| 1. |
- 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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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Li, Qizhao, et al.
(författare)
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Regioselectively Halogenated Expanded Porphyrinoids as Building Blocks for Constructing Porphyrin-Porphyrinoid Heterodyads with Tunable Energy Transfer
- 2019
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Ingår i: Journal of the American Chemical Society. - : AMER CHEMICAL SOC. - 0002-7863 .- 1520-5126. ; 141:13, s. 5294-5302
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Tidskriftsartikel (refereegranskat)abstract
- Expanded porphyrins have been attracting increasing attention owing to their unique optical and electrochemical properties as well as switchable aromaticity. Toward material applications, regioselective functionalization of the expanded porphyrins at their periphery is indeed challenging due to the presence of multiple reactive sites. Herein, a set of regioselective halogenated isomers (L5-Br-A/B/C) of neo-confused isosmaragdyrin (L5) are synthesized by a combination of the halogenation reaction of L5 and sequential macrocycleto-macrocycle transformation reactions of its halogenated isomers. On this basis, the regioselectively functionalized isosmaragdyrins are utilized as building blocks for constructing multichromophoric porphyrinoids, specifically, heterodyads L5-ZnP-A/B/C, in which a common zinc porphyrin is linked at three different pyrrolic positions of isosmaragdyrins, respectively, by Sonogashira coupling reactions. The highly efficient energy cascade from porphyrin to isosmaragdyrin is elucidated using steady-state/time-resolved spectroscopies and theoretical calculations. Notably, the energy transfer processes from the porphyrin to the isosmaragdyrin moieties as well as the excitation energy transfer rates in L5-ZnP-A/B/C are highly dependent on the linking sites by through-bond and Forster-type resonance energy transfer mechanisms. The site-selective functionalization and subsequent construction of a set of heterodyads of the expanded porphyrinoid would provide opportunities for developing new materials for optoelectronic applications.
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| 4. |
- Li, Qizhao, et al.
(författare)
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Skeletal Rearrangement of Twisted Thia-Norhexaphyrin : Multiply Annulated Polypyrrolic Aromatic Macrocycles
- 2019
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Ingår i: Angewandte Chemie International Edition. - : WILEY-V C H VERLAG GMBH. - 1433-7851 .- 1521-3773. ; 58:18, s. 5925-5929
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Tidskriftsartikel (refereegranskat)abstract
- A hybrid thia-norhexaphyrin comprising a directly linked N-confused pyrrole and thiophene unit (1) revealed unique macrocycle transformations to afford multiply inner-annulated aromatic macrocycles. Oxidation with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone triggered a cleavage of the C-S bond of the thiophene unit, accompanied with skeletal rearrangement to afford unique pi-conjugated products: a thiopyrrolo-pentaphyrin embedded with a pyrrolo[1,2]isothiazole (2), a sulfur-free pentaphyrin incorporating an indolizine moiety (3), and a thiopyranyltriphyrinoid containing a 2H-thiopyran unit (4). Furthermore, 2 underwent desulfurization reactions to afford a fused pentaphyrin containing a pyrrolizine moiety (5) under mild conditions. Using expanded porphyrin scaffolds, oxidative thiophene cleavage and desulfurization of the hitherto unknown N-confused core-modified macrocycles would be a practical approach for developing unique polypyrrolic aromatic macrocycles.
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| 5. |
- Tang, Sui, et al.
(författare)
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Association of plant-based diet index with sleep quality in middle-aged and older adults : The Healthy Dance Study
- 2023
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Ingår i: Sleep Health. - : Elsevier. - 2352-7218 .- 2352-7226. ; 9:5, s. 698-703
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: To investigate the association between plant-based diet indices and sleep quality in Chinese middle-aged and older adults.Methods: The study included 2424 participants aged 45 years and older. Dietary data were collected using a semi-quantitative food frequency questionnaire, and sleep quality was assessed by the Pittsburgh Sleep Quality Index scale. Plant-based diet was categorized based on 3 indices (score range, 17-85) covering 17 food groups: the overall plant-based diet index, healthful plant-based diet index, and unhealthful plant-based diet index. The associations between these plant-based diet indices and sleep quality were examined using logistic and linear regression analyses.Results: After controlling for sociodemographic, lifestyle, and multiple disease-related factors, participants in the highest quartile of the healthful plant-based diet index had 0.55 higher odds of better sleep quality (95% CI: 0.42, 0.72; P-trend < .001). In contrast, participants in the highest quartile of the unhealthful plant-based diet index had 2.03 higher odds of poor sleep quality (95% CI: 1.51, 2.72; P-trend < .001). In addition, plant-based diet index and healthful plant-based diet index were inversely associated with Pittsburgh Sleep Quality Index scores, while unhealthful plant-based diet index and Pittsburgh Sleep Quality Index scores were positively associated.Conclusions: We found unhealthy plant-based diets are significantly associated with poor sleep quality. Adherence to overall plant-based diets, especially healthy plant-based diets, was positively associated with optimal sleep quality.(c) 2023 National Sleep Foundation. Published by Elsevier Inc. All rights reserved.
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| 6. |
- Xiong, Wenjuan, et al.
(författare)
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SiNx films and membranes for photonic and MEMS applications
- 2020
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Ingår i: Journal of materials science. Materials in electronics. - : Springer Science and Business Media LLC. - 0957-4522 .- 1573-482X. ; 31, s. 90-97
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Tidskriftsartikel (refereegranskat)abstract
- This work presents a novel process to form SiN x films and process for membranes with excellent mechanical properties for micro-electro-mechanical systems application as well as integration as IR waveguide for photonic application. The SiN x films were fabricated in SiNgen apparatus which is a single wafer chamber equipment compared to conventional low pressure chemical vapor deposition furnace process. The films showed low stress, good mechanical properties, but the synthesis also eradicates the issues of particle contamination. Through optimizing of the growth parameters and post annealing profile, low stress (40 Mpa) SiN x film could be finally deposited when annealing temperature rose up to 1150 °C. The stress relaxation is a result of more Si nano-crystalline which was formed during annealing, according to the FTIR results. The mechanical properties, Young’s modulus and hardness, were 210 Gpa and 20 Gpa respectively. For the waveguide application, a stack of three layers, SiO 2 /SiN x /SiO 2 was formed where the optimized layer thicknesses were used for minimum optical loss according to simulation feedback. After deposition of the first two layers in the stack, the samples were annealed in range of 900–1150 °C in order to release the stress. Chemical mechanical polish technique was applied to planarize the nitride layer prior to the oxide cladding layer. Such wafers can be used to bond to Si or Ge to manufacture advanced substrates.
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| 7. |
- Du, Ningchao, et al.
(författare)
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Phytoestrogens protect joints in collagen induced arthritis by increasing IgG glycosylation and reducing osteoclast activation
- 2020
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Ingår i: International Immunopharmacology. - London : Elsevier. - 1567-5769 .- 1878-1705. ; 83
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Tidskriftsartikel (refereegranskat)abstract
- Based on previous studies, we know that estrogen can protect the joints from arthritis development by increasing IgG glycosylation and inhibiting osteoclast activation. Phytoestrogens, especially genistein and daidzein, are structurally similar to estradiol that can bind to estrogen receptors (ERs). However, how phytoestrogens affect IgG glycosylation and osteoclast activation in vivo are not investigated so far. In this study, we used 20 mg/kg genistein or daidzein to gavage the female DBA1/J mice in collagen induced arthritis (CIA). We assessed arthritis and bone erosion by clinical scores, histopathology, and micro-CT analysis. Inflammatory cells such as neutrophils, B cells, macrophages and T cells in the peripheral blood were analyzed by flow cytometry. Phagocytic function of peritoneal macrophages was assessed by using FITC-labeled Escherichia coli. New monoclonal antibodies against CII were produced, purified and analyzed. Glycosylation levels of polyclonal and monoclonal IgG were detected by lectin-ELISA. Quantitative PCR was used to analyze the genes related to IgG glycosylation (B4galt1, St6gal1) and osteoclasts (TRAP, NFATC1, c-Fos). Expression of NF-κB and Akt signaling pathways as well as downstream transcription factors NFATc1 and c-Fos was studied by Western blot. Our results show that phytoestrogens protect mice from CIA by increasing IgG glycosylation leading to amelioration of inflammation and inhibiting the NF-κB pathway and NFATc1/c-Fos to decrease the activity of osteoclasts. In conclusion, phytoestrogens can protect bone and joints in CIA mice by increasing IgG glycosylation and inhibiting osteoclast activity. © 2020 Elsevier B.V.
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| 8. |
- Li, Fei, et al.
(författare)
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Iron(III) complexes with a tripodal N3O ligand containing an internal base as a model for catechol intradiol-cleaving dioxygenases
- 2007
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 46:22, s. 9364-9371
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Tidskriftsartikel (refereegranskat)abstract
- A bis(mu-alkoxo)-bridged dinuclear iron(III) complex [Fe(L)(NO3)](2)(NO3)(2) [1; HL = NN-bis(2-pyridylmethyl)-N-(2hydroxyethyl)amine] of the tripodal N3O ligand was prepared as a biomimetic model for the intradiol-cleaving dioxygenase enzymes. The reaction of 1 and catechol in the presence of excess triethylamine gave the catecholate (CAT) chelate b is(u -al koxo) -bridged dinuclear iron(Ill) complex [Fe(L)(CAT)12 (2). The molecular structures of complexes 1 and 2 were determined by X-ray crystallography. Diiron complexes 1 and 2 contain the same bis(u-alkoxo)diiron diamond core. All heteroatoms (N3O) of the ligand are coordinated to the iron center in complex 1 with two pyridine nitrogen atoms on the axial bonds, while one of the pyridyl arms of the ligand is left uncoordinated in complex 2. The interaction of the diiron complex 1 and 3,5-di-tert-butylcatechol (H2DBC) was investigated by electronic and mass spectroscopy. Complex 1 displays the intradiol-cleaving dioxygenase activity, and the coordinate ethoxyl arm of the ligand is capable of accepting the proton from catechol, which mimics the function of Tyr447 in the. protocatechuate 3,4-dioxygenase as an internal base. The spectrop h oto metric titration experiment indicates the relatively low demand of the external base (0.8 equiv based on Fe3+) for attaining the highest dioxygenase activity of complex 1. The reaction rate of the reactive intermediate [Fe(HL)(DBC)](+) with dioxygen is 0.38 M-1 s(-1) determined by kinetic studies.
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| 9. |
- Li, Juan, et al.
(författare)
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Unravelling the novel sex determination genotype with ‘ZY’ and a distinctive 2.15–2.95 Mb inversion among poplar species through haplotype-resolved genome assembly and comparative genomics analysis
- 2024
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998.
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Tidskriftsartikel (refereegranskat)abstract
- Populus tomentosa, an indigenous tree species, is widely distributed and cultivated over 1,000,000 km2 in China, contributing significantly to forest production, ecological conservation and urban–rural greening. Although a reference genome is available for P. tomentosa, the intricate interspecific hybrid origins, chromosome structural variations (SVs) and sex determination mechanisms remain confusion and unclear due to its broad and even overlapping geographical distribution, extensive morphological variations and cross infiltration among white poplar species. We conducted a haplotype-resolved de novo assembly of P. tomentosa elite individual GM107, which comprises subgenomes a and b with a total genome size of 714.9 Mb. We then analysed the formation of hybrid species and the phylogenetic evolution and sex differentiation across the entire genus. Phylogenomic analyses suggested that GM107 likely originated from a hybridisation event between P. alba (♀) and P. davidiana (♂) approximately 3.8 Mya. A total of 1551 chromosome SVs were identified between the two subgenomes. More noteworthily, a distinctive inversion structure spanning 2.15–2.95 Mb was unveiled among Populus, Tacamahaca, Turaga, Aigeiros poplar species and Salix, highlighting a unique evolutionary feature. Intriguingly, a novel sex genotype of the ZY type, which represents a crossover between XY and ZW systems, was identified and confirmed through both natural and artificial hybrids populations. These novel insights offer significant theoretical value for the study of the species' evolutionary origins and serve as a valuable resource for ecological genetics and forest biotechnology.
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| 10. |
- Li, Qianjin, et al.
(författare)
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Synthesis of highly selective molecularly imprinted nanoparticles by a solid-phase imprinting strategy for fluorescence turn-on recognition of phospholipid
- 2022
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Ingår i: Sensors and actuators. B, Chemical. - : Elsevier. - 0925-4005 .- 1873-3077. ; 368
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Tidskriftsartikel (refereegranskat)abstract
- Molecularly imprinted polymers (MIPs) are artificial receptors with template tailored recognition sites complementary to the targets. The versatility of this molecular imprinting technique has been hampered by the lack of practical synthetic procedures to prepare highly selective MIP nanoparticles targeting phospholipids, which are challenging to be imprinted due to their amphiphilic structure. Here, a novel sedimentation-based solid phase imprinting strategy is introduced relying on polymerization in the presence of template-modified silica nanospheres (SNs). To demonstrate this concept, the sphingosine-1-phosphate receptor agonist fingolimod phosphate (FP) was coupled to SNs which were dispersed in the prepolymerization medium consisting of the fluorescent functional monomer 1,8-bis(N-vinylimidazol-N'-methyl)anthracene bromide and the crosslinking monomer ethyleneglycol dimethacrylate. High dilution polymerization of the dispersion under agitation followed by simple sedimentation-based separation of the SN template resulted in the isolation of surface imprinted fluorescent MIP nanoparticles (FMIP NPs) in a high yield (17 %). The FMIP NPs displayed fluorescence enhancement in response to the template with a high imprinting factor (IF=9) under the experimental conditions and good specificity, and could recognize FP in human serum with recoveries of 68-74 %. Moreover, the template-modified SNs could be recycled for reuse. Such molecular imprinting strategy opens a new approach to produce highly selective artificial receptors targeting phospholipids.
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| 11. |
- Li, Qizhao, et al.
(författare)
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Twisted-Planar-Twisted expanded porphyrinoid dimer as a rudimentary reaction-based methanol indicator
- 2020
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Directly linked porphyrin dimers have attracted considerable attention because of their intriguing electronic features. Most emphasis has been placed on either dimers with large dihedral angles between the constituent planar monomeric subunits or those with overall planarity, referred to as "Planar-Twisted-Planar" and "Planar-Planar-Planar", respectively. Herein, we report a "Twisted-Planar-Twisted" framework, the hexaphyrin dimer D that exists in a trans configuration. Treatment of D with MeOH affords two isomeric dimers, MD1 and MD2, both of which incorporate a methoxy moiety and exist in cis orientations with respect to the tethering linkage. The methanol-promoted conversion is accompanied by a readily discernible color change from green to brown and is not induced to an appreciable level by other alcohols. Dimer D thus acts as a rudimentary, albeit highly selective, reaction-based methanol indicator. This work provides a promising approach for constructing reaction-based chemosensors using porphyrinoid dimers of nonplanar subunits with biased reactivity. Directly linked porphyrin dimers show intriguing electronic features but emphasis has been placed on planar monomeric units. Here, the authors report a Twisted-Planar-Twisted framework which can undergo a cis-trans transformation accompanied by a colour change in presence of methanol, making this framework applicable as a methanol sensor.
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| 12. |
- Mokhtari, Dariush, et al.
(författare)
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Imatinib mesilate-induced phosphatidylinositol 3-kinase signalling and improved survival in insulin-producing cells : role of Src homology 2-containing inositol 5'-phosphatase interaction with c-Abl
- 2013
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Ingår i: Diabetologia. - : Springer Science and Business Media LLC. - 0012-186X .- 1432-0428. ; 56:6, s. 1327-1338
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Tidskriftsartikel (refereegranskat)abstract
- AIMS/HYPOTHESIS: It is not clear how small tyrosine kinase inhibitors, such as imatinib mesilate, protect against diabetes and beta cell death. The aim of this study was to determine whether imatinib, as compared with the non-cAbl-inhibitor sunitinib, affects pro-survival signalling events in the phosphatidylinositol 3-kinase (PI3K) pathway. METHODS: Human EndoC-βH1 cells, murine beta TC-6 cells and human pancreatic islets were used for immunoblot analysis of insulin receptor substrate (IRS)-1, Akt and extracellular signal-regulated kinase (ERK) phosphorylation. Phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3] plasma membrane concentrations were assessed in EndoC-βH1 and MIN6 cells using evanescent wave microscopy. Src homology 2-containing inositol 5'-phosphatase 2 (SHIP2) tyrosine phosphorylation and phosphatase and tensin homologue deleted on chromosome 10 (PTEN) serine phosphorylation, as well as c-Abl co-localisation with SHIP2, were studied in HEK293 and EndoC-βH1 cells by immunoprecipitation and immunoblot analysis. Gene expression was assessed using RT-PCR. Cell viability was measured using vital staining. RESULTS: Imatinib stimulated ERK(thr202/tyr204) phosphorylation in a c-Abl-dependent manner. Imatinib, but not sunitinib, also stimulated IRS-1(tyr612), Akt(ser473) and Akt(thr308) phosphorylation. This effect was paralleled by oscillatory bursts in plasma membrane PI(3,4,5)P3 levels. Wortmannin induced a decrease in PI(3,4,5)P3 levels, which was slower in imatinib-treated cells than in control cells, indicating an effect on PI(3,4,5)P3-degrading enzymes. In line with this, imatinib decreased the phosphorylation of SHIP2 but not of PTEN. c-Abl co-immunoprecipitated with SHIP2 and its binding to SHIP2 was largely reduced by imatinib but not by sunitinib. Imatinib increased total β-catenin levels and cell viability, whereas sunitinib exerted negative effects on cell viability. CONCLUSIONS/INTERPRETATION: Imatinib inhibition of c-Abl in beta cells decreases SHIP2 activity, which results in enhanced signalling downstream of PI3 kinase.
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| 13. |
- Roy, Sushmita, et al.
(författare)
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Identification of functional elements and regulatory circuits by Drosophila modENCODE.
- 2010
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 330:6012, s. 1787-1797
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Tidskriftsartikel (refereegranskat)abstract
- To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.
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| 14. |
- Song, Lin, et al.
(författare)
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Thalamic gray matter volume mediates the association between KIBRA polymorphism and olfactory function among older adults : a population-based study
- 2022
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Ingår i: Cerebral Cortex. - : Oxford University Press (OUP). - 1047-3211 .- 1460-2199. ; 33:7, s. 3664-3673
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Tidskriftsartikel (refereegranskat)abstract
- The kidney and brain expressed protein (KIBRA) rs17070145 polymorphism is associated with both structure and activation of the olfactory cortex. However, no studies have thus far examined whether KIBRA can be linked with olfactory function and whether brain structure plays any role in the association. We addressed these questions in a population-based cross-sectional study among rural-dwelling older adults. This study included 1087 participants derived from the Multidomain Interventions to Delay Dementia and Disability in Rural China, who underwent the brain MRI scans in August 2018 to October 2020; of these, 1016 took the 16-item Sniffin’ Sticks identification test and 634 (62.40%) were defined with olfactory impairment (OI). Data were analyzed using the voxel-based morphometry analysis and general linear, logistic, and structural equation models. The KIBRA rs17070145 C-allele (CC or CT vs. TT genotype) was significantly associated with greater gray matter volume (GMV) mainly in the bilateral orbitofrontal cortex and left thalamus (P < 0.05) and with the multi-adjusted odds ratio of 0.73 (95% confidence interval 0.56–0.95) for OI. The left thalamic GMV could mediate 8.08% of the KIBRA-olfaction association (P < 0.05). These data suggest that the KIBRA rs17070145 C-allele is associated with a reduced likelihood of OI among older adults, partly mediated through left thalamic GMV.
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| 15. |
- Wu, Xiuchen, et al.
(författare)
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Exposures to temperature beyond threshold disproportionately reduce vegetation growth in the northern hemisphere
- 2019
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Ingår i: National Science Review. - : Oxford University Press (OUP). - 2095-5138 .- 2053-714X. ; 6:4, s. 786-795
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Tidskriftsartikel (refereegranskat)abstract
- In recent decades, terrestrial vegetation in the northern hemisphere (NH) has been exposed to warming and more extremely high temperatures. However, the consequences of these changes for terrestrial vegetation growth remain poorly quantified and understood. By examining a satellite-based vegetation index, tree-ring measurements and land-surface model simulations, we discovered a consistent convex pattern in the responses of vegetation growth to temperature exposure (TE) for forest, shrub and grass in both the temperate (30°−50° N) and boreal (50°−70° N) NH during the period of 1982−2012. The response of vegetation growth to TE for the three vegetation types in both the temperate and boreal NH increased convergently with increasing temperature, until vegetation type-dependent temperature thresholds were reached. A TE beyond these temperature thresholds resulted in disproportionately weak positive or even strong negative responses. Vegetation growth in the boreal NH was more vulnerable to extremely high-temperature events than vegetation growth in the temporal NH. The non-linear responses discovered here provide new insights into the dynamics of northern terrestrial ecosystems in a warmer world.
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| 16. |
- Xin, Yiwei, et al.
(författare)
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Fusobacterium nucleatum- induced exosomal HOTTIP promotes gastric cancer progression through the microRNA-885-3p/EphB2 axis
- 2023
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Ingår i: Cancer Science. - : John Wiley & Sons. - 1347-9032 .- 1349-7006. ; 114:6, s. 2360-2374
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies have reported that Fusobacterium nucleatum (Fn) is associated with gastric cancer (GC). Cancer-derived exosomes contain key regulatory noncoding RNAs and are a crucial medium of intercellular communication. However, the function and regulatory mechanism of exosomes (Fn-GCEx) secreted from Fn-infected GC cells remains unclear. In this study, Fn-GCEx enhanced the proliferation, migration, and invasion capacity of GC cells in vitro, as well as tumor growth and metastasis in vivo. HOTTIP was also upregulated in GC cells treated with Fn-GCEx. Moreover, knockdown of HOTTIP weakened the effects of Fn-GCEx in recipient GC cells. Mechanistically, HOTTIP promoted EphB2 expression by sponging microRNA (miR)-885-3p, thus activating the PI3K/AKT pathway in Fn-GCEx treated GC cells. Overall, Fn infection induced the upregulation of exosomal HOTTIP from GC cells that subsequently promoted GC progression through the miR-885-3p/EphB2/PI3K/AKT axis. Herein, we identify a potential molecular pathway and therapeutic target for GC.
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| 17. |
- Yu, Wenjin, et al.
(författare)
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Deep Learning-Based Classification of Cancer Cell in Leptomeningeal Metastasis on Cytomorphologic Features of Cerebrospinal Fluid
- 2022
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Ingår i: Frontiers in Oncology. - : Frontiers Media SA. - 2234-943X. ; 12, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Background: It is a critical challenge to diagnose leptomeningeal metastasis (LM), given its technical difficulty and the lack of typical symptoms. The existing gold standard of diagnosing LM is to use positive cerebrospinal fluid (CSF) cytology, which consumes significantly more time to classify cells under a microscope.Objective: This study aims to establish a deep learning model to classify cancer cells in CSF, thus facilitating doctors to achieve an accurate and fast diagnosis of LM in an early stage.Method: The cerebrospinal fluid laboratory of Xijing Hospital provides 53,255 cells from 90 LM patients in the research. We used two deep convolutional neural networks (CNN) models to classify cells in the CSF. A five-way cell classification model (CNN1) consists of lymphocytes, monocytes, neutrophils, erythrocytes, and cancer cells. A four-way cancer cell classification model (CNN2) consists of lung cancer cells, gastric cancer cells, breast cancer cells, and pancreatic cancer cells. Here, the CNN models were constructed by Resnet-inception-V2. We evaluated the performance of the proposed models on two external datasets and compared them with the results from 42 doctors of various levels of experience in the human-machine tests. Furthermore, we develop a computer-aided diagnosis (CAD) software to generate cytology diagnosis reports in the research rapidly.Results: With respect to the validation set, the mean average precision (mAP) of CNN1 is over 95% and that of CNN2 is close to 80%. Hence, the proposed deep learning model effectively classifies cells in CSF to facilitate the screening of cancer cells. In the human-machine tests, the accuracy of CNN1 is similar to the results from experts, with higher accuracy than doctors in other levels. Moreover, the overall accuracy of CNN2 is 10% higher than that of experts, with a time consumption of only one-third of that consumed by an expert. Using the CAD software saves 90% working time of cytologists.Conclusion: A deep learning method has been developed to assist the LM diagnosis with high accuracy and low time consumption effectively. Thanks to labeled data and step-by-step training, our proposed method can successfully classify cancer cells in the CSF to assist LM diagnosis early. In addition, this unique research can predict cancer’s primary source of LM, which relies on cytomorphologic features without immunohistochemistry. Our results show that deep learning can be widely used in medical images to classify cerebrospinal fluid cells. For complex cancer classification tasks, the accuracy of the proposed method is significantly higher than that of specialist doctors, and its performance is better than that of junior doctors and interns. The application of CNNs and CAD software may ultimately aid in expediting the diagnosis and overcoming the shortage of experienced cytologists, thereby facilitating earlier treatment and improving the prognosis of LM.
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| 18. |
- Zhang, Yinping, et al.
(författare)
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Ten cities cross-sectional questionnaire survey of children asthma and other allergies in China
- 2013
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Ingår i: Chinese Science Bulletin. - : Springer Science and Business Media LLC. - 1001-6538 .- 1861-9541. ; 58:34, s. 4182-4189
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Tidskriftsartikel (refereegranskat)abstract
- Asthma, rhinitis and eczema (allergic or non-allergic) have increased throughout the world during the last decades, especially among children. Changes in the indoor environment are suspected to be important causes. China has experienced a dramatic change in indoor environmental exposures during the past two decades. However, such changes and their associations with children's asthma and other health aspects have not been thoroughly studied. China, Children, Homes, Health (CCHH), Phase I, was a cross-sectional questionnaire survey of 48219 children 1-8 years old in 10 Chinese cities during 2010-2012. The questionnaire includes the International Study of Asthma and Allergies in Childhood (ISAAC) core health questions and additional questions regarding housing, life habits and outdoor environment. In health analyses, children aged 3-6 years old were included. The prevalences of doctor diagnosed asthma varied from 1.7% to 9.8% (mean 6.8%), a large increase from 0.91% in 1999 and 1.50% in 2000. The prevalence of wheeze, rhinitis and atopic eczema (last 12 months) varied from 13.9% to 23.7%, 24.0% to 50.8% and 4.8% to 15.8%, respectively. Taiyuan had the lowest prevalences of all illnesses and Shanghai the highest, except for wheezewhere the highest value was for Urumqi. We found (1) no obvious association between disease prevalences and ambient PM10 concentrations and (2) higher prevalences of disease in humid climates with hot summers and cold winters, but with no centrally heated buildings. Associations between the diseases and economic status as indexed by Gross Domestic Product (GDP) requires further study.
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| 19. |
- Cai, Tingting, et al.
(författare)
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Human cortical neural correlates of visual fatigue during binocular depth perception : An fNIRS study
- 2017
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Ingår i: PLOS ONE. - : PUBLIC LIBRARY SCIENCE. - 1932-6203. ; 12:2
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Tidskriftsartikel (refereegranskat)abstract
- Functional near-infrared spectroscopy (fNIRS) was adopted to investigate the cortical neural correlates of visual fatigue during binocular depth perception for different disparities (from 0.1 degrees to 1.5 degrees). By using a slow event-related paradigm, the oxyhaemoglobin (HbO) responses to fused binocular stimuli presented by the random-dot stereogram (RDS) were recorded over the whole visual dorsal area. To extract from an HbO curve the characteristics that are correlated with subjective experiences of stereopsis and visual fatigue, we proposed a novel method to fit the time-course HbO curve with various response functions which could reflect various processes of binocular depth perception. Our results indicate that the parietal-occipital cortices are spatially correlated with binocular depth perception and that the process of depth perception includes two steps, associated with generating and sustaining stereovision. Visual fatigue is caused mainly by generating stereovision, while the amplitude of the haemodynamic response corresponding to sustaining stereovision is correlated with stereopsis. Combining statistical parameter analysis and the fitted time-course analysis, fNIRS could be a promising method to study visual fatigue and possibly other multi-process neural bases.
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| 20. |
- Chen, Gongbo, et al.
(författare)
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All-cause, cardiovascular, and respiratory mortality and wildfire-related ozone : a multicountry two-stage time series analysis
- 2024
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Ingår i: The Lancet Planetary Health. - : Elsevier. - 2542-5196. ; 8:7, s. e452-e462
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Tidskriftsartikel (refereegranskat)abstract
- Background: Wildfire activity is an important source of tropospheric ozone (O3) pollution. However, no study to date has systematically examined the associations of wildfire-related O3 exposure with mortality globally.Methods: We did a multicountry two-stage time series analysis. From the Multi-City Multi-Country (MCC) Collaborative Research Network, data on daily all-cause, cardiovascular, and respiratory deaths were obtained from 749 locations in 43 countries or areas, representing overlapping periods from Jan 1, 2000, to Dec 31, 2016. We estimated the daily concentration of wildfire-related O3 in study locations using a chemical transport model, and then calibrated and downscaled O3 estimates to a resolution of 0·25° × 0·25° (approximately 28 km2 at the equator). Using a random-effects meta-analysis, we examined the associations of short-term wildfire-related O3 exposure (lag period of 0–2 days) with daily mortality, first at the location level and then pooled at the country, regional, and global levels. Annual excess mortality fraction in each location attributable to wildfire-related O3 was calculated with pooled effect estimates and used to obtain excess mortality fractions at country, regional, and global levels.Findings: Between 2000 and 2016, the highest maximum daily wildfire-related O3 concentrations (≥30 μg/m3) were observed in locations in South America, central America, and southeastern Asia, and the country of South Africa. Across all locations, an increase of 1 μg/m3 in the mean daily concentration of wildfire-related O3 during lag 0–2 days was associated with increases of 0·55% (95% CI 0·29 to 0·80) in daily all-cause mortality, 0·44% (–0·10 to 0·99) in daily cardiovascular mortality, and 0·82% (0·18 to 1·47) in daily respiratory mortality. The associations of daily mortality rates with wildfire-related O3 exposure showed substantial geographical heterogeneity at the country and regional levels. Across all locations, estimated annual excess mortality fractions of 0·58% (95% CI 0·31 to 0·85; 31 606 deaths [95% CI 17 038 to 46 027]) for all-cause mortality, 0·41% (–0·10 to 0·91; 5249 [–1244 to 11 620]) for cardiovascular mortality, and 0·86% (0·18 to 1·51; 4657 [999 to 8206]) for respiratory mortality were attributable to short-term exposure to wildfire-related O3.Interpretation: In this study, we observed an increase in all-cause and respiratory mortality associated with short-term wildfire-related O3 exposure. Effective risk and smoke management strategies should be implemented to protect the public from the impacts of wildfires.
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| 21. |
- Chen, Gongbo, et al.
(författare)
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Mortality risk attributable to wildfire-related PM2·5 pollution : a global time series study in 749 locations
- 2021
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Ingår i: The Lancet Planetary Health. - : Elsevier. - 2542-5196. ; 5:9, s. e579-e587
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Many regions of the world are now facing more frequent and unprecedentedly large wildfires. However, the association between wildfire-related PM2·5 and mortality has not been well characterised. We aimed to comprehensively assess the association between short-term exposure to wildfire-related PM2·5 and mortality across various regions of the world.METHODS: For this time series study, data on daily counts of deaths for all causes, cardiovascular causes, and respiratory causes were collected from 749 cities in 43 countries and regions during 2000-16. Daily concentrations of wildfire-related PM2·5 were estimated using the three-dimensional chemical transport model GEOS-Chem at a 0·25° × 0·25° resolution. The association between wildfire-related PM2·5 exposure and mortality was examined using a quasi-Poisson time series model in each city considering both the current-day and lag effects, and the effect estimates were then pooled using a random-effects meta-analysis. Based on these pooled effect estimates, the population attributable fraction and relative risk (RR) of annual mortality due to acute wildfire-related PM2·5 exposure was calculated.FINDINGS: 65·6 million all-cause deaths, 15·1 million cardiovascular deaths, and 6·8 million respiratory deaths were included in our analyses. The pooled RRs of mortality associated with each 10 μg/m3 increase in the 3-day moving average (lag 0-2 days) of wildfire-related PM2·5 exposure were 1·019 (95% CI 1·016-1·022) for all-cause mortality, 1·017 (1·012-1·021) for cardiovascular mortality, and 1·019 (1·013-1·025) for respiratory mortality. Overall, 0·62% (95% CI 0·48-0·75) of all-cause deaths, 0·55% (0·43-0·67) of cardiovascular deaths, and 0·64% (0·50-0·78) of respiratory deaths were annually attributable to the acute impacts of wildfire-related PM2·5 exposure during the study period.INTERPRETATION: Short-term exposure to wildfire-related PM2·5 was associated with increased risk of mortality. Urgent action is needed to reduce health risks from the increasing wildfires.
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| 22. |
- Chen, Min, et al.
(författare)
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Yeast increases glycolytic flux to support higher growth rates accompanied by decreased metabolite regulation and lower protein phosphorylation
- 2023
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 120:25
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Tidskriftsartikel (refereegranskat)abstract
- Supply of Gibbs free energy and precursors are vital for cellular function and cell metabolism have evolved to be tightly regulated to balance their supply and consumption. Precursors and Gibbs free energy are generated in the central carbon metabolism (CCM), and fluxes through these pathways are precisely regulated. However, how fluxes through CCM pathways are affected by posttranslational modification and allosteric regulation remains poorly understood. Here, we integrated multi-omics data collected under nine different chemostat conditions to explore how fluxes in the CCM are regulated in the yeast Saccharomyces cerevisiae. We deduced a pathway- and metabolism-specific CCM flux regulation mechanism using hierarchical analysis combined with mathematical modeling. We found that increased glycolytic flux associated with an increased specific growth rate was accompanied by a decrease in flux regulation by metabolite concentrations, including the concentration of allosteric effectors, and a decrease in the phosphorylation level of glycolytic enzymes.
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| 23. |
- Chen, Tianyi, et al.
(författare)
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Maternal exposure to PM2.5/BC during pregnancy predisposes children to allergic rhinitis which varies by regions and exclusive breastfeeding
- 2022
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Ingår i: Environment International. - : Elsevier. - 0160-4120 .- 1873-6750. ; 165
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundIncreasing prevalence of childhood allergic rhinitis(AR) needs a deeper understanding on the potential adverse effects of early life exposure to air pollution.ObjectivesThe main aim was to evaluate the effects of maternal exposure to PM2.5 and chemical constituents during pregnancy on preschool children’s AR, and further to explore the modification effects of regions and exclusive breastfeeding.MethodsA multi-center population-based study was performed in 6 cities from 3 regions of China in 2011–2012. Maternal exposure to ambient PM2.5 and main chemical constituents(BC, OM, SO42−, NO3−, NH4+) during pregnancy was assessed and a longitudinal prospective analysis was applied on preschool children’s AR. The modification effects of regions and exclusive breastfeeding were investigated.ResultsA total of 8.8% and 9.8% of children reported doctor-diagnosed allergic rhinitis(DDAR) and current hay fever, respectively, and 48.6% had less than 6 months of exclusive breastfeeding. The means of PM2.5 during pregnancy were 52.7 μg/m3, 70.3 μg/m3 and 76.4 μg/m3 in the east, north and central south of China, respectively. Multilevel log-binomial model regression showed that each interquartile range(IQR) increase of PM2.5 during pregnancy was associated with an average increase in prevalence ratio (PR) of DDAR by 1.43(95% confidence interval(CI): 1.11, 1.84) and current hay fever by 1.79(95% CI: 1.26, 2.55), respectively. Among chemical constituents, black carbon (BC) had the strongest associations. Across 3 regions, the eastern cities had the highest associations, followed by those in the central south and the north. For those equal to or longer than 6 months of exclusive breastfeeding, the associations were significantly reduced.ConclusionsChildren in east of China had the highest risks of developing AR per unit increase of maternal exposure to PM2.5 during pregnancy, especially BC constituent. Remarkable decline was found in association with an increase in breastfeeding for ≥6 months, in particular in east of China.
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| 24. |
- Cheng, Hong, et al.
(författare)
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Home environment exposure and sick building syndrome (SBS) symptoms among adults in southern China : Health associations in 2010 and 2019
- 2024
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Ingår i: Building and Environment. - : Elsevier. - 0360-1323 .- 1873-684X. ; 248
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Tidskriftsartikel (refereegranskat)abstract
- We studied time trends in home environment and sick building syndrome (SBS) symptoms in a repeat study in five cities in southern China. Moreover, we studied associations between home environment exposure and SBS symptoms. Parents from randomly selected day care centers were invited. One parent per family answered a questionnaire on the home environment and their own SBS symptoms. Data collection was performed in two surveys in 2010 and 2019 (27,292 participants in 2010 and 32,073 in 2019). We used two-level logistic regression to analyze health associations. Asthma decreased from 1.7% to 1.5% (P < 0.05) but allergic rhinitis increased from 6.5% to 16.4% (P < 0.001). All SBS symptoms decreased from 2010 to 2019 (all P < 0.001). Most aspects of the home environment improved from 2010 to 2019 but there were less cleaning, more cats, dogs, and urbanization in 2019. Redecoration, new furniture, and pests were associated with most types of SBS symptoms, similarly in 2010 and 2019. Environmental tobacco smoke (ETS) was associated with SBS symptoms in 2019 only. In conclusion, prevalence of SBS symptoms among young parents in southern China decreased from 2010 to 2019 but allergic rhinitis increased. Cockroaches, rats, mice, mosquitoes or flies can be consistent biological risk factors for SBS symptoms. Redecoration, buying new furniture and traffic air pollution are other risk factors for SBS symptoms. Daily cleaning, frequently putting bedding to sunshine, and having a fan in the bathroom can be protective factors. ETS is an emerging risk factor for SBS symptoms.
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| 25. |
- Daranciang, Dan, et al.
(författare)
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Ultrafast Photovoltaic Response in Ferroelectric Nanolayers
- 2012
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Ingår i: Physical Review Letters. - 1079-7114. ; 108:8
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Tidskriftsartikel (refereegranskat)abstract
- We show that light drives large-amplitude structural changes in thin films of the prototypical ferroelectric PbTiO3 via direct coupling to its intrinsic photovoltaic response. Using time-resolved x-ray scattering to visualize atomic displacements on femtosecond time scales, photoinduced changes in the unit-cell tetragonality are observed. These are driven by the motion of photogenerated free charges within the ferroelectric and can be simply explained by a model including both shift and screening currents, associated with the displacement of electrons first antiparallel to and then parallel to the ferroelectric polarization direction.
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