| 1. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
- Agirre, Jon, et al.
(författare)
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The CCP4 suite: integrative software for macromolecular crystallography
- 2023
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Ingår i: Acta Crystallographica Section D. - : INT UNION CRYSTALLOGRAPHY. - 2059-7983. ; 79, s. 449-461
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Tidskriftsartikel (refereegranskat)abstract
- The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
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| 4. |
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| 5. |
- Arun, K. G., et al.
(författare)
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New horizons for fundamental physics with LISA
- 2022
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Ingår i: Living Reviews in Relativity. - : Springer Science and Business Media LLC. - 1433-8351 .- 2367-3613. ; 25:1
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Forskningsöversikt (refereegranskat)abstract
- The Laser Interferometer Space Antenna (LISA) has the potential to reveal wonders about the fundamental theory of nature at play in the extreme gravity regime, where the gravitational interaction is both strong and dynamical. In this white paper, the Fundamental Physics Working Group of the LISA Consortium summarizes the current topics in fundamental physics where LISA observations of gravitational waves can be expected to provide key input. We provide the briefest of reviews to then delineate avenues for future research directions and to discuss connections between this working group, other working groups and the consortium work package teams. These connections must be developed for LISA to live up to its science potential in these areas.
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| 6. |
- Chen, Hongjie, et al.
(författare)
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Large-scale cross-cancer fine-mapping of the 5p15.33 region reveals multiple independent signals
- 2021
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Ingår i: Human Genetics and Genomics Advances. - : Cell Press. - 2666-2477. ; 2:3
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWASs) have identified thousands of cancer risk loci revealing many risk regions shared across multiple cancers. Characterizing the cross-cancer shared genetic basis can increase our understanding of global mechanisms of cancer development. In this study, we collected GWAS summary statistics based on up to 375,468 cancer cases and 530,521 controls for fourteen types of cancer, including breast (overall, estrogen receptor [ER]-positive, and ER-negative), colorectal, endometrial, esophageal, glioma, head/neck, lung, melanoma, ovarian, pancreatic, prostate, and renal cancer, to characterize the shared genetic basis of cancer risk. We identified thirteen pairs of cancers with statistically significant local genetic correlations across eight distinct genomic regions. Specifically, the 5p15.33 region, harboring the TERT and CLPTM1L genes, showed statistically significant local genetic correlations for multiple cancer pairs. We conducted a cross-cancer fine-mapping of the 5p15.33 region based on eight cancers that showed genome-wide significant associations in this region (ER-negative breast, colorectal, glioma, lung, melanoma, ovarian, pancreatic, and prostate cancer). We used an iterative analysis pipeline implementing a subset-based meta-analysis approach based on cancer-specific conditional analyses and identified ten independent cross-cancer associations within this region. For each signal, we conducted cross-cancer fine-mapping to prioritize the most plausible causal variants. Our findings provide a more in-depth understanding of the shared inherited basis across human cancers and expand our knowledge of the 5p15.33 region in carcinogenesis.
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| 7. |
- Chen, Zhishan, et al.
(författare)
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Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
- 2024
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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| 8. |
- Fernandez-Rozadilla, Ceres, et al.
(författare)
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Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries
- 2023
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 55, s. 89-99
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Tidskriftsartikel (refereegranskat)abstract
- Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.
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| 9. |
- Figtree, Gemma A., et al.
(författare)
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Clinical Pathway for Coronary Atherosclerosis in Patients Without Conventional Modifiable Risk Factors JACC State-of-the-Art Review
- 2023
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Ingår i: Journal of the American College of Cardiology. - : ELSEVIER SCIENCE INC. - 0735-1097 .- 1558-3597. ; 82:13, s. 1343-1359
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Forskningsöversikt (refereegranskat)abstract
- Reducing the incidence and prevalence of standard modifiable cardiovascular risk factors (SMuRFs) is critical to tackling the global burden of coronary artery disease (CAD). However, a substantial number of individuals develop coronary atherosclerosis despite no SMuRFs. SMuRFless patients presenting with myocardial infarction have been observed to have an unexpected higher early mortality compared to their counterparts with at least 1 SMuRF. Evidence for optimal management of these patients is lacking. We assembled an international, multidisciplinary team to develop an evidence-based clinical pathway for SMuRFless CAD patients. A modified Delphi method was applied. The resulting pathway confirms underlying atherosclerosis and true SMuRFless status, ensures evidence-based secondary prevention, and considers additional tests and interventions for less typical contributors. This dedicated pathway for a previously overlooked CAD population, with an accompanying registry, aims to improve outcomes through enhanced adherence to evidence-based secondary prevention and additional diagnosis of modifiable risk factors observed. (c) 2023 The Authors. Published by Elsevier on behalf of the American College of Cardiology Foundation. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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| 10. |
- Lindström, Sara, et al.
(författare)
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Genome-wide analyses characterize shared heritability among cancers and identify novel cancer susceptibility regions
- 2023
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press. - 0027-8874 .- 1460-2105. ; 115:6, s. 712-732
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The shared inherited genetic contribution to risk of different cancers is not fully known. In this study, we leverage results from 12 cancer genome-wide association studies (GWAS) to quantify pairwise genome-wide genetic correlations across cancers and identify novel cancer susceptibility loci.METHODS: We collected GWAS summary statistics for 12 solid cancers based on 376 759 participants with cancer and 532 864 participants without cancer of European ancestry. The included cancer types were breast, colorectal, endometrial, esophageal, glioma, head and neck, lung, melanoma, ovarian, pancreatic, prostate, and renal cancers. We conducted cross-cancer GWAS and transcriptome-wide association studies to discover novel cancer susceptibility loci. Finally, we assessed the extent of variant-specific pleiotropy among cancers at known and newly identified cancer susceptibility loci.RESULTS: We observed widespread but modest genome-wide genetic correlations across cancers. In cross-cancer GWAS and transcriptome-wide association studies, we identified 15 novel cancer susceptibility loci. Additionally, we identified multiple variants at 77 distinct loci with strong evidence of being associated with at least 2 cancer types by testing for pleiotropy at known cancer susceptibility loci.CONCLUSIONS: Overall, these results suggest that some genetic risk variants are shared among cancers, though much of cancer heritability is cancer-specific and thus tissue-specific. The increase in statistical power associated with larger sample sizes in cross-disease analysis allows for the identification of novel susceptibility regions. Future studies incorporating data on multiple cancer types are likely to identify additional regions associated with the risk of multiple cancer types.
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| 11. |
- McAlpine, Stuart, et al.
(författare)
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SIBELIUS-DARK : a galaxy catalogue of the local volume from a constrained realization simulation
- 2022
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 512:4, s. 5823-5847
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Tidskriftsartikel (refereegranskat)abstract
- We present SIBELIUS-DARK, a constrained realization simulation of the local volume to a distance of 200 Mpc from the Milky Way. SIBELIUS-DARK is the first study of the ‘Simulations Beyond The Local Universe’ (SIBELIUS) project, which has the goal of embedding a model Local Group-like system within the correct cosmic environment. The simulation is dark-matter-only, with the galaxy population calculated using the semi-analytic model of galaxy formation, GALFORM. We demonstrate that the large-scale structure that emerges from the SIBELIUS constrained initial conditions matches well the observational data. The inferred galaxy population of SIBELIUS-DARK also match well the observational data, both statistically for the whole volume and on an object-by-object basis for the most massive clusters. For example, the K-band number counts across the whole sky, and when divided between the northern and southern Galactic hemispheres, are well reproduced by SIBELIUS-DARK. We find that the local volume is somewhat unusual in the wider context of ΛCDM: it contains an abnormally high number of supermassive clusters, as well as an overall large-scale underdensity at the level of ≈5 per cent relative to the cosmic mean. However, whilst rare, the extent of these peculiarities does not significantly challenge the ΛCDM model. SIBELIUS-DARK is the most comprehensive constrained realization simulation of the local volume to date, and with this paper we publicly release the halo and galaxy catalogues at z = 0, which we hope will be useful to the wider astronomy community.
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| 12. |
- Sawala, Till, et al.
(författare)
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Setting the stage : structures from Gaussian random fields
- 2021
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 501:4, s. 4759-4776
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Tidskriftsartikel (refereegranskat)abstract
- We study structure formation in a set of cosmological simulations to uncover the scales in the initial density field that gave rise to the formation of present-day structures. Our simulations share a common primordial power spectrum (here Lambda cold dark matter, Lambda CDM), but the introduction of hierarchical variations of the phase information allows us to systematically study the scales that determine the formation of structure at later times. We consider the variance in z = 0 statistics such as the matter power spectrum and halo mass function. We also define a criterion for the existence of individual haloes across simulations, and determine what scales in the initial density field contain sufficient information for the non-linear formation of unique haloes. We study how the characteristics of individual haloes such as the mass and concentration, as well as the position and velocity, are affected by variations on different scales, and give scaling relations for haloes of different mass. Finally, we use the example of a cluster-mass halo to show how our hierarchical parametrization of the initial density field can be used to create variants of particular objects. With properties such as mass, concentration, kinematics, and substructure of haloes set on distinct and well-determined scales, and its unique ability to introduce variations localized in real space, our method is a powerful tool to study structure formation in cosmological simulations.
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| 13. |
- Sawala, Till, et al.
(författare)
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The Milky Way’s plane of satellites is consistent with ΛCDM
- 2023
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Ingår i: Nature Astronomy. - : Springer Science and Business Media LLC. - 2397-3366. ; 7:4, s. 481-491
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Tidskriftsartikel (refereegranskat)abstract
- The Milky Way is surrounded by 11 ‘classical’ satellite galaxies in a remarkable configuration: a thin plane that is possibly rotationally supported. Such a structure is thought to be highly unlikely to arise in the standard (ΛCDM) cosmological model (Λ cold dark matter model, where Λ is the cosmological constant). While other apparent discrepancies between predictions and observations of Milky Way satellite galaxies may be explained either through baryonic effects or by invoking alternative forms of dark matter particles, there is no known mechanism for making rotating satellite planes within the dispersion-supported dark matter haloes predicted to surround galaxies such as the Milky Way. This is the so-called ‘plane of satellites problem’, which challenges not only the ΛCDM model but the entire concept of dark matter. Here we show that the reportedly exceptional anisotropy of the Milky Way satellites is explained, in large part, by their lopsided radial distribution combined with the temporary conjunction of the two most distant satellites, Leo I and Leo II. Using Gaia proper motions, we show that the orbital pole alignment is much more common than previously reported, and reveal the plane of satellites to be transient rather than rotationally supported. Comparing with new simulations, where such short-lived planes are common, we find the Milky Way satellites to be compatible with standard model expectations.
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| 14. |
- Sawala, Till, et al.
(författare)
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The SIBELIUS Project : E Pluribus Unum
- 2022
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 509:1, s. 1432-1446
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Tidskriftsartikel (refereegranskat)abstract
- We introduce 'Simulations Beyond The Local Universe' (SIBELIUS) that connect the Local Group (LG) to its cosmic environment. We show that introducing hierarchical small-scale perturbations to a density field constrained on large scales by observations provides an efficient way to explore the sample space of LG analogues. From more than 60 000 simulations, we identify a hierarchy of LG characteristics emanating from different scales: the total mass, orientation, orbital energy, and the angular momentum are largely determined by modes above lambda = 1.6 comoving Mpc (cMpc) in the primordial density field. Smaller scale variations are mostly manifest as perturbations to the MW-M31 orbit, and we find that the observables commonly used to describe the LG - the MW M31 separation and radial velocity - are transient and depend on specifying scales down to 0.2 cMpc in the primordial density field. We further find that the presence of M33/LMC analogues significantly affects the MW-M31 orbit and its sensitivity to small-scale perturbations. We construct initial conditions that lead to the formation of an LG whose primary observables precisely match the current observations.
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| 15. |
- Zhang, Wei, et al.
(författare)
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Observation of the proton emitter 11657La59
- 2022
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Ingår i: Communications Physics. - : Springer Science and Business Media LLC. - 2399-3650. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- The quantum tunneling and emission of a single constituent nucleon provide a beautifully simple and unique window into the complex properties of atomic nuclei at the extreme edge of nuclear existence. In particular, for odd-odd proton emitting nuclides, the associated decay energy and partial half-life can be used to probe the correlations between the valence neutrons and protons which have been theoretically predicted to favour a new type of nuclear superfluidity, isoscalar neutron-proton pairing, for which the experimental “smoking gun" remains elusive. In the present work, proton emission from the lanthanum isotope 1165757116La59, 23 neutrons away from the only stable isotope 1395757139La82, is reported. 116La nuclei were synthesised in the fusion-evaporation reaction 58Ni(64Zn, p5n)116La and identified via their proton radioactivity using the mass spectrometer MARA (Mass Analysing Recoil Apparatus) and the silicon detectors placed at its focal plane. Comparisons of the measured proton energy (Ep = 718 ± 9 keV) and half-life (T1/2 = 50 ± 22 ms) with values calculated using the Universal Decay Law approach indicate that the proton is emitted with an orbital angular momentum l = 2 and that its emission probability is enhanced relative to its closest, less exotic, odd-even lanthanum isotope (1175757117La60) while the proton-emission Q-value is lower. We propose this to be a possible signature for the presence of strong neutron-proton pair correlations in this exotic, neutron deficient system. The observations of γ decays from isomeric states in 116La and 117La are also reported.
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| 16. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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