Publications by authors named "Fei Long"

185 Publications

The missing link: covalent linkages in structural models.

Acta Crystallogr D Struct Biol 2021 Jun 19;77(Pt 6):727-745. Epub 2021 May 19.

Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.

Covalent linkages between constituent blocks of macromolecules and ligands have been subject to inconsistent treatment during the model-building, refinement and deposition process. This may stem from a number of sources, including difficulties with initially detecting the covalent linkage, identifying the correct chemistry, obtaining an appropriate restraint dictionary and ensuring its correct application. The analysis presented herein assesses the extent of problems involving covalent linkages in the Protein Data Bank (PDB). Not only will this facilitate the remediation of existing models, but also, more importantly, it will inform and thus improve the quality of future linkages. By considering linkages of known type in the CCP4 Monomer Library (CCP4-ML), failure to model a covalent linkage is identified to result in inaccurate (systematically longer) interatomic distances. Scanning the PDB for proximal atom pairs that do not have a corresponding type in the CCP4-ML reveals a large number of commonly occurring types of unannotated potential linkages; in general, these may or may not be covalently linked. Manual consideration of the most commonly occurring cases identifies a number of genuine classes of covalent linkages. The recent expansion of the CCP4-ML is discussed, which has involved the addition of over 16 000 and the replacement of over 11 000 component dictionaries using AceDRG. As part of this effort, the CCP4-ML has also been extended using AceDRG link dictionaries for the aforementioned linkage types identified in this analysis. This will facilitate the identification of such linkage types in future modelling efforts, whilst concurrently easing the process involved in their application. The need for a universal standard for maintaining link records corresponding to covalent linkages, and references to the associated dictionaries used during modelling and refinement, following deposition to the PDB is emphasized. The importance of correctly modelling covalent linkages is demonstrated using a case study, which involves the covalent linkage of an inhibitor to the main protease in various viral species, including SARS-CoV-2. This example demonstrates the importance of properly modelling covalent linkages using a comprehensive restraint dictionary, as opposed to just using a single interatomic distance restraint or failing to model the covalent linkage at all.
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http://dx.doi.org/10.1107/S2059798321003934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8171067PMC
June 2021

Modelling covalent linkages in CCP4.

Acta Crystallogr D Struct Biol 2021 Jun 19;77(Pt 6):712-726. Epub 2021 May 19.

Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.

In this contribution, the current protocols for modelling covalent linkages within the CCP4 suite are considered. The mechanism used for modelling covalent linkages is reviewed: the use of dictionaries for describing changes to stereochemistry as a result of the covalent linkage and the application of link-annotation records to structural models to ensure the correct treatment of individual instances of covalent linkages. Previously, linkage descriptions were lacking in quality compared with those of contemporary component dictionaries. Consequently, AceDRG has been adapted for the generation of link dictionaries of the same quality as for individual components. The approach adopted by AceDRG for the generation of link dictionaries is outlined, which includes associated modifications to the linked components. A number of tools to facilitate the practical modelling of covalent linkages available within the CCP4 suite are described, including a new restraint-dictionary accumulator, the Make Covalent Link tool and AceDRG interface in Coot, the 3D graphical editor JLigand and the mechanisms for dealing with covalent linkages in the CCP4i2 and CCP4 Cloud environments. These integrated solutions streamline and ease the covalent-linkage modelling workflow, seamlessly transferring relevant information between programs. Current recommended practice is elucidated by means of instructive practical examples. By summarizing the different approaches to modelling linkages that are available within the CCP4 suite, limitations and potential pitfalls that may be encountered are highlighted in order to raise awareness, with the intention of improving the quality of future modelled covalent linkages in macromolecular complexes.
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http://dx.doi.org/10.1107/S2059798321001753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8171069PMC
June 2021

Predicting the performance of anaerobic digestion using machine learning algorithms and genomic data.

Water Res 2021 Jul 22;199:117182. Epub 2021 Apr 22.

Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, USA. Electronic address:

Modeling of anaerobic digestion (AD) is crucial to better understand the process dynamics and to improve the digester performance. This is an essential yet difficult task due to the complex and unknown interactions within the system. The application of well-developed data mining technologies, such as machine learning (ML) and microbial gene sequencing techniques are promising in overcoming these challenges. In this study, we investigated the feasibility of 6 ML algorithms using genomic data and their corresponding operational parameters from 8 research groups to predict methane yield. For classification models, random forest (RF) achieved accuracies of 0.77 using operational parameters alone and 0.78 using genomic data at the bacterial phylum level alone. The combination of operational parameters and genomic data improved the prediction accuracy to 0.82 (p<0.05). For regression models, a low root mean square error of 0.04 (relative root mean square error =8.6%) was acquired by neural network using genomic data at the bacterial phylum level alone. Feature importance analysis by RF suggested that Chloroflexi, Actinobacteria, Proteobacteria, Fibrobacteres, and Spirochaeta were the top 5 most important phyla although their relative abundances were ranging only from 0.1% to 3.1%. The important features identified could provide guidance for early warning and proactive management of microbial communities. This study demonstrated the promising application of ML techniques for predicting and controlling AD performance.
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http://dx.doi.org/10.1016/j.watres.2021.117182DOI Listing
July 2021

Differential expression of sputum and serum autoantibodies in patients with chronic obstructive pulmonary disease.

Am J Physiol Lung Cell Mol Physiol 2021 Jun 28;320(6):L1169-L1182. Epub 2021 Apr 28.

Department of Pathology and Molecular Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada.

Chronic obstructive pulmonary disease (COPD) is a complex and progressive respiratory disease. Autoimmune processes have been hypothesized to contribute to disease progression; however, the presence of autoantibodies in the serum has been variable. Given that COPD is a lung disease, we sought to investigate whether autoantibodies in sputum supernatant would better define pulmonary autoimmune processes. Matched sputum and serum samples were obtained from the Airways Disease Endotyping for Personalized Therapeutics (ADEPT) study and at the Guangzhou Institute of Respiratory Health (GIRH). Samples were collected from patients with varying severity of COPD, asymptomatic smokers, and healthy control subjects. IgG and IgM autoantibodies were detected in sputum and serum of all subjects in both cohorts using a broad-spectrum autoantigen array. No differences were observed in sputum autoantibodies between COPD and asymptomatic smokers in either cohort. In contrast, 16% of detectable sputum IgG autoantibodies were decreased in subjects with COPD compared to healthy controls in the ADEPT cohort. Compared to asymptomatic smokers, approximately 13% of detectable serum IgG and 40% of detectable serum IgM autoantibodies were differentially expressed in GIRH COPD subjects. Of the differentially expressed specificities, anti-nuclear autoantibodies were predominately decreased. A weak correlation between increased serum IgM anti-tissue autoantibodies and a measure of airspace enlargement was observed. The differential expression of specificities varied between the cohorts. In closing, using a comprehensive autoantibody array, we demonstrate that autoantibodies are present in subjects with COPD, asymptomatic smokers, and healthy controls. Cohorts displayed high levels of heterogeneity, precluding the utilization of autoantibodies for diagnostic purposes.
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http://dx.doi.org/10.1152/ajplung.00518.2020DOI Listing
June 2021

BloodCaps: A capsule network based model for the multiclassification of human peripheral blood cells.

Comput Methods Programs Biomed 2021 Apr 7;202:105972. Epub 2021 Feb 7.

School of Big Data & Software Engineering, Chongqing University, Chongqing 401331, China. Electronic address:

Background And Objective: The classification of human peripheral blood cells yields significance in the detection of inflammation, infections and blood cell disorders such as leukemia. Limitations in traditional algorithms for blood cell classification and increased computational processing power have allowed machine learning methods to be utilized for this clinically prevalent task.

Methods: In the current work, we present BloodCaps, a capsule based model designed for the accurate multiclassification of a diverse and broad spectrum of blood cells.

Results: Implemented on a large-scale dataset of 8 categories of human peripheral blood cells, the proposed architecture achieved an overall accuracy of 99.3%, outperforming convolutional neural networks such as AlexNet(81.5%), VGG16(97.8%), ResNet-18(95.9%) and InceptionV3(98.4%). Furthermore, we devised three new datasets(low-resolution dataset, small dataset, and low-resolution small dataset) from the original dataset, and tested BloodCaps in comparison with AlexNet, VGG16, ResNet-18, and InceptionV3. To further validate the applicability of our proposed model, we tested BloodCaps on additional public datasets such as the All IDB2, BCCD, and Cell Vision datasets. Compared with the reported results, BloodCaps showed the best performance in all three scenarios.

Conclusions: The proposed method proved superior in octal classification among all three datasets. We believe the proposed method represents a promising tool to improve the diagnostic performance of clinical blood examinations.
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http://dx.doi.org/10.1016/j.cmpb.2021.105972DOI Listing
April 2021

MiR-133b inhibits colorectal cancer metastasis via lncRNA-LUCAT1.

Future Oncol 2021 Mar 5;17(9):1013-1023. Epub 2021 Feb 5.

Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, 410013, China.

Colorectal cancer (CRC) is a common malignant tumor of the digestive system. Metastasis is the leading cause of poor prognosis of CRC patients, warranting further study of the molecular mechanism of metastasis in CRC and identification of new therapeutic targets. MiR-133b has been proven to play an important role in tumorigenesis by directly targeting coding genes. However, whether miR-133b can regulate tumorigenesis via long noncoding RNA (lncRNA) remains unclear. We systematically analyzed the expression level and correlation of miR-133b and LUCAT1 in cancer tissues and adjacent tissues from 30 patients with CRC. The effects of miR-133b and LUCAT1 on the invasive ability of CRC cells were detected by a transwell assay. The relationship between miR-133b and LUCAT1 was investigated by cells transfection experiments, rescue experiments and luciferase reporter assays. The binding of LUCAT1 and EZH2 was detected by RNA immunoprecipitation assay. MiR-133b was expressed at low levels in CRC tissues, and LUCAT1 was highly expressed, with an inverse correlation between them. LUCAT1 promoted the migration and invasion of HCT116 and SW620 cells. Overexpression of LUCAT1 attenuated the inhibition of cell migration and invasion induced by miR-133b. However, the dual luciferase assay showed that miR-133b did not directly target LUCAT1. MiR-133b affects CRC metastasis via the LUCAT1/EZH2 complex. MiR-133b and LUCAT1 may be potential targets for antimetastasis therapy in CRC.
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http://dx.doi.org/10.2217/fon-2020-0420DOI Listing
March 2021

Comprehensive landscape and future perspectives of circular RNAs in colorectal cancer.

Mol Cancer 2021 02 3;20(1):26. Epub 2021 Feb 3.

Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan, 410013, P.R. China.

Colorectal cancer (CRC) is a common hereditary tumor that is often fatal. Its pathogenesis involves multiple genes, including circular RNAs (circRNAs). Notably, circRNAs constitute a new class of noncoding RNAs (ncRNAs) with a covalently closed loop structure and have been characterized as stable, conserved molecules that are abundantly expressed in tissue/development-specific patterns in eukaryotes. Based on accumulating evidence, circRNAs are aberrantly expressed in CRC tissues, cells, exosomes, and blood from patients with CRC. Moreover, numerous circRNAs have been identified as either oncogenes or tumor suppressors that mediate tumorigenesis, metastasis and chemoradiation resistance in CRC. Although the regulatory mechanisms of circRNA biogenesis and functions remain fairly elusive, interesting results have been obtained in studies investigating CRC. In particular, the expression of circRNAs in CRC is comprehensively modulated by multiple factors, such as splicing factors, transcription factors, specific enzymes and cis-acting elements. More importantly, circRNAs exert pivotal effects on CRC through various mechanisms, including acting as miRNA sponges or decoys, interacting with RNA binding proteins, and even translating functional peptides. Finally, circRNAs may serve as promising diagnostic and prognostic biomarkers and potential therapeutic targets in the clinical practice of CRC. In this review, we discuss the dysregulation, functions and clinical significance of circRNAs in CRC and further discuss the molecular mechanisms by which circRNAs exert their functions and how their expression is regulated. Based on this review, we hope to reveal the functions of circRNAs in the initiation and progression of cancer and highlight the future perspectives on strategies targeting circRNAs in cancer research.
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http://dx.doi.org/10.1186/s12943-021-01318-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7856739PMC
February 2021

Evaluation of a novel Cardiac Peri-Operative Transfusion Trigger Scoring system in patients with coronary artery disease.

BMC Cardiovasc Disord 2021 01 19;21(1):40. Epub 2021 Jan 19.

Department of Anesthesiology, The First Affiliated Hospital of Xinjiang Medical University, 37 Liyushan South Road, Xinshi District, Urumqi, 830054, Xinjiang, China.

Background: A simple and accurate scoring system to guide perioperative blood transfusion in patients with coronary artery disease (CAD) undergoing cardiac surgery is lacking. The trigger point for blood transfusions for these patients may be different from existing transfusion guidelines. This study aimed to evaluate the safety and efficacy of a new scoring strategy for use in guiding transfusion decisions in patients with CAD.

Methods: A multicenter randomized controlled trial was conducted at three third-level grade-A hospitals from January 2015 to May 2018. Data of 254 patients in a Cardiac Peri-Operative Transfusion Trigger Score (cPOTTS) group and 246 patients in a group receiving conventional evaluation of the need for transfusion (conventional group) were analysed. The requirements for transfusion and the per capita consumption of red blood cells (RBCs) were compared between groups.

Results: Baseline characteristics of the two groups were comparable. Logistic regression analyses revealed no significant differences between the two groups in primary outcomes (1-year mortality and perioperative ischemic cardiac events), secondary outcomes (shock, infections, and renal impairment), ICU admission, and ICU stay duration. However, patients in the cPOTTS group had significantly shorter hospital stays, lower hospital costs, lower utilization rate and lower per capita consumption of transfused RBCs than controls. Stratified analyses revealed no significant differences between groups in associations between baseline characteristics and perioperative ischemic cardiac events, except for hemofiltration or dialysis and NYHA class in I.

Conclusions: This novel scoring system offered a practical and straightforward guideline of perioperative blood transfusion in patients with CAD. Trial registration chiCTR1800016561(2017/7/19).
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http://dx.doi.org/10.1186/s12872-021-01854-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7814977PMC
January 2021

Performance prediction of ZVI-based anaerobic digestion reactor using machine learning algorithms.

Waste Manag 2021 Feb 22;121:59-66. Epub 2020 Dec 22.

Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, United States. Electronic address:

The use of zero-valent iron (ZVI) to enhance anaerobic digestion (AD) systems is widely advocated as it improves methane production and system stability. Accurate modeling of ZVI-based AD reactor is conducive to predicting methane production potential, optimizing operational strategy, and gathering reference information for industrial design in place of time-consuming and laborious tests. In this study, three machine learning (ML) algorithms, namely random forest (RF), extreme gradient boosting (XGBoost), and deep learning (DL), were evaluated for their feasibility of predicting the performance of ZVI-based AD reactors based on the operating parameters collected in 9 published articles. XGBoost demonstrated the highest accuracy in predicting total methane production, with a root mean squared error (RMSE) of 21.09, compared to 26.03 and 27.35 of RF and DL, respectively. The accuracy represented by mean absolute percentage error also showed the same trend, with 14.26%, 15.14% and 17.82% for XGBoost, RF and DL, respectively. Through the feature importance generated by XGBoost, the parameters of total solid of feedstock (TS), sCOD, ZVI dosage and particle size were identified as the dominant parameters that affect the methane production, with feature importance weights of 0.339, 0.238, 0.158, and 0.116, respectively. The digestion time was further introduced into the above-established model to predict the cumulative methane production. With the expansion of training dataset, DL outperformed XGBoost and RF to show the lowest RMSEs of 11.83 and 5.82 in the control and ZVI-added reactors, respectively. This study demonstrates the potential of using ML algorithms to model ZVI-based AD reactors.
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http://dx.doi.org/10.1016/j.wasman.2020.12.003DOI Listing
February 2021

A Stable and Indurative Superhydrophobic Film with Excellent Anti-Bioadhesive Performance for 6061 Al Protection.

Materials (Basel) 2020 Dec 6;13(23). Epub 2020 Dec 6.

State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.

Superhydrophobic surfaces have attracted intensive attention in the antifouling field because of their excellent anti-bioadhesive performance and environmental friendliness. However, promising surfaces have met great challenges of poor mechanical robustness under harsh serving conditions. Herein, an organic-inorganic composite strategy, that the silane-modified TiO nanoparticles are compounded into the porous framework provided by the stable and indurative aluminum oxide film, is proposed to address the common serious problem in superhydrophobic surfaces. Different from the traditional superhydrophobic surfaces, this composite film possesses a ~18 μm thick layer which can provide strong support to silane-modified TiO nanoparticles. The resulting film can reserve superhydrophobicity to the surface even after a thickness loss of ~15 μm under continuous abrasion. At the same time, the results of the bacterial adhesive tests also verify that the film has the same long-term anti-bioadhesive performance. The film with superhydrophobicity, excellent anti-bioadhesive property, and stable robustness will make it a promising candidate for serving in a harsh environment, and the design concept of this film could be applied to various substrates.
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http://dx.doi.org/10.3390/ma13235564DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7731204PMC
December 2020

Enhancement of microbiome management by machine learning for biological wastewater treatment.

Microb Biotechnol 2021 01 22;14(1):59-62. Epub 2020 Nov 22.

School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.

Here, we propose to develop microbiome-based machine learning models to predict the response of biological wastewater treatment systems to environmental or operational disturbances or to design specific microbiomes to achieve a desired system function. These machine learning models can be used to enhance the stability of microbiome-based biological systems and warn against the failure of these systems.
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http://dx.doi.org/10.1111/1751-7915.13707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7888473PMC
January 2021

Stability Analysis for Delayed Neural Networks via a Novel Negative-Definiteness Determination Method.

IEEE Trans Cybern 2020 Nov 17;PP. Epub 2020 Nov 17.

The stability of neural networks with a time-varying delay is studied in this article. First, a relaxed Lyapunov-Krasovskii functional (LKF) is presented, in which the positive-definiteness requirement of the augmented quadratic term and the delay-product-type terms are set free, and two double integral states are augmented into the single integral terms at the same time. Second, a new negative-definiteness determination method is put forward for quadratic functions by utilizing Taylor's formula and the interval-decomposition approach. This method encompasses the previous negative-definiteness determination approaches and has less conservatism. Finally, the proposed LKF and the negative-definiteness determination method are applied to the stability analysis of neural networks with a time-varying delay, whose advantages are shown by two numerical examples.
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http://dx.doi.org/10.1109/TCYB.2020.3031087DOI Listing
November 2020

The Application of Decellularized Adipose Tissue Promotes Wound Healing.

Tissue Eng Regen Med 2020 12 9;17(6):863-874. Epub 2020 Nov 9.

Department of Plastic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Shuaifuyuan 1#, Dongcheng District, Beijing, 100730, China.

Background: Due to adipose-derived stem cells (ASCs) being easy to obtain, their rapid proliferation rate, and their multidirectional differentiation capabilities, they have been widely used in the field of regenerative medicine. With the progress of decellularized adipose tissue (DAT) and adipose tissue engineering research, the role of DAT in promoting angiogenesis has gradually been emphasized.

Methods: We examined the biological characteristics and biosafety of DAT and evaluated the stem cell maintenance ability and promotion of growth factor secretion through conducting in vitro and in vivo studies.

Results: The tested ASCs showed high rat:es of proliferation and adhered well to DAT. The expression levels of essential genes for cell stem maintenance, including OCT4, SOX2, and Nanog were low at 2-24 h and much higher at 48 and 96 h. The Adipogenic expression level of markers for ASCs proliferation including PPARγ, C/EPBα, and LPL increased from 2 to 96 h. Co-culture of ASCs and DAT increased the secretion of local growth factors, such as VEGF, PDGF-bb, bFGF, HGF, EGF, and FDGF-bb, and secretion gradually increased from 0 to 48 h. A model of full-thickness skin defects on the back of nude mice was established, and the co-culture of ASCs and DAT showed the best in vivo treatment effect.

Conclusion: The application of DAT promotes wound healing, and DAT combined with ASCs may be a promising material in adipose tissue engineering and regenerative medicine.
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http://dx.doi.org/10.1007/s13770-020-00286-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710820PMC
December 2020

Anaerobic reduction of high-polarity nitroaromatic compounds by electrochemically active bacteria: Roles of Mtr respiratory pathway, molecular polarity, mediator and membrane permeability.

Environ Pollut 2021 Jan 28;268(Pt B):115943. Epub 2020 Oct 28.

Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China. Electronic address:

Electrochemically active bacteria (EAB) are effective for the bioreduction of nitroaromatic compounds (NACs), but the exact reduction mechanisms are unclear yet. Therefore, 3-nitrobenzenesulfonate (NBS) was used to explore the biodegradation mechanism of NACs by EAB. Results show that NBS could be anaerobically degraded by Shewanella oneidensis MR-1. The generation of aminoaromatic compounds was accompanied with the NBS reduction, indicating that NBS was biodegraded via reductive approach by S. oneidensis MR-1. The impacts of NBS concentration and cell density on the NBS reduction were evaluated. The removal of NBS depends mainly on the transmembrane electron transfer of S. oneidensis MR-1. Impairment of Mtr respiratory pathway was found to mitigate the reduction of NBS, suggesting that the anaerobic biodegradation of NBS occurred extracellularly. Knocking out cymA severely impaired the extracellular reduction ability of S. oneidensis MR-1. However, the phenotype of ΔcymA mutant could be compensated by the exogenous electron mediators, implying the trans-outer membrane diffusion of mediators into the periplasmic space. This work provides a new insight into the anaerobic reduction of aromatic contaminants by EAB.
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http://dx.doi.org/10.1016/j.envpol.2020.115943DOI Listing
January 2021

Hydrogen production from lignocellulosic hydrolysate in an up-scaled microbial electrolysis cell with stacked bio-electrodes.

Bioresour Technol 2021 Jan 28;320(Pt A):124314. Epub 2020 Oct 28.

Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97333, USA. Electronic address:

Hydrogen production from renewable resources via microbial electrolysis cells (MECs) is a promising approach for sustainable energy production. Yet high hydrogen yield from real feedstocks has not been demonstrated in up-scaled MECs. In this study, a 10-L single chamber MEC with a high electrode surface area to volume ratio (66 m/m) was constructed and electroactive cathodic biofilms were enriched for hydrogen evolution reaction. A high hydrogen yield of 91% was achieved using lignocellulosic hydrolysate with a hydrogen production rate of 0.71 L/L/D at an organic loading rate of 0.4 g/D. The anodic and cathodic microbial communities, with Enterococcus spp. as the known electroactive bacteria, were capable of achieving current densities of 13.7 A/m and 16.5 A/m, respectively. A machine learning algorithm was used to investigate the correlation between community data and electrochemical performance, and the critical genera on determining current density were identified.
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http://dx.doi.org/10.1016/j.biortech.2020.124314DOI Listing
January 2021

Analysis and Prediction of Corrosion of Refractory Materials by Sodium Salts during Waste Liquid Incineration-Thermodynamic Study.

Materials (Basel) 2020 Oct 23;13(21). Epub 2020 Oct 23.

National Engineering Laboratory for Biomass Power Generation Equipment, School of New Energy, North China Electric Power University, Beijing 102206, China.

Incineration of high-content sodium salt organic waste liquid will corrode the refractory material in the incinerator, causing the refractory material to peel off and be damaged. A thermodynamics method was used to study the thermodynamic properties of three common sodium salts (NaCl, NaCO and NaSO) on the corrosion of refractory materials (MgO·CrO, MgO·AlO, AlO, MgO and CrO). The results determined that MgO has the best corrosion resistance and is not corroded by the three sodium salts. On this basis, the thermodynamic corrosion experiments of NaCl corrosion of magnesium oxide at three temperatures of 600, 1000 and 1200 °C were carried out. Analysis of the corrosion product by X-ray diffraction (XRD) showed no corrosion product formation. Studies have shown that thermodynamic calculation can accurately predict the thermodynamic mechanism of alkali metal corrosion to refractory materials, and MgO is a good anti-alkali metal corrosion refractory material.
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http://dx.doi.org/10.3390/ma13214729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7660194PMC
October 2020

One-Pot Hydrothermal Synthesis of La-Doped ZnInS Microspheres with Improved Visible-Light Photocatalytic Performance.

Nanomaterials (Basel) 2020 Oct 14;10(10). Epub 2020 Oct 14.

Department of Nano Convergence Engineering, Jeonbuk National University, Jeonju 54896, Korea.

Impurity element doping is extensively taken as one of the most efficient strategies to regulate the electronic structure as well as the rate of photogenerated charge separation of photocatalysts. Herein, a one-pot hydrothermal synthesis process was exploited to obtain La-doped ZnInS microspheres, aiming at gaining insight into the role that doping ions played in the improvement of pollutant photodegradation. Systematical characterization means, comprising of X-ray photoelectron spectroscopy (XPS), ultraviolet-visible (UV-vis) diffuse reflection spectroscopy and Raman spectra, combination with high-resolution transmission electron microscopy (HRTEM), were employed to in depth reveal the concomitancy of La ions and ZnInS crystal lattice. The results showed that the La-doped ZnInS samples exhibited a slightly wider and stronger spectral absorption than pristine ZnInS; and the specific surface area of doped ZnInS samples was a bit larger. The La-doped ZnInS electrodes showed improved photocurrent response, and the photocurrent density reached a maximum value at La content of 1.5 wt%. As expected, La-doped ZnInS samples exhibited a remarkable enhancement of photocatalytic behaviour toward the photodegradation of tetracycline hydrochloride (TCH) and methyl orange (MO). The prominently enhanced photoactivity of doped ZnInS samples was due to the synergistic effect of the elevated visible-light absorption ability and effective photogenerated charge carriers' separation.
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http://dx.doi.org/10.3390/nano10102026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7602468PMC
October 2020

Dissociation between airway and systemic autoantibody responses in chronic obstructive pulmonary disease.

Ann Transl Med 2020 Aug;8(15):918

State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.

Background: Autoimmune processes have been implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). However, the relationship between airway and systemic autoantibody responses remains unclear. The aim of this study was to elucidate this relationship in patients with stable COPD by investigating the correlation patterns between sputum and serum autoantibodies.

Methods: In this cross-sectional study, sputum supernatant and serum obtained from 47 patients with stable COPD were assayed for the presence of IgG antibodies against ten autoantigens: Smith antigen (Sm), ribosomal phosphoprotein P0 (P0), Ro/Sjögren syndrome type A antigen (Ro/SSA), La/Sjögren syndrome type B antigen (La/SSB), DNA topoisomerase I (Scl-70), histidyl-tRNA synthetase (Jo-1), U1 small nuclear ribonucleoprotein (U1-SnRNP), thyroid peroxidase (TPO), proteinase-3 (PR3), and myeloperoxidase (MPO). A second cohort of 55 stable COPD patients was recruited for validation, and a group of 59 non-COPD controls and a group of 20 connective-tissue disease-associated interstitial lung disease (CTD-ILD) patients were also recruited for comparison. Hierarchical clustering and network analysis were used to evaluate the correlation patterns between sputum and serum autoantibody profiles.

Results: Both hierarchical clustering and network analysis showed that sputum and serum autoantibody profiles were distinct in either analytic COPD cohort or validation cohort. In contrast, the autoantibodies of the two compartments in non-COPD controls and CTD-ILD patients were inadequately distinguished using either hierarchical clustering or network analysis. Many autoantibodies in the sputum were found to have significant correlations with lung function, symptom score and frequency of prior exacerbations in COPD patients, but the antibodies in the serum were not.

Conclusions: We observed a dissociation between sputum autoantibodies and serum autoantibodies in patients with stable COPD, suggesting that airway and systemic immune status may play very different roles in the disease. Sputum autoantibodies are more clinically relevant than serum autoantibodies. Focusing on airway autoimmunity may help improve understanding of the immunopathological mechanism of COPD.
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http://dx.doi.org/10.21037/atm-20-944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7475442PMC
August 2020

Identification of circular RNA hsa_circ_0044556 and its effect on the progression of colorectal cancer.

Cancer Cell Int 2020 1;20:427. Epub 2020 Sep 1.

Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan China.

Background: Circular RNAs (circRNAs) are a novel class of noncoding RNAs. Increasing evidence indicates that circRNAs play an important role in the occurrence and development of tumors. However, the role of circRNA hsa_circ_0044556 in the progression of colorectal cancer (CRC) remains unclear.

Methods: First, we searched for differentially expressed circRNAs using a circRNA microarray in paired CRC and adjacent normal tissues. The circRNA hsa_circ_0044556 was screened out from the existing CRC circRNA microarray in the Gene Expression Omnibus database and our microarray. The clinical significance of hsa_circ_0044556 expression level in CRC patients was then investigated. Finally, the functions of the targets of this circRNA were determined in CRC cell lines.

Results: Hsa_circ_0044556 was highly expressed in CRC patients and was positively correlated with tumor stage and lymph node metastasis. In CRC cell lines, the proliferation, migration, and invasion of cancer cells were inhibited by knocking down hsa_circ_0044556 expression.

Conclusion: Hsa_circ_0044556 promoted the progression of CRC. It is possible that hsa_circ_0044556 will become a novel biomarker or therapeutic target for CRC.
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http://dx.doi.org/10.1186/s12935-020-01523-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7465356PMC
September 2020

Current smoking status is associated with reduced sputum immunoglobulin M and G expression in COPD.

Eur Respir J 2021 Feb 4;57(2). Epub 2021 Feb 4.

State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China.

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http://dx.doi.org/10.1183/13993003.02338-2019DOI Listing
February 2021

Genetic diversity, forensic feature, and phylogenetic analysis of Guizhou Tujia population via 19 X-STRs.

Mol Genet Genomic Med 2020 11 2;8(11):e1473. Epub 2020 Sep 2.

Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China.

Background: X-chromosome short tandem repeats (X-STRs) with unique sex-linkage inheritance models play a complementary role in forensic science. Guizhou is a multiethnic province located in southwest China and some genetic evidence focusing on X-STRs for various minorities was reported. However, population data of Guizhou Tujia are scarce.

Methods: A total of 507 Guizhou Tujia individuals were profiled using the AGCU X-19 STR kit. Allele frequencies and forensic parameters were calculated. Additionally, population genetic relationships between Guizhou Tujia and other 19 populations were explored.

Results: A total of 257 alleles with the allele frequencies ranged from 0.0013 to 0.6098 were found. The combined power of discrimination in males and females and mean exclusion chances in all case scenarios were all greater than 0.99999. Population comparisons showed Guizhou Tujia had a homogeneity with all Han populations from different administrative regions, and other ethnic populations residing in Guizhou, while had obviously genetic heterogeneity with the Altaic family populations except Xibe.

Conclusion: Nineteen X-STRs can afford a reliable and informative database of Guizhou Tujia population for human identification and paternity testing, especially in complex biological relations. The genetic relationships of Chinese are significantly influenced by the geographic position and ethnolinguistic origin.
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http://dx.doi.org/10.1002/mgg3.1473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7667307PMC
November 2020

Hematopoietic Progenitor Kinase1 (HPK1) Mediates T Cell Dysfunction and Is a Druggable Target for T Cell-Based Immunotherapies.

Cancer Cell 2020 10 28;38(4):551-566.e11. Epub 2020 Aug 28.

School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Human Brain Protection, Tsinghua University, 100084 Beijing, China. Electronic address:

Ameliorating T cell exhaustion and enhancing effector function are promising strategies for the improvement of immunotherapies. Here, we show that the HPK1-NFκB-Blimp1 axis mediates T cell dysfunction. High expression of MAP4K1 (which encodes HPK1) correlates with increased T cell exhaustion and with worse patient survival in several cancer types. In MAP4K1 mice, tumors grow slower than in wild-type mice and infiltrating T cells are less exhausted and more active and proliferative. We further show that genetic depletion, pharmacological inhibition, or proteolysis targeting chimera (PROTAC)-mediated degradation of HPK1 improves the efficacy of CAR-T cell-based immunotherapies in diverse preclinical mouse models of hematological and solid tumors. These strategies are more effective than genetically depleting PD-1 in CAR-T cells. Thus, we demonstrate that HPK1 is a mediator of T cell dysfunction and an attractive druggable target to improve immune therapy responses.
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http://dx.doi.org/10.1016/j.ccell.2020.08.001DOI Listing
October 2020

Overexpressed GATA3 enhances the sensitivity of colorectal cancer cells to oxaliplatin through regulating MiR-29b.

Cancer Cell Int 2020 24;20:339. Epub 2020 Jul 24.

Department of Oncology, Changhai Hospital of Shanghai, The Second Military Medical University, 168 Changhai Road, Yangpu District, Shanghai, 200433 China.

Background: GATA binding protein 3 (GATA3) and miR-29b are related to colorectal cancer (CRC). The current study explored the regulatory relationship between GATA3 and miR-29b, and the mechanism of the two in the drug resistance of CRC cells to oxaliplatin.

Method: Apoptosis of CRC cells induced by oxaliplatin at various doses was detected by flow cytometry. CRC cells were separately transfected with overexpression and knockdown of GATA3, miR-29b agomir and antagomir, and treated by oxaliplatin to detect the cell viability and apoptosis by performing Cell Couting Kit-8 (CCK-8) and flow cytometry. The expression levels of GATA3, caspase3 and cleaved caspase3 were determined by Western blot, and the expression of miR-29b was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Animal experiments were performed to examine the changes of transplanted tumors in nude mouse xenograft studies and observed by in vivo imaging. TUNEL staining was performed to detect tumor cell apoptosis.

Result: Both GATA3 and miR-29b agomir inhibited the activity of the CRC cells, promoted apoptosis and Cleaved caspase3 expression, and reduced the resistance of the cells to chemotherapy drug oxaliplatin. Although GATA3 could up-regulate miR-29b expression, the tumor-suppressive effect of GATA3 was partially reversed by miR-29b antagomir. In vivo experiments showed that down-regulating the expression of GATA3 promoted the growth rate and volume of transplanted tumors, while overexpressing GATA3 had no significant effect on tumor growth. TUNEL staining results showed that knocking down or overexpression of GATA3 did not cause significant changes to apoptotic bodies of CRC cells, while oxaliplatin treatment increased the number of apoptotic bodies.

Conclusion: GATA3 inhibits the cell viability of CRC cells, promotes apoptosis, and reduces oxaliplatin resistance of CRC cells through regulating miR-29b.
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http://dx.doi.org/10.1186/s12935-020-01424-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7379773PMC
July 2020

Elucidation of the active ingredients of against hemorrhage based on network pharmacology and tail snipping model in mice.

Pharmazie 2020 08;75(8):381-384

College of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing; ; Email:

This study aimed to elucidate the active ingredients of (LH), the overground part of (Benth.) Kudo, against hemorrhage based on network pharmacology and tail snipping model in mice. A total of 118 hemorrhage-related target genes were identified by retrieving public databases, and 39 genes were identified as the hub genes of hemorrhage based on protein-protein interaction and module analyses. The interactions between 67 potentially active ingredients in LH and 7 genes in the 39 hub genes were established and analyzed through molecular docking and Cytoscape. A total of 21 ingredients were involved in the interactions, and were divided into three categories: iridoid (15 ingredients), flavonoid (2 ingredients) and other category (4 ingredients). Based on the "multi-ingredient, multi-target" characteristic of traditional Chinese medicines (TCMs), the results of network pharmacology indicated that iridoid might be the key active ingredient group of LH against hemorrhage. The contribution of iridoid to the hemostatic effect of LH was investigated by the tail snipping model in mice. The results showed that iridoid was the key active ingredient group of LH against hemorrhage, which confirmed the prediction in network pharmacology. Additionally, the previous reports also supported this prediction. In conclusion, the finding of the present study indicates that iridoid is the key hemostatic ingredient group of LH. This work provides valuable references for investigation of the hemostatic ingredients of LH based on the holistic theory of TCMs. Meanwhile, this work also provides further insight into the development of hemostatic drugs based on LH.
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http://dx.doi.org/10.1691/ph.2020.0507DOI Listing
August 2020

To use indwelling drainage or not in dual-plane breast augmentation mammoplasty patients: A comparative study.

Medicine (Baltimore) 2020 Jul;99(29):e21305

Department of Information Engineering, Chaoshan Polytechnic College, Puning, Guangdong, China.

To explore the necessity of indwelling drainage in dual-plane breast augmentation mammoplasty patients.Female patients (123 in total) were selected from June 2015 to June 2018 in the Department of Plastic Surgery at Peking Union Medical College Hospital and were randomly divided into 2 different groups: the with drainage group (WD group, 57 patients) and the without drainage group (WOD group, 66 patients). In the 2 groups, the operation time, postoperative stay, and hospitalization expenses were recorded. The BREAST-Q Version 2.0 Augmentation Module Pre- and Postoperative Scales (Chinese Version) were used to evaluate psychosocial well-being, sexual well-being, physical well-being, and satisfaction with breasts preoperatively and postoperatively (1 year after operation).Before the operation, no significant differences were found in psychosocial well-being, sexual well-being, physical well-being, or satisfaction with breasts between these 2 groups. In the WOD group, postoperative stay and hospitalization expenses were remarkably decreased, but the operation time was similar, compared with the WD group. Compared with before the operation, both groups had significantly increased scores in psychosocial well-being, sexual well-being, and satisfaction with breasts after the operation. However, no significant differences were found between the 2 groups. No complications were found in any of the patients.Although the operation time was not significantly decreased, patients without drainage could save much more time and money and simultaneously reach similar postoperative effects in psychosocial well-being, sexual well-being, physical well-being, and satisfaction with breasts. Therefore, drainage may not be necessary in patients who undergo dual-plane breast augmentation mammoplasty.
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http://dx.doi.org/10.1097/MD.0000000000021305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7373562PMC
July 2020

Overexpression of microRNA-203 Suppresses Proliferation, Invasion, and Migration while Accelerating Apoptosis of CSCC Cell Line SCL-1.

Mol Ther Nucleic Acids 2020 Sep 1;21:428-440. Epub 2020 May 1.

Department of Plastic and Aesthetic Surgery, Peking Union Medical College Hospital, Beijing 100730, P.R. China. Electronic address:

Cutaneous squamous cell carcinoma (CSCC) is a malignant proliferation of cutaneous epithelium that has been observed to have an alarming rise in incidence. Numerous studies have demonstrated microRNAs (miRNAs or miRs) as important biomarkers in the diagnosis, prognosis, and treatment of CSCC. This study aims to investigate the effects of miR-203 on the behaviors of CSCC cells and possible mechanisms associated with protein regulator of cytokinesis-1 (PRC1) and Wnt/β-catenin signaling pathway. PRC1 was suggested as a target of miR-203 in squamous cell carcinoma cell line 1 (SCL-1) cells by dual-luciferase reporter gene assay. Based on the immunohistochemical staining and qRT-PCR, PRC1 was abundantly expressed while miR-203 was poorly expressed in CSCC tissues. miR-203 mimic or inhibitor was transfected into SCL-1 cells to upregulate or downregulate its expression. Upregulation of miR-203 downregulated PRC1 expression to block the Wnt/β-catenin signaling pathway. By conducting 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT), scratch test, and Transwell and flow cytometric analyses, miR-203 was witnessed to restrain SCL-1 cell proliferation, migration, and invasion while accelerating their apoptosis. The rescue experiments addressed that inhibition of the Wnt/β-catenin signaling pathway conferred the anti-tumor effect of miR-203. These results establish a tumor-suppressive role for miR-203 in CSCC cell line SCL-1. Hence, miR-203 has promising potential as a therapeutic target for CSCC.
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http://dx.doi.org/10.1016/j.omtn.2020.04.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7358222PMC
September 2020

Sputum and serum autoantibody profiles and their clinical correlation patterns in COPD patients with and without eosinophilic airway inflammation.

J Thorac Dis 2020 Jun;12(6):3085-3100

State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.

Background: Autoimmunity plays a role in the pathogenesis of chronic obstructive pulmonary disease (COPD). However, the autoantibody responses and their clinical correlation patterns in COPD patients with and without airway eosinophilic inflammation are unknown. The aim of this study was to compare the autoantibody profiles and their clinical associations in stable COPD patients, stratified by airway inflammatory phenotypes.

Methods: Matched sputum and serum, obtained from 62 stable COPD patients and 14 age-matched controls, were assayed for the presence of IgG and IgM antibodies against 13 autoantigens using protein array. A sputum eosinophil count ≥3% was used as cut-off value to stratify COPD patients into eosinophilic and non-eosinophilic groups. Correlation network analysis was used to evaluate the correlation patterns among autoantibody and clinical variables in each group.

Results: There were no significant differences of clinical parameters and autoantibody levels between the two COPD groups. In non-eosinophilic COPD, sputum anti-CytochromeC_IgG and anti-Aggrecan_IgM were significantly higher than those in healthy controls, and prior exacerbation was positively associated with lung function and sputum anti-Collagen-IV_IgG. While in eosinophilic COPD, sputum/serum anti-heat shock protein (HSP)47_IgG, serum anti-HSP70_IgG and serum anti-Amyloid-beta_IgG were significantly lower than those in healthy controls, and no significant correlation between prior exacerbations and lung function was found. Differences were also observed in network hubs, with the network for non-eosinophilic COPD possessing 9 hubs comprising two lung function parameters and seven autoantibodies, compared with eosinophilic COPD possessing 12 hubs all comprising autoantibodies.

Conclusions: Autoantibody responses were heterogeneous and differentially correlated with the exacerbation risk and other clinical parameters in COPD patients of different inflammatory phenotypes. These findings provide useful insight into the need for personalized management for preventing COPD exacerbations.
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http://dx.doi.org/10.21037/jtd-20-545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7330801PMC
June 2020

The role of circular RNAs in hematological malignancies.

Genomics 2020 11 4;112(6):4000-4008. Epub 2020 Jul 4.

Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China. Electronic address:

Circular RNAs (circRNAs) are a class of noncoding RNAs (ncRNAs) that lack a 5' end cap or a 3' end poly-(A) tail and form a circular structure through covalent bonds. Compared to linear RNAs, circRNAs are more conservative and stable, and their distribution is spatiotemporally regulated. circRNAs, as a new type of competitive endogenous RNA (ceRNA), are involved in many disease processes and are also related to the occurrence and development of tumors. Over the past three years, the role of circRNAs in hematological malignancies has received increasing attention. Related research has shown that circRNAs may regulate the occurrence and development of hematological malignancies and contribute to drug resistance through a variety of molecular mechanisms. Therefore, to lay the foundation and point out directions for further research on circRNAs, this article systematically reviews the research progress on circRNAs in leukemia, lymphoma, and myeloma.
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http://dx.doi.org/10.1016/j.ygeno.2020.06.051DOI Listing
November 2020

Serum ferritin as an independent risk factor for severity in COVID-19 patients.

J Infect 2020 10 24;81(4):647-679. Epub 2020 Jun 24.

Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China. Electronic address:

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http://dx.doi.org/10.1016/j.jinf.2020.06.053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313486PMC
October 2020

ExoBCD: a comprehensive database for exosomal biomarker discovery in breast cancer.

Brief Bioinform 2021 May;22(3)

Key Laboratory of Clinical Laboratory Diagnostics, College of Laboratory Medicine, Chongqing Medical University, Chongqing, China.

Effective and safe implementation of precision oncology for breast cancer is a vital strategy to improve patient outcomes, which relies on the application of reliable biomarkers. As 'liquid biopsy' and novel resource for biomarkers, exosomes provide a promising avenue for the diagnosis and treatment of breast cancer. Although several exosome-related databases have been developed, there is still lacking of an integrated database for exosome-based biomarker discovery. To this end, a comprehensive database ExoBCD (https://exobcd.liumwei.org) was constructed with the combination of robust analysis of four high-throughput datasets, transcriptome validation of 1191 TCGA cases and manual mining of 950 studies. In ExoBCD, approximately 20 900 annotation entries were integrated from 25 external sources and 306 exosomal molecules (49 potential biomarkers and 257 biologically interesting molecules). The latter could be divided into 3 molecule types, including 121 mRNAs, 172 miRNAs and 13 lncRNAs. Thus, the well-linked information about molecular characters, experimental biology, gene expression patterns, overall survival, functional evidence, tumour stage and clinical use were fully integrated. As a data-driven and literature-based paradigm proposed of biomarker discovery, this study also demonstrated the corroborative analysis and identified 36 promising molecules, as well as the most promising prognostic biomarkers, IGF1R and FRS2. Taken together, ExoBCD is the first well-corroborated knowledge base for exosomal studies of breast cancer. It not only lays a foundation for subsequent studies but also strengthens the studies of probing molecular mechanisms, discovering biomarkers and developing meaningful clinical use.
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http://dx.doi.org/10.1093/bib/bbaa088DOI Listing
May 2021