| 1. |
- Sarneel, Judith M., et al.
(författare)
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Reading tea leaves worldwide : decoupled drivers of initial litter decomposition mass-loss rate and stabilization
- 2024
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Ingår i: Ecology Letters. - : John Wiley & Sons. - 1461-023X .- 1461-0248. ; 27:5
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Tidskriftsartikel (refereegranskat)abstract
- The breakdown of plant material fuels soil functioning and biodiversity. Currently, process understanding of global decomposition patterns and the drivers of such patterns are hampered by the lack of coherent large-scale datasets. We buried 36,000 individual litterbags (tea bags) worldwide and found an overall negative correlation between initial mass-loss rates and stabilization factors of plant-derived carbon, using the Tea Bag Index (TBI). The stabilization factor quantifies the degree to which easy-to-degrade components accumulate during early-stage decomposition (e.g. by environmental limitations). However, agriculture and an interaction between moisture and temperature led to a decoupling between initial mass-loss rates and stabilization, notably in colder locations. Using TBI improved mass-loss estimates of natural litter compared to models that ignored stabilization. Ignoring the transformation of dead plant material to more recalcitrant substances during early-stage decomposition, and the environmental control of this transformation, could overestimate carbon losses during early decomposition in carbon cycle models.
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| 2. |
- Mondal, I. C., et al.
(författare)
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Organosulfur/Selenium-Based Highly Fluorogenic Molecular Probes for Live-Cell Nucleolus Imaging
- 2022
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Ingår i: Chemistry - An Asian Journal. - : Wiley. - 1861-4728 .- 1861-471X. ; 17:7
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Tidskriftsartikel (refereegranskat)abstract
- We present fluorogenic cationic organo chalcogens that are highly selective to RNA. We have demonstrated that the conformational dynamics and subsequently the optical properties of these dyes can be controlled to facilitate efficient bioimaging. We report the application of organoselenium and organosulfur-based cell-permeable red-emissive probes bearing a favorable cyclic sidearm for selective and high contrast imaging of cell nucleoli. The probes exhibit high quantum yield upon interacting with RNA in an aqueous solution. An in-depth multiscale simulation study reveals that the prominent rotational freezing of the electron-donating sidearm of the probes in the microenvironment of RNA helps in attaining more planar conformation when compared to DNA. It exerts a greater extent of intramolecular charge transfer and hence leads to enhanced fluorescence emission. A systematic structure-interaction relationship study highlighted the impact of heavy-chalcogens toward the improved emissive properties of the probes.
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| 3. |
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| 4. |
- Ramesh, M., et al.
(författare)
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Thiophene-Based Dual Modulators of Aβ and Tau Aggregation
- 2021
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Ingår i: ChemBioChem. - : Wiley. - 1439-4227 .- 1439-7633. ; 22:23, s. 3348-3357
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Tidskriftsartikel (refereegranskat)abstract
- Alzheimer's disease is characterized by the accumulation of amyloid beta (Aβ) and Tau aggregates in the brain, which induces various pathological events resulting in neurodegeneration. There have been continuous efforts to develop modulators of the Aβ and Tau aggregation process to halt or modify disease progression. A few small-molecule-based inhibitors that target both Aβ and Tau pathology have been reported. Here, we report the screening of a targeted library of small molecules to modulate Aβ and Tau aggregation together with their in vitro, in silico and cellular studies. In vitro ThT fluorescence assay, dot blot assay, gel electrophoresis and transmission electron microscopy (TEM) results have shown that thiophene-based lead molecules effectively modulate Aβ aggregation and inhibit Tau aggregation. In silico studies performed by employing molecular docking, molecular dynamics and binding-free energy calculations have helped in understanding the mechanism of interaction of the lead thiophene compounds with Aβ and Tau fibril targets. In cellulo studies revealed that the lead candidate is biocompatible and effectively ameliorates neuronal cells from Aβ and Tau-mediated amyloid toxicity.
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| 5. |
- Choudhury, Chinmayee, et al.
(författare)
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Structure-based drug repurposing : Traditional and advanced AI/ML-aided methods
- 2022
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Ingår i: Drug Discovery Today. - : Elsevier BV. - 1359-6446 .- 1878-5832. ; 27:7, s. 1847-1861
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Forskningsöversikt (refereegranskat)abstract
- The current global health emergency in the form of the Coronavirus 2019 (COVID-19) pandemic has highlighted the need for fast, accurate, and efficient drug discovery pipelines. Traditional drug discovery projects relying on in vitro high-throughput screening (HTS) involve large investments and sophisticated experimental set-ups, affordable only to big biopharmaceutical companies. In this scenario, application of efficient state-of-the-art computational methods and modern artificial intelligence (AI)-based algorithms for rapid screening of repurposable chemical space [approved drugs and natural products (NPs) with proven pharmacokinetic profiles] to identify the initial leads is a powerful option to save resources and time. Structure-based drug repurposing is a popular in silico repurposing approach. In this review, we discuss traditional and modern AI-based computational methods and tools applied at various stages for structure-based drug discovery (SBDD) pipelines. Additionally, we highlight the role of generative models in generating molecules with scaffolds from repurposable chemical space.
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| 6. |
- Dispenza, Clelia, et al.
(författare)
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On the origin of functionalization in one-pot radiation synthesis of nanogels from aqueous polymer solutions
- 2016
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Ingår i: RSC Advances. - : Royal Society of Chemistry. - 2046-2069. ; 6:4, s. 2582-2591
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Tidskriftsartikel (refereegranskat)abstract
- Radiation-engineered poly(N-vinyl pyrrolidone) nanogels are very interesting biocompatible nanocarriers for i.v. administration of therapeutics and contrast agents for bioimaging. The manufacturing process is fast and effective, it grants excellent control of particle size and simultaneous sterilization of the formed nanogels. Interestingly, primary amino groups and carboxyl groups, useful for (bio) conjugation, are also formed in a dose-dependent fashion. In this paper, by means of both numerical simulations and experiments, the origin of nanogel size control and functionalization is investigated. This understanding offers a new dimension for the design and production of radiation-sculptured multifunctional nanocarriers from aqueous solutions of polymers.
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| 7. |
- Murugan, N. A., et al.
(författare)
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Artificial intelligence in virtual screening : Models versus experiments
- 2022
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Ingår i: Drug Discovery Today. - : Elsevier BV. - 1359-6446 .- 1878-5832. ; 27:7, s. 1913-1923
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Forskningsöversikt (refereegranskat)abstract
- A typical drug discovery project involves identifying active compounds with significant binding potential for selected disease-specific targets. Experimental high-throughput screening (HTS) is a traditional approach to drug discovery, but is expensive and time-consuming when dealing with huge chemical libraries with billions of compounds. The search space can be narrowed down with the use of reliable computational screening approaches. In this review, we focus on various machine-learning (ML) and deep-learning (DL)-based scoring functions developed for solving classification and ranking problems in drug discovery. We highlight studies in which ML and DL models were successfully deployed to identify lead compounds for which the experimental validations are available from bioassay studies.
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| 8. |
- Natarajan Arul, Murugan, et al.
(författare)
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How crucial are finite temperature and solvent effects on structure and absorption spectra of Si10?
- 2012
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 116:50, s. 26618-26624
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated finite temperature and solvent effects on the structure, and optical absorption properties of the Si10 cluster, as a model for functionalized clusters used in biomedical applications. Among the many isomers possible for Si10 clusters we have studied tetracapped trigonal prism (TCTP) with C3v symmetry, which previously has been reported to be the global minimum structure, using the Car-Parrinello hybrid QM/MM technique. We observe that Si10 remains to be in the TCTP structure in the gas phase, while in solvents we see dominant population of a distorted TCTP conformer which has a similar structure like TCTP except for one of the surface atoms changing its face center position to the edge. We find that there is frequent conformational transitions between these two structures. In the presence of solvents, the interatomic distances are lowered significantly compared to the case of gas phase. While solvent effects appear not to be very significant for the prediction of the excitation energy in the silicon cluster, we find that temperature effects have a substantial influence on its structure and optical properties.
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