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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
    detail.hit.zdb_id: 2496706-3
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  • 2
    In: Water, MDPI AG, Vol. 15, No. 18 ( 2023-09-11), p. 3227-
    Abstract: To examine the impacts of various straw mulching techniques, this study used the indoor soil column test as the primary research method and the field test as the validation test on the salinity dynamics of saline and alkaline soils. The experiment in this study was designed with five treatments: SC means for straw covered on the soil surface; DB means for straw buried 40 cm below the soil surface; S1D1, S2D1, and S1D2 represent the ratio of soil surface cover to the amount of straw buried 40 cm below the soil surface as 1:1, 2:1, and 1:2, respectively. The results of the indoor soil column test showed that all kinds of straw mulching techniques could effectively reduce soil moisture evaporation, and the straw mulching and deep burial mode was more effective: after 45 days of evaporation, compared with that of CK, the cumulative evaporation of soil moisture were reduced by 29.61%, 27.49%, 37.87%, 65.85%, and 54.58% for SC, DB, S1D1, S2D1, and S1D2, respectively; the straw mulching and deep burial mode could reduce the soil evaporation intensity more effectively than the single-layer straw mulching mode: the mean soil evaporation rates of CK, SC, DB, S1D1, S2D1 and S1D2 after 45 days of evaporation were 1.27 mm/day, 0.90 mm/day, 0.92 mm/day, 0.80 mm/day, 0.43 mm/day, and 0.58 mm/day; various straw mulching techniques could inhibit the accumulation of salts in the surface soil and effectively regulate the distribution of salts in the soil profile, among which the straw mulching and deep burial mode had the best effect of salinity suppression: after 30 days of evaporation, the re-salinization levels of the 0–40 cm soil layer of SC, DB, S1D1, S2D1, and S1D2 were reduced by 66.78%, 43.08%, 33.95%, 92.04% and 45.94% compared with that in the CK, respectively; there was a significant positive correlation between cumulative evaporation of soil moisture and cumulative soil salinity, which implied that cumulative soil salinity increased with the increase in cumulative evaporation of soil moisture. The results of the field experiment justified the results of the indoor soil column test: after four months of evaporation, the field moisture contents of CK, SC, DB, S1D1, S2D1, and S1D2 in the 0–20 cm soil layer were 14.77%, 3.51%, 15.10%, 15.26%, 18.73%, and 2.94%, respectively; during the experimental period, the salt inhibition rate of SC, DB, S1D1, S2D1 and S1D2 in 0–20 cm soil layer were 35.46%, 44.76%, 50.98%, 54.80% and 37.30%, respectively. Therefore, in a comprehensive view, S2D1 treatment had the best effect of salt and vapor suppression on saline soil. This study is of great significance for the resource utilization of straw waste, the improvement of water utilization and efficiency, and the management of soil salinization.
    Type of Medium: Online Resource
    ISSN: 2073-4441
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2521238-2
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  • 3
    In: Microchemical Journal, Elsevier BV, Vol. 160 ( 2021-01), p. 105775-
    Type of Medium: Online Resource
    ISSN: 0026-265X
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2021
    detail.hit.zdb_id: 1471165-5
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  • 4
    In: Cell Regeneration, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2022-11-02)
    Abstract: Intestinal organoids, derived from intestinal stem cell self-organization, recapitulate the tissue structures and behaviors of the intestinal epithelium, which hold great potential for the study of developmental biology, disease modeling, and regenerative medicine. The intestinal epithelium is exposed to dynamic mechanical forces which exert profound effects on gut development. However, the conventional intestinal organoid culture system neglects the key role of mechanical microenvironments but relies solely on biological factors. Here, we show that adding cyclic stretch to intestinal organoid cultures remarkably up-regulates the signature gene expression and proliferation of intestinal stem cells. Furthermore, mechanical stretching stimulates the expansion of SOX9 + progenitors by activating the Wnt/β-Catenin signaling. These data demonstrate that the incorporation of mechanical stretch boosts the stemness of intestinal stem cells, thus benefiting organoid growth. Our findings have provided a way to optimize an organoid generation system through understanding cross-talk between biological and mechanical factors, paving the way for the application of mechanical forces in organoid-based models.
    Type of Medium: Online Resource
    ISSN: 2045-9769
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2682438-3
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  • 5
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 49, No. D1 ( 2021-01-08), p. D86-D91
    Abstract: Long non-coding RNAs (lncRNAs) play important functional roles in many diverse biological processes. However, not all expressed lncRNAs are functional. Thus, it is necessary to manually collect all experimentally validated functional lncRNAs (EVlncRNA) with their sequences, structures, and functions annotated in a central database. The first release of such a database (EVLncRNAs) was made using the literature prior to 1 May 2016. Since then (till 15 May 2020), 19 245 articles related to lncRNAs have been published. In EVLncRNAs 2.0, these articles were manually examined for a major expansion of the data collected. Specifically, the number of annotated EVlncRNAs, associated diseases, lncRNA-disease associations, and interaction records were increased by 260%, 320%, 484% and 537%, respectively. Moreover, the database has added several new categories: 8 lncRNA structures, 33 exosomal lncRNAs, 188 circular RNAs, and 1079 drug-resistant, chemoresistant, and stress-resistant lncRNAs. All records have checked against known retraction and fake articles. This release also comes with a highly interactive visual interaction network that facilitates users to track the underlying relations among lncRNAs, miRNAs, proteins, genes and other functional elements. Furthermore, it provides links to four new bioinformatics tools with improved data browsing and searching functionality. EVLncRNAs 2.0 is freely available at https://www.sdklab-biophysics-dzu.net/EVLncRNAs2/.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    IOS Press ; 2021
    In:  Technology and Health Care Vol. 29 ( 2021-03-25), p. 103-114
    In: Technology and Health Care, IOS Press, Vol. 29 ( 2021-03-25), p. 103-114
    Abstract: BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.
    Type of Medium: Online Resource
    ISSN: 0928-7329 , 1878-7401
    Language: Unknown
    Publisher: IOS Press
    Publication Date: 2021
    detail.hit.zdb_id: 2043772-9
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  • 7
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2016
    In:  Cellular and Molecular Life Sciences Vol. 73, No. 15 ( 2016-8), p. 2949-2957
    In: Cellular and Molecular Life Sciences, Springer Science and Business Media LLC, Vol. 73, No. 15 ( 2016-8), p. 2949-2957
    Type of Medium: Online Resource
    ISSN: 1420-682X , 1420-9071
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
    detail.hit.zdb_id: 1458497-9
    SSG: 12
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  • 8
    In: Sensors and Actuators B: Chemical, Elsevier BV, Vol. 326 ( 2021-01), p. 128991-
    Type of Medium: Online Resource
    ISSN: 0925-4005
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2021
    detail.hit.zdb_id: 1500731-5
    detail.hit.zdb_id: 1021505-0
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  • 9
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2015
    In:  Scientific Reports Vol. 5, No. 1 ( 2015-11-16)
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 5, No. 1 ( 2015-11-16)
    Abstract: The 14-3-3σ proteins are a family of ubiquitous conserved eukaryotic regulatory molecules involved in the regulation of mitogenic signal transduction, apoptotic cell death and cell cycle control. A lot of small-molecule inhibitors have been identified for 14-3-3 protein-protein interactions (PPIs). In this work, we carried out molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method to study the binding mechanism between a 14-3-3σ protein and its eight inhibitors. The ranking order of our calculated binding free energies is in agreement with the experimental results. We found that the binding free energies are mainly from interactions between the phosphate group of the inhibitors and the hydrophilic residues. To improve the binding free energy of Rx group, we designed the inhibitor R9 with group R9 = 4-hydroxypheny. However, we also found that the binding free energy of inhibitor R9 is smaller than that of inhibitor R1. By further using the steer molecular dynamics (SMD) simulations, we identified a new hydrogen bond between the inhibitor R8 and residue Arg64 in the pulling paths. The information obtained from this study may be valuable for future rational design of novel inhibitors and provide better structural understanding of inhibitor binding to 14-3-3σ proteins.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2615211-3
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  • 10
    Online Resource
    Online Resource
    MDPI AG ; 2018
    In:  International Journal of Molecular Sciences Vol. 19, No. 11 ( 2018-11-09), p. 3524-
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 19, No. 11 ( 2018-11-09), p. 3524-
    Abstract: ToxIN is a triangular structure formed by three protein toxins (ToxNs) and three specific noncoding RNA antitoxins (ToxIs). To respond to stimuli, ToxI is preferentially degraded, releasing the ToxN. Thus, the dynamic character is essential in the normal function interactions between ToxN and ToxI. Here, equilibrated molecular dynamics (MD) simulations were performed to study the stability of ToxN and ToxI. The results indicate that ToxI adjusts the conformation of 3′ and 5′ termini to bind to ToxN. Steered molecular dynamics (SMD) simulations combined with the recently developed thermodynamic integration in 3nD (TI3nD) method were carried out to investigate ToxN unbinding from the ToxIN complex. The potentials of mean force (PMFs) and atomistic pictures suggest the unbinding mechanism as follows: (1) dissociation of the 5′ terminus from ToxN, (2) missing the interactions involved in the 3′ terminus of ToxI without three nucleotides (G31, A32, and A33), (3) starting to unfold for ToxI, (4) leaving the binding package of ToxN for three nucleotides of ToxI, (5) unfolding of ToxI. This work provides information on the structure-function relationship at the atomistic level, which is helpful for designing new potent antibacterial drugs in the future.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    Language: English
    Publisher: MDPI AG
    Publication Date: 2018
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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