| 1. |
- 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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| 2. |
- Wang, H. Y., et al.
(författare)
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Cellular Analysis and Comparative Transcriptomics Reveal the Tolerance Mechanisms of Candida tropicalis Toward Phenol
- 2020
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Phenol is a ubiquitous pollutant and can contaminate natural water resources. Hence, the removal of phenol from wastewater is of significant importance. A series of biological methods were used to remove phenol based on the natural ability of microorganisms to degrade phenol, but the tolerance mechanism of phenol-degraded strains to phenol are not very clear. Morphological observation on Candida tropicalis showed that phenol caused the reactive oxygen species (ROS) accumulation, damaging the mitochondrial and the endoplasmic reticulum. On the basis of transcriptome data and cell wall susceptibility analysis, it was found that C. tropicalis prevented phenol-caused cell damage through improvement of cell wall resistance, maintenance of high-fidelity DNA replication, intracellular protein homeostasis, organelle integrity, and kept the intracellular phenol concentration at a low level through cell-wall remodeling and removal of excess phenol via MDR/MXR transporters. The knowledge obtained will promote the genetic modification of yeast strains in general to tolerate the high concentrations of phenol and improve their efficiency of phenol degradation.
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| 3. |
- Kristan, M., et al.
(författare)
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The Eighth Visual Object Tracking VOT2020 Challenge Results
- 2020
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Ingår i: Computer Vision. - Cham : Springer International Publishing. - 9783030682378 ; , s. 547-601
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Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2020 is the eighth annual tracker benchmarking activity organized by the VOT initiative. Results of 58 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The VOT2020 challenge was composed of five sub-challenges focusing on different tracking domains: (i) VOT-ST2020 challenge focused on short-term tracking in RGB, (ii) VOT-RT2020 challenge focused on “real-time” short-term tracking in RGB, (iii) VOT-LT2020 focused on long-term tracking namely coping with target disappearance and reappearance, (iv) VOT-RGBT2020 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2020 challenge focused on long-term tracking in RGB and depth imagery. Only the VOT-ST2020 datasets were refreshed. A significant novelty is introduction of a new VOT short-term tracking evaluation methodology, and introduction of segmentation ground truth in the VOT-ST2020 challenge – bounding boxes will no longer be used in the VOT-ST challenges. A new VOT Python toolkit that implements all these novelites was introduced. 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 (http://votchallenge.net ).
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| 4. |
- Zhou, J. M., et al.
(författare)
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Digoxin is associated with worse outcomes in patients with heart failure with reduced ejection fraction
- 2020
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Ingår i: Esc Heart Failure. - : Wiley. - 2055-5822. ; 7:1, s. 139-147
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Tidskriftsartikel (refereegranskat)abstract
- Aims The aim of this study was to investigate the impact of digoxin use on the outcomes of patients with heart failure with reduced ejection fraction (HFrEF) and its possible interaction with atrial fibrillation or use of currently guideline-recommended treatments in the real world in China. Methods and results Patients hospitalized with HFrEF from 45 hospitals participating in the China National Heart Failure Registration Study (CN-HF) were enrolled to assess the all-cause mortality, HF mortality, all-cause re-hospitalization, and HF re-hospitalization associated with digoxin use. Eight hundred eighty-two eligible HFrEF patients in the CN-HF registry were included: 372 patients with digoxin and 510 patients without digoxin. Among them, 794 (90.0%) patients were followed up for the endpoint events, with a median follow-up of 28.6 months. Kaplan-Meier survival analysis showed that the all-cause mortality (P < 0.001) and all-cause re-hospitalization (P = 0.020) were significantly higher in digoxin group than non-digoxin group, while HF mortality (P = 0.232) and HF re-hospitalization (P = 0.098) were similar between the two groups. The adjusted Cox proportional-hazards regression analysis demonstrated that digoxin use remained as an independent risk factor for increased all-cause mortality [hazard ratio (HR) 1.76; 95% confidence interval (CI) 1.27-2.44; P = 0.001] and all-cause re-hospitalization (HR 1.27; 95% CI 1.03-1.57; P = 0.029) in HFrEF patients and the predictive value of digoxin for all-cause mortality irrespective of rhythm or in combination with other guideline-recommended therapies. Conclusions Digoxin use is independently associated with increased risk of all-cause mortality and all-cause re-hospitalization in HFrEF patients.
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| 5. |
- De Leoz, M. L. A., et al.
(författare)
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NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods
- 2020
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476. ; 19:1, s. 11-30
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Tidskriftsartikel (refereegranskat)abstract
- A broad-based interlaboratory study of glycosylation profiles of a reference and modified IgG antibody involving 103 reports from 76 laboratories. Glycosylation is a topic of intense current interest in the development of biopharmaceuticals because it is related to drug safety and efficacy. This work describes results of an interlaboratory study on the glycosylation of the Primary Sample (PS) of NISTmAb, a monoclonal antibody reference material. Seventy-six laboratories from industry, university, research, government, and hospital sectors in Europe, North America, Asia, and Australia submitted a total of 103 reports on glycan distributions. The principal objective of this study was to report and compare results for the full range of analytical methods presently used in the glycosylation analysis of mAbs. Therefore, participation was unrestricted, with laboratories choosing their own measurement techniques. Protein glycosylation was determined in various ways, including at the level of intact mAb, protein fragments, glycopeptides, or released glycans, using a wide variety of methods for derivatization, separation, identification, and quantification. Consequently, the diversity of results was enormous, with the number of glycan compositions identified by each laboratory ranging from 4 to 48. In total, one hundred sixteen glycan compositions were reported, of which 57 compositions could be assigned consensus abundance values. These consensus medians provide community-derived values for NISTmAb PS. Agreement with the consensus medians did not depend on the specific method or laboratory type. The study provides a view of the current state-of-the-art for biologic glycosylation measurement and suggests a clear need for harmonization of glycosylation analysis methods.
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| 8. |
- Li, J., et al.
(författare)
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Study of selective isotropic etching Si1−xGex in process of nanowire transistors
- 2020
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Ingår i: Journal of materials science. Materials in electronics. - : Springer Science and Business Media LLC. - 0957-4522 .- 1573-482X. ; 31:1, s. 134-143
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Tidskriftsartikel (refereegranskat)abstract
- On approach towards the end of technology roadmap, a revolutionary approach towards the nanowire transistors is favorable due to the full control of carrier transport. The transistor design moves toward vertically or laterally stacked Gate-All-Around (GAA) where Si or SiGe can be used as channel material. This study presents a novel isotropic inductively coupled plasma (ICP) dry etching of Si1−xGex (0.10 ≤ x ≤ 0.28) in SiGe/Si multilayer structures (MLSs) with high selectivity to Si, SiO2, Si3N4 and SiON which can be applied in advanced 3D transistors and Micro-Electro-Mechanical System (MEMS) in future. The profile of SiGe etching for different thicknesses, compositions and locations in MLSs using dry or wet etch have been studied. A special care has been spent for layer quality of Si, strain relaxation of SiGe layers as well as residual contamination during the etching. In difference with dry etching methods (downstream remote plasma), the conventional ICP source in situ is used where CF4/O2/He gas mixture was used as the etching gas to obtain higher selectivity. Based on the reliability of ICP technique a range of etching rate 25–50 nm/min can be obtained for accurate isotropic etching of Si1−xGex, to form cavity in advanced 3D transistor processes in future.
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| 9. |
- Li, J., et al.
(författare)
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Study of silicon nitride inner spacer formation in process of gate-all-around nano-transistors
- 2020
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Ingår i: Nanomaterials. - : MDPI AG. - 2079-4991. ; 10:4
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Tidskriftsartikel (refereegranskat)abstract
- Stacked SiGe/Si structures are widely used as the units for gate-all-around nanowire transistors (GAA NWTs) which are a promising candidate beyond fin field effective transistors (FinFETs) technologies in near future. These structures deal with a several challenges brought by the shrinking of device dimensions. The preparation of inner spacers is one of the most critical processes for GAA nano-scale transistors. This study focuses on two key processes: Inner spacer film conformal deposition and accurate etching. The results show that low pressure chemical vapor deposition (LPCVD) silicon nitride has a good film filling effect; a precise and controllable silicon nitride inner spacer structure is prepared by using an inductively coupled plasma (ICP) tool and a new gas mixtures of CH2F2/CH4/O2/Ar. Silicon nitride inner spacer etch has a high etch selectivity ratio, exceeding 100:1 to Si and more than 30:1 to SiO2. High anisotropy with an excellent vertical/lateral etch ratio exceeding 80:1 is successfully demonstrated. It also provides a solution to the key process challenges of nano-transistors beyond 5 nm node. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
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| 10. |
- Meng, Y., et al.
(författare)
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Fractal superconducting nanowire avalanche photodetector at 1550 nm with 60% system detection efficiency and 1.05 polarization sensitivity
- 2020
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Ingår i: Optics Letters. - : Optical Society of America. - 0146-9592 .- 1539-4794. ; 45:2, s. 471-474
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Tidskriftsartikel (refereegranskat)abstract
- Superconducting nanowire (nanostrip) single-photon detectors (SNSPDs) have shown unprecedented detection efficiency and timing properties, but simultaneously achieving polarization-insensitive high detection efficiency, low dark-count rate (DCR), fast speed, and low timing jitter remains a challenge. Here we report on our design, fabrication, and characterization of a cascaded superconducting avalanche photodetector composed of 40 nm wide NbTiN nanowires patterned into fractal curves. At the base temperature of 2.7 K, the device exhibits 60 ± 3% system detection efficiency at the wavelength of 1550 nm, 1.05 polarization sensitivity, 220 cps DCR, 4 ns recovery time, and 45 ps timing jitter. This Letter not only demonstrates these combined properties on a single detector that was unobtainable previously, but also shows that that current-crowding effect remarkably permits decent internal detection efficiency. These counter-intuitive results expand the understanding pertaining to the device physics of SNSPDs.
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