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  • Oxford University Press (OUP)  (9)
  • 2020-2024  (9)
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  • Oxford University Press (OUP)  (9)
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  • 2020-2024  (9)
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  • 1
    Online Resource
    Online Resource
    Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021
    Oxford University Press (OUP) ; 2021
    In:  Nucleic Acids Research Vol. 49, No. D1 ( 2021-01-08), p. D18-D28
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 49, No. D1 ( 2021-01-08), p. D18-D28
    Abstract: The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching its core database resources through big data deposition, integration and translation. In the past year, considerable efforts have been devoted to 2019nCoVR, a newly established resource providing a global landscape of SARS-CoV-2 genomic sequences, variants, and haplotypes, as well as Aging Atlas, BrainBase, GTDB (Glycosyltransferases Database), LncExpDB, and TransCirc (Translation potential for circular RNAs). Meanwhile, a series of resources have been updated and improved, including BioProject, BioSample, GWH (Genome Warehouse), GVM (Genome Variation Map), GEN (Gene Expression Nebulas) as well as several biodiversity and plant resources. Particularly, BIG Search, a scalable, one-stop, cross-database search engine, has been significantly updated by providing easy access to a large number of internal and external biological resources from CNCB-NGDC, our partners, EBI and NCBI. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkaa1022
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1472175-2
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  • 2
    Online Resource
    Online Resource
    Energetic transients joint analysis system for multi-INstrument (ETJASMIN) for GECAM – I. Positional, temporal, and spectral analyses
    Oxford University Press (OUP) ; 2022
    In:  Monthly Notices of the Royal Astronomical Society Vol. 514, No. 2 ( 2022-06-17), p. 2397-2406
    Details
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 514, No. 2 ( 2022-06-17), p. 2397-2406
    Abstract: Gravitational wave high-energy Electromagnetic Counterpart All-sky Monitor (GECAM) is a dedicated mission, launched in December 2020, for gamma-ray transients, including gamma-ray bursts (GRBs) and soft gamma repeater (SGR) bursts in the multimessenger and multiwavelength astronomy era. Since GECAM consists of two independent spacecrafts (or say instruments), and the framework of data analysis for multiple spacecrafts is distinctive from that for only one spacecraft, which is the case for most GRB missions, we developed a dedicated pipeline called Energetic Transients Joint Analysis System for Multi-INstrument (ETJASMIN) for GECAM mission. This pipeline has been naturally extended to incorporate data from other gamma-ray instruments, including the operating missions, such as Insight-HXMT/HE, Fermi/GBM, Swift/BAT, INTEGRAL/SPI-ACS, Konus-Wind, and GRID, as well as the forthcoming missions, such as SVOM/GRM and HEBS. In this paper, we present this pipeline with a focus on the data analysis procedures, methodology, and results in terms of the localization, verification (classification), spectral, and temporal analyses of gamma-ray transients. We show that this pipeline could provide more accurate, reliable, and comprehensive results than that of individual spacecraft, which is beneficial for gamma-ray transients observation.
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    URL: Article
    DOI: 10.1093/mnras/stac999
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2016084-7
    SSG: 16,12
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  • 3
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    Discovery of the linear energy dependence of the spectral lag of X-ray bursts from SGR J1935+2154
    Oxford University Press (OUP) ; 2023
    In:  Monthly Notices of the Royal Astronomical Society Vol. 521, No. 4 ( 2023-03-31), p. 5308-5333
    Details
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 521, No. 4 ( 2023-03-31), p. 5308-5333
    Abstract: Spectral lag of the low-energy photons with respect to the high-energy ones is a common astrophysical phenomenon (such as gamma-ray bursts and the Crab Pulsar) and may serve as a key probe to the underlying radiation mechanism. However, spectral lag in keV range of the magnetar bursts has not been systematically studied yet. In this work, we perform a detailed spectral lag analysis with the Li et al.’s Cross-Correlation Function (Li-CCF) method for SGR J1935+2154 bursts observed by Insight-Hard X-ray Modulation Telescope (HXMT), Gravitational Wave High-energy Electromagnetic Counterpart All-sky Monitor (GECAM), and Fermi/Gamma-ray Burst Monitor (GBM) from 2014 July to 2022 January. We discover that the spectral lags of about 61 per cent (non-zero significance & gt;1σ) bursts from SGR J1935+2154 are linearly dependent on the photon energy (E) with tlag(E) = α(E/keV) + C, which may be explained by a linear change of the temperature of the blackbody-emitting plasma with time. The distribution of the slope (α) approximately follows a Gaussian function with mean and standard deviation of 0.02 ms keV−1 (i.e. high-energy photons arrive earlier) and 0.02 ms keV−1, respectively. We also find that the distribution can be well fitted with three Gaussians with mean values of ∼−10.009, 0.013, and 0.039 ms keV−1, which may correspond to different origins of the bursts. These spectral lag features may have important implications on the magnetar bursts.
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    URL: Article
    DOI: 10.1093/mnras/stad885
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2016084-7
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  • 4
    Online Resource
    Online Resource
    Ground-based calibration and characterization of LaBr3-SiPM-based gamma-ray detector on GECAM satellite: 8–160 keV
    Oxford University Press (OUP) ; 2023
    In:  Monthly Notices of the Royal Astronomical Society Vol. 525, No. 3 ( 2023-09-01), p. 3399-3412
    Details
    In: Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP), Vol. 525, No. 3 ( 2023-09-01), p. 3399-3412
    Abstract: As the main detector of the Gravitational wave high-energy Electromagnetic Counterpart All-sky Monitor mission (GECAM), the calibration of the energy response and detection efficiency of the gamma-ray detector (GRD) is the main content of the ground-based calibration. This article mainly focuses on the calibration of the energy response and detection efficiency in the 8–160 keV with a refined measurement around the absorption edges of the lanthanum bromide crystal ($\rm {LaBr_3}$). The GRD performances for different crystal types, data acquisition modes, working modes, and incident positions are also analysed in detail. We show that the calibration campaign is comprehensive, the detector performance meets the flight requirements, and the calibration results generally agree with simulations as expected. The detector’s model was corrected by the ground-based calibration, which led to the establishment of the calibration data base.
    Type of Medium: Online Resource
    ISSN: 0035-8711 , 1365-2966
    URL: Article
    DOI: 10.1093/mnras/stad2439
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2016084-7
    SSG: 16,12
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  • 5
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    Macrophage NFATc3 prevents foam cell formation and atherosclerosis: evidence and mechanisms
    Oxford University Press (OUP) ; 2021
    In:  European Heart Journal Vol. 42, No. 47 ( 2021-12-14), p. 4847-4861
    Details
    In: European Heart Journal, Oxford University Press (OUP), Vol. 42, No. 47 ( 2021-12-14), p. 4847-4861
    Abstract: Our previous study demonstrated that Ca2+ influx through the Orai1 store-operated Ca2+ channel in macrophages contributes to foam cell formation and atherosclerosis via the calcineurin–ASK1 pathway, not the classical calcineurin–nuclear factor of activated T-cell (NFAT) pathway. Moreover, up-regulation of NFATc3 in macrophages inhibits foam cell formation, suggesting that macrophage NFATc3 is a negative regulator of atherogenesis. Hence, this study investigated the precise role of macrophage NFATc3 in atherogenesis. Methods and results Macrophage-specific NFATc3 knockout mice were generated to determine the effect of NFATc3 on atherosclerosis in a mouse model of adeno-associated virus-mutant PCSK9-induced atherosclerosis. NFATc3 expression was decreased in macrophages within human and mouse atherosclerotic lesions. Moreover, NFATc3 levels in peripheral blood mononuclear cells from atherosclerotic patients were negatively associated with plaque instability. Furthermore, macrophage-specific ablation of NFATc3 in mice led to the atherosclerotic plaque formation, whereas macrophage-specific NFATc3 transgenic mice exhibited the opposite phenotype. NFATc3 deficiency in macrophages promoted foam cell formation by potentiating SR-A- and CD36-meditated lipid uptake. NFATc3 directly targeted and transcriptionally up-regulated miR-204 levels. Mature miR-204-5p suppressed SR-A expression via canonical regulation. Unexpectedly, miR-204-3p localized in the nucleus and inhibited CD36 transcription. Restoration of miR-204 abolished the proatherogenic phenotype observed in the macrophage-specific NFATc3 knockout mice, and blockade of miR-204 function reversed the beneficial effects of NFATc3 in macrophages. Conclusion Macrophage NFATc3 up-regulates miR-204 to reduce SR-A and CD36 levels, thereby preventing foam cell formation and atherosclerosis, indicating that the NFATc3/miR-204 axis may be a potential therapeutic target against atherosclerosis.
    Type of Medium: Online Resource
    ISSN: 0195-668X , 1522-9645
    URL: Article
    DOI: 10.1093/eurheartj/ehab660
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2001908-7
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  • 6
    Online Resource
    Online Resource
    Characterization of Changes and Driver Microbes in Gut Microbiota During Healthy Aging Using a Captive Monkey Model
    Oxford University Press (OUP) ; 2022
    In:  Genomics, Proteomics & Bioinformatics Vol. 20, No. 2 ( 2022-04-01), p. 350-365
    Details
    In: Genomics, Proteomics & Bioinformatics, Oxford University Press (OUP), Vol. 20, No. 2 ( 2022-04-01), p. 350-365
    Abstract: Recent population studies have significantly advanced our understanding of how age shapes the gut microbiota. However, the actual role of age could be inevitably confounded due to the complex and variable environmental factors in human populations. A well-controlled environment is thus necessary to reduce undesirable confounding effects, and recapitulate age-dependent changes in the gut microbiota of healthy primates. Herein we performed 16S rRNA gene sequencing, characterized the age-associated gut microbial profiles from infant to elderly crab-eating macaques reared in captivity, and systemically revealed the lifelong dynamic changes of the primate gut microbiota. While the most significant age-associated taxa were mainly found as commensals such as Faecalibacterium, the abundance of a group of suspicious pathogens such as Helicobacter was exclusively increased in infants, underlining their potential role in host development. Importantly, topology analysis indicated that the network connectivity of gut microbiota was even more age-dependent than taxonomic diversity, and its tremendous decline with age could probably be linked to healthy aging. Moreover, we identified key driver microbes responsible for such age-dependent network changes, which were further linked to altered metabolic functions of lipids, carbohydrates, and amino acids, as well as phenotypes in the microbial community. The current study thus demonstrates the lifelong age-dependent changes and their driver microbes in the primate gut microbiota, and provides new insights into their roles in the development and healthy aging of their hosts.
    Type of Medium: Online Resource
    ISSN: 1672-0229 , 2210-3244
    URL: Article
    DOI: 10.1016/j.gpb.2021.09.009
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2233708-8
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  • 7
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    Distribution and prognostic impact of M1 macrophage on esophageal squamous cell carcinoma
    Oxford University Press (OUP) ; 2021
    In:  Carcinogenesis Vol. 42, No. 4 ( 2021-04-30), p. 537-545
    Details
    In: Carcinogenesis, Oxford University Press (OUP), Vol. 42, No. 4 ( 2021-04-30), p. 537-545
    Abstract: Macrophages are a double-edged sword with potential cancer-promoting and anticancer effects. Controversy remains regarding the effect of macrophages, especially M1 macrophages, on tumor promotion and suppression. We aimed to investigate the role of M1 macrophages in the occurrence and progression of esophageal squamous cell carcinoma (ESCC). Analyzing the data in Gene Expression Omnibus database by the CIBERSORT algorithm found that M1 macrophages were one of the important components of many immune cells in ESCCs, and the increase in their number was obviously negatively correlated with tumor T staging. This result was verified by our experimental data: the density of CD68/HLA-DR double-stained M1 macrophages in ESCC tumor nest and tumor stroma was significantly higher than that in cancer-adjacent normal (CAN) tissues. The density of M1 macrophages in ESCC tumor nest was negatively correlated with the patient’s lymph node metastasis and clinical stage (P & lt; 0.05), and the negative tendency was more obvious for M1 macrophages in ESCC tumor stroma (P & lt; 0.001). Exposure to M1 macrophage-conditioned medium inhibited ESCC cell migration and invasion ability significantly (P & lt; 0.05). Moreover, the increased M1 macrophage density in ESCC tumor stroma correlated positively with good prognosis of ESCC. M1 macrophages were involved in inhibiting ESCC cell migration and invasion, which could serve as a good prognostic factor in patients with ESCC.
    Type of Medium: Online Resource
    ISSN: 0143-3334 , 1460-2180
    URL: Article
    DOI: 10.1093/carcin/bgaa128
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1474206-8
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  • 8
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    Early cardiac involvement in patients with acute COVID-19 infection identified by multiparametric cardiovascular magnetic resonance imaging
    Oxford University Press (OUP) ; 2021
    In:  European Heart Journal - Cardiovascular Imaging Vol. 22, No. 8 ( 2021-07-20), p. 844-851
    Details
    In: European Heart Journal - Cardiovascular Imaging, Oxford University Press (OUP), Vol. 22, No. 8 ( 2021-07-20), p. 844-851
    Abstract: In order to determine acute cardiac involvement in patients with COVID-19, we quantitatively evaluated tissue characteristics and mechanics by non-invasive cardiac magnetic resonance (CMR) in a cohort of patients within the first 10 days of the onset of COVID symptoms. Methods and results Twenty-five patients with reverse transcription polymerase chain reaction confirmed COVID-19 and at least one marker of cardiac involvement [cardiac symptoms, abnormal electrocardiograph (ECG), or abnormal cardiac biomarkers] and 25 healthy age- and gender-matched control subjects were recruited to the study. Patients were divided into those with elevated (n = 8) or normal TnI (n = 17). There were significant differences in global longitudinal strain among patients who were positive and negative for hs-TnI, and controls [−12.3 (−13.3, −11.5)%, −13.1 (−14.2, −9.8)%, and −15.7 (−18.3, −12.7)%, P = 0.004] . Native myocardial T1 relaxation times in patients with positive and negative hs-TnI manifestation (1169.8 ± 12.9 and 1113.2 ± 31.2 ms) were significantly higher than the normal (1065 ± 57 ms) subjects, respectively (P  & lt; 0.001). The extracellular volume (ECV) of patients who were positive and negative for hs-TnI was higher than that of the normal controls [32 (31, 33)%, 29 (27, 30)%, and 26 (24, 27.5)%, P  & lt; 0.001]. In our study, quantitative T2 mapping in patients who were positive and negative for hs-TnI [51 (47.9, 52.8) and 48 (47, 49.4) ms] was significantly higher than the normal [42 (41, 45.2) ms] subjects (P  & lt; 0.001). Conclusion In patients with early-stage COVID-19, myocardial oedema, and functional abnormalities are a frequent finding, while irreversible regional injury such as necrosis may be infrequent.
    Type of Medium: Online Resource
    ISSN: 2047-2404 , 2047-2412
    URL: Article
    DOI: 10.1093/ehjci/jeab042
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2042482-6
    detail.hit.zdb_id: 2647943-6
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  • 9
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    Endoscopic management of delayed bleeding after polypectomy of small colorectal polyps: two or more clips may be safe
    Oxford University Press (OUP) ; 2022
    In:  Gastroenterology Report Vol. 10 ( 2022-01-25)
    Details
    In: Gastroenterology Report, Oxford University Press (OUP), Vol. 10 ( 2022-01-25)
    Abstract: The resection of small colorectal polyps (≤10 mm) is routine for endoscopists. However, the management of one of its main complications, namely delayed (within 14 days) postpolypectomy bleeding (DPPB), has not been clearly demonstrated. We aimed to assess the role of coloscopy in the management of DPPB from small colorectal polyps and identify the associated factors for initial hemostatic success. Methods We conducted a retrospective study of 69 patients who developed DPPB after the removal of colorectal polyps of ≤10 mm and underwent hemostatic colonoscopy at the Sixth Affiliated Hospital of Sun Yat-sen University (Guangzhou, China) between April 2013 and June 2021. Demographics, clinical variables, and colonoscopic features were collected independently. We applied univariate and multivariate analyses to assess factors associated with initial hemostatic success. Results General colonoscopy without oral bowel preparation was successfully performed in all the patients, with a median duration of 23.9 (12.5–37.9) minutes. Among 69 patients, 62 (89.9%) achieved hemostasis after initial hemostatic colonoscopy and 7 (10.1%) rebled 2.7 ± 1.1 days after initial colonoscopic hemostasis and had rebleeding successfully controlled by one additional colonoscopy. No colonoscopy-related adverse events occurred. Multivariate analysis showed that management with at least two clips was the only independent prognostic factor for initial hemostatic success (odds ratio, 0.17; 95% confidence interval, 0.03–0.91; P = 0.04). All the patients who had at least two clips placed at the initial hemostatic colonoscopy required no further hemostatic intervention. Conclusions Colonoscopy is a safe, effective, and not too time-consuming approach for the management of patients with DPPB of small colorectal polyps and management with the placement of at least two hemoclips may be beneficial.
    Type of Medium: Online Resource
    ISSN: 2052-0034
    URL: Article
    DOI: 10.1093/gastro/goab051
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2710871-5
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