| 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. |
- Bousquet, J, et al.
(författare)
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Nrf2-interacting nutrients and COVID-19: time for research to develop adaptation strategies
- 2020
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Ingår i: Clinical and translational allergy. - : Wiley. - 2045-7022. ; 10:1, s. 58-
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Tidskriftsartikel (refereegranskat)abstract
- There are large between- and within-country variations in COVID-19 death rates. Some very low death rate settings such as Eastern Asia, Central Europe, the Balkans and Africa have a common feature of eating large quantities of fermented foods whose intake is associated with the activation of the Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) anti-oxidant transcription factor. There are many Nrf2-interacting nutrients (berberine, curcumin, epigallocatechin gallate, genistein, quercetin, resveratrol, sulforaphane) that all act similarly to reduce insulin resistance, endothelial damage, lung injury and cytokine storm. They also act on the same mechanisms (mTOR: Mammalian target of rapamycin, PPARγ:Peroxisome proliferator-activated receptor, NFκB: Nuclear factor kappa B, ERK: Extracellular signal-regulated kinases and eIF2α:Elongation initiation factor 2α). They may as a result be important in mitigating the severity of COVID-19, acting through the endoplasmic reticulum stress or ACE-Angiotensin-II-AT1R axis (AT1R) pathway. Many Nrf2-interacting nutrients are also interacting with TRPA1 and/or TRPV1. Interestingly, geographical areas with very low COVID-19 mortality are those with the lowest prevalence of obesity (Sub-Saharan Africa and Asia). It is tempting to propose that Nrf2-interacting foods and nutrients can re-balance insulin resistance and have a significant effect on COVID-19 severity. It is therefore possible that the intake of these foods may restore an optimal natural balance for the Nrf2 pathway and may be of interest in the mitigation of COVID-19 severity.
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| 3. |
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| 4. |
- Chumak, A. V., et al.
(författare)
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Advances in Magnetics Roadmap on Spin-Wave Computing
- 2022
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Ingår i: IEEE Transactions on Magnetics. - 0018-9464. ; 58:6
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Tidskriftsartikel (refereegranskat)abstract
- Magnonics addresses the physical properties of spin waves and utilizes them for data processing. Scalability down to atomic dimensions, operation in the GHz-to-THz frequency range, utilization of nonlinear and nonreciprocal phenomena, and compatibility with CMOS are just a few of many advantages offered by magnons. Although magnonics is still primarily positioned in the academic domain, the scientific and technological challenges of the field are being extensively investigated, and many proof-of-concept prototypes have already been realized in laboratories. This roadmap is a product of the collective work of many authors that covers versatile spin-wave computing approaches, conceptual building blocks, and underlying physical phenomena. In particular, the roadmap discusses the computation operations with Boolean digital data, unconventional approaches like neuromorphic computing, and the progress towards magnon-based quantum computing. The article is organized as a collection of sub-sections grouped into seven large thematic sections. Each sub-section is prepared by one or a group of authors and concludes with a brief description of current challenges and the outlook of further development for each research direction. Author
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| 5. |
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| 6. |
- Mlecnik, B, et al.
(författare)
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Clinical Performance of the Consensus Immunoscore in Colon Cancer in the Asian Population from the Multicenter International SITC Study
- 2022
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Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 14:18
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: In this study, we evaluated the prognostic value of Immunoscore in patients with stage I–III colon cancer (CC) in the Asian population. These patients were originally included in an international study led by the Society for Immunotherapy of Cancer (SITC) on 2681 patients with AJCC/UICC-TNM stages I–III CC. METHODS: CD3+ and cytotoxic CD8+ T-lymphocyte densities were quantified in the tumor and invasive margin by digital pathology. The association of Immunoscore with prognosis was evaluated for time to recurrence (TTR), disease-free survival (DFS), and overall survival (OS). RESULTS: Immunoscore stratified Asian patients (n = 423) into different risk categories and was not impacted by age. Recurrence-free rates at 3 years were 78.5%, 85.2%, and 98.3% for a Low, Intermediate, and High Immunoscore, respectively (HR[Low-vs-High] = 7.26 (95% CI 1.75−30.19); p = 0.0064). A High Immunoscore showed a significant association with prolonged TTR, OS, and DFS (p < 0.05). In Cox multivariable analysis stratified by center, Immunoscore association with TTR was independent (HR[Low-vs-Int+High] = 2.22 (95% CI 1.10–4.55) p = 0.0269) of the patient’s gender, T-stage, N-stage, sidedness, and MSI status. A significant association of a High Immunoscore with prolonged TTR was also found among MSS (HR[Low-vs-Int+High] = 4.58 (95% CI 2.27−9.23); p ≤ 0.0001), stage II (HR[Low-vs-Int+High] = 2.72 (95% CI 1.35−5.51); p = 0.0052), low-risk stage-II (HR[Low-vs-Int+High] = 2.62 (95% CI 1.21−5.68); p = 0.0146), and high-risk stage II patients (HR[Low-vs-Int+High] = 3.11 (95% CI 1.39−6.91); p = 0.0055). CONCLUSION: A High Immunoscore is significantly associated with the prolonged survival of CC patients within the Asian population.
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| 7. |
- Barthelmi, K., et al.
(författare)
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Atomistic defects as single-photon emitters in atomically thin MoS2
- 2020
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 117:7
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Tidskriftsartikel (refereegranskat)abstract
- Precisely positioned and scalable single-photon emitters (SPEs) are highly desirable for applications in quantum technology. This Perspective discusses single-photon-emitting atomistic defects in monolayers of MoS2 that can be generated by focused He-ion irradiation with few nanometers positioning accuracy. We present the optical properties of the emitters and the possibilities to implement them into photonic and optoelectronic devices. We showcase the advantages of the presented emitters with respect to atomistic positioning, scalability, long (microsecond) lifetime, and a homogeneous emission energy within ensembles of the emitters. Moreover, we demonstrate that the emitters are stable in energy on a timescale exceeding several weeks and that temperature cycling narrows the ensembles' emission energy distribution.
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| 8. |
- Rosati, Roberto, 1984, et al.
(författare)
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Temporal Evolution of Low-Temperature Phonon Sidebands in Transition Metal Dichalcogenides
- 2020
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Ingår i: ACS Photonics. - : American Chemical Society (ACS). - 2330-4022. ; 7:10, s. 2756-2764
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Tidskriftsartikel (refereegranskat)abstract
- Low-temperature photoluminescence (PL) of hBN-encapsulated monolayer tungsten diselenide (WSe2) shows a multitude of sharp emission peaks below the bright exciton. Some of them have been recently identified as phonon sidebands of momentum-dark states. However, the exciton dynamics behind the emergence of these sidebands has not been revealed yet. In this joint theory-experiment study, we theoretically predict and experimentally observe time-resolved PL, providing microscopic insights into the thermalization of hot excitons formed after optical excitation. In very good agreement between theory and experiment, we demonstrate a spectral red-shift of phonon sidebands on a time scale of tens of picoseconds, reflecting the phonon-driven thermalization of hot excitons in momentum-dark states. Furthermore, we predict the emergence of a transient phonon sideband that vanishes in the stationary PL. The obtained microscopic insights are applicable to a broad class of 2D materials with multiple exciton valleys.
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| 9. |
- Binggeli, Christian, et al.
(författare)
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A puzzling non-detection of [O III] and [C II] from a z ≈ 7.7 galaxy observed with ALMA
- 2021
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 646
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Tidskriftsartikel (refereegranskat)abstract
- Context. Characterizing the galaxy population in the early Universe holds the key to understanding the evolution of these objects and the role they played in cosmic reionization. However, there have been very few observations at the very highest redshifts to date. Aims. In order to shed light on the properties of galaxies in the high-redshift Universe and their interstellar media, we observe the Lyman-α emitting galaxy z7_GSD_3811 at z = 7.664 with bands 6 and 8 at the Atacama Large Millimeter/submillimeter Array (ALMA). Methods. We target the far-infrared [O iii] 88 µm and [C ii] 158 µm emission lines and dust continuum in the star-forming galaxy z7_GSD_3811 with ALMA. We combine these measurements with earlier observations in the rest-frame ultraviolet (UV) in order to characterize the object and compare the results to those of earlier studies that observed [O iii] and [C ii] emission in high-redshift galaxies. Results. The [O iii] 88 µm and [C ii] 158 µm emission lines are undetected at the position of z7_GSD_3811, with 3σ upper limits of 1.6 × 108 L and 4.0 × 107 L, respectively. We do not detect any dust continuum in band 6 nor band 8. The measured rms in the band 8 and band 6 continua are 26 and 9.9 µJy beam−1, respectively. Similar to several other high-redshift galaxies, z7_GSD_3811 exhibits low [C ii] emission for its star formation rate compared to local galaxies. Furthermore, our upper limit on the [O iii] line luminosity is lower than the previously observed [O iii] lines in high-redshift galaxies with similar UV luminosities. Our ALMA band 6 and 8 dust continuum observations imply that z7_GSD_3811 likely has a low dust content, and our non-detections of the [O iii] and [C ii] lines could indicate that z7_GSD_3811 has a low metallicity (Z. 0.1 Z).
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| 10. |
- Jones, Alfred J. H., et al.
(författare)
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Visualizing band structure hybridization and superlattice effects in twisted MoS2/WS2 heterobilayers
- 2022
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Ingår i: Current Opinion in Chemical Engineering. - : IOP Publishing Ltd. - 2211-3398. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- A mismatch of atomic registries between single-layer transition metal dichalcogenides (TMDs) in a two-dimensional (2D) van der Waals heterostructure produces a moire superlattice with a periodic potential, which can be fine-tuned by introducing a twist angle between the materials. This approach is promising both for controlling the interactions between the TMDs and for engineering their electronic band structures, yet direct observation of the changes to the electronic structure introduced with varying twist angle has so far been missing. Here, we probe heterobilayers comprised of single-layer MoS2 and WS2 with twist angles ranging from 2 degrees to 20 degrees and determine the twist angle-dependent evolution of the electronic band structure using micro-focused angle-resolved photoemission spectroscopy. We find strong interlayer hybridization between MoS2 and WS2 electronic states at the (Gamma) over bar -point of the Brillouin zone, leading to a shift of the valence band maximum in the heterostructure. Replicas of the hybridized states are observed at the center of twist angle-dependent moire mini Brillouin zones. We confirm that these replica features arise from the inherent moire potential by comparing our experimental observations with density functional theory calculations of the superlattice dispersion. Our direct visualization of these features underscores the potential of using twisted heterobilayer semiconductors to engineer hybrid electronic states and superlattices that alter the electronic and optical properties of 2D heterostructures for a wide range of twist angles.
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| 11. |
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| 12. |
- Pasquale, Gabriele, et al.
(författare)
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Flat-Band-Induced Many-Body Interactions and Exciton Complexes in a Layered Semiconductor
- 2022
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 22:22, s. 8883-8891
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Tidskriftsartikel (refereegranskat)abstract
- Interactions among a collection of particles generate many-body effects in solids that result in striking modifications of material properties. The heavy carrier mass that yields strong interactions and gate control of carrier density over a wide range makes two-dimensional semiconductors an exciting playground to explore many-body physics. The family of III-VI metal monochalcogenides emerges as a new platform for this purpose because of its excellent optical properties and the flat valence band dispersion. In this work, we present a complete study of charge-tunable excitons in few-layer InSe by photoluminescence spectroscopy. From the optical spectra, we establish that free excitons in InSe are more likely to be captured by ionized donors leading to the formation of bound exciton complexes. Surprisingly, a pronounced red shift of the exciton energy accompanied by a decrease of the exciton binding energy upon hole-doping reveals a significant band gap renormalization induced by the presence of the Fermi reservoir.
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| 13. |
- Tagarelli, Fedele, et al.
(författare)
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Electrical control of hybrid exciton transport in a van der Waals heterostructure
- 2023
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Ingår i: Nature Photonics. - 1749-4885 .- 1749-4893. ; 17:7, s. 615-621
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Tidskriftsartikel (refereegranskat)abstract
- Interactions between out-of-plane dipoles in bosonic gases enable the long-range propagation of excitons. The lack of direct control over collective dipolar properties has so far limited the degrees of tunability and the microscopic understanding of exciton transport. In this work we modulate the layer hybridization and interplay between many-body interactions of excitons in a van der Waals heterostructure with an applied vertical electric field. By performing spatiotemporally resolved measurements supported by microscopic theory, we uncover the dipole-dependent properties and transport of excitons with different degrees of hybridization. Moreover, we find constant emission quantum yields of the transporting species as a function of excitation power with radiative decay mechanisms dominating over nonradiative ones, a fundamental requirement for efficient excitonic devices. Our findings provide a complete picture of the many-body effects in the transport of dilute exciton gases, and have crucial implications for studying emerging states of matter such as Bose–Einstein condensation and optoelectronic applications based on exciton propagation.
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| 14. |
- Taniguchi, Kotomi, et al.
(författare)
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Digging into the Interior of Hot Cores with the ALMA (DIHCA). III. The Chemical Link between NH 2 CHO, HNCO, and H 2 CO
- 2023
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Ingår i: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 950:1
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Tidskriftsartikel (refereegranskat)abstract
- We have analyzed the NH2CHO, HNCO, H2CO, and CH3CN (13CH3CN) molecular lines at an angular resolution of ∼0.″3 obtained by the Atacama Large Millimeter/submillimeter Array Band 6 toward 30 high-mass star-forming regions. The NH2CHO emission has been detected in 23 regions, while the other species have been detected toward 29 regions. A total of 44 hot molecular cores (HMCs) have been identified using the moment 0 maps of the CH3CN line. The fractional abundances of the four species have been derived at each HMC. In order to investigate pure chemical relationships, we have conducted a partial correlation test to exclude the effect of temperature. Strong positive correlations between NH2CHO and HNCO (ρ = 0.89) and between NH2CHO and H2CO (0.84) have been found. These strong correlations indicate their direct chemical links; dual-cyclic hydrogen addition and abstraction reactions between HNCO and NH2CHO and gas-phase formation of NH2CHO from H2CO. Chemical models including these reactions can reproduce the observed abundances in our target sources.
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| 15. |
- Viti, Leonardo, et al.
(författare)
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Thermoelectric graphene photodetectors with sub-nanosecond response times at terahertz frequencies
- 2020
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Ingår i: Nanophotonics. - : Walter de Gruyter GmbH. - 2192-8614 .- 2192-8606. ; 10:1, s. 89-98
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Tidskriftsartikel (refereegranskat)abstract
- Ultrafast and sensitive (noise equivalent power <1 nW Hz-1/2) light-detection in the terahertz (THz) frequency range (0.1-10 THz) and at room-temperature is key for applications such as time-resolved THz spectroscopy of gases, complex molecules and cold samples, imaging, metrology, ultra-high-speed data communications, coherent control of quantum systems, quantum optics and for capturing snapshots of ultrafast dynamics, in materials and devices, at the nanoscale. Here, we report room-temperature THz nano-receivers exploiting antenna-coupled graphene field effect transistors integrated with lithographically-patterned high-bandwidth (∼100 GHz) chips, operating with a combination of high speed (hundreds ps response time) and high sensitivity (noise equivalent power ≤120 pW Hz-1/2) at 3.4 THz. Remarkably, this is achieved with various antenna and transistor architectures (single-gate, dual-gate), whose operation frequency can be extended over the whole 0.1-10 THz range, thus paving the way for the design of ultrafast graphene arrays in the far infrared, opening concrete perspective for targeting the aforementioned applications.
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| 16. |
- Viti, Leonardo, et al.
(författare)
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Thermoelectric graphene photodetectors with sub-nanosecond response times at terahertz frequencies
- 2021
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Ingår i: Frontiers in Optics and Photonics. - : De Gruyter. ; , s. 89-98
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Ultrafast and sensitive (noise equivalent power <1 nW Hz-1/2) light-detection in the terahertz (THz) frequency range (0.1-10 THz) and at room-temperature is key for applications such as time-resolved THz spectroscopy of gases, complex molecules and cold samples, imaging, metrology, ultra-high-speed data communications, coherent control of quantum systems, quantum optics and for capturing snapshots of ultrafast dynamics, in materials and devices, at the nanoscale. Here, we report room-temperature THz nano-receivers exploiting antenna-coupled graphene field effect transistors integrated with lithographically-patterned high-bandwidth (-100 GHz) chips, operating with a combination of high speed (hundreds ps response time) and high sensitivity (noise equivalent power <120 pW Hz-1/2) at 3.4 THz. Remarkably, this is achieved with various antenna and transistor architectures (single-gate, dual-gate), whose operation frequency can be extended over the whole 0.1-10 THz range, thus paving the way for the design of ultrafast graphene arrays in the far infrared, opening concrete perspective for targeting the aforementioned applications.
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