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  • Oxford University Press (OUP)  (14)
  • Biodiversity Research  (14)
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  • Oxford University Press (OUP)  (14)
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  • Biodiversity Research  (14)
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  • 1
    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
    SSG: 12
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  • 2
    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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    Online Resource
  • 3
    Online Resource
    Online Resource
    Effects of Azadirachtin on Hemolymph Protein Expression in 〈I〉Ostrinia furnacalis〈/I〉 (Lepidoptera: Crambidae)
    Oxford University Press (OUP) ; 2007
    In:  Annals of the Entomological Society of America Vol. 100, No. 2 ( 2007-03-01), p. 245-250
    Details
    In: Annals of the Entomological Society of America, Oxford University Press (OUP), Vol. 100, No. 2 ( 2007-03-01), p. 245-250
    Type of Medium: Online Resource
    ISSN: 0013-8746 , 0013-8746
    URL: Article
    DOI: 10.1603/0013-8746(2007)100[245:EOAOHP]2.0.CO;2
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2007
    detail.hit.zdb_id: 2175906-6
    detail.hit.zdb_id: 2028805-0
    SSG: 12
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    Online Resource
  • 4
    Online Resource
    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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  • 5
    Online Resource
    Online Resource
    Analysis of 20-OH-Ecdysone Titers in Ostrinia furnacalis Affected by Azadirachtin Using Capillary Zone Electrophoresis
    Oxford University Press (OUP) ; 2012
    In:  Annals of the Entomological Society of America Vol. 105, No. 6 ( 2012-11-01), p. 890-895
    Details
    In: Annals of the Entomological Society of America, Oxford University Press (OUP), Vol. 105, No. 6 ( 2012-11-01), p. 890-895
    Abstract: A novel technique of insect ecdysone analysis was established by capillary zone electrophoresis using 20-hydroxy ecdysone (purity ≥93%) as a standard sample. It showed that 20-hydroxy ecdysone and other trace impurities were completely separated within 5 min with an electrolyte containing 10 mmol/L borate, at pH 9.18, 20 kV applied voltage and 0.5 psi × 5 s injected volume. Under this optimal condition, effects of azadirachtin on ecdysone in the hemolymph of Ostrinia furnacalis (Guenee) were investigated. The results showed that the peak values of 20-hydroxy ecdysone were strongly suppressed by azadirachtin and the titers remained at a lower level than those in the control samples. When compared with high-performance liquid chromatography, the primary advantages of capillary zone electrophoresis include a much shorter analysis time and detection limit and the elimination of complex pretreatment of samples.
    Type of Medium: Online Resource
    ISSN: 1938-2901 , 0013-8746
    URL: Article
    DOI: 10.1603/AN11177
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2012
    detail.hit.zdb_id: 2175906-6
    detail.hit.zdb_id: 2028805-0
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  • 6
    Online Resource
    Online Resource
    Trivalent Arsenic Inhibits the Functions of Chaperonin Complex
    Oxford University Press (OUP) ; 2010
    In:  Genetics Vol. 186, No. 2 ( 2010-10-01), p. 725-734
    Details
    In: Genetics, Oxford University Press (OUP), Vol. 186, No. 2 ( 2010-10-01), p. 725-734
    Abstract: The exact molecular mechanisms by which the environmental pollutant arsenic works in biological systems are not completely understood. Using an unbiased chemogenomics approach in Saccharomyces cerevisiae, we found that mutants of the chaperonin complex TRiC and the functionally related prefoldin complex are all hypersensitive to arsenic compared to a wild-type strain. In contrast, mutants with impaired ribosome functions were highly arsenic resistant. These observations led us to hypothesize that arsenic might inhibit TRiC function, required for folding of actin, tubulin, and other proteins postsynthesis. Consistent with this hypothesis, we found that arsenic treatment distorted morphology of both actin and microtubule filaments. Moreover, arsenic impaired substrate folding by both bovine and archaeal TRiC complexes in vitro. These results together indicate that TRiC is a conserved target of arsenic inhibition in various biological systems.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    URL: Article
    DOI: 10.1534/genetics.110.117655
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2010
    detail.hit.zdb_id: 1477228-0
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    OLE1 reduces cadmium-induced oxidative damage in Saccharomyces cerevisiae
    Oxford University Press (OUP) ; 2018
    In:  FEMS Microbiology Letters Vol. 365, No. 18 ( 2018-09-01)
    Details
    In: FEMS Microbiology Letters, Oxford University Press (OUP), Vol. 365, No. 18 ( 2018-09-01)
    Type of Medium: Online Resource
    ISSN: 1574-6968
    URL: Article
    DOI: 10.1093/femsle/fny193
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 1501716-3
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  • 8
    Online Resource
    Online Resource
    Effects of abiotic stress and crop management on cereal grain composition: implications for food quality and safety
    Oxford University Press (OUP) ; 2015
    In:  Journal of Experimental Botany Vol. 66, No. 5 ( 2015-3), p. 1145-1156
    Details
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 66, No. 5 ( 2015-3), p. 1145-1156
    Type of Medium: Online Resource
    ISSN: 1460-2431 , 0022-0957
    URL: Article
    DOI: 10.1093/jxb/eru473
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
    detail.hit.zdb_id: 1466717-4
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Structural basis of Staphylococcus aureus Cas9 inhibition by AcrIIA14
    Oxford University Press (OUP) ; 2021
    In:  Nucleic Acids Research Vol. 49, No. 11 ( 2021-06-21), p. 6587-6595
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 49, No. 11 ( 2021-06-21), p. 6587-6595
    Abstract: Bacteriophages have evolved a range of anti-CRISPR proteins (Acrs) to escape the adaptive immune system of prokaryotes, therefore Acrs can be used as switches to regulate gene editing. Herein, we report the crystal structure of a quaternary complex of AcrIIA14 bound SauCas9–sgRNA–dsDNA at 2.22 Å resolution, revealing the molecular basis for AcrIIA14 recognition and inhibition. Our structural and biochemical data analysis suggest that AcrIIA14 binds to a non-conserved region of SauCas9 HNH domain that is distinctly different from AcrIIC1 and AcrIIC3, with no significant effect on sgRNA or dsDNA binding. Further, our structural data shows that the allostery of the HNH domain close to the substrate DNA is sterically prevented by AcrIIA14 binding. In addition, the binding of AcrIIA14 triggers the conformational allostery of the HNH domain and the L1 linker within the SauCas9, driving them to make new interactions with the target-guide heteroduplex, enhancing the inhibitory ability of AcrIIA14. Our research both expands the current understanding of anti-CRISPRs and provides additional culues for the rational use of the CRISPR-Cas system in genome editing and gene regulation.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkab487
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    Rank-in: enabling integrative analysis across microarray and RNA-seq for cancer
    Oxford University Press (OUP) ; 2021
    In:  Nucleic Acids Research Vol. 49, No. 17 ( 2021-09-27), p. e99-e99
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 49, No. 17 ( 2021-09-27), p. e99-e99
    Abstract: Though transcriptomics technologies evolve rapidly in the past decades, integrative analysis of mixed data between microarray and RNA-seq remains challenging due to the inherent variability difference between them. Here, Rank-In was proposed to correct the nonbiological effects across the two technologies, enabling freely blended data for consolidated analysis. Rank-In was rigorously validated via the public cell and tissue samples tested by both technologies. On the two reference samples of the SEQC project, Rank-In not only perfectly classified the 44 profiles but also achieved the best accuracy of 0.9 on predicting TaqMan-validated DEGs. More importantly, on 327 Glioblastoma (GBM) profiles and 248, 523 heterogeneous colon cancer profiles respectively, only Rank-In can successfully discriminate every single cancer profile from normal controls, while the others cannot. Further on different sizes of mixed seq-array GBM profiles, Rank-In can robustly reproduce a median range of DEG overlapping from 0.74 to 0.83 among top genes, whereas the others never exceed 0.72. Being the first effective method enabling mixed data of cross-technology analysis, Rank-In welcomes hybrid of array and seq profiles for integrative study on large/small, paired/unpaired and balanced/imbalanced samples, opening possibility to reduce sampling space of clinical cancer patients. Rank-In can be accessed at http://www.badd-cao.net/rank-in/index.html.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkab554
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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