| 1. |
- Rajewsky, N., et al.
(författare)
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LifeTime and improving European healthcare through cell-based interceptive medicine
- 2020
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 587:7834, s. 377-386
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Tidskriftsartikel (refereegranskat)abstract
- LifeTime aims to track, understand and target human cells during the onset and progression of complex diseases and their response to therapy at single-cell resolution. This mission will be implemented through the development and integration of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during progression from health to disease. Analysis of such large molecular and clinical datasets will discover molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. Timely detection and interception of disease embedded in an ethical and patient-centered vision will be achieved through interactions across academia, hospitals, patient-associations, health data management systems and industry. Applying this strategy to key medical challenges in cancer, neurological, infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.
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| 2. |
- Callaway, EM, et al.
(författare)
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A multimodal cell census and atlas of the mammalian primary motor cortex
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 598:7879, s. 86-102
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Tidskriftsartikel (refereegranskat)abstract
- Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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| 3. |
- Savage, J. E., et al.
(författare)
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Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence
- 2018
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 50:7, s. 912-919
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Tidskriftsartikel (refereegranskat)abstract
- Intelligence is highly heritable 1 and a major determinant of human health and well-being 2 . Recent genome-wide meta-analyses have identified 24 genomic loci linked to variation in intelligence 3-7, but much about its genetic underpinnings remains to be discovered. Here, we present a large-scale genetic association study of intelligence (n = 269,867), identifying 205 associated genomic loci (190 new) and 1,016 genes (939 new) via positional mapping, expression quantitative trait locus (eQTL) mapping, chromatin interaction mapping, and gene-based association analysis. We find enrichment of genetic effects in conserved and coding regions and associations with 146 nonsynonymous exonic variants. Associated genes are strongly expressed in the brain, specifically in striatal medium spiny neurons and hippocampal pyramidal neurons. Gene set analyses implicate pathways related to nervous system development and synaptic structure. We confirm previous strong genetic correlations with multiple health-related outcomes, and Mendelian randomization analysis results suggest protective effects of intelligence for Alzheimer's disease and ADHD and bidirectional causation with pleiotropic effects for schizophrenia. These results are a major step forward in understanding the neurobiology of cognitive function as well as genetically related neurological and psychiatric disorders.
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| 4. |
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| 5. |
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| 6. |
- Bakken, TE, et al.
(författare)
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Comparative cellular analysis of motor cortex in human, marmoset and mouse
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 598:7879, s. 111-
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Tidskriftsartikel (refereegranskat)abstract
- The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch–seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.
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| 7. |
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| 11. |
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| 13. |
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| 14. |
- Goodridge, JP, et al.
(författare)
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Remodeling of secretory lysosomes during education tunes functional potential in NK cells
- 2019
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 514-
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Tidskriftsartikel (refereegranskat)abstract
- Inhibitory signaling during natural killer (NK) cell education translates into increased responsiveness to activation; however, the intracellular mechanism for functional tuning by inhibitory receptors remains unclear. Secretory lysosomes are part of the acidic lysosomal compartment that mediates intracellular signalling in several cell types. Here we show that educated NK cells expressing self-MHC specific inhibitory killer cell immunoglobulin-like receptors (KIR) accumulate granzyme B in dense-core secretory lysosomes that converge close to the centrosome. This discrete morphological phenotype is independent of transcriptional programs that regulate effector function, metabolism and lysosomal biogenesis. Meanwhile, interference of signaling from acidic Ca2+ stores in primary NK cells reduces target-specific Ca2+-flux, degranulation and cytokine production. Furthermore, inhibition of PI(3,5)P2 synthesis, or genetic silencing of the PI(3,5)P2-regulated lysosomal Ca2+-channel TRPML1, leads to increased granzyme B and enhanced functional potential, thereby mimicking the educated state. These results indicate an intrinsic role for lysosomal remodeling in NK cell education.
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| 15. |
- Hochgerner, H, et al.
(författare)
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STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array
- 2017
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7:1, s. 16327-
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Tidskriftsartikel (refereegranskat)abstract
- Single-cell RNA-seq has become routine for discovering cell types and revealing cellular diversity, but archived human brain samples still pose a challenge to current high-throughput platforms. We present STRT-seq-2i, an addressable 9600-microwell array platform, combining sampling by limiting dilution or FACS, with imaging and high throughput at competitive cost. We applied the platform to fresh single mouse cortical cells and to frozen post-mortem human cortical nuclei, matching the performance of a previous lower-throughput platform while retaining a high degree of flexibility, potentially also for other high-throughput applications.
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| 16. |
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| 17. |
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| 18. |
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| 19. |
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| 20. |
- Jouhilahti, EM, et al.
(författare)
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The human PRD-like homeobox gene LEUTX has a central role in embryo genome activation
- 2016
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Ingår i: Development (Cambridge, England). - : The Company of Biologists. - 1477-9129 .- 0950-1991. ; 143:19, s. 3459-3469
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Tidskriftsartikel (refereegranskat)abstract
- Leucine twenty homeobox gene (LEUTX) is a PAIRED (PRD)-like homeobox gene that is expressed nearly exclusively in human preimplantation embryos. We previously identified a novel transcription start site for the predicted human LEUTX gene based on the transcriptional analysis of human preimplantation embryos. The novel variant encodes a protein with a complete homeodomain. Here we provide a detailed description of the molecular cloning of the complete homeodomain-containing LEUTX. Using a human embryonic stem cell overexpression model we show that the complete homeodomain isoform is functional and sufficient to activate the transcription of a large fraction of the genes found upregulated in human embryo genome activation, whereas the previously predicted partial homeodomain isoform is largely inactive. Another PRD-like transcription factor, DPRX, appears as a powerful repressor of transcription. We propose a two-stage model of human EGA in which LEUTX acts as a transcriptional activator at 4-cell stage, and DPRX as a balancing repressor at 8-cell stage. We conclude that LEUTX is a candidate regulator of human embryo genome activation.
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| 21. |
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| 23. |
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| 24. |
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| 25. |
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| 26. |
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| 27. |
- Regev, A, et al.
(författare)
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The Human Cell Atlas
- 2017
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Ingår i: eLife. - : ELIFE SCIENCES PUBLICATIONS LTD. - 2050-084X. ; 6
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Tidskriftsartikel (refereegranskat)
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| 28. |
- Tervaniemi, MH, et al.
(författare)
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NOD-like receptor signaling and inflammasome-related pathways are highlighted in psoriatic epidermis
- 2016
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6, s. 22745-
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Tidskriftsartikel (refereegranskat)abstract
- Psoriatic skin differs distinctly from normal skin by its thickened epidermis. Most gene expression comparisons utilize full-thickness biopsies, with substantial amount of dermis. We assayed the transcriptomes of normal, lesional and non-lesional psoriatic epidermis, sampled as split-thickness skin grafts, with 5′-end RNA sequencing. We found that psoriatic epidermis contains more mRNA per total RNA than controls and took this into account in the bioinformatic analysis. The approach highlighted innate immunity-related pathways in psoriasis, including NOD-like receptor (NLR) signaling and inflammasome activation. We demonstrated that the NLR signaling genes NOD2, PYCARD, CARD6 and IFI16 are upregulated in psoriatic epidermis and strengthened these findings by protein expression. Interestingly, PYCARD, the key component of the inflammasome, showed an altered expression pattern in the lesional epidermis. The profiling of non-lesional skin highlighted PSORS4 and mitochondrially encoded transcripts, suggesting that their gene expression is altered already before the development of lesions. Our data suggest that all components needed for the active inflammasome are present in the keratinocytes of psoriatic skin. The characterization of inflammasome pathways provides further opportunities for therapy. Complementing previous transcriptome studies, our approach gives deeper insight into the gene regulation in psoriatic epidermis.
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| 29. |
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| 30. |
- Wang, YQ, et al.
(författare)
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A cell fitness selection model for neuronal survival during development
- 2019
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 4137-
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Tidskriftsartikel (refereegranskat)abstract
- Developmental cell death plays an important role in the construction of functional neural circuits. In vertebrates, the canonical view proposes a selection of the surviving neurons through stochastic competition for target-derived neurotrophic signals, implying an equal potential for neurons to compete. Here we show an alternative cell fitness selection of neurons that is defined by a specific neuronal heterogeneity code. Proprioceptive sensory neurons that will undergo cell death and those that will survive exhibit different molecular signatures that are regulated by retinoic acid and transcription factors, and are independent of the target and neurotrophins. These molecular features are genetically encoded, representing two distinct subgroups of neurons with contrasted functional maturation states and survival outcome. Thus, in this model, a heterogeneous code of intrinsic cell fitness in neighboring neurons provides differential competitive advantage resulting in the selection of cells with higher capacity to survive and functionally integrate into neural networks.
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| 31. |
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| 32. |
- Borm, LE, et al.
(författare)
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Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH
- 2023
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Ingår i: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 41:2, s. 222-
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Tidskriftsartikel (refereegranskat)abstract
- Methods to spatially profile the transcriptome are dominated by a trade-off between resolution and throughput. Here we develop a method named Enhanced ELectric Fluorescence in situ Hybridization (EEL FISH) that can rapidly process large tissue samples without compromising spatial resolution. By electrophoretically transferring RNA from a tissue section onto a capture surface, EEL speeds up data acquisition by reducing the amount of imaging needed, while ensuring that RNA molecules move straight down toward the surface, preserving single-cell resolution. We apply EEL on eight entire sagittal sections of the mouse brain and measure the expression patterns of up to 440 genes to reveal complex tissue organization. Moreover, EEL can be used to study challenging human samples by removing autofluorescent lipofuscin, enabling the spatial transcriptome of the human visual cortex to be visualized. We provide full hardware specifications, all protocols and complete software for instrument control, image processing, data analysis and visualization.
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| 33. |
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| 34. |
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| 35. |
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| 36. |
- Hallén, Anders., et al.
(författare)
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Ion implantation of silicon carbide
- 2002
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Ingår i: Nuclear Instruments and Methods in Physics Research Section B. - 0168-583X .- 1872-9584. ; 186, s. 186-194
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Tidskriftsartikel (refereegranskat)abstract
- Ion implantation is an important technique for a successful implementation of commercial SiC devices. Much effort has also been devoted to optimising implantation and annealing parameters to improve the electrical device characteristics. However, there is a severe lack of understanding of the fundamental implantation process and the generation and annealing kinetics of point defects and defect complexes. Only very few of the most elementary intrinsic point defects have been unambiguously identified so far. To reach a deeper understanding of the basic mechanisms SiC samples have been implanted with a broad range of ions, energies, doses, etc., and the resulting defects and damage produced in the lattice have been studied with a multitude of characterisation techniques. In this contribution we will review some of the results generated recently and also try to indicate where more research is needed. In particular, deep level transient spectroscopy (DLTS) has been used to investigate point defects at very low doses and transmission electron microscopy (TEM) and Rutherford backscattering spectrometry (RBS) are used for studying the damage build-up at high doses.
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| 37. |
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| 38. |
- Islam, S, et al.
(författare)
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Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
- 2011
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 21:7, s. 1160-1167
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Tidskriftsartikel (refereegranskat)abstract
- Our understanding of the development and maintenance of tissues has been greatly aided by large-scale gene expression analysis. However, tissues are invariably complex, and expression analysis of a tissue confounds the true expression patterns of its constituent cell types. Here we describe a novel strategy to access such complex samples. Single-cell RNA-seq expression profiles were generated, and clustered to form a two-dimensional cell map onto which expression data were projected. The resulting cell map integrates three levels of organization: the whole population of cells, the functionally distinct subpopulations it contains, and the single cells themselves—all without need for known markers to classify cell types. The feasibility of the strategy was demonstrated by analyzing the transcriptomes of 85 single cells of two distinct types. We believe this strategy will enable the unbiased discovery and analysis of naturally occurring cell types during development, adult physiology, and disease.
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| 39. |
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| 40. |
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| 41. |
- Janson, M S, et al.
(författare)
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Diffusion of dopants and impurities in device structures of SiC, SiGe and Si
- 2001
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Ingår i: DIFFUSIONS IN MATERIALS. ; , s. 597-609
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Konferensbidrag (refereegranskat)abstract
- Silicon Carbide (SiC) has a high thermal stability and for most elements temperatures in excess of 2000 degreesC are anticipated to reach reasonable diffusivities (greater than or equal to 10(-13) cm(2)/s). We demonstrate, however, that light elements, like hydrogen and lithium, exhibit a considerable mobility already at less than or equal to 400 degreesC, Technologically, the principal interest in these light elements arises because of their ability to electrically passivate shallow acceptors and donors as well as deep level defects in common semiconductors (SiC, Si, GaAs). Indeed, for both hydrogen and lithium the diffusion kinetics is shown to be strongly affected by trapping and de-trapping at boron impurities in the SiC layers. Evidence is also provided that hydrogen migrates as a positively charged ion in p-type SiC. Furthermore, similar to that in crystalline silicon, transient enhanced diffusion of ion-implanted boron is observed in SiC. The initial boron diffusivity during postimplant annealing at 1600 degreesC is enhanced by more than two orders of magnitude compared to equilibrium conditions. For Silicon Germanium (SiGe) diffusion of the n-type dopants Sb and P is studied. Comparing results from strained and relaxed SiGe layers annealed under inert and oxidizing conditions it is unambiguously shown that the diffusion of Sb is almost exclusively mediated by vacancies. On the other hand, P diffusion is predominantly assisted by Si self-interstitials and in this case compositional and strain effects in the SiGe layers are competing.
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| 42. |
- Janson, M S, et al.
(författare)
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Dissociation energy of the passivating hydrogen-aluminum complex in 4H-SiC
- 2001
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Ingår i: Materials Science Forum. ; , s. 427-430
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The thermal stability of the passivating hydrogen-aluminum complex ((HAl)-H-2) in 4H-silicon carbide has been studied by determining the effective diffusion constant for hydrogen in an AI-doped epitaxial layer. Assuming a complex comprised of one H-2 and one AI acceptor ion, the extracted diffusivities provide the dissociation frequency of the complex. The extracted frequencies cover three orders of magnitude and yield a close to perfect fit to an Arrhenius equation with the extracted dissociation energy for the (HAl)-H-2-complex equal to 1.66 (+/-0.05) eV and a pre-exponential attempt frequency nu (0) = 1.7x10(13) s(-1) in good agreement with the expected value for a first order dissociation process.
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| 43. |
- Janson, Martin S., et al.
(författare)
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Electric-field-assisted migration and accumulation of hydrogen in silicon carbide
- 2000
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 61:11, s. 7195-7198
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Tidskriftsartikel (refereegranskat)abstract
- The diffusion of deuterium (H-2) in epitaxial 4H-SiC layers with buried highly Al-acceptor doped regions has been studied by secondary ion mass spectrometry. H-2 was introduced in the near surface region by the use of 20-keV implantation after which the samples were thermally annealed. As a result, an anomalous accumulation of H-2 in the high doped layers was observed. To explain the accumulation kinetics, a model is proposed where positively charged H-2 ions are driven into the high doped layer and become trapped there by the strong electric field at the edges. This effect is important for other semiconductors as well, since hydrogen is a common impurity present at high concentrations in many semiconductors.
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| 44. |
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| 45. |
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| 46. |
- Konstantinov, A., et al.
(författare)
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Investigation of lo-hi-lo and delta-doped silicon carbide structures
- 2001
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Ingår i: Materials Research Society Symposium - Proceedings. - Boston, MA. ; , s. H2.4.1-H2.4.6
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Konferensbidrag (refereegranskat)abstract
- Feasibility of lo-hi-lo and delta-doped structures for evaluation of high-field silicon carbide material properties is investigated. Delta-doped structures are grown using the hot-wall CVD technique. Aluminum and nitrogen doping profiles are demonstrated with FWHM below 10 nm. Nitrogen doping transients are found to be slower than those for aluminum. The growth interrupt technique has been developed for achieving narrow nitrogen doping peaks. Lo-hi-lo structures were fabricated using the implantation-and-regrowth technique. Structures with confined avalanche multiplication are demonstrated using the lo-hi-lo and delta doping techniques. The effect of substrate imperfections on early avalanche breakdown is investigated using confined avalanche multiplication devices.
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| 47. |
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| 48. |
- Lake, BB, et al.
(författare)
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A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA
- 2017
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7:1, s. 6031-
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Tidskriftsartikel (refereegranskat)abstract
- Significant heterogeneities in gene expression among individual cells are typically interrogated using single whole cell approaches. However, tissues that have highly interconnected processes, such as in the brain, present unique challenges. Single-nucleus RNA sequencing (SNS) has emerged as an alternative method of assessing a cell’s transcriptome through the use of isolated nuclei. However, studies directly comparing expression data between nuclei and whole cells are lacking. Here, we have characterized nuclear and whole cell transcriptomes in mouse single neurons and provided a normalization strategy to reduce method-specific differences related to the length of genic regions. We confirmed a high concordance between nuclear and whole cell transcriptomes in the expression of cell type and metabolic modeling markers, but less so for a subset of genes associated with mitochondrial respiration. Therefore, our results indicate that single-nucleus transcriptome sequencing provides an effective means to profile cell type expression dynamics in previously inaccessible tissues.
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| 49. |
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| 50. |
- Linnarsson, M K, et al.
(författare)
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Diffusion of light elements in 4H-and 6H-SiC
- 1999
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Ingår i: Materials Science & Engineering. - 0921-5107 .- 1873-4944. ; 61-2, s. 275-280
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Tidskriftsartikel (refereegranskat)abstract
- Deuterium and lithium were introduced in p-type SiC by implantation of 20 keV H-2(+) or 30 keV Li-7(+) ions in order to form a diffusion source. The samples were subsequently annealed in vacuum in the temperature range 400-700 degrees C for 0.25 to 16 h. Secondary ion mass spectrometry (SIMS) was used to measure the deuterium and the lithium distribution after heat treatments. Both deuterium and lithium readily decorate the bombardment-induced defects in the vicinity of the ion implantation profile and they are also trapped, most likely by residual boron impurities, during diffusion into the bulk. An effective diffusion coefficient, reflecting the dissociation of trapped lithium, with an activation energy of 2.1 eV is extracted for lithium diffusion in p-type 6H SIG. Furthermore, a capture radius for trapping (most likely by boron) of deuterium is estimated as 10 Angstrom. (C) 1999 Elsevier Science S.A. All rights reserved.
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