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  • Oxford University Press (OUP)  (8)
  • Du, Qiang  (8)
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  • Oxford University Press (OUP)  (8)
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  • 1
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 50, No. D1 ( 2022-01-07), p. D27-D38
    Abstract: The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
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  • 2
    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
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
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    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 3
    In: Nucleic Acids Research, Oxford University Press (OUP), ( 2019-11-08)
    Abstract: The National Genomics Data Center (NGDC) provides a suite of database resources to support worldwide research activities in both academia and industry. With the rapid advancements in higher-throughput and lower-cost sequencing technologies and accordingly the huge volume of multi-omics data generated at exponential scales and rates, NGDC is continually expanding, updating and enriching its core database resources through big data integration and value-added curation. In the past year, efforts for update have been mainly devoted to BioProject, BioSample, GSA, GWH, GVM, NONCODE, LncBook, EWAS Atlas and IC4R. Newly released resources include three human genome databases (PGG.SNV, PGG.Han and CGVD), eLMSG, EWAS Data Hub, GWAS Atlas, iSheep and PADS Arsenal. In addition, four web services, namely, eGPS Cloud, BIG Search, BIG Submission and BIG SSO, have been significantly improved and enhanced. 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
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 186809-3
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 4
    In: Human Reproduction, Oxford University Press (OUP), Vol. 38, No. 4 ( 2023-04-03), p. 537-548
    Abstract: Is dietary total antioxidant capacity (DTAC) associated with the odds of developing asthenozoospermia in Chinese men? SUMMARY ANSWER There is no statistically significant association between DTAC indices and the odds of developing asthenozoospermia. WHAT IS KNOWN ALREADY Both diet and oxidative stress may be related to sperm quality; however, few studies have investigated the association between DTAC and sperm quality. STUDY DESIGN, SIZE, DURATION This case–control study was conducted from June 2020 to December 2020. Those diagnosed with asthenozoospermia were assigned to the case group, whereas those with normal sperm parameters were assigned to the control group. Data from a total of 553 cases and 586 controls were included in the final analysis. PARTICIPANTS/MATERIALS, SETTING, METHODS Men who had been referred to the infertility clinic of Shengjing Hospital of China Medical University were enrolled. Dietary intake was assessed using a validated food frequency questionnaire. DTAC was based on ferric-reducing ability of plasma (FRAP), total oxygen radical absorbance capacity (T-ORAC), hydrophilic oxygen radical absorbance capacity (H-ORAC), lipophilic oxygen radical absorbance capacity (L-ORAC), total phenolics (TP), total radical-trapping antioxidant parameter (TRAP), and Trolox equivalent antioxidant capacity (TEAC). Asthenozoospermia was defined according to the criteria published in the fifth edition of the World Health Organization laboratory manual for the examination and processing of human semen. MAIN RESULTS AND THE ROLE OF CHANCE No significant association was observed between the DTAC indices and the odds of asthenozoospermia after multivariable adjustment (T3 vs T1, odds ratio (OR) = 0.99, 95% CI: 0.73–1.33 for FRAP; OR = 1.05, 95% CI: 0.77–1.42 for T-ORAC; OR = 0.88, 95% CI: 0.65–1.18 for H-ORAC; OR = 0.98, 95% CI: 0.71–1.34 for L-ORAC; OR = 1.03, 95% CI: 0.76–1.39 for TP; OR = 1.18, 95% CI: 0.87–1.59 for TRAP; and OR = 1.15, 95% CI: 0.85–1.55 for TEAC). Both additive and multiplicative interaction analyses suggested that smoking might modify the association of T-ORAC with the odds of developing asthenozoospermia (relative excess risk due to interaction = 0.45, 95% CI: 0.07–0.83, attributable proportion due to interaction = 0.46, 95% CI: 0.07–0.84 for additive interaction; P = 0.033 for multiplicative interaction). LIMITATIONS, REASONS FOR CAUTION Recall bias and protopathic bias were inevitable in this retrospective case–control study. The estimation accuracy of the DTAC indices may have also affected the findings. WIDER IMPLICATIONS OF THE FINDINGS To the best of our knowledge, this is the first study to specifically investigate whether an association exists between DTAC and the odds of developing asthenozoospermia. Although no significant association was found, this study provides novel information pertaining to the fields of nutrition and human reproduction. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the JieBangGuaShuai Project of Liaoning Province (2021JH1/10400050), the Shengjing Hospital Clinical Research Project (M0071), and the Outstanding Scientific Fund of Shengjing Hospital (M1150). All authors have no competing interests to disclose. TRIAL REGISTRATION NUMBER N/A.
    Type of Medium: Online Resource
    ISSN: 0268-1161 , 1460-2350
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
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  • 5
    In: Human Molecular Genetics, Oxford University Press (OUP), Vol. 24, No. 19 ( 2015-10-01), p. 5628-5636
    Type of Medium: Online Resource
    ISSN: 0964-6906 , 1460-2083
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
    detail.hit.zdb_id: 1474816-2
    detail.hit.zdb_id: 1108742-0
    SSG: 12
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  • 6
    In: Human Reproduction Open, Oxford University Press (OUP), Vol. 2023, No. 3 ( 2023-06-01)
    Abstract: Are dietary phytochemicals associated with the risk of teratozoospermia? SUMMARY ANSWER Dietary intake of carotene, including total carotene, α-carotene, β-carotene as well as retinol equivalent, and lutein + zeaxanthin, were inversely correlated with the risk of teratozoospermia. WHAT IS KNOWN ALREADY Phytochemicals are natural plant derived bioactive compounds, which have been reported to be potentially associated with male reproductive health. To date, no study has investigated the association between phytochemical intake and the risk of teratozoospermia. STUDY DESIGN, SIZE, DURATION This hospital-based case–control study, which included 146 newly diagnosed teratozoospermia cases and 581 controls with normozoospermia from infertile couples, was conducted in a hospital-based infertility clinic in China, from June 2020 to December 2020. PARTICIPANTS/MATERIALS, SETTING, METHODS Dietary information was collected using a validated semi-quantitative 110-item food frequency questionnaire. Unconditional logistic regression was applied to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for the associations between phytochemical (i.e. phytosterol, carotene, flavonoid, isoflavone, anthocyanidin, lutein + zeaxanthin, and resveratrol) intake and the risk of teratozoospermia. MAIN RESULTS AND THE ROLE OF CHANCE We observed a decreased risk of teratozoospermia for the highest compared with the lowest tertile consumption of total carotene (OR = 0.40, 95% CI = 0.21–0.77), α-carotene (OR = 0.53, 95% CI = 0.30–0.93), β-carotene (OR = 0.47, 95% CI = 0.25–0.88), retinol equivalent (OR = 0.47, 95% CI = 0.24–0.90), and lutein + zeaxanthin (OR = 0.35, 95% CI = 0.19–0.66), with all of the associations showing evident linear trends (all P trend & lt;0.05). In addition, significant dose–response associations were observed between campestanol and α-carotene consumption and the risk of teratozoospermia. Moreover, there was a significant multiplicative interaction between BMI and lutein + zeaxanthin intake (P interaction & lt;0.05). LIMITATIONS, REASONS FOR CAUTION The cases and controls were not a random sample of the entire target population, which could lead to admission rate bias. Nevertheless, the controls were enrolled from the same infertility clinic, which could reduce the bias caused by selection and increase the comparability. Furthermore, our study only included a Chinese population, therefore caution is required regarding generalization of our findings to other populations. WIDER IMPLICATIONS OF THE FINDINGS Dietary phytochemicals, namely carotene, lutein, and zeaxanthin, might exert a positive effect on teratozoospermia. These phytochemicals are common in the daily diet and dietary supplements, and thus may provide a preventive intervention for teratozoospermia. STUDY FUNDING/COMPETING INTERESTS This study was funded by Natural Science Foundation of Liaoning Province (No. 2022-MS-219 to X.B.W.), Outstanding Scientific Fund of Shengjing Hospital (No. M1150 to Q.J.W.), Clinical Research Cultivation Project of Shengjing Hospital (No. M0071 to B.C.P.), and JieBangGuaShuai Project of Liaoning Province (No. 2021JH1/1040050 to Y.H.Z.). All authors declared that there was no conflict of interest. TRIAL REGISTRATION NUMBER N/A.
    Type of Medium: Online Resource
    ISSN: 2399-3529
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2899901-0
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  • 7
    In: Human Reproduction Open, Oxford University Press (OUP), Vol. 2023, No. 3 ( 2023-06-01)
    Abstract: Are dietary fat and fatty acid (FA) intakes related to the odds of asthenozoospermia? SUMMARY ANSWER Plant-based fat consumption was associated with decreased asthenozoospermia odds, while the consumption of animal-based monounsaturated fatty acid (MUFA) was positively related to asthenozoospermia odds. WHAT IS KNOWN ALREADY Dietary fat and FA are significant ingredients of a daily diet, which have been demonstrated to be correlated to the reproductive health of men. However, to date, evidence on fat and FA associations with the odds of asthenozoospermia is unclear. STUDY DESIGN, SIZE, DURATION The hospital-based case–control study was performed in an infertility clinic from June 2020 to December 2020. Briefly, 549 asthenozoospermia cases and 581 controls with normozoospermia were available for final analyses. PARTICIPANTS/MATERIALS, SETTING, METHODS We collected dietary data through a verified food frequency questionnaire of 110 food items. Asthenozoospermia cases were ascertained according to the World Health Organization guidelines. To investigate the correlations of dietary fat and FA consumptions with the odds of asthenozoospermia, we calculated the odds ratios (ORs) and corresponding 95% CIs through unconditional logistic regression models. MAIN RESULTS AND THE ROLE OF CHANCE Relative to the lowest tertile of consumption, the highest tertile of plant-based fat intake was inversely correlated to the odds of asthenozoospermia (OR = 0.68, 95% CI = 0.50–0.91), with a significant dose–response relation (OR = 0.85, 95% CI = 0.75–0.97, per standard deviation increment). Inversely, animal-based MUFA intake (OR = 1.49, 95% CI = 1.04–2.14) was significantly correlated to increased odds of asthenozoospermia, and an evident dose–response relation was also detected (OR = 1.24, 95% CI = 1.05-1.45, per standard deviation increment). Subgroup analyses showed similar patterns of associations to those of the primary results. Moreover, we observed significant interactions on both multiplicative and additive scales between animal-based MUFA and cigarette smoking. LIMITATIONS, REASONS FOR CAUTION Selection bias and recall bias were unavoidable in any of the observational studies. As we failed to obtain the information of trans-fatty acid (TFA) consumption, the relation of TFA intake and asthenozoospermia odds was unclear. WIDER IMPLICATIONS OF THE FINDINGS This study indicated that different sources of fat and FAs might exert different effects on the etiology of asthenozoospermia, and cigarette smoking could exacerbate the adverse effect of high animal-based MUFA intake on asthenozoospermia. Our findings provide novel evidence pertaining to the fields of prevention of asthenozoospermia through decreasing animal-derived fat and FA consumptions and smoking cessation. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the JieBangGuaShuai Project of Liaoning Province, Natural Science Foundation of Liaoning Province, Clinical Research Cultivation Project of Shengjing Hospital, and Outstanding Scientific Fund of Shengjing Hospital. All authors have no conflict of interest to declare. TRIAL REGISTRATION NUMBER N/A.
    Type of Medium: Online Resource
    ISSN: 2399-3529
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2899901-0
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  • 8
    In: Human Reproduction Open, Oxford University Press (OUP), Vol. 2023, No. 4 ( 2023-09-10)
    Abstract: Is dietary non-enzymatic antioxidant capacity related to semen quality? SUMMARY ANSWER The only statistically significant association of semen quality parameters with dietary total antioxidant capacity (DTAC) detected was an inverse association between DTAC and ejaculate volume. WHAT IS KNOWN ALREADY Growing interest exists regarding the role of diet in influencing semen quality. While DTAC is linked to favorable health outcomes, its association with semen quality, especially among men attending infertility clinics, remains understudied. STUDY DESIGN, SIZE, DURATION This cross-sectional study was carried out between June and December of 2020. In total, 1715 participants were included in the final analysis. PARTICIPANTS/MATERIALS, SETTING, METHODS Men who attended an infertility clinic in China were enrolled. Experienced clinical technicians performed the semen analysis. The DTAC indices included the ferric-reducing ability of plasma, oxygen radical absorbance capacity, total reactive antioxidant potential, and Trolox equivalent antioxidant capacity. The quantile regression model was used for multivariate analysis. MAIN RESULTS AND THE ROLE OF CHANCE After adjustment for a variety of confounding variables, a significant inverse association was identified between DTAC and ejaculate volume (βcontinuous FRAP = −0.015, 95% CI = −0.023, −0.006, βT3 vs T1 = −0.193, 95% CI = −0.379, −0.006, Ptrend = 0.007; βcontinuous TRAP = −0.019, 95% CI = −0.041, 0.002, βT3 vs T1 = −0.291, 95% CI = −0.469, −0.112, Ptrend = 0.002). The majority of DTAC indices have no statistically significant association with semen quality parameters. LIMITATIONS, REASONS FOR CAUTION We cannot infer causality because of the nature of the cross-sectional study design. The robustness of the conclusion may be compromised by the exactness of non-enzymatic antioxidant capacity estimation. WIDER IMPLICATIONS OF THE FINDINGS Our findings demonstrated no association between DTAC indices and semen quality parameters among men attending an infertility clinic, except for ejaculate volume. Even though our findings are mostly non-significant, they contribute novel knowledge to the field of study while also laying the groundwork for future well-designed studies. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the JieBangGuaShuai Project of Liaoning Province [grant number 2021JH1/10400050], the Clinical Research Cultivation Project of Shengjing Hospital [grant number M1590] , and the Outstanding Scientific Fund of Shengjing Hospital [grant number M1150]. The sponsors had no role in study design, or in the collection, analysis, and interpretation of data, or in the writing of the report, or in the decision to submit the article for publication. There are no conflicts of interest to declare. TRIAL REGISTRATION NUMBER N/A.
    Type of Medium: Online Resource
    ISSN: 2399-3529
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2899901-0
    Location Call Number Limitation Availability
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