| 1. |
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| 2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Journal article (peer-reviewed)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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| 4. |
- Aad, G, et al.
(author)
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- 2015
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swepub:Mat__t
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| 16. |
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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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In: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
-
Journal article (peer-reviewed)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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| 17. |
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- 2019
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Journal article (peer-reviewed)
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| 18. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
Journal article (peer-reviewed)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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| 19. |
- Jiang, Bin, et al.
(author)
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Observation of an acoustic topological Euler insulator with meronic waves
- 2024
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In: Science Bulletin. - : Elsevier BV. - 2095-9273. ; 69:11, s. 1653-1659
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Journal article (peer-reviewed)abstract
- Topological band theory has conventionally been concerned with the topology of bands around a single gap. Only recently non-Abelian topologies that thrive on involving multiple gaps were studied, unveiling a new horizon in topological physics beyond the conventional paradigm. Here, we report on the first experimental realization of a topological Euler insulator phase with unique meronic characterization in an acoustic metamaterial. We demonstrate that this topological phase has several nontrivial features: First, the system cannot be described by conventional topological band theory, but has a nontrivial Euler class that captures the unconventional geometry of the Bloch bands in the Brillouin zone. Second, we uncover in theory and probe in experiments a meronic configuration of the bulk Bloch states for the first time. Third, using a detailed symmetry analysis, we show that the topological Euler insulator evolves from a non-Abelian topological semimetal phase via. the annihilation of Dirac points in pairs in one of the band gaps. With these nontrivial properties, we establish concretely an unconventional bulk-edge correspondence which is confirmed by directly measuring the edge states via. pump-probe techniques. Our work thus unveils a nontrivial topological Euler insulator phase with a unique meronic pattern and paves the way as a platform for non-Abelian topological phenomena.
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| 20. |
- Lensink, Marc F., et al.
(author)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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In: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Journal article (peer-reviewed)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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| 21. |
- Lin, Jia, et al.
(author)
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Pressure-induced semiconductor-to-metal phase transition of a charge-ordered indium halide perovskite
- 2019
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:47, s. 23404-23409
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Journal article (peer-reviewed)abstract
- Phase transitions in halide perovskites triggered by external stimuli generate significantly different material properties, providing a great opportunity for broad applications. Here, we demonstrate an In-based, charge-ordered (In+/In3+) inorganic halide perovskite with the composition of Cs2In(I)In(III)Cl-6 in which a pressure-driven semiconductor-to-metal phase transition exists. The single crystals, synthesized via a solid-state reaction method, crystallize in a distorted perovskite structure with space group I4/m with a = 17.2604(12) angstrom, c = 11.0113(16) angstrom if both the strong reflections and superstructures are considered. The supercell was further confirmed by rotation electron diffraction measurement. The pressure-induced semiconductor-to-metal phase transition was demonstrated by high-pressure Raman and absorbance spectroscopies and was consistent with theoretical modeling. This type of charge-ordered inorganic halide perovskite with a pressure-induced semiconductor-to-metal phase transition may inspire a range of potential applications.
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| 22. |
- Luo, Yifei, et al.
(author)
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Technology Roadmap for Flexible Sensors
- 2023
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In: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
-
Research review (peer-reviewed)abstract
- Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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| 23. |
- Warren, Wesley C, et al.
(author)
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The genome of a songbird
- 2010
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 757-762
-
Journal article (peer-reviewed)abstract
- The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.
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| 24. |
- Aaltonen, T., et al.
(author)
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Combination of CDF and D0 measurements of the W boson helicity in top quark decays
- 2012
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 85:7, s. 071106-
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Journal article (peer-reviewed)abstract
- We report the combination of recent measurements of the helicity of the W boson from top quark decay by the CDF and D0 collaborations, based on data samples corresponding to integrated luminosities of 2.7-5.4 fb(-1) of p (p) over bar collisions collected during Run II of the Fermilab Tevatron collider. Combining measurements that simultaneously determine the fractions of W bosons with longitudinal (f(0)) and right-handed (f(+)) helicities, we find f(0) = 0.722 +/- 0.081[+/- 0.062(stat) +/- 0.052(syst)] and f(+) = -0.033 +/- 0.046[+/- 0.034(stat) +/- 0.031(syst)]. Combining measurements where one of the helicity fractions is fixed to the value expected in the standard model, we find f(0) = 0.682 +/- 0.057[+/- 0.035(stat) +/- 0.046(syst)] for fixed f(+) and f(+) = -0.015 +/- 0.035[+/- 0.018(stat) +/- 0.030(syst)] for fixed f(0). The results are consistent with standard model expectations.
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| 25. |
- Aaltonen, T., et al.
(author)
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Combination of Tevatron Searches for the Standard Model Higgs Boson in the W+W- Decay Mode
- 2010
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 104:6, s. 061802-
-
Journal article (peer-reviewed)abstract
- We combine searches by the CDF and D0 Collaborations for a Higgs boson decaying to W+W-. The data correspond to an integrated total luminosity of 4.8 (CDF) and 5.4 (D0) fb(-1) of p (p) over bar collisions at root s = 1.96 TeV at the Fermilab Tevatron collider. No excess is observed above background expectation, and resulting limits on Higgs boson production exclude a standard model Higgs boson in the mass range 162-166 GeV at the 95% C.L.
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| 26. |
- Aaltonen, T., et al.
(author)
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Evidence for a Particle Produced in Association with Weak Bosons and Decaying to a Bottom-Antibottom Quark Pair in Higgs Boson Searches at the Tevatron
- 2012
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 109:7, s. 071804-
-
Journal article (peer-reviewed)abstract
- We combine searches by the CDF and D0 Collaborations for the associated production of a Higgs boson with a W or Z boson and subsequent decay of the Higgs boson to a bottom-antibottom quark pair. The data, originating from Fermilab Tevatron p (p) over bar collisions at root s = 1.96 TeV, correspond to integrated luminosities of up to 9.7 fb(-1). The searches are conducted for a Higgs boson with mass in the range 100-150 GeV/c(2). We observe an excess of events in the data compared with the background predictions, which is most significant in the mass range between 120 and 135 GeV/c(2). The largest local significance is 3.3 standard deviations, corresponding to a global significance of 3.1 standard deviations. We interpret this as evidence for the presence of a new particle consistent with the standard model Higgs boson, which is produced in association with a weak vector boson and decays to a bottom-antibottom quark pair.
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| 27. |
- Abramson, Alex, et al.
(author)
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Ingestible transiently anchoring electronics for microstimulation and conductive signaling
- 2020
-
In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 6:35
-
Journal article (peer-reviewed)abstract
- Ingestible electronic devices enable noninvasive evaluation and diagnosis of pathologies in the gastrointestinal (GI) tract but generally cannot therapeutically interact with the tissue wall. Here, we report the development of an orally administered electrical stimulation device characterized in ex vivo human tissue and in in vivo swine models, which transiently anchored itself to the stomach by autonomously inserting electrically conductive, hooked probes. The probes provided stimulation to the tissue via timed electrical pulses that could be used as a treatment for gastric motility disorders. To demonstrate interaction with stomach muscle tissue, we used the electrical stimulation to induce acute muscular contractions. Pulses conductively signaled the probes' successful anchoring and detachment events to a parenterally placed device. The ability to anchor into and electrically interact with targeted GI tissues controlled by the enteric nervous system introduces opportunities to treat a multitude of associated pathologies.
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| 28. |
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| 29. |
- Brownstein, Catherine A., et al.
(author)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Journal article (peer-reviewed)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 30. |
- Bu, Junling, et al.
(author)
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Catalytic promiscuity of O-methyltransferases from Corydalis yanhusuo leading to the structural diversity of benzylisoquinoline alkaloids
- 2022
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In: Horticulture Research. - : Oxford University Press (OUP). - 2662-6810 .- 2052-7276. ; 9
-
Journal article (peer-reviewed)abstract
- O-methyltransferases play essential roles in producing structural diversity and improving the biological properties of benzylisoquinoline alkaloids (BIAs) in plants. In this study, Corydalis yanhusuo, a plant used in traditional Chinese medicine due to the analgesic effects of its BIA-active compounds, was employed to analyze the catalytic characteristics of O-methyltransferases in the formation of BIA diversity. Seven genes encoding O-methyltransferases were cloned, and functionally characterized using seven potential BIA substrates. Specifically, an O-methyltransferase (CyOMT2) with highly efficient catalytic activity of both 4′- and 6-O-methylations of 1-BIAs was found. CyOMT6 was found to perform two sequential methylations at both 9- and 2-positions of the essential intermediate of tetrahydroprotoberberines, (S)-scoulerine. Two O-methyltransferases (CyOMT5 and CyOMT7) with wide substrate promiscuity were found, with the 2-position of tetrahydroprotoberberines as the preferential catalytic site for CyOMT5 (named scoulerine 2-O-methyltransferase) and the 6-position of 1-BIAs as the preferential site for CyOMT7. In addition, results of integrated phylogenetic molecular docking analysis and site-directed mutation suggested that residues at sites 172, 306, 313, and 314 in CyOMT5 are important for enzyme promiscuity related to O-methylations at the 6- and 7-positions of isoquinoline. Cys at site 253 in CyOMT2 was proved to promote the methylation activity of the 6-position and to expand substrate scopes. This work provides insight into O-methyltransferases in producing BIA diversity in C. yanhusuo and genetic elements for producing BIAs by metabolic engineering and synthetic biology.
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| 31. |
- Cai, Baoping, et al.
(author)
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Application of Bayesian Networks in Reliability Evaluation
- 2019
-
In: IEEE Transactions on Industrial Informatics. - : IEEE. - 1551-3203 .- 1941-0050. ; 15:4, s. 2146-2157
-
Journal article (peer-reviewed)abstract
- The Bayesian network (BN) is a powerful model for probabilistic knowledge representation and inference and is increasingly used in the field of reliability evaluation. This paper presents a bibliographic review of BNs that have been proposed for reliability evaluation in the last decades. Studies are classified from the perspective of the objects of reliability evaluation, i.e., hardware, structures, software, and humans. For each classification, the construction and validation of a BN-based reliability model are emphasized. The general procedural steps for BN-based reliability evaluation, including BN structure modeling, BN parameter modeling, BN inference, and model verification and validation, are investigated. Current gaps and challenges in reliability evaluation with BNs are explored, and a few upcoming research directions that are of interest to reliability researchers are identified.
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| 32. |
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| 33. |
- Ding, Aixiang, et al.
(author)
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Complex-Formation-Enhanced Fluorescence Quenching Effect for Efficient Detection of Picric Acid
- 2014
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In: Chemistry - A European Journal. - : Wiley-VCH Verlag. - 0947-6539 .- 1521-3765. ; 20:38, s. 12215-12222
-
Journal article (peer-reviewed)abstract
- Amine-functionalized alpha-cyanostilbene derivatives (Z)-2-(4-aminophenyl)-3-(4-butoxyphenyl) acrylonitrile (ABA) and (Z)-3-(4-butoxyphenyl)-2-[4-(butylamino) phenyl] acrylonitrile (BBA) were designed for specific recognition of picric acid (PA), an environmental and biological pollutant. The 1:1 host-guest complexes formed between the chemosensors and PA enhanced fluorescence quenching, thus leading to sensitive and selective detection in aqueous media and the solid phase.
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| 34. |
- Du, Yong, et al.
(author)
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Investigation of the Heteroepitaxial Process Optimization of Ge Layers on Si (001) by RPCVD
- 2021
-
In: Nanomaterials. - : MDPI AG. - 2079-4991. ; 11:4
-
Journal article (peer-reviewed)abstract
- This work presents the growth of high-quality Ge epilayers on Si (001) substrates using a reduced pressure chemical vapor deposition (RPCVD) chamber. Based on the initial nucleation, a low temperature high temperature (LT-HT) two-step approach, we systematically investigate the nucleation time and surface topography, influence of a LT-Ge buffer layer thickness, a HT-Ge growth temperature, layer thickness, and high temperature thermal treatment on the morphological and crystalline quality of the Ge epilayers. It is also a unique study in the initial growth of Ge epitaxy; the start point of the experiments includes Stranski-Krastanov mode in which the Ge wet layer is initially formed and later the growth is developed to form nuclides. Afterwards, a two-dimensional Ge layer is formed from the coalescing of the nuclides. The evolution of the strain from the beginning stage of the growth up to the full Ge layer has been investigated. Material characterization results show that Ge epilayer with 400 nm LT-Ge buffer layer features at least the root mean square (RMS) value and it's threading dislocation density (TDD) decreases by a factor of 2. In view of the 400 nm LT-Ge buffer layer, the 1000 nm Ge epilayer with HT-Ge growth temperature of 650 degrees C showed the best material quality, which is conducive to the merging of the crystals into a connected structure eventually forming a continuous and two-dimensional film. After increasing the thickness of Ge layer from 900 nm to 2000 nm, Ge surface roughness decreased first and then increased slowly (the RMS value for 1400 nm Ge layer was 0.81 nm). Finally, a high-temperature annealing process was carried out and high-quality Ge layer was obtained (TDD=2.78 x 10(7) cm(-2)). In addition, room temperature strong photoluminescence (PL) peak intensity and narrow full width at half maximum (11 meV) spectra further confirm the high crystalline quality of the Ge layer manufactured by this optimized process. This work highlights the inducing, increasing, and relaxing of the strain in the Ge buffer and the signature of the defect formation.
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| 35. |
- Du, Y., et al.
(author)
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Strain modulation of selectively and/or globally grown ge layers
- 2021
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In: Nanomaterials. - : MDPI AG. - 2079-4991. ; 11:6
-
Journal article (peer-reviewed)abstract
- This article presents a novel method to grow a high-quality compressive-strain Ge epilayer on Si using the selective epitaxial growth (SEG) applying the RPCVD technique. The procedures are composed of a global growth of Ge layer on Si followed by a planarization using CMP as initial process steps. The growth parameters of the Ge layer were carefully optimized and after cycle-annealing treatments, the threading dislocation density (TDD) was reduced to 3 × 107 cm−2 . As a result of this process, a tensile strain of 0.25% was induced, whereas the RMS value was as low as 0.81 nm. Later, these substrates were covered by an oxide layer and patterned to create trenches for selective epitaxy growth (SEG) of the Ge layer. In these structures, a type of compressive strain was formed in the SEG Ge top layer. The strain amount was −0.34%; meanwhile, the TDD and RMS surface roughness were 2 × 106 cm−2 and 0.68 nm, respectively. HRXRD and TEM results also verified the existence of compressive strain in selectively grown Ge layer. In contrast to the tensile strained Ge layer (globally grown), enhanced PL intensity by a factor of more than 2 is partially due to the improved material quality. The significantly high PL intensity is attributed to the improved crystalline quality of the selectively grown Ge layer. The change in direct bandgap energy of PL was observed, owing to the compressive strain introduced. Hall measurement shows that a selectively grown Ge layer possesses room temperature hole mobility up to 375 cm2/Vs, which is approximately 3 times larger than that of the Ge (132 cm2/Vs). Our work offers fundamental guidance for the growth of high-quality and compressive strain Ge epilayer on Si for future Ge-based optoelectronics integration applications.
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| 36. |
- Gezari, S., et al.
(author)
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iPTF Discovery of the Rapid Turn-on of a Luminous Quasar
- 2017
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In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 835:2
-
Journal article (peer-reviewed)abstract
- We present a radio-quiet quasar at z = 0.237 discovered turning on by the intermediate Palomar Transient Factory (iPTF). The transient, iPTF 16bco, was detected by iPTF in the nucleus of a galaxy with an archival Sloan Digital Sky Survey spectrum with weak narrow-line emission characteristic of a low-ionization nuclear emission-line region (LINER). Our follow-up spectra show the dramatic appearance of broad Balmer lines and a power-law continuum characteristic of a luminous (L-bol approximate to 10(45) erg s(-1)) type 1 quasar 12 yr later. Our photometric monitoring with PTF from 2009-2012 and serendipitous X-ray observations from the XMM-Newton Slew Survey in 2011 and 2015 constrain the change of state to have occurred less than 500 days before the iPTF detection. An enhanced broad H alpha/[O III] lambda 5007 line ratio in the type 1 state relative to other changing-look quasars also is suggestive of the most rapid change of state yet observed in a quasar. We argue that the > 10 increase in Eddington ratio inferred from the brightening in UV and X-ray continuum flux is more likely due to an intrinsic change in the accretion rate of a preexisting accretion disk than an external mechanism such as variable obscuration, microlensing, or the tidal disruption of a star. However, further monitoring will be helpful in better constraining the mechanism driving this change of state. The rapid turn-on of the quasar is much shorter than the viscous infall timescale of an accretion disk and requires a disk instability that can develop around a similar to 10(8) M circle dot black hole on timescales less than 1 yr.
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| 37. |
- Gu, Qiang, et al.
(author)
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VKORC1-1639G>A, CYP2C9, EPHX1691A>G genotype, body weight, and age are important predictors for warfarin maintenance doses in patients with mechanical heart valve prostheses in southwest China
- 2010
-
In: European Journal of Clinical Pharmacology. - : Springer Science and Business Media LLC. - 0031-6970 .- 1432-1041. ; 66:12, s. 1217-1227
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Journal article (peer-reviewed)abstract
- There were great interindividual differences in warfarin maintenance dosage (ranging from 0.6 to 8.4 mg/day) among the 127 patients with mechanical heart valve prostheses. VKORC1-1639G>A, CYP2C9, EPHX1691A>G polymorphism, body weight, and age were found to affect the dose demands. Multiple linear regression models incorporating genetic polymorphisms of VKORC1, CYP2C9, EPHX1691A>G, and the nongenetic factors of age and body weight were developed, and explained up to 76.8% of the total variation (adjusted R (2) of 0.743) in warfarin maintenance doses in southwest Chinese patients with mechanical heart valve prostheses.
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| 38. |
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| 39. |
- Huang, X. Z., et al.
(author)
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Oxidative stress induced by titanium dioxide nanoparticles increases under seawater acidification in the thick shell mussel Mytilus coruscus
- 2018
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In: Marine Environmental Research. - 0141-1136. ; 137, s. 49-59
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Journal article (peer-reviewed)abstract
- Biochemical responses of the mussel Mytflrn coruscus exposed to different concentrations of titanium dioxide nanoparticles (nano-Ti0(2)) (0, 2.5, 10mgL(-1)) and two pH levels (pH 8.1 and pH 7.3) for 14 days. Mussel responses were also investigated after a 7 days recovery period (pH 8.1 and no nanoparticle). Exposure to nanoTi0(2) led changes in antioxidant indexes (superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione (GSH)), biotransformation enzyme activity (GST) and malondialdehyde level (MDA) in gills and digestive glands. An increase in MDA level and a decrease in SOD and GSH activities were observed in gill of mussels exposed to 10 mg L-n1 nano-TiO2. This effect was more severe in mussels kept at pH 7.3 as compared to pH 8.1. A different response was observed in the digestive gland as SOD, CAT and GSH levels increased in mussels exposed to nano-TiO2. These contrasting results in digestive glands and gills were only evident at high concentration of nano-TiO2 and low pH. A 7 days recovery period was not sufficient to fully restore SOD, GPx, GST, GSH and MDA levels to levels before exposure to nano-TiO2 and low pH. Overall, our results confirmed that seawater acidification modulates effects of nanoparticles in mussels, and that gills are more sensitive to these stressors as compared with digestive glands.
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| 40. |
- Hung, T., et al.
(author)
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Sifting for Sapphires : Systematic Selection of Tidal Disruption Events in iPTF
- 2018
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In: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 238:2
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Journal article (peer-reviewed)abstract
- We present results from a systematic selection of tidal disruption events (TDEs) in a wide-area (4800 deg(2)), g+ R band, Intermediate Palomar Transient Factory experiment. Our selection targets typical optically selected TDEs: bright (> 60% flux increase) and blue transients residing in the centers of red galaxies. Using photometric selection criteria to down-select from a total of 493 nuclear transients to a sample of 26 sources, we then use follow-up UV imaging with the Neil Gehrels Swift Telescope, ground-based optical spectroscopy, and light curve fitting to classify them as 14 Type Ia supernovae (SNe Ia), 9 highly variable active galactic nuclei (AGNs), 2 confirmed TDEs, and 1 potential core-collapse supernova. We find it possible to filter AGNs by employing a more stringent transient color cut (g - r < -0.2 mag); further, UV imaging is the best discriminator for filtering SNe, since SNe Ia can appear as blue, optically, as TDEs in their early phases. However, when UV-optical color is unavailable, higher-precision astrometry can also effectively reduce SNe contamination in the optical. Our most stringent optical photometric selection criteria yields a 4.5: 1 contamination rate, allowing for a manageable number of TDE candidates for complete spectroscopic follow-up and real-time classification in the Zwicky Transient Facility era. We measure a TDE per galaxy rate of 1.7(-1.3)(+2.9) 10(-4) gal yr(-1) (90% CL in Poisson statistics). This does not account for TDEs outside our selection criteria, and thus may not reflect the total TDE population, which is yet to be fully mapped.
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| 41. |
- Hyde, K. D., et al.
(author)
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Global consortium for the classification of fungi and fungus-like taxa
- 2023
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In: MYCOSPHERE. - : Mushroom Research Foundation. - 2077-7000 .- 2077-7019. ; 14:1, s. 1960-2012
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Journal article (peer-reviewed)abstract
- The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-career and early-career mycologists and plant pathologists. The Consortium will publish a biannual update of the Outline of Fungi and fungus-like taxa, to act as an international scheme for other scientists. Notes on all newly published taxa at or above the level of species will be prepared and published online on the Outline of Fungi website (https://www.outlineoffungi.org/), and these will be finally published in the biannual edition of the Outline of Fungi and fungus-like taxa. Comments on recent important taxonomic opinions on controversial topics will be included in the biannual outline. For example, 'to promote a more stable taxonomy in Fusarium given the divergences over its generic delimitation', or 'are there too many genera in the Boletales?' and even more importantly, 'what should be done with the tremendously diverse 'dark fungal taxa?' There are undeniable differences in mycologists' perceptions and opinions regarding species classification as well as the establishment of new species. Given the pluralistic nature of fungal taxonomy and its implications for species concepts and the nature of species, this consortium aims to provide a platform to better refine and stabilise fungal classification, taking into consideration views from different parties. In the future, a confidential voting system will be set up to gauge the opinions of all mycologists in the Consortium on important topics. The results of such surveys will be presented to the International Commission on the Taxonomy of Fungi (ICTF) and the Nomenclature Committee for Fungi (NCF) with opinions and percentages of votes for and against. Criticisms based on scientific evidence with regards to nomenclature, classifications, and taxonomic concepts will be welcomed, and any recommendations on specific taxonomic issues will also be encouraged; however, we will encourage professionally and ethically responsible criticisms of others' work. This biannual ongoing project will provide an outlet for advances in various topics of fungal classification, nomenclature, and taxonomic concepts and lead to a community-agreed classification scheme for the fungi and fungus-like taxa. Interested parties should contact the lead author if they would like to be involved in future outlines.
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| 42. |
- Ke, You, et al.
(author)
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Defect Passivation for Red Perovskite Light-Emitting Diodes with Improved Brightness and Stability
- 2019
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In: The Journal of Physical Chemistry Letters. - : AMER CHEMICAL SOC. - 1948-7185. ; 10:3, s. 380-385
-
Journal article (peer-reviewed)abstract
- Efficient and stable red perovskite light-emitting diodes (PeLEDs) are important for realizing full-color display and lighting. Red PeLEDs can be achieved either by mixed-halide or low-dimensional perovskites. However, the device performance, especially the brightness, is still low owing to phase separation or poor charge transport issues. Here, we demonstrate red PeLEDs based on three-dimensional (3D) mixed-halide perovskites where the defects are passivated by using 5-aminovaleric acid. The red PeLEDs with an emission peak at 690 nm exhibit an external quantum efficiency of 8.7% and a luminance of 1408 cd m(-2). A maximum luminance of 8547 cd m(-2) can be further achieved as tuning the emission peak to 662 nm, representing the highest brightness of red PeLEDs. Moreover, those LEDs exhibit a half-life of up to 8 h under a high constant current density of 100 mA cm(-2), which is over 10 times improvement compared to literature results.
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| 43. |
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| 44. |
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| 45. |
- Kong, Z., et al.
(author)
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Growth and Strain Modulation of GeSn Alloys for Photonic and Electronic Applications
- 2022
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In: Nanomaterials. - : MDPI AG. - 2079-4991. ; 12:6
-
Journal article (peer-reviewed)abstract
- GeSn materials have attracted considerable attention for their tunable band structures and high carrier mobilities, which serve well for future photonic and electronic applications. This research presents a novel method to incorporate Sn content as high as 18% into GeSn layers grown at 285–320◦C by using SnCl4 and GeH4 precursors. A series of characterizations were performed to study the material quality, strain, surface roughness, and optical properties of GeSn layers. The Sn content could be calculated using lattice mismatch parameters provided by X-ray analysis. The strain in GeSn layers was modulated from fully strained to partially strained by etching Ge buffer into Ge/GeSn heterostructures . In this study, two categories of samples were prepared when the Ge buffer was either laterally etched onto Si wafers, or vertically etched Ge/GeSnOI wafers which bonded to the oxide. In the latter case, the Ge buffer was initially etched step-by-step for the strain relaxation study. Meanwhile, the Ge/GeSn heterostructure in the first group of samples was patterned into the form of micro-disks. The Ge buffer was selectively etched by using a CF4/O2 gas mixture using a plasma etch tool. Fully or partially relaxed GeSn micro-disks showed photoluminescence (PL) at room temperature. PL results showed that red-shift was clearly observed from the GeSn microdisk structure, indicating that the compressive strain in the as-grown GeSn material was partially released. Our results pave the path for the growth of high quality GeSn layers with high Sn content, in addition to methods for modulating the strain for lasing and detection of short-wavelength infrared at room temperature.
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| 46. |
- Li, C., et al.
(author)
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Growth and Selective Etch of Phosphorus-Doped Silicon/Silicon–Germanium Multilayers Structures for Vertical Transistors Application
- 2020
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In: Nanoscale Research Letters. - : Springer. - 1931-7573 .- 1556-276X. ; 15:1
-
Journal article (peer-reviewed)abstract
- Vertical gate-all-around field-effect transistors (vGAAFETs) are considered as the potential candidates to replace FinFETs for advanced integrated circuit manufacturing technology at/beyond 3-nm technology node. A multilayer (ML) of Si/SiGe/Si is commonly grown and processed to form vertical transistors. In this work, the P-incorporation in Si/SiGe/Si and vertical etching of these MLs followed by selective etching SiGe in lateral direction to form structures for vGAAFET have been studied. Several strategies were proposed for the epitaxy such as hydrogen purging to deplete the access of P atoms on Si surface, and/or inserting a Si or Si0.93Ge0.07 spacers on both sides of P-doped Si layers, and substituting SiH4 by SiH2Cl2 (DCS). Experimental results showed that the segregation and auto-doping could also be relieved by adding 7% Ge to P-doped Si. The structure had good lattice quality and almost had no strain relaxation. The selective etching between P-doped Si (or P-doped Si0.93Ge0.07) and SiGe was also discussed by using wet and dry etching. The performance and selectivity of different etching methods were also compared. This paper provides knowledge of how to deal with the challenges or difficulties of epitaxy and etching of n-type layers in vertical GAAFETs structure. © 2020, The Author(s).
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| 47. |
- Li, Junjie, et al.
(author)
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A Novel Dry Selective Isotropic Atomic Layer Etching of SiGe for Manufacturing Vertical Nanowire Array with Diameter Less than 20 nm
- 2020
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In: Materials. - : MDPI AG. - 1996-1944. ; 13:3
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Journal article (peer-reviewed)abstract
- Semiconductor nanowires have great application prospects in field effect transistors and sensors. In this study, the process and challenges of manufacturing vertical SiGe/Si nanowire array by using the conventional lithography and novel dry atomic layer etching technology. The final results demonstrate that vertical nanowires with a diameter less than 20 nm can be obtained. The diameter of nanowires is adjustable with an accuracy error less than 0.3 nm. This technology provides a new way for advanced 3D transistors and sensors.
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| 48. |
- Li, J., et al.
(author)
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Study of silicon nitride inner spacer formation in process of gate-all-around nano-transistors
- 2020
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In: Nanomaterials. - : MDPI AG. - 2079-4991. ; 10:4
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Journal article (peer-reviewed)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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| 49. |
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