| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)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. |
- Ariyawansa, Hiran A., et al.
(författare)
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Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
- 2015
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Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 75, s. 27-274
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Tidskriftsartikel (refereegranskat)abstract
- This paper is a compilation of notes on 142 fungal taxa, including five new families, 20 new genera, and 100 new species, representing a wide taxonomic and geographic range. The new families, Ascocylindricaceae, Caryosporaceae and Wicklowiaceae (Ascomycota) are introduced based on their distinct lineages and unique morphology. The new Dothideomycete genera Pseudomassariosphaeria (Amniculicolaceae), Heracleicola, Neodidymella and P s e u d o m i c ros p h a e r i o p s i s ( D id y m e l l a c e a e ) , P s e u d o p i t h o m y c e s ( D i d y m o s p h a e r i a c e a e ) , Brunneoclavispora, Neolophiostoma and Sulcosporium (Halotthiaceae), Lophiohelichrysum (Lophiostomataceae), G a l l i i c o l a , Popul o c re s c e n t i a a nd Va g i c o l a (Phaeosphaeriaceae), Ascocylindrica (Ascocylindricaceae), E l o n g a t o p e d i c e l l a t a ( R o u s s o e l l a c e a e ) , Pseudoasteromassaria (Latoruaceae) and Pseudomonodictys (Macrodiplodiopsidaceae) are introduced. The newly described species of Dothideomycetes (Ascomycota) are Pseudomassariosphaeria bromicola (Amniculicolaceae), Flammeascoma lignicola (Anteagloniaceae), Ascocylindrica marina (Ascocylindricaceae) , Lembosia xyliae (Asterinaceae), Diplodia crataegicola and Diplodia galiicola ( B o t r yosphae r i a cea e ) , Caryospor a aquat i c a (Caryosporaceae), Heracleicola premilcurensis and Neodi dymell a thai landi cum (Didymellaceae) , Pseudopithomyces palmicola (Didymosphaeriaceae), Floricola viticola (Floricolaceae), Brunneoclavispora bambusae, Neolophiostoma pigmentatum and Sulcosporium thailandica (Halotthiaceae), Pseudoasteromassaria fagi (Latoruaceae), Keissleriella dactylidicola (Lentitheciaceae), Lophiohelichrysum helichrysi (Lophiostomataceae), Aquasubmersa japonica (Lophiotremataceae) , Pseudomonodictys tectonae (Macrodiplodiopsidaceae), Microthyrium buxicola and Tumidispora shoreae (Microthyriaceae), Alloleptosphaeria clematidis, Allophaeosphaer i a c y t i s i , Allophaeosphae r i a subcylindrospora, Dematiopleospora luzulae, Entodesmium artemisiae, Galiicola pseudophaeosphaeria, Loratospora(Basidiomycota) are introduced together with a new genus Neoantrodiella (Neoantrodiellaceae), here based on both morphology coupled with molecular data. In the class Agaricomycetes, Agaricus pseudolangei, Agaricus haematinus, Agaricus atrodiscus and Agaricus exilissimus (Agaricaceae) , Amanita m e l l e i a l b a , Amanita pseudosychnopyramis and Amanita subparvipantherina (Amanitaceae), Entoloma calabrum, Cora barbulata, Dictyonema gomezianum and Inocybe granulosa (Inocybaceae), Xerocomellus sarnarii (Boletaceae), Cantharellus eucalyptorum, Cantharellus nigrescens, Cantharellus tricolor and Cantharellus variabilicolor (Cantharellaceae), Cortinarius alboamarescens, Cortinarius brunneoalbus, Cortinarius ochroamarus, Cortinarius putorius and Cortinarius seidlii (Cortinariaceae), Hymenochaete micropora and Hymenochaete subporioides (Hymenochaetaceae), Xylodon ramicida (Schizoporaceae), Colospora andalasii (Polyporaceae), Russula guangxiensis and Russula hakkae (Russulaceae), Tremella dirinariae, Tremella graphidis and Tremella pyrenulae (Tremellaceae) are introduced. Four new combinations Neoantrodiella gypsea, Neoantrodiella thujae (Neoantrodiellaceae), Punctulariopsis cremeoalbida, Punctulariopsis efibulata (Punctulariaceae) are also introduced here for the division Basidiomycota. Furthermore Absidia caatinguensis, Absidia koreana and Gongronella koreana (Cunninghamellaceae), Mortierella pisiformis and Mortierella formosana (Mortierellaceae) are newly introduced in the Zygomycota, while Neocallimastix cameroonii and Piromyces irregularis (Neocallimastigaceae) ar e i n t roduced i n the Neocallimastigomycota. Reference specimens or changes in classification and notes are provided for Alternaria ethzedia, Cucurbitaria ephedricola, Austropleospora, Austropleospora archidendri, Byssosphaeria rhodomphala, Lophiostoma caulium, Pseudopithomyces maydicus, Massariosphaeria, Neomassariosphaeria and Pestalotiopsis montellica.
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| 5. |
- Tang, Ting-Ting, et al.
(författare)
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Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure.
- 2011
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 6:9, s. e24272-
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Tidskriftsartikel (refereegranskat)abstract
- Animal studies suggest that regulatory T (T(reg)) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T(reg) cells in patients with chronic heart failure (CHF). However, the mechanisms behind T(reg-)cell defects remained unknown. We here sought to elucidate the mechanism of T(reg-)cell defects in CHF patients.
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| 6. |
- Berzunza, Gabriel, et al.
(författare)
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The k-cut model in deterministic and random trees
- 2021
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Ingår i: The Electronic Journal of Combinatorics. - : ELECTRONIC JOURNAL OF COMBINATORICS. - 1097-1440 .- 1077-8926. ; 28:1
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Tidskriftsartikel (refereegranskat)abstract
- The k-cut number of rooted graphs was introduced by Cai et al. as a generalization of the classical cutting model by Meir and Moon. In this paper, we show that all moments of the k-cut number of conditioned Galton-Watson trees converge after proper rescaling, which implies convergence in distribution to the same limit law regardless of the offspring distribution of the trees. This extends the result of Janson. Using the same method, we also show that the k-cut number of various random or deterministic trees of logarithmic height converges in probability to a constant after rescaling, such as random split-trees, uniform random recursive trees, and scale-free random trees.
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| 7. |
- Berzunza Ojeda, Gabriel, et al.
(författare)
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The fluctuations of the giant cluster for percolation on random split trees
- 2022
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Ingår i: Latin American Journal of Probability and Mathematical Statistics. - : Institute for Applied and Pure Mathematics (IMPA). - 1980-0436. ; 19:1, s. 665-700
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Tidskriftsartikel (refereegranskat)abstract
- A split tree of cardinality n is constructed by distributing n “balls” in a subset ofvertices of an infinite tree which encompasses many types of random trees such as m-ary searchtrees, quad trees, median-of-(2k + 1) trees, fringe-balanced trees, digital search trees and randomsimplex trees. In this work, we study Bernoulli bond percolation on arbitrary split trees of large butfinite cardinality n. We show for appropriate percolation regimes that depend on the cardinalityn of the split tree that there exists a unique giant cluster, the fluctuations of the size of the giantcluster as n → ∞ are described by an infinitely divisible distribution that belongs to the class ofstable (asymmetric) Cauchy laws. This work generalizes the results for the random m-ary recursivetrees by Berzunza (2015). Our approach is based on a remarkable decomposition of the size of thegiant percolation cluster as a sum of essentially independent random variables which may be usefulfor studying percolation on other trees with logarithmic height; for instance in this work we studyalso the case of regular trees.
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| 8. |
- Cai, Fanfan, et al.
(författare)
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Characteristics and mechanisms of low-alloy high-strength steel corrosion behavior under barnacle adhesion based on a comparison experiment
- 2023
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Ingår i: Corrosion Science. - : Elsevier BV. - 0010-938X. ; 217
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Tidskriftsartikel (refereegranskat)abstract
- A comparative experiment was set up in a field site and laboratory to study the effect of barnacles (model organisms of macrofouling) on the corrosion behavior of a low-alloy high-strength steel. The results indicated that barnacle adhesion can slow the corrosion rate of steel in an immersion environment by hindering the diffusion of corrosive ions. It was found that barnacle adhesion had a significant promotion effect on localized corrosion. Due to steel’s high corrosion rate, the corrosion-impeding effect was improved, and the promotioneffect on localized corrosion was weakened. The study proposed a corrosion mechanism model influenced by barnacles.
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| 9. |
- Cai, Xing Shi, et al.
(författare)
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A note on the asymptotic expansion of the Lerch's transcendent
- 2019
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Ingår i: Integral transforms and special functions. - : TAYLOR & FRANCIS LTD. - 1065-2469 .- 1476-8291. ; 30:10, s. 844-855
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Tidskriftsartikel (refereegranskat)abstract
- In Ferreira and Lopez [Asymptotic expansions of the Hurwitz-Lerch zeta function. J Math Anal Appl. 2004;298(1):210-224], the authors derived an asymptotic expansion of the Lerch's transcendent Phi(z, s, a) for large vertical bar a vertical bar, valid for Ra > 0, Rs > 0 and z is an element of C \ [1, infinity). In this paper, we study the special case z >= 1 not covered in Ferreira and Lopez [Asymptotic expansions of the Hurwitz-Lerch zeta function. J Math Anal Appl. 2004; 298(1): 210-224], deriving a complete asymptotic expansion of the Lerch's transcendent Phi(z, s, a) for z > 1 and Rs > 0 as Ra goes to infinity. We also show that when a is a positive integer, this expansion is convergent for Rz >= 1. As a corollary, we get a full asymptotic expansion for the sum Sigma(m)(n=1) z(n)/n(s) for fixed z > 1 as m -> infinity. Some numerical results show the accuracy of the approximation.
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| 10. |
- Cai, Xing Shi, et al.
(författare)
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Cutting resilient networks - complete binary trees
- 2019
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Ingår i: The Electronic Journal of Combinatorics. - : ELECTRONIC JOURNAL OF COMBINATORICS. - 1097-1440 .- 1077-8926. ; 26:4
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Tidskriftsartikel (refereegranskat)abstract
- In our previous work [2, 3], we introduced the random k-cut number for rooted graphs. In this paper, we show that the distribution of the k-cut number in complete binary trees of size n, after rescaling, is asymptotically a periodic function of lg n - lg lg n. Thus there are different limit distributions for different subsequences, where these limits are similar to weakly 1-stable distributions. This generalizes the result for the case k = 1, i.e., the traditional cutting model, by Janson [12].
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| 11. |
- Cai, Xing Shi, et al.
(författare)
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Inversions in Split Trees and Conditional Galton-Watson Treest
- 2019
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Ingår i: Combinatorics, probability & computing. - 0963-5483 .- 1469-2163. ; 28:3, s. 335-364
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Tidskriftsartikel (refereegranskat)abstract
- We study I(T), the number of inversions in a tree T with its vertices labelled uniformly at random, which is a generalization of inversions in permutations. We first show that the cumulants of I(T) have explicit formulas involving the k-total common ancestors of T (an extension of the total path length). Then we consider X-n, the normalized version of I(T-n), for a sequence of trees T-n. For fixed T-n's, we prove a sufficient condition for X-n to converge in distribution. As an application, we identify the limit of X-n for complete b-ary trees. For T(n )being split trees [16], we show that X-n converges to the unique solution of a distributional equation. Finally, when T-n's are conditional Galton-Watson trees, we show that X-n converges to a random variable defined in terms of Brownian excursions. By exploiting the connection between inversions and the total path length, we are able to give results that significantly strengthen and broaden previous work by Panholzer and Seitz [46].
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| 12. |
- Cai, Xing Shi, et al.
(författare)
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kappa-cut on paths and some trees
- 2019
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Ingår i: Electronic Journal of Probability. - : UNIV WASHINGTON, DEPT MATHEMATICS. - 1083-6489. ; 24:53
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Tidskriftsartikel (refereegranskat)abstract
- We define the (random) kappa-cut number of a rooted graph to model the difficulty of the destruction of a resilient network. The process is as the cut model of Meir and Moon [21] except now a node must be cut kappa times before it is destroyed. The first order terms of the expectation and variance of chi(n), the kappa-cut number of a path of length n, are proved. We also show that chi(n), after rescaling, converges in distribution to a limit B-kappa, which has a complicated representation. The paper then briefly discusses the kappa-cut number of some trees and general graphs. We conclude by some analytic results which may be of interest.
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| 13. |
- Cai, Xing Shi, et al.
(författare)
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Non-fringe subtrees in conditioned Galton-Watson trees
- 2018
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Ingår i: The Electronic Journal of Combinatorics. - 1097-1440 .- 1077-8926. ; 25:3
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Tidskriftsartikel (refereegranskat)abstract
- We study S(T-n), the number of subtrees in a conditioned Galton-Watson tree of size n. With two very different methods, we show that log(S(T-n)) has a Central Limit Law and that the moments of S(T-n) are of exponential scale.
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| 14. |
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| 15. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 16. |
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| 17. |
- Feitosa, Mary F., et al.
(författare)
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Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries
- 2018
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Ingår i: PLOS ONE. - : Public library science. - 1932-6203. ; 13:6
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Tidskriftsartikel (refereegranskat)abstract
- Heavy alcohol consumption is an established risk factor for hypertension; the mechanism by which alcohol consumption impact blood pressure (BP) regulation remains unknown. We hypothesized that a genome-wide association study accounting for gene-alcohol consumption interaction for BP might identify additional BP loci and contribute to the understanding of alcohol-related BP regulation. We conducted a large two-stage investigation incorporating joint testing of main genetic effects and single nucleotide variant (SNV)-alcohol consumption interactions. In Stage 1, genome-wide discovery meta-analyses in approximate to 131 K individuals across several ancestry groups yielded 3,514 SNVs (245 loci) with suggestive evidence of association (P <1.0 x 10(-5)). In Stage 2, these SNVs were tested for independent external replication in individuals across multiple ancestries. We identified and replicated (at Bonferroni correction threshold) five novel BP loci (380 SNVs in 21 genes) and 49 previously reported BP loci (2,159 SNVs in 109 genes) in European ancestry, and in multi-ancestry meta-analyses (P < 5.0 x 10(-8)). For African ancestry samples, we detected 18 potentially novel BP loci (P< 5.0 x 10(-8)) in Stage 1 that warrant further replication. Additionally, correlated meta-analysis identified eight novel BP loci (11 genes). Several genes in these loci (e.g., PINX1, GATA4, BLK, FTO and GABBR2 have been previously reported to be associated with alcohol consumption. These findings provide insights into the role of alcohol consumption in the genetic architecture of hypertension.
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| 18. |
- Guo, Hui-Hui, et al.
(författare)
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Alleviation of allergic asthma by rosmarinic acid via gut-lung axis
- 2024
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Ingår i: Phytomedicine. - : Elsevier. - 0944-7113 .- 1618-095X. ; 126
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Tidskriftsartikel (refereegranskat)abstract
- Background: Asthma affects 3% of the global population, leading to over 0.25 million deaths. Due to its complexity, asthma is difficult to cure or prevent, and current therapies have limitations. This has led to a growing demand for alternative asthma treatments. We found rosmarinic acid (RosA) as a potential new drug candidate from natural medicine. However, RosA has poor bioavailability and remains mainly in the gastrointestinal tract after oral administration, suggesting the involvement of gut microbiota in its bioactivity. Purpose: To investigate the mechanism of RosA in alleviating allergic asthma by gut-lung axis. Methods: We used 16S rRNA gene sequencing and metabolites analysis to investigate RosA's modulation of gut microbiota. Techniques of molecular biology and metabolomics were employed to study the pharmacological mechanism of RosA. Cohousing was used to confirm the involvement of gut microbiota in RosA-induced improvement of allergic asthma. Results: RosA decreased cholate levels from spore-forming bacteria, leading to reduced 5-hydroxytryptamine (5HT) synthesis, bronchoconstriction, vasodilation, and inflammatory cell infiltration. It also increased short-chain fatty acids (SCFAs) levels, facilitating the expression of intestinal tight junction proteins to promote intestinal integrity. SCFAs upregulated intestinal monocarboxylate transporters (MCTs), thereby improving their systemic delivery to reduce Th2/ILC2 mediated inflammatory response and suppress eosinophil influx and mucus production in lung. Additionally, RosA inhibited lipopolysaccharide (LPS) production and translocation, leading to reduced TLR4-NF kappa B mediated pulmonary inflammation and oxidative stress. Conclusions: The anti-asthmatic mechanism of oral RosA is primarily driven by modulation of gut microbiotaderived 5-HT, SCFAs, and LPS, achieving a combined synergistic effect. RosA is a safe, effective, and reliable drug candidate that could potentially replace glucocorticoids for asthma treatment.
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| 19. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 20. |
- Krishnasamy, Ezhilmathi, et al.
(författare)
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Multi-GPU Implementations of Parallel 3D Sweeping Algorithms with Application to Geological Folding
- 2015
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Ingår i: INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, ICCS 2015 COMPUTATIONAL SCIENCE AT THE GATES OF NATURE. - : ELSEVIER SCIENCE BV. ; , s. 1494-1503
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Konferensbidrag (refereegranskat)abstract
- This paper studies the CUDA programming challenges with using multiple GPUs inside a single machine to carry out plane-by-plane updates in parallel 3D sweeping algorithms. In particular, care must be taken to mask the overhead of various data movements between the GPUs. Multiple OpenMP threads on the CPU side should be combined multiple CUDA streams per GPU to hide the data transfer cost related to the halo computation on each 2D plane. Moreover, the technique of peer-to-peer data motion can be used to reduce the impact of 3D volumetric data shuffles that have to be done between mandatory changes of the grid partitioning. We have investigated the performance improvement of 2-and 4-GPU implementations that are applicable to 3D anisotropic front propagation computations related to geological folding. In comparison with a straightforward multi-GPU implementation, the overall performance improvement due to masking of data movements on four GPUs of the Fermi architecture was 23%. The corresponding improvement obtained on four Kepler GPUs was 47%.
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| 21. |
- Kristan, Matej, et al.
(författare)
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The Visual Object Tracking VOT2016 Challenge Results
- 2016
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Ingår i: COMPUTER VISION - ECCV 2016 WORKSHOPS, PT II. - Cham : SPRINGER INT PUBLISHING AG. - 9783319488813 - 9783319488806 ; , s. 777-823
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2016 aims at comparing short-term single-object visual trackers that do not apply pre-learned models of object appearance. Results of 70 trackers are presented, with a large number of trackers being published at major computer vision conferences and journals in the recent years. The number of tested state-of-the-art trackers makes the VOT 2016 the largest and most challenging benchmark on short-term tracking to date. For each participating tracker, a short description is provided in the Appendix. The VOT2016 goes beyond its predecessors by (i) introducing a new semi-automatic ground truth bounding box annotation methodology and (ii) extending the evaluation system with the no-reset experiment.
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| 22. |
- Ljungkvist, Karl, 1986-
(författare)
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Finite Element Computations on Multicore and Graphics Processors
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, techniques for efficient utilization of modern computer hardwarefor numerical simulation are considered. In particular, we study techniques for improving the performance of computations using the finite element method.One of the main difficulties in finite-element computations is how to perform the assembly of the system matrix efficiently in parallel, due to its complicated memory access pattern. The challenge lies in the fact that many entries of the matrix are being updated concurrently by several parallel threads. We consider transactional memory, an exotic hardware feature for concurrent update of shared variables, and conduct benchmarks on a prototype multicore processor supporting it. Our experiments show that transactions can both simplify programming and provide good performance for concurrent updates of floating point data.Secondly, we study a matrix-free approach to finite-element computation which avoids the matrix assembly. In addition to removing the need to store the system matrix, matrix-free methods are attractive due to their low memory footprint and therefore better match the architecture of modern processors where memory bandwidth is scarce and compute power is abundant. Motivated by this, we consider matrix-free implementations of high-order finite-element methods for execution on graphics processors, which have seen a revolutionary increase in usage for numerical computations during recent years due to their more efficient architecture. In the implementation, we exploit sum-factorization techniques for efficient evaluation of matrix-vector products, mesh coloring and atomic updates for concurrent updates, and a geometric multigrid algorithm for efficient preconditioning of iterative solvers. Our performance studies show that on the GPU, a matrix-free approach is the method of choice for elements of order two and higher, yielding both a significantly faster execution, and allowing for solution of considerably larger problems. Compared to corresponding CPU implementations executed on comparable multicore processors, the GPU implementation is about twice as fast, suggesting that graphics processors are about twice as power efficient as multicores for computations of this kind.
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| 23. |
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| 24. |
- Luo, Xuhao, et al.
(författare)
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Intrinsic polarization-sensitive organic photodetector with self-assembled all-polymer heterojunction
- 2022
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 121:23
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Tidskriftsartikel (refereegranskat)abstract
- Intrinsic polarization-sensitive photodetectors (IPPDs) have attracted considerable attention in recent years due to their simplicity in configuration, making them ideal candidates for compact and integrated polarization-sensitive sensing and imaging systems. Photoactive films with intrinsic optical anisotropy are necessary for IPPDs. This study reports an achievement of photoactive films based on all-polymer heterojunction films with in-plane optical anisotropy using a simple bottom-up self-assembly method. Both the donor (TQ1) and acceptor (N2200) polymers have the same spatial orientation with distinct anisotropy, approaching a dichroic ratio (DR) of 8. Polarization-sensitive light absorption is due to the uniaxially oriented polymer chains, which are dominated by lamellar packing with edge-on orientation. For IPPDs based on this anisotropic all-polymer heterojunction film, a photocurrent anisotropy was found with a polarized photocurrent ratio of 2.6. The detectivity of these IPPDs was found to be 1.9 × 1011 Jones (@ ∼600 nm, 0 V bias). Our work shows that oriented polymer donor-acceptor films fabricated using bottom-up self-assembly have great potential in applications, such as polarization detection.
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| 25. |
- Nordén, Markus, 1975-
(författare)
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Multithreaded PDE Solvers on Non-Uniform Memory Architectures
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A trend in parallel computer architecture is that systems with a large shared memory are becoming more and more popular. A shared memory system can be either a uniform memory architecture (UMA) or a cache coherent non-uniform memory architecture (cc-NUMA). In the present thesis, the performance of parallel PDE solvers on cc-NUMA computers is studied. In particular, we consider the shared namespace programming model, represented by OpenMP. Since the main memory is physically, or geographically distributed over several multi-processor nodes, the latency for local memory accesses is smaller than for remote accesses. Therefore, the geographical locality of the data becomes important. The focus of the present thesis is to study multithreaded PDE solvers on cc-NUMA systems, in particular their memory access pattern with respect to geographical locality. The questions posed are: (1) How large is the influence on performance of the non-uniformity of the memory system? (2) How should a program be written in order to reduce this influence? (3) Is it possible to introduce optimizations in the computer system for this purpose? The main conclusion is that geographical locality is important for performance on cc-NUMA systems. This is shown experimentally for a broad range of PDE solvers as well as theoretically using a model involving characteristics of computer systems and applications. Geographical locality can be achieved through migration directives that are inserted by the programmer or — possibly in the future — automatically by the compiler. On some systems, it can also be accomplished by means of transparent, hardware initiated migration and replication. However, a necessary condition that must be fulfilled if migration is to be effective is that the memory access pattern must not be "speckled", i.e. as few threads as possible shall make accesses to each memory page. We also conclude that OpenMP is competitive with MPI on cc-NUMA systems if care is taken to get a favourable data distribution.
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| 26. |
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| 27. |
- Phukhamsakda, Chayanard, et al.
(författare)
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The numbers of fungi: contributions from traditional taxonomic studies and challenges of metabarcoding
- 2022
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Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 114:1, s. 327-386
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Tidskriftsartikel (refereegranskat)abstract
- The global diversity of fungi has been estimated using several different approaches. There is somewhere between 2–11 million estimated species, but the number of formally described taxa is around 150,000, a tiny fraction of the total. In this paper, we examine 12 ascomycete genera as case studies to establish trends in fungal species descriptions, and introduce new species in each genus. To highlight the importance of traditional morpho-molecular methods in publishing new species, we introduce novel taxa in 12 genera that are considered to have low species discovery. We discuss whether the species are likely to be rare or due to a lack of extensive sampling and classification. The genera are Apiospora, Bambusicola, Beltrania, Capronia, Distoseptispora, Endocalyx, Neocatenulostroma, Neodeightonia, Paraconiothyrium, Peroneutypa, Phaeoacremonium and Vanakripa. We discuss host-specificity in selected genera and compare the number of species epithets in each genus with the number of ITS (barcode) sequences deposited in GenBank and UNITE. We furthermore discuss the relationship between the divergence times of these genera with those of their hosts. We hypothesize whether there might be more species in these genera and discuss hosts and habitats that should be investigated for novel species discovery.
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| 28. |
- Ruilope, LM, et al.
(författare)
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Design and Baseline Characteristics of the Finerenone in Reducing Cardiovascular Mortality and Morbidity in Diabetic Kidney Disease Trial
- 2019
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Ingår i: American journal of nephrology. - : S. Karger AG. - 1421-9670 .- 0250-8095. ; 50:5, s. 345-356
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Tidskriftsartikel (refereegranskat)abstract
- <b><i>Background:</i></b> Among people with diabetes, those with kidney disease have exceptionally high rates of cardiovascular (CV) morbidity and mortality and progression of their underlying kidney disease. Finerenone is a novel, nonsteroidal, selective mineralocorticoid receptor antagonist that has shown to reduce albuminuria in type 2 diabetes (T2D) patients with chronic kidney disease (CKD) while revealing only a low risk of hyperkalemia. However, the effect of finerenone on CV and renal outcomes has not yet been investigated in long-term trials. <b><i>Patients and</i></b> <b><i>Methods:</i></b> The Finerenone in Reducing CV Mortality and Morbidity in Diabetic Kidney Disease (FIGARO-DKD) trial aims to assess the efficacy and safety of finerenone compared to placebo at reducing clinically important CV and renal outcomes in T2D patients with CKD. FIGARO-DKD is a randomized, double-blind, placebo-controlled, parallel-group, event-driven trial running in 47 countries with an expected duration of approximately 6 years. FIGARO-DKD randomized 7,437 patients with an estimated glomerular filtration rate ≥25 mL/min/1.73 m<sup>2</sup> and albuminuria (urinary albumin-to-creatinine ratio ≥30 to ≤5,000 mg/g). The study has at least 90% power to detect a 20% reduction in the risk of the primary outcome (overall two-sided significance level α = 0.05), the composite of time to first occurrence of CV death, nonfatal myocardial infarction, nonfatal stroke, or hospitalization for heart failure. <b><i>Conclusions:</i></b> FIGARO-DKD will determine whether an optimally treated cohort of T2D patients with CKD at high risk of CV and renal events will experience cardiorenal benefits with the addition of finerenone to their treatment regimen. Trial Registration: EudraCT number: 2015-000950-39; ClinicalTrials.gov identifier: NCT02545049.
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| 29. |
- Takeuchi, Fumihiko, et al.
(författare)
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Interethnic analyses of blood pressure loci in populations of East Asian and European descent
- 2018
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Blood pressure (BP) is a major risk factor for cardiovascular disease and more than 200 genetic loci associated with BP are known. Here, we perform a multi-stage genome-wide association study for BP (max N = 289,038) principally in East Asians and meta-analysis in East Asians and Europeans. We report 19 new genetic loci and ancestry-specific BP variants, conforming to a common ancestry-specific variant association model. At 10 unique loci, distinct non-rare ancestry-specific variants colocalize within the same linkage disequilibrium block despite the significantly discordant effects for the proxy shared variants between the ethnic groups. The genome-wide transethnic correlation of causal-variant effect-sizes is 0.898 and 0.851 for systolic and diastolic BP, respectively. Some of the ancestry-specific association signals are also influenced by a selective sweep. Our results provide new evidence for the role of common ancestry-specific variants and natural selection in ethnic differences in complex traits such as BP.
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| 30. |
- Wang, Fang, et al.
(författare)
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Emerging contaminants: A One Health perspective
- 2024
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Ingår i: Innovation. - 2666-6758. ; 5
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Forskningsöversikt (refereegranskat)abstract
- Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.
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| 31. |
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| 32. |
- Weber, Werner, et al.
(författare)
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The EMC2 Project on Embedded Microcontrollers: Technical Progress after two years
- 2016
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Since April 2014 the Artemis/ECSEL project EMC2 is running and provides significant results. EMC2 stands for “Embedded Multi-Core Systems for Mixed Criticality Applications in Dynamic and Changeable Real-Time Environments”. In this paper we report recent progress on technical work in the different workpackages and use cases. We highlight progress in the research on system architecture, design methodology, platform and operating systems, and in qualification and certification. Application cases in the fields of automotive, avionics, health care, and industry are presented exploiting the technical results achieved.
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| 33. |
- Xing, Li-Da, et al.
(författare)
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Asianopodus-type footprints from the Hekou Group of Honggu District, Lanzhou City, Gansu, China and the “heel” of large theropod tracks
- 2014
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Ingår i: Palaeoworld. - : Elsevier BV. - 1871-174X .- 1875-5887. ; 23:3-4, s. 304-313
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Tidskriftsartikel (refereegranskat)abstract
- An increasing number of dinosaur tracksites have been reported from the Cretaceous Hekou Group deposits of the Lanzhou-Minhe Basin in theGansu Province region. These include small sites such as the Huazhuang tracksite, from the Honggu District reported here, the Zhongpu tracksitewith multiple track levels but few well-preserved tracks, other small tracksites currently under investigation, and the large and diverse LiujixiaNational Dinosaur Geopark site at Yanguoxia, where intensive study is ongoing. Collectively these sites reveal that ichnofaunas in the HekouGroup are widespread and diverse. The Huazhuang tracksite yields a small assemblage of moderately well-preserved theropod tracks assigned toAsianopodus. This is the first report of Asianopodus from the Hekou Group. Huazhuang Asianopodus belongs to the Eubrontes morphotype. Thelarge theropod tracks from Lanzhou-Minhe Basin were left by large theropod trackmakers with the same general foot morphology. The specimensare described in detail and compared with other theropod track morphotypes from the Lower Cretaceous of China and elsewhere. In general,although the metatarsophalangeal pads of some Jurassic Eubrontes-type tracks are aligned with the axis of digit III, this feature appears mostcommon in the Early Cretaceous theropod (Eubrontes-type) tracks.
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| 34. |
- Xing, Zhe, et al.
(författare)
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Altered Surface Hydrophilicity on Copolymer Scaffolds Stimulate the Osteogenic Differentiation of Human Mesenchymal Stem Cells
- 2020
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Ingår i: Polymers. - : MDPI. - 2073-4360. ; 12:7
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Tidskriftsartikel (refereegranskat)abstract
- Background: Recent studies have suggested that both poly(l-lactide-co-1,5-dioxepan-2-one) (or poly(LLA-co-DXO)) and poly(l-lactide-co-epsilon-caprolactone) (or poly(LLA-co-CL)) porous scaffolds are good candidates for use as biodegradable scaffold materials in the field of tissue engineering; meanwhile, their surface properties, such as hydrophilicity, need to be further improved. Methods: We applied several different concentrations of the surfactant Tween 80 to tune the hydrophilicity of both materials. Moreover, the modification was applied not only in the form of solid scaffold as a film but also a porous scaffold. To investigate the potential application for tissue engineering, human bone marrow mesenchymal stem cells (hMSCs) were chosen to test the effect of hydrophilicity on cell attachment, proliferation, and differentiation. First, the cellular cytotoxicity of the extracted medium from modified scaffolds was investigated on HaCaT cells. Then, hMSCs were seeded on the scaffolds or films to evaluate cell attachment, proliferation, and osteogenic differentiation. The results indicated a significant increasing of wettability with the addition of Tween 80, and the hMSCs showed delayed attachment and spreading. PCR results indicated that the differentiation of hMSCs was stimulated, and several osteogenesis related genes were up-regulated in the 3% Tween 80 group. Poly(LLA-co-CL) with 3% Tween 80 showed an increased messenger Ribonucleic acid (mRNA) level of late-stage markers such as osteocalcin (OC) and key transcription factor as runt related gene 2 (Runx2). Conclusion: A high hydrophilic scaffold may speed up the osteogenic differentiation for bone tissue engineering.
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| 35. |
- Yang, Jia-Xiang, et al.
(författare)
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Facile synthesis, optical properties and theoretical calculation of two novel two-photon absorption chromophores
- 2010
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Ingår i: Journal of Luminescence. - : Elsevier BV. - 0022-2313 .- 1872-7883. ; 130:4, s. 654-659
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Tidskriftsartikel (refereegranskat)abstract
- Two heterocycle-based derivatives that can be used as two-photon absorption chromophore, 9-butyl-3-(2,6-diphenylpyridin-4-yl)-9H-carbazole (BDPYC) and 9-butyl-3-(4-(2, 6-diphenylpyridin-4-yl)styryl)-9H-carbazole (BDPSC) have been successfully synthesized and fully characterized by elemental analysis, IR, H-1 NMR, C-13 NMR and MS. The molecules possess D-pi-A structures, but have different pi bridge. The 9-butylcarbazole is used as a donor (D), and the pyridine ring is used as an acceptor (A). One- and two-photon absorption and excited fluorescence properties in various solvents were experimentally investigated. Two-photon initiated optical data recording experiments have been carried Out under 740 nm laser radiation, and the possible mechanism of optical data storage is discussed based on theoretical calculations.
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