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- Munoz-Gil, G., et al.
(författare)
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Objective comparison of methods to decode anomalous diffusion
- 2021
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Deviations from Brownian motion leading to anomalous diffusion are found in transport dynamics from quantum physics to life sciences. The characterization of anomalous diffusion from the measurement of an individual trajectory is a challenging task, which traditionally relies on calculating the trajectory mean squared displacement. However, this approach breaks down for cases of practical interest, e.g., short or noisy trajectories, heterogeneous behaviour, or non-ergodic processes. Recently, several new approaches have been proposed, mostly building on the ongoing machine-learning revolution. To perform an objective comparison of methods, we gathered the community and organized an open competition, the Anomalous Diffusion challenge (AnDi). Participating teams applied their algorithms to a commonly-defined dataset including diverse conditions. Although no single method performed best across all scenarios, machine-learning-based approaches achieved superior performance for all tasks. The discussion of the challenge results provides practical advice for users and a benchmark for developers. Deviations from Brownian motion leading to anomalous diffusion are ubiquitously found in transport dynamics but often difficult to characterize. Here the authors compare approaches for single trajectory analysis through an open competition, showing that machine learning methods outperform classical approaches.
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- Gaetani, L., et al.
(författare)
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Cerebrospinal fluid neurofilament light chain tracks cognitive impairment in multiple sclerosis
- 2019
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Ingår i: Journal of Neurology. - : Springer Science and Business Media LLC. - 0340-5354 .- 1432-1459. ; 266:9, s. 2157-2163
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Tidskriftsartikel (refereegranskat)abstract
- Background Cognitive impairment (CI) is a disabling symptom of multiple sclerosis (MS). Axonal damage disrupts neural circuits and may play a role in determining CI, but its detection and monitoring are not routinely performed. Cerebrospinal fluid (CSF) neurofilament light chain (NfL) is a promising marker of axonal damage in MS. Objective To retrospectively examine the relationship between CSF NfL and CI in MS patients. Methods CSF NfL concentration was measured in 28 consecutive newly diagnosed MS patients who underwent a neuropsychological evaluation with the Brief Repeatable Battery of Neuropsychological tests (BRBN). Results CSF NfL was higher in patients with overall CI (947.8 +/- 400.7 vs 518.4 +/- 424.7 pg/mL, p < 0.01), and with impairment in information processing speed (IPS) (820.8 +/- 413.6 vs 513.6 +/- 461.4 pg/mL, p < 0.05) and verbal fluency (1292 +/- 511 vs 582.8 +/- 395.4 pg/mL, p < 0.05), and it positively correlated with the number of impaired BRBN tests (r = 0.48, p = 0.01) and cognitive domains (r = 0.47, p = 0.01). Multivariate analyses taking into account potential confounders confirmed these findings. Conclusion CSF NfL is higher in MS patients with CI and impaired IPS and verbal fluency. Large myelinated axons injury, causing neural disconnection, may be an important determinant of CI in MS and can be reliably measured through CSF NfL.
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- Kabakci, Zeynep, et al.
(författare)
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Pharmacophore-guided discovery of CDC25 inhibitors causing cell cycle arrest and tumor regression
- 2019
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- CDC25 phosphatases play a key role in cell cycle transitions and are important targets for cancer therapy. Here, we set out to discover novel CDC25 inhibitors. Using a combination of computational methods, we defined a minimal common pharmacophore in established CDC25 inhibitors and performed virtual screening of a proprietary library. Based on the availability of crystal structures for CDC25A and CDC25B, we implemented a molecular docking strategy and carried out hit expansion/optimization. Enzymatic assays revealed that naphthoquinone scaffolds were the most promising CDC25 inhibitors among selected hits. At the molecular level, the compounds acted through a mixed-type mechanism of inhibition of phosphatase activity, involving reversible oxidation of cysteine residues. In 2D cell cultures, the compounds caused arrest of the cell cycle at the G1/S or at the G2/M transition. Mitotic markers analysis and time-lapse microscopy confirmed that CDK1 activity was impaired and that mitotic arrest was followed by death. Finally, the compounds induced differentiation, accompanied by decreased stemness properties, in intestinal crypt stem cell-derived Apc/K-Ras-mutant mouse organoids, and led to tumor regression and reduction of metastatic potential in zebrafish embryo xenografts used as in vivo model.
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- Lindberg, A., et al.
(författare)
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Cold stress stimulates algae to produce value-added compounds
- 2022
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Ingår i: Bioresource Technology Reports. - : Elsevier. - 2589-014X. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Two cold-tolerant microalgae, Chlorella vulgaris and Scenedesmus sp., were grown at 22 and 5 °C. At the lower temperature, the microalgae showed substantial biochemical and morphological changes. The soluble sugar profile in response to low-temperature cultivation was very different in the two strains. C. vulgaris increased both the sucrose and raffinose family oligosaccharides (RFOs) content at 5 °C while Scenedesmus sp. drastically reduced the sucrose content. Both strains increased the total fatty acid methyl ester (FAME) content when grown at 5 °C. However, the FAME profiles were very different: C. vulgaris mainly increased C18:1 and less so C18:3, while Scenedesmus sp. decreased C18:1 but greatly increased C18:3. The morphology of C. vulgaris changed slightly at the lower temperature, while Scenedesmus sp. showed substantial changes in the size and shape. Low temperature triggered the synthesis of unsaturated fatty acids that are essential for human nutrition.
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- Olsson, Jesper, et al.
(författare)
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Co-digestion of cultivated microalgae and sewage sludge from municipal waste water treatment
- 2014
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Ingår i: Bioresource Technology. - : Elsevier BV. - 0960-8524 .- 1873-2976. ; 171:1, s. 203-210
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Tidskriftsartikel (refereegranskat)abstract
- In this study two wet microalgae cultures and one dried microalgae culture were co-digested in different proportions with sewage sludge in mesophilic and thermophilic conditions. The aim was to evaluate if the co-digestion could lead to an increased efficiency of methane production compared to digestion of sewage sludge alone. The results showed that co-digestion with both wet and dried microalgae, in certain proportions, increased the biochemical methane potential (BMP) compared with digestion of sewage sludge alone in mesophilic conditions. The BMP was significantly higher than the calculated BMP in many of the mixtures. This synergetic effect was statistically significant in a mixture containing 63% (w/w VS based) undigested sewage sludge and 37% (w/w VS based) wet algae slurry, which produced 23% more methane than observed with undigested sewage sludge alone. The trend was that thermophilic co-digestion of microalgae and undigested sewage sludge did not give the same synergy.
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