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- 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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| 6. |
- Thomas, HS, et al.
(författare)
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- 2019
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swepub:Mat__t
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- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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- Tabiri, S, et al.
(författare)
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- 2021
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swepub:Mat__t
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- 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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| 15. |
- da Silva Schneider, André, et al.
(författare)
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A Parameterized Neutrino Emission Model to Study Mass Ejection in Failed Core-collapse Supernovae
- 2023
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 942:1
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Tidskriftsartikel (refereegranskat)abstract
- Some massive stars end their lives as failed core-collapse supernovae (CCSNe) and become black holes (BHs). Although in this class of phenomena the stalled supernova (SN) shock is not revived, the outer stellar envelope can still be partially ejected. This occurs because the hydrodynamic equilibrium of the star is disrupted by the gravitational mass loss of the protoneutron star (PNS) due to neutrino emission. We develop a simple parameterized model that emulates PNS evolution and its neutrino emission and use it to simulate failed CCSNe in spherical symmetry for a wide range of progenitor stars. Our model allows us to study mass ejection of failed CCSNe where the PNS collapses into a BH within ∼100 ms and up to ∼106 s. We perform failed CCSNe simulations for 262 different pre-SN progenitors and determine how the energy and mass of the ejecta depend on progenitor properties and the equation of state (EOS) of dense matter. In the case of a future failed CCSN observation, the trends obtained in our simulations can be used to place constraints on the pre-SN progenitor characteristics, the EOS, and on PNS properties at BH formation time.
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| 16. |
- da Silva Schneider, André, et al.
(författare)
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Equation of State and Progenitor Dependence of Stellar-mass Black Hole Formation
- 2020
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 894:1
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Tidskriftsartikel (refereegranskat)abstract
- The core collapse of a massive star results in the formation of a proto-neutron star (PNS). If enough material is accreted onto a PNS, it will become gravitationally unstable and further collapse into a black hole (BH). We perform a systematic study of failing core-collapse supernovae in spherical symmetry for a wide range of pre-supernova progenitor stars and equations of state (EOSs) of nuclear matter. We analyze how variations in progenitor structure and the EOS of dense matter above nuclear saturation density affect the PNS evolution and subsequent BH formation. Comparisons of core collapse for a given progenitor star and different EOSs show that the path traced by the PNS in mass-specific entropy phase space M-grav(PNS) - (s) over bar is well correlated with the progenitor compactness and is almost EOS independent, apart from the final end point. Furthermore, BH formation occurs, to a very good approximation, soon after the PNS overcomes the maximum gravitational mass supported by a hot NS with constant specific entropy equal to (s) over bar. These results show a path to constraining the temperature dependence of the EOS through the detection of neutrinos from a failed galactic supernova.
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| 18. |
- Eggenberger Andersen, Oliver, et al.
(författare)
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Equation-of-state Dependence of Gravitational Waves in Core-collapse Supernovae
- 2021
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 923:2
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Tidskriftsartikel (refereegranskat)abstract
- Gravitational waves (GWs) provide unobscured insight into the birthplace of neutron stars and black holes in core-collapse supernovae (CCSNe). The nuclear equation of state (EOS) describing these dense environments is yet uncertain, and variations in its prescription affect the proto−neutron star (PNS) and the post-bounce dynamics in CCSN simulations, subsequently impacting the GW emission. We perform axisymmetric simulations of CCSNe with Skyrme-type EOSs to study how the GW signal and PNS convection zone are impacted by two experimentally accessible EOS parameters, (1) the effective mass of nucleons, m⋆, which is crucial in setting the thermal dependence of the EOS, and (2) the isoscalar incompressibility modulus, Ksat. While Ksat shows little impact, the peak frequency of the GWs has a strong effective mass dependence due to faster contraction of the PNS for higher values of m⋆ owing to a decreased thermal pressure. These more compact PNSs also exhibit more neutrino heating, which drives earlier explosions and correlates with the GW amplitude via accretion plumes striking the PNS, exciting the oscillations. We investigate the spatial origin of the GWs and show the agreement between a frequency-radial distribution of the GW emission and a perturbation analysis. We do not rule out overshoot from below via PNS convection as another moderately strong excitation mechanism in our simulations. We also study the combined effect of effective mass and rotation. In all our simulations we find evidence for a power gap near ∼1250 Hz; we investigate its origin and report its EOS dependence.
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| 20. |
- Hunter, KE, et al.
(författare)
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Transforming Obesity Prevention for CHILDren (TOPCHILD) Collaboration: protocol for a systematic review with individual participant data meta-analysis of behavioural interventions for the prevention of early childhood obesity
- 2022
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Ingår i: BMJ open. - : BMJ. - 2044-6055. ; 12:1, s. e048166-
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Tidskriftsartikel (refereegranskat)abstract
- Behavioural interventions in early life appear to show some effect in reducing childhood overweight and obesity. However, uncertainty remains regarding their overall effectiveness, and whether effectiveness differs among key subgroups. These evidence gaps have prompted an increase in very early childhood obesity prevention trials worldwide. Combining the individual participant data (IPD) from these trials will enhance statistical power to determine overall effectiveness and enable examination of individual and trial-level subgroups. We present a protocol for a systematic review with IPD meta-analysis to evaluate the effectiveness of obesity prevention interventions commencing antenatally or in the first year after birth, and to explore whether there are differential effects among key subgroups.Methods and analysisSystematic searches of Medline, Embase, Cochrane Central Register of Controlled Trials, Cumulative Index to Nursing and Allied Health Literature (CINAHL), PsycInfo and trial registries for all ongoing and completed randomised controlled trials evaluating behavioural interventions for the prevention of early childhood obesity have been completed up to March 2021 and will be updated annually to include additional trials. Eligible trialists will be asked to share their IPD; if unavailable, aggregate data will be used where possible. An IPD meta-analysis and a nested prospective meta-analysis will be performed using methodologies recommended by the Cochrane Collaboration. The primary outcome will be body mass index z-score at age 24±6 months using WHO Growth Standards, and effect differences will be explored among prespecified individual and trial-level subgroups. Secondary outcomes include other child weight-related measures, infant feeding, dietary intake, physical activity, sedentary behaviours, sleep, parenting measures and adverse events.Ethics and disseminationApproved by The University of Sydney Human Research Ethics Committee (2020/273) and Flinders University Social and Behavioural Research Ethics Committee (HREC CIA2133-1). Results will be relevant to clinicians, child health services, researchers, policy-makers and families, and will be disseminated via publications, presentations and media releases.PROSPERO registration numberCRD42020177408.
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| 21. |
- Johnson, BJ, et al.
(författare)
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Unpacking the behavioural components and delivery features of early childhood obesity prevention interventions in the TOPCHILD Collaboration: a systematic review and intervention coding protocol
- 2022
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Ingår i: BMJ open. - : BMJ. - 2044-6055. ; 12:1, s. e048165-
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Tidskriftsartikel (refereegranskat)abstract
- Little is known about how early (eg, commencing antenatally or in the first 12 months after birth) obesity prevention interventions seek to change behaviour and which components are or are not effective. This study aims to (1) characterise early obesity prevention interventions in terms of target behaviours, delivery features and behaviour change techniques (BCTs), (2) explore similarities and differences in BCTs used to target behaviours and (3) explore effectiveness of intervention components in preventing childhood obesity.Methods and analysisAnnual comprehensive systematic searches will be performed in Epub Ahead of Print/MEDLINE, Embase, Cochrane (CENTRAL), CINAHL, PsycINFO, as well as clinical trial registries. Eligible randomised controlled trials of behavioural interventions to prevent childhood obesity commencing antenatally or in the first year after birth will be invited to join the Transforming Obesity in CHILDren Collaboration. Standard ontologies will be used to code target behaviours, delivery features and BCTs in both published and unpublished intervention materials provided by trialists. Narrative syntheses will be performed to summarise intervention components and compare applied BCTs by types of target behaviours. Exploratory analyses will be undertaken to assess effectiveness of intervention components.Ethics and disseminationThe study has been approved by The University of Sydney Human Research Ethics Committee (project no. 2020/273) and Flinders University Social and Behavioural Research Ethics Committee (project no. HREC CIA2133-1). The study’s findings will be disseminated through peer-reviewed publications, conference presentations and targeted communication with key stakeholders.PROSPERO registration numberCRD42020177408.
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| 23. |
- Shrine, N, et al.
(författare)
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Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk
- 2023
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Ingår i: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 55:3, s. 410-
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Tidskriftsartikel (refereegranskat)abstract
- Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by ≥2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies for selected associated variants as well as trait and pathway-specific genetic risk scores to infer possible consequences of intervening in pathways underlying lung function. We highlight new putative causal variants, genes, proteins and pathways, including those targeted by existing drugs. These findings bring us closer to understanding the mechanisms underlying lung function and COPD, and should inform functional genomics experiments and potentially future COPD therapies.
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| 24. |
- Zha, Shuai, et al.
(författare)
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Progenitor Dependence of Hadron-quark Phase Transition in Failing Core-collapse Supernovae
- 2021
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 911:2
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Tidskriftsartikel (refereegranskat)abstract
- We study the consequences of a hadron-quark phase transition (PT) in failing core-collapse supernovae (CCSNe) that give birth to stellar-mass black holes (BH). We perform a suite of neutrino-transport general-relativistic hydrodynamic simulations in spherical symmetry with 21 progenitor models and a hybrid equation of state (EoS) including hadrons and quarks. We find that the effect of the PT on the CCSN postbounce dynamics is a function of the bounce compactness parameter xi(2.2). For xi(2.2) greater than or similar to 0.24, the PT leads to a second dynamical collapse of the protocompact star (PCS). While BH formation starts immediately after this second collapse for models with xi(2.2) greater than or similar to 0.51, the PCS experiences a second bounce and oscillations for models with 0.24 less than or similar to x xi(2.2) less than or similar to 0.51. These models emit potent oscillatory neutrino signals with a period of similar to 1 ms for tens of milliseconds after the second bounce, which can be a strong indicator of the PT in failing CCSNe if detected in the future. However, no shock revival occurs and BH formation inevitably takes place in our spherically symmetric simulations. Furthermore, via a diagram of mass-specific entropy evolution of the PCS, the progenitor dependence can be understood through the appearance of a third family of compact stars emerging at large entropy induced by the PT.
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