| 1. |
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| 2. |
- 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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| 3. |
- 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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| 4. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 5. |
- Abolfathi, Bela, et al.
(författare)
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The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
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Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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| 6. |
- Aguado, D. S., et al.
(författare)
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The Fifteenth Data Release of the Sloan Digital Sky Surveys : First Release of MaNGA-derived Quantities, Data Visualization Tools, and Stellar Library
- 2019
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics Publishing (IOPP). - 0067-0049 .- 1538-4365. ; 240:2
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Tidskriftsartikel (refereegranskat)abstract
- Twenty years have passed since first light for the Sloan Digital Sky Survey (SDSS). Here, we release data taken by the fourth phase of SDSS (SDSS-IV) across its first three years of operation (2014 July-2017 July). This is the third data release for SDSS-IV, and the 15th from SDSS (Data Release Fifteen; DR15). New data come from MaNGA-we release 4824 data cubes, as well as the first stellar spectra in the MaNGA Stellar Library (MaStar), the first set of survey-supported analysis products (e.g., stellar and gas kinematics, emission-line and other maps) from the MaNGA Data Analysis Pipeline, and a new data visualization and access tool we call "Marvin." The next data release, DR16, will include new data from both APOGEE-2 and eBOSS; those surveys release no new data here, but we document updates and corrections to their data processing pipelines. The release is cumulative; it also includes the most recent reductions and calibrations of all data taken by SDSS since first light. In this paper, we describe the location and format of the data and tools and cite technical references describing how it was obtained and processed. The SDSS website (www.sdss.org) has also been updated, providing links to data downloads, tutorials, and examples of data use. Although SDSS-IV will continue to collect astronomical data until 2020, and will be followed by SDSS-V (2020-2025), we end this paper by describing plans to ensure the sustainability of the SDSS data archive for many years beyond the collection of data.
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| 7. |
- Blanton, Michael R., et al.
(författare)
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Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
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Ingår i: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
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Tidskriftsartikel (refereegranskat)abstract
- We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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| 8. |
- Chen, Xuan, et al.
(författare)
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Prevalence of Abdominal Obesity in Chinese Middle-Aged and Older Adults with a Normal Body Mass Index and Its Association with Type 2 Diabetes Mellitus : A Nationally Representative Cohort Study from 2011 to 2018
- 2021
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Ingår i: Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy. - 1178-7007. ; 14, s. 4829-4841
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Tidskriftsartikel (refereegranskat)abstract
- Background: Few studies have focused on the prevalence of abdominal obesity in Chinese middle-aged and older adults with a normal body mass index (BMI). Furthermore, it is still unclear whether abdominal obesity is an independent risk factor for type 2 diabetes mellitus (T2DM). Participants with a normal BMI are usually neglected during assessments of abdominal obesity-associated T2DM risk since the current recommendations for medical interventions are mainly focused on overall body mass index rather than fat deposition patterns. Methods: In this study, 7942 normal-BMI participants aged over 45 years from the China Health and Retirement Longitudinal Study were included to assess the prevalence of abdominal obesity defined by waist circumference (WC) or waist-to-height ratio (WHtR). In addition, 4348 normal-BMI individuals with no diabetes at baseline were included to evaluate the association between abdominal obesity and the risk of T2DM with the Cox proportional hazards model. Results: The prevalence (95% confidence interval, CI) of increased WC and substantially increased WC among adults with a normal BMI was 22.0% (21.1%-22.9%) and 18.1% (17.3%-19.0%), respectively. The adjusted hazard ratios and 95% CIs for T2DM incidence were 1.39 (1.05–1.85) and 1.89 (1.42–2.53) for those with increased WC and substantially increased WC, respectively, compared to the individuals with a normal WC. Similar HRs were obtained for the association between WHtR and the risk of T2DM. In prediabetic patients, the HRs (95% CIs) for new-onset T2DM for those with increased WC and substantially increased WC were 1.85 (1.27–2.69) and 2.46 (1.67–3.61), respectively, when compared with individuals with normal WC. This positive association was observed in women but not in men or adults with normal glucose tolerance (NGT). Conclusion: Abdominal obesity is highly prevalent among middle-aged and older Chinese adults with a normal BMI, and maintaining a normal waist circumference may be beneficial in the prevention of T2DM.
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| 9. |
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| 10. |
- Karlsson, Max, et al.
(författare)
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Mixed halide perovskites for spectrally stable and high-efficiency blue light-emitting diodes
- 2021
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Bright and efficient blue emission is key to further development of metal halide perovskite light-emitting diodes. Although modifying bromide/chloride composition is straightforward to achieve blue emission, practical implementation of this strategy has been challenging due to poor colour stability and severe photoluminescence quenching. Both detrimental effects become increasingly prominent in perovskites with the high chloride content needed to produce blue emission. Here, we solve these critical challenges in mixed halide perovskites and demonstrate spectrally stable blue perovskite light-emitting diodes over a wide range of emission wavelengths from 490 to 451 nanometres. The emission colour is directly tuned by modifying the halide composition. Particularly, our blue and deep-blue light-emitting diodes based on three-dimensional perovskites show high EQE values of 11.0% and 5.5% with emission peaks at 477 and 467 nm, respectively. These achievements are enabled by a vapour-assisted crystallization technique, which largely mitigates local compositional heterogeneity and ion migration.
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| 11. |
- Li, Xiaochun, et al.
(författare)
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Bidirectional associations of intellectual and social activities with cognitive function among middle-aged and elderly adults in China
- 2022
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Ingår i: Journal of Affective Disorders. - : Elsevier BV. - 0165-0327. ; 319, s. 83-89
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Tidskriftsartikel (refereegranskat)abstract
- Background: Previous studies evaluating the association between leisure activities and cognitive function produced conflicting results. Different types of leisure activities may have different effects on cognition, and very few studies have explored their bidirectional associations. Our study aimed to explore whether intellectual and social activities had bidirectional associations with cognitive function among the middle-aged and elderly adults in China. Methods: Data was derived from the China Health and Retirement Longitudinal Study. The data in this study were based on 11,549 participants aged 45 or older whose intellectual and social activities and cognitive function were assessed at baseline. Cross-lagged panel model was used to examine the temporal relationship of intellectual and social activities with cognitive function. Results: Totally, 5624 participants completed the third follow-up in 2018. The results showed that the better the cognitive function they had at baseline, the more intellectual activities they were engage in (β = 0.044, P < 0.001) and vice versa (β = 0.042, P = 0.001). Additionally, better cognitive function at baseline was significantly associated with more engagement in social activities (β = 0.028, P = 0.030); in contrast, higher engagement in social activities at baseline was not related to better cognitive function (β = −0.008, P = 0.523). Limitations: Engagement in social and intellectual activities was assessed via questionnaire. Conclusions: Our findings indicated that there was a bidirectional relationship between intellectual activities and cognitive function. However, participation in social activities did not slow down the decline in cognitive function. Participating in intellectual activities, compared to social activities, is especially beneficial for cognitive function.
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| 12. |
- Sun, Xiao-dong, et al.
(författare)
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Implementing a novel capture and ligation probe-PCR method in mass screen and treatment to support malaria elimination efforts in the China-Myanmar border region
- 2023
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Ingår i: Malaria Journal. - : BioMed Central (BMC). - 1475-2875. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundMass screening and treatment (MSAT) for malaria elimination lacks an ideal diagnostic tool to allow sensitive and affordable test of the target population in the field. This study evaluated whether Capture and Ligation Probe-PCR (CLIP-PCR) could be used in a field MSAT in Laiza City, Myanmar.MethodsOn day 0, two dried blood spots were collected from each participant. On day 1, all samples were screened for Plasmodium in a 20 m(2) laboratory with workbench, a biosafety cabinet, a refrigerator, a benchtop shaking incubator and a qPCR machine, by four technicians using CLIP-PCR with sample pooling, at a health clinic of the Chinese bordering town of Nabang. On day 2, all positives were followed up and treated.ResultsOf 15,038 persons (65% of the total population) screened, 204 (1.36%) were CLIP-PCR positives. Among them, 188, 14, and 2 were infected with Plasmodium vivax, Plasmodium falciparum, and P. vivax/P. falciparum mix, respectively. The testing capacity was 538 persons/day, with a cost of US$0.92 /person. The proportion of submicroscopic infection was 64.7%. All positive individuals received treatment within 72 h after blood collection.ConclusionUsing CLIP-PCR in MSAT in low transmission settings can support the malaria elimination efforts in the China-Myanmar border region.
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| 13. |
- Zhao, Xiaofeng, et al.
(författare)
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Response of Nd3+ and Sm3+ precipitating into rhabdophane and the leaching mechanism of associated monazite ceramics
- 2023
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Ingår i: Journal of The American Ceramic Society. - : John Wiley & Sons. - 0002-7820 .- 1551-2916. ; 106:2, s. 1287-1298
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Tidskriftsartikel (refereegranskat)abstract
- Rhabdophane has been considered an important permeable reactive barrier to isolate groundwater radionuclides, and evaluating its precipitation response to different species of radionuclide in acid solutions is critical. In this work, the effects of pH values on the precipitation behavior of Nd3+ and Sm3+ into La-rhabdophane are systematically investigated. Some specific issues such as ions removal, precipitation reaction kinetics, and crystal growth affected ions incorporation are discussed in detail, along with uncovering the veil of the Ln (La, Nd, and Sm) leaching mechanism of associated La0.666Nd0.167Sm0.167PO4 monazite ceramic based on dissolution experiments and density functional theory. The results reveal that Nd3+ and Sm3+ can be removed more than 98% in pH = 1 solution within 12 h, whereas uneven precipitation process to form unexpected stoichiometric ratio of rhabdophane has been observed in 30-50 nm short crystal. Grain growth effects based on spark plasma sintering can contribute to homogenize the materials composition with obtaining La0.666Nd0.167Sm0.167PO4 monazite ceramics. Furthermore, the binding energy of Ln-O in (1 0 0) surface of monazite plays an important role in controlling the leaching stability of Ln(3+), associated with the leaching activities are energetically favorable in the order of La > Nd > Sm for La0.666Nd0.167Sm0.167PO4 monazite.
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| 14. |
- Amin, Risul, et al.
(författare)
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The kidney injury caused by the onset of acute graft-versus-host disease is associated with down-regulation of alpha Klotho
- 2020
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Ingår i: International Immunopharmacology. - : Elsevier BV. - 1567-5769 .- 1878-1705. ; 78
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Tidskriftsartikel (refereegranskat)abstract
- Acute graft-versus-host disease (aGVHD) and kidney injury are the major complications after allogeneic hematopoietic stem cell transplantation (HSCT). Although the underlying mechanisms for the development of these complications are not yet fully understood, it has been proposed that emergence of aGVHD contributes to the development of kidney injury after HSCT. We have shown previously that aGVHD targets the kidney in a biphasic manner: at the onset, inflammatory genes are up-regulated, while when aGVHD becomes established, donor lymphocytes infiltrate the kidney. Here, we characterize renal manifestations at the onset of aGVHD. Mice receiving allogeneic bone marrow and spleen cells displayed symptoms of aGVHD and elevated serum levels of tumor necrosis factor alpha (TNF-alpha) and interferon gamma (IFN-gamma) within 4 days. There was concurrent kidney injury with the following characteristics: (1) elevated expression of the kidney injury biomarker, neutrophil gelatinase-associated lipocalin (NGAL), (2) accumulation of hetero-lysosomes in proximal tubule epithelial cells, and (3) reductions in alpha Klotho mRNA and protein and increased serum levels of fibroblast growth factor 23 (Fgf23), phosphate and urea. This situation resembled acute renal injury caused by bacterial lipopolysaccharide. We conclude that the onset of aGVHD is associated with kidney injury involving down-regulation of alpha Klotho, a sight that may inspire novel therapeutic approaches.
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| 15. |
- An, Rui, et al.
(författare)
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Photostability and Photodegradation Processes in Colloidal CsPbI3 Perovskite Quantum Dots
- 2018
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Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 10:45, s. 39222-39227
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Tidskriftsartikel (refereegranskat)abstract
- All-inorganic CsPbI3 perovskite quantum dots (QDs) have attracted intense attention for their successful application in photovoltaics (PVs) and optoelectronics that are enabled by their superior absorption capability and great photoluminescence (PL) properties. However, their photostability remains a practical bottleneck and further optimization is highly desirable. Here, we studied the photostability of as-obtained colloidal CsPbI3 QDs suspended in hexane. We found that light illumination does induce photodegradation of CsPbI3 QDs. Steady-state spectroscopy, X-ray diffraction, Fourier transform infrared spectroscopy, transmission electron microscopy, and transient absorption spectroscopy verified that light illumination leads to detachment of the capping agent, collapse of the CsPbI3 QD surface, and finally aggregation of surface Pb0. Both dangling bonds containing surface and Pb0 serve as trap states causing PL quenching with a dramatic decrease of PL quantum yield. Our work provides a detailed insight about the correlation between the structural and photophysical consequences of the photodegradation process in CsPbI3 QDs and may lead to the optimization of such QDs toward device applications.
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| 16. |
- Arcavi, Iair, et al.
(författare)
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Energetic eruptions leading to a peculiar hydrogen-rich explosion of a massive star
- 2017
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 551:7679, s. 210-213
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Tidskriftsartikel (refereegranskat)abstract
- Every supernova so far observed has been considered to be the terminal explosion of a star. Moreover, all supernovae with absorption lines in their spectra show those lines decreasing in velocity over time, as the ejecta expand and thin, revealing slower-moving material that was previously hidden. In addition, every supernova that exhibits the absorption lines of hydrogen has one main light-curve peak, or a plateau in luminosity, lasting approximately 100 days before declining(1). Here we report observations of iPTF14hls, an event that has spectra identical to a hydrogen-rich core-collapse supernova, but characteristics that differ extensively from those of known supernovae. The light curve has at least five peaks and remains bright for more than 600 days; the absorption lines show little to no decrease in velocity; and the radius of the line-forming region is more than an order of magnitude bigger than the radius of the photosphere derived from the continuum emission. These characteristics are consistent with a shell of several tens of solar masses ejected by the progenitor star at supernova-level energies a few hundred days before a terminal explosion. Another possible eruption was recorded at the same position in 1954. Multiple energetic pre-supernova eruptions are expected to occur in stars of 95 to 130 solar masses, which experience the pulsational pair instability(2-5). That model, however, does not account for the continued presence of hydrogen, or the energetics observed here. Another mechanism for the violent ejection of mass in massive stars may be required.
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| 17. |
- Bao, Zijia, et al.
(författare)
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A helical polypyrrole nanotube interwoven zeolitic imidazolate framework and its derivative as an oxygen electrocatalyst
- 2022
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Ingår i: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1359-7345 .- 1364-548X. ; 58:80, s. 11288-11291
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Tidskriftsartikel (refereegranskat)abstract
- A helical polypyrrole nanotube interwoven zeolitic imidazolate framework (ZIF) has been prepared for the first time. After pyrolysis, the helical carbon could act as highly active sites, while the 3D-connected nanoarchitecture contributed to fast charge transfer. The derived carbon material exhibits high activity for the ORR and good performance for a Zn–air battery.
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| 18. |
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| 19. |
- Bentham, James, et al.
(författare)
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A century of trends in adult human height
- 2016
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Ingår i: eLIFE. - 2050-084X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.522.7) and 16.5 cm (13.319.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
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| 20. |
- Bentham, James, et al.
(författare)
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A century of trends in adult human height
- 2016
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Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3– 19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8– 144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
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| 21. |
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| 22. |
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| 23. |
- Bodén, Stina, et al.
(författare)
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Dietary patterns, untargeted metabolite profiles and their association with colorectal cancer risk
- 2024
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322 .- 2045-2322. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- We investigated data-driven and hypothesis-driven dietary patterns and their association to plasma metabolite profiles and subsequent colorectal cancer (CRC) risk in 680 CRC cases and individually matched controls. Dietary patterns were identified from combined exploratory/confirmatory factor analysis. We assessed association to LC–MS metabolic profiles by random forest regression and to CRC risk by multivariable conditional logistic regression. Principal component analysis was used on metabolite features selected to reflect dietary exposures. Component scores were associated to CRC risk and dietary exposures using partial Spearman correlation. We identified 12 data-driven dietary patterns, of which a breakfast food pattern showed an inverse association with CRC risk (OR per standard deviation increase 0.89, 95% CI 0.80–1.00, p = 0.04). This pattern was also inversely associated with risk of distal colon cancer (0.75, 0.61–0.96, p = 0.01) and was more pronounced in women (0.69, 0.49–0.96, p = 0.03). Associations between meat, fast-food, fruit soup/rice patterns and CRC risk were modified by tumor location in women. Alcohol as well as fruit and vegetables associated with metabolite profiles (Q2 0.22 and 0.26, respectively). One metabolite reflecting alcohol intake associated with increased CRC risk, whereas three metabolites reflecting fiber, wholegrain, and fruit and vegetables associated with decreased CRC risk.
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| 24. |
- Danaei, Goodarz, et al.
(författare)
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Effects of diabetes definition on global surveillance of diabetes prevalence and diagnosis: a pooled analysis of 96 population-based studies with 331288 participants
- 2015
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Ingår i: The Lancet Diabetes & Endocrinology. - 2213-8595 .- 2213-8587. ; 3:8, s. 624-637
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Tidskriftsartikel (refereegranskat)abstract
- Background Diabetes has been defined on the basis of different biomarkers, including fasting plasma glucose (FPG), 2-h plasma glucose in an oral glucose tolerance test (2hOGTT), and HbA(1c). We assessed the effect of different diagnostic definitions on both the population prevalence of diabetes and the classification of previously undiagnosed individuals as having diabetes versus not having diabetes in a pooled analysis of data from population-based health examination surveys in different regions. Methods We used data from 96 population-based health examination surveys that had measured at least two of the biomarkers used for defining diabetes. Diabetes was defined using HbA(1c) (HbA(1c) >= 6 . 5% or history of diabetes diagnosis or using insulin or oral hypoglycaemic drugs) compared with either FPG only or FPG-or-2hOGTT definitions (FPG >= 7 . 0 mmol/L or 2hOGTT >= 11 . 1 mmol/L or history of diabetes or using insulin or oral hypoglycaemic drugs). We calculated diabetes prevalence, taking into account complex survey design and survey sample weights. We compared the prevalences of diabetes using different definitions graphically and by regression analyses. We calculated sensitivity and specificity of diabetes diagnosis based on HbA1c compared with diagnosis based on glucose among previously undiagnosed individuals (ie, excluding those with history of diabetes or using insulin or oral hypoglycaemic drugs). We calculated sensitivity and specificity in each survey, and then pooled results using a random-effects model. We assessed the sources of heterogeneity of sensitivity by meta-regressions for study characteristics selected a priori. Findings Population prevalence of diabetes based on FPG- or-2hOGTT was correlated with prevalence based on FPG alone (r= 0 . 98), but was higher by 2-6 percentage points at different prevalence levels. Prevalence based on HbA(1c) was lower than prevalence based on FPG in 42 . 8% of age-sex-survey groups and higher in another 41 . 6%; in the other 15 . 6%, the two definitions provided similar prevalence estimates. The variation across studies in the relation between glucose-based and HbA(1c)-based prevalences was partly related to participants' age, followed by natural logarithm of per person gross domestic product, the year of survey, mean BMI, and whether the survey population was national, subnational, or from specific communities. Diabetes defined as HbA(1c) 6 . 5% or more had a pooled sensitivity of 52 . 8% (95% CI 51 . 3-54 . 3%) and a pooled specificity of 99 . 74% (99 . 71-99 . 78%) compared with FPG 7 . 0 mmol/L or more for diagnosing previously undiagnosed participants; sensitivity compared with diabetes defined based on FPG-or-2hOGTT was 30 . 5% (28 . 7-32 . 3%). None of the preselected study-level characteristics explained the heterogeneity in the sensitivity of HbA(1c) versus FPG. Interpretation Different biomarkers and definitions for diabetes can provide different estimates of population prevalence of diabetes, and differentially identify people without previous diagnosis as having diabetes. Using an HbA(1c)-based definition alone in health surveys will not identify a substantial proportion of previously undiagnosed people who would be considered as having diabetes using a glucose-based test.
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| 25. |
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| 26. |
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| 27. |
- Dou, Shihan, et al.
(författare)
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Decorrelate Irrelevant, Purify Relevant : Overcome Textual Spurious Correlations from a Feature Perspective
- 2022
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Konferensbidrag (refereegranskat)abstract
- Natural language understanding (NLU) models tend to rely on spurious correlations (i.e., dataset bias) to achieve high performance on in-distribution datasets but poor performance on out-of-distribution ones. Most of the existing debiasing methods often identify and weaken these samples with biased features (i.e., superficial surface features that cause such spurious correlations). However, down-weighting these samples obstructs the model in learning from the non-biased parts of these samples. To tackle this challenge, in this paper, we propose to eliminate spurious correlations in a fine-grained manner from a feature space perspective. Specifically, we introduce Random Fourier Features and weighted re-sampling to decorrelate the dependencies between features to mitigate spurious correlations. After obtaining decorrelated features, we further design a mutual-information-based method to purify them, which forces the model to learn features that are more relevant to tasks. Extensive experiments on two well-studied NLU tasks demonstrate that our method is superior to other comparative approaches.
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| 28. |
- Du, Mulong, et al.
(författare)
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Cyp2a6 activity and cigarette consumption interact in smoking-related lung cancer susceptibility
- 2024
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Ingår i: Cancer Research. - : American Association For Cancer Research (AACR). - 0008-5472 .- 1538-7445. ; 84:4, s. 616-625
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Tidskriftsartikel (refereegranskat)abstract
- Cigarette smoke, containing both nicotine and carcinogens, causes lung cancer. However, not all smokers develop lung cancer, highlighting the importance of the interaction between host susceptibility and environmental exposure in tumorigenesis. Here, we aimed to delineate the interaction between metabolizing ability of tobacco carcinogens and smoking intensity in mediating genetic susceptibility to smoking-related lung tumorigenesis. Single-variant and gene-based associations of 43 tobacco carcinogen–metabolizing genes with lung cancer were analyzed using summary statistics and individual-level genetic data, followed by causal inference of Mendelian randomization, mediation analysis, and structural equation modeling. Cigarette smoke–exposed cell models were used to detect gene expression patterns in relation to specific alleles. Data from the International Lung Cancer Consortium (29,266 cases and 56,450 controls) and UK Biobank (2,155 cases and 376,329 controls) indicated that the genetic variant rs56113850 C>T located in intron 4 of CYP2A6 was significantly associated with decreased lung cancer risk among smokers (OR = 0.88, 95% confidence interval = 0.85–0.91, P = 2.18 X 10-16), which might interact (Pinteraction = 0.028) with and partially be mediated (ORindirect = 0.987) by smoking status. Smoking intensity accounted for 82.3% of the effect of CYP2A6 activity on lung cancer risk but entirely mediated the genetic effect of rs56113850. Mechanistically, the rs56113850 T allele rescued the downregulation of CYP2A6 caused by cigarette smoke exposure, potentially through preferential recruitment of transcription factor helicase-like transcription factor. Together, this study provides additional insights into the interplay between host susceptibility and carcinogen exposure in smoking-related lung tumorigenesis.
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| 29. |
- El-Serafi, Ahmed, 1977-, et al.
(författare)
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Vitamin D levels and busulphan kinetics in patients undergoing hematopoietic stem cell transplantation, a multicenter study
- 2021
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Ingår i: Bone Marrow Transplantation. - : SPRINGERNATURE. - 0268-3369 .- 1476-5365. ; 56, s. 807-817
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Tidskriftsartikel (refereegranskat)abstract
- Vitamin D (Vit-D), an essential nutrient, interacts with different drugs including chemotherapeutic agents like busulphan, an alkylating agent used for conditioning prior to stem cell transplantation. The correlation between Vit-D plasma levels and busulphan clearance was investigated in an uncontrolled prospective study in patients and mice. Plasma 25(OH)D levels were measured and busulphan pharmacokinetics calculated in 81 patients. Adults received oral busulphan (n = 34) while children received busulphan orally (n = 19) or intravenously (n = 28). Patients received no Vit-D supplementation. To confirm our findings, pharmacokinetics after a single dose of busulphan (oral or intravenous) were evaluated in two groups of mice (n = 60) receiving high or standard-level Vit-D supplementation. Both busulphan clearance (P < 0.0001) and 25(OH)D levels (P = 0.0004) were significantly higher in adults compared to children. A significant negative correlation (P = 0.041) was found between busulphan clearance and 25(OH)D levels in children treated orally. No such correlation was observed in adults or in children receiving intravenous busulphan. In addition, no significant effect of Vit-D levels on busulphan pharmacokinetics in mice regardless of the administration route. In conclusion, 25(OH)D can affect oral busulphan pharmacokinetics in children and its level should be considered when personalizing oral busulphan treatment. Further studies are warranted to confirm the underlying mechanisms.
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| 30. |
- Estrada, Karol, et al.
(författare)
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Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
- 2012
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 44:5, s. 491-501
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Tidskriftsartikel (refereegranskat)abstract
- Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top BMD-associated markers for replication in 50,933 independent subjects and for association with risk of low-trauma fracture in 31,016 individuals with a history of fracture (cases) and 102,444 controls. We identified 56 loci (32 new) associated with BMD at genome-wide significance (P < 5 × 10(-8)). Several of these factors cluster within the RANK-RANKL-OPG, mesenchymal stem cell differentiation, endochondral ossification and Wnt signaling pathways. However, we also discovered loci that were localized to genes not known to have a role in bone biology. Fourteen BMD-associated loci were also associated with fracture risk (P < 5 × 10(-4), Bonferroni corrected), of which six reached P < 5 × 10(-8), including at 18p11.21 (FAM210A), 7q21.3 (SLC25A13), 11q13.2 (LRP5), 4q22.1 (MEPE), 2p16.2 (SPTBN1) and 10q21.1 (DKK1). These findings shed light on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility.
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| 31. |
- Feng, Ruizhi, et al.
(författare)
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Mutations in TUBB8 and Human Oocyte Meiotic Arrest.
- 2016
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Ingår i: The New England journal of medicine. - 1533-4406. ; 374:3, s. 223-232
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Tidskriftsartikel (refereegranskat)abstract
- Background Human reproduction depends on the fusion of a mature oocyte with a sperm cell to form a fertilized egg. The genetic events that lead to the arrest of human oocyte maturation are unknown. Methods We sequenced the exomes of five members of a four-generation family, three of whom had infertility due to oocyte meiosis I arrest. We performed Sanger sequencing of a candidate gene, TUBB8, in DNA samples from these members, additional family members, and members of 23 other affected families. The expression of TUBB8 and all other β-tubulin isotypes was assessed in human oocytes, early embryos, sperm cells, and several somatic tissues by means of a quantitative reverse-transcriptase-polymerase-chain-reaction assay. We evaluated the effect of the TUBB8 mutations on the assembly of the heterodimer consisting of one α-tubulin polypeptide and one β-tubulin polypeptide (α/β-tubulin heterodimer) in vitro, on microtubule architecture in HeLa cells, on microtubule dynamics in yeast cells, and on spindle assembly in mouse and human oocytes. Results We identified seven mutations in the primate-specific gene TUBB8 that were responsible for oocyte meiosis I arrest in 7 of the 24 families. TUBB8 expression is unique to oocytes and the early embryo, in which this gene accounts for almost all the expressed β-tubulin. The mutations affect chaperone-dependent folding and assembly of the α/β-tubulin heterodimer, disrupt microtubule behavior on expression in cultured cells, alter microtubule dynamics in vivo, and cause catastrophic spindle-assembly defects and maturation arrest on expression in mouse and human oocytes. Conclusions TUBB8 mutations have dominant-negative effects that disrupt microtubule behavior and oocyte meiotic spindle assembly and maturation, causing female infertility. (Funded by the National Basic Research Program of China and others.).
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| 32. |
- He, Li, et al.
(författare)
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In silico promoter analysis and functional validation identify CmZFH, the co-regulator of hypoxia-responsive genes CmScylla and CmLPCAT
- 2022
-
Ingår i: Insect Biochemistry and Molecular Biology. - : Elsevier. - 0965-1748 .- 1879-0240. ; 140
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Tidskriftsartikel (refereegranskat)abstract
- Oxygen (O2) plays an essential role in aerobic organisms including terrestrial insects. Under hypoxic stress, the cowpea bruchid (Callosobruchus maculatus) ceases feeding and growth. However, larvae, particularly 4th instar larvae exhibit very high tolerance to hypoxia and can recover normal growth once brought to normoxia. To better understand the molecular mechanism that enables insects to cope with low O2 stress, we performed RNA-seq to distinguish hypoxia-responsive genes in midguts and subsequently identified potential common cis-elements in promoters of hypoxia-induced and -repressed genes, respectively. Selected elements were subjected to gel-shift and transient transfection assays to confirm their cis-regulatory function. Of these putative common cis-elements, AREB6 appeared to regulate the expression of CmLPCAT and CmScylla, two hypoxia-induced genes. CmZFH, the putative AREB6-binding protein, was hypoxia-inducible. Transient expression of CmZFH in Drosophila S2 cells activated CmLPCAT and CmScylla, and their induction was likely through interaction of CmZFH with AREB6. Binding to AREB6 was further confirmed by bacterially expressed CmZFH recombinant protein. Deletion analyses indicated that the N-terminal zinc-finger cluster of CmZFH was the key AREB6-binding domain. Through in silico and experimental exploration, we discovered novel transcriptional regulatory components associated with gene expression dynamics under hypoxia that facilitated insect survival.
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| 33. |
- Huo, Meiling, et al.
(författare)
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A heteroepitaxially grown two-dimensional metal-organic framework and its derivative for the electrocatalytic oxygen reduction reaction
- 2022
-
Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry (RSC). - 2050-7488 .- 2050-7496. ; 10:19, s. 10408-10416
-
Tidskriftsartikel (refereegranskat)abstract
- Two-dimensional (2D) metal–organic frameworks (MOFs) have become a hot topic recently due to their high surface area, larger number of exposed active sites, and improved conductivity. Combining different 2D MOFs could introduce new physical and chemical properties. Here, we have synthesized a heteroepitaxially grown 2D zeolitic imidazolate framework with a leaf-like morphology (ZIF-L). ZIF-L has a layer-by-layer dense structure, which possesses a high content of N and metal ions as active sites. ZIF-L-Co is heteroepitaxially grown on ZIF-L-Zn, while ZIF-L-Zn@ZIF-Co has been successfully prepared. After pyrolysis, the heteroepitaxially grown MOF derived ultra-small Co nanoparticle immobilized nitrogen doped carbon (NC) material (HM-Co@NC) exhibits superior oxygen reduction reaction (ORR) activity (Eonset = 0.998 V, E1/2 = 0.905 V) and better stability than Pt/C, achieving well-qualified assemblies for use in rechargeable Zn–air batteries.
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| 34. |
- Jia, Xiaomin, et al.
(författare)
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Single crystal metal-organic framework constructed by vertically self-pillared nanosheets and its derivative for oriented lithium plating
- 2021
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Ingår i: Cuihuà xuébào. - : Elsevier BV. - 0253-9837 .- 1872-2067. ; 42:9, s. 1553-1560
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Tidskriftsartikel (refereegranskat)abstract
- This vertically self-pillared (VSP) structure extends the application range of traditional porous materials with facile mass/ion transport and enhanced reaction kinetics. Here, we prepare a single crystal metal-organic framework (MOF), employing the ZIF-67 structure as a proof of concept, which is constructed by vertically self-pillared nanosheets (VSP-MOF). We further converted VSP-MOF into VSP-cobalt sulfide (VSP-CoS2) through a sulfidation process. Catalysis plays an important role in almost all battery technologies; for metallic batteries, lithium anodes exhibit a high theoretical specific capacity, low density, and low redox potential. However, during the half-cell reaction (Li++e=Li), uncontrolled dendritic Li penetrates the separator and solid electrolyte interphase layer. When employed as a composite scaffold for lithium metal deposition, there are many advantage to using this framework: 1) the VSP-CoS2 substrate provides a high specific surface area to dissipate the ion flux and mass transfer and acts as a pre-catalyst, 2) the catalytic Co center favors the charge transfer process and preferentially binds the Li+ with the enhanced electrical fields, and 3) the VSP structure guides the metallic propagation along the nanosheet 2D orientation without the protrusive dendrites. All these features enable the VSP structure in metallic batteries with encouraging performances.
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| 35. |
- Kan, Siyi, et al.
(författare)
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Risk of intact forest landscape loss goes beyond global agricultural supply chains
- 2023
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Ingår i: One Earth. - : Elsevier BV. - 2590-3322 .- 2590-3330. ; 6:1, s. 55-65
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Tidskriftsartikel (refereegranskat)abstract
- The continued loss of unfragmented intact forest landscapes (IFLs) despite numerous global conservation initiatives indicates the need for improved knowledge of proximate and underlying drivers. Yet the role of non-agricultural activities in forest degradation and fragmentation has not received adequate attention. We focus on IFL loss caused by various economic activities and investigate the influence of global consumption and trade via the multi-regional input-output model. For IFL loss associated with the 2014 world economy, over 60% was related to final consumption of non-agricultural products. More than one-third of IFL loss was linked to export, primarily from Russia, Canada, and tropical regions to mainland China, the EU, and the United States. Of IFL loss associated with export, 51% and 26% was directly caused by logging and mining or energy extraction, respectively. The dispersed nature of IFL loss drivers and their indirect links to individual final consumers call for stronger government engagement and supply chain interventions.
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| 36. |
- Kanoni, Stavroula, et al.
(författare)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
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Ingår i: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
-
Tidskriftsartikel (refereegranskat)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 37. |
- Kristan, Matej, et al.
(författare)
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The first visual object tracking segmentation VOTS2023 challenge results
- 2023
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Ingår i: 2023 IEEE/CVF International conference on computer vision workshops (ICCVW). - : Institute of Electrical and Electronics Engineers Inc.. - 9798350307443 - 9798350307450 ; , s. 1788-1810
-
Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking Segmentation VOTS2023 challenge is the eleventh annual tracker benchmarking activity of the VOT initiative. This challenge is the first to merge short-term and long-term as well as single-target and multiple-target tracking with segmentation masks as the only target location specification. A new dataset was created; the ground truth has been withheld to prevent overfitting. New performance measures and evaluation protocols have been created along with a new toolkit and an evaluation server. Results of the presented 47 trackers indicate that modern tracking frameworks are well-suited to deal with convergence of short-term and long-term tracking and that multiple and single target tracking can be considered a single problem. A leaderboard, with participating trackers details, the source code, the datasets, and the evaluation kit are publicly available at the challenge website1
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| 38. |
- Liang, Zuozhong, et al.
(författare)
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Novel insight into the epitaxial growth mechanism of six-fold symmetrical beta-Co(OH)(2)/Co(OH)F hierarchical hexagrams and their water oxidation activity
- 2018
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Ingår i: Electrochimica Acta. - : Elsevier BV. - 0013-4686 .- 1873-3859. ; 271, s. 526-536
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Tidskriftsartikel (refereegranskat)abstract
- The six-fold symmetry widely presents in both natural and artificial architectures. Understanding the growth mechanism of six-fold symmetrical materials is of fundamental interest and significance. Herein, we report the formation process of beta-Co(OH)(2)/Co(OH)F hierarchical hexagrams with a six-fold symmetrical arrangement. Our results demonstrate that hexagonal beta-Co(OH)(2) plates are first formed under the reaction condition. These hexagonal plates then act as templates for the growth of Co(OH)F nanorods. The intermediate material is therefore composed of plate-like beta-Co(OH)(2) hexagonal cores appended with six rod-like Co(OH)F branches, giving the beta-Co(OH)(2)/Co(OH)F hybrid. After prolonged reaction, the beta-Co(OH)(2) hexagons can be completely converted, leading to authentic six-branched Co(OH)F nanorods as the final product. Consequently, for both intermediate and final materials, the Co(OH)F nanorods are arranged with a six-fold symmetry. Importantly, these Co(OH)F nanorods grow along beta-Co(OH)(2) hexagon edges as lateral branches instead of perpendicular to hexagons. This uncommon epitaxial growth mechanism is considered to be a result of the matching between the b-axis of Co(OH)F crystals and the a-axis of beta-Co(OH)(2) crystals, which is beneficial for the electrocatalysis. The beta-Co(OH)(2)/Co(OH)F hierarchical hexagrams show enhanced water oxidation activity compared to the pure beta-Co(OH)(2) and Co(OH)F.
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| 39. |
- Liang, Zuozhong, et al.
(författare)
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Quasi-single-crystalline CoO hexagrams with abundant defects for highly efficient electrocatalytic water oxidation
- 2018
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 9:34, s. 6961-6968
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Tidskriftsartikel (refereegranskat)abstract
- Defects and structural long-range ordering have been recognized as two crucial characters for advanced electrocatalysts. However, these two features have rarely been achieved together. Herein, we report the preparation of single-crystalline CoO hexagrams and demonstrate their exceptional electrocatalytic properties for water oxidation. The quasi-single-crystalline CoO hexagrams, prepared at the critical phase transition point of -Co(OH)(2)/Co(OH)F hexagrams, possess both abundant oxygen vacancies as defects and structural long-range ordering. The matching between the b-axis of Co(OH)F crystals and the a-axis of -Co(OH)(2) crystals is critical for the formation of the CoO hexagram single crystals. The quasi-single-crystalline CoO hexagrams with abundant defects are highly efficient for water oxidation by delivering a 10 mA cm(-2) current density at a low overpotential of 269 mV in a 1 M KOH aqueous solution.
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| 40. |
- Liu, Hui, et al.
(författare)
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Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
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| 41. |
- Niu, Jiqiang, et al.
(författare)
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Aerodynamic simulation of effects of one- and two-side windbreak walls on a moving train running on a double track railway line subjected to strong crosswind
- 2022
-
Ingår i: Journal of Wind Engineering and Industrial Aerodynamics. - : Elsevier BV. - 0167-6105. ; 221
-
Tidskriftsartikel (refereegranskat)abstract
- High-speed railway lines are widely distributed worldwide. The surrounding wind environment of such railway lines is complex, which significantly affects the safety of high-speed train operations. Using a combination of the computational fluid dynamics method of improved delayed detached eddy simulation and sliding grid technology, the effects of one- and two-side windbreak walls on the unsteady aerodynamic performance of a high-speed train running under a crosswind on a double-track railway line with an embankment and the flow-field characteristics around the train were systematically studied. The grid independence and numerical methods used in this study were verified. The results showed that when the windbreak wall was absent, the aerodynamic performance of the train running on the upstream railway line was the poorest, while the train running on the downstream railway line exhibited large aerodynamic fluctuations. The windbreak wall significantly reduced the aerodynamic force and its fluctuation; the one- and two-side windbreak walls had different effects on the unsteady aerodynamic performance of trains running on the upstream and downstream railway lines under a crosswind. The one-side windbreak wall could restrain the aerodynamic fluctuation of the train more and is thus preferred from the perspective of construction effort and cost.
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| 42. |
- Ren, Luyao, et al.
(författare)
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- 2023
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome.RESULTS: We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data.CONCLUSIONS: The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
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| 43. |
- Sui, Jiong-Ming, et al.
(författare)
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Isolation and characterization of a stress responsive small GTP-binding protein AhRabG3b in peanut (Arachis hypogaea L.)
- 2013
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Ingår i: Euphytica. - : Springer Science and Business Media LLC. - 0014-2336 .- 1573-5060. ; 189:2, s. 161-172
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Tidskriftsartikel (refereegranskat)abstract
- Rab7 is a member of small GTP-binding protein family involved in intracellular vesicle trafficking from late endosome to vacuole, some of them are found to be responsive by different environmental stresses. Here we report the isolation of a Rab7 (RabG3b) cDNA from peanut (Arachis hypogaea). Overexpression of the open reading frame (ORF) of Rab7 cDNA encoding 205 amino acids in E. coli conferred the cells tolerance to various abiotic stresses. Transcription of AhRabG3b was differentially up-regulated by different environmental stimuli such as cold, dehydration, NaCl and the plant hormone ABA. Overexpression of the AhRabG3b exhibited enhanced tolerance to drought and salinity stresses in transgenic peanut. These results suggested that the AhRabG3b be a potential candidate gene responsible for both salinity and dehydration tolerance in cultivated peanut.
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| 44. |
- Tang, Ting-Ting, et al.
(författare)
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Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure.
- 2011
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 6:9, s. e24272-
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Tidskriftsartikel (refereegranskat)abstract
- Animal studies suggest that regulatory T (T(reg)) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T(reg) cells in patients with chronic heart failure (CHF). However, the mechanisms behind T(reg-)cell defects remained unknown. We here sought to elucidate the mechanism of T(reg-)cell defects in CHF patients.
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| 45. |
- Vidman, Linda, et al.
(författare)
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Untargeted plasma metabolomics and risk of colorectal cancer : an analysis nested within a large-scale prospective cohort
- 2023
-
Ingår i: Cancer & Metabolism. - : BioMed Central (BMC). - 2049-3002. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Colorectal cancer (CRC) is a leading cause of cancer-related death worldwide, but if discovered at an early stage, the survival rate is high. The aim of this study was to identify novel markers predictive of future CRC risk using untargeted metabolomics.Methods: This study included prospectively collected plasma samples from 902 CRC cases and 902 matched cancer-free control participants from the population-based Northern Sweden Health and Disease Study (NSHDS), which were obtained up to 26 years prior to CRC diagnosis. Using reverse-phase liquid chromatography-mass spectrometry (LC-MS), data comprising 5015 metabolic features were obtained. Conditional logistic regression was applied to identify potentially important metabolic features associated with CRC risk. In addition, we investigated if previously reported metabolite biomarkers of CRC risk could be validated in this study population.Results: In the univariable analysis, seven metabolic features were associated with CRC risk (using a false discovery rate cutoff of 0.25). Two of these could be annotated, one as pyroglutamic acid (odds ratio per one standard deviation increase = 0.79, 95% confidence interval, 0.70-0.89) and another as hydroxytigecycline (odds ratio per one standard deviation increase = 0.77, 95% confidence interval, 0.67-0.89). Associations with CRC risk were also found for six previously reported metabolic biomarkers of prevalent and/or incident CRC: sebacic acid (inverse association) and L-tryptophan, 3-hydroxybutyric acid, 9,12,13-TriHOME, valine, and 13-OxoODE (positive associations).Conclusions: These findings suggest that although the circulating metabolome may provide new etiological insights into the underlying causes of CRC development, its potential application for the identification of individuals at higher risk of developing CRC is limited.
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| 46. |
- Wang, Yanzhi, et al.
(författare)
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Anchoring Fe Species on the Highly Curved Surface of S and N Co-Doped Carbonaceous Nanosprings for Oxygen Electrocatalysis and a Flexible Zinc-Air Battery
- 2024
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Ingår i: Angewandte Chemie International Edition. - 1433-7851 .- 1521-3773. ; 63:7
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Tidskriftsartikel (refereegranskat)abstract
- Oxygen reduction reaction (ORR) is of critical significance in the advancement of fuel cells and zinc-air batteries. The iron-nitrogen (Fe−Nx) sites exhibited exceptional reactivity towards ORR. However, the task of designing and controlling the local structure of Fe species for high ORR activity and stability remains a challenge. Herein, we have achieved successful immobilization of Fe species onto the highly curved surface of S, N co-doped carbonaceous nanosprings (denoted as FeNS/Fe3C@CNS). The induction of this twisted configuration within FeNS/Fe3C@CNS arose from the assembly of chiral templates. For electrocatalytic ORR tests, FeNS/Fe3C@CNS exhibits a half-wave potential (E1/2) of 0.91 V in alkaline medium and a E1/2 of 0.78 V in acidic medium. The Fe single atoms and Fe3C nanoparticles are coexistent and play as active centers within FeNS/Fe3C@CNS. The highly curved surface, coupled with S substitution in the coordination layer, served to reduce the energy barrier for ORR, thereby enhancing the intrinsic catalytic activity of the Fe single-atom sites. We also assembled a wearable flexible Zn-air battery using FeNS/Fe3C@CNS as electrocatalysts. This work provides new insights into the construction of highly curved surfaces within carbon materials, offering high electrocatalytic efficacy and remarkable performance for flexible energy conversion devices.
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| 47. |
- Wang, Yanzhi, et al.
(författare)
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Fe Single-atom Sites in Two-Dimensional Nitrogen-doped Porous Carbon for Electrocatalytic Oxygen Reduction
- 2022
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Ingår i: ChemCatChem. - : Wiley. - 1867-3880 .- 1867-3899. ; 14:14
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Tidskriftsartikel (refereegranskat)abstract
- The development of electrocatalysts for oxygen reduction reaction (ORR) is important for energy conversion devices, such as fuel cells, and metal-air batteries. Here, we have developed a confined space strategy to prepare a two-dimensional (2D) leaf-like nitrogen (N)-containing porous carbon as a single-atom catalyst substrate. ZIF−L materials have been confined in a thin silica layer to regulate the pyrolysis. The obtained Fe single atoms doped N-containing porous carbons (Fe SAs/N−C) maintain the 2D morphology and have Fe single-atom active sites. Correspondingly, Fe SAs/N−C exhibits excellent ORR performance (E1/2 of 0.907 V), which is more positive than those of commercially available Pt/C (0.874 V) and most reported non-noble metal catalysts. The durability test shows that Fe SAs/N−C exhibits good stability during electrocatalytic process. This rational design shows a new strategy to prepare 2D catalyst supports with single-atom active sites.
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| 48. |
- Wang, Yanzhi, et al.
(författare)
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Two-Dimensional Metal-Organic Frameworks with Unique Oriented Layers for Oxygen Reduction Reaction : Tailoring the Activity through Exposed Crystal Facets
- 2022
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Ingår i: CCS CHEMISTRY. - : Chinese Chemical Society. - 2096-5745. ; 4:5, s. 1633-1642
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Tidskriftsartikel (refereegranskat)abstract
- As one of the most important families of porous materials, metal-organic frameworks (MOFs) have well-defined atomic structures. This provides ideal models for investigating and understanding the relationships between structures and catalytic activities at the molecular level. However, the active sites on the edges of two-dimensional (2D) MOFs have rarely been studied, as they are less exposed to the surfaces. Here, for the first time, we synthesized and observed that the 2D layers could align perpendicular to the surface of a 2D zeolitic imidazolate framework L (ZIF-L) with a leaf-like morphology. Owing to this unique orientation, the active sites on the edges of the 2D crystal structure could mostly be exposed to the surfaces. Interestingly, when another layer of ZIF-L-Co was grown heteroepitaxially onto ZIF-L-Zn (ZIF-L-Zn@ZIF-L-Co), the two layers shared a common b axis but rotated by 90 degrees in the ac plane. This demonstrated that we could control exposed facets of the 2D MOFs. The ZIF-L-Co with more exposed edge active sites exhibited high electrocatalytic activity for oxygen reduction reaction. This work provides a new concept of designing unique oriented layers in 2D MOFs to expose more edge-active sites for efficient electrocatalysis. [GRAPHICS] .
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| 49. |
- Wu, Chuansha, et al.
(författare)
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Modification of Food Allergy on the Associations between Early Life Exposure to Size-Specific Particulate Matter and Childhood Allergic Rhinitis
- 2024
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 58:4, s. 1813-1822
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies have reported the association between particulate matter (PM) and childhood allergic rhinitis (AR). However, it is unclear whether food allergy (FA) modifies the PM-AR association. We aimed at evaluating the effect of the modification of FA on PM-AR association in preschool children. We adopted a cross-sectional study and conducted a questionnaire survey among preschool children aged 3-6 years in 7 cities in China from June 2019 to June 2020 to collect information on AR and FA. We used a combination of multilevel logistic regression and restricted cubic spline functions to quantitatively assess whether FA modifies the associations between size-specific PM exposure (1 x 1 km) and the risk of AR. The adjusted odds ratios (ORs) for AR among the children with FA as per a 10 mu g/m(3) increase in early life PM1, PM2.5, and PM10 were significantly higher than the corresponding ORs among the children without FA [e.g., OR: 1.58, 95% CI: (1.32, 1.90) vs 1.29, 95% CI: (1.18, 1.41), per 10 mu g/m(3) increase in PM1]. The interactions between FA and size-specific PM exposure and their effects on AR were statistically significant (all p-int < 0.001). FA, as an important part of the allergic disease progression, may modify the PM-AR association in preschool children.
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| 50. |
- Wu, Pianpian, et al.
(författare)
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Elevated temperature and browning increase dietary methylmercury, but decrease essential fatty acids at the base of lake food webs
- 2021
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Climate change scenarios predict increases in temperature and organic matter supply from land to water, which affect trophic transfer of nutrients and contaminants in aquatic food webs. How essential nutrients, such as polyunsaturated fatty acids (PUFA), and potentially toxic contaminants, such as methylmercury (MeHg), at the base of aquatic food webs will be affected under climate change scenarios, remains unclear. The objective of this outdoor mesocosm study was to examine how increased water temperature and terrestrially-derived dissolved organic matter supply (tDOM; i.e., lake browning), and the interaction of both, will influence MeHg and PUFA in organisms at the base of food webs (i.e. seston; the most edible plankton size for zooplankton) in subalpine lake ecosystems. The interaction of higher temperature and tDOM increased the burden of MeHg in seston (< 40 mu m) and larger sized plankton (microplankton; 40-200 mu m), while the MeHg content per unit biomass remained stable. However, PUFA decreased in seston, but increased in microplankton, consisting mainly of filamentous algae, which are less readily bioavailable to zooplankton. We revealed elevated dietary exposure to MeHg, yet decreased supply of dietary PUFA to aquatic consumers with increasing temperature and tDOM supply. This experimental study provides evidence that the overall food quality at the base of aquatic food webs deteriorates during ongoing climate change scenarios by increasing the supply of toxic MeHg and lowering the dietary access to essential nutrients of consumers at higher trophic levels.
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