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  • Oxford University Press (OUP)  (7)
  • English  (7)
  • 1
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    Prospective observational cohort study on grading the severity of postoperative complications in global surgery research
    Oxford University Press (OUP) ; 2019
    In:  British Journal of Surgery Vol. 106, No. 2 ( 2019-01-08), p. e73-e80
    Details
    In: British Journal of Surgery, Oxford University Press (OUP), Vol. 106, No. 2 ( 2019-01-08), p. e73-e80
    Abstract: The Clavien–Dindo classification is perhaps the most widely used approach for reporting postoperative complications in clinical trials. This system classifies complication severity by the treatment provided. However, it is unclear whether the Clavien–Dindo system can be used internationally in studies across differing healthcare systems in high- (HICs) and low- and middle-income countries (LMICs). Methods This was a secondary analysis of the International Surgical Outcomes Study (ISOS), a prospective observational cohort study of elective surgery in adults. Data collection occurred over a 7-day period. Severity of complications was graded using Clavien–Dindo and the simpler ISOS grading (mild, moderate or severe, based on guided investigator judgement). Severity grading was compared using the intraclass correlation coefficient (ICC). Data are presented as frequencies and ICC values (with 95 per cent c.i.). The analysis was stratified by income status of the country, comparing HICs with LMICs. Results A total of 44 814 patients were recruited from 474 hospitals in 27 countries (19 HICs and 8 LMICs). Some 7508 patients (16·8 per cent) experienced at least one postoperative complication, equivalent to 11 664 complications in total. Using the ISOS classification, 5504 of 11 664 complications (47·2 per cent) were graded as mild, 4244 (36·4 per cent) as moderate and 1916 (16·4 per cent) as severe. Using Clavien–Dindo, 6781 of 11 664 complications (58·1 per cent) were graded as I or II, 1740 (14·9 per cent) as III, 2408 (20·6 per cent) as IV and 735 (6·3 per cent) as V. Agreement between classification systems was poor overall (ICC 0·41, 95 per cent c.i. 0·20 to 0·55), and in LMICs (ICC 0·23, 0·05 to 0·38) and HICs (ICC 0·46, 0·25 to 0·59). Conclusion Caution is recommended when using a treatment approach to grade complications in global surgery studies, as this may introduce bias unintentionally.
    Type of Medium: Online Resource
    ISSN: 0007-1323 , 1365-2168
    URL: Article
    DOI: 10.1002/bjs.11025
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2006309-X
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  • 2
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    Negative regulation of root-knot nematode parasitic behavior by root-derived volatiles of wild relatives of Cucumis metuliferus CM3
    Oxford University Press (OUP) ; 2022
    In:  Horticulture Research Vol. 9 ( 2022-01-05)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 9 ( 2022-01-05)
    Abstract: Root-knot nematodes (RKN; Meloidogyne spp.) cause a significant decrease in the yield of cucumber crops every year. Cucumis metuliferus is an important wild germplasm that has resistance to RKN in which plant root volatiles are thought to play a role. However, the underlying molecular mechanism is unclear. To investigate it, we used the resistant C. metuliferus line CM3 and the susceptible cucumber line Xintaimici (XTMC). CM3 roots repelled Meloidogyne incognita second-stage larvae (J2s), while the roots of XTMC plants attracted the larvae. CM3 and XTMC were found to contain similar amounts of root volatiles, but many volatiles, including nine hydrocarbons, three alcohols, two aldehydes, two ketones, one ester, and one phenol, were only detected in CM3 roots. It was found that one of these, (methoxymethyl)-benzene, could repel M. incognita, while creosol and (Z)-2-penten-1-ol could attract M. incognita. Interestingly, creosol and (Z)-2-penten-1-ol effectively killed M. incognita at high concentrations. Furthermore, we found that a mixture of CM3 root volatiles increased cucumber resistance to M. incognita. The results provide insights into the interaction between the host and plant-parasitic nematodes in the soil, with some compounds possibly acting as nematode biofumigation, which can be used to manage nematodes.
    Type of Medium: Online Resource
    ISSN: 2052-7276
    URL: Article
    DOI: 10.1093/hr/uhac051
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2781828-7
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  • 3
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    Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS
    Oxford University Press (OUP) ; 2021
    In:  Briefings in Bioinformatics Vol. 22, No. 3 ( 2021-05-20)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 22, No. 3 ( 2021-05-20)
    Abstract: Transcriptional switch (TS) is a widely observed phenomenon caused by changes in the relative expression of transcripts from the same gene, in spatial, temporal or other dimensions. TS has been associated with human diseases, plant development and stress responses. Its investigation is often hampered by a lack of suitable tools allowing comprehensive and flexible TS analysis for high-throughput RNA sequencing (RNA-Seq) data. Here, we present deepTS, a user-friendly web-based implementation that enables a fully interactive, multifunctional identification, visualization and analysis of TS events for large-scale RNA-Seq datasets from pairwise, temporal and population experiments. deepTS offers rich functionality to streamline RNA-Seq-based TS analysis for both model and non-model organisms and for those with or without reference transcriptome. The presented case studies highlight the capabilities of deepTS and demonstrate its potential for the transcriptome-wide TS analysis of pairwise, temporal and population RNA-Seq data. We believe deepTS will help research groups, regardless of their informatics expertise, perform accessible, reproducible and collaborative TS analyses of large-scale RNA-Seq data.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbaa137
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2036055-1
    SSG: 12
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  • 4
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    Storing biological sequence databases in relational form
    Oxford University Press (OUP) ; 2000
    In:  Bioinformatics Vol. 16, No. 3 ( 2000-03-01), p. 288-289
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 16, No. 3 ( 2000-03-01), p. 288-289
    Abstract: Summary: We have created a set of applications using Perl and Java in combination with XML technology to install biological sequence databases into an Oracle RDBMS. An easy-to-use interface using Java has been created for database query and other tools developed to integrate with our in-house bioinformatics applications. Availability: The database schema, DTD file, and source codes are available from the authors via email. Contact: guochun_xie@merck.com
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/16.3.288
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2000
    detail.hit.zdb_id: 1468345-3
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  • 5
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    Antibody-Based Methods Reveal the Protein Expression Properties of Glucosinolate Sulfatase 1 and 2 in Plutella xylostella
    Oxford University Press (OUP) ; 2022
    In:  Journal of Insect Science Vol. 22, No. 6 ( 2022-11-01)
    Details
    In: Journal of Insect Science, Oxford University Press (OUP), Vol. 22, No. 6 ( 2022-11-01)
    Abstract: The glucosinolates (GLs) and myrosinase defensive systems in cruciferous plants were circumvented by Plutella xylostella using glucosinolate sulfatases (PxGSSs) during pest-plant interaction. Despite identifying three duplicated GSS-encoding genes in P. xylostella, limited information regarding their spatiotemporal and induced expression is available. Here, we investigated the tissue- and stage-specific expression and induction in response to GLs of PxGSS1 and PxGSS2 (PxGSS1/2) at the protein level, which shares a high degree of similarity in protein sequences. Western blotting (WB) analysis showed that PxGSS1/2 exhibited a higher protein level in mature larvae, their guts, and gut content. A significantly high protein and transcript levels of PxGSS1/2 were also detected in the salivary glands using WB and qRT-PCR. The immunofluorescence (IF) and immunohistochemistry (IHC) results confirmed that PxGSS1/2 is widely expressed in the larval body. The IHC was more appropriate than IF when autofluorescence interference was present in collected samples. Furthermore, the content of PxGSS1/2 did not change significantly under treatments of GL mixture from Arabidopsis thaliana ecotype Col-0, or commercial ally (sinigrin), 4-(methylsulfinyl)butyl, 3-(methylsulfinyl)propyl, and indol-3-ylmethyl GLs indicating that the major GLs from leaves of A. thaliana Col-0 failed to induce the expression of proteins for both PxGSS1 and PxGSS2. Our study systemically characterized the expression properties of PxGSS1/2 at the protein level, which improves our understanding of PxGSS1/2-center adaptation in P. xylostella during long-term insect-plant interaction.
    Type of Medium: Online Resource
    ISSN: 1536-2442
    URL: Article
    DOI: 10.1093/jisesa/ieac070
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2049098-7
    SSG: 12
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  • 6
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    Methylorubrum rhodesianum M520 as a biocontrol agent against Meloidogyne incognita (Tylenchida: Heteroderidae) J2s infecting cucumber roots
    Oxford University Press (OUP) ; 2023
    In:  Journal of Applied Microbiology Vol. 134, No. 2 ( 2023-02-16)
    Details
    In: Journal of Applied Microbiology, Oxford University Press (OUP), Vol. 134, No. 2 ( 2023-02-16)
    Abstract: Root-knot nematodes (RKNs) are plant pathogens that cause huge economic losses worldwide. The biological management of RKNs may be a sustainable alternative to chemical control methods. Here, the biocontrol potential of Methylorubrum rhodesianum M520 against the RKN Meloidogyne incognita was investigated to theoretically support its application as a biocontrol agent in field production. Methods and results In-vitro assays showed 91.9% mortality of M. incognita second-stage juveniles in the presence of strain M520 and that the hatching rate of M. incognita eggs was 21.7% lower than that of eggs treated with sterile water. In pot experiments, the M520 treatment caused 70.8% reduction in root-knots and increased plant shoot length and stem and root fresh weights, compared to control plant values. In split-root experiments, cucumber roots treated with M520 showed 25.6% decrease in root gall number, compared to that in control roots. Conclusion M520 has multiple mechanisms against RKNs and might be used as a biocontrol agent against M. incognita in cucumber, laying a foundation for further studying M520 biocontrol against RKNs.
    Type of Medium: Online Resource
    ISSN: 1365-2672
    URL: Article
    DOI: 10.1093/jambio/lxad001
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2020421-8
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  • 7
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    Evolutionary Implications of the RNA N 6-Methyladenosine Methylome in Plants
    Oxford University Press (OUP) ; 2022
    In:  Molecular Biology and Evolution Vol. 39, No. 1 ( 2022-01-07)
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 39, No. 1 ( 2022-01-07)
    Abstract: Epigenetic modifications play important roles in genome evolution and innovation. However, most analyses have focused on the evolutionary role of DNA modifications, and little is understood about the influence of posttranscriptional RNA modifications on genome evolution. To explore the evolutionary significance of RNA modifications, we generated transcriptome-wide profiles of N6-methyladenosine (m6A), the most prevalent internal modification of mRNA, for 13 representative plant species spanning over half a billion years of evolution. These data reveal the evolutionary conservation and divergence of m6A methylomes in plants, uncover the preference of m6A modifications on ancient orthologous genes, and demonstrate less m6A divergence between orthologous gene pairs with earlier evolutionary origins. Further investigation revealed that the evolutionary divergence of m6A modifications is related to sequence variation between homologs from whole-genome duplication and gene family expansion from local-genome duplication. Unexpectedly, a significant negative correlation was found between the retention ratio of m6A modifications and the number of family members. Moreover, the divergence of m6A modifications is accompanied by variation in the expression level and translation efficiency of duplicated genes from whole- and local-genome duplication. Our work reveals new insights into evolutionary patterns of m6A methylomes in plant species and their implications, and provides a resource of plant m6A profiles for further studies of m6A regulation and function in an evolutionary context.
    Type of Medium: Online Resource
    ISSN: 0737-4038 , 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msab299
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2024221-9
    SSG: 12
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