from Ce(3+) to Tb(3+) arose from dipole-dipole interaction with a critical distance of approximately 17.6 Å.
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http://dx.doi.org/10.1016/j.saa.2015.04.108DOI Listing
October 2015
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