| 3011. |
- Mattsson, Karin, et al.
(författare)
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Comparison of pre-treatment methods and heavy density liquids to optimize microplastic extraction from natural marine sediments
- 2022
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- The ubiquitous occurrence of anthropogenic particles, including microplastics in the marine environment, has, over the last years, gained worldwide attention. As a result, many methods have been developed to estimate the amount and type of microplastics in the marine environment. However, there are still no standardized protocols for how different marine matrices should be sampled or how to extract and identify these particles, making meaningful data comparison hard. Buoyant microplastics are influenced by winds and currents, and concentrations could hence be expected to be highly variable over time. However, since both high density and most of the initially buoyant microplastics are known to eventually sink and settle on the seafloor, marine sediments are proposed as a suitable matrix for microplastics monitoring. Several principles, apparatuses, and protocols for extracting microplastics from marine sediments have been presented, but extensive comparison of the different steps in the protocols using real environmental samples is lacking. Thus, in this study, different pre-treatment and subsequent density separation protocols for extraction of microplastics from replicate samples of marine sediment were compared. Two pre-treatment methods, one using inorganic chemicals (NaClO+KOH+Na4P2O7) and one using porcine pancreatic enzymes, as well as one with no pre-treatment of the sediment, were compared in combination with two commonly used high-density saline solutions used for density separation, sodium chloride (NaCl) and zinc chloride (ZnCl2). Both pre-treatment methods effectively removed organic matter, and both saline solutions extracted lighter plastic particles such as polyethylene (PE) and polypropylene (PP). The most efficient combination, chemical pre-treatment and density separation with ZnCl2, was found to extract>15 times more particles (≥100µm) from the sediment than other treatment combinations, which could largely be explained by the high presence and efficient extraction of PVC particles. © 2022. The Author(s).
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| 3012. |
- Matula, J, et al.
(författare)
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Resolving complex cartilage structures in developmental biology via deep learning-based automatic segmentation of X-ray computed microtomography images
- 2022
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1, s. 8728-
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Tidskriftsartikel (refereegranskat)abstract
- The complex shape of embryonic cartilage represents a true challenge for phenotyping and basic understanding of skeletal development. X-ray computed microtomography (μCT) enables inspecting relevant tissues in all three dimensions; however, most 3D models are still created by manual segmentation, which is a time-consuming and tedious task. In this work, we utilised a convolutional neural network (CNN) to automatically segment the most complex cartilaginous system represented by the developing nasal capsule. The main challenges of this task stem from the large size of the image data (over a thousand pixels in each dimension) and a relatively small training database, including genetically modified mouse embryos, where the phenotype of the analysed structures differs from the norm. We propose a CNN-based segmentation model optimised for the large image size that we trained using a unique manually annotated database. The segmentation model was able to segment the cartilaginous nasal capsule with a median accuracy of 84.44% (Dice coefficient). The time necessary for segmentation of new samples shortened from approximately 8 h needed for manual segmentation to mere 130 s per sample. This will greatly accelerate the throughput of μCT analysis of cartilaginous skeletal elements in animal models of developmental diseases.
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| 3013. |
- Matveev, V. V., et al.
(författare)
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Investigation of Melts of Polybutylcarbosilane Dendrimers by 1H NMR Spectroscopy
- 2017
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Melts of polybutylcarbosilane (PBC) dendrimers from third (G3) up to sixth (G6) generations are investigated by 1H NMR spectroscopy in a wide temperature range up to 493 K. At room temperature, NMR spectra of G3-G5 dendrimers exhibit resolved, solution-like spectra ("liquid" phase). In contrast, the spectrum of the G6 dendrimer is characterized by a single unresolved broad line at whole temperature range, which supports the presence of an anomalous phase state of G6 at temperatures higher than glass transition temperature. For the first time, an unexpected transition of G5 dendrimer from a molecular liquid state to an anomalous state/phase upon temperature increase has been detected using NMR data. Specifically, an additional wide background line appears in the G5 spectrum above 473 K, and this line corresponds to a G5 state characterized by restricted molecular mobility, i.e., a state similar to the "anomalous" phase of G6 melt. The fraction of the G5 dendrimers in "anomalous" phase at 493 K is approximately 40%. Analysis of the spectral shapes suggests that changes in the G5 dendrimers are reversible with temperature.
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| 3014. |
- Mauritsson, Karl, et al.
(författare)
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A new flexible model for maintenance and feeding expenses that improves description of individual growth in insects
- 2023
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Metabolic theories in ecology interpret ecological patterns at different levels through the lens of metabolism, typically applying allometric scaling to describe energy use. This requires a sound theory for individual metabolism. Common mechanistic growth models, such as ‘von Bertalanffy’, ‘dynamic energy budgets’ and the ‘ontogenetic growth model’ lack some potentially important aspects, especially regarding regulation of somatic maintenance. We develop a model for ontogenetic growth of animals, applicable to ad libitum and food limited conditions, based on an energy balance that expresses growth as the net result of assimilation and metabolic costs for maintenance, feeding and food processing. The most important contribution is the division of maintenance into a ‘non-negotiable’ and a ‘negotiable’ part, potentially resulting in hyperallometric scaling of maintenance and downregulated maintenance under food restriction. The model can also account for effects of body composition and type of growth at the cellular level. Common mechanistic growth models often fail to fully capture growth of insects. However, our model was able to capture empirical growth patterns observed in house crickets.
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| 3015. |
- Mavri, A, et al.
(författare)
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Apixaban concentration variability and relation to clinical outcomes in real-life patients with atrial fibrillation
- 2021
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1, s. 13908-
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Tidskriftsartikel (refereegranskat)abstract
- In some clinical situations, measurements of anticoagulant effect of apixaban may be needed. We investigated the inter- and intra-individual apixaban variability in patients with atrial fibrillation and correlated these results with clinical outcome. We included 62 patients receiving either 5 mg (A5, n = 32) or 2.5 mg (A2.5, n = 30) apixaban twice-daily. We collected three trough and three peak blood samples 6–8 weeks apart. Apixaban concentration was measured by liquid chromatography-tandem mass-spectrometry (LC–MS/MS) and by anti-Xa. Patients on A2.5 were older, had lower creatinine clearance, higher CHA2DS2VASc (4.7 ± 1.0 vs. 3.4 ± 1.7) and lower trough (85 ± 39 vs. 117 ± 53 ng/mL) and peak (170 ± 56 vs. 256 ± 91 ng/mL) apixaban concentrations than patients on A5 (all p < 0.01). In patients on A5, LC–MS/MS showed a significant difference between through levels and between peak levels (p < 0.01). During apixaban treatment, 21 patients suffered bleeding (2 major). There was no association between bleeding and apixaban concentrations or variability. Four patients who suffered thromboembolic event had lower peak apixaban concentrations than patients without it (159 ± 13 vs. 238 ± 88 ng/mL, p = 0.05). We concluded, that there was a significant intra- and inter-individual variability in apixaban trough and peak concentrations. Neither variability nor apixaban concentrations were associated with clinical outcomes.
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| 3016. |
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| 3017. |
- Mayrhofer, Markus, et al.
(författare)
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Rawcopy: Improved copy number analysis with Affymetrix arrays
- 2016
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6, s. 36158-
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Tidskriftsartikel (refereegranskat)abstract
- Microarray data is subject to noise and systematic variation that negatively affects the resolution of copy number analysis. We describe Rawcopy, an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). Noise characteristics of a large number of reference samples are used to estimate log ratio and B-allele frequency for total and allele-specific copy number analysis. Rawcopy achieves better signal-to-noise ratio and higher proportion of validated alterations than commonly used free and proprietary alternatives. In addition, Rawcopy visualizes each microarray sample for assessment of technical quality, patient identity and genome-wide absolute copy number states. Software and instructions are available at http://rawcopy.org.
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| 3018. |
- Mazidi, Mohsen, 1989, et al.
(författare)
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Food Patterns are Associated with Likelihood of CKD in US Adults
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the association between dietary patterns and prevalent chronic kidney diseases (CKD), in participants of the 2005-2012 US National Health and Nutrition Examination Survey (NHANES) conducted between 2005 and 2012, who had measured data on dietary intake and kidney function. Analyse of covariance (ANCOVA) and logistic regression models were employed to account for the survey design and sample weights. A total of 21,649 eligible participants (634 with and 20,015 without prevalent CKD) were included in the final analysis. Three food patterns together explained 50.8% of the variance of the dietary nutrients consumption. The first food pattern was representative of a diet containing high levels of saturated and mono-unsaturated fatty acids; the second food pattern comprised vitamins and trace elements; and the third food pattern was mainly representative of polyunsaturated fatty acids. The odd of prevalent CKD decreased across increasing quarters of vitamins and trace elements, so that the top quarter was associated with a 53% (95%CI: 42-62%) lower odds of CKD in age, sex and race adjusted logistic regression models. These results suggest that vitamins and trace elements intake are associated with lower risk of prevalent CKD.
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| 3019. |
- Mazurkewich, Scott, 1982, et al.
(författare)
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Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae
- 2020
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Chitin is one of the most abundant renewable organic materials found on earth. The chitin utilization locus in Flavobacterium johnsoniae, which encodes necessary proteins for complete enzymatic depolymerization of crystalline chitin, has recently been characterized but no detailed structural information on the enzymes was provided. Here we present protein structures of the F. johnsoniae chitobiase (FjGH20) and chitinase B (FjChiB). FjGH20 is a multi-domain enzyme with a helical domain not before observed in other chitobiases and a domain organization reminiscent of GH84 (beta -N-acetylglucosaminidase) family members. The structure of FjChiB reveals that the protein lacks loops and regions associated with exo-acting activity in other chitinases and instead has a more solvent accessible substrate binding cleft, which is consistent with its endo-chitinase activity. Additionally, small angle X-ray scattering data were collected for the internal 70 kDa region that connects the N- and C-terminal chitinase domains of the unique 158 kDa multi-domain chitinase A (FjChiA). The resulting model of the molecular envelope supports bioinformatic predictions of the region comprising six domains, each with similarities to either Fn3-like or Ig-like domains. Taken together, the results provide insights into chitin utilization by F. johnsoniae and reveal structural diversity in bacterial chitin metabolism.
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| 3020. |
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