| 1. |
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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Xu, Chao-Qun, et al.
(författare)
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Genome sequence of Malania oleifera, a tree with great value for nervonic acid production
- 2019
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Ingår i: GigaScience. - : Oxford University Press. - 2047-217X. ; 8:2
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Tidskriftsartikel (refereegranskat)abstract
- Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings We generated 51 Gb and 135Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted approximate to 82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. Conclusions Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.
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| 4. |
- Meng, Pingping, et al.
(författare)
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Efficient removal of perfluorooctane sulfonate from aqueous film-forming foam solution by aeration-foam collection
- 2018
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Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 203, s. 263-270
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Tidskriftsartikel (refereegranskat)abstract
- Aqueous film-forming foams (AFFFs) used in fire-fighting are one of the main contamination sources of perfluorooctane sulfonate (PFOS) to the subterranean environment, requiring high costs for remediation. In this study, a method that combined aeration and foam collection was presented to remove PFOS from a commercially available AFFF solution. The method utilized the strong surfactant properties of PFOS that cause it to be highly enriched at air-water interfaces. With an aeration flow rate of 75 mL/min, PFOS removal percent reached 96% after 2 h, and the PFOS concentration in the collected foam was up to 6.5 mmol/L, beneficial for PFOS recovery and reuse. Increasing the aeration flow rate, ionic strength and concentration of co-existing surfactant, as well as decreasing the initial PFOS concentration, increased the removal percents of PFOS by increasing the foam volume, but reduced the enrichment of PFOS in the foams. With the assistance of a co-existing hydrocarbon surfactant, PFOS removal percent was above 99.9% after aeration-foam collection for 2 h and the enrichment factor exceeded 8400. Aeration-foam collection was less effective for short-chain perfluoroalkyl substances due to their relatively lower surface activity. Aeration-foam collection was found to be effective for the removal of high concentrations of PFOS from AFFF-contaminated wastewater, and the concentrated PFOS in the collected foam can be reused.
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| 5. |
- Riera-Galindo, Sergi, et al.
(författare)
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Impact of Singly Occupied Molecular Orbital Energy on the n-Doping Efficiency of Benzimidazole Derivatives
- 2019
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Ingår i: ACS Applied Materials and Interfaces. - : AMER CHEMICAL SOC. - 1944-8244 .- 1944-8252. ; 11:41, s. 37981-37990
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the impact of singly occupied molecular orbital (SOMO) energy on the n-doping efficiency of benzimidazole derivatives. By designing and synthesizing a series of new air-stable benzimidazole-based dopants with different SOMO energy levels, we demonstrated that an increase of the dopant SOMO energy by only similar to 0.3 eV enhances the electrical conductivity of a benchmark electron-transporting naphthalenediimide-bithiophene polymer by more than 1 order of magnitude. By combining electrical, X-ray diffraction, and electron paramagnetic resonance measurements with density functional theory calculations and analytical transport simulations, we quantitatively characterized the conductivity, Seebeck coefficient, spin density, and crystallinity of the doped polymer as a function of the dopant SOMO energy. Our findings strongly indicate that charge and energy transport are dominated by the (relative) position of the SOMO level, whereas morphological differences appear to play a lesser role. These results set molecular-design guidelines for next-generation n-type dopants.
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| 6. |
- Shen, Qian, et al.
(författare)
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The Genome of Artemisia annua Provides Insight into the Evolution of Asteraceae Family and Artemisinin Biosynthesis
- 2018
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Ingår i: Molecular Plant. - : Cell Press. - 1674-2052 .- 1752-9867. ; 11:6, s. 776-788
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Tidskriftsartikel (refereegranskat)abstract
- Artemisia annua, commonly known as sweet wormwood or Qinghao, is a shrub native to China and has long been used for medicinal purposes. A. annua is now cultivated globally as the only natural source of a potent anti-malarial compound, artemisinin. Here, we report a high-quality draft assembly of the 1.74-gigabase genome of A. annua, which is highly heterozygous, rich in repetitive sequences, and contains 63 226 protein-coding genes, one of the largest numbers among the sequenced plant species. We found that, as one of a few sequenced genomes in the Asteraceae, the A. annua genome contains a large number of genes specific to this large angiosperm clade. Notably, the expansion and functional diversification of genes encoding enzymes involved in terpene biosynthesis are consistent with the evolution of the artemisinin biosynthetic pathway. We further revealed by transcriptome profiling that A. annua has evolved the sophisticated transcriptional regulatory networks underlying artemisinin biosynthesis. Based on comprehensive genomic and transcriptomic analyses we generated transgenic A. annua lines producing high levels of artemisinin, which are now ready for large-scale production and thereby will help meet the challenge of increasing global demand of artemisinin.
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| 7. |
- Sidén, Johan, 1975-, et al.
(författare)
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Design of High-Directivity Wideband Microstrip Directional Coupler With Fragment-Type Structure
- 2015
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Ingår i: IEEE transactions on microwave theory and techniques. - 0018-9480 .- 1557-9670. ; 63:12, s. 3962-3970
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Tidskriftsartikel (refereegranskat)abstract
- A novel design for a microstrip wideband directional coupler is proposedby using fragment-type structures. The use of a fragment-type structuremay provide satisfactory flexibility and excellent performance. For agiven design space, a fragment-type wideband coupler can be designed byfirst gridding the space into fragment cells and then metallizing thefragment cells selected by a multi-objective optimization searchingalgorithm, such as a multi-objective evolutionary algorithm based ondecomposition combined with enhanced genetic operators. Fordemonstration, a 20-dB wideband microstrip directional coupler isdesigned and verified by test. A 45% bandwidth centered at 2 GHz hasbeen measured in terms of maximum variation of 0.5 dB in the 20-dBcoupling level. In the operation band, the designed coupler hasdirectivity above 37 dB, and a maximum directivity of 48 dB at 2 GHz. Inaddition, some technique aspects related to multi-objective optimizationsearching, such as effects of design space, control of coupling level,and efficiency consideration for optimization searching, are furtherdiscussed. Fragment-type structures may also be used to designhigh-performance wideband directional couplers of tight coupling level.
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| 8. |
- Wang, Bin, et al.
(författare)
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A primary estimate of global PCDD/F release based on the quantity and quality of national economic and social activities
- 2016
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Ingår i: Chemosphere. - Oxford, United Kingdom : Elsevier. - 0045-6535 .- 1879-1298. ; 151, s. 303-309
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Tidskriftsartikel (refereegranskat)abstract
- The correlations between polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) releases and factors relevant to human social-economic activities (HSEAs) were analyzed. The multiple linear regression model was successfully developed to estimate the total global PCDD/F release. The PCDD/F releases significantly correlated with population, area, GDP and GNI, suggesting that "quantity" of HSEAs have significantly contributed to the PCDD/F releases. On another aspect, advanced technologies are usually adopted in developed countries/regions, and hence reduce the PCDD/F release. The significant correlation between PCDD/F release and CO2 emission implies the potential of simultaneous reduction of CO2 emission and PCDD/F release. The total global PCDD/F release from 196 countries/regions was estimated to be 100.4 kg-TEQ yr(-1). The estimated annual PCDD/F release per unit area ranged from 0.007 to 28 mg-TEQ km(-2). Asia is estimated to have the highest PCDD/F release of 47.1 kg-TEQ yr(-1), almost half of the total world release. Oceania is estimated to have the smallest total release but the largest per-capita release. For the developed areas, such as Europe and North America, the PCDD/F release per unit GDP is lower, while for Africa, it is much higher.
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| 9. |
- Wang, Gang, et al.
(författare)
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Aggregation control in natural brush-printed conjugated polymer films and implications for enhancing charge transport
- 2017
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 114:47, s. E10066-E10073
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Tidskriftsartikel (refereegranskat)abstract
- Shear-printing is a promising processing technique in organic electronics for microstructure/charge transport modification and large-area film fabrication. Nevertheless, the mechanism by which shear-printing can enhance charge transport is not well-understood. In this study, a printing method using natural brushes is adopted as an informative tool to realize direct aggregation control of conjugated polymers and to investigate the interplay between printing parameters, macromolecule backbone alignment and aggregation, and charge transport anisotropy in a conjugated polymer series differing in architecture and electronic structure. This series includes (i) semicrystalline hole-transporting P3HT, (ii) semicrystalline electron transporting N2200, (iii) low-crystallinity hole-transporting PBDTT-FTTE, and (iv) low-crystallinity conducting PEDOT:PSS. The (semi-)conducting films are characterized by a battery of morphology and microstructure analysis techniques and by charge transport measurements. We report that remarkably enhanced mobilities/conductivities, as high as 5.7x/3.9x, are achieved by controlled growth of nanofibril aggregates and by backbone alignment, with the adjusted R-2 (R-adj(2)) correlation between aggregation and charge transport as high as 95%. However, while shear-induced aggregation is important for enhancing charge transport, backbone alignment alone does not guarantee charge transport anisotropy. The correlations between efficient charge transport and aggregation are clearly shown, while mobility and degree of orientation are not always well-correlated. These observations provide insights into macroscopic charge transport mechanisms in conjugated polymers and suggest guidelines for optimization.
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| 10. |
- Wang, Huijiao, et al.
(författare)
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Oxidation of emerging biocides and antibiotics in wastewater by ozonation and the electro-peroxone process
- 2019
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Ingår i: Chemosphere. - : Elsevier. - 0045-6535 .- 1879-1298. ; 235, s. 575-585
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Tidskriftsartikel (refereegranskat)abstract
- This study investigated the abatement of a number of antimicrobials frequently detected in municipal wastewater by conventional ozonation and a recently developed ozone-based advanced oxidation process, the electro-peroxone (E-peroxone) process. A synthetic water and a real secondary wastewater effluent were spiked with fourteen antimicrobials, including antibiotics and biocides, and then treated by the two processes. The results show that most of the antibiotics investigated (e.g., ofloxacin, trimethoprim, norfloxacin, and ciprofloxacin) readily react with ozone (O3) and could therefore be efficiently eliminated from the water matrices by direct O3 oxidation during both processes. In contrast, most of the biocides tested in this study (e.g., clotrimazole, pentamidine, bixafen, propiconazole, and fluconazole) were only moderately reactive, or non-reactive, with O3. Therefore, these biocides were removed at considerably lower rate than the antibiotics during the two ozone-based processes, with hydroxyl radical (OH) oxidation playing an important role in their abatement mechanisms. When compared with conventional ozonation, the E-peroxone process is defined by the in situ electrogeneration of hydrogen peroxide, which considerably enhances the transformation of O3 to OH. As a result, the E-peroxone process significantly accelerated the abatement of biocides and required a considerably shorter treatment time to eliminate all of the tested compounds from the water matrices than conventional ozonation. In addition, the E-peroxone process enhanced the contributions of OH fractions to the abatement of moderately ozone reactive benzotriazoles. These results demonstrate that the E-peroxone process holds promise as an effective tertiary treatment option for enhancing the abatement of ozone-resistant antimicrobials in wastewater.
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| 11. |
- Wang, Lu, et al.
(författare)
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Design of Chipless RFID Tag by Using Miniaturized Open-Loop Resonators
- 2018
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Ingår i: IEEE Transactions on Antennas and Propagation. - 0018-926X .- 1558-2221. ; 66:2, s. 618-626
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, an open-loop resonator with fragment-loading structure is used for the first time in the design of radar cross section-based chipless radio-frequency identification (RFID) tag. By optimizing the distribution of fragment patches in an open loop, a microstrip open-loop resonator can be miniaturized so that the data capacity of the chipless RFID tag designed using such a miniaturized loop resonator can be significantly increased. Moreover, the resonant frequency of the fragment-loaded resonator can be adjusted conveniently by removing or disconnecting some fragment patches, which provides great flexibility for data encoding of the chipless RFID tag. The proposed chipless RFID tag with miniaturized open-loop resonators is designed and tested and can acquire 3.56 bits per resonator and a coding density of approximately 745.1bits/λg 2. Several experimental results validate the proposed design as well as its implementation in a realistic environment.
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| 12. |
- Wang, Lu, et al.
(författare)
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High-performance tight coupling microstrip directional coupler with fragment-type compensated structure
- 2017
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Ingår i: IET Microwaves, Antennas & Propagation. - : Institution of Engineering and Technology (IET). - 1751-8725 .- 1751-8733. ; 11:7, s. 1057-1063
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Tidskriftsartikel (refereegranskat)abstract
- In this study, a design scheme for high-performance tight coupling microstrip coupler is proposed by adding a fragment-type compensated structure between two loosely coupled lines. Owing to its flexibility and adaptability, the fragment-type compensated structure can not only provide a quarter-wavelength phase shift for coupling enhancement, but also compensate the difference in the phase velocities of the even- and odd-modes for high directivity. Design of the fragment-type compensated structure can be implemented by multi-objective optimisation searching with several design objectives characterising tight coupling couplers. A high-efficiency optimisation searching strategy by using two-dimensional median filtering operator is employed to improve the efficiency of multi-objective optimisation. For demonstration, a high-performance 3-dB tight coupling directional coupler operating at 2 GHz is designed. The measurement data demonstrates a maximum directivity of 47 dB, above 25 dB directivity in a 21.5% bandwidth, a maximum variation of 0.3 dB in the coupling level and a maximum power division ratio of 0.6 dB, which indicate the overall performance better than the previously reported 3-dB couplers. In addition, a simplified theoretical analysis of the proposed coupler and full-wave simulated results are provided for better understanding of the fragment-type compensated structure.
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| 13. |
- Wang, Suhao, et al.
(författare)
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A Chemically Doped Naphthalenediimide-Bithiazole Polymer for n-Type Organic Thermoelectrics
- 2018
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Ingår i: Advanced Materials. - : WILEY-V C H VERLAG GMBH. - 0935-9648 .- 1521-4095. ; 30:31
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Tidskriftsartikel (refereegranskat)abstract
- The synthesis of a novel naphthalenediimide (NDI)-bithiazole (Tz2)-based polymer [P(NDI2OD-Tz2)] is reported, and structural, thin-film morphological, as well as charge transport and thermoelectric properties are compared to the parent and widely investigated NDI-bithiophene (T2) polymer [P(NDI2OD-T2)]. Since the steric repulsions in Tz2 are far lower than in T2, P(NDI2OD-Tz2) exhibits a more planar and rigid backbone, enhancing p-p chain stacking and intermolecular interactions. In addition, the electron-deficient nature of Tz2 enhances the polymer electron affinity, thus reducing the polymer donor-acceptor character. When n-doped with amines, P(NDI2OD-Tz2) achieves electrical conductivity (approximate to 0.1 S cm(-1)) and a power factor (1.5 mu W m(-1) K-2) far greater than those of P(NDI2OD-T2) (0.003 S cm(-1) and 0.012 mu W m(-1) K-2, respectively). These results demonstrate that planarized NDI-based polymers with reduced donor-acceptor character can achieve substantial electrical conductivity and thermoelectric response.
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| 14. |
- Xiao, Chao, et al.
(författare)
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RBBP6 increases radioresistance and serves as a therapeutic target for preoperative radiotherapy in colorectal cancer
- 2018
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Ingår i: Cancer Science. - : Blackwell Publishing. - 1347-9032 .- 1349-7006. ; 109:4, s. 1075-1087
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Tidskriftsartikel (refereegranskat)abstract
- Radiotherapy (RT) can be used as preoperative treatment to downstage initially unresectable locally rectal carcinoma, but the radioresistance and recurrence remain significant problems. Retinoblastoma binding protein 6 (RBBP6) has been implicated in the regulation of cell cycle, apoptosis and chemoresistance both in vitro and in vivo. This study investigated whether the inhibition of RBBP6 expression would improve radiosensitivity in human colorectal cancer cells. After SW620 and HT29 cells were exposed to radiation, the levels of RBBP6 mRNA and protein increased over time in both two cells. Moreover, a significant reduction in clonogenic survival and a decrease in cell viability in parallel with an obvious increase in cell apoptosis were demonstrated in irradiated RBBP6-knockdown cells. Besides, transfection with RBBP6 shRNA improved levels of G2-M phase arrest which blocked the cells in a more radiosensitive period of the cell cycle. These observations indicated that cell cycle and apoptosis mechanisms may be connected with tumor cell survival following radiotherapy. In vivo, tumor growth rate of nude mice in RBBP6-knockdown group was significantly slower than that in other groups. These results indicated that RBBP6 overexpression could resist colorectal cancer cells against radiation by regulating cell cycle and apoptosis pathways, and inhibition of RBBP6 could enhance radiosensitivity of human colorectal cancer.
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| 15. |
- Xu, Shuang Feng, et al.
(författare)
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Lactoferrin ameliorates dopaminergic neurodegeneration and motor deficits in MPTP-treated mice
- 2019
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Ingår i: Redox Biology. - : Elsevier BV. - 2213-2317. ; 21
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Tidskriftsartikel (refereegranskat)abstract
- Brain iron accumulation is common in patients with Parkinson's disease (PD). Iron chelators have been investigated for their ability to prevent neurodegenerative diseases with features of iron overload. Given the non-trivial side effects of classical iron chelators, lactoferrin (Lf), a multifunctional iron-binding globular glycoprotein, was screened to identify novel neuroprotective pathways against dopaminergic neuronal impairment. We found that Lf substantially ameliorated PD-like motor dysfunction in the subacute 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced mouse model of PD. We further showed that Lf could alleviate MPTP-triggered apoptosis of DA neurons, neuroinflammation, and histological alterations. As expected, we also found that Lf suppressed MPTP-induced excessive iron accumulation and the upregulation of divalent metal transporter (DMT1) and transferrin receptor (TFR), which is the main intracellular iron regulation protein, and subsequently improved the activity of several antioxidant enzymes. We probed further and determined that the neuroprotection provided by Lf was involved in the upregulated levels of brain-derived neurotrophic factor (BDNF), hypoxia-inducible factor 1α (HIF-1α) and its downstream protein, accompanied by the activation of extracellular regulated protein kinases (ERK) and cAMP response element binding protein (CREB), as well as decreased phosphorylation of c-Jun N-terminal kinase (JNK) and mitogen activated protein kinase (MAPK)/P38 kinase in vitro and in vivo. Our findings suggest that Lf may be an alternative safe drug in ameliorating MPTP-induced brain abnormalities and movement disorder.
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| 16. |
- Zhuang, Ting, et al.
(författare)
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SHARPIN stabilizes estrogen receptor a and promotes breast cancer cell proliferation
- 2017
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Ingår i: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 8:44, s. 77137-77151
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Tidskriftsartikel (refereegranskat)abstract
- Estrogen receptor a is expressed in the majority of breast cancers and promotes estrogen-dependent cancer progression. In our study, we identified the novel E3 ubiquitin ligase SHARPIN function to facilitate ERα signaling. SHARPIN is highly expressed in human breast cancer and correlates with ERα protein level by immunohistochemistry. SHARPIN expression level correlates with poor prognosis in ERα positive breast cancer patients. SHARPIN depletion based RNA-sequence data shows that ERα signaling is a potential SHARPIN target. SHARPIN depletion significantly decreases ERα protein level, ERα target genes expression and estrogen response element activity in breast cancer cells, while SHARPIN overexpression could reverse these effects. SHARPIN depletion significantly decreases estrogen stimulated cell proliferation in breast cancer cells, which effect could be further rescued by ERα overexpression. Further mechanistic study reveals that SHARPIN mainly localizes in the cytosol and interacts with ERα both in the cytosol and the nuclear. SHARPIN regulates ERα signaling through protein stability, not through gene expression. SHARPIN stabilizes ERα protein via prohibiting ERα protein poly-ubiquitination. Further study shows that SHARPIN could facilitate the mono-ubiquitinaiton of ERα at K302/303 sites and facilitate ERE luciferase activity. Together, our findings propose a novel ERα modulation mechanism in supporting breast cancer cell growth, in which SHARPIN could be one suitable target for development of novel therapy for ERα positive breast cancer.
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| 17. |
- Aldrin-Kirk, Patrick, et al.
(författare)
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DREADD Modulation of Transplanted DA Neurons Reveals a Novel Parkinsonian Dyskinesia Mechanism Mediated by the Serotonin 5-HT6 Receptor
- 2016
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Ingår i: Neuron. - : Elsevier BV. - 0896-6273. ; 90:5, s. 955-968
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Tidskriftsartikel (refereegranskat)abstract
- Transplantation of DA neurons is actively pursued as a restorative therapy in Parkinson's disease (PD). Pioneering clinical trials using transplants of fetal DA neuroblasts have given promising results, although a number of patients have developed graft-induced dyskinesias (GIDs), and the mechanism underlying this troublesome side effect is still unknown. Here we have used a new model where the activity of the transplanted DA neurons can be selectively modulated using a bimodal chemogenetic (DREADD) approach, allowing either enhancement or reduction of the therapeutic effect. We show that exclusive activation of a cAMP-linked (Gs-coupled) DREADD or serotonin 5-HT6 receptor, located on the grafted DA neurons, is sufficient to induce GIDs. These findings establish a mechanistic link between the 5-HT6 receptor, intracellular cAMP, and GIDs in transplanted PD patients. This effect is thought to be mediated through counteraction of the D2 autoreceptor feedback inhibition, resulting in a dysplastic DA release from the transplant.
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| 18. |
- Andersson, Anna, et al.
(författare)
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The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias.
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:4, s. 192-330
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Tidskriftsartikel (refereegranskat)abstract
- Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia with a poor prognosis. To define its mutational landscape, we performed whole-genome, exome, RNA and targeted DNA sequencing on 65 infants (47 MLL-R and 18 non-MLL-R cases) and 20 older children (MLL-R cases) with leukemia. Our data show that infant MLL-R ALL has one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations. Despite this paucity of mutations, we detected activating mutations in kinase-PI3K-RAS signaling pathway components in 47% of cases. Surprisingly, these mutations were often subclonal and were frequently lost at relapse. In contrast to infant cases, MLL-R leukemia in older children had more somatic mutations (mean of 6.5 mutations/case versus 1.3 mutations/case, P = 7.15 × 10(-5)) and had frequent mutations (45%) in epigenetic regulators, a category of genes that, with the exception of MLL, was rarely mutated in infant MLL-R ALL.
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| 19. |
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| 20. |
- Chen, Gang, et al.
(författare)
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EDF-VD Scheduling of Flexible Mixed-Criticality System With Multiple-Shot Transitions
- 2018
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Ingår i: IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. - 0278-0070 .- 1937-4151. ; 37:11, s. 2393-2403
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Tidskriftsartikel (refereegranskat)abstract
- The existing mixed-criticality (MC) real-time task models assume that once any high-criticality task overruns, all high-criticality jobs execute up to their most pessimistic WCET estimations simultaneously in a one-shot manner. This is very pessimistic in the sense of unnecessary resource overbooking. In this paper, we propose a more generalized mixed-critical real-time task model, called flexible MC model with multiple-shot transitions (FMC-MST), to address this problem. In FMC-MST, high-criticality tasks can transit multiple intermediate levels to handle less pessimistic overruns independently and to nonuni-formly scale the deadline on each level. We develop a run-time schedulability analysis for FMC-MST under EDF-VD scheduling, in which a better tradeoff between the penalties of low-criticality tasks and the overruns of high-criticality tasks is achieved to improve the service quality of low-criticality tasks. We also develop a resource optimization technique to find resource-efficient level-insertion configurations for FMC-MST task systems under MC timing constraints. Experiments demonstrate the effectiveness of FMC-MST compared with the state-of-the-art techniques.
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| 21. |
- Chen, Gang, et al.
(författare)
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On the kinematic algebra for BCJ numerators beyond the MHV sector
- 2019
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Ingår i: Journal of High Energy Physics (JHEP). - : Springer. - 1126-6708 .- 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- The duality between color and kinematics present in scattering amplitudes of Yang-Mills theory strongly suggests the existence of a hidden kinematic Lie algebra that controls the gauge theory. While associated BCJ numerators are known on closed forms to any multiplicity at tree level, the kinematic algebra has only been partially explored for the simplest of four-dimensional amplitudes: up to the MHV sector. In this paper we introduce a framework that allows us to characterize the algebra beyond the MHV sector. This allows us to both constrain some of the ambiguities of the kinematic algebra, and better control the generalized gauge freedom that is associated with the BCJ numerators. Specifically, in this paper, we work in dimension-agnostic notation and determine the kinematic algebra valid up to certain ? ((epsilon i .epsilon j )(2)) terms that in four dimensions compute the next-to-MHV sector involving two scalars. The kinematic algebra in this sector is simple, given that we introduce tensor currents that generalize standard Yang-Mills vector currents. These tensor currents control the generalized gauge freedom, allowing us to generate multiple different versions of BCJ numerators from the same kinematic algebra. The framework should generalize to other sectors in Yang-Mills theory.
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| 22. |
- Chen, Gang, et al.
(författare)
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Utilization-Based Scheduling of Flexible Mixed-Criticality Real-Time Tasks
- 2018
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Ingår i: IEEE Transactions on Computers. - : IEEE COMPUTER SOC. - 0018-9340 .- 1557-9956. ; 67:4, s. 543-558
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Tidskriftsartikel (refereegranskat)abstract
- Mixed-criticality models are an emerging paradigm for the design of real-time systems because of their significantly improved resource efficiency. However, formal mixed-criticality models have traditionally been characterized by two impractical assumptions: once any high-criticality task overruns, all low-criticality tasks are suspended and all other high-criticality tasks are assumed to exhibit high-criticality behaviors at the same time. In this paper, we propose a more realistic mixed-criticality model, called the flexible mixed-criticality (FMC) model, in which these two issues are addressed in a combined manner. In this new model, only the overrun task itself is assumed to exhibit high-criticality behavior, while other high-criticality tasks remain in the same mode as before. The guaranteed service levels of low-criticality tasks are gracefully degraded with the overruns of high-criticality tasks. We derive a utilization-based technique to analyze the schedulability of this new mixed-criticality model under EDF-VD scheduling. During run time, the proposed test condition serves an important criterion for dynamic service level tuning, by means of which the maximum available execution budget for low-criticality tasks can be directly determined with minimal overhead while guaranteeing mixed-criticality schedulability. Experiments demonstrate the effectiveness of the FMC scheme compared with state-of-the-art techniques.
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| 23. |
- Davidsson, Marcus, et al.
(författare)
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A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Detailed characterization and mapping of oligonucleotide function in vivo is generally a very time consuming effort that only allows for hypothesis driven subsampling of the full sequence to be analysed. Recent advances in deep sequencing together with highly efficient parallel oligonucleotide synthesis and cloning techniques have, however, opened up for entirely new ways to map genetic function in vivo. Here we present a novel, optimized protocol for the generation of universally applicable, barcode labelled, plasmid libraries. The libraries are designed to enable the production of viral vector preparations assessing coding or non-coding RNA function in vivo. When generating high diversity libraries, it is a challenge to achieve efficient cloning, unambiguous barcoding and detailed characterization using low-cost sequencing technologies. With the presented protocol, diversity of above 3 million uniquely barcoded adeno-associated viral (AAV) plasmids can be achieved in a single reaction through a process achievable in any molecular biology laboratory. This approach opens up for a multitude of in vivo assessments from the evaluation of enhancer and promoter regions to the optimization of genome editing. The generated plasmid libraries are also useful for validation of sequencing clustering algorithms and we here validate the newly presented message passing clustering process named Starcode.
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| 24. |
- Davidsson, Marcus, et al.
(författare)
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A systematic capsid evolution approach performed in vivo for the design of AAV vectors with tailored properties and tropism
- 2019
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 1091-6490. ; 116:52, s. 27053-27062
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Tidskriftsartikel (refereegranskat)abstract
- Adeno-associated virus (AAV) capsid modification enables the generation of recombinant vectors with tailored properties and tropism. Most approaches to date depend on random screening, enrichment, and serendipity. The approach explored here, called BRAVE (barcoded rational AAV vector evolution), enables efficient selection of engineered capsid structures on a large scale using only a single screening round in vivo. The approach stands in contrast to previous methods that require multiple generations of enrichment. With the BRAVE approach, each virus particle displays a peptide, derived from a protein, of known function on the AAV capsid surface, and a unique molecular barcode in the packaged genome. The sequencing of RNA-expressed barcodes from a single-generation in vivo screen allows the mapping of putative binding sequences from hundreds of proteins simultaneously. Using the BRAVE approach and hidden Markov model-based clustering, we present 25 synthetic capsid variants with refined properties, such as retrograde axonal transport in specific subtypes of neurons, as shown for both rodent and human dopaminergic neurons.
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| 25. |
- Davidsson, Marcus, et al.
(författare)
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Molecular barcoding of viral vectors enables mapping and optimization of mRNA trans-splicing
- 2018
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Ingår i: RNA. - : Cold Spring Harbor Laboratory. - 1355-8382 .- 1469-9001. ; 24:5, s. 673-687
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Tidskriftsartikel (refereegranskat)abstract
- Genome editing has proven to be highly potent in the generation of functional gene knockouts in dividing cells. In the CNS however, efficient technologies to repair sequences are yet to materialize. Reprogramming on the mRNA level is an attractive alternative as it provides means to perform in situ editing of coding sequences without nuclease dependency. Furthermore, de novo sequences can be inserted without the requirement of homologous recombination. Such reprogramming would enable efficient editing in quiescent cells (e.g., neurons) with an attractive safety profile for translational therapies. In this study, we applied a novel molecular-barcoded screening assay to investigate RNA trans-splicing in mammalian neurons. Through three alternative screening systems in cell culture and in vivo, we demonstrate that factors determining trans-splicing are reproducible regardless of the screening system. With this screening, we have located the most permissive trans-splicing sequences targeting an intron in the Synapsin I gene. Using viral vectors, we were able to splice full-length fluorophores into the mRNA while retaining very low off-target expression. Furthermore, this approach also showed evidence of functionality in the mouse striatum. However, in its current form, the trans-splicing events are stochastic and the overall activity lower than would be required for therapies targeting loss-of-function mutations. Nevertheless, the herein described barcode-based screening assay provides a unique possibility to screen and map large libraries in single animals or cell assays with very high precision.
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