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  • Oxford University Press (OUP)  (27)
  • 2020-2024  (27)
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  • Oxford University Press (OUP)  (27)
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  • 2020-2024  (27)
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  • 1
    Online Resource
    Online Resource
    Single-Cell Transcriptomic Sequencing Analyses of Cell Heterogeneity During Osteogenesis of Human Adipose-Derived Mesenchymal Stem Cells
    Oxford University Press (OUP) ; 2021
    In:  Stem Cells Vol. 39, No. 11 ( 2021-11-01), p. 1478-1488
    Details
    In: Stem Cells, Oxford University Press (OUP), Vol. 39, No. 11 ( 2021-11-01), p. 1478-1488
    Abstract: Mesenchymal stem cells (MSCs) are known for their multilineage differentiation potential with immune-modulatory properties. The molecular underpinnings of differentiation remain largely undefined. In this study, we investigated the cellular and molecular features of chemically induced osteogenesis from MSC isolated from human adipose tissue (human adipose MSCs, hAMSCs) using single-cell RNA-sequencing (scRNA-seq). We found that a near complete differentiation of osteogenic clusters from hAMSCs under a directional induction. Both groups of cells are heterogeneous, and some of the hAMSCs cells are intrinsically prepared for osteogenesis, while variant OS clusters seems in cooperation with a due division of the general function. We identified a set of genes related to cell stress response highly expressed during the differentiation. We also characterized a series of transitional transcriptional waves throughout the process from hAMSCs to osteoblast and specified the unique gene networks and epigenetic status as key markers of osteogenesis.
    Type of Medium: Online Resource
    ISSN: 1066-5099 , 1549-4918
    URL: Article
    DOI: 10.1002/stem.3442
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
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    detail.hit.zdb_id: 1143556-2
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    SSG: 12
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  • 2
    Online Resource
    Online Resource
    CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing
    Oxford University Press (OUP) ; 2023
    In:  Nucleic Acids Research Vol. 51, No. W1 ( 2023-07-05), p. W93-W107
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 51, No. W1 ( 2023-07-05), p. W93-W107
    Abstract: The CRISPR-Cas system is a highly adaptive and RNA-guided immune system found in bacteria and archaea, which has applications as a genome editing tool and is a valuable system for studying the co-evolutionary dynamics of bacteriophage interactions. Here introduces CRISPRimmunity, a new web server designed for Acr prediction, identification of novel class 2 CRISPR-Cas loci, and dissection of key CRISPR-associated molecular events. CRISPRimmunity is built on a suite of CRISPR-oriented databases providing a comprehensive co-evolutionary perspective of the CRISPR-Cas and anti-CRISPR systems. The platform achieved a high prediction accuracy of 0.997 for Acr prediction when tested on a dataset of 99 experimentally validated Acrs and 676 non-Acrs, outperforming other existing prediction tools. Some of the newly identified class 2 CRISPR-Cas loci using CRISPRimmunity have been experimentally validated for cleavage activity in vitro. CRISPRimmunity offers the catalogues of pre-identified CRISPR systems to browse and query, the collected resources or databases to download, a well-designed graphical interface, a detailed tutorial, multi-faceted information, and exportable results in machine-readable formats, making it easy to use and facilitating future experimental design and further data mining. The platform is available at http://www.microbiome-bigdata.com/CRISPRimmunity. Moreover, the source code for batch analysis are published on Github (https://github.com/HIT-ImmunologyLab/CRISPRimmunity).
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkad425
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1472175-2
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  • 3
    Online Resource
    Online Resource
    HLA Zygosity Increases Risk of Hepatitis B Virus-Associated Hepatocellular Carcinoma
    Oxford University Press (OUP) ; 2021
    In:  The Journal of Infectious Diseases Vol. 224, No. 10 ( 2021-11-22), p. 1796-1805
    Details
    In: The Journal of Infectious Diseases, Oxford University Press (OUP), Vol. 224, No. 10 ( 2021-11-22), p. 1796-1805
    Abstract: Diversity in the HLA genes might be associated with disease outcomes—the heterozygote advantage hypothesis. We tested this hypothesis in relation to hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC). Methods We utilized DNA from & gt; 10 000 Taiwanese individuals with current or past HBV infection to examine the association between HLA diversity and critical natural history steps in the progression from HBV infection to HCC. Individuals were classified as homozygotes at a given locus when imputed to carry the same 4-digit allele for the 2 HLA alleles at that locus. Results Increase in number of homozygous HLA class II loci was associated with an increased risk of chronic HBV infection (Ptrend = 1.18 × 10–7). Among chronic HBV carriers, increase in number of homozygous HLA class II loci was also associated with an increased risk of HBV-associated HCC (Ptrend = .031). For individual HLA loci, HLA-DQB1 homozygosity was significantly associated with HCC risk (adjusted hazard ratio = 1.40; 95% confidence interval, 1.06–1.84). We also found that zygosity affects risk of HCC through its ability to affect viral control. Conclusions Homozygosity at HLA class II loci, particularly HLA-DQB1, is associated with a higher risk of HBV-associated HCC.
    Type of Medium: Online Resource
    ISSN: 0022-1899 , 1537-6613
    URL: Article
    DOI: 10.1093/infdis/jiab207
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1473843-0
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  • 4
    Online Resource
    Online Resource
    GmPIN-dependent polar auxin transport is involved in soybean nodule development
    Oxford University Press (OUP) ; 2021
    In:  The Plant Cell Vol. 33, No. 9 ( 2021-09-24), p. 2981-3003
    Details
    In: The Plant Cell, Oxford University Press (OUP), Vol. 33, No. 9 ( 2021-09-24), p. 2981-3003
    Abstract: To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that are fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed the impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that the establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia.
    Type of Medium: Online Resource
    ISSN: 1040-4651 , 1532-298X
    URL: Article
    DOI: 10.1093/plcell/koab183
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 623171-8
    detail.hit.zdb_id: 2004373-9
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Nasal Spray of Neutralizing Monoclonal Antibody 35B5 Confers Potential Prophylaxis Against Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Small-Scale Clinical Trial
    Oxford University Press (OUP) ; 2023
    In:  Clinical Infectious Diseases Vol. 76, No. 3 ( 2023-02-08), p. e336-e341
    Details
    In: Clinical Infectious Diseases, Oxford University Press (OUP), Vol. 76, No. 3 ( 2023-02-08), p. e336-e341
    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs), especially the Delta and Omicron variants, have been reported to show significant resistance to approved neutralizing monoclonal antibodies (mAbs) and vaccines. We previously identified a mAb named 35B5 that harbors broad neutralization to SARS-CoV-2 VOCs. Herein, we explored the protection efficacy of a 35B5-based nasal spray against SARS-CoV-2 VOCs in a small-scale clinical trial. Methods We enrolled 30 healthy volunteers who were nasally administered the modified 35B5 formulation. At 12, 24, 48, and 72 hours after nasal spray, the neutralization efficacy of nasal mucosal samples was assayed with pseudoviruses coated with SARS-CoV-2 spike protein of the wild-type strain or the Alpha, Beta, Delta, or Omicron variants. Results The nasal mucosal samples collected within 24 hours after nasal spray effectively neutralized SARS-CoV-2 VOCs (including Delta and Omicron). Meanwhile, the protection efficacy was 60% effective and 20% effective at 48 and 72 hours after nasal spray, respectively. Conclusions A single nasal spray of 35B5 formation conveys 24-hour effective protection against SARS-CoV-2 VOCs, including the Alpha, Beta, Delta, or Omicron variants. Thus, 35B5 nasal spray might be potential in strengthening SARS-CoV-2 prevention, especially in high-risk populations. Clinical Trials Registration 2022-005-02-KY.
    Type of Medium: Online Resource
    ISSN: 1058-4838 , 1537-6591
    URL: Article
    DOI: 10.1093/cid/ciac448
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2002229-3
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  • 6
    Online Resource
    Online Resource
    Clioquinol induces S-phase cell cycle arrest through the elevation of the calcium level in human neurotypic SH-SY5Y cells
    Oxford University Press (OUP) ; 2020
    In:  Metallomics Vol. 12, No. 2 ( 2020-02-26), p. 173-182
    Details
    In: Metallomics, Oxford University Press (OUP), Vol. 12, No. 2 ( 2020-02-26), p. 173-182
    Abstract: Clioquinol is recently considered to be the most promising drug for treating cancer and neurodegenerative diseases. However, its mode of action varies from different disease models. In this study, we found that clioquinol inhibited cell growth in human neurotypic SHSY-5Y cells, which was attributed to both S-phase cell-cycle arrest and autophagic cell death. Clioquinol increased the intracellular contents of iron and zinc as well as calcium as measured by ICP-AES. Staining of Fluo-3 confirmed an increase in the level of calcium. Analysis of the metal-binding ability of clioquinol showed that it was not a chelating agent of calcium ions and the elevation of intracellular calcium content is not achieved by clioquinol as an ionophore. CaCl2 could simulate or even aggravate the cytotoxicity of clioquinol and it increased S-phase cell cycle arrest induced by clioquinol in a concentration dependent manner. Staining of acridine orange demonstrated that autophagy induced by clioquinol was not affected by addition of calcium ions. In contrast, the intracellular calcium ion chelator BAPTA-am abolished the clioquinol-induced S phase arrest and reduced the cell death caused by clioquinol. The WB assay of cell cycle-related proteins (CDK2, p21 and p27) further confirmed that S phase arrest is positively correlated with intracellular calcium elevation, which was due to the alterations of the mRNA and protein levels of calcium pumps (SERCA and SPCA). Taken together, these data indicate that clioquinol regulates the level of intracellular calcium ions to induce S-phase cell cycle arrest in human SH-SY5Y cells. Our results demonstrate for the first time that an increase of intracellular calcium content is one of the mechanisms of clioquinol in the inhibition of human neurotypic SHSY-5Y cells.
    Type of Medium: Online Resource
    ISSN: 1756-5901 , 1756-591X
    URL: Article
    DOI: 10.1039/c9mt00260j
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2474317-3
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  • 7
    Online Resource
    Online Resource
    The 100 most cited articles on pancreatic neuroendocrine tumors from 2000 to 2020: a bibliometric analysis
    Oxford University Press (OUP) ; 2022
    In:  Japanese Journal of Clinical Oncology Vol. 52, No. 3 ( 2022-03-03), p. 251-259
    Details
    In: Japanese Journal of Clinical Oncology, Oxford University Press (OUP), Vol. 52, No. 3 ( 2022-03-03), p. 251-259
    Abstract: The present study attempted to identify 100 most cited articles on pancreatic neuroendocrine tumors and characterize them via bibliometric analysis whereby it would provide an insight into the progress and trend in this field. Methods Records regarding pancreatic neuroendocrine tumors and published between 2000 and 2020 were retrieved in 2021 through the Web of Science to identify the 100 most cited articles. Results The 100 articles were screened in 17 434 records. The number of citations of the top-cited articles ranged from 151 to 1867. These articles were published in 47 journals among which the Journal of Clinical Oncology produced the most articles (n = 10). The USA contributed most of the articles (n = 44). Articles enrolled came from 58 institutions; the University of California System of the USA came to the top (n = 7). More than half of the articles were clinical studies (n = 55), basic science research reports accounting for a quarter. In clinical topics (n = 73), treatment issues were the most concerned (n = 21), in which more articles focused on targeted inhibitors. Articles about gene mutation were cited most frequently in basic science topics (n = 27). Conclusions This bibliometric analysis reflected the brief the progress and highlighted current trend in pancreatic neuroendocrine tumor research, providing references for further study.
    Type of Medium: Online Resource
    ISSN: 1465-3621
    URL: Article
    DOI: 10.1093/jjco/hyab205
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1494610-5
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  • 8
    Online Resource
    Online Resource
    Structure of the Gonghe Sedimentary Basin in the northeastern Tibetan Plateau: evidence from teleseismic P waves recorded by a dense seismic array
    Oxford University Press (OUP) ; 2023
    In:  Geophysical Journal International Vol. 235, No. 2 ( 2023-07-27), p. 1697-1711
    Details
    In: Geophysical Journal International, Oxford University Press (OUP), Vol. 235, No. 2 ( 2023-07-27), p. 1697-1711
    Abstract: The Gonghe Basin in the northeast Tibetan Plateau presents significant potential for hot dry rock (HDR) geothermal resources. A 1990 Mw 6.4 earthquake in the basin furthers the need for an improved understanding of its sedimentary structure. In this study, we utilize data from a dense seismic array of 88 short-period seismometers deployed at an interstation spacing of approximately 3 km to scrutinize the sedimentary structure of the Gonghe Basin. By analysing teleseismic P waveforms, we identify P-to-S converted waves (Ps wave) originating from the sedimentary basement. We then determine the delay time between the Ps waves and the direct P waves (P wave) through waveform cross-correlation. By integrating this delay time with empirical velocity structure models, HDR borehole data and results from teleseismic receiver function analysis, we derive a sediment thickness model of the Gonghe Basin for the Qabqa geothermal area. Our findings reveal a gradual increase in sediment thickness from around 500 m in the east to approximately 3000 m in the west, which is consistent with other geophysical surveys and borehole data. The thick sediments in the basin could potentially serve as an excellent thermal storage cover for HDR. The strong ground motion simulation using our sediment thickness model shows that thick sediments can amplify seismic waves, increasing the risk of seismic hazards. Moreover, our study indicates that the clear Ps waves can be effectively extracted to construct a dependable sediment thickness model using teleseismic P waves recorded by a short-period dense seismic array.
    Type of Medium: Online Resource
    ISSN: 0956-540X , 1365-246X
    URL: Article
    DOI: 10.1093/gji/ggad327
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
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    detail.hit.zdb_id: 2006420-2
    detail.hit.zdb_id: 1002799-3
    SSG: 16,13
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  • 9
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    Online Resource
    A benchmark for automatic medical consultation system: frameworks, tasks and datasets
    Oxford University Press (OUP) ; 2023
    In:  Bioinformatics Vol. 39, No. 1 ( 2023-01-01)
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 39, No. 1 ( 2023-01-01)
    Abstract: In recent years, interest has arisen in using machine learning to improve the efficiency of automatic medical consultation and enhance patient experience. In this article, we propose two frameworks to support automatic medical consultation, namely doctor–patient dialogue understanding and task-oriented interaction. We create a new large medical dialogue dataset with multi-level fine-grained annotations and establish five independent tasks, including named entity recognition, dialogue act classification, symptom label inference, medical report generation and diagnosis-oriented dialogue policy. Results We report a set of benchmark results for each task, which shows the usability of the dataset and sets a baseline for future studies. Availability and implementation Both code and data are available from https://github.com/lemuria-wchen/imcs21. Supplementary information Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4803 , 1367-4811
    URL: Article
    DOI: 10.1093/bioinformatics/btac817
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 10
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    Online Resource
    The transporter PHO84/NtPT1 is a target of aluminum to affect phosphorus absorption in Saccharomyces cerevisiae and Nicotiana tabacum L
    Oxford University Press (OUP) ; 2023
    In:  Metallomics
    Details
    In: Metallomics, Oxford University Press (OUP)
    Abstract: The molecular mechanism of aluminum toxicity in biological systems is not completely understood. Saccharomyces cerevisiae is one of the most used model organisms in the study of environmental metal toxicity. Using an unbiased metallomic approach in yeast, we found that aluminum treatment caused phosphorus deprivation, and the lack of phosphorus increased as the pH of the environment decreased compared to the control strain. By screening the PHO pathway in yeast with the synthetic lethality of a new phosphorus-restricted aluminum-sensitive gene, we observed that pho84Δ mutation conferred severe growth defect to aluminum under low-phosphorus conditions, and the addition of phosphate alleviated this sensitivity. Subsequently, the data showed that PHO84 determined the intracellular aluminum-induced phosphorus deficiency, and the expression of PHO84 was positively correlated with aluminum stress, which was mediated by phosphorus through the coordinated regulation of PHO4/PHO2. Moreover, aluminum reduced phosphorus absorption and inhibited tobacco plant growth in acidic media. In addition, the high-affinity phosphate transporter NtPT1 in tobacco exhibited similar effects to PHO84, and overexpression of NtPT1 conferred aluminum resistance in yeast cells. Taken together, positive feedback regulation of the PHO pathway centered on the high-affinity phosphate transporters is a highly conservative mechanism in response to aluminum toxicity. The results may provide a basis for aluminum-resistant microorganisms or plant engineering and acidic soil treatment.
    Type of Medium: Online Resource
    ISSN: 1756-591X
    URL: Article
    DOI: 10.1093/mtomcs/mfad069
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2474317-3
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