| 1. |
- 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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| 2. |
- Sun, Fengbo, et al.
(author)
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1,5-Diiodocycloctane: a cyclane solvent additive that can extend the exciton diffusion length in thick film organic solar cells
- 2024
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In: Energy and Environmental Sciences. - 1754-5692 .- 1754-5706. ; 17:5, s. 1916-1930
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Journal article (peer-reviewed)abstract
- The short exciton diffusion length associated with most state-of-the-art organic semiconductors used in organic solar cells (OSCs) imposes severe limits on the exciton transport in the larger donor/acceptor domains and the exciton dissociation at the interface, which hinder further improvements in the power conversion efficiencies (PCE) of the thick-film devices. In this study, a new cyclane, 1,5-diiodocycloctane (DICO), was employed as a solvent additive to effectively extend the exciton LD within the bulk-heterojunction blend, which can function with the multiple photovoltaic materials system. Due to the great enhancement of molecular stacking and exclusively large domain sizes of photovoltaic materials with the assistance of the DICO additive, the trap density in devices is significantly reduced, thereby nearly doubling the LD in the thick film OSCs. Notably, the DICO-processed PM6/L8-BO-based OSC showed high thickness tolerance for the bulk-heterojunction (BHJ) layer, delivering a high PCE of 19.1% in the case of a 110 nm thick film and still maintaining an excellent PCE of 17.2% in the case of a 300 nm thick film. Crucially, a noticeably increased stability of the multiple materials system was observed in the DICO-processed OSCs. These findings enrich the additive family with new cyclane systems to extend the exciton LD in thick film OSCs with high performance.
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| 3. |
- Ding, Jiangwei, et al.
(author)
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All Roads Lead to Rome? : Genes Causing Dravet Syndrome and Dravet Syndrome-Like Phenotypes
- 2022
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In: Frontiers in Neurology. - : Frontiers Media S.A.. - 1664-2295. ; 13
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Research review (peer-reviewed)abstract
- Background: Dravet syndrome (DS) is a severe epileptic encephalopathy mainly caused by haploinsufficiency of the gene SCN1A, which encodes the voltage-gated sodium channel NaV1. 1 in the brain. While SCN1A mutations are known to be the primary cause of DS, other genes that may cause DS are poorly understood. Several genes with pathogenic mutations result in DS or DS-like phenotypes, which may require different drug treatment approaches. Therefore, it is urgent for clinicians, especially epilepsy specialists to fully understand these genes involved in DS in addition to SCN1A. Particularly for healthcare providers, a deep understanding of these pathogenic genes is useful in properly selecting and adjusting drugs in a more effective and timely manner.Objective: The purpose of this study was to identify genes other than SCN1A that may also cause DS or DS-like phenotypes. Methods: A comprehensive search of relevant Dravet syndrome and severe myoclonic epilepsy in infancy was performed in PubMed, until December 1, 2021. Two independent authors performed the screening for potentially eligible studies. Disagreements were decided by a third, more professional researcher or by all three. The results reported by each study were narratively summarized.Results: A PubMed search yielded 5,064 items, and other sources search 12 records. A total of 29 studies published between 2009 and 2021 met the inclusion criteria. Regarding the included articles, seven studies on PCDH19, three on SCN2A, two on SCN8A, five on SCN1B, two on GABRA1, three on GABRB3, three on GABRG2, and three on STXBP1 were included. Only one study was recorded for CHD2, CPLX1, HCN1 and KCNA2, respectively. It is worth noting that a few articles reported on more than one epilepsy gene.Conclusion: DS is not only identified in variants of SCN1A, but other genes such as PCDH19, SCN2A, SCN8A, SCN1B, GABRA1, GABRB3, GABRG2, KCNA2, CHD2, CPLX1, HCN1A, STXBP1 can also be involved in DS or DS-like phenotypes. As genetic testing becomes more widely available, more genes associated with DS and DS-like phenotypes may be identified and gene-based diagnosis of subtypes of phenotypes in this spectrum may improve the management of these diseases in the future.
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| 4. |
- Hoogendoorn, Billy W., et al.
(author)
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Cellulose-assisted electrodeposition of zinc for morphological control in battery metal recycling
- 2022
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In: Materials Advances. - : Royal Society of Chemistry (RSC). - 2633-5409.
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Journal article (peer-reviewed)abstract
- Cellulose nanofibers (CNF) are demonstrated as an effective tool for converting electrodeposits into more easily detachable dendritic deposits useful in recycling zinc ion batteries via electrowinning. The incorporation of CNF at concentrations ranging from 0.01 to 0.5 g/L revealed a progressively extensive formation of a nacre-like dendritic zinc structure that did not form in its absence. Increasing CNF-concentrations from 0.01 to 0.5 g/L resulted in more extensive dendritic structures forming. The explanation to the observed phenomenon is the CNFs ability to strongly interact with the metal ions, i.e., restricting the mobility of the ions towards the electrowinning electrode. At the highest concentration of CNF (0.5 g/L), in combination with the lowest current density (150 A/m2), the electrodeposition was limited to the extent that formed deposits were almost non-existent. The electrodeposition in the presence of CNF was further evaluated at different temperatures: 20, 40 and 60°C. The dendritic formation was increasingly suppressed with increasing temperatures, and at a temperature of 60°C, the electrodeposited morphologies could not be differentiated from the morphologies formed in the absence of the cellulose. The results stemmed from a greater mobility of the metal ions at elevated temperatures, while at the same time suggests an inability of the CNF to strongly associate the metal ions at the elevated temperatures. High-pressure blasted titanium electrodes were used a reference material for accurate comparisons, and electron microscopy (FE-SEM) and X-ray diffraction were used to characterize the zinc morphologies and crystallite sizes, respectively. The article reports the first investigation on how dispersions of highly crystalline cellulose nanofibers can be used as a renewable and functional additive during the recycling of battery metal ions. The metal-ion/cellulose interactions may also allow for structural control in electrodeposition for other applications.
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| 5. |
- Hoogendoorn, Billy W., et al.
(author)
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Ultra-low Concentration of Cellulose Nanofibers (CNFs) for Enhanced Nucleation and Yield of ZnO Nanoparticles
- 2022
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In: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 38:41, s. 12480-12490
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Journal article (peer-reviewed)abstract
- Cellulose nanofibers (CNFs) were used in aqueous synthesis protocols for zinc oxide (ZnO) to affect the formation of the ZnO particles. Different concentrations of CNFs were evaluated in two different synthesis protocols producing distinctly different ZnO morphologies (flowers and sea urchins) as either dominantly oxygen-or zinc-terminated particles. The CNF effects on the ZnO formation were investigated by implementing a heat-treatment method at 400 degrees C that fully removed the cellulose material without affecting the ZnO particles made in the presence of CNFs. The inorganic phase formations were monitored by extracting samples during the enforced precipitations to observe changes in the ZnO morphologies. A decrease in the size of the ZnO particles could be observed for all synthesis protocols, already occurring at small additions of CNFs. At as low as 0.1 g/L CNFs, the particle size decreased by 50% for the flower-shaped particles and 45% for the sea-urchin-shaped particles. The formation of smaller particles was accompanied by increased yield by 13 and 15% due to the CNFs' ability to enhance the nucleation, resulting in greater mass of ZnO divided among a larger number of particles. The enhanced nucleation could also be verified as useful for preventing secondary morphologies from forming, which grew on the firstly precipitated particles. The suppression of secondary growths' was due to the more rapid inorganic phase formation during the early phases of the reactions and the faster consumption of dissolved salts, leaving smaller amounts of metal salts present at later stages of the reactions. The findings show that using cellulose to guide inorganic nanoparticle growth can be predicted as an emerging field in the preparation of functional inorganic micro/nanoparticles. The observations are highly relevant in any industrial setting for the large-scale and resource-efficient production of ZnO.
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| 6. |
- Lensink, Marc F., et al.
(author)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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In: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Journal article (peer-reviewed)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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| 7. |
- Liu, Anbu, et al.
(author)
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DDR1/2 enhance KIT activation and imatinib resistance of primary and secondary KIT mutants in gastrointestinal stromal tumors
- 2024
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In: Molecular Carcinogenesis. - 0899-1987. ; 63:1, s. 75-93
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Journal article (peer-reviewed)abstract
- Gastrointestinal stromal tumors (GISTs) are predominantly initiated by KIT mutations. In this study, we observed that discoidin domain receptors 1 and 2 (DDR1 and DDR2) exhibited high expression in GISTs, were associated with KIT, and enhanced the activation of both wild-type KIT and primary KIT mutants. Inhibition of DDR1/2 led to a reduction in the activation of KIT and its downstream signaling molecules, ultimately impairing GIST cell survival and proliferation in vitro. Consequently, treatment of mice carrying germline KIT/V558A mutation with DDR1/2 inhibitor significantly impeded tumor growth, and the combined use of DDR1/2 inhibitor and imatinib, the first-line targeted therapeutic agent for GISTs, markedly enhanced tumor growth suppression. In addition, DDR1/2 inhibition resulted in decreased KIT expression, while KIT inhibition led to upregulation of DDR1/2 expression in GISTs. The presence of DDR1/2 also decreased the sensitivity of wild-type KIT or primary KIT mutants to imatinib, indicating a possible role for DDR1/2 in promoting GIST survival during KIT-targeted therapy. The development of drug-resistant secondary KIT mutations is a primary factor contributing to GIST recurrence following targeted therapy. Similar to primary KIT mutants, DDR1/2 can associate with and enhance the activation of secondary KIT mutants, further diminishing their sensitivity to imatinib. In summary, our data demonstrate that DDR1/2 contribute to KIT activation in GISTs and strengthen resistance to imatinib for both primary and secondary KIT mutants, providing a rationale for further exploration of DDR1/2 targeting in GIST treatment.
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| 8. |
- Tang, Sui, et al.
(author)
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Association of plant-based diet index with sleep quality in middle-aged and older adults : The Healthy Dance Study
- 2023
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In: Sleep Health. - : Elsevier. - 2352-7218 .- 2352-7226. ; 9:5, s. 698-703
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Journal article (peer-reviewed)abstract
- Objectives: To investigate the association between plant-based diet indices and sleep quality in Chinese middle-aged and older adults.Methods: The study included 2424 participants aged 45 years and older. Dietary data were collected using a semi-quantitative food frequency questionnaire, and sleep quality was assessed by the Pittsburgh Sleep Quality Index scale. Plant-based diet was categorized based on 3 indices (score range, 17-85) covering 17 food groups: the overall plant-based diet index, healthful plant-based diet index, and unhealthful plant-based diet index. The associations between these plant-based diet indices and sleep quality were examined using logistic and linear regression analyses.Results: After controlling for sociodemographic, lifestyle, and multiple disease-related factors, participants in the highest quartile of the healthful plant-based diet index had 0.55 higher odds of better sleep quality (95% CI: 0.42, 0.72; P-trend < .001). In contrast, participants in the highest quartile of the unhealthful plant-based diet index had 2.03 higher odds of poor sleep quality (95% CI: 1.51, 2.72; P-trend < .001). In addition, plant-based diet index and healthful plant-based diet index were inversely associated with Pittsburgh Sleep Quality Index scores, while unhealthful plant-based diet index and Pittsburgh Sleep Quality Index scores were positively associated.Conclusions: We found unhealthy plant-based diets are significantly associated with poor sleep quality. Adherence to overall plant-based diets, especially healthy plant-based diets, was positively associated with optimal sleep quality.(c) 2023 National Sleep Foundation. Published by Elsevier Inc. All rights reserved.
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