| 1. |
- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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| 2. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 3. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 4. |
- Axfors, Cathrine, et al.
(author)
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Association between convalescent plasma treatment and mortality in COVID-19 : a collaborative systematic review and meta-analysis of randomized clinical trials
- 2021
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In: BMC Infectious Diseases. - : BioMed Central (BMC). - 1471-2334. ; 21:1
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Research review (peer-reviewed)abstract
- Background: Convalescent plasma has been widely used to treat COVID-19 and is under investigation in numerous randomized clinical trials, but results are publicly available only for a small number of trials. The objective of this study was to assess the benefits of convalescent plasma treatment compared to placebo or no treatment and all-cause mortality in patients with COVID-19, using data from all available randomized clinical trials, including unpublished and ongoing trials (Open Science Framework, ). Methods: In this collaborative systematic review and meta-analysis, clinical trial registries (ClinicalTrials.gov, WHO International Clinical Trials Registry Platform), the Cochrane COVID-19 register, the LOVE database, and PubMed were searched until April 8, 2021. Investigators of trials registered by March 1, 2021, without published results were contacted via email. Eligible were ongoing, discontinued and completed randomized clinical trials that compared convalescent plasma with placebo or no treatment in COVID-19 patients, regardless of setting or treatment schedule. Aggregated mortality data were extracted from publications or provided by investigators of unpublished trials and combined using the Hartung-Knapp-Sidik-Jonkman random effects model. We investigated the contribution of unpublished trials to the overall evidence. Results: A total of 16,477 patients were included in 33 trials (20 unpublished with 3190 patients, 13 published with 13,287 patients). 32 trials enrolled only hospitalized patients (including 3 with only intensive care unit patients). Risk of bias was low for 29/33 trials. Of 8495 patients who received convalescent plasma, 1997 died (23%), and of 7982 control patients, 1952 died (24%). The combined risk ratio for all-cause mortality was 0.97 (95% confidence interval: 0.92; 1.02) with between-study heterogeneity not beyond chance (I-2 = 0%). The RECOVERY trial had 69.8% and the unpublished evidence 25.3% of the weight in the meta-analysis. Conclusions: Convalescent plasma treatment of patients with COVID-19 did not reduce all-cause mortality. These results provide strong evidence that convalescent plasma treatment for patients with COVID-19 should not be used outside of randomized trials. Evidence synthesis from collaborations among trial investigators can inform both evidence generation and evidence application in patient care.
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| 5. |
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| 6. |
- Eichhorn, S. J., et al.
(author)
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Current international research into cellulose as a functional nanomaterial for advanced applications
- 2022
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In: Journal of Materials Science. - : Springer Nature. - 0022-2461 .- 1573-4803. ; 57:10, s. 5697-5767
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Journal article (peer-reviewed)abstract
- This review paper provides a recent overview of current international research that is being conducted into the functional properties of cellulose as a nanomaterial. A particular emphasis is placed on fundamental and applied research that is being undertaken to generate applications, which are now becoming a real prospect given the developments in the field over the last 20 years. A short introduction covers the context of the work, and definitions of the different forms of cellulose nanomaterials (CNMs) that are most widely studied. We also address the terminology used for CNMs, suggesting a standard way to classify these materials. The reviews are separated out into theme areas, namely healthcare, water purification, biocomposites, and energy. Each section contains a short review of the field within the theme and summarizes recent work being undertaken by the groups represented. Topics that are covered include cellulose nanocrystals for directed growth of tissues, bacterial cellulose in healthcare, nanocellulose for drug delivery, nanocellulose for water purification, nanocellulose for thermoplastic composites, nanocellulose for structurally colored materials, transparent wood biocomposites, supercapacitors and batteries.
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| 11. |
- Massironi, A., et al.
(author)
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Valorization of pumpkin seed hulls, cucurbitin extraction strategies and their comparative life cycle assessment
- 2023
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In: Journal of Cleaner Production. - : Elsevier BV. - 0959-6526 .- 1879-1786. ; 427
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Journal article (peer-reviewed)abstract
- In most cases, final agricultural products such as vegetables, fruits, and cereals are associated with the industrial generation of byproducts that are usually unexploited to express all their potential value or, in the worst but common case, directly disposed of as wastes. Even after industrial processing, plant biomasses still represent an invaluable source of unique and human-useful compounds. Within the circular economy, the valorization of industrial wasted biomasses is considered an opportunity to provide new higher-value products with a concomitant solution to waste accumulation issues. In this framework, pointing to circularity, the seed hulls industrial residuals discarded as waste deriving from Cucurbita pepo L. (pumpkin) are hereby investigated to be re-entered in a circular valorization chain. After a full characterization of the biomass residual, the focus was set on cucurbitin, a biologically active non-proteic amino acid found only in the Cucurbita species. The present research investigates different water-based strategies for cucurbitin extraction and enrichment. LCA comparative analysis has been performed to evaluate the environmental impacts of the extractions and assess the most sustainable strategy to yield cucurbitin.
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| 12. |
- Forzieri, Giovanni, et al.
(author)
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The Database of European Forest Insect and Disease Disturbances: DEFID2
- 2023
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In: Global Change Biology. - 1365-2486. ; 29:21, s. 6040-6065
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Journal article (peer-reviewed)abstract
- Insect and disease outbreaks in forests are biotic disturbances that can profoundly alter ecosystem dynamics. In many parts of the world, these disturbance regimes are intensifying as the climate changes and shifts the distribution of species and biomes. As a result, key forest ecosystem services, such as carbon sequestration, regulation of water flows, wood production, protection of soils, and the conservation of biodiversity, could be increasingly compromised. Despite the relevance of these detrimental effects, there are currently no spatially detailed databases that record insect and disease disturbances on forests at the pan-European scale. Here, we present the new Database of European Forest Insect and Disease Disturbances (DEFID2). It comprises over 650,000 harmonized georeferenced records, mapped as polygons or points, of insects and disease disturbances that occurred between 1963 and 2021 in European forests. The records currently span eight different countries and were acquired through diverse methods (e.g., ground surveys, remote sensing techniques). The records in DEFID2 are described by a set of qualitative attributes, including severity and patterns of damage symptoms, agents, host tree species, climate-driven trigger factors, silvicultural practices, and eventual sanitary interventions. They are further complemented with a satellite-based quantitative characterization of the affected forest areas based on Landsat Normalized Burn Ratio time series, and damage metrics derived from them using the LandTrendr spectral–temporal segmentation algorithm (including onset, duration, magnitude, and rate of the disturbance), and possible interactions with windthrow and wildfire events. The DEFID2 database is a novel resource for many large-scale applications dealing with biotic disturbances. It offers a unique contribution to design networks of experiments, improve our understanding of ecological processes underlying biotic forest disturbances, monitor their dynamics, and enhance their representation in land-climate models. Further data sharing is encouraged to extend and improve the DEFID2 database continuously. The database is freely available at https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/FOREST/DISTURBANCES/DEFID2/.
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| 13. |
- Marzorati, S., et al.
(author)
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“Zero Waste” and “Green” Approaches towards Valorisation of Vegetable Residues
- 2022
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In: Chemical Engineering Transactions. - : Italian Association of Chemical Engineering - AIDIC. - 1974-9791 .- 2283-9216. ; 92, s. 577-582
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Journal article (peer-reviewed)abstract
- Among the waste valorisation strategies, particular attention is given to plant and agri-food biomasses. They are particularly valuable since they are produced in large amounts worldwide and have been widely studied since ancient times for the richness in secondary metabolites, displaying strong bioactive properties. Within this context, the following biomasses have been selected and processed for the present study: • Residues from medicinal plants (Cucurbita pepo L. seeds and Serenoa repens L. fruits). Given the selectivity of the method employed from the company processing the commercial oils, the residual biomasses are expected to still contain a significant amount of valuable natural products. • Coffee silverskin, the only by-product of coffee roasting process. Silverskin has already been investigated as combustible, fertilizer and animal feed, but our work points out the relevance of its phytochemical profile in terms of polar compounds dealing with its antioxidant properties. The aim of the study was to set up a green methodology minimizing the use of organic solvents, employing a green extraction technique, supercritical CO2, selectively enriching the extracts of target high value compounds. Plant biomasses were chosen in order to assess different methodologies, based on the same supercritical fluid technique, able to demonstrate the feasibility to target separately narrow windows of compounds, differentiated by their polarities.
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| 14. |
- Yilmaz Turan, Secil, et al.
(author)
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Enzymatic production of hydrogels from corn bran feruloylated arabinoxylan with protective effects against reactive oxygen species
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Other publication (other academic/artistic)abstract
- The feruloylated nature of cereal bran arabinoxylans (AX) enables the production of strong hydrogen networks to be used as matrices for food and biomedical applications with protective effects against reactive oxygen species. Here we comparatively examine the physicochemical properties and radical scavenging activity of hydrogels developed from corn bran AX with high ferulic acid content following enzymatic crosslinking by laccase and peroxidase. Both enzymatic systems resulted in strong hydrogels with distinct kinetics, properties and ultrastructure. Peroxidase-mediated crosslinking exhibited much faster kinetics during hydrogel formation, whereas laccase-crosslinking provided a stronger network. Structural characterization by size exclusion chromatography, small angle X-ray scattering, and microscopy revealed that laccase formed aggregates with higher clustering strength, while peroxidase led to the occurrence of larger covalent polymer aggregates. As a proof of concept, we demonstrated that the AXhydrogels had adequate biocompatibility and demonstrated protective effects against oxidative stress on colon cells under in vitro conditions. The peroxidase-crosslinked hydrogel achieved a higher antioxidative effect. This study demonstrates the distinct effect of enzymatic crosslinking routes of highly feruloylated AX, resulting in hydrogels with tailored morphological, structural and rheological properties. Moreover, the AX hydrogels display excellent radical scavenging activity against cellular oxidative stress, which constitutes a proof of concept for their potential application in cell delivery, encapsulation and bio-fabrication.
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| 15. |
- Yilmaz Turan, Secil, et al.
(author)
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Hydrogels with protective effects against cellular oxidative stress via enzymatic crosslinking of feruloylated arabinoxylan from corn fibre
- 2022
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In: Green Chemistry. - : Royal Society of Chemistry (RSC). - 1463-9262 .- 1463-9270. ; 24:23, s. 9114-9127
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Journal article (peer-reviewed)abstract
- Biocatalytical upgrading of side streams from agricultural biomass into multifunctional materials constitutes a very attractive option to increase the circularity of food and material systems. We propose the design of radical scavenging hydrogels with mechanical integrity and protective effects against reactive oxygen species by enzymatic crosslinking of arabinoxylans (AX) with high ferulic acid content extracted from corn fibre using subcritical water. We have compared the influence of two enzymatic systems, laccase/O-2 and peroxidase/H2O2, on the biochemical structure, multiscale assembly, physicochemical properties, and radical scavenging activity of the polysaccharide hydrogels. Peroxidase crosslinking results in instant hydrogel formation, whereas laccase shows slower crosslinking kinetics, resulting in a more elastic gel network. Characterization by size exclusion chromatography, small angle X-ray scattering, and microscopy revealed structural differences in the network organization of the hydrogels produced by the two enzymes. Laccase crosslinking leads to smaller polymeric aggregates, promoting their progressive organization in network clusters that impact the overall ultrastructure. Conversely, the fast crosslinking induced by peroxidase results in higher porosity and forms larger and potentially more heterogeneous aggregates, which seem to hinder their subsequent association in clusters. Both AX hydrogels exhibit adequate biocompatibility and protective effects against in vitro cellular oxidative stress compared to an alginate reference. This constitutes a proof of concept of the potential application of radical scavenging hydrogels from agricultural side streams for biomedical and nutritional applications in wound healing, cellular repair and targeted delivery.
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| 16. |
- Yilmaz Turan, Secil, 1986-, et al.
(author)
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Revealing the mechanisms of hydrogel formation by laccase crosslinking and regeneration of feruloylated arabinoxylan from wheat bran
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Other publication (other academic/artistic)abstract
- Feruloylated arabinoxylan (FAX) from cereal brans has large potential to generate multifunctional materials with customized macromolecular and nanostructural architectures and techno-functional properties. Here we investigate the biochemical and structural mechanisms of hydrogel formation of wheat bran FAX following enzymatic crosslinking by laccase and a subsequent regeneration procedure involving freeze-drying and resuspension of the crosslinkedFAX in different pH buffers, using a battery of biochemical, rheological and biophysical techniques. The laccase crosslinking induced the conversion of ferulic acid units into a wide diversity of dimeric forms, leading to an increased molecular weight and a closer-packing of the FAX chains. The regeneration step resulted in a remarkable increase in the viscosity and viscoelasticity for all tested pH, especially under acidic conditions. The amount of crystallinity ofFAX increased by enzymatic crosslinking, it was however not influenced by the regeneration step. The structural characterization revealed that enzymatic crosslinking, in addition to the formation of covalent crosslinks, increases the physical intermolecular interactions between adjacent FAXdomains, and the regeneration forms larger clusters with higher dynamic moduli. Our results reveal that both chemical and physical mechanisms influence the network formation and multiscale assembly of wheat bran FAX hydrogels, thus modulating their rheological properties fundamental for their use in food and biomedical applications.
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| 17. |
- Yilmaz Turan, Secil, et al.
(author)
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Revealing the mechanisms of hydrogel formation by laccase crosslinking and regeneration of feruloylated arabinoxylan from wheat bran
- 2022
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In: Food Hydrocolloids. - : Elsevier BV. - 0268-005X .- 1873-7137. ; 128
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Journal article (peer-reviewed)abstract
- Feruloylated arabinoxylan (FAX) from cereal brans has large potential to generate multifunctional materials with customized macromolecular and nanostructural architectures and techno-functional properties. Here we investigate the chemical and structural mechanisms of hydrogel formation of wheat bran FAX following enzymatic crosslinking by laccase and a subsequent regeneration procedure involving freeze-drying and resuspension of the crosslinked FAX in different pH buffers, using a battery of biochemical, rheological and physical techniques. The laccase crosslinking induced the conversion of ferulic acid units into a wide diversity of dimeric forms, leading to an increased molecular weight and a closer-packing of the FAX chains. The regeneration step resulted in a remarkable increase in the viscosity and viscoelasticity for all tested pH values. The amount of crystallinity of FAX increased by enzymatic crosslinking, it was however decreased by the regeneration step. The structural characterization revealed that enzymatic crosslinking, in addition to the formation of covalent crosslinks, influences the physical intermolecular interactions between adjacent FAX domains, and the regeneration forms larger clusters with higher dynamic moduli. Our results reveal that both chemical and physical mechanisms influence the network formation and multiscale assembly of wheat bran FAX hydrogels, thus modulating their rheological properties fundamental for their use in food and biomedical applications.
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