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  • 1
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    Online Resource
    Molecular ecological network analyses
    Springer Science and Business Media LLC ; 2012
    In:  BMC Bioinformatics Vol. 13, No. 1 ( 2012-12)
    Details
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2012-12)
    Abstract: Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Results Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now ( http://ieg2.ou.edu/MENA ). Conclusions The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.
    Type of Medium: Online Resource
    ISSN: 1471-2105
    URL: Article
    DOI: 10.1186/1471-2105-13-113
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2012
    detail.hit.zdb_id: 2041484-5
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  • 2
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    Discovery of Novel Agents on Spindle Assembly Checkpoint to Sensitize Vinorelbine-Induced Mitotic Cell Death against Human Non-Small Cell Lung Cancers
    MDPI AG ; 2020
    In:  International Journal of Molecular Sciences Vol. 21, No. 16 ( 2020-08-05), p. 5608-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 21, No. 16 ( 2020-08-05), p. 5608-
    Abstract: Non-small cell lung cancer (NSCLC) accounts about 80% of all lung cancers. More than two-thirds of NSCLC patients have inoperable, locally advanced or metastatic tumors. Non-toxic agents that synergistically potentiate cancer-killing activities of chemotherapeutic drugs are in high demand. YL-9 was a novel and non-cytotoxic compound with the structure related to sildenafil but showing much less activity against phosphodiesterase type 5 (PDE5). NCI-H460, an NSCLC cell line with low PDE5 expression, was used as the cell model. YL-9 synergistically potentiated vinorelbine-induced anti-proliferative and apoptotic effects in NCI-H460 cells. Vinorelbine induced tubulin acetylation and Bub1-related kinase (BUBR1) phosphorylation, a necessary component in spindle assembly checkpoint. These effects, as well as BUBR1 cleavage, were substantially enhanced in co-treatment with YL-9. Several mitotic arrest signals were enhanced under combinatory treatment of vinorelbine and YL-9, including an increase of mitotic spindle abnormalities, increased cyclin B1 expression, B-cell lymphoma 2 (Bcl-2) phosphorylation and increased phosphoproteins. Moreover, YL-9 also displayed synergistic activity in combining with vinorelbine to induce apoptosis in A549 cells which express PDE5. In conclusion. the data suggest that YL-9 is a novel agent that synergistically amplifies vinorelbine-induced NSCLC apoptosis through activation of spindle assembly checkpoint and increased mitotic arrest of the cell cycle. YL-9 shows the potential for further development in combinatory treatment against NSCLC.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms21165608
    Language: English
    Publisher: MDPI AG
    Publication Date: 2020
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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  • 3
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    Image_1.tif
    Frontiers Media SA ; 2022
    In:  Frontiers in Oncology Vol. 12 ( 2022-4-22)
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    In: Frontiers in Oncology, Frontiers Media SA, Vol. 12 ( 2022-4-22)
    Abstract: The advantage of adjuvant chemotherapy for upper urinary tract urothelial cancer (UTUC) has been reported, whereas its impact on upper tract cancer with variant histology remains unclear. We aimed to answer the abovementioned question with our real-world data. Design, Setting, and Participants Patients who underwent radical nephroureterectomy (RNU) and were confirmed to have variant UTUC were retrospectively evaluated for eligibility of analysis. In the Taiwan UTUC Collaboration database, we identified 245 patients with variant UTUC among 3,109 patients with UTUC who underwent RNU after excluding patients with missing clinicopathological information. Intervention Those patients with variant UTUC were grouped based on their history of receiving adjuvant chemotherapy or not. Outcome Measurements and Statistical Analysis Propensity score matching was used to reduce the treatment assignment bias. Multivariable Cox regression model was used for the analysis of overall, cancer-specific, and disease-free survival. Results and Limitations For the patients with variant UTUC who underwent adjuvant chemotherapy compared with those without chemotherapy, survival benefit was identified in overall survival in univariate analysis (hazard ratio (HR), 0.527; 95% confidence interval (CI), 0.285–0.973; p = 0.041). In addition, in multivariate analysis, patients with adjuvant chemotherapy demonstrated significant survival benefits in cancer-specific survival (OS; HR, 0.454; CI, 0.208–0.988; p = 0.047), and disease-free survival (DFS; HR, 0.324; 95% CI, 0.155–0.677; ( p = 0.003). The main limitations of the current study were its retrospective design and limited case number. Conclusions Adjuvant chemotherapy following RNU significantly improved cancer-related survivals in patients with UTUC with variant histology.
    Type of Medium: Online Resource
    ISSN: 2234-943X
    URL: Article
    URL: Article
    DOI: 10.3389/fonc.2022.843715
    DOI: 10.3389/fonc.2022.843715.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2649216-7
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  • 4
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    Reproducibility and quantitation of amplicon sequencing-based detection
    Springer Science and Business Media LLC ; 2011
    In:  The ISME Journal Vol. 5, No. 8 ( 2011-8), p. 1303-1313
    Details
    In: The ISME Journal, Springer Science and Business Media LLC, Vol. 5, No. 8 ( 2011-8), p. 1303-1313
    Type of Medium: Online Resource
    ISSN: 1751-7362 , 1751-7370
    URL: Article
    DOI: 10.1038/ismej.2011.11
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
    detail.hit.zdb_id: 2299378-2
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  • 5
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    Patterns and causes of species richness: a general simulation model for macroecology
    Wiley ; 2009
    In:  Ecology Letters Vol. 12, No. 9 ( 2009-09), p. 873-886
    Details
    In: Ecology Letters, Wiley, Vol. 12, No. 9 ( 2009-09), p. 873-886
    Abstract: Understanding the causes of spatial variation in species richness is a major research focus of biogeography and macroecology. Gridded environmental data and species richness maps have been used in increasingly sophisticated curve‐fitting analyses, but these methods have not brought us much closer to a mechanistic understanding of the patterns. During the past two decades, macroecologists have successfully addressed technical problems posed by spatial autocorrelation, intercorrelation of predictor variables and non‐linearity. However, curve‐fitting approaches are problematic because most theoretical models in macroecology do not make quantitative predictions, and they do not incorporate interactions among multiple forces. As an alternative, we propose a mechanistic modelling approach. We describe computer simulation models of the stochastic origin, spread, and extinction of species’ geographical ranges in an environmentally heterogeneous, gridded domain and describe progress to date regarding their implementation. The output from such a general simulation model (GSM) would, at a minimum, consist of the simulated distribution of species ranges on a map, yielding the predicted number of species in each grid cell of the domain. In contrast to curve‐fitting analysis, simulation modelling explicitly incorporates the processes believed to be affecting the geographical ranges of species and generates a number of quantitative predictions that can be compared to empirical patterns. We describe three of the ‘control knobs’ for a GSM that specify simple rules for dispersal, evolutionary origins and environmental gradients. Binary combinations of different knob settings correspond to eight distinct simulation models, five of which are already represented in the literature of macroecology. The output from such a GSM will include the predicted species richness per grid cell, the range size frequency distribution, the simulated phylogeny and simulated geographical ranges of the component species, all of which can be compared to empirical patterns. Challenges to the development of the GSM include the measurement of goodness of fit (GOF) between observed data and model predictions, as well as the estimation, optimization and interpretation of the model parameters. The simulation approach offers new insights into the origin and maintenance of species richness patterns, and may provide a common framework for investigating the effects of contemporary climate, evolutionary history and geometric constraints on global biodiversity gradients. With further development, the GSM has the potential to provide a conceptual bridge between macroecology and historical biogeography.
    Type of Medium: Online Resource
    ISSN: 1461-023X , 1461-0248
    URL: Issue
    URL: Article
    DOI: 10.1111/ele.2009.12.issue-9
    DOI: 10.1111/j.1461-0248.2009.01353.x
    Language: English
    Publisher: Wiley
    Publication Date: 2009
    detail.hit.zdb_id: 2020195-3
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  • 6
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    Random Sampling Process Leads to Overestimation of β-Diversity of Microbial Communities
    American Society for Microbiology ; 2013
    In:  mBio Vol. 4, No. 3 ( 2013-07)
    Details
    In: mBio, American Society for Microbiology, Vol. 4, No. 3 ( 2013-07)
    Abstract: Due to the vast diversity and uncultivated status of the majority of microorganisms, microbial detection, characterization, and quantitation are of great challenge. Although large-scale metagenome sequencing technology such as PCR-based amplicon sequencing has revolutionized the studies of microbial communities, it suffers from several inherent drawbacks, such as a high number of sequencing errors, biases, poor quantitation, and very high percentages of technical variations, which could greatly overestimate microbial biodiversity. Based on general sampling theory, this study provided the first explicit evidence to demonstrate the importance of random sampling processes in estimating microbial β-diversity, which has not been adequately recognized and addressed in microbial ecology. Since most ecological studies are involved in random sampling, the conclusions learned from this study should also be applicable to other ecological studies in general. In summary, the results presented in this study should have important implications for examining microbial biodiversity to address both basic theoretical and applied management questions.
    Type of Medium: Online Resource
    ISSN: 2161-2129 , 2150-7511
    URL: Article
    DOI: 10.1128/mBio.00324-13
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2013
    detail.hit.zdb_id: 2557172-2
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  • 7
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    Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community
    American Society for Microbiology ; 2013
    In:  mBio Vol. 4, No. 2 ( 2013-05)
    Details
    In: mBio, American Society for Microbiology, Vol. 4, No. 2 ( 2013-05)
    Abstract: Microorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of stochastic processes in generating microbial biodiversity is rarely appreciated. Moreover, while microorganisms mediate many ecosystem processes, the relationship between microbial diversity and ecosystem functioning remains largely elusive. Using a well-controlled laboratory system, this study provides empirical support for the dominant role of stochastic assembly in creating variations of microbial diversity and the first explicit evidence for the critical role of community assembly in influencing ecosystem functioning. The results presented in this study represent important contributions to the understanding of the mechanisms, especially stochastic processes, involved in shaping microbial biodiversity.
    Type of Medium: Online Resource
    ISSN: 2161-2129 , 2150-7511
    URL: Article
    DOI: 10.1128/mBio.00584-12
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2013
    detail.hit.zdb_id: 2557172-2
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  • 8
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    Efficacy of Cryoballoon Ablation for Atrial Fibrillation and Recurrence Predictors in an Asian Cohort
    MDPI AG ; 2022
    In:  Journal of Personalized Medicine Vol. 12, No. 5 ( 2022-04-30), p. 732-
    Details
    In: Journal of Personalized Medicine, MDPI AG, Vol. 12, No. 5 ( 2022-04-30), p. 732-
    Abstract: Background: Cryoballoon ablation (CBA) for atrial fibrillation (AF) is a rhythm control procedure used in clinical trials, mostly in Western countries. Its efficacy and the predictors of AF recurrence after CBA remain unclear for Asian populations. We aimed to investigate the efficacy of CBA and the predictors of AF recurrence after CBA in Asian AF patients. Methods: We included consecutive AF patients undergoing CBA for rhythm control between 2014 and 2020. The baseline characteristics, including AF types, symptom severity, and left atrial diameter (LAD), were analyzed. Holter’s monitoring and 12-lead ECG were performed to document AF recurrence. A multivariate Cox hazards regression model was used to evaluate the risk of AF recurrence. Results: A total of 120 AF patients (aged 61.9 ± 9.3 years) were included. The percentage of patients free from AF in the year following CBA was 74.2%. Among the three independent predictors of AF recurrence within one year were the presence of persistent AF (p = 0.025), an LAD ≥ 4.75 cm (p = 0.016), and pre-procedural cardioversion (p = 0.025). All patients survived and none had a stroke after CBA. Conclusion: CBA for AF is an effective and safe procedure in Asian populations. The presence of persistent AF, an LAD ≥ 4.75 cm, and severe symptoms are predictors of AF recurrence in the year following CBA.
    Type of Medium: Online Resource
    ISSN: 2075-4426
    URL: Article
    DOI: 10.3390/jpm12050732
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2662248-8
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  • 9
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    Chalcones Display Anti-NLRP3 Inflammasome Activity in Macrophages through Inhibition of Both Priming and Activation Steps—Structure-Activity-Relationship and Mechanism Studies
    MDPI AG ; 2020
    In:  Molecules Vol. 25, No. 24 ( 2020-12-16), p. 5960-
    Details
    In: Molecules, MDPI AG, Vol. 25, No. 24 ( 2020-12-16), p. 5960-
    Abstract: Chalcones are responsible for biological activity throughout fruits, vegetables, and medicinal plants in preventing and treating a variety of inflammation-related diseases. However, their structure-activity relationship (SAR) in inhibiting inflammasome activation has not been explored. We synthesized numerous chalcones and determined their SAR on lipopolysaccharide (LPS)-primed ATP-induced NLRP3 inflammasome activation. 11Cha1 displayed good inhibitory activity on release reaction of caspase-1, IL-1β, and IL-18. It significantly inhibited LPS-induced phosphorylation and proteolytic degradation of IĸB-α and nuclear translocation of NF-ĸB, but had little effect on mitogen-activated protein kinases (MAPKs) activities. Furthermore, 11Cha1 blocked LPS-induced up-regulation of NLRP3, pro-caspase-1, ASC, IL-18, and IL-1β, indicating the suppression on priming step of inflammasome activation. ASC dimerization and oligomerization are considered to be direct evidence for inflammasome activation. 11Cha1 profoundly inhibited ATP-induced formation of ASC dimers, trimers, and oligomers, and the assembly of ASC, pro-caspase-1, and NLRP3 in inflammasome formation. Decrease of intracellular K+ levels is the common cellular activity elicited by all NLRP3 inflammasome activators. 11Cha1 substantially diminished ATP-mediated K+ efflux, confirming the anti-NLRP3 inflammasome activity of 11Cha1. In summary, the SAR of chalcone derivatives in anti-inflammasome activities was examined. Besides, 11Cha1 inhibited both priming and activation steps of NLRP3 inflammasome activation. It inhibited NF-ĸB activation and subsequently suppressed the up-regulation of NLRP3 inflammasome components including NLRP3, ASC, pro-caspase-1, pro-IL-18, and pro-IL-1β. Next, 11Cha1 blocked ATP-mediated K+ efflux and suppressed the assembly and activation of NLRP3 inflammasome, leading to the inhibition of caspase-1 activation and proteolytic cleavage, maturation, and secretion of IL-1β and IL-18.
    Type of Medium: Online Resource
    ISSN: 1420-3049
    URL: Article
    DOI: 10.3390/molecules25245960
    Language: English
    Publisher: MDPI AG
    Publication Date: 2020
    detail.hit.zdb_id: 2008644-1
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  • 10
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    Use of statistical methods to find the polysaccharide structural characteristics and the relationships between monosaccharide composition ratio and macrophage stimulatory activity of regionally different strains of Lentinula edodes
    Elsevier BV ; 2007
    In:  Analytica Chimica Acta Vol. 584, No. 1 ( 2007-02), p. 50-56
    Details
    In: Analytica Chimica Acta, Elsevier BV, Vol. 584, No. 1 ( 2007-02), p. 50-56
    Type of Medium: Online Resource
    ISSN: 0003-2670
    URL: Article
    DOI: 10.1016/j.aca.2006.10.051
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2007
    detail.hit.zdb_id: 52-8
    detail.hit.zdb_id: 1483436-4
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