| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Zhou, Xian-Jing, et al.
(författare)
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Thermo-sensitive Microgels Supported Gold Nanoparticles as Temperature-mediated Catalyst
- 2019
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Ingår i: Chinese Journal of Polymer Science. - : Springer Science and Business Media LLC. - 0256-7679 .- 1439-6203. ; 37:3, s. 235-242
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Tidskriftsartikel (refereegranskat)abstract
- Microgels with a thermo-sensitive poly(N-isopropylacrylamide) (polyNIPAm) backbone and bis-imidazolium (VIM) ionic cross-links, denoted as poly(NIPAm-co-VIM), were successfully prepared. The as-synthesized ionic microgels were converted to nanoreactors, denoted as Au@PNI MGs, upon generation and immobilization of gold nanoparticles (Au NPs) of 5-8 nm in size into poly(NIPAm-co-VIM). The content of Au NPs in microgels could be regulated by controlling the 1,6-dibromohexane/vinylimidazole molar ratio in the quaternization reaction. The microgel-based nanoreactors were morphologically spherical and uniform in size, and presented reversible thermo-sensitive behavior with volume phase transition temperatures (VPTTs) at 39-40 degrees C. The Au@PNI MGs were used for the reduction of 4-nitrophenol, of which the catalytic activity could be modulated by temperature.
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| 4. |
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| 5. |
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| 6. |
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| 7. |
- Cai, Baoping, et al.
(författare)
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Application of Bayesian Networks in Reliability Evaluation
- 2019
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Ingår i: IEEE Transactions on Industrial Informatics. - : IEEE. - 1551-3203 .- 1941-0050. ; 15:4, s. 2146-2157
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Tidskriftsartikel (refereegranskat)abstract
- The Bayesian network (BN) is a powerful model for probabilistic knowledge representation and inference and is increasingly used in the field of reliability evaluation. This paper presents a bibliographic review of BNs that have been proposed for reliability evaluation in the last decades. Studies are classified from the perspective of the objects of reliability evaluation, i.e., hardware, structures, software, and humans. For each classification, the construction and validation of a BN-based reliability model are emphasized. The general procedural steps for BN-based reliability evaluation, including BN structure modeling, BN parameter modeling, BN inference, and model verification and validation, are investigated. Current gaps and challenges in reliability evaluation with BNs are explored, and a few upcoming research directions that are of interest to reliability researchers are identified.
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| 8. |
- Dou, Jin-Hu, et al.
(författare)
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Atomically precise single-crystal structures of electrically conducting 2D metal-organic frameworks
- 2021
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Ingår i: Nature Materials. - : Springer Science and Business Media LLC. - 1476-1122 .- 1476-4660. ; 20, s. 222-228
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Tidskriftsartikel (refereegranskat)abstract
- Electrically conducting 2D metal-organic frameworks (MOFs) have attracted considerable interest, as their hexagonal 2D lattices mimic graphite and other 2D van der Waals stacked materials. However, understanding their intrinsic properties remains a challenge because their crystals are too small or of too poor quality for crystal structure determination. Here, we report atomically precise structures of a family of 2D pi-conjugated MOFs derived from large single crystals of sizes up to 200 mu m, allowing atomic-resolution analysis by a battery of high-resolution diffraction techniques. A designed ligand core rebalances the in-plane and out-of-plane interactions that define anisotropic crystal growth. We report two crystal structure types exhibiting analogous 2D honeycomb-like sheets but distinct packing modes and pore contents. Single-crystal electrical transport measurements distinctively demonstrate anisotropic transport normal and parallel to the pi-conjugated sheets, revealing a clear correlation between absolute conductivity and the nature of the metal cation and 2D sheet packing motif. Two-dimensional MOFs can possess porosity and electrical conductivity but are difficult to grow as single crystals. Here, by balancing in-plane and out-of-plane interactions, single crystals of sizes up to 200 mu m are grown, allowing in-plane transport measurements and atomic-resolution analysis.
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| 9. |
- George, Julie, et al.
(författare)
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Comprehensive genomic profiles of small cell lung cancer
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 524:7563, s. 47-U73
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Tidskriftsartikel (refereegranskat)abstract
- We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Dex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
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| 10. |
- Gu, Qiang, et al.
(författare)
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VKORC1-1639G>A, CYP2C9, EPHX1691A>G genotype, body weight, and age are important predictors for warfarin maintenance doses in patients with mechanical heart valve prostheses in southwest China
- 2010
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Ingår i: European Journal of Clinical Pharmacology. - : Springer Science and Business Media LLC. - 0031-6970 .- 1432-1041. ; 66:12, s. 1217-1227
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Tidskriftsartikel (refereegranskat)abstract
- There were great interindividual differences in warfarin maintenance dosage (ranging from 0.6 to 8.4 mg/day) among the 127 patients with mechanical heart valve prostheses. VKORC1-1639G>A, CYP2C9, EPHX1691A>G polymorphism, body weight, and age were found to affect the dose demands. Multiple linear regression models incorporating genetic polymorphisms of VKORC1, CYP2C9, EPHX1691A>G, and the nongenetic factors of age and body weight were developed, and explained up to 76.8% of the total variation (adjusted R (2) of 0.743) in warfarin maintenance doses in southwest Chinese patients with mechanical heart valve prostheses.
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| 11. |
- He, Tao, et al.
(författare)
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Kinetically Controlled Reticular Assembly of a Chemically Stable Mesoporous Ni(II)-Pyrazolate Metal-Organic Framework
- 2020
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 142:31, s. 13491-13499
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Tidskriftsartikel (refereegranskat)abstract
- The application scope of metal-organic frameworks (MOFs) is severely restricted by their weak chemical stability and limited pore size. A robust MOF with large mesopores is highly desired, yet poses a great synthetic challenge. Herein, two chemically stable Ni(II)-pyrazolate MOFs, BUT-32 and -33, were constructed from a conformation-matched elongated pyrazolate ligand through the isoreticular expansion. The two MOFs share the same sodalite-type net, but have different pore sizes due to the network interpenetration in BUT-32. Controlled syntheses of the two MOFs have been achieved through precisely tuning reaction conditions, where the microporous BUT-32 was demonstrated to be a thermodynamically stable product while the mesoporous BUT-33 is kinetically favored. To date, BUT-32 represents the first example of Ni-4-pyrazolate MOF whose structure was unambiguously determined by single-crystal X-ray diffraction. Interestingly, the kinetic product BUT-33 integrates 2.6 nm large mesopores with accessible Ni(II) active sites and remarkable chemical stability even in 4 M NaOH aqueous solution and 1 M Grignard reagent. This MOF thus demonstrated an excellent catalytic performance in carbon-carbon coupling reactions, superior to other Ni(II)-MOFs including BUT-32. These findings highlight the importance of kinetic control in the reticular synthesis of mesoporous MOFs, as well as their superiority in heterogeneous catalysis.
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| 12. |
- Htet, Cho Sandar, et al.
(författare)
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Effect of Local Structural Distortions on Antiferroelectric-Ferroelectric Phase Transition in Dilute Solid Solutions of K xNa1- xNbO3
- 2022
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 61:50, s. 20277-20287
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Tidskriftsartikel (refereegranskat)abstract
- The fundamental principles that govern antiferroelectric (AFE)-ferroelectric (FE) transitions are not well understood for many solid solutions of perovskite compounds. For example, crystal chemical considerations based on the average Goldschmidt tolerance factor or ionic polarizability do not precisely predict the boundary between the AFE and FE phases in dilute solid solutions of alkali niobates, such as KxNa1-xNbO3(x ≤ 0.02). Here, based on detailed structural analysis from neutron total scattering experiments, we provide insights about how the relative local distortions around the A- and B-sites of the ABO3perovskite structure affect the AFE/FE order of the average crystallographic phases in KxNa1-xNbO3. We show that a higher (lower) ratio of B-site-centered distortions over A-site-centered distortions drives transition toward a long-range FE (AFE) phase, which is based on a competition between the long-range polarizing field of the Nb-O dipoles and the disordering effect of local distortions around the A-site. Our study provides a predictive tool for designing complex solid-solution perovskites with tunable (anti)ferroelectric polarization properties, which can be of interest for various energy-related applications such as high-density energy storage and solid-state cooling.
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| 13. |
- Islam, Mohammad Mirazul, et al.
(författare)
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Effects of gamma radiation sterilization on the structural and biological properties of decellularized corneal xenografts
- 2019
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Ingår i: Acta Biomaterialia. - : Elsevier. - 1742-7061 .- 1878-7568. ; 96, s. 330-344
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Tidskriftsartikel (refereegranskat)abstract
- To address the shortcomings associated with corneal transplants, substantial efforts have been focused on developing new modalities such as xenotransplantion. Xenogeneic corneas are anatomically and biomechanically similar to the human cornea, yet their applications require prior decellularization to remove the antigenic components to avoid rejection. In the context of bringing decellularized corneas into clinical use, sterilization is a crucial step that determines the success of the transplantation. Well-standardized sterilization methods, such as gamma irradiation (GI), have been applied to decellularized porcine corneas (DPC) to avoid graft-associated infections in human recipients. However, little is known about the effect of GI on decellularized corneal xenografts. Here, we evaluated the radiation effect on the ultrastructure, optical, mechanical and biological properties of DPC. Transmission electron microscopy revealed that gamma irradiated decellularized porcine cornea (G-DPC) preserved its structural integrity. Moreover, the radiation did not reduce the optical properties of the tissue. Neither DPC nor G-DPC led to further activation of complement system compared to native porcine cornea when exposed to plasma. Although, DPC were mechanically comparable to the native tissue, GI increased the mechanical strength, tissue hydrophobicity and resistance to enzymatic degradation. Despite these changes, human corneal epithelial, stromal, endothelial and hybrid neuroblastoma cells grew and differentiated on DPC and G-DPC. Thus, GI may achieve effective tissue sterilization without affecting critical properties that are essential for corneal transplant survival. (C) 2019 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
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| 14. |
- Kong, Jing, et al.
(författare)
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A Local Atomic Mechanism for Monoclinic-Tetragonal Phase Boundary Creation in Li-Doped Na0.5K0.5NbO3Ferroelectric Solid Solution
- 2022
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 61:10, s. 4335-4349
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Tidskriftsartikel (refereegranskat)abstract
- ABO3 perovskites display a wide range of phase transitions, which are driven by A/B-site centered polyhedral distortions and/or BO6 octahedral tilting. Since heterogeneous substitutions at the A/B-site can locally alter both polyhedral distortions and/or tilting, they are often used to create phase boundary regions in solid solutions of ABO3, where the functional properties are highly enhanced. However, the relationships between doping-induced atomistic structural changes and the creation of phase boundaries are not always clear. One prominent example of this is the Li-doped K0.5Na0.5NbO3 (KNNL), which is considered a promising alternative to traditional Pb-based ferroelectrics. Although the electromechanical properties of KNNL are enhanced for compositions near the morphotropic phase boundary (MPB), the atomistic mechanism for phase transitions is not well understood. Here, we combined neutron total scattering experiments and density functional theory to investigate the long-range average and short-range (∼10 Å) structural changes in KNNL. We show that the average monoclinic-to-tetragonal (M-T) transition across the MPB in KNNL can be described as an order-disorder-type change, which is driven by competition between a longer-range polarization field of monoclinic structural units and local distortions of the disordered AO12 polyhedra. The current study demonstrates a way to clarify dopant-induced local distortions near phase boundaries in complex solid solution systems, which will be important for the rational design of new environmentally sustainable ferroelectrics.
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| 15. |
- Kong, Jing, et al.
(författare)
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Scaling behavior of order parameters for the hybrid improper ferroelectric (Ca,Sr)3Ti2 O7
- 2023
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Ingår i: Physical Review B. - 2469-9950. ; 107:22
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Tidskriftsartikel (refereegranskat)abstract
- We show that in contrast to the conventional view of a mean-field Landau-type behavior, the oxygen octahedral tilt (R) and polarization (P) in the A3B2O7 Ruddlesden-Popper hybrid improper ferroelectric (Ca,Sr)3Ti2O7 exhibits the scaling behavior of a 2D Ising class near the para-to-ferroelectric transition temperature (Tc). We also show that P exhibits an additional transition from a 2D Ising to a 3D mean-field critical behavior at a temperature Td
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| 16. |
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| 17. |
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| 18. |
- Lee, James J, et al.
(författare)
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Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals.
- 2018
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 50:8, s. 1112-1121
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Tidskriftsartikel (refereegranskat)abstract
- Here we conducted a large-scale genetic association analysis of educational attainment in a sample of approximately 1.1million individuals and identify 1,271independent genome-wide-significant SNPs. For the SNPs taken together, we found evidence of heterogeneous effects across environments. The SNPs implicate genes involved in brain-development processes and neuron-to-neuron communication. In a separate analysis of the X chromosome, we identify 10independent genome-wide-significant SNPs and estimate a SNP heritability of around 0.3% in both men and women, consistent with partial dosage compensation. A joint (multi-phenotype) analysis of educational attainment and three related cognitive phenotypes generates polygenic scores that explain 11-13% of the variance in educational attainment and 7-10% of the variance in cognitive performance. This prediction accuracy substantially increases the utility of polygenic scores as tools in research.
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| 19. |
- Li, Junjie, et al.
(författare)
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A Novel Dry Selective Isotropic Atomic Layer Etching of SiGe for Manufacturing Vertical Nanowire Array with Diameter Less than 20 nm
- 2020
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Ingår i: Materials. - : MDPI AG. - 1996-1944. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- Semiconductor nanowires have great application prospects in field effect transistors and sensors. In this study, the process and challenges of manufacturing vertical SiGe/Si nanowire array by using the conventional lithography and novel dry atomic layer etching technology. The final results demonstrate that vertical nanowires with a diameter less than 20 nm can be obtained. The diameter of nanowires is adjustable with an accuracy error less than 0.3 nm. This technology provides a new way for advanced 3D transistors and sensors.
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| 20. |
- 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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| 21. |
- Luo, Yifei, et al.
(författare)
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Technology Roadmap for Flexible Sensors
- 2023
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Ingår i: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
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Forskningsöversikt (refereegranskat)abstract
- Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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| 22. |
- Marlton, Frederick P., et al.
(författare)
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Broad Distribution of Local Polar States Generates Large Electrothermal Properties in Pb-Free Relaxor Ferroelectrics
- 2021
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Ingår i: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 33:22
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Tidskriftsartikel (refereegranskat)abstract
- Electrothermal energy conversion provides attractive solutions for global energy management, such as energy harvesting from waste heat using pyroelectric energy conversion (PEC) and efficient cooling of portable electronics or data servers using the electrocaloric effect. Relaxor ferroelectrics are attractive for electrothermal energy conversion because of their large pyroelectric coefficients over a wide temperature range. Although Pb-based relaxors are well-known, toxicity concerns have mandated the intense search for Pb-free alternatives. Here, we engineered (Ba,Ca)TiO3-based relaxors based on a multisite doping strategy, which show promising electrothermal performance, viz. a maximum PEC efficiency of 14% and electrocaloric refrigeration capacity of 115 J/kg. Using local-scale structural analysis, we provide an atomistic model for large electrothermal properties in the newly designed Pb-free ferroelectrics, whereby a temperature-independent continuous distribution of cation displacement directions creates easy pathways for microscopic polarization reorientation. This research provides key structural insight for future atomic-scale engineering of environmentally sustainable ferroelectrics in energy applications.
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| 23. |
- Nie, Shuai, et al.
(författare)
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Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color
- 2023
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Ingår i: Horticulture Research. - : Oxford University Press. - 2662-6810 .- 2052-7276. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.
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| 24. |
- 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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| 25. |
- Prokopenko, Inga, et al.
(författare)
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Variants in MTNR1B influence fasting glucose levels
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 41:1, s. 77-81
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Tidskriftsartikel (refereegranskat)abstract
- To identify previously unknown genetic loci associated with fasting glucose concentrations, we examined the leading association signals in ten genome-wide association scans involving a total of 36,610 individuals of European descent. Variants in the gene encoding melatonin receptor 1B (MTNR1B) were consistently associated with fasting glucose across all ten studies. The strongest signal was observed at rs10830963, where each G allele (frequency 0.30 in HapMap CEU) was associated with an increase of 0.07 (95% CI = 0.06-0.08) mmol/l in fasting glucose levels (P = 3.2 x 10(-50)) and reduced beta-cell function as measured by homeostasis model assessment (HOMA-B, P = 1.1 x 10(-15)). The same allele was associated with an increased risk of type 2 diabetes (odds ratio = 1.09 (1.05-1.12), per G allele P = 3.3 x 10(-7)) in a meta-analysis of 13 case-control studies totaling 18,236 cases and 64,453 controls. Our analyses also confirm previous associations of fasting glucose with variants at the G6PC2 (rs560887, P = 1.1 x 10(-57)) and GCK (rs4607517, P = 1.0 x 10(-25)) loci.
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| 26. |
- Sun, Yuhao, et al.
(författare)
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The Contribution of Genetic Risk and Lifestyle Factors in the Development of Adult-Onset Inflammatory Bowel Disease : A Prospective Cohort Study
- 2023
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Ingår i: American Journal of Gastroenterology. - : Lippincott Williams & Wilkins. - 0002-9270 .- 1572-0241. ; 118:3, s. 511-522
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: The joint associations across genetic risk, modifiable lifestyle factors, and inflammatory bowel disease (IBD) remains unclear.METHODS: Genetic susceptibility to Crohn's disease (CD) and ulcerative colitis (UC) was estimated by polygenic risk scores and further categorized into high, intermediate, and low genetic risk categories. Weighted healthy lifestyle scores were constructed based on 5 common lifestyle factors and categorized into favorable (4 or 5 healthy lifestyle factors), intermediate (3 healthy lifestyle factors), and unfavorable (0-2 healthy lifestyle factors) groups. Cox proportional hazards regression model was used to estimate the hazard ratios (HR) and 95% confidence interval (CI) for their associations.RESULTS: During the 12-year follow-up, 707 cases with CD and 1576 cases with UC were diagnosed in the UK Biobank cohort. Genetic risk and unhealthy lifestyle categories were monotonically associated with CD and UC risk with no multiplicative interaction between them. The HR of CD and UC were 2.24 (95% CI 1.75-2.86) and 2.15 (95% CI 1.82-2.53) for those with a high genetic risk, respectively. The HR of CD and UC for individuals with an unfavorable lifestyle were 1.94 (95% CI 1.61-2.33) and 1.98 (95% CI 1.73-2.27), respectively. The HR of individuals with a high genetic risk but a favorable lifestyle (2.33, 95% CI 1.58-3.44 for CD, and 2.05, 95% CI 1.58-2.66 for UC) were reduced nearly by half, compared with those with a high genetic risk but an unfavorable lifestyle (4.40, 95% CI 2.91-6.66 for CD and 4.44, 95% CI 3.34-5.91 for UC).DISCUSSION: Genetic and lifestyle factors were independently associated with susceptibility to incident CD and UC. Adherence to a favorable lifestyle was associated with a nearly 50% lower risk of CD and UC among participants at a high genetic risk.
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| 27. |
- Tian, Xue-Chan, et al.
(författare)
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Unique gene duplications and conserved microsynteny potentially associated with resistance to wood decay in the Lauraceae
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.
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| 28. |
- Wang, Li, et al.
(författare)
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A functional mechanism for a non-coding variant near AGTR2 associated with risk for preterm birth.
- 2023
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Ingår i: BMC medicine. - 1741-7015. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Preterm birth (PTB), defined as delivery before 37 gestational weeks, imposes significant public health burdens. A recent maternal genome-wide association study of spontaneous PTB identified a noncoding locus near the angiotensin II receptor type 2 (AGTR2) gene. Genotype-Tissue Expression data revealed that alleles associated with decreased AGTR2 expression in the uterus were linked to an increased risk of PTB and shortened gestational duration. We hypothesized that a causative variant in this locus modifies AGTR2 expression by altering transcription factor (TF) binding.To investigate this hypothesis, we performed bioinformatics analyses and functional characterizations at the implicated locus. Potential causal single nucleotide polymorphisms (SNPs) were prioritized, and allele-dependent binding of TFs was predicted. Reporter assays were employed to assess the enhancer activity of the top PTB-associated non-coding variant, rs7889204, and its impact on TF binding.Our analyses revealed that rs7889204, a top PTB-associated non-coding genetic variant is one of the strongest eQTLs for the AGTR2 gene in uterine tissue samples. We observed differential binding of CEBPB (CCAAT enhancer binding protein beta) and HOXA10 (homeobox A10) to the alleles of rs7889204. Reporter assays demonstrated decreased enhancer activity for the rs7889204 risk "C" allele.Collectively, these results demonstrate that decreased AGTR2 expression caused by reduced transcription factor binding increases the risk for PTB and suggest that enhancing AGTR2 activity may be a preventative measure in reducing PTB risk.
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| 29. |
- Yan, Xue-Mei, et al.
(författare)
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Unraveling the evolutionary dynamics of the TPS gene family in land plants
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.
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| 30. |
- Yang, Chih-Wen, et al.
(författare)
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Epitaxial Growth and Determination of Band Alignment of Bi2Te3–WSe2 Vertical van der Waals Heterojunctions
- 2020
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Ingår i: ACS Materials Letters. - : American Chemical Society (ACS). - 2639-4979. ; 2:10, s. 1351-1359
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Tidskriftsartikel (refereegranskat)abstract
- Artificial heterojunctions formed by vertical stacking of dissimilar two-dimensional (2D) transition metal dichalcogenide (TMD) monolayer materials in a chosen sequence hold tantalizing prospects for futuristic atomically thin circuits. The emergence of 2D topological insulators (TI), including Bi2Te3, Bi2Se3, and Sb2Te3, represents a new class of 2D building blocks and can complement the existing artificial heterojunctions as a result of their intriguing surface states protected by the time-reversal symmetry. However, the determination of band alignments of such 2D TI/TMD vertical heterojunctions, the key parameter for designing HJ-based electronic/photonic devices, which lies in the development of epitaxy growth, remains in its infancy. Here, we demonstrate the epitaxy growth of 2D TI/TMD vertical heterojunctions comprised of Bi2Te3/WSe2 with atomically clean interfaces that are spectroscopically accessible, and theoretically tractable. Cross-sectional scanning transmission electron microscopy (STEM) images and the presence of interlayer-coupled characteristics from Raman spectroscopy collectively confirm the neat stacking of Bi2Te3/WSe2 with the absence of unwanted containments. Microbeam X-ray photoelectron spectroscopy (ΌXPS) measurement coupled with the density functional theory (DFT) calculations and electrical characteristics of field effect transistors quantitatively reveals the type-II alignment of vertically stacked of quintuple layers (QL) Bi2Te3/WSe2. Meanwhile, the type-III band emerges when transitioning to multi-quintuple layer (MQL) Bi2Te3/WSe2. The finding here provides a well-defined example of the epitaxy growth paradigm, the interlayer coupling-electronic properties relationship, for these emerging 2D TI/TMDs vertical heterojunctions. © 2020 American Chemical Society.
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| 31. |
- Zhao, Shi-Wei, et al.
(författare)
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Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub
- 2023
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.
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| 32. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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