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. |
- Zhao, Sen, et al.
(författare)
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Expanding the mutation and phenotype spectrum of MYH3-associated skeletal disorders
- 2022
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Ingår i: NPJ genomic medicine. - : Nature Publishing Group. - 2056-7944. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Pathogenic variants in MYH3 cause distal arthrogryposis type 2A and type 2B3 as well as contractures, pterygia and spondylocarpotarsal fusion syndromes types 1A and 1B. These disorders are ultra-rare and their natural course and phenotypic variability are not well described. In this study, we summarize the clinical features and genetic findings of 17 patients from 10 unrelated families with vertebral malformations caused by dominant or recessive pathogenic variants in MYH3. Twelve novel pathogenic variants in MYH3 (NM_002470.4) were identified: three of them were de novo or inherited in autosomal dominant way and nine were inherited in autosomal recessive way. The patients had vertebral segmentation anomalies accompanied with variable joint contractures, short stature and dysmorphic facial features. There was a significant phenotypic overlap between dominant and recessive MYH3-associated conditions regarding the degree of short stature as well as the number of vertebral fusions. All monoallelic variants caused significantly decreased SMAD3 phosphorylation, which is consistent with the previously proposed pathogenic mechanism of impaired canonical TGF-β signaling. Most of the biallelic variants were predicted to be protein-truncating, while one missense variant c.4244T>G,p.(Leu1415Arg), which was inherited in an autosomal recessive way, was found to alter the phosphorylation level of p38, suggesting an inhibition of the non-canonical pathway of TGF-β signaling. In conclusion, the identification of 12 novel pathogenic variants and overlapping phenotypes in 17 affected individuals from 10 unrelated families expands the mutation and phenotype spectrum of MYH3-associated skeletal disorders. We show that disturbances of canonical or non-canonical TGF-β signaling pathways are involved in pathogenesis of MYH3-associated skeletal fusion (MASF) syndrome.
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3. |
- Shi, Wenming, et al.
(författare)
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Urinary phthalate metabolites in relation to childhood asthmatic and allergic symptoms in Shanghai
- 2018
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Ingår i: Environment International. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0160-4120 .- 1873-6750. ; 121, s. 276-286
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Tidskriftsartikel (refereegranskat)abstract
- Background: Few studies can be found on phthalate exposure in relation to childhood asthma and allergic symptoms from Mainland China, where a persistent increase in prevalence of childhood asthma and allergic disease has been observed. Objectives: This study aimed to assess the exposure levels to phthalates and its relationship with asthmatic and allergic symptoms among children in Shanghai, which has the highest prevalence of childhood asthma in Mainland China. Methods: A follow-up study (2013-2014) of 434 children aged 5-10 years was conducted, based on the China, Children, Homes, Health (CCHH) study (2011-2012) in Shanghai, China. Information on asthmatic and allergic symptoms (wheeze, rhinitis, and eczema) were collected using validated questionnaires. Ten phthalate metabolites in morning urine samples were analyzed by high-performance liquid chromatography with triple quadrupole tandem mass spectrometry (HPLC-MS/MS). Multivariable logistic regression was used to estimate the associations between symptoms and urinary phthalate metabolites controlling for demographics, family history of allergic diseases and other covariates. Results: Nine out of 10 phthalate metabolites were detected in all subjects (average detection rate of 93.2%). By multivariable logistic regression analyses, the 4th quartile of Mono-n-butyl phthalate (MnBP) (reference: 1st quartile) had adjusted prevalence odds ratios (aPORs) and 95% confidence intervals (95%CIs) of 2.27(1.06-4.88), 2.14(1.02-4.46) and 2.98(1.19-7.50) for wheeze, rhinitis and eczema, respectively, while those of Mono-isobutyl phthalate (MiBP) were 2.23(1.08-4.62) and 2.96(1.02-8.60) for rhinitis and eczema, respectively. The highest quartile of mono-2-ethyl-5-hydroxyhexyl phthalate(MEHHP) and mono 2 ethyl 5 ox ohexyl phthalate(MEOHP) had aPORs and 95%CIs of 3.10(1.10-8.74) and 2.63(1.02-6.80) for eczema, respectively. By summing up the 4 low molecular weight metabolites (Sigma 4LMWP) and all 9 metabolites (Sigma(9)Total), the highest quartiles of Sigma 4LMWP and Sigma(9)Total were significantly associated with all symptoms. In most of the above associations, a significantly increasing trend from the 1st to the 4th quartile was observed. Subjects with 2 or 3 concomitant symptoms (reference: no symptoms) had significant positive associations with a higher level (the 4th quartile) of phthalate metabolites. Conclusions: Low MW metabolites such as MnBP and MiBP, high MW DEHP and the total amount of phthalate metabolites might have adverse health effects on asthma and allergic symptoms in Chinese children.
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4. |
- Wang, Hao, et al.
(författare)
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In-situ growth of low-dimensional perovskite-based insular nanocrystals for highly efficient light emitting diodes
- 2023
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Ingår i: Light. - : SPRINGERNATURE. - 2095-5545 .- 2047-7538. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Regulation of perovskite growth plays a critical role in the development of high-performance optoelectronic devices. However, judicious control of the grain growth for perovskite light emitting diodes is elusive due to its multiple requirements in terms of morphology, composition, and defect. Herein, we demonstrate a supramolecular dynamic coordination strategy to regulate perovskite crystallization. The combined use of crown ether and sodium trifluoroacetate can coordinate with A site and B site cations in ABX(3) perovskite, respectively. The formation of supramolecular structure retard perovskite nucleation, while the transformation of supramolecular intermediate structure enables the release of components for slow perovskite growth. This judicious control enables a segmented growth, inducing the growth of insular nanocrystal consist of low-dimensional structure. Light emitting diode based on this perovskite film eventually brings a peak external quantum efficiency up to 23.9%, ranking among the highest efficiency achieved. The homogeneous nano-island structure also enables high-efficiency large area (1 cm(2)) device up to 21.6%, and a record high value of 13.6% for highly semi-transparent ones.
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5. |
- Zhang, Dezhi, et al.
(författare)
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Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)
- 2023
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Ingår i: SYSTEMATIC BIOLOGY. - 1063-5157 .- 1076-836X.
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Tidskriftsartikel (refereegranskat)abstract
- Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of 4 Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and similar to 39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which-in combination-support the following tree topology: ([{E. godlewskii, E. cia}, E. cioides], E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.
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6. |
- Jash, Sukanta, et al.
(författare)
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Cis P-tau is a central circulating and placental etiologic driver and therapeutic target of preeclampsia
- 2023
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Ingår i: Nature Communications. - : NATURE PORTFOLIO. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Preeclampsia (PE) is the leading cause of maternal and fetal mortality globally and may trigger dementia later in life in mothers and their offspring. However, the etiological drivers remain elusive. Cis P-tau is an early etiological driver and blood biomarker in pre-clinical Alzheimers and after vascular or traumatic brain injury, which can be targeted by stereo-specific antibody, with clinical trials ongoing. Here we find significant cis P-tau in the placenta and serum of PE patients, and in primary human trophoblasts exposed to hypoxia or sera from PE patients due to Pin1 inactivation. Depletion of cis P-tau from PE patient sera by the antibody prevents their ability to disrupt trophoblast invasion and endovascular activity and to cause the PE-like pathological and clinical features in pregnant humanized tau mice. Our studies uncover that cis P-tau is a central circulating etiological driver and its stereo-specific antibody is valuable for early PE diagnosis and treatment.
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7. |
- Li, Chenxi, et al.
(författare)
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Aligning silver nanowire films with cellulose nanocrystal nematics
- 2021
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Ingår i: Optical Materials Express. - : The Optical Society. - 2159-3930 .- 2159-3930. ; 11:10, s. 3321-3331
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Tidskriftsartikel (refereegranskat)abstract
- Anisotropic plasmonic films are a desirable material for many optoelectronic ap-plications. Here, we propose a method to align silver nanowires (AgNWs) with the help of uniaxial nematic alignment of cellulose nanocrystal (CNC) liquid crystals (LCs) that can preserve their LC orientation in solid film. AgNWs are doped into uniaxial nematic CNC LCs, where AgNWs are oriented parallel to the director of shear-aligned CNCs without aggregation. The AgNWs orientations are determined by polarized optical and dark field microscopic images. The alignment of AgNWs is characterized by the scalar order parameter S , and the measured S around 0.59 for aligned AgNWs presents an improved anisotropy with the assistance of uniaxial nematic CNC LCs. The electrical property of aligned AgNWs is examined by the four-probe method and exhibits the maximum ratio of anisotropic sheet resistance around 5, consistent with the simulated percolation probability performance using the Monte Carlo computation. Our results show that the uniaxial nematic CNC LCs can act as an effective template in aligning AgNWs, which is compatible with 3D printing and microfluidics, and allows for the preparation of low-cost, innovative optical materials and devices.
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8. |
- Li, Chenxi, et al.
(författare)
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pH dependence of the chirality of nematic cellulose nanocrystals
- 2019
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Cellulose nanocrystals produced by acid hydrolysis of native cellulose form a well-known chiral nematic liquid crystal phase. The mechanism involved in the formation of chirality has been the subject of a vigorous discussion. The pH and concentration dependence of the phase is studied using cellulose nanocrystal droplets within a silicon oil suspension, which allows for convenient real-time microscale manipulation of phase behaviors and properties. We demonstrate the existence of nematic phases at both low and high pH regions consistent with the Stroobants - Lekkerkerker - Odijk theory. Our results confirm electrostatic interactions play a critical role in controlling the strength of the chirality.
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9. |
- Li, Chenxi, et al.
(författare)
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Preparation and liquid crystal phase properties of discotic cellulose nanoparticles
- 2019
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Ingår i: Cellulose. - : SPRINGER. - 0969-0239 .- 1572-882X. ; 26:18, s. 9543-9552
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the behavior of fluids with inhomogeneous structural properties is critical for many industrial and biological materials. Sulfuric acid hydrolysis of cotton with ultrasonic treatment and low-speed centrifugation during purification yields "spiky" discotic cellulose particles. Amorphous cellulose remained in solution and forms discotic units which may be nucleated by crystalline rods. Scanning electron microscope and transmission electron microscope images confirm the discotic nature of the cellulose. High speed centrifugation could recover rod-like cellulose nanocrystals from the discotic cellulose nanoparticle solution. 3.6 wt% discotic cellulose nanoparticles formed the typical nematic phase and the liquid crystal texture became more structured with increasing concentration. Our results showed that spontaneous structuring of amorphous cellulose can lead to phase behavior that cannot be achieved using just rod-like cellulose nanocrystals. Graphic abstract Mixtures containing amorphous and crystalline cellulose can form discotic cellulose nanoparticles. These solutions can form nematic phase (A), a structured columnar-like phase (B), and a glassy phase [GRAPHICS] .
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10. |
- Li, Chenxi, et al.
(författare)
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Preparation of optical waveplates from cellulose nanocrystal nematics on patterned polydimethylsiloxane substrates
- 2019
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Ingår i: Optical Materials Express. - : Optical Society of America. - 2159-3930 .- 2159-3930. ; 9:12, s. 4614-4623
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Tidskriftsartikel (refereegranskat)abstract
- Optical waveplates play an essential role in controlling polarization in various applications. We show the feasibility of facile production of optical waveplates from plant-based cellulose nanocrystal (CNC) nematics. We align CNC nematic liquid crystals doped with polyethylene glycol on periodically patterned polydimethylsiloxane substrates on large scale by shearing forces and prepare a 1/4 lambda and a 1/2 lambda CNC waveplates for 530 nm by bonding two slices of CNC nematic films with half-period displacement. The optical performance of the CNC waveplates is investigated by Mueller matrix analysis and is examined by measuring the transmission spectra of the waveplate between two polarizers, and optical extinction and birefringence of CNCs are extracted from the measured spectra. Our CNC waveplates of arbitrary phase difference are flexible and can be tailored into any desirable shape conveniently.
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11. |
- Qu, Yanhua, 1974-, et al.
(författare)
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The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau
- 2021
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 10.1073/pnas.2012398118:13, s. e2012398118-e2012398118
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Tidskriftsartikel (refereegranskat)abstract
- Species in a shared environment tend to evolve similar adaptations under the influence of their phylogenetic context. Using snowfinches, a monophyletic group of passerine birds (Passeridae), we study the relative roles of ancestral and species-specific adaptations to an extreme high-elevation environment, the Qinghai–Tibet Plateau. Our ancestral trait reconstruction shows that the ancestral snowfinch occupied high elevations and had a larger body mass than most nonsnowfinches in Passeridae. Subsequently, this phenotypic adaptation diversified in the descendant species. By comparing high-quality genomes from representatives of the three phylogenetic lineages, we find that about 95% of genes under positive selection in the descendant species are different from those in the ancestor. Consistently, the biological functions enriched for these species differ from those of their ancestor to various degrees (semantic similarity values ranging from 0.27 to 0.5), suggesting that the three descendant species have evolved divergently from the initial adaptation in their common ancestor. Using a functional assay to a highly selective gene, DTL, we demonstrate that the nonsynonymous substitutions in the ancestor and descendant species have improved the repair capacity of ultraviolet-induced DNA damage. The repair kinetics of the DTL gene shows a twofold to fourfold variation across the ancestor and the descendants. Collectively, this study reveals an exceptional case of adaptive evolution to high-elevation environments, an evolutionary process with an initial adaptation in the common ancestor followed by adaptive diversification of the descendant species.
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12. |
- Shi, Feng, et al.
(författare)
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A multi-proxy reconstruction of spatial and temporal variations in Asian summer temperatures over the last millennium
- 2015
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Ingår i: Climatic Change. - : Springer Science and Business Media LLC. - 0165-0009 .- 1573-1480. ; 131:4, s. 663-674
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Tidskriftsartikel (refereegranskat)abstract
- To investigate climate variability in Asia during the last millennium, the spatial and temporal evolution of summer (June–July–August; JJA) temperature in eastern and south-central Asia is reconstructed using multi-proxy records and the regularized expectation maximization (RegEM) algorithm with truncated total least squares (TTLS), under a point-by-point regression (PPR) framework. The temperature index reconstructions show that the late 20th century was the warmest period in Asia over the past millennium. The temperature field reconstructions illustrate that temperatures in central, eastern, and southern China during the 11th and 13th centuries, and in western Asia during the 12th century, were significantly higher than those in other regions, and comparable to levels in the 20th century. Except for the most recent warming, all identified warm events showed distinct regional expressions and none were uniform over the entire reconstruction area. The main finding of the study is that spatial temperature patterns have, on centennial time-scales, varied greatly over the last millennium. Moreover, seven climate model simulations, from the Coupled Model Intercomparison Project Phase 5 (CMIP5), over the same region of Asia, are all consistent with the temperature index reconstruction at the 99 % confidence level. Only spatial temperature patterns extracted as the first empirical orthogonal function (EOF) from the GISS-E2-R and MPI-ESM-P model simulations are significant and consistent with the temperature field reconstruction over the past millennium in Asia at the 90 % confidence level. This indicates that both the reconstruction and the simulations depict the temporal climate variability well over the past millennium. However, the spatial simulation or reconstruction capability of climate variability over the past millennium could be still limited. For reconstruction, some grid points do not pass validation tests and reveal the need for more proxies with high temporal resolution, accurate dating, and sensitive temperature signals, especially in central Asia and before AD 1400.
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13. |
- Shi, Feng, et al.
(författare)
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Interdecadal to Multidecadal Variability of East Asian Summer Monsoon Over the Past Half Millennium
- 2022
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Ingår i: Journal of Geophysical Research - Atmospheres. - 2169-897X .- 2169-8996. ; 127:20
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Tidskriftsartikel (refereegranskat)abstract
- The East Asian summer monsoon (EASM) plays a crucial role for ecosystems and societies in East Asia past, present, and future. However, substantial uncertainties remain regarding EASM variability on interdecadal to multidecadal timescales because of the short length of instrumental data in East Asia. This study extended the EASM circulation index in the modern meteorological studies to the paleoclimate over the past half-millennium (1470-1998 CE) to reconcile the understanding of the EASM variability in paleoclimate and modern meteorological studies. The EASM index is reconstructed based on the common signal from the three main types of the proxy records (the tree rings, speleothems, and historical documentary data) related to EASM. The reconstructed EASM index captures the simultaneous changes of the "Meiyu precipitation" and the southwesterly anomalies in South China on interdecadal to multidecadal timescales, which is a dynamic pattern visible and well-documented in the modern meteorology. Analysis of the reconstructed EASM index suggests that the interdecadal to multidecadal EASM variability is closely associated with the Pacific-Japan teleconnection pattern, which acts as a bridge between the negative phase of the Pacific Decadal Oscillation and the anomalous anticyclonic circulation over the western North Pacific. It also indicates that the EASM variability over the recent 30 years (1992-2021 CE) falls within the range of natural variability over the past half-millennium.
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14. |
- Shi, Feng, et al.
(författare)
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Interdecadal to Multidecadal Variability of East Asian Summer Monsoon Over the Past Half Millennium
- 2022
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Ingår i: Journal of Geophysical Research - Atmospheres. - : American Geophysical Union (AGU). - 2169-897X .- 2169-8996. ; 127:20
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Tidskriftsartikel (refereegranskat)abstract
- The East Asian summer monsoon (EASM) plays a crucial role for ecosystems and societies in East Asia past, present, and future. However, substantial uncertainties remain regarding EASM variability on interdecadal to multidecadal timescales because of the short length of instrumental data in East Asia. This study extended the EASM circulation index in the modern meteorological studies to the paleoclimate over the past half-millennium (1470–1998 CE) to reconcile the understanding of the EASM variability in paleoclimate and modern meteorological studies. The EASM index is reconstructed based on the common signal from the three main types of the proxy records (the tree rings, speleothems, and historical documentary data) related to EASM. The reconstructed EASM index captures the simultaneous changes of the “Meiyu precipitation” and the southwesterly anomalies in South China on interdecadal to multidecadal timescales, which is a dynamic pattern visible and well-documented in the modern meteorology. Analysis of the reconstructed EASM index suggests that the interdecadal to multidecadal EASM variability is closely associated with the Pacific-Japan teleconnection pattern, which acts as a bridge between the negative phase of the Pacific Decadal Oscillation and the anomalous anticyclonic circulation over the western North Pacific. It also indicates that the EASM variability over the recent 30 years (1992–2021 CE) falls within the range of natural variability over the past half-millennium.
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15. |
- Wang, Nan, et al.
(författare)
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Colloidal directional structures at a nematic liquid crystal–air interface
- 2023
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Ingår i: Liquid crystals (Print). - : Taylor and Francis Ltd.. - 0267-8292 .- 1366-5855. ; 50:11-12, s. 1930-1937
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Tidskriftsartikel (refereegranskat)abstract
- We present a variety of structures formed by colloidal droplets at a nematic liquid crystal–air interface, where the elastic dipole–dipole, quadrupole–quadrupole and dipole–quadrupole interactions are all essentially involved. The colloidal structures observed not only include chains with kinks or clusters but also comprise directional structures, such as directional chains and branches, whose direction is associated with the tilting director in the liquid crystal layer. The dipole–quadrupole interaction, originating from the polydispersity of the droplets, plays a central role for the formation of these directional structures. Clusters consisting of directional branches and chains are also observed and found to be fractal statistically.
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16. |
- Wang, Nan, et al.
(författare)
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Controlled Multistep Self-Assembling of Colloidal Droplets at a Nematic Liquid Crystal-Air Interface
- 2019
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Ingår i: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 123:8
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Tidskriftsartikel (refereegranskat)abstract
- We present a controlled cascade of self-assemblings of colloidal droplets at a nematic liquid crystal-air interface into large-scale ordered structures. Changing the tilt of the droplet-induced elastic dipoles via its dependence on the nematic film thickness, we are able to control the dipole-dipole interaction and thus the self-assembling regime. For a progressively large tilt, droplets form anisotropic lattices, which then transform into arrays of repulsive chains, then to bands of half-period-shifted densely bound chains. These structures with chain order at the inner scale aggregate into different large-scale clusters that have a pronounced circular pattern and are stabilized by the many-body elastocapillary attraction.
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17. |
- Zhao, Chenxi, et al.
(författare)
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Effects of fracture network distribution on excavation-induced coupled responses of pore pressure perturbation and rock mass deformation
- 2022
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Ingår i: Computers and geotechnics. - : Elsevier BV. - 0266-352X .- 1873-7633. ; 145
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Tidskriftsartikel (refereegranskat)abstract
- We perform a numerical study of the spatio-temporal evolution of rock damages and fracture displacements around underground excavation in fractured rocks. We model fracture networks based on a power law model and explore different values of the length exponent and fracture intensity. An elasto-brittle constitutive relation is employed to characterise the deformation/failure of intact rocks, while a non-linear stress–displacement relation is used to mimic the normal/shear displacement of pre-existing fractures. Fluid flow through fractured porous media is simulated based on Darcy’s law. Both direct coupling (via poroelasticity) and indirect coupling (via changes of rock mass properties) are considered, with excavation-induced stress alteration, pore pressure variation, damage evolution, and fracture deformation realistically captured. It is observed that, fracture systems dominated by large fractures in general accommodate significant sliding along pre-existing fractures but minor damage in intact rocks, while fracture systems governed by small fractures can have profound damage and slippage simultaneously. Excavation-induced stress variation near the tunnel can instantly cause pore pressure fluctuations in low-permeability rock matrix, promoting fracture shear and rock damage. In addition, we investigate the microseismicity generated during and after the excavation as well as analyse the mechanisms of excavation and drainage-induced disturbances. Our results have important implications for underground excavation activities involved in many geoengineering applications.
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