Publications by authors named "Zhang Zhang"

439 Publications

The Adjunctive Effect of Acupuncture for Advanced Cancer Patients in a Collaborative Model of Palliative Care: Study Protocol for a 3-Arm Randomized Trial.

Integr Cancer Ther 2021 Jan-Dec;20:15347354211012749

The University of Hong Kong, Hong Kong, China.

Background: Cancer is the second leading cause of death before the age of 70. Improved cancer survival has put increasing demands on cancer care. Palliative care is the specialized multi-disciplinary care providing relief from the pain, symptoms, and stress of serious illness. The study aims to evaluate the adjunctive effect of acupuncture for advanced cancer patients in a collaborative model of palliative care.

Methods/design: This is a single-blinded, randomized, sham-controlled trial. One hundred twenty advanced cancer patients undergoing palliative care will be randomized in a ratio of 2:1:1 to manual acupuncture plus standard care group (ASC), sham acupuncture plus standard care group (SSC), and standard care group (SC). Patients in ASC and SSC will receive 9 sessions of acupuncture or sham acupuncture for 3 weeks, and will be followed up for 2 months. The primary measure is the change from baseline score of the Edmonton Symptom Assessment System at 3 weeks. The secondary measures include the Brief Fatigue Inventory, Hospital Anxiety and Depression Scale, Insomnia Severity Index, Numeric Rating Scale, and European Organization for Research and Treatment of Cancer Quality of Life 15 items Questionnaire for Palliative Care.

Discussion: The finding of this trial will provide high-quality evidence on the adjunctive effect of acupuncture to standard care on advanced cancer patients undergoing palliative care.

Trial Registration: Clinicaltrials.gov, NCT04398875 (https://www.clinicaltrials.gov/ct2/show/NCT04398875), Registered on 21 May 2020.
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http://dx.doi.org/10.1177/15347354211012749DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8113363PMC
May 2021

Integrated bioinformatic analysis and experiment confirmation of the antagonistic effect and molecular mechanism of ginsenoside Rh2 in metastatic osteosarcoma.

J Pharm Biomed Anal 2021 Apr 19;201:114088. Epub 2021 Apr 19.

Key Laboratory of Diagnostic Medicine Designated by the Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China. Electronic address:

This study aimed to compare the gene expression variation of clinical primary osteosarcoma (OS) and metastatic OS, identify expression profiles and signal pathways related to disease classification, and systematically evaluate the potential anticancer effect and molecular mechanism of ginsenoside Rh2 on OS. A raw dataset (GSE14359), which excluded GSM359137 and GSM359138, was downloaded from the Gene Expression Omnibus. Differentially expressed genes (DEGs) and principal component analysis (PCA) were obtained with limma. Pathways enrichment analysis was understood by GSEA app. Rh2-associated targets were harvested and mapped through PharmMapper and Cytoscape 3.4.0. The toxicity of Rh2 was determined using crystal staining and MTT assay on 143B and MG63 cell lines. The relative protein expression was confirmed through Western blot analysis. The mitochondrial membrane potential (△Ψm) was evaluated by JC-1 fluorescence staining. The cell mobility was measured via wound healing and transwell assays. A total of 752 genes were upregulated, while 161 genes were downregulated. GSEA and PCA displayed significant function enrichment and classification. Through PharmMapper and Cytoscape 3.4.0, Rh2 was found to target the mitogen activated protein kinase (MAPK) and PI3K signaling pathways, which are the key pathways in the metastasis of OS. Furthermore, Rh2 induced a concentration-dependent decrease in cell viability and early apoptosis associated with ΔΨm decline, while a non-lethal dose of Rh2 weakened the metastatic capability. Moreover, systematic evaluation showed that promoting the MAPK signaling pathway and inhibiting PI3K/Akt/mTOR were correlated with the anticancer effects of Rh2 on metastatic OS. In conclusion, transcriptome-derived approaches may be beneficial in diagnosing early metastases, and Rh2, a multi-targeting agent, shows promising application potential in suppressing metastatic OS in an MAPK- and PI3K/Akt/mTOR-dependent manner.
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http://dx.doi.org/10.1016/j.jpba.2021.114088DOI Listing
April 2021

Protective Effect of Pre-treatment Against Experimental Cerebral Ischemia Injury via Regulating GSK-3β/HO-1 Pathway.

Front Pharmacol 2021 16;12:640297. Epub 2021 Apr 16.

Department of Biology, Faculty of Science, Hong Kong Baptist University (HKBU), Hong Kong Special Administrative Region (HKSAR), Kowloon Tong, China.

() a famous formula in traditional Chinese medicine, has been clinically used for centuries for treating cerebral diseases, but the protective effects of pre-treatment with on cerebral ischemia have not yet been reported. The present study aimed to test such protective effects and elucidate the underlying mechanisms on cerebral ischemia in rats by phenotypic approaches (i.e. including the neurological functional score, cerebral infarct area, neuron apoptosis, and brain oxidative stress status) and target-based approaches (i.e. involving the GSK-3β/HO-1 pathway). AGNHW was administered orally at the doses of 386.26, 772.52, and 1545.04 mg/kg respectively for 7 days to male Sprague-Dawley rats and then cerebral ischemia was induced by middle cerebral artery occlusion (MCAO) for 1.5 h. Pre-treatment with AGNHW significantly ameliorated ischemic damage to the brain in a dose-dependent manner, including reduction of the neurological deficit score and infarct area. AGNHW pre-treatment increased the number of Nissl cells, NeuN and DCX cells, and decreased the number of Tunel cells. Moreover, AGNHW reversed the up-regulation of ROS and MDA induced by cerebral ischemia. AGNHW pre-treatment increased the expression of p-GSK-3β(Ser9)/GSK-3β (glycogen synthase kinase-3β) ratio and heme oxygenase-1 (HO-1). These results firstly revealed that short-term pre-treatment of AGNHW could significantly protect the rats from injury caused by cerebral ischemia-reperfusion, which support further clinical studies for disease prevention. The protective effect of AGNWH pre-treatment could be associated with its antioxidant properties by the activation of GSK-3β-mediated HO-1 pathway.
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http://dx.doi.org/10.3389/fphar.2021.640297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085595PMC
April 2021

Investigation of Covalent Warheads in the Design of 2-Aminopyrimidine-based FGFR4 Inhibitors.

ACS Med Chem Lett 2021 Apr 22;12(4):647-652. Epub 2021 Mar 22.

School of Pharmacy, Jinan University, #601 Huangpu Avenue West, Guangzhou 510632, China.

Covalent kinase inhibitors are rapidly emerging as a class of therapeutics with clinical benefits. Herein we report a series of selective 2-aminopyrimidine-based fibroblast growth factor receptor 4 (FGFR4) inhibitors exploring different types of cysteine-targeting warheads. The structure-activity relationship study revealed that the chemically tuned warheads α-fluoro acrylamide, vinylsulfonamide, and acetaldehyde amine were suitable as covalent warheads for the design of selective FGFR4 inhibitors. Compounds , , and selectively suppressed FGFR4 enzymatic activity with IC values of 53 ± 18, 45 ± 11, and 16 ± 4 nM, respectively, while sparing FGFR1/2/3. X-ray crystal structure and MALDI-TOF studies demonstrated that compound bearing the α-fluoro acrylamide binds to FGFR4 with an irreversible binding mode, whereas compound with an acetaldehyde amine binds to FGFR4 with a reversible covalent mode. and might provide some fundamental structural information for the rational design of new selective FGFR4 inhibitors.
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http://dx.doi.org/10.1021/acsmedchemlett.1c00052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8040253PMC
April 2021

20()-protopanaxadiol and oleanolic acid ameliorate cognitive deficits in APP/PS1 transgenic mice by enhancing hippocampal neurogenesis.

J Ginseng Res 2021 Mar 16;45(2):325-333. Epub 2020 Jul 16.

Department of Biology, Faculty of Science, Hong Kong Baptist University (HKBU), Kowloon Tong, Hong Kong Special Administrative Region (HKSAR), China.

Background: Alzheimer's disease (AD) is one of the most prevalent neurodegenerative disorders. Enhancing hippocampal neurogenesis by promoting proliferation and differentiation of neural stem cells (NSCs) is a promising therapeutic strategy for AD. 20()-protopanaxadiol (PPD) and oleanolic acid (OA) are small, bioactive compounds found in ginseng that can promote NSC proliferation and neural differentiation . However, it is currently unknown whether PPD or OA can attenuate cognitive deficits by enhancing hippocampal neurogenesis in a transgenic APP/PS1 AD mouse model. Here, we administered PPD or OA to APP/PS1 mice and monitored the effects on cognition and hippocampal neurogenesis.

Methods: We used the Morris water maze, Y maze, and open field tests to compare the cognitive capacities of treated and untreated APP/PS1 mice. We investigated hippocampal neurogenesis using Nissl staining and BrdU/NeuN double labeling. NSC proliferation was quantified by Sox2 labeling of the hippocampal dentate gyrus. We used western blotting to determine the effects of PPD and OA on Wnt/GSK3β/β-catenin pathway activation in the hippocampus.

Results: Both PPD and OA significantly ameliorated the cognitive impairments observed in untreated APP/PS1 mice. Furthermore, PPD and OA significantly promoted hippocampal neurogenesis and NSC proliferation. At the mechanistic level, PPD and OA treatments resulted in Wnt/GSK-3β/β-catenin pathway activation in the hippocampus.

Conclusion: PPD and OA ameliorate cognitive deficits in APP/PS1 mice by enhancing hippocampal neurogenesis, achieved by stimulating the Wnt/GSK-3β/β-catenin pathway. As such, PPD and OA are promising novel therapeutic agents for the treatment of AD and other neurodegenerative diseases.
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http://dx.doi.org/10.1016/j.jgr.2020.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8020272PMC
March 2021

90% yield production of polymer nano-memristor for in-memory computing.

Nat Commun 2021 Mar 31;12(1):1984. Epub 2021 Mar 31.

Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.

Polymer memristors with light weight and mechanical flexibility are preeminent candidates for low-power edge computing paradigms. However, the structural inhomogeneity of most polymers usually leads to random resistive switching characteristics, which lowers the production yield and reliability of nanoscale devices. In this contribution, we report that by adopting the two-dimensional conjugation strategy, a record high 90% production yield of polymer memristors has been achieved with miniaturization and low power potentials. By constructing coplanar macromolecules with 2D conjugated thiophene derivatives to enhance the π-π stacking and crystallinity of the thin film, homogeneous switching takes place across the entire polymer layer, with fast responses in 32 ns, D2D variation down to 3.16% ~ 8.29%, production yield approaching 90%, and scalability into 100 nm scale with tiny power consumption of ~ 10 J/bit. The polymer memristor array is capable of acting as both the arithmetic-logic element and multiply-accumulate accelerator for neuromorphic computing tasks.
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http://dx.doi.org/10.1038/s41467-021-22243-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8012610PMC
March 2021

[Exploration of yeast biodiversity and development of industrial applications].

Sheng Wu Gong Cheng Xue Bao 2021 Mar;37(3):806-815

State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.

Yeast are comprised of diverse single-cell fungal species including budding yeast Saccharomyces cerevisiae and various nonconventional yeasts. Budding yeast is well known as an important industrial microorganism, which has been widely applied in various fields, such as biopharmaceutical and health industry, food, light industry and biofuels production. In the recent years, various yeast strains from different ecological environments have been isolated and characterized. Novel species have been continuously identified, and strains with diverse physiological characteristics such as stress resistance and production of bioactive compounds were selected, which proved abundant biodiversity of natural yeast resources. Genome mining of yeast strains, as well as multi-omics analyses (transcriptome, proteome and metabolome, etc.) can reveal diverse genetic diversity for strain engineering. The genetic resources including genes encoding various enzymes and regulatory proteins, promoters, and other elements, can be employed for development of robust strains. In addition to exploration of yeast natural diversity, phenotypes that are more suitable for industrial applications can be obtained by generation of a variety of genetic diversity through mutagenesis, laboratory adaptation, metabolic engineering, and synthetic biology design. The optimized genetic elements can be used to efficiently improve strain performance. Exploration of yeast biodiversity and genetic diversity can be employed to build efficient cell factories and produce biological enzymes, vaccines, various natural products as well as other valuable products. In this review, progress on yeast diversity is summarized, and the future prospects on efficient development and utilization of yeast biodiversity are proposed. The methods and schemes described in this review also provide a reference for exploration of diversity of other industrial microorganisms and development of efficient strains.
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http://dx.doi.org/10.13345/j.cjb.200650DOI Listing
March 2021

WITHDRAWN: In Memory of Vladimir B. Bajic (1952-2019).

Genomics Proteomics Bioinformatics 2021 Mar 17. Epub 2021 Mar 17.

Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.

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http://dx.doi.org/10.1016/j.gpb.2019.12.003DOI Listing
March 2021

Indication of the prognosis of pulmonary hypertension by using CMR function parameters.

Eur Radiol 2021 Mar 18. Epub 2021 Mar 18.

Department of Radiology, Tianjin Medical University General Hospital, 154 Anshan Road, Tianjin, 300052, China.

Objective: This study aimed to compare the cardiac function among different sub-types of pulmonary hypertension (PH) and to explore the independent predictors of major adverse cardiovascular events (MACE).

Methods: Eighty-seven PH patients diagnosed by right heart catheterization (RHC) were recruited. Patients underwent cardiac magnetic resonance (CMR) and RHC examination within 2 weeks. The CMR images were analyzed to calculate the cardiac functional parameters including right ventricle (RV) and left ventricle (LV) end-diastolic volume index (EDVI), end-systolic volume index (ESVI), stroke volume index (SVI), ejection fraction (EF), tricuspid annular plane systolic excursion (TAPSE), and myocardial mass (MM). The median follow-up time was 46.5 months (interquartile range: 26-65.5 months), and the endpoints were the occurrence of MACE.

Results: RVEDVI, LVEDVI, and LVESVI were higher in congenital heart disease-related PH (CHD-PH) than in other sub-types (p < 0.05). RVMM, RVSVI, and RVCI were highest in CHD-PH. There was no significant difference in the prognosis among different sub-types (p > 0.05). Comparing with the non-MACE group, RVEF, TAPSE, and LVSVI significantly decreased in the MACE group, while the RVESVI significantly increased (p < 0.05). TAPSE ≤ 15.65 mm and LVSVI ≤ 30.27 mL/m were significant independent predictors of prognosis in PH patients.

Conclusion: CHD-PH had a higher RV function reserve but lowest LVEF comparing to other subgroups. TAPSE and LVSVI could contribute to the prediction of MACE in PH patients.

Key Points: • CMR imaging is a noninvasive and accurate tool to assess ventricular function. • CHD-PH had higher RV function reserve but lowest LVEF. • TAPSE and LVSVI could contribute to the prediction of MACE in PH patients.
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http://dx.doi.org/10.1007/s00330-021-07835-8DOI Listing
March 2021

Liposarcoma in children and young adults: a clinicopathologic and molecular study of 23 cases in one of the largest institutions of China.

Virchows Arch 2021 Mar 18. Epub 2021 Mar 18.

Department of Pathology, West China Hospital, Sichuan University, Guoxuexiang 37, Chengdu, 610041, Sichuan, China.

The incidence of pediatric liposarcoma is rare and most published cases lack systematic genetic analyses. We present clinicopathologic and genetic features of 23 liposarcomas aged <22 years. The study cohort comprised 10 males and 13 females (M:F=1:1.3) aged 11-21 years (median 17 years). The tumors predominantly occurred at the extremities (16/23; 69.6%), followed by the head/neck (2/23; 8.7%), chest (2/23; 8.7%), waist (2/23, 8.7%), and retroperitoneum (1/23; 4.3%). The tumor subtypes were sixteen myxoid liposarcoma (ML), one well-differentiated liposarcoma (WDL), two dedifferentiated liposarcoma (DDL), one pleomorphic liposarcoma (PL), and three myxoid pleomorphic liposarcoma (MPL) cases. Fluorescence in situ hybridization analysis identified MDM2/CDK4 amplification in all WDL/DDL cases (3/3; 100%) and DDIT3 rearrangement in all ML cases (13/13; 100%). Whole-exome sequencing indicated that one PL case and one MPL case exhibited RB1 loss. The two tested MPL cases had TP53 mutation and one of them harbored a TP53 germline mutation. Follow-up information was available for 20 patients (20/23; 87.0%) with a median follow-up duration of 42.5 months (range, 13-120 months). Three patients exhibited tumor progression (3/20;15.0%). Seventeen patients (17/20; 85.0%) survived with no evidence of disease. One MPL case (1/20; 5.0%) died of the disease. In conclusion, despite some overlaps, the occurrence, distribution of subtype, and prognosis of liposarcoma are overall different in children and adults. Most MLs and ALT/WDL/DDLs showed similar genetic aberrations with adult counterparts. Molecular features of MPL overlapped with those of conventional PL. The genetic characteristics including Tp53 status of MPL need further investigation.
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http://dx.doi.org/10.1007/s00428-021-03076-8DOI Listing
March 2021

Comprehensive Analysis of Expression Regulation for RNA m6A Regulators With Clinical Significance in Human Cancers.

Front Oncol 2021 23;11:624395. Epub 2021 Feb 23.

National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing, China.

Background: N6-methyladenosine (m6A), the most abundant chemical modification on eukaryotic messenger RNA (mRNA), is modulated by three class of regulators namely "writers," "erasers," and "readers." Increasing studies have shown that aberrant expression of m6A regulators plays broad roles in tumorigenesis and progression. However, it is largely unknown regarding the expression regulation for RNA m6A regulators in human cancers.

Results: Here we characterized the expression profiles of RNA m6A regulators in 13 cancer types with The Cancer Genome Atlas (TCGA) data. We showed that , , and were down-regulated in most cancers, whereas and were up-regulated in 12 cancer types except for thyroid carcinoma (THCA). Survival analysis further revealed that low expression of several m6A regulators displayed longer overall survival times. Then, we analyzed microRNA (miRNA)-regulated and DNA methylation-regulated expression changes of m6A regulators in pan-cancer. In total, we identified 158 miRNAs and 58 DNA methylation probes (DMPs) involved in expression regulation for RNA m6A regulators. Furthermore, we assessed the survival significance of those regulatory pairs. Among them, 10 miRNAs and 7 DMPs may promote cancer initiation and progression; conversely, 3 miRNA/mRNA pairs in kidney renal clear cell carcinoma (KIRC) may exert tumor-suppressor function. These findings are indicative of their potential prognostic values. Finally, we validated two of those miRNA/mRNA pairs (hsa-miR-1307-3p/ and hsa-miR-204-5p/) that could serve a critical role for potential clinical application in KIRC patients.

Conclusions: Our findings highlighted the importance of upstream regulation (miRNA and DNA methylation) governing m6A regulators' expression in pan-cancer. As a result, we identified several informative regulatory pairs for prognostic stratification. Thus, our study provides new insights into molecular mechanisms of m6A modification in human cancers.
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http://dx.doi.org/10.3389/fonc.2021.624395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7946859PMC
February 2021

The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR.

Genomics Proteomics Bioinformatics 2020 Dec 3. Epub 2020 Dec 3.

China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

On January 22, 2020, China National Center for Bioinformation (CNCB) released the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access information resource for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline. Of particular note, 2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and their detailed statistics for each virus isolate, and congregates the quality score, functional annotation, and population frequency for each variant. Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019 (COVID-19), including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC. Furthermore, by linking with relevant databases in CNCB, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with NCBI. Collectively, SARS-CoV-2 is updated daily to collect the latest information on genome sequences, variants, haplotypes, and literature for a timely reflection, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.
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http://dx.doi.org/10.1016/j.gpb.2020.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836967PMC
December 2020

Resilience patterns and transitions in the Be Resilient To Breast Cancer trial: an exploratory latent profile transition analysis.

Psychooncology 2021 Mar 10. Epub 2021 Mar 10.

South China University of Technology, Guangzhou, Guangdong Province, China.

Objective: Be Resilient to Breast Cancer (BRBC), a theoretically-derived, resilience-based, culturally-tailored, supportive-expressive group therapy (SEGT), has been developed to help promote patients' resilience in breast cancer. Data from patients receiving BRBC intervention was utilized to explore and define characteristics of resilience patterns and their transitions over time.

Methods: Resilience was used as a primary outcome and 391 patients completed Resilience Scale Specific to Cancer at enrollment (T0), 2 months (T1), 6 months(T2), and 12 months (T3) after intervention. latent profile transition analysis was performed to model the change in resilience and predict positive transitioning probabilities between resilience patterns (from one pattern to another pattern with a higher level) over time.

Results: One hundred and forty four resilience patterns were identified after BRBC intervention. 33.1%, 50.3%, and 40.5% of patients experienced positive resilience transitions from T0 to T1, T1 to T2, and T2 to T3, respectively. Patients with middle age, unmarried status, higher education level, and less advanced tumor stage were more likely to experience positive resilience transitions.

Conclusion: Different transitions of resilience patterns are observed after BRBC intervention. Age, marital status, education, and tumor stage may be four factors affecting the efficacy of SEGT intervention in breast cancer.
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http://dx.doi.org/10.1002/pon.5668DOI Listing
March 2021

Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades.

Genomics Proteomics Bioinformatics 2021 Feb 10. Epub 2021 Feb 10.

China National Center for Bioinformation, Beijing 100101, China; National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

COVID-19 and its causative pathogen SARS-CoV-2 have rushed the world into a staggering pandemic in a few months, and a global fight against both has been intensifying. Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code to molecular mechanisms, based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on the replicase-transcriptase complex. Our analysis starts with primary sequence information, identity-based phylogeny based on 22,051 SARS-CoV-2 sequences, and evaluation of sequence variation patterns as mutation spectra and its 12 permutations among organized clades. All are tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings are listed as follows. (1) The most dominant mutation is C-to-U permutation, whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity, albeit assumed most slightly deleterious. (2) The second abundance group includes three negative-strand mutations (U-to-C, A-to-G, and G-to-A) and a positive-strand mutation (G-to-U) due to DNA repair mechanisms after cellular abasic events. (3) A clade-associated biased mutation trend is found attributable to elevated level of negative-sense strand synthesis. (4) Within-clade permutation variation is very informative for associating non-synonymous mutations and viral proteome changes. These findings demand a platform where emerging mutations are mapped onto mostly subtle but fast-adjusting viral proteomes and transcriptomes, to provide biological and clinical information after logical convergence for effective pharmaceutical and diagnostic applications. Such actions are in desperate need, especially in the middle of the War against COVID-19.
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http://dx.doi.org/10.1016/j.gpb.2020.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7875716PMC
February 2021

Retinal cross-section motion correction in three-dimensional retinal optical coherence tomography.

J Biophotonics 2021 Feb 12:e202000443. Epub 2021 Feb 12.

School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou, China.

Motion correction is an important issue in ophthalmic optical coherence tomography (OCT), and can improve the ability of data sets to reflect the physiological structures of tissues and make visualization and subsequent analysis easier. In this study, we present a novel method to correct the cross-sectional motion artifacts in retinal OCT volumes. Motion along the x-direction (fast-scan direction) is corrected through the normalized cross-correlation algorithm, while axial motion compensation is performed using the polynomial fitting method on the inner segment/outer segment (IS/OS) layer segmented by the shortest path faster algorithm (SPFA). The results of volunteers with central serous chorioretinopathy demonstrate that the proposed method effectively corrects motion artifacts in OCT volumes and may have potential application value in the evaluation of ophthalmic diseases such as diabetic retinopathy, glaucoma and age-related macular degeneration.
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http://dx.doi.org/10.1002/jbio.202000443DOI Listing
February 2021

Detection of SARS-CoV-2 in Simultaneously Collected Tear and Throat Swab Samples from the Patients with 2019- new SARS-CoV-2 Infection Disease: A Single Center Cross-sectional Study.

Ophthalmic Epidemiol 2021 Jan 24:1-7. Epub 2021 Jan 24.

Department of Ophthalmology, Central Theater General Hospital, Wuhan, China.

: This study aimed to evaluate whether Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can be detected in the tears in the eyes of Coronavirus Disease 2019 (COVID-2019) infected patients and compare the detection consistency of two simultaneously collected samples, from the tears and throat swabs.: A total of 35 COVID-2019 patients were included in this cross-sectional case series study. Throat samples from all enrolled patients were collected with sampling swab, and simultaneously, tear samples were collected with sampling swab from 9 patients (No.1-9) and with Schirmer's strip from the remaining patients (No.10-35) (bilateral eyes for all patients). Sample collecting and testing were performed in three separate time points: first from patients No.1-9, second from patients No.10-29, and third from patients No. 30-35. Reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay was performed.: Among enrolled patients, 29 (No.1-29) had mild or moderate clinical symptoms and 6 (No.30-35) had severe symptoms. The mean time interval from the sample collection day to diagnosis confirmation day was 9.71 ± 6.50 days (ranged from 3 to 29 days). None of the patients had conjunctivitis. Nineteen out of 35 (54.3%) throat samples presented positive Rt-PCR results. Three (no.13,21,31) out of 35 (8.6%) tear samples presented positive RT-PCR results. Two (no.21, 31) of these three patients were throat swab positive and one (No. 13) was negative. The consistency analysis indicated that tears and throat samples showed poor consistency (Kappa = -0.009, = .9).The cycle threshold value (Ct-value) of tear samples collected by sampling swab was significantly higher than that by Schirmer's strip (t = 2.288, = .03).: In spite of the low SARS-CoV-2 positive detection rate of tear samples from COVID-2019 patients, we cannot fully rule out the transmission by ocular surface. Whether tear testing can be used as an aid in judging of SARS-CoV-2 infection need further investigation.
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http://dx.doi.org/10.1080/09286586.2021.1875011DOI Listing
January 2021

Ultrasensitive electrochemical biosensor for attomolar level detection of let 7a based on toehold mediated strand displacement reaction circuits and molecular beacon mediated circular strand displacement polymerization.

Anal Chim Acta 2021 Feb 30;1147:108-115. Epub 2020 Dec 30.

Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China. Electronic address:

In this study, an ultrasensitive electrochemical miRNA biosensor based on toehold mediated strand displacement reaction circuits (SDRCs) and molecular beacon mediated isothermal circular strand displacement polymerization reaction (ICSDPR) has been proposed. During the SDRCs module, the cascade strand displacement reaction induces the recycling of the target let 7a and generation of a large amount of strand A (SA). The SA recognition opens the hairpin capture probe immobilized on the gold electrode, thus, varying the distance between the redox molecules and electrode surface. The primer mediated ICSDPR is observed to further generate a large amount of SA, thus, leading to a reduction in the signal. Considering these merits, the proposed method is observed to exhibit a log-linear linearity from 10 aM to 100 pM and ultrahigh sensitivity towards let 7a down to 6.2 aM, with a capability of distinguishing the let 7a family members, thereby, providing a new electrochemical route for early cancer screening.
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http://dx.doi.org/10.1016/j.aca.2020.12.057DOI Listing
February 2021

The synthesis and biological evaluation of sanguinarine derivatives as anti-non-small cell lung cancer agents.

RSC Med Chem 2020 Feb 12;11(2):293-296. Epub 2020 Feb 12.

International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE) , School of Pharmacy , Jinan University , 601 Huangpu Avenue West , Guangzhou 510632 , China . Email:

A novel series of sanguinarine (SA) derivatives were synthesized and evaluated as anti-non-small cell lung cancer (NSCLC) agents. The compounds inhibited A549 and H1975 NSCLC cells with IC values of 0.96 - >30 μM and 0.79 - >30 μM, respectively. Compounds exhibited low micromolar inhibitory activity and indicated that the C6-position of SA was tolerated to be substituted by hydrophilic groups and CN. Further investigation of their mechanism of action showed that compound induced apoptosis of A549 and H1975 cells by inhibiting the Akt signaling pathway and elevating the reactive oxygen species (ROS). This study provided a strategy for developing new anti-cancer agents.
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http://dx.doi.org/10.1039/c9md00494gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7489057PMC
February 2020

Experimental and Theoretical Studies on Effects of Structural Modification of Tin Nanoclusters for Third-Order Nonlinear Optical Properties.

Inorg Chem 2021 Feb 14;60(3):1885-1892. Epub 2021 Jan 14.

State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, PR China.

Tin oxide based materials have attracted much attention as new sources for nonlinear optical (NLO) devices, while the electronic mechanism behind the structure and nonlinearity is still unclear. In this work, by precisely controlling different functionalization ligands, here a series of binuclear [(BuSn)(TEOA)L] (L = monocarboxylic acid ligand) complexes have been synthesized and characterized; we also adopted a new method to make the metal clusters and PMMA blend together for NLO testing. Importantly, the electronic structure, static third-order NLO properties, sum over states (SOS) have been studied by both experimental and density function theory (DFT) analysis. The effects for general NLO polarizability under various conditions, including different substitutions ligands and replacement of the metal cores, have been further investigated. The results indicate the static second hyperpolarizabilities (γ) is inversely proportional to the band gap decreases. Notably, the theory predicts that the third-order nonlinear coefficient will double through the synergistic effects of pull-push groups. The hole-electron analysis of the main excited states indicates the simultaneous introduction of pull-push electron groups into the system cause the excitation of the valence layer from LE to LLCT, which also leads to significant increase in the γ value of complex . This work demonstrates that an efficient adjustment for the intensity of NLO polarizability can be achieved by regulating the substitutions and the material structures, providing a new potential for the application of tin-oxo clusters in the field of nonlinear optics.
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http://dx.doi.org/10.1021/acs.inorgchem.0c03331DOI Listing
February 2021

Optical Micro/Nanofiber-Enabled Compact Tactile Sensor for Hardness Discrimination.

ACS Appl Mater Interfaces 2021 Jan 13;13(3):4560-4566. Epub 2021 Jan 13.

State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310027, China.

Optical micro/nanofibers (MNFs) can be applied for ultrasensitive tactile sensing with fast response and compact size, which are attractive for restoring tactile information in minimally invasive robotic surgery and tissue palpation. Herein, we present a compact tactile sensor (CTS) with a diameter of 1.5 mm enabled by an optical MNF. The CTS provides continuous readouts for high-fidelity transduction of touch and pressure stimuli into interpretable optical signals, which permit instantaneous sensing of contact and pressure with pressure-sensing sensitivity as high as 0.108 mN and a resolution of 0.031 mN. Working in pressing mode, the CTS can discriminate the difference in the hardness of two poly(dimethylsiloxane) (PDMS) slats (with shore A of 36 and 40) directly, a hardness resolving ability even beyond the human hands. Benefitting from the fast response feature, the CTS can also be operated in either scanning or tapping mode, making it feasible for hardness identification by analyzing the shape of the response curve. As a proof of concept, the hardness discrimination of a pork liver and an adductor muscle was experimentally demonstrated. Such MNF-enabled compact tactile sensors may pave the way for hardness sensing in tissue palpation, surgical robotics, and object identification.
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http://dx.doi.org/10.1021/acsami.0c20392DOI Listing
January 2021

Responses of Caenorhabditis elegans to various surface modifications of alumina nanoparticles.

Environ Pollut 2021 Feb 22;271:116335. Epub 2020 Dec 22.

Institute of Soil and Water Resource and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China. Electronic address:

The surface modifications of nanoparticles (NPs), are well-recognized parameters that affect the toxicity, while there has no study on toxicity of AlO NPs with different surface modification. Therefore, for the first time, this study pays attention to evaluating the toxicity and potential mechanism of pristine AlO NPs (p-AlO), hydrophilic (w-AlO) and lipophilic (o-AlO) modifications of AlO NPs both in vitro and in vivo. Applied concentrations of 10, 20, 40, 80,100 and 200 μg/mL for 24 h exposure on Caenorhabditis elegans (C. elegans), while 100 μg/mL of AlO NPs significantly decreased the survival rate. Using multiple toxicological endpoints, we found that o-AlO NPs (100 μg/mL) could induce more severe toxicity than p-AlO and w-AlO NPs. After uptake by C. elegans, o-AlO NPs increased the intestinal permeability, easily swallow and further destroy the intestinal membrane cells. Besides, cytotoxicity evaluation revealed that o-AlO NPs (100 μg/mL) are more toxic than p-AlO and w-AlO. Once inside the cell, o-AlO NPs could attack mitochondria and induce the over-production of reactive oxygen species (ROS), which destroy the intracellular redox balance and lead to apoptosis. Furthermore, the transcriptome sequencing and RT-qPCR data also demonstrated that the toxicity of o-AlO NPs is highly related to the damage of cell membrane and the imbalance of intracellular redox. Generally, our study has offered a comprehensive sight to the adverse effects of different surface modifications of AlO NPs on environmental organisms and the possible underlying mechanisms.
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http://dx.doi.org/10.1016/j.envpol.2020.116335DOI Listing
February 2021

Minimum clinical important difference for resilience scale specific to cancer: a prospective analysis.

Health Qual Life Outcomes 2020 Dec 9;18(1):381. Epub 2020 Dec 9.

South China University of Technology, Guangzhou, 510641, Guangdong Province, China.

Background: The minimum clinical important differences (MCIDs) of resilience instruments in patients with cancer have not been comprehensively described. This study was designed to evaluate MCIDs of 10-item and 25-item resilience scales specific to cancer (RS-SC-10 and RS-SC-25).

Methods: From June 2015 to December 2018, RS-SCs were longitudinally measured in 765 patients with different cancer diagnoses at baseline (T0) and 3 months later (T1). The EORTC QLQ-C30, Connor-Davidson Resilience Scale, Hospital Anxiety and Depression Scale, and Allostatic Load Index were measured concurrently as anchors. Anchor-based methods (linear regression, within-group), distribution-based methods(within-group), and receiver operating characteristic curves (ROCs, within-subject) were performed to evaluate the MCIDs.

Results: 623 of 765 (84.1%) patients had paired RS-SCs scores. Moderate correlations were identified between the change in RS-SCs and change in anchors (r = 0.38-0.44, all p < 0.001). Linear regression estimated + 8.9 and - 6.7 as the MCIDs of RS-SC-25, and + 3.4 and - 2.5 for RS-SC-10. Distribution-based methods estimated + 9.9 and - 9.9 as the MCIDs of RS-SC-25, and + 4.0 and - 4.0 for RS-SC-10. ROC estimated + 5.5 and - 4.5 as the MCIDs of RS-SC-25, and + 2.0 and - 1.5 for RS-SC-10.

Conclusions: The most reliable MCID is around 5 points for RS-SC-25 and 2 points for RS-SC-10. RS-SCs are more responsive to the worsening status of resilience in patients with cancer and these estimates could be useful in future resilience-based intervention trials.
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http://dx.doi.org/10.1186/s12955-020-01631-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7724855PMC
December 2020

Designing high-performance hypergolic propellants based on materials genome.

Sci Adv 2020 Dec 4;6(49). Epub 2020 Dec 4.

Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.

A new generation of rocket propellants for deep space exploration, ionic liquid propellants, with long endurance and high stability, is attracting more and more attention. However, a major defect of ionic liquid propellants that restricts their application is the inadequate hypergolic reactivity between the fuel and the oxidant, and this defect results in local burnout and accidental explosions during the launch process. We propose a visualization model to show the features of structure, density, thermal stability, and hypergolic activity for estimating propellant performances and their application abilities. This propellant materials genome and visualization model greatly improves the efficiency and quality of developing high-performance propellants, which benefits the discovery of new advanced functional molecules in the field of energetic materials.
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http://dx.doi.org/10.1126/sciadv.abb1899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7717915PMC
December 2020

Crystal structure of the yeast heterodimeric ADAT2/3 deaminase.

BMC Biol 2020 12 3;18(1):189. Epub 2020 Dec 3.

MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, 510275, Guangdong, People's Republic of China.

Background: The adenosine-to-inosine (A-to-I) editing in anticodons of tRNAs is critical for wobble base-pairing during translation. This modification is produced via deamination on A34 and catalyzed by the adenosine deaminase acting on tRNA (ADAT) enzyme. Eukaryotic ADATs are heterodimers composed of the catalytic subunit ADAT2 and the structural subunit ADAT3, but their molecular assemblies and catalytic mechanisms are largely unclear.

Results: Here, we report a 2.8-Å crystal structure of Saccharomyces cerevisiae ADAT2/3 (ScADAT2/3), revealing its heterodimeric assembly and substrate recognition mechanism. While each subunit clearly contains a domain resembling their prokaryotic homolog TadA, suggesting an evolutionary gene duplication event, they also display accessory domains for additional structural or functional purposes. The N-lobe of ScADAT3 exhibits a positively charged region with a potential role in the recognition and binding of tRNA, supported by our biochemical analysis. Interestingly, ScADAT3 employs its C-terminus to block tRNA's entry into its pseudo-active site and thus inactivates itself for deamination despite the preservation of a zinc-binding site, a mechanism possibly shared only among yeasts.

Conclusions: Combining the structural with biochemical, bioinformatic, and in vivo functional studies, we propose a stepwise model for the pathway of deamination by ADAT2/3. Our work provides insight into the molecular mechanism of the A-to-I editing by the eukaryotic ADAT heterodimer, especially the role of ADAT3 in catalysis.
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http://dx.doi.org/10.1186/s12915-020-00920-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7713142PMC
December 2020

Deformable Liposomal Hydrogel for Dermal and Transdermal Delivery of Meloxicam.

Int J Nanomedicine 2020 24;15:9319-9335. Epub 2020 Nov 24.

Center for Dermal Research and Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.

Background And Aim: Meloxicam (MX) is a potent hydrophobic non-steroidal anti-inflammatory drug used to reduce inflammation and pain. However, its oral dosage form can cause many adverse gastrointestinal effects. In the present study, a poloxamer P407 based hydrogel system containing transfersomes or flavosomes has been prepared as a potential therapeutic vehicle for the topical delivery of MX.

Methods: In this study, MX was encapsulated in conventional liposomes, transfersomes, and flavosomes. The obtained liposomal vesicles were characterized in terms of size, drug entrapment efficiency, zeta potential, and stability. These MX-loaded liposomal formulations were further incorporated into a poloxamer P407 gel and evaluated using rheological properties, a stability study and an ex vivo permeation study through human cadaver skin by both HPLC analysis and confocal laser scanning microscopy (CLSM).

Results: The developed deformable liposomes exhibited homogeneous vesicle sizes less than 120 nm with a higher entrapment efficiency as compared to conventional liposomes. The deformable liposomal gel formulations showed improved permeability compared to a conventional liposomal gel and a liposome-free gel. The enhancement effect was also clearly visible by CLSM.

Conclusion: These deformable liposomal hydrogel formulations can be a promising alternative to conventional oral delivery of MX by topical administration. Notably, flavosome-loaded gel formulations displayed the highest permeability through the deeper layers of the skin and shortened lag time, indicating a potential faster on-site pain relief and anti-inflammatory effect.
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http://dx.doi.org/10.2147/IJN.S274954DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7700092PMC
December 2020

Pyrido[2, 3-d]pyrimidin-7(8H)-ones as new selective orally bioavailable Threonine Tyrosine Kinase (TTK) inhibitors.

Eur J Med Chem 2021 Feb 16;211:113023. Epub 2020 Nov 16.

International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China. Electronic address:

A series of pyrido [2, 3-d]pyrimidin-7(8H)-ones were designed and synthesized as new selective orally bioavailable Threonine Tyrosine Kinase (TTK) inhibitors. One of the representative compounds, 5o, exhibited strong binding affinity with a K value of 0.15 nM, but was significantly less potent against a panel of 402 wild-type kinases at 100 nM. The compound also potently inhibited the kinase activity of TTK with an IC value of 23 nM, induced chromosome missegregation and aneuploidy, and suppressed proliferation of a panel of human cancer cell lines with low μM IC values. Compound 5o demonstrated good oral pharmacokinetic properties with a bioavailability value of 45.3% when administered at a dose of 25 mg/kg in rats. Moreover, a combination therapy of 5o with paclitaxel displayed promising in vivo efficacy against the HCT-116 human colon cancer xenograft model in nude mice with a Tumor Growth Inhibition (TGI) value of 78%. Inhibitor 5o may provide a new research tool for further validating therapeutic potential of TTK inhibition.
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http://dx.doi.org/10.1016/j.ejmech.2020.113023DOI Listing
February 2021

Clinicopathologic characteristics of HER2-positive metaplastic squamous cell carcinoma of the breast.

J Clin Pathol 2020 Nov 19. Epub 2020 Nov 19.

Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.

Aims: The aim of this study was to analyse the clinicopathological features and prognosis of human epidermal growth factor receptor-2 (HER2)-positive metaplastic squamous cell carcinoma (MSCC).

Methods: Fifty-eight patients with MSCC of the breast who were classified into 45 triple-negative and 13 HER2-positive subgroups diagnosed at the West China Hospital, Sichuan University, from 2004 to 2018, were enrolled. Clinicopathological features were collected and compared between HER2-positive MSCC, triple-negative MSCC, HER2-positive invasive breast carcinoma of no special type (NST) and triple-negative NST groups. In the prognostic survival analysis, HER2-positive MSCCs was compared with triple-negative MSCCs, HER2-positive NSTs and triple-negative NSTs.

Results: Compared with triple-negative MSCCs, more patients with Ki-67 low expression were in HER2-positive MSCCs (p<0.05). More patients with HER2-positive MSCC than patients with HER2-positive NST were postmenopausal (p<0.05). Compared among HER2-positive MSCCs, triple-negative MSCCs and triple-negative NSTs, patients of HER2-positive MSCCs with high Ki-67 expression were the least, and HER2-positive MSCCs had more strongly associated with postmenopausal disease status (p<0.05). In survival analyses, HER2-positive MSCCs had a high risk of recurrence and poor prognosis (p<0.05). Lymph node status was significantly associated with the disease-free survival of patients with HER2-positive MSCC.

Conclusion: In conclusion, our study indicates that HER2-positive MSCC is an aggressive disease with unique clinicopathological characteristics. Both HER2-positive status and an SCC component are critical factors for poor prognosis. HER2-positive MSCC and triple-negative MSCC are distinct subgroups. Corresponding targeted therapy recommendations should be made for this HER2-positive MSCC group.
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http://dx.doi.org/10.1136/jclinpath-2020-206468DOI Listing
November 2020

Genome Variation Map: a worldwide collection of genome variations across multiple species.

Nucleic Acids Res 2021 01;49(D1):D1186-D1191

China National Center for Bioinformation, Beijing 100101, China.

The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. It aims to collect and integrate genome variations for a wide range of species, accepts submissions of different variation types from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Compared with the previous version, particularly, a total of 22 species, 115 projects, 55 935 samples, 463 429 609 variants, 66 220 associations and 56 submissions (as of 7 September 2020) were newly added in the current version of GVM. In the current release, GVM houses a total of ∼960 million variants from 41 species, including 13 animals, 25 plants and 3 viruses. Moreover, it incorporates 64 819 individual genotypes and 260 393 manually curated high-quality genotype-to-phenotype associations. Since its inception, GVM has archived genomic variation data of 43 754 samples submitted by worldwide users and served >1 million data download requests. Collectively, as a core resource in the National Genomics Data Center, GVM provides valuable genome variations for a diversity of species and thus plays an important role in both functional genomics studies and molecular breeding.
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http://dx.doi.org/10.1093/nar/gkaa1005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778933PMC
January 2021

Multiplex real-time PCR using double-strand primers and probes for the detection of nucleic acids.

Anal Methods 2020 11 28;12(44):5392-5396. Epub 2020 Oct 28.

Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, China.

Multiplex PCR encounters difficulties in primer designing with all the primer pairs working at the same annealing temperature. In this study, we have developed a double-strand primer-mediated multiple strand displacement reaction for the detection of SARS-COV-2 ORF, N and E genes (as examples). The double primer is composed of a 5'-modified fluorophore strand, which does not impact polymerase extension and a 3'-modified quencher strand, which cannot impact elongation. At the annealing temperature, the fluorophore strand combined with the template, extended and resulted in fluorescence signal release. Results showed that the double-strand primer relatively exhibits a wide annealing temperature range and good compatibility between three pairs of primers and probes. These merits allow the simple and multiplex real-time fluorescence quantification of nucleic acids. The detection limit was 400 copies/mL, and the detection time was approximately 2 h. In addition to its extreme specificity and simplicity, this method has a wide range of applications such as multiple PCR and SNP detection.
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http://dx.doi.org/10.1039/d0ay01661fDOI Listing
November 2020

An online coronavirus analysis platform from the National Genomics Data Center.

Zool Res 2020 Nov;41(6):705-708

China National Center for Bioinformation & National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

Since the first reported severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in December 2019, coronavirus disease 2019 (COVID-19) has become a global pandemic, spreading to more than 200 countries and regions worldwide. With continued research progress and virus detection, SARS-CoV-2 genomes and sequencing data have been reported and accumulated at an unprecedented rate. To meet the need for fast analysis of these genome sequences, the National Genomics Data Center (NGDC) of the China National Center for Bioinformation (CNCB) has established an online coronavirus analysis platform, which includes assembly, BLAST alignment, genome annotation, variant identification, and variant annotation modules. The online analysis platform can be freely accessed at the 2019 Novel Coronavirus Resource (2019nCoVR) (https://bigd.big.ac.cn/ncov/online/tools).
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http://dx.doi.org/10.24272/j.issn.2095-8137.2020.065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671910PMC
November 2020