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  • Oxford University Press (OUP)  (4)
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  • Oxford University Press (OUP)  (4)
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  • 1
    Online Resource
    Online Resource
    Metabolic RNA labeling for probing RNA dynamics in bacteria
    Oxford University Press (OUP) ; 2020
    In:  Nucleic Acids Research Vol. 48, No. 22 ( 2020-12-16), p. 12566-12576
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 48, No. 22 ( 2020-12-16), p. 12566-12576
    Abstract: Metabolic labeling of RNAs with noncanonical nucleosides that are chemically active, followed by chemoselective conjugation with imaging probes or enrichment tags, has emerged as a powerful method for studying RNA transcription and degradation in eukaryotes. However, metabolic RNA labeling is not applicable for prokaryotes, in which the complexity and distinctness of gene regulation largely remain to be explored. Here, we report 2′-deoxy-2′-azidoguanosine (AzG) as a noncanonical nucleoside compatible with metabolic labeling of bacterial RNAs. With AzG, we develop AIR-seq (azidonucleoside-incorporated RNA sequencing), which enables genome-wide analysis of transcription upon heat stress in Escherichia coli. Furthermore, AIR-seq coupled with pulse-chase labeling allows for global analysis of bacterial RNA degradation. Finally, we demonstrate that RNAs of mouse gut microbiotas can be metabolically labeled with AzG in living animals. The AzG-enabled metabolic RNA labeling should find broad applications in studying RNA biology in various bacterial species.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkaa1111
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure
    Oxford University Press (OUP) ; 2014
    In:  Bioinformatics Vol. 30, No. 14 ( 2014-07-15), p. 2073-2075
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 30, No. 14 ( 2014-07-15), p. 2073-2075
    Abstract: Summary: Correlated mutations constitute a fundamental idea in evolutionary biology, and understanding correlated mutations will, in turn, facilitate an understanding of the genetic mechanisms governing evolution. CorMut is an R package designed to compute correlated mutations in the unit of codon or amino acid mutation. Three classical methods were incorporated, and the computation results can be represented as correlation mutation networks. CorMut also enables the comparison of correlated mutations between two different evolutionary conditions. Availability and implementation: CorMut is released under the GNU General Public License within bioconductor project, and freely available at http://bioconductor.org/packages/release/bioc/html/CorMut.html . Contact:  mal@chinaaids.cn or yshao08@gmail.com
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/btu154
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2014
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Deep learning based on preoperative magnetic resonance (MR) images improves the predictive power of survival models in primary spinal cord astrocytomas
    Oxford University Press (OUP) ; 2023
    In:  Neuro-Oncology Vol. 25, No. 6 ( 2023-06-02), p. 1157-1165
    Details
    In: Neuro-Oncology, Oxford University Press (OUP), Vol. 25, No. 6 ( 2023-06-02), p. 1157-1165
    Abstract: Prognostic models for spinal cord astrocytoma patients are lacking due to the low incidence of the disease. Here, we aim to develop a fully automated deep learning (DL) pipeline for stratified overall survival (OS) prediction based on preoperative MR images. Methods A total of 587 patients diagnosed with intramedullary tumors were retrospectively enrolled in our hospital to develop an automated pipeline for tumor segmentation and OS prediction. The automated pipeline included a T2WI-based tumor segmentation model and 3 cascaded binary OS prediction models (1-year, 3-year, and 5-year models). For the tumor segmentation model, 439 cases of intramedullary tumors were used to model training and testing using a transfer learning strategy. A total of 138 patients diagnosed with astrocytomas were included to train and test the OS prediction models via 10 × 10-fold cross-validation using CNNs. Results The dice of the tumor segmentation model with the test set was 0.852. The results indicated that the best input of OS prediction models was a combination of T2W and T1C images and the tumor mask. The 1-year, 3-year, and 5-year automated OS prediction models achieved accuracies of 86.0%, 84.0%, and 88.0% and AUCs of 0.881 (95% CI 0.839–0.918), 0.862 (95% CI 0.827–0.901), and 0.905 (95% CI 0.867–0.942), respectively. The automated DL pipeline achieved 4-class OS prediction ( & lt;1 year, 1–3 years, 3–5 years, and & gt;5 years) with 75.3% accuracy. Conclusions We proposed an automated DL pipeline for segmenting spinal cord astrocytomas and stratifying OS based on preoperative MR images.
    Type of Medium: Online Resource
    ISSN: 1522-8517 , 1523-5866
    URL: Article
    DOI: 10.1093/neuonc/noac280
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2094060-9
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  • 4
    Online Resource
    Online Resource
    Rationale and Design of a Cluster Randomized Trial of a Village Doctor-Led Intervention on Hypertension Control in China
    Oxford University Press (OUP) ; 2021
    In:  American Journal of Hypertension Vol. 34, No. 8 ( 2021-08-09), p. 831-839
    Details
    In: American Journal of Hypertension, Oxford University Press (OUP), Vol. 34, No. 8 ( 2021-08-09), p. 831-839
    Abstract: In China, hypertension prevalence is high and increasing while the control rate is low, especially in rural areas. Traditionally, village doctors play an important role in infectious disease control and delivering essential health services to rural residents. We aim to test the effectiveness of a village doctor-led multifaceted intervention compared with usual care on blood pressure (BP) control and cardiovascular disease (CVD) among rural residents with hypertension in China. METHODS In the China Rural Hypertension Control Project (CRHCP), a cluster randomized trial, 163 villages were randomly assigned to the village doctor-led intervention and 163 villages to control. A total of 33,995 individuals aged ≥40 years with an untreated BP ≥140/90 mm Hg or treated BP ≥130/80 mm Hg or with an untreated BP ≥130/80 mm Hg and a history of clinical CVD were recruited into the study. The village doctor-led multifaceted intervention is designed to overcome barriers at the healthcare system, provider, patient, and community levels. Village doctors receive training on standard BP measurement, protocol-based hypertension treatment, and health coaching. They also receive technical support and supervision from hypertension specialists/primary care physicians and performance-based financial incentives. Study participants receive health coaching on home BP monitoring, lifestyle changes, and adherence to medications. The primary outcome is BP control ( & lt;130/80 mm Hg) at 18 months in phase 1 and CVD events over 36 months in phase 2. CONCLUSIONS The CRHCP will provide critically important data on the effectiveness, implementation, and sustainability of a hypertension control strategy in rural China for reducing the BP-related CVD burden. CLINICAL TRIALS REGISTRATION Trial Number NCT03527719.
    Type of Medium: Online Resource
    ISSN: 0895-7061 , 1941-7225
    URL: Article
    DOI: 10.1093/ajh/hpab038
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1479505-X
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