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| 4. |
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| 5. |
- 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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| 6. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 7. |
- Jones, Benedict C, et al.
(författare)
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To which world regions does the valence-dominance model of social perception apply?
- 2021
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Ingår i: Nature Human Behaviour. - : Springer Science and Business Media LLC. - 2397-3374. ; 5:1, s. 159-169
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Tidskriftsartikel (refereegranskat)abstract
- Over the past 10 years, Oosterhof and Todorov's valence-dominance model has emerged as the most prominent account of how people evaluate faces on social dimensions. In this model, two dimensions (valence and dominance) underpin social judgements of faces. Because this model has primarily been developed and tested in Western regions, it is unclear whether these findings apply to other regions. We addressed this question by replicating Oosterhof and Todorov's methodology across 11 world regions, 41 countries and 11,570 participants. When we used Oosterhof and Todorov's original analysis strategy, the valence-dominance model generalized across regions. When we used an alternative methodology to allow for correlated dimensions, we observed much less generalization. Collectively, these results suggest that, while the valence-dominance model generalizes very well across regions when dimensions are forced to be orthogonal, regional differences are revealed when we use different extraction methods and correlate and rotate the dimension reduction solution. PROTOCOL REGISTRATION: The stage 1 protocol for this Registered Report was accepted in principle on 5 November 2018. The protocol, as accepted by the journal, can be found at https://doi.org/10.6084/m9.figshare.7611443.v1 .
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| 8. |
- Kristanl, Matej, et al.
(författare)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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Ingår i: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 9. |
- Palmer, Nicholette D, et al.
(författare)
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A genome-wide association search for type 2 diabetes genes in African Americans.
- 2012
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Ingår i: PloS one. - San Francisco : Public Library of Science (PLoS). - 1932-6203. ; 7:1, s. e29202-
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Tidskriftsartikel (refereegranskat)abstract
- African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.
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| 10. |
- Qi, Xiuying, et al.
(författare)
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Prevalence and Correlates of Latent Autoimmune Diabetes in Adults in Tianjin, China A population-based cross-sectional study
- 2011
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Ingår i: Diabetes Care. - : American Diabetes Association. - 0149-5992 .- 1935-5548. ; 34:1, s. 66-70
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: Data on latent autoimmune diabetes in adults (LADA) from population-based studies are sparse. We sought to investigate the prevalence and correlates of LADA. RESEARCH DESIGN AND METHODS: A total of 8,109 participants, who were aged >= 15 years and living in Tianjin, China, were assessed to identify individuals with type 2 diabetes (American Diabetes Association Criteria, 1997) and further to detect patients with LADA. LADA was ascertained by 1) the presence of type 2 diabetes and age >= 35 years, 2) the lack of a requirement for insulin at least 6 months after the diagnosis of type 2 diabetes, and 3) serum GAD antibody positivity. Data were analyzed using multinomial logistic regression with adjustment for potential confounders. RESULTS: Of all participants, 498 (6.1%) were patients with type 2 diabetes. Of them, 46 (9.2%) were found to have LADA. The prevalence of LADA was 0.6% (46 of 8,109), and tended to increase with age up to 50-59 years in all participants. The odds ratios (95% CI) of LADA related to hypertension, family history of diabetes, waist-to-hip ratio >= 0.85, and major stressful events were 1.93 (1.02-3.65), 17.59 (9.08-34.06), 5.37 (2.31-12.49), and 4.09 (1.75-9.52), respectively. CONCLUSIONS: The prevalence of LADA is similar to 9% in patients with type 2 diabetes. Hypertension, family history of diabetes, central obesity, and major stressful events may be associated with the occurrence of LADA.
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| 11. |
- Ren, Lin-Ling, et al.
(författare)
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Subcellular relocalization and positive selection play key Roles in the retention of duplicate genes of populus class III peroxidase family
- 2014
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Ingår i: The Plant Cell. - : Oxford University Press (OUP). - 1040-4651 .- 1532-298X. ; 26:6, s. 2404-2419
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Tidskriftsartikel (refereegranskat)abstract
- Gene duplication is the primary source of new genes and novel functions. Over the course of evolution, many duplicate genes lose their function and are eventually removed by deletion. However, some duplicates have persisted and evolved diverse functions. A particular challenge is to understand how this diversity arises and whether positive selection plays a role. In this study, we reconstructed the evolutionary history of the class III peroxidase (PRX) genes from the Populus trichocarpa genome. PRXs are plant-specific enzymes that play important roles in cell wall metabolism and in response to biotic and abiotic stresses. We found that two large tandem-arrayed clusters of PRXs evolved from an ancestral cell wall type PRX to vacuole type, followed by tandem duplications and subsequent functional specification. Substitution models identified seven positively selected sites in the vacuole PRXs. These positively selected sites showed significant effects on the biochemical functions of the enzymes. We also found that positive selection acts more frequently on residues adjacent to, rather than directly at, a critical active site of the enzyme, and on flexible regions rather than on rigid structural elements of the protein. Our study provides new insights into the adaptive molecular evolution of plant enzyme families.
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| 12. |
- Shao, Wen-Ze, et al.
(författare)
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On potentials of regularized Wasserstein generative adversarial networks for realistic hallucination of tiny faces
- 2019
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Ingår i: Neurocomputing. - : ELSEVIER. - 0925-2312 .- 1872-8286. ; 364, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Super-resolution of facial images, a.k.a. face hallucination, has been intensively studied in the past decades due to the increasingly emerging analysis demands in video surveillance, e.g., face detection, verification, identification. However, the actual performance of most previous hallucination approaches will drop dramatically when a very low-res tiny face is provided, due to the challenging multimodality of the problem as well as lack of an informative prior as a strong semantic guidance. Inspired by the latest progress in deep unsupervised learning, this paper focuses on tiny faces of size 16 x 16 pixels, hallucinating them to their 8 x upsampling versions by exploring the potentials of Wasserstein generative adversarial networks (WGAN). Besides a pixel-wise L2 regularization term imposed to the generative model, it is found that our advocated autoencoding generator with both residual and skip connections is a critical component for WGAN representing the facial contour and semantic content to a reasonable precision. With the additional Lipschitz penalty and architectural considerations for the critic in WGAN, the proposed approach finally achieves state-of-the-art hallucination performance in terms of both visual perception and objective assessment. The cropped CelebA face dataset is primarily used to aid the tuning and analysis of the new method, termed as tfh-WGAN. Experimental results demonstrate that the proposed approach not only achieves realistic hallucination of tiny faces, but also adapts to pose, expression, illuminance and occluded variations to a great degree.
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| 13. |
- Zhang, Huai, et al.
(författare)
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A global survey on the use of the international classification of diseases codes for metabolic dysfunction-associated fatty liver disease.
- 2024
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Ingår i: Hepatology international. - 1936-0541.
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Tidskriftsartikel (refereegranskat)abstract
- With the implementation of the 11th edition of the International Classification of Diseases (ICD-11) and the publication of the metabolic dysfunction-associated fatty liver disease (MAFLD) nomenclature in 2020, it is important to establish consensus for the coding of MAFLD in ICD-11. This will inform subsequent revisions of ICD-11.Using the Qualtrics XM and WJX platforms, questionnaires were sent online to MAFLD-ICD-11 coding collaborators, authors of papers, and relevant association members.A total of 890 international experts in various fields from 61 countries responded to the survey. We also achieved full coverage of provincial-level administrative regions in China. 77.1% of respondents agreed that MAFLD should be represented in ICD-11 by updating NAFLD, with no significant regional differences (77.3% in Asia and 76.6% in non-Asia, p=0.819). Over 80% of respondents agreed or somewhat agreed with the need to assign specific codes for progressive stages of MAFLD (i.e. steatohepatitis) (92.2%), MAFLD combined with comorbidities (84.1%), or MAFLD subtypes (i.e., lean, overweight/obese, and diabetic) (86.1%).This global survey by a collaborative panel of clinical, coding, health management and policy experts, indicates agreement that MAFLD should be coded in ICD-11. The data serves as a foundation for corresponding adjustments in the ICD-11 revision.
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| 14. |
- Zhao, Li-Juan, et al.
(författare)
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Lysine demethylase LSD1 delivered via small extracellular vesicles promotes gastric cancer cell stemness
- 2021
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Ingår i: EMBO Reports. - : EMBO. - 1469-221X .- 1469-3178. ; 22:8
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Tidskriftsartikel (refereegranskat)abstract
- Several studies have examined the functions of nucleic acids in small extracellular vesicles (sEVs). However, much less is known about the protein cargos of sEVs and their functions in recipient cells. This study demonstrates the presence of lysine-specific demethylase 1 (LSD1), which is the first identified histone demethylase, in the culture medium of gastric cancer cells. We show that sEVs derived from gastric cancer cells and the plasma of patients with gastric cancer harbor LSD1. The shuttling of LSD1-containing sEVs from donor cells to recipient gastric cancer cells promotes cancer cell stemness by positively regulating the expression of Nanog, OCT4, SOX2, and CD44. Additionally, sEV-delivered LSD1 suppresses oxaliplatin response of recipient cells in vitro and in vivo, whereas LSD1-depleted sEVs do not. Taken together, we demonstrate that LSD1-loaded sEVs can promote stemness and chemoresistance to oxaliplatin. These findings suggest that the LSD1 content of sEV could serve as a biomarker to predict oxaliplatin response in gastric cancer patients.
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| 15. |
- Ablikim, M., et al.
(författare)
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Observation of the decay psi(3686) -> Lambda(Sigma)over-bar(+/-) pi(-/+) + c.c
- 2013
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 88:11, s. 112007-
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Tidskriftsartikel (refereegranskat)abstract
- Using a sample of 1:06 X 10(8) psi(3686) events collected with the BESIII detector, we present the first observation of the decays of psi(3686) -> Lambda(Sigma) over bar (+) pi(-) + c.c. and psi(3686) -> Lambda(Sigma) over bar (-) pi(+) + c.c. The branching fractions are measured to be B(psi(3686) -> Lambda(Sigma) over bar (+) pi(-) + c.c.) = (1.40 +/- 0.03 +/- 0.13) X 10(-4) and B(psi(3686) -> Lambda (Sigma) over bar (-) pi(+) + c.c.) = (1.54 +/- 0.04 +/- 0.13) X 10(-4) where the first errors are statistical and the second ones systematic.
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| 16. |
- Ablikim, M., et al.
(författare)
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Search for eta(c)(2S)h(c) -> p(p)over-bar decays and measurements of the chi(cJ) -> p(p)over-bar branching fractions
- 2013
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 88:11, s. 112001-
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Tidskriftsartikel (refereegranskat)abstract
- Using a sample of 1.06 x 10(8)psi(3686) events collected with the BESIII detector at BEPCII, the decays eta(c)(2S) -> p (p) over bar and h(c) -> p (p) over bar are searched for, where eta(c)(2S) and h(c) are reconstructed in the decay chains psi(3686) -> gamma eta(c)(2S), eta(c)(2S) -> p (p) over bar and psi(3686) -> pi(0)h(c), h(c) -> p (p) over bar, respectively. No significant signals are observed. The upper limits of the product branching fractions are determined to be B(psi(3686) -> gamma eta(c)(2S)) x B(eta(c)(2S) -> p (p) over bar) < 1.4 x 10(-6) and B(psi(3686) -> pi(0)h(c)) x B(h(c) -> p<(p)over bar>) < 1.3 x 10(-7) at the 90% C.L.. The branching fractions for chi(cJ) -> p<(p)over bar> (J = 0, 1, 2) are also measured to be (24.5 +/- 0.8 +/- 1.3, 8.6 +/- 0.5 +/- 0.5, 8.4 +/- 0.5 +/- 0.5) x 10(-5), which are the world's most precise measurements.
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| 17. |
- 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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| 18. |
- Bentham, James, et al.
(författare)
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A century of trends in adult human height
- 2016
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Ingår i: eLIFE. - 2050-084X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.522.7) and 16.5 cm (13.319.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
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| 19. |
- Bentham, James, et al.
(författare)
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A century of trends in adult human height
- 2016
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Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 5
-
Tidskriftsartikel (refereegranskat)abstract
- Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3– 19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8– 144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
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| 20. |
- Berndt, Sonja I., et al.
(författare)
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Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
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Tidskriftsartikel (refereegranskat)abstract
- Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
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| 21. |
- Cai, Jing, et al.
(författare)
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Characterization of offline analysis of particulate matter with FIGAERO-CIMS
- 2023
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Ingår i: Atmospheric Measurement Techniques (AMT). - : Copernicus GmbH. - 1867-8610 .- 1867-8548 .- 1867-1381. ; 16:5, s. 1147-1165
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Tidskriftsartikel (refereegranskat)abstract
- Measurements of the molecular composition of organic aerosol (OA) constituents improve our understanding of sources, formation processes, and physicochemical properties of OA. One instrument providing such data at a time resolution of minutes to hours is the chemical ionization time-of-flight mass spectrometer with filter inlet for gases and aerosols (FIGAERO-CIMS). The technique collects particles on a filter, which are subsequently desorbed, and the evaporated molecules are ionized and analyzed in the mass spectrometer. However, long-term measurements using this technique and/or field deployments at several sites simultaneously require substantial human and financial resources. The analysis of filter samples collected outside the instrument (offline) may provide a more cost-efficient alternative and makes this technology available for the large number of particle filter samples collected routinely at many different sites globally. Filter-based offline use of the FIGAERO-CIMS limits this method, albeit to particle-phase analyses, which is likely at a reduced time resolution compared to online deployments. Here we present the application and assessment of offline FIGAERO-CIMS, using Teflon and quartz fiber filter samples that were collected in autumn 2018 in urban Beijing. We demonstrate the feasibility of the offline application with a “sandwich” sample preparation for the over 900 identified organic compounds with (1) high signal-to-noise ratios, (2) high repeatability, and (3) linear signal response to the filter loadings. Comparable overall signals were observed between the quartz fiber and Teflon filters for 12 and 24h samples but with larger signals for semi-volatile compounds for the quartz fiber filters, likely due to adsorption artifacts. We also compare desorption profile (thermogram) shapes for the two filter materials. Thermograms are used to derive volatility qualitatively based on the desorption temperature at which the maximum signal intensity of a compound is observed (Tmax). While we find that Tmax can be determined with high repeatability (±5.7∘C) from the duplicate tests for one filter type, we observe considerable differences in Tmax between the quartz and Teflon filters, warranting further investigation into the thermal desorption characteristics of different filter types. Overall, this study provides a basis for expanding OA molecular characterization by FIGAERO-CIMS to situations where and when deployment of the instrument itself is not possible.
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| 22. |
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| 23. |
- Ding, Xue Bing, et al.
(författare)
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Impaired meningeal lymphatic drainage in patients with idiopathic Parkinson’s disease
- 2021
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:3, s. 411-418
-
Tidskriftsartikel (refereegranskat)abstract
- Animal studies implicate meningeal lymphatic dysfunction in the pathogenesis of neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease (PD). However, there is no direct evidence in humans to support this role1–5. In this study, we used dynamic contrast-enhanced magnetic resonance imaging to assess meningeal lymphatic flow in cognitively normal controls and patients with idiopathic PD (iPD) or atypical Parkinsonian (AP) disorders. We found that patients with iPD exhibited significantly reduced flow through the meningeal lymphatic vessels (mLVs) along the superior sagittal sinus and sigmoid sinus, as well as a notable delay in deep cervical lymph node perfusion, compared to patients with AP. There was no significant difference in the size (cross-sectional area) of mLVs in patients with iPD or AP versus controls. In mice injected with α-synuclein (α-syn) preformed fibrils, we showed that the emergence of α-syn pathology was followed by delayed meningeal lymphatic drainage, loss of tight junctions among meningeal lymphatic endothelial cells and increased inflammation of the meninges. Finally, blocking flow through the mLVs in mice treated with α-syn preformed fibrils increased α-syn pathology and exacerbated motor and memory deficits. These results suggest that meningeal lymphatic drainage dysfunction aggravates α-syn pathology and contributes to the progression of PD.
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| 24. |
- Fan, Jianming, et al.
(författare)
-
Hydrothermal-assisted synthesis of Li-rich layered oxide microspheres with high capacity and superior rate-capability as a cathode for lithium-ion batteries
- 2015
-
Ingår i: Electrochimica Acta. - 0013-4686. ; 173, s. 7-16
-
Tidskriftsartikel (refereegranskat)abstract
- Li-rich layered oxide materials possess high voltage and high specific capacity, which makes them attractive cathode candidates for lithium-ion batteries. However, they still suffer from a poor rate capability, which seriously blocks their widespread practical applications. In this work, Li(Li0.167Mn0.5Co0.167Ni0.167)O2 microspheres were synthesized by a hydrothermal-assisted method, in which Ni-Co-Mn-based microspherical precursors obtained by a hydrothermal process with polyethylene glycol-600 (PEG-600) as a surfactant were mixed with lithium sources and then sintered to yield the final products. It is found that the as-prepared Li-rich layered oxide microspheres exhibit high discharge capacity and superior rate performance: delivering an initial discharge capacity of 292 mAh g−1 at a current density of 20 mA g−1, 189 mAh g−1 at a current density of 600 mA g−1 and 142 mAh g−1 at a current density of 2000 mA g−1 (10C), which are better than that of the sample as-prepared by co-precipitation method. The high discharge capacity and improved rate-capability were beneficial from the microspheres assembled by uniform primary particles around 250 nm, more reversible redox and better electrode kinetics comparing to that of the co-precipitation sample. The preparation strategy reported here may offer hints for achieving various advanced Li-rich layered composite materials that would be used in high-performance energy storage.
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| 25. |
- Fan, Xinfeng, et al.
(författare)
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Tibetan Plateau Runoff and Evapotranspiration Dataset by an observation-constrained cryosphere-hydrology model
- 2024
-
Ingår i: SCIENTIFIC DATA. - 2052-4463. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- Runoff and evapotranspiration (ET) are pivotal constituents of the water, energy, and carbon cycles. This research presents a 5-km monthly gridded runoff and ET dataset for 1998-2017, encompassing seven headwaters of Tibetan Plateau rivers (Yellow, Yangtze, Mekong, Salween, Brahmaputra, Ganges, and Indus) (hereinafter TPRED). The dataset was generated using the advanced cryosphere-hydrology model WEB-DHM, yielding a Nash coefficient ranging from 0.77 to 0.93 when compared to the observed discharges. The findings indicate that TPRED's monthly runoff notably outperforms existing datasets in capturing hydrological patterns, as evidenced by robust metrics such as the correlation coefficient (CC) (0.944-0.995), Bias (-0.68-0.53), and Root Mean Square Error (5.50-15.59 mm). Additionally, TPRED's monthly ET estimates closely align with expected seasonal fluctuations, as reflected by a CC ranging from 0.94 to 0.98 when contrasted with alternative ET products. Furthermore, TPRED's annual values exhibit commendable concordance with operational products across multiple dimensions. Ultimately, the TPRED will have great application on hydrometeorology, carbon transport, water management, hydrological modeling, and sustainable development of water resources.
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| 26. |
- Ge, Qi, et al.
(författare)
-
Structure-Based Low-Rank Model With Graph Nuclear Norm Regularization for Noise Removal
- 2017
-
Ingår i: IEEE Transactions on Image Processing. - : Institute of Electrical and Electronics Engineers (IEEE). - 1057-7149 .- 1941-0042. ; 26:7, s. 3098-3112
-
Tidskriftsartikel (refereegranskat)abstract
- Nonlocal image representation methods, including group-based sparse coding and block-matching 3-D filtering, have shown their great performance in application to low-level tasks. The nonlocal prior is extracted from each group consisting of patches with similar intensities. Grouping patches based on intensity similarity, however, gives rise to disturbance and inaccuracy in estimation of the true images. To address this problem, we propose a structure-based low-rank model with graph nuclear norm regularization. We exploit the local manifold structure inside a patch and group the patches by the distance metric of manifold structure. With the manifold structure information, a graph nuclear norm regularization is established and incorporated into a low-rank approximation model. We then prove that the graph-based regularization is equivalent to a weighted nuclear norm and the proposed model can be solved by a weighted singular-value thresholding algorithm. Extensive experiments on additive white Gaussian noise removal and mixed noise removal demonstrate that the proposed method achieves a better performance than several state-of-the-art algorithms.
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| 27. |
- Ge, Qi, et al.
(författare)
-
Unsupervised Joint Image Denoising and Active Contour Segmentation in Multidimensional Feature Space
- 2016
-
Ingår i: Mathematical problems in engineering (Print). - : Hindawi Limited. - 1024-123X .- 1563-5147.
-
Tidskriftsartikel (refereegranskat)abstract
- We describe a new method for simultaneous image denoising and level set-based active contour segmentation using multidimensional features. We consider an image to be a surface embedded in a Riemannian manifold. By defining a metric in the embedded space, which in our case includes multidimensional image features as well as a level set-based active contour model, a minimization problem in the image space can be obtained through the Polyakov action framework. The resulting minimization problem is solved with a dual algorithm for efficiency. Benefits of this new method include the fact that it is independent of any artificial “running” parameters, and experiments using both synthetic and real images show that the method is robust with respect to noise and blurry object boundaries.
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| 28. |
- Gharibi, Arash, et al.
(författare)
-
Tunable transient evolutional behaviours of a four-level atomic vapour and the application to photonic logic gates
- 2009
-
Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 42:5, s. 055502-
-
Tidskriftsartikel (refereegranskat)abstract
- The evolutional optical behaviours (turn-on dynamics) of a four-level N-configuration atomic system are considered based on the transient solution to the equations of motion of atomic probability amplitudes. It is shown that the quantum interference between the signal and control fields can lead to the controllable absorption and transparency properties of the atomic vapour. One of the most remarkable properties of the present scheme is that the absorption (or transmittance) of the probe light in the atomic vapour depends on the intensity ratio of the signal field to the control field, and thus the tunable optical features (transparency or opaqueness to the probe light) can be realized by tuning the quantum interferences between the signal and control fields. The present mechanism can be applicable to designs of some new photonic and quantum optical devices such as logic and functional devices as well as optical switches. Two typical photonic logic gates (NOT and NOR gates) designed based on the tunable four-level optical responses are presented as illustrative examples.
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| 29. |
- Guan, Qi, et al.
(författare)
-
Eutrophication changes in fifty large lakes on the Yangtze Plain of China derived from MERIS and OLCI observations
- 2020
-
Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257. ; 246
-
Tidskriftsartikel (refereegranskat)abstract
- The eutrophication problems in lakes on the Yangtze Plain of China have attracted global concern. However, a comprehensive assessment of the eutrophication status and its evolution is still lacking for these regional lakes, mostly because of technical difficulties and/or insufficient data to cover the large region. Our study attempts to fill this knowledge gap by using the entire archive of remote sensing images from two satellite ocean color missions (MEdium Resolution Imaging Spectrometer, or MERIS (2003−2011), and Ocean and Land Color Instrument, or OLCI (2017–2018)), together with in situ data on remote sensing reflectance and chlorophyll-a (Chla) concentrations across various lakes on the Yangtze Plain. A machine learning-based piecewise Chla algorithm was developed in this study, with special considerations to improve algorithm performance under lower Chla conditions. Remotely sensed Chla and algal bloom areas were then used to classify the eutrophication status of 50 large lakes on the Yangtze Plain, and the frequent satellite observations enabled us to estimate the probability of eutrophication occurrence (PEO) for each examined lake. The long-term mean Chla ranged from 17.58 mg m−3 to 43.86 mg m−3 on the Yangtze Plain, and severe floating algal blooms were found in 7 lakes. All 50 lakes had high climatological PEO values (50%) during the study period, indicating a generally high probability of eutrophication in lakes on the Yangtze Plain. However, 21 out of 51 lakes exhibited statistically significant (p < .05) decreasing trends in PEO during the observation period, suggesting an overall improvement in the water quality of lakes on the Yangtze Plain in recent years. The methods developed here are expected to contribute to real-time monitoring of drinking water safety for local regions, and the long-term results provide valuable baseline information for future lake conservation and restoration efforts.
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| 30. |
- Guan, Qi, et al.
(författare)
-
Long-term changes of nitrogen leaching and the contributions of terrestrial nutrient sources to lake eutrophication dynamics on the Yangtze Plain of China
- 2023
-
Ingår i: Biogeosciences. - 1726-4170. ; 20:8, s. 1635-1648
-
Tidskriftsartikel (refereegranskat)abstract
- Over the past half-century, drastically increased chemical fertilizers have entered agricultural ecosystems to promote crop production on the Yangtze Plain, potentially enhancing agricultural nutrient sources for eutrophication in freshwater ecosystems. However, long-term trends of nitrogen dynamics in terrestrial ecosystems and their impacts on eutrophication changes in this region remain poorly studied. Using a process-based ecosystem model, we investigated the temporal and spatial patterns of nitrogen use efficiency (NUE) and nitrogen leaching on the Yangtze Plain from 1979-2018. The agricultural NUE for the Yangtze Plain significantly decreased from 50g€¯% in 1979 to 25g€¯% in 2018, with the largest decline of NUE in soybean, rice, and rapeseed. Simultaneously, the leached nitrogen from cropland and natural land increased, with annual rates of 4.5 and 0.22g€¯kgg€¯Ng€¯ha-1g€¯yr-2, respectively, leading to an overall increase of nitrogen inputs to the 50 large lakes. We further examined the correlations between terrestrial nutrient sources (i.e., the leached nitrogen, total phosphorus sources, and industrial wastewater discharge) and the satellite-observed probability of eutrophication occurrence (PEO) at an annual scale and showed that PEO was positively correlated with the changes in terrestrial nutrient sources for most lakes. Agricultural nitrogen and phosphorus sources were found to explain the PEO trends in lakes in the western and central part of the Yangtze Plain, and industrial wastewater discharge was associated with the PEO trends in eastern lakes. Our results revealed the importance of terrestrial nutrient sources for long-term changes in eutrophic status over the 50 lakes of the Yangtze Plain. This calls for region-specific sustainable nutrient management (i.e., nitrogen and phosphorus applications in agriculture and industry) to improve the water quality of lake ecosystems.
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| 31. |
- Guan, Qi, et al.
(författare)
-
Trends in River Total Suspended Sediments Driven by Dams and Soil Erosion : A Comparison Between the Yangtze and Mekong Rivers
- 2022
-
Ingår i: Water Resources Research. - 0043-1397. ; 58:10
-
Tidskriftsartikel (refereegranskat)abstract
- Global river systems are experiencing rapid changes in sediment transport under growing anthropogenic and climatic stresses. However, the response of sediment discharge to the coupled influence of anthropogenic and natural factors and the associated impacts on the fluvial geomorphology in the Yangtze and Mekong rivers are not comprehensively assessed. Here, we recalibrated a seamless retrieval algorithm of the total suspended sediment (TSS) concentrations using in situ data and concurrent satellite data sets to analyze spatiotemporal patterns of the TSS concentrations in the lower Yangtze and Mekong rivers. Combined with soil erosion rates estimated by the Revised Universal Soil Loss Equation for the past 20 years, we examined the contributions of different factors to TSS trends. The results show that TSS concentrations in the Yangtze River decreased from 0.47 g L−1 in 2000 to 0.23 g L−1 in 2018 due to the construction of the Three Gorges Dam (TGD), especially in the Jingjiang reach, with a declining magnitude of 0.3 g L−1 (∼56%) since the TGD began operating. The Mekong River experienced increasing TSS concentration trends upstream and decreasing trends downstream from 2000 to 2018, possibly attributed to increased upstream soil erosion and decreased downstream water discharge. Declining TSS concentrations in both rivers have driven varying degrees of river channel erosion over the past two decades. This study investigated long-term changes in the TSS concentrations and soil erosion in the Yangtze and Mekong rivers, and the results provide baseline information for the sustainable development of river sediment delivery.
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| 32. |
- Han, Xue-Min, et al.
(författare)
-
Evolution and Function of the Populus SABATH Family Reveal That a Single Amino Acid Change Results in a Substrate Switch
- 2018
-
Ingår i: Plant and Cell Physiology. - : Oxford University Press. - 0032-0781 .- 1471-9053. ; 59:2, s. 392-403
-
Tidskriftsartikel (refereegranskat)abstract
- Evolutionary mechanisms of substrate specificities of enzyme families remain poorly understood. Plant SABATH methyltransferases catalyze methylation of the carboxyl group of various low molecular weight metabolites. Investigation of the functional diversification of the SABATH family in plants could shed light on the evolution of substrate specificities in this enzyme family. Previous studies identified 28 SABATH genes from the Populus trichocarpa genome. In this study, we re-annotated the Populus SABATH gene family, and performed molecular evolution, gene expression and biochemical analyses of this large gene family. Twenty-eight Populus SABATH genes were divided into three classes with distinct divergences in their gene structure, expression responses to abiotic stressors and enzymatic properties of encoded proteins. Populus class I SABATH proteins converted IAA to methyl-IAA, class II SABATH proteins converted benzoic acid (BA) and salicylic acid (SA) to methyl-BA and methyl-SA, while class III SABATH proteins converted farnesoic acid (FA) to methyl-FA. For Populus class II SABATH proteins, both forward and reverse mutagenesis studies showed that a single amino acid switch between PtSABATH4 and PtSABATH24 resulted in substrate switch. Our findings provide new insights into the evolution of substrate specificities of enzyme families.
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| 33. |
- Heid, Iris M, et al.
(författare)
-
Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution
- 2010
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:11, s. 949-960
-
Tidskriftsartikel (refereegranskat)abstract
- Waist-hip ratio (WHR) is a measure of body fat distribution and a predictor of metabolic consequences independent of overall adiposity. WHR is heritable, but few genetic variants influencing this trait have been identified. We conducted a meta-analysis of 32 genome-wide association studies for WHR adjusted for body mass index (comprising up to 77,167 participants), following up 16 loci in an additional 29 studies (comprising up to 113,636 subjects). We identified 13 new loci in or near RSPO3, VEGFA, TBX15-WARS2, NFE2L3, GRB14, DNM3-PIGC, ITPR2-SSPN, LY86, HOXC13, ADAMTS9, ZNRF3-KREMEN1, NISCH-STAB1 and CPEB4 (P = 1.9 × 10⁻⁹ to P = 1.8 × 10⁻⁴⁰) and the known signal at LYPLAL1. Seven of these loci exhibited marked sexual dimorphism, all with a stronger effect on WHR in women than men (P for sex difference = 1.9 × 10⁻³ to P = 1.2 × 10⁻¹³). These findings provide evidence for multiple loci that modulate body fat distribution independent of overall adiposity and reveal strong gene-by-sex interactions.
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| 34. |
- Huang, Jing, et al.
(författare)
-
Differences in driver takeover performance and physiological responses in conditionally automated driving: Links to emotional instability
- 2024
-
Ingår i: Transportation Research Part F: Traffic Psychology and Behaviour. - 1369-8478. ; 105, s. 73-86
-
Tidskriftsartikel (refereegranskat)abstract
- When the automated driving system reaches its technical limit, drivers will have to take over control from the vehicle within a limited time. The drivers’ emotional instability may affect whether they can safely control the vehicle during takeover transitions. Accordingly, this paper explores the association between emotional instability and physiological responses and driver takeover performance. 42 drivers engaged in negative emotion induced by movie clips were involved in a sequence of takeover events in a driving simulator. Personality questionnaires were used to assess the driver's level of emotional instability. Their physiological data before the takeover request (TOR) and operational behavior data fragments for the takeover process were extracted. The results demonstrated that integration of subjective evaluations with electroencephalogram (EEG) and electrocardiogram (ECG) signals allows for more objective measurement of drivers’ level of emotional instability. The statistical analyses indicated that emotional instability has a significant effect on drivers’ heartbeat interval, heart rate, the frequency bands of θ(4–8 Hz), α(8–12 Hz), β(13–30 Hz), γ (30–50 Hz) and lateral takeover performance. Those findings of differences in driver physiological responses and takeover performance under emotional instability may provide additional support for the design of driver state monitoring and adaptive warning systems.
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| 35. |
- Huang, Juan, et al.
(författare)
-
Differential metabolic profiles of ginsenosides in artificial gastric juice using ultra-high-pressure liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometry
- 2022
-
Ingår i: BMC Biomedical chromotography. - : John Wiley & Sons. - 0269-3879 .- 1099-0801. ; 36:12
-
Tidskriftsartikel (refereegranskat)abstract
- Ginsenosides have poor oral bioavailability and undergo rapid biological transformation in the complex gastrointestinal environment. Most studies on the metabolism of ginsenosides have focused on gut bacteria, yet gastric juice remains a nonnegligible factor. Metabolic profiles of ginsenoside monomers formed in artificial gastric juice were separately investigated and qualitatively identified using ultra-high-pressure liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometry (UHPLC-LTQ-Orbitrap MSn). A common pattern of their metabolic pathways was established, showing that ginsenosides were transformed via deglycosylation, hydration, and dehydration pathways. Two major structure types, 20(S), 20(R)-protopanaxatriols and 20(S), 20(R)-protopanaxadiols, basically shared similar transformation pathways and yielded deglycosylated, hydrated, and dehydrated products. Fragmentation patterns of major ginsenosides were also discussed. Consequently, gastric juice, as the primary link in ginsenoside metabolism and as important as the intestinal flora, produces considerable amounts of degraded ginsenosides, providing a partial explanation for the low bioavailabilities of primary ginsenosides.
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| 36. |
- Huang, Ke, et al.
(författare)
-
Tailoring magnetic order via atomically stacking 3d/5d electrons to achieve high-performance spintronic devices
- 2020
-
Ingår i: Applied Physics Reviews. - : AMER INST PHYSICS. - 1931-9401. ; 7:1
-
Forskningsöversikt (refereegranskat)abstract
- The ability to tune magnetic orders, such as magnetic anisotropy and topological spin texture, is desired to achieve high-performance spintronic devices. A recent strategy has been to employ interfacial engineering techniques, such as the introduction of spin-correlated interfacial coupling, to tailor magnetic orders and achieve novel magnetic properties. We chose a unique polar-nonpolar LaMnO3/SrIrO3 superlattice because Mn (3d)/Ir (5d) oxides exhibit rich magnetic behaviors and strong spin-orbit coupling through the entanglement of their 3d and 5d electrons. Through magnetization and magnetotransport measurements, we found that the magnetic order is interface-dominated as the superlattice period is decreased. We were able to then effectively modify the magnetization, tilt of the ferromagnetic easy axis, and symmetry transition of the anisotropic magnetoresistance of the LaMnO3/SrIrO3 superlattice by introducing additional Mn (3d) and Ir (5d) interfaces. Further investigations using in-depth first-principles calculations and numerical simulations revealed that these magnetic behaviors could be understood by the 3d/5d electron correlation and Rashba spin-orbit coupling. The results reported here demonstrate a new route to synchronously engineer magnetic properties through the atomic stacking of different electrons, which would contribute to future applications in high-capacity storage devices and advanced computing.
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| 37. |
- Jayasiri, Subashini C., et al.
(författare)
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The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts
- 2015
-
Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 74:1, s. 3-18
-
Tidskriftsartikel (refereegranskat)abstract
- Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.
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| 38. |
- Jiang, Bing-Xin, et al.
(författare)
-
Fabrication and bonding of In bumps on Micro-LED with 8 μ m pixel pitch
- 2024
-
Ingår i: ENGINEERING RESEARCH EXPRESS. - 2631-8695. ; 6:2
-
Tidskriftsartikel (refereegranskat)abstract
- Indium (In) is currently used to fabricate metal bumps on micro-light-emitting diode (Micro-LED) chips due to its excellent physical properties. However, as Micro-LED pixel size and pitch decrease, achieving high-quality In bumps on densely packed Micro-LED chips often presents more challenges. This paper describes the process of fabricating In bumps on micro-LEDs using thermal evaporation, highlighting an issue where In tends to grow laterally within the photoresist pattern, ultimately blocking the pattern and resulting in undersized and poorly dense In bumps on the Micro-LED chip. To address this issue, we conducted numerous experiments to study the height variation of In bumps within a range of photoresist aperture sizes (3 mu m -7 mu m) under two different resist thickness conditions (3.8 mu m and 4.8 mu m). The results showed that the resist thickness had a certain effect on the height of In bumps on the Micro-LED chip electrodes. Moreover, we found that, with the photoresist pattern size increasing under constant resist thickness conditions, the height and quality of the bumps significantly improved. Based on this finding, we rationalized the adjustment of the photoresist pattern size within a limited emission platform range to compensate for the height difference of In bumps caused by different resist thicknesses between the cathode and anode regions. Consequently, well-shaped and dense In bumps with a maximum height of up to 4.4 mu m were fabricated on 8 mu m pitch Micro-LED chips. Afterwards, we bonded the Micro-LED chip with indium bumps to the CMOS chip, and we found that we could successfully control the CMOS chip to drive the Micro-LED chip to display specific characters through the Flexible Printed Circuit (FPC). This work is of significant importance for the fabrication of In bumps on Micro-LED chips with pitches below 10 mu m and subsequent bonding processes.
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| 39. |
- Kanoni, Stavroula, et al.
(författare)
-
Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
-
Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
-
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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| 40. |
- Kristan, Matej, et al.
(författare)
-
The Sixth Visual Object Tracking VOT2018 Challenge Results
- 2019
-
Ingår i: Computer Vision – ECCV 2018 Workshops. - Cham : Springer Publishing Company. - 9783030110086 - 9783030110093 ; , s. 3-53
-
Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative. Results of over eighty trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis and a “real-time” experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. A long-term tracking subchallenge has been introduced to the set of standard VOT sub-challenges. The new subchallenge focuses on long-term tracking properties, namely coping with target disappearance and reappearance. A new dataset has been compiled and a performance evaluation methodology that focuses on long-term tracking capabilities has been adopted. The VOT toolkit has been updated to support both standard short-term and the new long-term tracking subchallenges. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website (http://votchallenge.net).
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| 41. |
- Lango Allen, Hana, et al.
(författare)
-
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
- 2010
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 467:7317, s. 832-8
-
Tidskriftsartikel (refereegranskat)abstract
- Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P<0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.
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| 42. |
- Li, Constance H., et al.
(författare)
-
Sex differences in oncogenic mutational processes
- 2020
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
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| 43. |
- Li, Qi, 1990, et al.
(författare)
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A Study on Storage Characteristics of Pristine Li-rich Layered Oxide Li1.20Mn0.54Co0.13Ni0.13O2: Effect of Storage Temperature and Duration
- 2015
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Ingår i: Electrochimica Acta. - 0013-4686. ; 154, s. 249-158
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Tidskriftsartikel (refereegranskat)abstract
- Lithium-ion batteries always suffer from serious capability decay, especially when stored at high temperature and/or for prolonged duration. In this work, electrochemical performance for Li-rich layered oxides Li1.20Mn0.54Co0.13Ni0.13O2 was systematically investigated as a function of temperature and duration. Plenty of techniques like SEM, EDS, EIS, ARC, Raman, XRD, and XPS were utilized to characterize the structures, valence states, compositions, particle sizes, and morphologies of the layered oxides with varying temperature and duration. The results reveal that room temperature storage may alter surface kinetics, but hardly influence the electrochemical performance. While in the case of high temperature storage in pristine state, cycling stability is highly dependent on the storage duration. The degradation mechanism at high temperature storage with prolonged duration is demonstrated to be the accumulation of surface species like LiF/LixPFyOz initiated by the strong reactions between LiPF6 electrolyte and electrode. The results reported here may shed light on predicting electrochemical performance by surface analysis and also provide vital hints on enhancing the high-temperature storage stability of Li-rich layered oxides.
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| 44. |
- Li, Shenpan, et al.
(författare)
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Hepatic injury and ileitis associated with gut microbiota dysbiosis in mice upon F–53B exposure
- 2024
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Ingår i: Environmental Research. - : Elsevier. - 0013-9351 .- 1096-0953. ; 248
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Tidskriftsartikel (refereegranskat)abstract
- Chlorinated polyfluorinated ether sulfonate (F–53B), a substitute of perfluorooctane sulfonic acid (PFOS), has attracted significant attention for its link to hepatotoxicity and enterotoxicity. Nevertheless, the underlying mechanisms of F–53B-induced enterohepatic toxicity remain incompletely understood. This study aimed to explore the role of F–53B exposure on enterohepatic injury based on the gut microbiota, pathological and molecular analysis in mice. Here, we exposed C57BL/6 mice to F–53B (0, 4, 40, and 400 μg/L) for 28 days. Our findings revealed a significant accumulation of F–53B in the liver, followed by small intestines, and feces. In addition, F–53B induced pathological collagen fiber deposition and lipoid degeneration, up-regulated the expression of fatty acid β-oxidation-related genes (PPARα and PPARγ, etc), while simultaneously down-regulating pro-inflammatory genes (Nlrp3, IL-1β, and Mcp1) in the liver. Meanwhile, F–53B induced ileal mucosal barrier damage, and an up-regulation of pro-inflammatory genes and mucosal barrier-related genes (Muc1, Muc2, Claudin1, Occludin, Mct1, and ZO-1) in the ileum. Importantly, F–53B distinctly altered gut microbiota compositions by increasing the abundance of Akkermansia and decreasing the abundance of Prevotellaceae_NK3B31_group in the feces. F–53B-altered microbiota compositions were significantly associated with genes related to fatty acid β-oxidation, inflammation, and mucosal barrier. In summary, our results demonstrate that F–53B is capable of inducing hepatic injury, ileitis, and gut microbiota dysbiosis in mice, and the gut microbiota dysbiosis may play an important role in the F–53B-induced enterohepatic toxicity.
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| 45. |
- Liang, Qi, et al.
(författare)
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First-Principles Exploration of Hazardous Gas Molecule Adsorption on Pure and Modified Al60N60 Nanoclusters
- 2020
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Ingår i: Nanomaterials. - : MDPI. - 2079-4991. ; 10:11
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Tidskriftsartikel (refereegranskat)abstract
- In this work, we use the first-principles method to study in details the characteristics of the adsorption of hazardous NO2, NO, CO2, CO and SO2 gas molecules by pure and heteroatom (Ti, Si, Mn) modified Al60N60 nanoclusters. It is found that the pure Al60N60 cluster is not sensitive to CO. When NO2, NO, CO2, CO and SO2 are adsorbed on Al60N60 cluster'stop.b, edge.a(p), edge.a(h), edge.a(p) andedge.a(h) sites respectively, the obtained configuration is the most stable for each gas. Ti, Si and Mn atoms prefer to stay on the top sites of Al60N60 cluster when these heteroatoms are used to modify the pure clusters. The adsorption characteristics of above hazardous gas molecules on these hetero-atom modified nanoclusters are also revealed. It is found that when Ti-Al60N60 cluster adsorbs CO and SO2, the energy gap decreases sharply and the change rate of gap is 62% and 50%, respectively. The Ti-modified Al60N60 improves the adsorption sensitivity of the cluster to CO and SO2. This theoretical work is proposed to predict and understand the basic adsorption characteristics of AlN-based nanoclusters for hazardous gases, which will help and guide researchers to design better nanomaterials for gas adsorption or detection.
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| 46. |
- Liang, Zuozhong, et al.
(författare)
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Novel insight into the epitaxial growth mechanism of six-fold symmetrical beta-Co(OH)(2)/Co(OH)F hierarchical hexagrams and their water oxidation activity
- 2018
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Ingår i: Electrochimica Acta. - : Elsevier BV. - 0013-4686 .- 1873-3859. ; 271, s. 526-536
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Tidskriftsartikel (refereegranskat)abstract
- The six-fold symmetry widely presents in both natural and artificial architectures. Understanding the growth mechanism of six-fold symmetrical materials is of fundamental interest and significance. Herein, we report the formation process of beta-Co(OH)(2)/Co(OH)F hierarchical hexagrams with a six-fold symmetrical arrangement. Our results demonstrate that hexagonal beta-Co(OH)(2) plates are first formed under the reaction condition. These hexagonal plates then act as templates for the growth of Co(OH)F nanorods. The intermediate material is therefore composed of plate-like beta-Co(OH)(2) hexagonal cores appended with six rod-like Co(OH)F branches, giving the beta-Co(OH)(2)/Co(OH)F hybrid. After prolonged reaction, the beta-Co(OH)(2) hexagons can be completely converted, leading to authentic six-branched Co(OH)F nanorods as the final product. Consequently, for both intermediate and final materials, the Co(OH)F nanorods are arranged with a six-fold symmetry. Importantly, these Co(OH)F nanorods grow along beta-Co(OH)(2) hexagon edges as lateral branches instead of perpendicular to hexagons. This uncommon epitaxial growth mechanism is considered to be a result of the matching between the b-axis of Co(OH)F crystals and the a-axis of beta-Co(OH)(2) crystals, which is beneficial for the electrocatalysis. The beta-Co(OH)(2)/Co(OH)F hierarchical hexagrams show enhanced water oxidation activity compared to the pure beta-Co(OH)(2) and Co(OH)F.
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| 47. |
- Lindgren, Cecilia M, et al.
(författare)
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Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution.
- 2009
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Ingår i: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 5:6, s. e1000508-
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Tidskriftsartikel (refereegranskat)abstract
- To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist-hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9x10(-11)) and MSRA (WC, P = 8.9x10(-9)). A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6x10(-8)). The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.
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| 48. |
- Liu, Ruishun, et al.
(författare)
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Cryosphere-Hydrometeorology Observations for a Water Tower Unit on the Tibetan Plateau Using the BeiDou-3 Navigation Satellite System
- 2024
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Ingår i: BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY. - 0003-0007 .- 1520-0477. ; 105:3
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Tidskriftsartikel (refereegranskat)abstract
- Life and civilization in arid regions depend on the availability of freshwater. Arid alpine river basins, where hydrological processes are highly sensitive to rapid warming, act as vital water towers for lowland oases. However, scientific understanding of precipitation variability and related cryosphere-hydrology processes is extremely limited because of the scarcity of in situ observations. The upper Danghe River basin (UDB; similar to 14,000 km2) is an arid and westerly dominated basin on the northeastern Tibetan Plateau and is the water source for the Dunhuang Oasis in China. We have established a comprehensive cryosphere-hydrometeorology observation network in the basin since 2014. At present, the network consists of 21 automatic rain gauges, 22 soil freeze-thaw monitoring stations, 4 automatic weather stations (AWS), and a 50-m gradient meteorological tower with an eddy covariance system. In particular, the 18 sites, located in remote areas without public networks, are equipped with new -generation BeiDou-3 communication terminals that enable the observations to be easily, safely, and reliably read and quality controlled in near-real time from offices in the city or at home. This integrated observation network over the UDB that facilitates the monitoring of cryosphere-hydrology processes, land-atmosphere interactions, and local weather processes. In addition, the observations are helpful for the objective evaluation, and continual improvement, of hydrological models, satellite -retrieval products, and reanalysis datasets. Finally, the network is expected to promote a better understanding of the status and role of water towers in arid zones and to provide basic data support for the sustainable development of the Dunhuang Oasis and the Belt and Road.
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| 49. |
- Locke, Adam E, et al.
(författare)
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Genetic studies of body mass index yield new insights for obesity biology.
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 518:7538, s. 197-401
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Tidskriftsartikel (refereegranskat)abstract
- Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10(-8)), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ∼2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.
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| 50. |
- Lu, Yingchang, et al.
(författare)
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New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk
- 2016
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- To increase our understanding of the genetic basis of adiposity and its links to cardiometabolic disease risk, we conducted a genome-wide association meta-analysis of body fat percentage (BF%) in up to 100,716 individuals. Twelve loci reached genome-wide significance (P<5 × 10(-8)), of which eight were previously associated with increased overall adiposity (BMI, BF%) and four (in or near COBLL1/GRB14, IGF2BP1, PLA2G6, CRTC1) were novel associations with BF%. Seven loci showed a larger effect on BF% than on BMI, suggestive of a primary association with adiposity, while five loci showed larger effects on BMI than on BF%, suggesting association with both fat and lean mass. In particular, the loci more strongly associated with BF% showed distinct cross-phenotype association signatures with a range of cardiometabolic traits revealing new insights in the link between adiposity and disease risk.
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