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  • 1
    In: Database, Oxford University Press (OUP), Vol. 2019 ( 2019-01-01)
    Abstract: Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.
    Type of Medium: Online Resource
    ISSN: 1758-0463
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
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  • 2
    In: World Journal of Urology, Springer Science and Business Media LLC, Vol. 42, No. 1 ( 2024-01-10)
    Type of Medium: Online Resource
    ISSN: 1433-8726
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2024
    detail.hit.zdb_id: 1463303-6
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  • 3
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 382, No. 6674 ( 2023-12)
    Abstract: Dimerization of thymine bases to form a cyclobutane-pyrimidine dimer (CPD) is a common ultraviolet light–induced DNA lesion. Photolyases catalyze light-triggered repair of CPD-DNA, thus contributing to genome stability in many organisms. Combining time-resolved crystallography and computational analyses, we report an atomic visualization of the photolyase-catalyzed DNA repair process. We captured electron transfer at low picoseconds, chemical steps at picoseconds to nanoseconds, active-site recovery at nanoseconds to microseconds, and reannealing of the double-stranded DNA (dsDNA) at submilliseconds, forging new ground in DNA repair, structural biology, and enzymology. RATIONALE Mechanistic models from previous spectroscopic studies set a framework for using time-resolved serial femtosecond crystallography (TR-SFX) to visualize this catalytic process. This technique provides a concise view of not only the repair chemistry but also hitherto unknown postrepair events. RESULTS Two series of TR-SFX experiments were performed, one from picoseconds to nanoseconds and the other from nanoseconds to microseconds (see the figure). Our visualization of the repair of a CPD begins at 100 ps, with Arg 256 (R256) becoming dynamic and moving to stabilize the CPD, which suggests the initiation of the forward electron transfer from the reduced, anionic hydroquinone state of flavin adenine dinucleotide (FADH − ) to the CPD. At 650 ps, the C5–C5′ bond of the CPD is predominantly split, and at 1 ns, the C6–C6′ is likewise split. Recovery of R256, a five-water cluster (5WC), and the FADH − coenzyme occurs during the next 500 ns, returning to their respective resting-state conformations. The repaired thymine bases remain in the active site during this time and then start to return to reanneal with the dsDNA in the microsecond range. The 200-μs structures show the coexistence of a back-flipping intermediate and the reannealed product before its final release from the enzyme. CONCLUSION Our results uncover the atomic mechanism of how DNA photolyases repair DNA in real time. These data reveal an ordered breaking of the covalent C–C bonds and opening of the cyclobutane ring, as well as the concomitant conformational changes of the photolyase and its FAD coenzyme. Defined intermediates were also captured when the enzyme-product complex was recovering and repaired product bases were departing from the active site to pair with their complementary bases in the dsDNA. Elucidation of the main processes and key intermediates in the DNA repair reaction catalyzed by photolyase. Selected intermediates (cyan) of the repair process are overlaid with the structure of the dark state (gray) to illustrate structural changes during catalysis. T7 and T8 are the thymine-7 and thymine-8, the damaged 5′- and 3′-thymines of the CPD lesion in the DNA strand. TT refers to the two thymines together.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2023
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    SSG: 11
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  • 4
    In: Virology Journal, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2023-12-07)
    Abstract: During coronavirus infection, in addition to the well-known coronavirus genomes and subgenomic mRNAs, an abundance of defective viral genomes (DVGs) can also be synthesized. In this study, we aimed to examine whether DVGs can encode proteins in infected cells. Nanopore direct RNA sequencing and liquid chromatography-tandem mass spectrometry (LC–MS/MS) analysis were employed. With the protein databases generated by nanopore direct RNA sequencing and the cell lysates derived from the RNA–protein pull-down assay, six DVG-encoded proteins were identified by LC–MS/MS based on the featured fusion peptides caused by recombination during DVG synthesis. The results suggest that the coronavirus DVGs have the capability to encode proteins. Consequently, future studies determining the biological function of DVG-encoded proteins may contribute to the understanding of their roles in coronavirus pathogenesis and the development of antiviral strategies.
    Type of Medium: Online Resource
    ISSN: 1743-422X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
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  • 5
    In: Journal of Virology, American Society for Microbiology, Vol. 96, No. 10 ( 2022-05-25)
    Abstract: Removal of 5′ cap on cellular mRNAs by the African swine fever virus (ASFV) decapping enzyme g5R protein (g5Rp) is beneficial to viral gene expression during the early stages of infection. As the only nucleoside diphosphate-linked moiety X (Nudix) decapping enzyme encoded in the ASFV genome, g5Rp works in both the degradation of cellular mRNA and the hydrolyzation of the diphosphoinositol polyphosphates. Here, we report the structures of dimeric g5Rp and its complex with inositol hexakisphosphate (InsP 6 ). The two g5Rp protomers interact head to head to form a dimer, and the dimeric interface is formed by extensive polar and nonpolar interactions. Each protomer is composed of a unique N-terminal helical domain and a C-terminal classic Nudix domain. As g5Rp is an mRNA-decapping enzyme, we identified key residues, including K 8 , K 94 , K 95 , K 98 , K 175 , R 221 , and K 243 located on the substrate RNA binding interfaces of g5Rp which are important to RNA binding and decapping enzyme activity. Furthermore, the g5Rp-mediated mRNA decapping was inhibited by InsP 6 . The g5Rp-InsP 6 complex structure showed that the InsP 6 molecules occupy the same regions that primarily mediate g5Rp-RNA interaction, elucidating the roles of InsP 6 in the regulation of the viral decapping activity of g5Rp in mRNA degradation. Collectively, these results provide the structural basis of interaction between RNA and g5Rp and highlight the inhibitory mechanism of InsP 6 on mRNA decapping by g5Rp. IMPORTANCE ASF is a highly contagious hemorrhagic viral disease in domestic pigs which causes high mortality. Currently, there are still no effective vaccines or specific drugs available against this particular virus. The protein g5Rp is the only viral mRNA-decapping enzyme, playing an essential role in the machinery assembly of mRNA regulation and translation initiation. In this study, we solved the crystal structures of g5Rp dimer and complex with InsP 6 . Structure-based mutagenesis studies revealed critical residues involved in a candidate RNA binding region, which also play pivotal roles in complex with InsP 6 . Notably, InsP 6 can inhibit g5Rp activity by competitively blocking the binding of substrate mRNA to the enzyme. Our structure-function studies provide the basis for potential anti-ASFV inhibitor designs targeting the critical enzyme.
    Type of Medium: Online Resource
    ISSN: 0022-538X , 1098-5514
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
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  • 6
    In: Transboundary and Emerging Diseases, Wiley, Vol. 69, No. 4 ( 2022-07)
    Type of Medium: Online Resource
    ISSN: 1865-1674 , 1865-1682
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
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    detail.hit.zdb_id: 2408860-2
    SSG: 22
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  • 7
    In: Human Reproduction, Oxford University Press (OUP), Vol. 37, No. 6 ( 2022-05-30), p. 1297-1310
    Abstract: Are sleep characteristics associated with outcomes of IVF/ICSI treatment? SUMMARY ANSWER Nocturnal sleep & lt;7 h/night and disturbed sleep are related to impaired oocyte and embryo yield, while longer nocturnal sleep might reduce the chance of a successful pregnancy, and the associations between nocturnal sleep duration and IVF/ICSI outcomes are modified by maternal age and subjective sleep quality. WHAT IS KNOWN ALREADY Disturbed sleep and circadian rhythm contribute to impaired fecundity in the general population, but the effects of sleep characteristics on IVF/ICSI outcomes are largely unknown. STUDY DESIGN, SIZE, DURATION This study was conducted among 1276 women undergoing IVF/ICSI treatment between December 2018 and September 2019 based on the Tongji Reproductive and Environmental cohort. Owing to the limited number of multiple cycles, we included only the outcomes of their first IVF/ICSI cycle in the current analysis. PARTICIPANTS/MATERIALS, SETTING, METHODS Data on sleep characteristics were collected via questionnaires on the day of oocyte retrieval. IVF/ICSI outcomes were abstracted from medical records. Quasi-Poisson, quasi-binomial or logistic regression models were used to assess the relations between sleep characteristics and reproductive outcomes after adjusting for relevant confounders. We also performed stratified analyses by subjective sleep quality (good versus poor) and maternal age (≤30 versus & gt;30 years). MAIN RESULTS AND THE ROLE OF CHANCE Compared with women who slept 7 to & lt;8 h/night, those who slept & lt;7 h/night exhibited decreases in the number of retrieved and mature oocytes of 11.5% (95% CI: −21.3%, −0.48%) and 11.9% (95% CI: −22.4%, −0.03%), respectively. A mid-sleep time (MST) earlier than 2:21 a.m. ( & lt;2:21 a.m.) or later than 3:00 a.m. (≥3:00 a.m.) and poor subjective sleep quality were inversely associated with the fertilization rate. Women who had trouble falling asleep more than three times per week had a lower number of mature oocytes (−10.5%, 95% CI: −18.6%, −1.6%), normal fertilized oocytes (−14.8%, 95% CI: −23.7%, −4.8%) and good-quality embryos (−15.1%, 95% CI: −25.4%, −3.5%) than those who had no such trouble. In addition, women who slept 9 to & lt;10 h/night had a lower chance of clinical pregnancy compared to women who slept 7 to & lt;8 h/night (odds ratio = 0.65, 95% CI: 0.44, 0.98). In the stratified analyses, the positive associations of nocturnal sleep duration with the number of good-quality embryos and fertilization rate existed only among the women with poor subjective sleep quality (P for interaction = 0.02 and 0.03, respectively). Additionally, we found that the positive associations of nocturnal sleep duration with implantation or clinical pregnancy only existed among women aged over 30 years (P for interaction = 0.04 and 0.01, respectively). LIMITATIONS, REASONS FOR CAUTION Sleep characteristics are self-reported, which may lead to misclassification. MST serves as a proxy of chronotype and may be non-differentially misclassified resulting in an underestimate of the association of interest. Measuring sleep characteristics on the day of oocyte retrieval may lead to bias. Chance findings cannot be excluded because of the limited number of women with & lt;7 h or ≥10 h nocturnal sleep and multiple testing. Our results may be biased by other confounders and may not be generalizable to women of other ethnicities. WIDER IMPLICATIONS OF THE FINDINGS Unhealthy sleep characteristics, including short nocturnal sleep, inappropriate sleep time, poor subjective sleep quality and having trouble falling asleep, may impair oocyte quantity and its potential to mature or be fertilized. Long nocturnal sleep might reduce the chance of clinical pregnancy among infertile females, especially women younger than 30 years old. Prolonged nocturnal sleep duration may be a potential beneficial behavior for improving IVF/ICSI outcomes for women aged over 30 years and women with poor subjective sleep quality, which requires further investigation. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the National Natural Science Foundation of China (81771654) and the National Key R & D Program of China (No. 2018YFC1004201). There are no conflicts of interest to declare. TRIAL REGISTRATION NUMBER N/A.
    Type of Medium: Online Resource
    ISSN: 0268-1161 , 1460-2350
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
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    detail.hit.zdb_id: 1484864-8
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  • 8
    In: Nature Chemistry, Springer Science and Business Media LLC, Vol. 14, No. 6 ( 2022-06), p. 677-685
    Type of Medium: Online Resource
    ISSN: 1755-4330 , 1755-4349
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2508771-X
    detail.hit.zdb_id: 2464596-5
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  • 9
    Online Resource
    Online Resource
    Elsevier BV ; 2007
    In:  Materials Research Bulletin Vol. 42, No. 11 ( 2007-11), p. 1897-1904
    In: Materials Research Bulletin, Elsevier BV, Vol. 42, No. 11 ( 2007-11), p. 1897-1904
    Type of Medium: Online Resource
    ISSN: 0025-5408
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2007
    detail.hit.zdb_id: 1491970-9
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  • 10
    In: Journal of Virology, American Society for Microbiology, Vol. 93, No. 11 ( 2019-06)
    Abstract: Enterovirus 71 (EV71) infection is generally associated with hand-foot-and-mouth disease (HFMD) and may cause severe neurological disorders and even death. An effective murine oral infection model for studying the pathogenesis of various clinical EV71 isolates is lacking. We developed a transgenic (Tg) mouse that expresses an EV71 receptor, that is, human scavenger receptor class B member 2 (hSCARB2), in a pattern highly similar to that of endogenous murine SCARB2 (mSCARB2) protein. A FLAG-tagged SCARB2 cDNA fragment composed of exons 3 to 12 was inserted into a murine Scarb2 gene-containing bacterial artificial chromosome (BAC) clone, and the resulting transgene was used for establishment of chimeric receptor-expressing Tg mice. Tg mice intragastrically (i.g.) infected with clinical isolates of EV71 showed neurological symptoms, such as ataxia and paralysis, and fatality. There was an age-dependent decrease in susceptibility to viral infection. Pathological characteristics of the infected Tg mice resembled those of encephalomyelitis in human patients. Viral infection was accompanied by microglial activation. Clodronate treatment of the brain slices from Tg mice enhanced viral replication, while lipopolysaccharide treatment significantly inhibited it, suggesting an antiviral role for microglia during EV71 infection. Taken together, this Tg mouse provides a model that closely mimics natural infection for studying EV71 pathogenesis and for evaluating the efficacy of vaccines or other antiviral drugs. IMPORTANCE The availability of a murine model of EV71 infection is beneficial for the understanding of pathogenic mechanisms and the development and assessment of vaccines and antiviral drugs. However, the lack of a murine oral infection model thwarted the study of pathogenesis induced by clinically relevant EV71 strains that are transmitted via the oral-oral or oral-fecal route. Our Tg mice could be intragastrically infected with clinically relevant EV71 strains in an efficient way and developed neurological symptoms and pathological changes strikingly resembling those of human infection. Moreover, these mice showed an age-dependent change in susceptibility that is similar to the human case. This Tg mouse, when combined with the use of other genetically modified mice, potentially contributes to studying the relationship between developmental changes in immunity and susceptibility to virus.
    Type of Medium: Online Resource
    ISSN: 0022-538X , 1098-5514
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2019
    detail.hit.zdb_id: 1495529-5
    detail.hit.zdb_id: 80174-4
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