| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- 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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| 3. |
- Leebens-Mack, James H., et al.
(författare)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Tidskriftsartikel (refereegranskat)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 4. |
- Chen, Hui, 1992, et al.
(författare)
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Doppler-Enabled Single-Antenna Localization and Mapping Without Synchronization
- 2022
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Ingår i: GLOBECOM - IEEE Global Telecommunications Conference. ; , s. 6469-6474
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Konferensbidrag (refereegranskat)abstract
- Radio localization is a key enabler for joint communication and sensing in the fifth/sixth generation (5G/6G) communication systems. With the help of multipath components (MPCs), localization and mapping tasks can be done with a single base station (BS) and single unsynchronized user equipment (UE) if both of them are equipped with an antenna array. However, the antenna array at the UE side increases the hardware and computational cost, preventing localization functionality. In this work, we show that with Doppler estimation and MPCs, localization and mapping tasks can be performed even with a singleantenna mobile UE. Furthermore, we show that the localization and mapping performance will improve and then saturate at a certain level with an increased UE speed. Both theoretical Cram´er-Rao bound analysis and simulation results show the potential of localization under mobility and the effectiveness of the proposed localization algorithm.
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| 5. |
- Ge, Yu, 1995, et al.
(författare)
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Experimental Validation of Single BS 5G mmWave Positioning and Mapping for Intelligent Transport
- 2024
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Ingår i: IEEE Transactions on Vehicular Technology. - 0018-9545 .- 1939-9359. ; In Press
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Tidskriftsartikel (refereegranskat)abstract
- Positioning with 5G signals generally requires connection to several base stations (BSs), which makes positioning more demanding in terms of infrastructure than communications. To address this issue, there have been several theoretical studies on single BS positioning, leveraging high-resolution angle and delay estimation and multipath exploitation possibilities at mmWave frequencies. This paper presents the first realistic experimental validation of such studies, involving a commercial 5G mmWave BS with a customized beam sweep procedure and a user equipment (UE) development kit mounted on a test vehicle. We present the relevant signal models, and signal processing methods, and validate these based on data collected in an outdoor science park environment. Our results indicate that positioning is possible, but the performance is limited by the knowledge of the position and orientation of the infrastructure and the multipath visibility and diversity
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| 6. |
- Bartoletti, Stefania, et al.
(författare)
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Introduction and fundamentals
- 2024
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Ingår i: Positioning and Location-based Analytics in 5G and Beyond. - 9781119911463 ; , s. 1-18
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- This chapter introduces the book and presents the main principles and fundamentals for positioning and location-based analytics, thus effectively providing the basis for the following chapters. After a brief introduction and motivation for the book, we present the main use cases, verticals, and applications for positioning and location-based analytics. Then, we provide the technical fundamentals for understanding positioning and navigation algorithms, as well as location-based analytics. An introduction to the architectural principles is presented. Finally, an outline of the book chapters is provided.
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| 7. |
- Bartoletti, Stefania, et al.
(författare)
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Positioning methods
- 2024
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Ingår i: Positioning and Location-based Analytics in 5G and Beyond. - 9781119911463 ; , s. 21-50
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- This chapter introduces the main positioning methods, starting from the state-of-the-art and following a statistical estimation perspective. This is followed by an in-depth treatment of radio positioning, first focusing on device-based positioning and then on device-free positioning. Finally, recent approaches based on artificial intelligence methods for positioning are detailed.
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| 8. |
- Chen, Hui, et al.
(författare)
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Doppler-Enabled Single-Antenna Localization and Mapping Without Synchronization
- 2022
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Ingår i: 2022 IEEE Global Communications Conference (GLOBECOM). - Piscataway : IEEE. - 9781665435406 ; , s. 6469-6474
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Konferensbidrag (refereegranskat)abstract
- Radio localization is a key enabler for joint communication and sensing in the fifth/sixth generation (SG/6G) communication systems. With the help of multipath components (MPCs), localization and mapping tasks can be done with a singlebase station (BS) and single unsynchronized user equipment (UE) if both of them are equipped with an antenna array. However, the antenna array at the UE side increases the hardware and computational cost, preventing localization functionality. In thiswork we show that with Doppler estimation and MPCs, localization and mapping tasks can be performed even with a single antenna mobile UE. Furthermore, we show that the localization and mapping performance will improve and then saturate ata certain level with an increased UE speed. Both theoretical Cramer-Rao bound analysis and simulation results show the potential of localization under mobility and the effectiveness of the proposed localization algorithm. © 2022 IEEE
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| 9. |
- Chen, Ling, et al.
(författare)
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Reliable and efficient RAR-based distributed model training in computing power network
- 2024
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Ingår i: Journal of Optical Communications and Networking. - 1943-0620 .- 1943-0639. ; 16:5, s. 527-540
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Tidskriftsartikel (refereegranskat)abstract
- The computing power network (CPN) is a novel network technology that integrates computing power from the cloud, edge, and terminals using IP/optical cross-layer networks for distributed computing. CPNs can provide an effective solution for distributed model training (DMT). As a bandwidth optimization architecture based on data parallelism, ring all-reduce (RAR) is widely used in DMT. However, any node or link failure on the ring can interrupt or block the requests deployed on the ring. Meanwhile, due to the resource competition of batch RAR-based DMT requests, inappropriate scheduling strategies will also lead to low training efficiency or congestion. As far as we know, there is currently no research that considers the survivability of rings in scheduling strategies for RAR-based DMT. To fill this gap, we propose a scheduling scheme for RAR-based DMT requests in CPNs to optimize the allocation of computing and wavelength resources considering the time dimension while ensuring reliability. In practical scenarios, service providers may focus on different performance metrics. We formulate an integer linear programming (ILP) model and a RAR-based DMT deployment algorithm (RDDA) to solve this problem considering four optimization objectives under the premise of the minimum blocking rate: minimum computing resource consumption, minimum wavelength resource consumption, minimum training time, and maximum reliability. Simulation results demonstrate that our model satisfies the reliability requirements while achieving corresponding optimal performance for DMT requests under four optimization objectives.
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| 10. |
- Cowgill, John, et al.
(författare)
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Structure and dynamics of differential ligand binding in the human ρ-type GABAA receptor
- 2023
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Ingår i: Neuron. - : Elsevier BV. - 0896-6273 .- 1097-4199. ; 111:21, s. 5-3450
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Tidskriftsartikel (refereegranskat)abstract
- The neurotransmitter γ-aminobutyric acid (GABA) drives critical inhibitory processes in and beyond the nervous system, partly via ionotropic type-A receptors (GABAARs). Pharmacological properties of ρ-type GABAARs are particularly distinctive, yet the structural basis for their specialization remains unclear. Here, we present cryo-EM structures of a lipid-embedded human ρ1 GABAAR, including a partial intracellular domain, under apo, inhibited, and desensitized conditions. An apparent resting state, determined first in the absence of modulators, was recapitulated with the specific inhibitor (1,2,5,6-tetrahydropyridin-4-yl)methylphosphinic acid and blocker picrotoxin and provided a rationale for bicuculline insensitivity. Comparative structures, mutant recordings, and molecular simulations with and without GABA further explained the sensitized but slower activation of ρ1 relative to canonical subtypes. Combining GABA with picrotoxin also captured an apparent uncoupled intermediate state. This work reveals structural mechanisms of gating and modulation with applications to ρ-specific pharmaceutical design and to our biophysical understanding of ligand-gated ion channels.
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