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  • Oxford University Press (OUP)  (20)
  • 1
    Online Resource
    Online Resource
    Protecting stable biological nomenclatural systems enables universal communication: A collective international appeal
    Oxford University Press (OUP) ; 2024
    In:  BioScience ( 2024-06-19)
    Details
    In: BioScience, Oxford University Press (OUP), ( 2024-06-19)
    Abstract: The fundamental value of universal nomenclatural systems in biology is that they enable unambiguous scientific communication. However, the stability of these systems is threatened by recent discussions asking for a fairer nomenclature, raising the possibility of bulk revision processes for “inappropriate” names. It is evident that such proposals come from very deep feelings, but we show how they can irreparably damage the foundation of biological communication and, in turn, the sciences that depend on it. There are four essential consequences of objective codes of nomenclature: universality, stability, neutrality, and transculturality. These codes provide fair and impartial guides to the principles governing biological nomenclature and allow unambiguous universal communication in biology. Accordingly, no subjective proposals should be allowed to undermine them.
    Type of Medium: Online Resource
    ISSN: 0006-3568 , 1525-3244
    URL: Article
    DOI: 10.1093/biosci/biae043
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 2066019-4
    SSG: 12
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  • 2
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    E -value: a superior alternative to P -value and its adjustments in DNA methylation studies
    Oxford University Press (OUP) ; 2023
    In:  Briefings in Bioinformatics Vol. 24, No. 4 ( 2023-07-20)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 24, No. 4 ( 2023-07-20)
    Abstract: DNA methylation plays a crucial role in transcriptional regulation. Reduced representation bisulfite sequencing (RRBS) is a technique of increasing use for analyzing genome-wide methylation profiles. Many computational tools such as Metilene, MethylKit, BiSeq and DMRfinder have been developed to use RRBS data for the detection of the differentially methylated regions (DMRs) potentially involved in epigenetic regulations of gene expression. For DMR detection tools, as for countless other medical applications, P-values and their adjustments are among the most standard reporting statistics used to assess the statistical significance of biological findings. However, P-values are coming under increasing criticism relating to their questionable accuracy and relatively high levels of false positive or negative indications. Here, we propose a method to calculate E-values, as likelihood ratios falling into the null hypothesis over the entire parameter space, for DMR detection in RRBS data. We also provide the R package ‘metevalue’ as a user-friendly interface to implement E-value calculations into various DMR detection tools. To evaluate the performance of E-values, we generated various RRBS benchmarking datasets using our simulator ‘RRBSsim’ with eight samples in each experimental group. Our comprehensive benchmarking analyses showed that using E-values not only significantly improved accuracy, area under ROC curve and power, over that of P-values or adjusted P-values, but also reduced false discovery rates and type I errors. In applications using real RRBS data of CRL rats and a clinical trial on low-salt diet, the use of E-values detected biologically more relevant DMRs and also improved the negative association between DNA methylation and gene expression.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbad241
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2036055-1
    SSG: 12
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  • 3
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    The substrates of Plk1, beyond the functions in mitosis
    Oxford University Press (OUP) ; 2010
    In:  Protein & Cell Vol. 1, No. 11 ( 2010-11), p. 999-1010
    Details
    In: Protein & Cell, Oxford University Press (OUP), Vol. 1, No. 11 ( 2010-11), p. 999-1010
    Type of Medium: Online Resource
    ISSN: 1674-800X , 1674-8018
    URL: Article
    DOI: 10.1007/s13238-010-0131-x
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2010
    detail.hit.zdb_id: 2543451-2
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  • 4
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    Computational approaches for detecting disease-associated alternative splicing events
    Oxford University Press (OUP) ; 2023
    In:  Briefings in Bioinformatics Vol. 24, No. 3 ( 2023-05-19)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 24, No. 3 ( 2023-05-19)
    Abstract: Alternative splicing (AS) is a key transcriptional regulation pathway. Recent studies have shown that AS events are associated with the occurrence of complex diseases. Various computational approaches have been developed for the detection of disease-associated AS events. In this review, we first describe the metrics used for quantitative characterization of AS events. Second, we review and discuss the three types of methods for detecting disease-associated splicing events, which are differential splicing analysis, aberrant splicing detection and splicing-related network analysis. Third, to further exploit the genetic mechanism of disease-associated AS events, we describe the methods for detecting genetic variants that potentially regulate splicing. For each type of methods, we conducted experimental comparison to illustrate their performance. Finally, we discuss the limitations of these methods and point out potential ways to address them. We anticipate that this review provides a systematic understanding of computational approaches for the analysis of disease-associated splicing.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbad106
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2036055-1
    SSG: 12
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  • 5
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    METTL14 Regulates Osteogenesis of Bone Marrow Mesenchymal Stem Cells via Inducing Autophagy Through m6A/IGF2BPs/Beclin-1 Signal Axis
    Oxford University Press (OUP) ; 2022
    In:  Stem Cells Translational Medicine Vol. 11, No. 9 ( 2022-09-21), p. 987-1001
    Details
    In: Stem Cells Translational Medicine, Oxford University Press (OUP), Vol. 11, No. 9 ( 2022-09-21), p. 987-1001
    Abstract: The development of osteoporosis is often accompanied by autophagy disturbance, which also causes new osteoblast defects from bone marrow mesenchymal stem cells (BMSCs). However, the underlying molecular mechanisms are still not fully understood. Methyltransferase-like 14 (METTL14) is the main enzyme for N6-methyladenosine (m6A), the most prevalent internal modification in mammalian mRNAs, and it has been implicated in many bioprocesses. Herein, we demonstrate that METTL14 plays a critical role in autophagy induction and hinders osteoporosis process whose expression is decreased both in human osteoporosis bone tissue and ovariectomy (OVX) mice. In vivo, METTL14+/− knockdown mice exhibit elevated bone loss and impaired autophagy similar to the OVX mice, while overexpression of METTL14 significantly promotes bone formation and inhibits the progression of osteoporosis caused by OVX surgery. In vitro, METTL14 overexpression significantly enhances the osteogenic differentiation ability of BMSCs through regulating the expression of beclin-1 depending on m6A modification and inducing autophagy; the opposite is true with METTL14 silencing. Subsequently, m6A-binding proteins IGF2BP1/2/3 recognize m6A-methylated beclin-1 mRNA and promote its translation via mediating RNA stabilization. Furthermore, METTL14 negatively regulates osteoclast differentiation. Collectively, our study reveals the METTL14/IGF2BPs/beclin-1 signal axis in BMSCs osteogenic differentiation and highlights the critical roles of METTL14-mediated m6A modification in osteoporosis.
    Type of Medium: Online Resource
    ISSN: 2157-6564 , 2157-6580
    URL: Article
    DOI: 10.1093/stcltm/szac049
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2642270-0
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  • 6
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    Fluid intake of adults in four Chinese cities
    Oxford University Press (OUP) ; 2012
    In:  Nutrition Reviews Vol. 70 ( 2012-11), p. S105-S110
    Details
    In: Nutrition Reviews, Oxford University Press (OUP), Vol. 70 ( 2012-11), p. S105-S110
    Type of Medium: Online Resource
    ISSN: 0029-6643
    URL: Issue
    URL: Article
    DOI: 10.1111/nure.2012.70.issue-s2
    DOI: 10.1111/j.1753-4887.2012.00520.x
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2012
    detail.hit.zdb_id: 2066844-2
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  • 7
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    Prevalence of Malnutrition, Its Risk Factors, and the Use of Nutrition Support in Patients with Inflammatory Bowel Disease
    Oxford University Press (OUP) ; 2022
    In:  Inflammatory Bowel Diseases Vol. 28, No. Supplement_2 ( 2022-06-02), p. S59-S66
    Details
    In: Inflammatory Bowel Diseases, Oxford University Press (OUP), Vol. 28, No. Supplement_2 ( 2022-06-02), p. S59-S66
    Abstract: Malnutrition is prevalent among patients with inflammatory bowel disease (IBD). Nutritional profiles among Asian patients with IBD have seldom been investigated. We assessed the prevalence of and risk factors for malnutrition, use of nutrition support, and sociopsychological status associated with malnutrition among patients with IBD in China. Methods Patients with ulcerative colitis and Crohn’s disease (CD) recruited from 43 tertiary referral hospitals were screened for malnutrition and nutrient deficiencies in this cross-sectional study. The use of nutrition support was recorded. The sociopsychological status was assessed by subjective questionnaires. Factors associated with malnutrition were analyzed, and multivariate regression was used to determine independent predictors for malnutrition. Results We recruited 1013 patients with a median age of 35.0 years, 58.5% of them had CD, and 61.4% of all patients were male. Overall, 49.5% (n = 501) of patients were diagnosed with malnutrition, including 57.0% of patients with CD, 38.8% of patients with ulcerative colitis, and 44.1% of patients with quiescent or mildly active disease. Nutrient deficiencies were prevalent despite the absence of malnutrition. Malnutrition was associated with adverse sociopsychological status, including decreased social support, higher perceived stress, and impaired quality of life. Moderate to severe disease activity and extensive disease were 2 independent risk factors for malnutrition. In total, 41.6% of patients received nutrition support, and patients with risk factors were more likely to receive nutrition support. Conclusions Malnutrition was highly prevalent and associated with adverse consequences in Chinese patients with IBD. Malnutrition screening and early initiation of nutrition support are essential components in IBD care.
    Type of Medium: Online Resource
    ISSN: 1078-0998 , 1536-4844
    URL: Article
    DOI: 10.1093/ibd/izab345
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
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  • 8
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    Anti-CRISPR AcrIIC5 is a dsDNA mimic that inhibits type II-C Cas9 effectors by blocking PAM recognition
    Oxford University Press (OUP) ; 2023
    In:  Nucleic Acids Research Vol. 51, No. 4 ( 2023-02-28), p. 1984-1995
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 51, No. 4 ( 2023-02-28), p. 1984-1995
    Abstract: Anti-CRISPR proteins are encoded by phages to inhibit the CRISPR-Cas systems of the hosts. AcrIIC5 inhibits several naturally high-fidelity type II-C Cas9 enzymes, including orthologs from Neisseria meningitidis (Nme1Cas9) and Simonsiella muelleri (SmuCas9). Here, we solve the structure of AcrIIC5 in complex with Nme1Cas9 and sgRNA. We show that AcrIIC5 adopts a novel fold to mimic the size and charge distribution of double-stranded DNA, and uses its negatively charged grooves to bind and occlude the protospacer adjacent motif (PAM) binding site in the target DNA cleft of Cas9. AcrIIC5 is positioned into the crevice between the WED and PI domains of Cas9, and one end of the anti-CRISPR interacts with the phosphate lock loop and a linker between the RuvC and BH domains. We employ biochemical and mutational analyses to build a model for AcrIIC5’s mechanism of action, and identify residues on both the anti-CRISPR and Cas9 that are important for their interaction and inhibition. Together, the structure and mechanism of AcrIIC5 reveal convergent evolution among disparate anti-CRISPR proteins that use a DNA-mimic strategy to inhibit diverse CRISPR-Cas surveillance complexes, and provide new insights into a tool for potent inhibition of type II-C Cas9 orthologs.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkad052
    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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  • 9
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    Comparison of accelerated and standard infliximab induction regimens in acute severe ulcerative colitis using propensity score analysis: a retrospective multicenter study in China
    Oxford University Press (OUP) ; 2023
    In:  Gastroenterology Report Vol. 12 ( 2023-12-22)
    Details
    In: Gastroenterology Report, Oxford University Press (OUP), Vol. 12 ( 2023-12-22)
    Abstract: The optimal regimen of infliximab salvage in acute severe ulcerative colitis (ASUC) patients remains controversial. This study aimed to compare accelerated and standard infliximab induction in Chinese ASUC patients, and to explore risk factors and concrete accelerated regimens for them. Methods Data were retrospectively collected from steroid-refractory ASUC patients receiving infliximab as rescue therapy at seven tertiary centers across China. Outcomes including colectomy and clinical remission (Mayo score ≤ 2 and every subscore ≤ 1 at Day 14) rates were compared between patients receiving accelerated and standard infliximab induction using propensity score adjustment for potential confounders. The dose–response relationship was explored by plotting restricted cubic splines. Logistic regression and Cox proportional hazards regression analyses were performed to determine risk factors for adverse outcomes. A systematic review and meta-analysis was also performed. Results A total of 76 patients were analysed: 29 received standard and 47 received accelerated induction. The accelerated group had a higher 90-day colectomy rate (17.8% vs 0%, P = 0.019) and lower clinical remission rate (27.7% vs 65.5%, P = 0.001). After adjusting for propensity score and institution, there was no significant difference in colectomy or clinical remission rates (both P & gt; 0.05). Dose–effect curves showed decreased colectomy hazard with higher cumulative infliximab dosage within 5 days, with no improvement observed for increasing cumulative infliximab dosage within 28 days. Multivariate logistic regression analyses revealed C-reactive protein of & gt;10 mg/L at infliximab initiation (odds ratio = 5.00, 95% confidence interval: 1.27–24.34) as an independent risk factor for no clinical remission. Meta-analysis also revealed no significant difference in colectomy rates at 3 months (P = 0.54). Conclusions After adjusting for confounders, there were no significant differences in colectomy or clinical remission rates between accelerated and standard infliximab induction among ASUC patients. Early administration of an intensified dosage within 5 days may be beneficial. Elevated C-reactive protein at infliximab initiation indicated need for intensive treatment.
    Type of Medium: Online Resource
    ISSN: 2052-0034
    URL: Article
    DOI: 10.1093/gastro/goae051
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2710871-5
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  • 10
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    L -Histidinium Chiral Ionic Liquid Functionalized β-Cyclodextrin as Chiral Selector in Capillary Electrophoresis
    Oxford University Press (OUP) ; 2021
    In:  Journal of Chromatographic Science Vol. 59, No. 4 ( 2021-03-19), p. 388-395
    Details
    In: Journal of Chromatographic Science, Oxford University Press (OUP), Vol. 59, No. 4 ( 2021-03-19), p. 388-395
    Abstract: Nowadays, ionic liquids (ILs) functionalized cyclodextrins (CDs) have drawn increasing attention in chiral separation. Herein, a novel β-CD derivative functionalized by L-histidinium IL, mono-6-deoxy-6-L-histidinium-β-cyclodextrin chloride (L-HMCDCl), was synthesized for the first time and utilized for enantioseparation of nefopam and chlorphenamine in capillary electrophoresis. The L-HMCDCl exhibited superior enantioselectivity compared with native β-CD. The effect of some key parameters such as chiral selector concentration, buffer pH and applied voltage on the enantioseparation was investigated in detail. In the interest of the chiral discrimination mechanism and the enhanced enantioselectivity of L-HMCDCl, molecular modeling with AutoDock was employed to study the interaction, which was in good agreement with experimental results.
    Type of Medium: Online Resource
    ISSN: 0021-9665 , 1945-239X
    URL: Article
    DOI: 10.1093/chromsci/bmaa115
    RVK:
    VA 5045
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2044085-6
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