| 1. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)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. |
- Ntalla, Ioanna, et al.
(author)
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Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction
- 2020
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Journal article (peer-reviewed)abstract
- The electrocardiographic PR interval reflects atrioventricular conduction, and is associated with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and cardiovascular mortality. Here we report a multi-ancestry (N=293,051) genome-wide association meta-analysis for the PR interval, discovering 202 loci of which 141 have not previously been reported. Variants at identified loci increase the percentage of heritability explained, from 33.5% to 62.6%. We observe enrichment for cardiac muscle developmental/contractile and cytoskeletal genes, highlighting key regulation processes for atrioventricular conduction. Additionally, 8 loci not previously reported harbor genes underlying inherited arrhythmic syndromes and/or cardiomyopathies suggesting a role for these genes in cardiovascular pathology in the general population. We show that polygenic predisposition to PR interval duration is an endophenotype for cardiovascular disease, including distal conduction disease, AF, and atrioventricular pre-excitation. These findings advance our understanding of the polygenic basis of cardiac conduction, and the genetic relationship between PR interval duration and cardiovascular disease. On the electrocardiogram, the PR interval reflects conduction from the atria to ventricles and also serves as risk indicator of cardiovascular morbidity and mortality. Here, the authors perform genome-wide meta-analyses for PR interval in multiple ancestries and identify 141 previously unreported genetic loci.
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| 3. |
- Alimena, Juliette, et al.
(author)
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Searching for long-lived particles beyond the Standard Model at the Large Hadron Collider
- 2020
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In: Journal of Physics G. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 47:9
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Journal article (peer-reviewed)abstract
- Particles beyond the Standard Model (SM) can generically have lifetimes that are long compared to SM particles at the weak scale. When produced at experiments such as the Large Hadron Collider (LHC) at CERN, these long-lived particles (LLPs) can decay far from the interaction vertex of the primary proton-proton collision. Such LLP signatures are distinct from those of promptly decaying particles that are targeted by the majority of searches for new physics at the LHC, often requiring customized techniques to identify, for example, significantly displaced decay vertices, tracks with atypical properties, and short track segments. Given their non-standard nature, a comprehensive overview of LLP signatures at the LHC is beneficial to ensure that possible avenues of the discovery of new physics are not overlooked. Here we report on the joint work of a community of theorists and experimentalists with the ATLAS, CMS, and LHCb experiments-as well as those working on dedicated experiments such as MoEDAL, milliQan, MATHUSLA, CODEX-b, and FASER-to survey the current state of LLP searches at the LHC, and to chart a path for the development of LLP searches into the future, both in the upcoming Run 3 and at the high-luminosity LHC. The work is organized around the current and future potential capabilities of LHC experiments to generally discover new LLPs, and takes a signature-based approach to surveying classes of models that give rise to LLPs rather than emphasizing any particular theory motivation. We develop a set of simplified models; assess the coverage of current searches; document known, often unexpected backgrounds; explore the capabilities of proposed detector upgrades; provide recommendations for the presentation of search results; and look towards the newest frontiers, namely high-multiplicity 'dark showers', highlighting opportunities for expanding the LHC reach for these signals.
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| 4. |
- Alseekh, Saleh, et al.
(author)
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Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices
- 2021
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In: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 18:7, s. 747-756
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Research review (peer-reviewed)abstract
- This Perspective, from a large group of metabolomics experts, provides best practices and simplified reporting guidelines for practitioners of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics. Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.
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| 5. |
- Anchordoqui, Luis A., et al.
(author)
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The Forward Physics Facility : Sites, experiments, and physics potential
- 2022
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In: Physics reports. - : Elsevier. - 0370-1573 .- 1873-6270. ; 968, s. 1-50
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Journal article (peer-reviewed)abstract
- The Forward Physics Facility (FPF) is a proposal to create a cavern with the space and infrastructure to support a suite of far-forward experiments at the Large Hadron Collider during the High Luminosity era. Located along the beam collision axis and shielded from the interaction point by at least 100 m of concrete and rock, the FPF will house experiments that will detect particles outside the acceptance of the existing large LHC experiments and will observe rare and exotic processes in an extremely low-background environment. In this work, we summarize the current status of plans for the FPF, including recent progress in civil engineering in identifying promising sites for the FPF and the experiments currently envisioned to realize the FPF's physics potential. We then review the many Standard Model and new physics topics that will be advanced by the FPF, including searches for long-lived particles, probes of dark matter and dark sectors, high-statistics studies of TeV neutrinos of all three flavors, aspects of perturbative and non-perturbative QCD, and high-energy astroparticle physics.
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| 6. |
- Barnekow, Elin, et al.
(author)
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A Swedish Familial Genome-Wide Haplotype Analysis Identified Five Novel Breast Cancer Susceptibility Loci on 9p24.3, 11q22.3, 15q11.2, 16q24.1 and Xq21.31
- 2023
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In: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 24:5
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Journal article (peer-reviewed)abstract
- Most breast cancer heritability is unexplained. We hypothesized that analysis of unrelated familial cases in a GWAS context could enable the identification of novel susceptibility loci. In order to examine the association of a haplotype with breast cancer risk, we performed a genome-wide haplotype association study using a sliding window analysis of window sizes 1–25 SNPs in 650 familial invasive breast cancer cases and 5021 controls. We identified five novel risk loci on 9p24.3 (OR 3.4; p 4.9 × 10−11), 11q22.3 (OR 2.4; p 5.2 × 10−9), 15q11.2 (OR 3.6; p 2.3 × 10−8), 16q24.1 (OR 3; p 3 × 10−8) and Xq21.31 (OR 3.3; p 1.7 × 10−8) and confirmed three well-known loci on 10q25.13, 11q13.3, and 16q12.1. In total, 1593 significant risk haplotypes and 39 risk SNPs were distributed on the eight loci. In comparison with unselected breast cancer cases from a previous study, the OR was increased in the familial analysis in all eight loci. Analyzing familial cancer cases and controls enabled the identification of novel breast cancer susceptibility loci.
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| 7. |
- Barnekow, Elin, et al.
(author)
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A Swedish Genome-Wide Haplotype Association Analysis Identifies a Novel Breast Cancer Susceptibility Locus in 8p21.2 and Characterizes Three Loci on Chromosomes 10, 11 and 16
- 2022
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In: Cancers. - : MDPI AG. - 2072-6694. ; 14:5
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Journal article (peer-reviewed)abstract
- Background: The heritability of breast cancer is partly explained but much of the genetic contribution remains to be identified. Haplotypes are often used as markers of ethnicity as they are preserved through generations. We have previously demonstrated that haplotype analysis, in addition to standard SNP association studies, could give novel and more detailed information on genetic cancer susceptibility.Methods: In order to examine the association of a SNP or a haplotype to breast cancer risk, we performed a genome wide haplotype association study, using sliding window analysis of window sizes 1-25 and 50 SNPs, in 3200 Swedish breast cancer cases and 5021 controls.Results: We identified a novel breast cancer susceptibility locus in 8p21.1 (OR 2.08; p 3.92 x 10(-8)), confirmed three known loci in 10q26.13, 11q13.3, 16q12.1-2 and further identified novel subloci within these three loci. Altogether 76 risk SNPs, 3302 risk haplotypes of window size 2-25 and 113 risk haplotypes of window size 50 at p < 5 x 10(-8) on chromosomes 8, 10, 11 and 16 were identified. In the known loci haplotype analysis reached an OR of 1.48 in overall breast cancer and in familial cases OR 1.68.Conclusions: Analyzing haplotypes, rather than single variants, could detect novel susceptibility loci even in small study populations but the method requires a fairly homogenous study population.
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| 8. |
- Baud, Patrick, et al.
(author)
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The Brittle-Ductile Transition in Porous Limestone : Failure Mode, Constitutive Modeling of Inelastic Deformation and Strain Localization
- 2021
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In: Journal of Geophysical Research: Solid Earth. - 2169-9313. ; 126:5
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Journal article (peer-reviewed)abstract
- Understanding of the mechanics of the brittle-ductile transition (BDT) in porous limestone is significantly more challenging than for sandstone because of the lack of consistent acoustic emission activity in limestone, meaning that one must rely on alternative techniques. In this paper, we investigate systematically the failure modes in Indiana limestone using X-ray microComputed Tomography imaging (μCT) and Digital Volume Correlation (DVC). Our new mechanical data show that the envelope for the onset of shear-enhanced compaction can be well approximated by an elliptical cap. The DVC analysis revealed the development of shear bands through the BDT, but no evidence of compaction bands. The shear band angles were between 29° and 46° with respect to the maximum principal stress. Compiling these new results with published data on Purbeck and Leitha limestones, we showed that inelastic compaction in each of these dual porosity allochemical limestones was in a good agreement with the normality condition, as defined in plasticity theory. Comparison of the observed failure modes with predictions based on bifurcation analysis showed that the shear band angles are consistently smaller than the theoretical predictions.
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| 9. |
- Heap, Michael J., et al.
(author)
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Imaging strain localisation in porous andesite using digital volume correlation
- 2020
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In: Journal of Volcanology and Geothermal Research. - : Elsevier BV. - 0377-0273. ; 404
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Journal article (peer-reviewed)abstract
- Strain localisation structures, such as shear fractures and compaction bands, are of importance due to their influence on permeability and therefore outgassing, a factor thought to influence eruptive style. In this study, we aim to develop a better understanding of strain localisation in porous volcanic rocks using X-ray tomographic images of samples of porous andesite (porosity = 0.26) acquired before and after deformation in the brittle and ductile regimes. These 3D images have been first analysed to provide 3D images of the porosity structure within the undeformed andesite, which consists of a large, well-connected porosity backbone alongside many smaller pores that are either isolated or connected to the porosity backbone by thin microstructural elements (e.g., microcracks). Following deformation, porosity profiles of the samples show localised dilation (porosity increase) and compaction (porosity reduction) within the samples deformed in the brittle and ductile regimes, respectively. Digital volume correlation (DVC) of the images before and after triaxial deformation was used to quantify the tensor strain fields, and the incremental divergence (volumetric strain) and curl (used as an indicator of shear strain) of the displacement fields were calculated from the DVC. These fields show that strain localisation in the sample deformed in the brittle regime manifested as a ~ 1 mm-wide, dilatational shear fracture oriented at an angle of 40–45° to the maximum principal stress. Pre- and post-deformation permeability measurements show that permeability of the sample deformed in the brittle regime increased from 3.9 × 10−12 to 4.9 × 10−12 m2, which is presumed to be related to the shear fracture. For the sample deformed in the ductile regime, strain localised into ~1 mm-thick, undulating compaction bands orientated sub-perpendicular to the maximum principal stress with little evidence of shear. Taken together, our data suggest that these bands formed during large stress drops seen in the mechanical data, within high-porosity zones within the sample, and within the large, well-connected porosity backbone. Pre- and post-deformation permeability measurements indicate that inelastic compaction decreased the permeability of the sample by a factor of ~3. The data of this study assist in the understanding of strain localisation in porous volcanic rocks, its influence on permeability (and therefore volcanic outgassing), and highlight an important role for DVC in studying strain localisation in volcanic materials.
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| 10. |
- Peña, Viviana, et al.
(author)
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Lithothamnion (Hapalidiales, Rhodophyta) in the changing Arctic and Subarctic : DNA sequencing of type and recent specimens provides a systematics foundation*
- 2021
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In: European journal of phycology. - : Taylor & Francis. - 0967-0262 .- 1469-4433. ; 56:4, s. 468-493
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Journal article (peer-reviewed)abstract
- Coralline red algae in the non-geniculate genera Clathromorphum, Phymatolithon and Lithothamnion are important benthic ecosystem engineers in the photic zone of the Arctic and Subarctic. In these regions, the systematics and biogeography of Clathromorphum and Phymatolithon have mostly been resolved whereas Lithothamnion has not, until now. Seventy-three specific and infraspecific names were given to Arctic and Subarctic Lithothamnion specimens in the late 19th and early 20th century by Frans R. Kjellman and Mikael H. Foslie. DNA sequences from 36 type specimens, five historical specimens, and an extensive sampling of recent collections resulted in the recognition of four Arctic and Subarctic Lithothamnion species, L. glaciale, L. lemoineae, L. soriferum and L. tophiforme. Three genes were sequenced, two plastid-encoded, rbcL and psbA, and the mitochondrial encoded COI-5P; rbcL and COI-5P segregated L. glaciale from L. tophiforme but psbA did not. Partial rbcL sequences obtained from type collections enabled us to correctly apply the earliest available names and to correctly place the remainder in synonymy. We were unable to sequence another 22 type specimens, but all of these are more recent names than those that are now applied. It is difficult to identify these species solely on morpho-anatomy as they can all occur as encrusting corallines or as maerl (rhodoliths). We demonstrate the importance of sequencing historical type specimens by showing that the recently proposed North-east Atlantic L. erinaceum is a synonym of one of the earliest published Arctic species of Lithothamnion, L. soriferum, itself incorrectly placed in synonymy under L. tophiforme based on morpho-anatomy. Based on sequenced specimens, we update the distributions and ecology of these species.
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