| 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. |
- Kristanl, Matej, et al.
(författare)
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The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
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Ingår i: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 5. |
- Ablikim, M., et al.
(författare)
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Measurements of cross section of e(+)e(-) -> p(p)over-bar pi(0) at center-of-mass energies between 4.008 and 4.600 GeV
- 2017
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Ingår i: Physics Letters B. - : ELSEVIER SCIENCE BV. - 0370-2693 .- 1873-2445. ; 771, s. 45-51
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Tidskriftsartikel (refereegranskat)abstract
- Based on e(+)e(-) annihilation data samples collected with the BESIII detector at the BEPCII collider at 13 center-of-mass energies from 4.008 to 4.600 GeV, measurements of the Born cross section of e(+)e(-) -> p (p) over bar pi(0) are performed. No significant resonant structure is observed in the measured energy dependence of the cross section. The upper limit on the Born cross section of e(+)e(-) -> Y (4260) -> p (p) over bar pi(0) at the 90% C. L. is determined to be 0.01 pb. The upper limit on the ratio of the branching fractions B(Y(4260) -> p (p) over bar pi(0))/B(Y(4260) -> pi(+)pi(-) j/Psi) at the 90% C. L. is determined to be 0.02%.
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| 6. |
- Mahajan, Anubha, et al.
(författare)
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Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation
- 2022
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Ingår i: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 54:5, s. 560-572
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Tidskriftsartikel (refereegranskat)abstract
- We assembled an ancestrally diverse collection of genome-wide association studies (GWAS) of type 2 diabetes (T2D) in 180,834 affected individuals and 1,159,055 controls (48.9% non-European descent) through the Diabetes Meta-Analysis of Trans-Ethnic association studies (DIAMANTE) Consortium. Multi-ancestry GWAS meta-analysis identified 237 loci attaining stringent genome-wide significance (P < 5 x 10(-9)), which were delineated to 338 distinct association signals. Fine-mapping of these signals was enhanced by the increased sample size and expanded population diversity of the multi-ancestry meta-analysis, which localized 54.4% of T2D associations to a single variant with >50% posterior probability. This improved fine-mapping enabled systematic assessment of candidate causal genes and molecular mechanisms through which T2D associations are mediated, laying the foundations for functional investigations. Multi-ancestry genetic risk scores enhanced transferability of T2D prediction across diverse populations. Our study provides a step toward more effective clinical translation of T2D GWAS to improve global health for all, irrespective of genetic background. Genome-wide association and fine-mapping analyses in ancestrally diverse populations implicate candidate causal genes and mechanisms underlying type 2 diabetes. Trans-ancestry genetic risk scores enhance transferability across populations.
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| 7. |
- Blokland, G. A. M., et al.
(författare)
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Sex-Dependent Shared and Nonshared Genetic Architecture Across Mood and Psychotic Disorders
- 2022
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Ingår i: Biological Psychiatry. - : Elsevier BV. - 0006-3223 .- 1873-2402. ; 91:1, s. 102-117
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Tidskriftsartikel (refereegranskat)abstract
- Background: Sex differences in incidence and/or presentation of schizophrenia (SCZ), major depressive disorder (MDD), and bipolar disorder (BIP) are pervasive. Previous evidence for shared genetic risk and sex differences in brain abnormalities across disorders suggest possible shared sex-dependent genetic risk. Methods: We conducted the largest to date genome-wide genotype-by-sex (G×S) interaction of risk for these disorders using 85,735 cases (33,403 SCZ, 19,924 BIP, and 32,408 MDD) and 109,946 controls from the PGC (Psychiatric Genomics Consortium) and iPSYCH. Results: Across disorders, genome-wide significant single nucleotide polymorphism–by-sex interaction was detected for a locus encompassing NKAIN2 (rs117780815, p = 3.2 × 10−8), which interacts with sodium/potassium-transporting ATPase (adenosine triphosphatase) enzymes, implicating neuronal excitability. Three additional loci showed evidence (p < 1 × 10−6) for cross-disorder G×S interaction (rs7302529, p = 1.6 × 10−7; rs73033497, p = 8.8 × 10−7; rs7914279, p = 6.4 × 10−7), implicating various functions. Gene-based analyses identified G×S interaction across disorders (p = 8.97 × 10−7) with transcriptional inhibitor SLTM. Most significant in SCZ was a MOCOS gene locus (rs11665282, p = 1.5 × 10−7), implicating vascular endothelial cells. Secondary analysis of the PGC-SCZ dataset detected an interaction (rs13265509, p = 1.1 × 10−7) in a locus containing IDO2, a kynurenine pathway enzyme with immunoregulatory functions implicated in SCZ, BIP, and MDD. Pathway enrichment analysis detected significant G×S interaction of genes regulating vascular endothelial growth factor receptor signaling in MDD (false discovery rate-corrected p < .05). Conclusions: In the largest genome-wide G×S analysis of mood and psychotic disorders to date, there was substantial genetic overlap between the sexes. However, significant sex-dependent effects were enriched for genes related to neuronal development and immune and vascular functions across and within SCZ, BIP, and MDD at the variant, gene, and pathway levels. © 2021 Society of Biological Psychiatry
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| 8. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 9. |
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| 10. |
- Yang, Xi-Xi, et al.
(författare)
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Theoretical study of the mechanism of the manganese catalase KatB
- 2019
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Ingår i: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 0949-8257 .- 1432-1327. ; 24:1, s. 103-115
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Tidskriftsartikel (refereegranskat)abstract
- The mechanism of the H2O2 disproportionation catalyzed by the manganese catalase (MnCat) KatB was studied using the hybrid density functional theory B3LYP and the quantum chemical cluster approach. Compared to the previous mechanistic study at the molecular level for the Thermus thermophilus MnCat (TTC), more modern methodology was used and larger models of increasing sizes were employed with the help of the high-resolution X-ray structure. In the reaction pathway suggested for KatB using the Large chemical model, the O-O homolysis of the first substrate H2O2 occurs through a -(1):(1) coordination mode and requires a barrier of 10.9kcal/mol. In the intermediate state of the bond cleavage, two hydroxides form as terminal ligands of the dimanganese cluster at the Mn-2(III,III) oxidation state. One of the two Mn(III)-OH- moieties and a second-sphere tyrosine stabilize the second substrate H2O2 in the second-sphere of the active site via hydrogen bonding interactions. The H2O2, unbound to the metals, is first oxidized into HO2 through a proton-coupled electron transfer (PCET) step with a barrier of 9.5kcal/mol. After the system switches to the triplet surface, the uncoordinated HO2 replaces the product water terminally bound to the Mn(II) and is then oxidized into O-2 spontaneously. Transition states with structural similarities to those obtained for TTC, where -(2)-OH-/O2- groups play important roles, were found to be higher in energy.
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| 11. |
- Gong, Hanmo, et al.
(författare)
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Gold nanoparticle transfer through photothermal effects in a metamaterial absorber by nanosecond laser
- 2014
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4, s. 6080-
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Tidskriftsartikel (refereegranskat)abstract
- A non-complicated, controllable method of metallic nanoparticle fabrication at low operating light power is proposed. The method is based on laser-induced forward transfer, using a metamaterial absorber as the donor to significantly enhance the photothermal effect and reduce the operating light fluence to 35 mJ/cm(2), which is much lower than that in previous works. A large number of metallic nanoparticles can be transferred by one shot of focused nanosecond laser pulses. Transferred nanoparticles exhibit good size uniformity and the sizes are controllable. The optical properties of transferred particles are characterized by dark-field spectroscopy and the experimental results agree with the simulation results.
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| 12. |
- Li, Cong, et al.
(författare)
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Expression of Twist associated to microcirculation patterns of human glioma correlated with progression and survival of the patient
- 2020
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Ingår i: NOVEL THERAPEUTIC ADVANCES IN GLIOBLASTOMA. - LONDON ENGLAND : Elsevier. - 9780128211144 ; , s. 201-217
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Bokkapitel (refereegranskat)abstract
- Twist is a transcription factor involved in the process of epithelial to mesenchymal transition (EMT) of carcinoma cells, and the promotion of invasion of gliomas through the mesenchymal adjusting process. However, its clinical significance in human glioma has not yet to be understood. To delineate the clinical-pathological significance and prognostic value of Twist, the expression of Twist was evaluated by Immunohistochemistry for 187 glioma samples. We found that Twist demonstrated frequent nuclear expression in the glioma samples and its expression levels were associated with tumor grade (P < 0.001). Furthermore, high Twist expression was correlated with a poor outcome in patients with glioma (P = 0.001), particularly with high grade glioma (P = 0.026). Interestingly, Twist expression showed positive correlation with microvascular density (MVD) (r = 0.145, P = 0.048) as well as vasculogenic mimicry (VM) (r = 0.273, P < 0.001) in the tumors. These results suggest that Twist could be a predictor for poor prognosis in glioma patients. Additionally, Twist expression was associated with two major microcirculation patterns: endothelial-dependent vessels and VM in glioma, indicating that Twist could be a potential molecular target for anti-glioma therapy.
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| 13. |
- Chen, David, et al.
(författare)
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Hydrologic alteration along the Middle and Upper East River (Dongjiang) basin, South China : a visually enhanced mining on the results of RVA method
- 2010
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Ingår i: Stochastic environmental research and risk assessment (Print). - : Springer Science and Business Media LLC. - 1436-3240 .- 1436-3259. ; 24, s. 9-18
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents a visually enhanced evaluation of the spatio-temporal patterns of the dam-induced hydrologic alteration in the middle and upper East River, south China over 1952-2002, using the range of variability approach (RVA) and visualization package XmdvTool. The impacts of climate variability on hydrological processes have been removed for wet and dry periods, respectively, so that we focus on the impacts of human activities (i.e., dam construction). The results indicate that: (1) along the East River, dams have greatly altered the natural flow regime, range condition and spatial variability; (2) six most remarkable indicators of hydrologic alteration induced by dam-construction are rise rate (1.16), 3-day maximum (0.91), low pulse duration (0.88), January (0.80), July (0.80) and February (0.79) mean flow of the East River during 1952-2002; and (3) spatiotemporal hydrologic alterations are different among three stations along Easter River. Under the influence of dam construction in the upstream, the degree of hydrologic changes from Lingxia, Heyuan to Longchuan station increases. This study reveals that visualization techniques for high-dimensional hydrological datasets together with RVA are beneficial for detecting spatio-temporal hydrologic changes.
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| 14. |
- Chen, Xi, et al.
(författare)
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Device noise reduction for Silicon nanowire field-effect-transistor based sensors by using a Schottky junction gate
- 2019
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Ingår i: ACS Sensors. - : American Chemical Society (ACS). - 2379-3694. ; 4:2, s. 427-433
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Tidskriftsartikel (refereegranskat)abstract
- The sensitivity of metal-oxide-semiconductor field-effect transistor (MOSFET) based nanoscale sensors is ultimately limited by noise induced by carrier trapping/detrapping processes at the gate oxide/semiconductor interfaces. We have designed a Schottky junction gated silicon nanowire field-effect transistor (SiNW-SJGFET) sensor, where the Schottky junction replaces the noisy oxide/semiconductor interface. Our sensor exhibits significantly reduced noise, 2.1×10-9 V2µm2/Hz at 1 Hz, compared to reference devices with the oxide/semiconductor interface operated at both inversion and depletion modes. Further improvement can be anticipated by wrapping the nanowire by such a Schottky junction thereby eliminating all oxide/semiconductor interfaces. Hence, a combination of the low-noise SiNW-SJGFET sensor device with a sensing surface of the Nernstian response limit holds promises for future high signal-to-noise ratio sensor applications.
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| 15. |
- Chen, Xi, et al.
(författare)
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Low-Noise Schottky Junction Trigate Silicon Nanowire Field-effect Transistor for Charge Sensing
- 2019
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Ingår i: IEEE Transactions on Electron Devices. - 0018-9383 .- 1557-9646. ; 66:9, s. 3994-4000
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Tidskriftsartikel (refereegranskat)abstract
- Silicon nanowire (SiNW) field-effect transistors (SiNWFETs) are of great potential as a high-sensitivity charge sensor. The signal-to-noise ratio (SNR) of an SiNWFET sensor is ultimately limited by the intrinsic device noise generated by carrier trapping/detrapping processes at the gate oxide/silicon interface. This carrier trapping/detrapping-induced noise can be significantly reduced by replacing the noisy oxide/silicon interface with a Schottky junction gate (SJG) on the top of the SiNW. In this paper, we present a tri-SJG SiNWFET (Tri-SJGFET) with the SJG formed on both the top surface and the two sidewalls of the SiNW so as to enhance the gate control over the SiNW channel. Both experiment and simulation confirm that the additional sidewall gates in a narrow Tri-SJGFET indeed can confine the conduction path within the bulk of the SiNW channel away from the interfaces and significantly improve the immunity to the traps at the bottom buried oxide/silicon interface. Therefore, the optimal low-frequency noise performance can be achieved without the need for any substrate bias. This new gating structure holds promises for further development of robust SiNWFET-based charge sensors with low noise and low operation voltage.
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| 16. |
- Chen, Xi, et al.
(författare)
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Multiplexed analysis of molecular and elemental ions using nanowire transistor sensors
- 2018
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Ingår i: Sensors and actuators. B, Chemical. - : Elsevier BV. - 0925-4005 .- 1873-3077. ; 270, s. 89-96
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Tidskriftsartikel (refereegranskat)abstract
- An integrated sensor chip with silicon nanowire ion-sensitive field-effect transistors for simultaneous and selective detection of both molecular and elemental ions in a single sample solution is demonstrated. The sensing selectivity is realized by functionalizing the sensor surface with tailor-made mixed-matrix membranes (MMM) incorporated with specific ionophores for the target ions. A biomimetic container molecule, named metal-organic supercontainer (MOSC), is selected as the ionophore for detection of methylene blue (MB+), a molecular ion, while a commercially available Na-ionophore is used for Na+, an elemental ion. The sensors show a near-Nernstian response with 56.4 ± 1.8 mV/dec down to a concentration limit of ∌1 ΌM for MB+ and 57.9 ± 0.7 mV/dec down to ∌60 ΌM for Na+, both with excellent reproducibility. Extensive control experiments on the MB+ sensor lead to identification of the critical role of the MOSC molecules in achieving a stable and reproducible potentiometric response. Moreover, the MB+-specific sensor shows remarkable selectivity against common interfering elemental ions in physiological samples, e.g., H+, Na+, and K+. Although the Na+-specific sensor is currently characterized by insufficient immunity to the interference by MB+, the root cause is identified and remedies generally applicable for hydrophobic molecular ions are discussed. River water experiments are also conducted to prove the efficacy of our sensors.
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| 17. |
- Chen, Xi, et al.
(författare)
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Nanosecond Photothermal Effects in Plasmonic Nanostructures
- 2012
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Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 6:3, s. 2550-2557
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Tidskriftsartikel (refereegranskat)abstract
- Photothermal effects in plasmonic nanostructures have great potentials in applications for photothermal cancer therapy, optical storage, thermo-photovoltaics, etc. However, the transient temperature behavior of a nanoscale material system during an ultrafast photothermal process has rarely been accurately investigated. Here a heat transfer model is constructed to investigate the temporal and spatial variation of temperature in plasmonic gold nanostructures. First, as a benchmark scenario, we study the light-induced heating of a gold nanosphere in water and calculate the relaxation time of the nanosphere excited by a modulated light. Second, we investigate heating and reshaping of gold nanoparticles in a more complex metamaterial absorber structure induced by a nanosecond pulsed light. The model shows that the temperature of the gold nanoparticles can be raised from room temperature to >795 K in just a few nanoseconds with a low light luminance, owing to enhanced light absorption through strong plasmonic resonance. Such quantitative predication of temperature change, which Is otherwise formidable to measure experimentally, can serve as an excellent guideline for designing devices for ultrafast photothermal applications.
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| 18. |
- Chen, Xi, et al.
(författare)
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Ordered Au nanocrystals on a substrate formed by light-induced rapid annealing
- 2014
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 6:3, s. 1756-1762
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Tidskriftsartikel (refereegranskat)abstract
- Light-induced rapid annealing (LIRA) is a widely used method to modify the morphology and crystallinity of noble metal nanoparticles, and the nanoparticles generally evolve into nanospheres. It is rather challenging to form faceted Au nanocrystals on a substrate using LIRA. Here the formation of spatially ordered Au nanocrystals using a continuous wave infrared laser is reported, assisted by a metamaterial perfect absorber. Faceted Au nanocrystals in truncated-octahedral or multi-twinned geometries can be obtained. The evolution of morphology and crystallinity of the Au nanoparticles during laser annealing is also revealed, where the crystal grain growth and the surface melting are shown to play key roles in nanocrystal formation. The evolution of morphology also gives the freedom of tuning the absorption spectrum of the metamaterial absorber. These findings provide a novel way for tailoring the morphology and crystallinity of metallic nanoparticles and may pave the way to fabricate refined nano-devices in many potential applications for optics, electronics, catalysis, surface-chemistry and biology.
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| 19. |
- Chen, Xi, et al.
(författare)
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Photothermal direct writing of metallic microstructure for frequency selective surface at terahertz frequencies
- 2012
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Ingår i: Proceedings of the 2012 International Workshop on Metamaterials, Meta 2012. - : IEEE. - 9781467328081 ; , s. 6464923-
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Konferensbidrag (refereegranskat)abstract
- Maskless photothermal direct writing technique was investigated to fabricate planar microscale metallic structures. In this technique, we use a tightly focused nanosecond pulsed infrared light to heat the metallic thin film on substrate. With sufficient volumic power density, the metal inside a "hot spot" could be removed from substrate. This technique benefits from not only the enhanced optical absorption, thanks to the surface plasmon resonance of metallic thin film, but also the reduced thermal conductivity, due to the frequent boundary scattering of phonons inside the thin film. To verify the performance of our direct writing technique, a cross-slot periodic array is scribed in gold thin film on silica substrate. Such a pattern can serve as a frequency selective surface at terahertz, which has many applications in terahertz radio system, e. g. rejecting thermal noise before terahertz receiver or serving as reflectors in Fabry-Perot etalon for astronomy spectroscopy.
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| 20. |
- Chen, Xi, et al.
(författare)
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Photothermal phenomena in plasmonics and metamaterials
- 2011
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Ingår i: ADVANCES IN OPTICAL THIN FILMS IV. - : SPIE. - 9780819487940 ; , s. 81681K-
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Konferensbidrag (refereegranskat)abstract
- Our recent theoretical and experimental investigation of the photothermal effect in a planar metamaterial absorber is reviewed in the present paper. The observed ultrasensitive photothermal heating in such an absorber nanostructure irradiated by a pulsed white-light source is elaborated with a simple yet compelling heat transfer model, which is subsequently solved with a finite-element method. The simulation results not only agree with the experimental finding, but also provide more detailed understanding of the temperature transition in the complex system.
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| 21. |
- Chen, Xi, et al.
(författare)
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Photothermal Switching of SOI Waveguide-Based Mach-Zehnder Interferometer with Integrated Plasmonic Nanoheater
- 2014
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Ingår i: Plasmonics. - : Springer. - 1557-1955 .- 1557-1963. ; 9:5, s. 1197-1205
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Tidskriftsartikel (refereegranskat)abstract
- We theoretically and numerically investigated the photothermal switching of a Mach-Zehnder interferometer (MZI) based on two Si waveguides integrated with plasmonic nanoheaters. The nanoheater is a composite nanowire with Au/Al2O3/Au three-layer structure, which is designed to have a highly efficient optical absorption peak at wavelength of 1,064 nm. Based on this finding, we further analyze a MZI built with two 40-μm-long symmetric waveguide branches, each integrated with a 20-μm-long nanoheater. The optical switching power of the MZI device is 190 mW (280 mW) for the capped (buried) channel waveguide, when pumped by a circular Gaussian beam with a waist of 10 μm. Alternatively, the switching power can be reduced to 38 mW (56 mW) by using an astigmatic Gaussian beam, with a semi-major axis of 10 μm and an aspect ratio of 5. The switching response time of the MZI is 0.7 μs (1.0 μs) for capped (buried) channel waveguide design. Our design opens a new route for optically driven non-contact optical on-off switching with sub-microsecond time response.
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| 22. |
- Chen, Xi, et al.
(författare)
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Photothermally tunable silicon-microring-based optical add-drop filter through integrated light absorber
- 2014
-
Ingår i: Optics Express. - 1094-4087. ; 22:21, s. 25233-25241
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Tidskriftsartikel (refereegranskat)abstract
- An optically pumped thermo-optic (TO) silicon ring add-drop filter with fast thermal response is experimentally demonstrated. We propose that metal-insulator-metal (MIM) light absorber can be integrated into silicon TO devices, acting as a localized heat source which can be activated remotely by a pump beam. The MIM absorber design introduces less thermal capacity to the device, compared to conventional electrically-driven approaches. Experimentally, the absorber-integrated add-drop filter shows an optical response time of 13.7 mu s following the 10%-90% rule (equivalent to a exponential time constant of 5 mu s) and a wavelength shift over pump power of 60 pm/mW. The photothermally tunable add-drop filter may provide new perspectives for all-optical routing and switching in integrated Si photonic circuits.
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| 23. |
- Chen, Xi, et al.
(författare)
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Photothermally tunable silicon-microring-based optical add-drop filter through integrated light absorber
- 2014
-
Ingår i: Optics Express. - : Optica Publishing Group. - 1094-4087. ; 22:21, s. 25233-25241
-
Tidskriftsartikel (refereegranskat)abstract
- An optically pumped thermo-optic (TO) silicon ring add-drop filter with fast thermal response is experimentally demonstrated. We propose that metal-insulator-metal (MIM) light absorber can be integrated into silicon TO devices, acting as a localized heat source which can be activated remotely by a pump beam. The MIM absorber design introduces less thermal capacity to the device, compared to conventional electrically-driven approaches. Experimentally, the absorber-integrated add-drop filter shows an optical response time of 13.7 μs following the 10%–90% rule (equivalent to a exponential time constant of 5 μs) and a wavelength shift over pump power of 60 pm/mW. The photothermally tunable add-drop filter may provide new perspectives for all-optical routing and switching in integrated Si photonic circuits.
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| 24. |
- Chen, Xi, et al.
(författare)
-
Photothermally tunable silicon microring-resonator-based optical add-drop filter
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- A themro-optic (TO) silicon photonic add-drop filterwith small switching power and fast response is experimentallydemonstrated. We propose that metal-insulator-metal (MIM)absorbers can be integrated into the silicon TO devices, acting asan efficient and localized heat source. The MIM absorber designintroduces less thermal capacity to the device, comparing to theelectrically driven heater used in conventional TO devices. As a keyelement in silicon photonics, microring resonators have applicationin wavelength-division-multiplexing (WDM) devices, owning to theirunique spectrum properties. In this work, a silicon microring add-dropfilter is equipped with a MIM absorber. Experimentally, the deviceshows a measured optical response time of 5.0 μs and pumping powerderivative of the wavelength shift of 60 pm/mW.
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| 25. |
- Chen, Xi
(författare)
-
Silicon Nanowire Field-Effect Devices as Low-Noise Sensors
- 2019
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In the past decades, silicon nanowire field-effect transistors (SiNWFETs) have been explored for label-free, highly sensitive, and real-time detections of chemical and biological species. The SiNWFETs are anticipated for sensing analyte at ultralow concentrations, even at single-molecule level, owing to their significantly improved charge sensitivity over large-area FETs. In a SiNWFET sensor, a change in electrical potential associated with biomolecular interactions in close proximity to the SiNW gate terminal can effectively control the underlying channel and modulate the drain-to-source current (IDS) of the SiNWFET. A readout signal is therefore generated. This signal is primarily determined by the surface properties of the sensing layer on the gate terminal, with sensitivity close up to the Nernstian limit widely demonstrated. To achieve a high signal-to-noise ratio (SNR), it is essential for the SiNWFETs to possess low noise of which intrinsic device noise is one of the major components. In metal-oxide-semiconductor (MOS)-type FETs, the intrinsic noise mainly results from carrier trapping/detrapping at the gate oxide/semiconductor interface and it is inversely proportional to the device area.This thesis presents a comprehensive study on design, fabrication, and noise reduction of SiNWFET-based sensors on silicon-on-oxide (SOI) substrate. A novel Schottky junction gated SiNWFET (SJGFET) is designed and experimentally demonstrated for low noise applications. Firstly, a robust process employing photo- and electron-beam mixed-lithography was developed to reliably produce sub-10 nm SiNW structures for SiNWFET fabrication. For a proof-of-concept demonstration, MOS-type SiNWFET sensors were fabricated and applied for multiplexed ion detection using ionophore-doped mixed-matrix membranes as sensing layers. To address the fundamental noise issue of the MOS-type SiNWFETs, SJGFETs were fabricated with a Schottky (PtSi/silicon) junction gate on the top surface of the SiNW channel, replacing the noisy gate oxide/silicon interface in the MOS-type SiNWFETs. The resultant SJGFETs exhibited a close-to-ideal gate coupling efficiency (60 mV/dec) and significantly reduced device noise compared to reference MOS-type SiNWFETs. Further optimization was performed by implementing a three-dimensional Schottky junction gate wrapping both top surface and two sidewalls of the SiNW channel. The tri-gate SJGFETs with optimized geometry exhibited significantly enhanced electrostatic control over the channel, thereby confined IDS in the SiNW bulk, which greatly improved the device noise immunity to the traps at bottom buried oxide/silicon interface. Finally, a lateral bipolar junction transistor (LBJT) was also designed and fabricated on a SOI substrate aiming for immediate sensor current amplification. Integrating SJGFETs with LBJTs is expected to significantly suppress environmental interference and improve the overall SNR especially under low sensor current situations.
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| 26. |
- Chen, Xi, et al.
(författare)
-
Simulating the integrated effects of topography and soil properties on runoff generation in hilly forested catchments, South China
- 2010
-
Ingår i: Hydrological Processes. - : Wiley. - 0885-6087 .- 1099-1085. ; 24:6, s. 714-725
-
Tidskriftsartikel (refereegranskat)abstract
- Estimation of runoff components associated with catchment topography and soil properties is critical for planning water resources utilization and evaluating hydrological changes due to artificially induced land surface manipulation. In this study, the modified TOPMODEL by Scanlon et al. (2000) was applied to simulate runoff-generating processes and to separate runoff components in two hilly forested catchments within the Dongjiang Basin of Southeast China. The modified TOPMODEL was improved by integrating an evapotranspiration package with the model algorithms. Influences of catchment topography and soil properties on runoff generation were analysed on the basis of explicit expression of catchment field capacity distribution derived from the topographic index and catchment average field capacity. Study results demonstrate that the model is capable of simulating hydrological processes and separate hydrological components in both hourly and daily time steps. Total runoff generation primarily depends on the effective storage capacity of unsaturated zone. A 50% decrease of the effective storage capacity from 0.22 to 0.11 m over the soil zone leads to a 6.6% increase in total runoff. Topography plays a dominant role in formation of runoff components. When the catchment mean slope increases by 87%, subsurface storm flow could increase by 50% whilst overland flow decreases by 7.5% and baseflow by 6.7%. Vertical changes of soil permeability influence runoff components as well. Decrease of the lower layer hydraulic transmissivity may result in 2-3% increase of overland flow and subsurface storm flow and 5% decrease of baseflow.
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| 27. |
- Chen, XÍ, et al.
(författare)
-
TDHQ Enabling Fine-granularity Adaptive Loading for SSB-DMT Systems
- 2018
-
Ingår i: IEEE Photonics Technology Letters. - : Institute of Electrical and Electronics Engineers Inc.. - 1041-1135 .- 1941-0174. ; 30:19, s. 1687-1690
-
Tidskriftsartikel (refereegranskat)abstract
- In this letter, we introduce time domain hybrid quadrature amplitude modulation (TDHQ) for the single sideband (SSB) discrete multi-tone (DMT) systems. Experimental results reveal that with a single precoding set and the proposed adaptive loading algorithm, the TDHQ scheme can achieve finer granularity and therefore smoother continuous growth of data rate than that with the conventional quadrature amplitude modulation (QAM). Besides, thanks to the frame construction and the tailored mapping rule, the scheme with TDHQ has an obviously better peak to average power ratio (PAPR).
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| 28. |
- Chen, Xi, et al.
(författare)
-
Top-bottom gate coupling effect on low frequency noise in a Schottky junction gated silicon nanowire field-effect transistor
- 2019
-
Ingår i: IEEE Journal of the Electron Devices Society. - 2168-6734. ; 7, s. 696-700
-
Tidskriftsartikel (refereegranskat)abstract
- In this letter, strong low frequency noise (LFN) reduction is observed when the buried oxide (BOX)/silicon interface of a Schottky junction gated silicon nanowire field-effect transistor (SJGFET) is depleted by a substrate bias. Such LFN reduction is mainly attributed to the dramatic reduction in Coulomb scattering when carriers are pushed away from the interface. The BOX/silicon interface depletion can also be achieved by sidewall Schottky junction gates in a narrow channel SJGFET, leading to an optimal LFN performance without the need of any substrate bias.
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| 29. |
- Chen, Xianhao, et al.
(författare)
-
WHEN FULL DUPLEX WIRELESS MEETS NON-ORTHOGONAL MULTIPLE ACCESS : OPPORTUNITIES AND CHALLENGES
- 2019
-
Ingår i: IEEE wireless communications. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 1536-1284 .- 1558-0687. ; 26:4, s. 148-155
-
Tidskriftsartikel (refereegranskat)abstract
- NOMA is a promising radio access technology for 5G wireless systems. The core of NOMA is to support multiple users in the same resource block via power or code domain multiplexing, which provides great enhancement in spectrum efficiency and connectivity. Meanwhile, with the recent advance in self-interference (SI) cancelation techniques, FD wireless communication has become a feasible technology enabling radios to receive and transmit simultaneously. This article aims to investigate the combination of these two emerging technologies. At first, several typical scenarios and protocols are presented to illustrate the application of the FD technique in NOMA systems. Then, a novel NOMA system with FD base stations (BSs) based on C-RAN is proposed. Furthermore, power allocation policies are discussed for the proposed scheme, and simulation results are provided to demonstrate its superiority. Finally, challenges and research opportunities of FD NOMA systems are also identified to stimulate future research.
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| 30. |
- Chen, Yiting, et al.
(författare)
-
Plasmonic analog of microstrip transmission line and effect of thermal annealing on its propagation loss
- 2013
-
Ingår i: Optics Express. - 1094-4087. ; 21:2, s. 1639-1644
-
Tidskriftsartikel (refereegranskat)abstract
- We fabricated a plasmonic analog of the microwave microstrip transmission line and measured its propagation loss before and after thermal annealing. It is found that its propagation loss at 980 nm wavelength can be reduced by more than 50%, from 0.45 to 0.20 dB/μm, after thermal annealing at 300 °C. The reduction in loss can be attributed to the improved gold surface condition and probably also to the change in the metal's inner structure. Less evident loss reduction is noticed at 1550 nm, which is owing to extremely small portion of the modal electric field located in the metal regions at this wavelength.
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| 31. |
- Chen, Yiting, et al.
(författare)
-
Plasmonic analog of microstrip transmission line and effect of thermal annealing on its propagation loss
- 2013
-
Ingår i: Optics Express. - : Optical Society of America. - 1094-4087. ; 21:2, s. 1639-1644
-
Tidskriftsartikel (refereegranskat)abstract
- We fabricated a plasmonic analog of the microwave microstrip transmission line and measured its propagation loss before and after thermal annealing. It is found that its propagation loss at 980 nm wavelength can be reduced by more than 50%, from 0.45 to 0.20 dB/μm, after thermal annealing at 300 °C. The reduction in loss can be attributed to the improved gold surface condition and probably also to the change in the metal’s inner structure. Less evident loss reduction is noticed at 1550 nm, which is owing to extremely small portion of the modal electric field located in the metal regions at this wavelength.
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| 32. |
- Deng, Min, et al.
(författare)
-
Genome-wide association analyses in Han Chinese identify two new susceptibility loci for amyotrophic lateral sclerosis
- 2013
-
Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 45:6, s. 697-
-
Tidskriftsartikel (refereegranskat)abstract
- To identify susceptibility genes for amyotrophic lateral sclerosis (ALS), we conducted a genome-wide association study (GWAS) in 506 individuals with sporadic ALS and 1,859 controls of Han Chinese ancestry. Ninety top SNPs suggested by the current GWAS and 6 SNPs identified by previous GWAS were analyzed in an independent cohort of 706 individuals with ALS and 1,777 controls of Han Chinese ancestry. We discovered two new susceptibility loci for ALS at 1q32 (CAMK1G, rs6703183, P-combined = 2.92 x 10(-8), odds ratio (OR) = 1.31) and 22p11 (CABIN1 and SUSD2, rs8141797, P-combined = 2.35 x 10(-9), OR = 1.52). These two loci explain 12.48% of the overall variance in disease risk in the Han Chinese population. We found no association evidence for the previously reported loci in the Han Chinese population, suggesting genetic heterogeneity of disease susceptibility for ALS between ancestry groups. Our study identifies two new susceptibility loci and suggests new pathogenic mechanisms of ALS.
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| 33. |
- Fu, Xi, et al.
(författare)
-
Associations between environmental characteristics, high-resolution indoor microbiome, metabolome and allergic and non-allergic rhinitis symptoms for junior high school students
- 2023
-
Ingår i: Environmental Science. - : Royal Society of Chemistry. - 2050-7887 .- 2050-7895. ; 25:4, s. 791-804
-
Tidskriftsartikel (refereegranskat)abstract
- Rhinitis is one of the most prevalent chronic diseases globally. Microbiome exposure affects the occurrence of rhinitis. However, previous studies did not differentiate allergic rhinitis (AR) and non-allergic rhinitis (NAR) in the microbial association analysis. In this study, we investigate 347 students in 8 junior high schools, Terengganu, Malaysia, who were categorized as healthy (70.9%), AR (13.8%) and NAR (15.3%) based on a self-administered questionnaire and skin prick tests of pollen, pet, mould and house dust mite allergens. Classroom microbial and metabolite exposure in vacuumed dust was characterized by PacBio long-read amplicon sequencing, quantitative PCR and LC-MS-based untargeted metabolomics. Our findings indicate a similar microbial association pattern between AR and NAR. The richness in Gammaproteobacteria was negatively associated with AR and NAR symptoms, whereas total fungal richness was positively associated with AR and NAR symptoms (p < 0.05). Brasilonema bromeliae and Aeromonas enteropelogenes were negatively associated with AR and NAR, and Deinococcus was positively associated with AR and NAR (p < 0.01). Pipecolic acid was protectively associated with AR and NAR symptoms (OR = 0.06 and 0.13, p = 0.009 and 0.045). A neural network analysis showed that B. bromeliae was co-occurring with pipecolic acid, suggesting that the protective role of this species may be mediated by releasing pipecolic acid. Indoor relative humidity and the weight of vacuum dust were associated with AR and NAR, respectively (p < 0.05), but the health effects were mediated by two protective bacterial species, Aliinostoc morphoplasticum and Ilumatobacter fluminis. Overall, our study reported a similar microbial association pattern between AR and NAR and also revealed the complex interactions between microbial species, environmental characteristics, and rhinitis symptoms.
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| 34. |
- Guo, Di, et al.
(författare)
-
Cholecystokinin-like peptide mediates satiety by inhibiting sugar attraction
- 2021
-
Ingår i: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 17:8
-
Tidskriftsartikel (refereegranskat)abstract
- Feeding is essential for animal survival and reproduction and is regulated by both internal states and external stimuli. However, little is known about how internal states influence the perception of external sensory cues that regulate feeding behavior. Here, we investigated the neuronal and molecular mechanisms behind nutritional state-mediated regulation of gustatory perception in control of feeding behavior in the brown planthopper and Drosophila. We found that feeding increases the expression of the cholecystokinin-like peptide, sulfakinin (SK), and the activity of a set of SK-expressing neurons. Starvation elevates the transcription of the sugar receptor Gr64f and SK negatively regulates the expression of Gr64f in both insects. Interestingly, we found that one of the two known SK receptors, CCKLR-17D3, is expressed by some of Gr64f-expressing neurons in the proboscis and proleg tarsi. Thus, we have identified SK as a neuropeptide signal in a neuronal circuitry that responds to food intake, and regulates feeding behavior by diminishing gustatory receptor gene expression and activity of sweet sensing GRNs. Our findings demonstrate one nutritional state-dependent pathway that modulates sweet perception and thereby feeding behavior, but our experiments cannot exclude further parallel pathways. Importantly, we show that the underlying mechanisms are conserved in the two distantly related insect species.
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| 35. |
- Hu, Hai-Xi, et al.
(författare)
-
Structural insights into HetR-PatS interaction involved in cyanobacterial pattern formation
- 2015
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
-
Tidskriftsartikel (refereegranskat)abstract
- The one-dimensional pattern of heterocyst in the model cyanobacterium Anabaena sp. PCC 7120 is coordinated by the transcription factor HetR and PatS peptide. Here we report the complex structures of HetR binding to DNA, and its hood domain (HetR(Hood)) binding to a PatS-derived hexapeptide (PatS6) at 2.80 and 2.10 angstrom, respectively. The intertwined HetR dimer possesses a couple of novel HTH motifs, each of which consists of two canonical alpha-helices in the DNA-binding domain and an auxiliary alpha-helix from the flap domain of the neighboring subunit. Two PatS6 peptides bind to the lateral clefts of HetR(Hood), and trigger significant conformational changes of the flap domain, resulting in dissociation of the auxiliary alpha-helix and eventually release of HetR from the DNA major grove. These findings provide the structural insights into a prokaryotic example of Turing model.
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| 36. |
- Hu, Qitao, et al.
(författare)
-
Current gain and low-frequency noise of symmetric lateral bipolar junction transistors on SOI
- 2018
-
Ingår i: 2018 48th European Solid-State Device Research Conference (ESSDERC). - 9781538654019 - 9781538654002 - 9781538654026 ; , s. 258-261
-
Konferensbidrag (refereegranskat)abstract
- This paper presents a comprehensive study of symmetric lateral bipolar junction transistors (LBJTs) fabricated on SOI substrate using a CMOS-compatible process; LBJTs find many applications including being a local signal amplifier for silicon-nanowire sensors. Our LBJTs are characterized by a peak gain (β) over 50 and low-frequency noise two orders of magnitude lower than what typically is of the SiO 2 /Si interface for a MOSFET. β is found to decrease at low base current due to recombination in the space charge region at the emitter-base junction and at the surrounding SiO 2 /Si interfaces. This decrease can be mitigated by properly biasing the substrate.
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| 37. |
- Hu, Zengyun, et al.
(författare)
-
CCHZ-DISO: A Timely New Assessment System for Data Quality or Model Performance From Da Dao Zhi Jian
- 2022
-
Ingår i: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 49:23
-
Tidskriftsartikel (refereegranskat)abstract
- With the rapid development of big data, assessment of data quality or model performance has become a hot scientific question. However, most existing lots of metrics focus on specific aspects of the assessment, and comprehensive assessment is rare. Therefore, it is very necessary to develop new assessment system. To address this problem, a new assessment system is constructed which is named after Chen, Chen, Hu, and Zhou (CCHZ)-distance between indices of simulation and observation (DISO) according to the contributions of Xi Chen, Deliang Chen, Zengyun Hu, and Qiming Zhou. CCHZ-DISO system builds on the Euclidean Distance and flexible determination of statistical metrics and their numbers. Due to its simplicity and flexibility, CCHZ-DISO can be readily and widely applied to any subject of science. Therefore, it follows the principle of the Chinese philosopher Lao Zi's Da Dao Zhi Jian which means that the most basic truth is very simple.
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| 38. |
- Hu, Zengyun, et al.
(författare)
-
DISO: A rethink of Taylor diagram
- 2019
-
Ingår i: International Journal of Climatology. - : Wiley. - 0899-8418 .- 1097-0088. ; 39:5, s. 2825-2832
-
Tidskriftsartikel (refereegranskat)abstract
- Climate models use quantitative methods to simulate the interactions of the important drivers of climate system, to reveal the corresponding physical mechanisms, and to project the future climate dynamics among atmosphere, oceans, land surface and ice, such as regional climate models and global climate models. A comprehensive assessment of these climate models is important to identify their different overall performances, such as the accuracy of the simulated temperature and precipitation against the observed field. However, until now, the comprehensive performances of these models have not been quantified by a comprehensive index except the existed single statistical index, such as correlation coefficient (r), absolute error (AE), and the root‐mean‐square error (RMSE). To address this issue, therefore, in this study, a new comprehensive index Distance between Indices of Simulation and Observation (DISO) is developed to describe the overall performances of different models against the observed field quantitatively. This new index DISO is a merge of different statistical metrics including r, AE, and RMSE according to the distance between the simulated model and observed field in a three‐dimension space coordinate system. From the relationship between AE, RMSE, and RMS difference (RMSD) (i.e., standard deviation [SD] of bias time series), the new index also has the information of RMSD which is the statistical index in Taylor diagram. An example is applied objectively to display the applications of DISO and Taylor diagram in identifying the overall performances of different simulated models. Overall, with the strong physical characteristic of the distance in three dimensional space and the strict mathematical proof, the new comprehensive index DISO can convey the performances among different models. It can be applied in the comparison between different model data and in tracking changes in their performances.
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| 39. |
- Hu, Zengyun, et al.
(författare)
-
“Dry gets drier, wet gets wetter”: A case study over the arid regions of central Asia
- 2019
-
Ingår i: International Journal of Climatology. - : Wiley. - 0899-8418 .- 1097-0088. ; 39:2, s. 1072-1091
-
Tidskriftsartikel (refereegranskat)abstract
- © 2018 Royal Meteorological Society The “dry gets drier, wet gets wetter” (DGDWGW) paradigm well describes the pattern of precipitation changes over the oceans. However, it has also been usually considered as a simplified pattern of regional changes in wet/dry under global warming, although GCMs mostly do not agree this pattern over land. To examine the validity of this paradigm over land and evaluate how usage of drought indices estimated from different hydrological variables affects detection of regional wet/dry trends, we take the arid regions of central Asia as a case study area and estimate the drying and wetting trends during the period of 1950–2015 based on multiple drought indices. These indices include the standardized precipitation index (SPI), the standardized precipitation evapotranspiration index (SPEI), the Palmer drought severity index (PDSI) and self-calibrating PDSI (sc_PDSI) with both the Thornthwaite (th) and Penman–Monteith (pm) equations in PDSI calculation (namely, PDSI_th, PDSI_pm, sc_PDSI_th and sc_PDSI_pm). The results show that there is an overall agreement among the indices in terms of inter-annual variation, especially for the PDSIs. All drought indices except SPI show a drying trend over the five states of central Asia (CAS5: including Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan and Uzbekistan). The four PDSIs and SPEI reveal a wetting tendency over the northwestern China (NW; including Xinjiang Uygur Autonomous Region and Hexi Corridor). The contrasting trends between CAS5 and NW can also be revealed in soil moisture (SM) variations. The nonlinear wet and dry variations are dominated by the 3–7 years oscillations for the indices. Relationships between the six indices and climate variables show the major drought drivers have regional features: with mean temperature (TMP), precipitation total (PRE) and potential evapotranspiration (PET) for CAS5, and PRE and PET for NW. Finally, our analyses indicate that the dry and wet variations are strongly correlated with the El Niño/Southern Oscillation (ENSO).
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| 40. |
- Huang, Wuqing, et al.
(författare)
-
PDE5 inhibition mitigates heart failure in hyperlipidemia
- 2024
-
Ingår i: Biomedicine and Pharmacotherapy. - 0753-3322. ; 175
-
Tidskriftsartikel (refereegranskat)abstract
- PDE5 inhibitors was reported to play a protective role in both regulating lipid metabolism and reducing heart failure (HF). This study aimed to clarify the effectiveness of PDE5 inhibitors against hyperlipidemia-related HF by combining evidence from population-based study and animal models. The nationwide cohort study found that post-diagnostic use of PDE5 inhibitors was associated with a significantly lower risk of HF compared with patients who used alprostadil, especially among individuals with hyperlipidemia (adjusted HR = 0.56, 95% CI = 0.40–0.78). In animal models, sildenafil significantly recovered the cardiac structure and function induced by AAB surgery, as well as reversed liver dysfunction and ameliorated hyperlipidemia induced by HFD via reducing the level of ALT, AST and serum lipids. Lipidomic analysis identified four lipid metabolites involved in sildenafil administration, including FA 16:3, LPC O-18:1, DG24:0_18:0 and SE28:1/20:4. This study revealed the protective effect of PDE5 inhibitors against HF in hyperlipidemia, indicating the potential of being repurposed as an adjuvant for HF prevention in patients with hyperlipidemia if these findings can be further confirmed in clinical trials.
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| 41. |
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| 42. |
- Kawakatsu, Taiji, et al.
(författare)
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Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions
- 2016
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Ingår i: Cell. - : Elsevier. - 0092-8674 .- 1097-4172. ; 166:2, s. 492-505
-
Tidskriftsartikel (refereegranskat)abstract
- The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.
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| 43. |
- Liao, Guangdong, et al.
(författare)
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Multi-Infection Patterns and Co-infection Preference of 27 Human Papillomavirus Types Among 137,943 Gynecological Outpatients Across China
- 2020
-
Ingår i: Frontiers in Oncology. - : Frontiers Media SA. - 2234-943X. ; 10
-
Tidskriftsartikel (refereegranskat)abstract
- Background: The epidemiological feature of human papillomavirus (HPV) infection is distinctive in China. We aimed to investigate the multi-infection patterns and co-infection preference of 27 HPV types among gynecological outpatients across China. Methods: Overall 137,943 gynecological outpatients were recruited from eight tertiary hospitals located in seven regions of China, between July 1st, 2014 and December 31st, 2016. The overall, region-specific, age-specific and type-specific prevalence of HPV infection were calculated, respectively. The pattern of HPV infection was also evaluated. Furthermore, rate ratio was calculated to evaluate the co-infection preference of any two HPV genotypes. Results: The overall prevalence of 27 HPVs' [17 high-risk (hr)/10 low-risk (lr)] infection was 23.5%. The age-specific HPV prevalence showed a "U-shaped" pattern. The most prevalent hrHPV genotypes were 16, 52, and 58. Multiple infections were detected in 25.8% of the HPV-positive women, in which dual infection was more prevalent. HPV 16/18 were likely to co-infected with HPV 31 but unlikely with HPV 52/58, i.e., the co-infection of HPV 16 with HPV 31 was high (3.5-fold), but low for HPV 58 (1.8-fold), and 52 (1.2-fold), while the co-infection of HPV 18 with HPV 31 was high (4.3-fold), but low for HPV 52 (1.9-fold), and 58 (1.7-fold). Conclusions: We found age-specific prevalence of HPV infection showed a "U-shaped" pattern for high and low risk HPV, suggesting the importance of screening among younger women and the necessary of detection among older women. We found a novel co-infection preference of HPV 16/18 with 31, 52, and 58, suggesting a need of developing and marketing prophylactic HPV vaccines that protect against more genotypes in China.
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| 44. |
- Ning, Yujie, et al.
(författare)
-
Comparative analysis of the gut microbiota composition between knee osteoarthritis and Kashin-Beck disease in Northwest China
- 2022
-
Ingår i: Arthritis Research & Therapy. - : BioMed Central. - 1478-6362. ; 24:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Osteoarthritis (OA) and Kashin-Beck disease (KBD) both are two severe osteochondral disorders. In this study, we aimed to compare the gut microbiota structure between OA and KBD patients.Methods: Fecal samples collected from OA and KBD patients were used to characterize the gut microbiota using 16S rDNA gene sequencing. To identify whether gut microbial changes at the species level are associated with the genes or functions of the gut bacteria between OA and KBD groups, metagenomic sequencing of fecal samples from OA and KBD subjects was performed.Results: The OA group was characterized by elevated Epsilonbacteraeota and Firmicutes levels. A total of 52 genera were identified to be significantly differentially abundant between the two groups. The genera Raoultella, Citrobacter, Flavonifractor, g__Lachnospiraceae_UCG-004, and Burkholderia-Caballeronia-Paraburkholderia were more abundant in the OA group. The KBD group was characterized by higher Prevotella_9, Lactobacillus, Coprococcus_2, Senegalimassilia, and Holdemanella. The metagenomic sequencing showed that the Subdoligranulum_sp._APC924/74, Streptococcus_parasanguinis, and Streptococcus_salivarius were significantly increased in abundance in the OA group compared to those in the KBD group, and the species Prevotella_copri, Prevotella_sp._CAG:386, and Prevotella_stercorea were significantly decreased in abundance in the OA group compared to those in the KBD group by using metagenomic sequencing.Conclusion: Our study provides a comprehensive landscape of the gut microbiota between OA and KBD patients and provides clues for better understanding the mechanisms underlying the pathogenesis of OA and KBD.
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| 45. |
- Ning, Yujie, et al.
(författare)
-
Genetic Variants and Protein Alterations of Selenium- and T-2 Toxin-Responsive Genes Are Associated With Chondrocytic Damage in Endemic Osteoarthropathy
- 2022
-
Ingår i: Frontiers in Genetics. - : Frontiers Media S.A.. - 1664-8021. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- The mechanism of environmental factors in Kashin-Beck disease (KBD) remains unknown. We aimed to identify single nucleotide polymorphisms (SNPs) and protein alterations of selenium- and T-2 toxin-responsive genes to provide new evidence of chondrocytic damage in KBD. This study sampled the cubital venous blood of 258 subjects including 129 sex-matched KBD patients and 129 healthy controls for SNP detection. We applied an additive model, a dominant model, and a recessive model to identify significant SNPs. We then used the Comparative Toxicogenomics Database (CTD) to select selenium- and T-2 toxin-responsive genes with the candidate SNP loci. Finally, immunohistochemistry was applied to verify the protein expression of candidate genes in knee cartilage obtained from 15 subjects including 5 KBD, 5 osteoarthritis (OA), and 5 healthy controls. Forty-nine SNPs were genotyped in the current study. The C allele of rs6494629 was less frequent in KBD than in the controls (OR = 0.63, p = 0.011). Based on the CTD database, PPARG, ADAM12, IL6, SMAD3, and TIMP2 were identified to interact with selenium, sodium selenite, and T-2 toxin. KBD was found to be significantly associated with rs12629751 of PPARG (additive model: OR = 0.46, p = 0.012; dominant model: OR = 0.45, p = 0.049; recessive model: OR = 0.18, p = 0.018), rs1871054 of ADAM12 (dominant model: OR = 2.19, p = 0.022), rs1800796 of IL6 (dominant model: OR = 0.30, p = 0.003), rs6494629 of SMAD3 (additive model: OR = 0.65, p = 0.019; dominant model: OR = 0.52, p = 0.012), and rs4789936 of TIMP2 (recessive model: OR = 5.90, p = 0.024). Immunohistochemistry verified significantly upregulated PPARG, ADAM12, SMAD3, and TIMP2 in KBD compared with OA and normal controls (p < 0.05). Genetic polymorphisms of PPARG, ADAM12, SMAD3, and TIMP2 may contribute to the risk of KBD. These genes could promote the pathogenesis of KBD by disturbing ECM homeostasis.
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| 46. |
- Pang, Yun-Jie, et al.
(författare)
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Theoretical Study of the Catalytic Mechanism of the Cu-Only Superoxide Dismutase
- 2023
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Ingår i: Journal of Physical Chemistry B. - 1520-6106 .- 1520-5207. ; 127:21, s. 4800-4807
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Tidskriftsartikel (refereegranskat)abstract
- The catalytic mechanisms for the wild-type and the mutated Cu-only superoxide dismutase were studied using the hybrid density functional B3LYP and a quantum chemical cluster approach. Optimal protonation states of the active site were examined for each stage of the catalytic cycle. For both the reductive and the oxidative half-reactions, the arrival of the substrate O-2(center dot-) was found to be accompanied by a chargecompensating H+ with exergonicities of -15.4 kcal center dot mol and -4.7 kcal center dot mol, respectively. The second-sphere Glu-110 and first-sphere His-93 were suggested to be the transient protonation site for the reductive and the oxidative half-reactions, respectively, which collaborates with the hydrogen bonding water chain to position the substrate near the redox-active copper center. For the reductive half-reaction, the rate-limiting step was found to be the inner-sphere electron transfer from the partially coordinated O-2(center dot-) to Cu-II with a barrier of 8.1 kcal center dot mol. The formed O-2 is released from the active site with an exergonicity of -14.9 kcal center dot mol. For the oxidative half-reaction, the inner-sphere electron transfer from CuI to the partially coordinated O-2(center dot-) was found to be accompanied by the proton transfer from the protonated His-93 and barrierless. The rate-limiting step was found to be the second proton transfer from the protonated Glu-110 to HO2 with a barrier of 7.3 kcal center dot mol. The barriers are reasonably consistent with experimental activities, and a proton-transfer rate-limiting step in the oxidative half-reaction could explain the experimentally observed pH-dependence. For the E110Q CuSOD, Asp-113 was suggested to be likely to serve as the transient protonation site in the reductive half-reaction. The rate-limiting barriers were found to be 8.0 and 8.6 kcal center dot mol, respectively, which could explain the slightly lower performance of E110X mutants. The results were found to be stable, with respect to the percentage of exact exchange in B3LYP.
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| 47. |
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| 48. |
- Qiu, Min, et al.
(författare)
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Nanostructured plasmonic devices and their applications
- 2013
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Ingår i: 2013 IEEE 6th International Conference on Advanced Infocomm Technology, ICAIT 2013. - : IEEE. - 9781479904655 ; , s. 79-80
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Konferensbidrag (refereegranskat)abstract
- In this talk, we will review our recent works on nanostructured plasmonic devices, and their applications in high performance light absorption, photothermal effects, and partly in photonic integrations.
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| 49. |
- Qiu, Min, et al.
(författare)
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Photothermal effects in a plasmonic metamaterial structure
- 2011
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Konferensbidrag (refereegranskat)abstract
- Heat generation due to photothermal effects in plasmonic nanostructures have generated many important applications, due to the strong enhancement of light absorption through plasmonic resonance at visible and near-infrared region. In this talk, we review our recent experimental efforts on photothermal effects in a metamaterial nanostructure, which has an ultrasensitive heating response owing to plasmonic resonance. We observed close-to-instantaneous fusion and re-shaping of the nanoparticles with a nanosecond pulse train. The generated heat profile has a subwavelength resolution, and the resonance wavelength can be in principle tailored to arbitrary wavelength region by choosing an appropriate geometry for the resonator structure.
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| 50. |
- Qiu, Min, et al.
(författare)
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Plasmonic enhanced photothermal effects and its applications
- 2014
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Konferensbidrag (refereegranskat)abstract
- We review here our recent studies on plasmonic enhanced photothermal effects in metallic nanostructure, and the applications of such effects. When light is shined on a prefect metamaterial absorber patterned with e-beam lithography, the gold nanoparticles (NPs) forming the absorber can be either transformed to nano-spherical-domes, or to truncated-octahedral shaped or multi-twined nanocrystals with large crystal grain sizes and flat boundary facets. The evolution of morphology and crystallinity of the gold NPs can be also observed. Evidences clearly show that the surface melting and the coalescence mechanism play a key role on nanocrystals formation. These melted gold nanospheres can even be transferred to another substrate, on which the transferred NPs exhibit excellent size uniformity. The strong photothermal effects can also be utilized to tune silicon photonics waveguides and resonators. It is shown that all-optical photothermal switching of Mach-Zehnder interferometers (MZI), silicon disk resonators, and silicon ring resonators is possible with the help of plasmonic nanoheaters. The switching response time and power consumption are all at reasonably low level.
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