| 1. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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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. |
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| 4. |
- 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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| 5. |
- Munn-Chernoff, M. A., et al.
(författare)
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Shared genetic risk between eating disorder- and substance-use-related phenotypes: Evidence from genome-wide association studies
- 2021
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Ingår i: Addiction Biology. - : Wiley. - 1355-6215 .- 1369-1600. ; 26:1
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Tidskriftsartikel (refereegranskat)abstract
- Eating disorders and substance use disorders frequently co-occur. Twin studies reveal shared genetic variance between liabilities to eating disorders and substance use, with the strongest associations between symptoms of bulimia nervosa and problem alcohol use (genetic correlation [r(g)], twin-based = 0.23-0.53). We estimated the genetic correlation between eating disorder and substance use and disorder phenotypes using data from genome-wide association studies (GWAS). Four eating disorder phenotypes (anorexia nervosa [AN], AN with binge eating, AN without binge eating, and a bulimia nervosa factor score), and eight substance-use-related phenotypes (drinks per week, alcohol use disorder [AUD], smoking initiation, current smoking, cigarettes per day, nicotine dependence, cannabis initiation, and cannabis use disorder) from eight studies were included. Significant genetic correlations were adjusted for variants associated with major depressive disorder and schizophrenia. Total study sample sizes per phenotype ranged from similar to 2400 to similar to 537 000 individuals. We used linkage disequilibrium score regression to calculate single nucleotide polymorphism-based genetic correlations between eating disorder- and substance-use-related phenotypes. Significant positive genetic associations emerged between AUD and AN (r(g) = 0.18; false discovery rate q = 0.0006), cannabis initiation and AN (r(g) = 0.23; q < 0.0001), and cannabis initiation and AN with binge eating (r(g) = 0.27; q = 0.0016). Conversely, significant negative genetic correlations were observed between three nondiagnostic smoking phenotypes (smoking initiation, current smoking, and cigarettes per day) and AN without binge eating (r(gs) = -0.19 to -0.23; qs < 0.04). The genetic correlation between AUD and AN was no longer significant after co-varying for major depressive disorder loci. The patterns of association between eating disorder- and substance-use-related phenotypes highlights the potentially complex and substance-specific relationships among these behaviors.
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| 6. |
- Ip, H. F., et al.
(författare)
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Genetic association study of childhood aggression across raters, instruments, and age
- 2021
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Ingår i: Translational Psychiatry. - : Springer Science and Business Media LLC. - 2158-3188. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Childhood aggressive behavior (AGG) has a substantial heritability of around 50%. Here we present a genome-wide association metaanalysis (GWAMA) of childhood AGG, in which all phenotype measures across childhood ages from multiple assessors were included. We analyzed phenotype assessments for a total of 328 935 observations from 87 485 children aged between 1.5 and 18 years, while accounting for sample overlap. We also meta-analyzed within subsets of the data, i.e., within rater, instrument and age. SNP-heritability for the overall meta-analysis (AGGoverall) was 3.31% (SE= 0.0038). We found no genome-wide significant SNPs for AGG(overall). The gene-based analysis returned three significant genes: ST3GAL3 (P= 1.6E-06), PCDH7 (P= 2.0E-06), and IPO13 (P= 2.5E-06). All three genes have previously been associated with educational traits. Polygenic scores based on our GWAMA significantly predicted aggression in a holdout sample of children (variance explained = 0.44%) and in retrospectively assessed childhood aggression (variance explained = 0.20%). Genetic correlations (rg) among rater-specific assessment of AGG ranged from r(g)= 0.46 between self- and teacher-assessment to r(g)d= 0.81 between mother- and teacher-assessment. We obtained moderate-to-strong rgs with selected phenotypes from multiple domains, but hardly with any of the classical biomarkers thought to be associated with AGG. Significant genetic correlations were observed with most psychiatric and psychological traits (range r(g): 0.19-1.00), except for obsessive-compulsive disorder. Aggression had a negative genetic correlation (r(g)=-0.5) with cognitive traits and age at first birth. Aggression was strongly genetically correlated with smoking phenotypes (range |r(g)| : 0.46-0.60). The genetic correlations between aggression and psychiatric disorders were weaker for teacher-reported AGG than for mother- and self-reported AGG. The current GWAMA of childhood aggression provides a powerful tool to interrogate the rater-specific genetic etiology of AGG.
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| 7. |
- Bryois, J., et al.
(författare)
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Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson’s disease
- 2020
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 52:5, s. 482-493
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies have discovered hundreds of loci associated with complex brain disorders, but it remains unclear in which cell types these loci are active. Here we integrate genome-wide association study results with single-cell transcriptomic data from the entire mouse nervous system to systematically identify cell types underlying brain complex traits. We show that psychiatric disorders are predominantly associated with projecting excitatory and inhibitory neurons. Neurological diseases were associated with different cell types, which is consistent with other lines of evidence. Notably, Parkinson’s disease was genetically associated not only with cholinergic and monoaminergic neurons (which include dopaminergic neurons) but also with enteric neurons and oligodendrocytes. Using post-mortem brain transcriptomic data, we confirmed alterations in these cells, even at the earliest stages of disease progression. Our study provides an important framework for understanding the cellular basis of complex brain maladies, and reveals an unexpected role of oligodendrocytes in Parkinson’s disease. © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.
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| 8. |
- Aghanim, N., et al.
(författare)
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Planck 2018 results I. Overview and the cosmological legacy of Planck
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 641
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Tidskriftsartikel (refereegranskat)abstract
- The European Space Agency's Planck satellite, which was dedicated to studying the early Universe and its subsequent evolution, was launched on 14 May 2009. It scanned the microwave and submillimetre sky continuously between 12 August 2009 and 23 October 2013, producing deep, high-resolution, all-sky maps in nine frequency bands from 30 to 857 GHz. This paper presents the cosmological legacy of Planck, which currently provides our strongest constraints on the parameters of the standard cosmological model and some of the tightest limits available on deviations from that model. The 6-parameter Lambda CDM model continues to provide an excellent fit to the cosmic microwave background data at high and low redshift, describing the cosmological information in over a billion map pixels with just six parameters. With 18 peaks in the temperature and polarization angular power spectra constrained well, Planck measures five of the six parameters to better than 1% (simultaneously), with the best-determined parameter (theta (*)) now known to 0.03%. We describe the multi-component sky as seen by Planck, the success of the Lambda CDM model, and the connection to lower-redshift probes of structure formation. We also give a comprehensive summary of the major changes introduced in this 2018 release. The Planck data, alone and in combination with other probes, provide stringent constraints on our models of the early Universe and the large-scale structure within which all astrophysical objects form and evolve. We discuss some lessons learned from the Planck mission, and highlight areas ripe for further experimental advances.
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| 9. |
- Akrami, Y., et al.
(författare)
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Planck intermediate results : LVII. Joint Planck LFI and HFI data processing
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 643
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Tidskriftsartikel (refereegranskat)abstract
- We present the NPIPE processing pipeline, which produces calibrated frequency maps in temperature and polarization from data from the Planck Low Frequency Instrument (LFI) and High Frequency Instrument (HFI) using high-performance computers. NPIPE represents a natural evolution of previous Planck analysis efforts, and combines some of the most powerful features of the separate LFI and HFI analysis pipelines. For example, following the LFI 2018 processing procedure, NPIPE uses foreground polarization priors during the calibration stage in order to break scanning-induced degeneracies. Similarly, NPIPE employs the HFI 2018 time-domain processing methodology to correct for bandpass mismatch at all frequencies. In addition, NPIPE introduces several improvements, including, but not limited to: inclusion of the 8% of data collected during repointing manoeuvres; smoothing of the LFI reference load data streams; in-flight estimation of detector polarization parameters; and construction of maximally independent detector-set split maps. For component-separation purposes, important improvements include: maps that retain the CMB Solar dipole, allowing for high-precision relative calibration in higher-level analyses; well-defined single-detector maps, allowing for robust CO extraction; and HFI temperature maps between 217 and 857 GHz that are binned into 0′.9 pixels (Nside = 4096), ensuring that the full angular information in the data is represented in the maps even at the highest Planck resolutions. The net effect of these improvements is lower levels of noise and systematics in both frequency and component maps at essentially all angular scales, as well as notably improved internal consistency between the various frequency channels. Based on the NPIPE maps, we present the first estimate of the Solar dipole determined through component separation across all nine Planck frequencies. The amplitude is (3366.6 ± 2.7) μK, consistent with, albeit slightly higher than, earlier estimates. From the large-scale polarization data, we derive an updated estimate of the optical depth of reionization of τ = 0.051 ± 0.006, which appears robust with respect to data and sky cuts. There are 600 complete signal, noise and systematics simulations of the full-frequency and detector-set maps. As a Planck first, these simulations include full time-domain processing of the beam-convolved CMB anisotropies. The release of NPIPE maps and simulations is accompanied with a complete suite of raw and processed time-ordered data and the software, scripts, auxiliary data, and parameter files needed to improve further on the analysis and to run matching simulations.
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| 10. |
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| 11. |
- Brennan, S. J., et al.
(författare)
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Photometric and spectroscopic evolution of the interacting transient AT 2016jbu(Gaia16cfr)
- 2022
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 513:4, s. 5642-5665
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Tidskriftsartikel (refereegranskat)abstract
- We present the results from a high-cadence, multiwavelength observation campaign of AT 2016jbu (aka Gaia16cfr), an interacting transient. This data set complements the current literature by adding higher cadence as well as extended coverage of the light-curve evolution and late-time spectroscopic evolution. Photometric coverage reveals that AT 2016jbu underwent significant photometric variability followed by two luminous events, the latter of which reached an absolute magnitude of MV ∼ −18.5 mag. This is similar to the transient SN 2009ip whose nature is still debated. Spectra are dominated by narrow emission lines and show a blue continuum during the peak of the second event. AT 2016jbu shows signatures of a complex, non-homogeneous circumstellar material (CSM). We see slowly evolving asymmetric hydrogen line profiles, with velocities of 500 km s−1 seen in narrow emission features from a slow-moving CSM, and up to 10 000 km s−1 seen in broad absorption from some high-velocity material. Late-time spectra (∼+1 yr) show a lack of forbidden emission lines expected from a core-collapse supernova and are dominated by strong emission from H, He I, and Ca II. Strong asymmetric emission features, a bumpy light curve, and continually evolving spectra suggest an inhibit nebular phase. We compare the evolution of H α among SN 2009ip-like transients and find possible evidence for orientation angle effects. The light-curve evolution of AT 2016jbu suggests similar, but not identical, circumstellar environments to other SN 2009ip-like transients.
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| 12. |
- Hosseinzadeh, Griffin, et al.
(författare)
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Weak Mass Loss from the Red Supergiant Progenitor of the Type II SN 2021yja
- 2022
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 935:1
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Tidskriftsartikel (refereegranskat)abstract
- We present high-cadence optical, ultraviolet (UV), and near-infrared data of the nearby (D approximate to 23 Mpc) Type II supernova (SN) 2021yja. Many Type II SNe show signs of interaction with circumstellar material (CSM) during the first few days after explosion, implying that their red supergiant (RSG) progenitors experience episodic or eruptive mass loss. However, because it is difficult to discover SNe early, the diversity of CSM configurations in RSGs has not been fully mapped. SN 2021yja, first detected within approximate to 5.4 hours of explosion, shows some signatures of CSM interaction (high UV luminosity and radio and x-ray emission) but without the narrow emission lines or early light-curve peak that can accompany CSM. Here we analyze the densely sampled early light curve and spectral series of this nearby SN to infer the properties of its progenitor and CSM. We find that the most likely progenitor was an RSG with an extended envelope, encompassed by low-density CSM. We also present archival Hubble Space Telescope imaging of the host galaxy of SN 2021yja, which allows us to place a stringent upper limit of less than or similar to 9 M-circle dot; on the progenitor mass. However, this is in tension with some aspects of the SN evolution, which point to a more massive progenitor. Our analysis highlights the need to consider progenitor structure when making inferences about CSM properties, and that a comprehensive view of CSM tracers should be made to give a fuller view of the last years of RSG evolution.
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| 13. |
- Peterson, A. Townsend, et al.
(författare)
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ENM2020 : A free online course and set of resources on modeling species niches and distributions
- 2022
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Ingår i: Biodiversity Informatics. - : The University of Kansas. - 1546-9735. ; 17, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- The field of distributional ecology has seen considerable recent attention, particularly surrounding the theory, protocols, and tools for Ecological Niche Modeling (ENM) or Species Distribution Modeling (SDM). Such analyses have grown steadily over the past two decades-including a maturation of relevant theory and key concepts-but methodological consensus has yet to be reached. In response, and following an online course taught in Spanish in 2018, we designed a comprehensive English-language course covering much of the underlying theory and methods currently applied in this broad field. Here, we summarize that course, ENM2020, and provide links by which resources produced for it can be accessed into the future. ENM2020 lasted 43 weeks, with presentations from 52 instructors, who engaged with >2500 participants globally through >14,000 hours of viewing and >90,000 views of instructional video and question-and-answer sessions. Each major topic was introduced by an "Overview" talk, followed by more detailed lectures on subtopics. The hierarchical and modular format of the course permits updates, corrections, or alternative viewpoints, and generally facilitates revision and reuse, including the use of only the Overview lectures for introductory courses. All course materials are free and openly accessible (CC-BY license) to ensure these resources remain available to all interested in distributional ecology.
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| 14. |
- Tobias, Deirdre K, et al.
(författare)
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Second international consensus report on gaps and opportunities for the clinical translation of precision diabetes medicine
- 2023
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Ingår i: Nature Medicine. - 1546-170X. ; 29:10, s. 2438-2457
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Forskningsöversikt (refereegranskat)abstract
- Precision medicine is part of the logical evolution of contemporary evidence-based medicine that seeks to reduce errors and optimize outcomes when making medical decisions and health recommendations. Diabetes affects hundreds of millions of people worldwide, many of whom will develop life-threatening complications and die prematurely. Precision medicine can potentially address this enormous problem by accounting for heterogeneity in the etiology, clinical presentation and pathogenesis of common forms of diabetes and risks of complications. This second international consensus report on precision diabetes medicine summarizes the findings from a systematic evidence review across the key pillars of precision medicine (prevention, diagnosis, treatment, prognosis) in four recognized forms of diabetes (monogenic, gestational, type 1, type 2). These reviews address key questions about the translation of precision medicine research into practice. Although not complete, owing to the vast literature on this topic, they revealed opportunities for the immediate or near-term clinical implementation of precision diabetes medicine; furthermore, we expose important gaps in knowledge, focusing on the need to obtain new clinically relevant evidence. Gaps include the need for common standards for clinical readiness, including consideration of cost-effectiveness, health equity, predictive accuracy, liability and accessibility. Key milestones are outlined for the broad clinical implementation of precision diabetes medicine.
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| 15. |
- Bar, N., et al.
(författare)
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A reference map of potential determinants for the human serum metabolome
- 2020
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Ingår i: Nature. - : Nature Research. - 0028-0836 .- 1476-4687. ; 588:7836, s. 135-140
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Tidskriftsartikel (refereegranskat)abstract
- The serum metabolome contains a plethora of biomarkers and causative agents of various diseases, some of which are endogenously produced and some that have been taken up from the environment1. The origins of specific compounds are known, including metabolites that are highly heritable2,3, or those that are influenced by the gut microbiome4, by lifestyle choices such as smoking5, or by diet6. However, the key determinants of most metabolites are still poorly understood. Here we measured the levels of 1,251 metabolites in serum samples from a unique and deeply phenotyped healthy human cohort of 491 individuals. We applied machine-learning algorithms to predict metabolite levels in held-out individuals on the basis of host genetics, gut microbiome, clinical parameters, diet, lifestyle and anthropometric measurements, and obtained statistically significant predictions for more than 76% of the profiled metabolites. Diet and microbiome had the strongest predictive power, and each explained hundreds of metabolites—in some cases, explaining more than 50% of the observed variance. We further validated microbiome-related predictions by showing a high replication rate in two geographically independent cohorts7,8 that were not available to us when we trained the algorithms. We used feature attribution analysis9 to reveal specific dietary and bacterial interactions. We further demonstrate that some of these interactions might be causal, as some metabolites that we predicted to be positively associated with bread were found to increase after a randomized clinical trial of bread intervention. Overall, our results reveal potential determinants of more than 800 metabolites, paving the way towards a mechanistic understanding of alterations in metabolites under different conditions and to designing interventions for manipulating the levels of circulating metabolites.
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| 16. |
- Hakkaart, C, et al.
(författare)
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Copy number variants as modifiers of breast cancer risk for BRCA1/BRCA2 pathogenic variant carriers
- 2022
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 5:1, s. 1061-
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Tidskriftsartikel (refereegranskat)abstract
- The contribution of germline copy number variants (CNVs) to risk of developing cancer in individuals with pathogenic BRCA1 or BRCA2 variants remains relatively unknown. We conducted the largest genome-wide analysis of CNVs in 15,342 BRCA1 and 10,740 BRCA2 pathogenic variant carriers. We used these results to prioritise a candidate breast cancer risk-modifier gene for laboratory analysis and biological validation. Notably, the HR for deletions in BRCA1 suggested an elevated breast cancer risk estimate (hazard ratio (HR) = 1.21), 95% confidence interval (95% CI = 1.09–1.35) compared with non-CNV pathogenic variants. In contrast, deletions overlapping SULT1A1 suggested a decreased breast cancer risk (HR = 0.73, 95% CI 0.59-0.91) in BRCA1 pathogenic variant carriers. Functional analyses of SULT1A1 showed that reduced mRNA expression in pathogenic BRCA1 variant cells was associated with reduced cellular proliferation and reduced DNA damage after treatment with DNA damaging agents. These data provide evidence that deleterious variants in BRCA1 plus SULT1A1 deletions contribute to variable breast cancer risk in BRCA1 carriers.
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| 17. |
- Meagher, N. S., et al.
(författare)
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Gene-Expression Profiling of Mucinous Ovarian Tumors and Comparison with Upper and Lower Gastrointestinal Tumors Identifies Markers Associated with Adverse Outcomes
- 2022
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Ingår i: Clinical Cancer Research. - 1078-0432. ; 28:24, s. 5383-5395
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Advanced-stage mucinous ovarian carcinoma (MOC) has poor chemotherapy response and prognosis and lacks biomarkers to aid stage I adjuvant treatment. Differentiating primaryMOC from gastrointestinal (GI) metastases to the ovary is also challenging due to phenotypic similarities. Clinicopathologic and geneexpression data were analyzed to identify prognostic and diagnostic features. Experimental Design: Discovery analyses selected 19 genes with prognostic/diagnostic potential. Validation was performed through the Ovarian Tumor Tissue Analysis consortium and GI cancer biobanks comprising 604 patients with MOC (n = 333), mucinous borderline ovarian tumors ( MBOT, n = 151), and upper GI (n = 65) and lower GI tumors (n = 55). Results: Infiltrative pattern of invasion was associated with decreased overall survival (OS) within 2 years from diagnosis, compared with expansile pattern in stage I MOC [hazard ratio ( HR), 2.77; 95% confidence interval (CI), 1.04-7.41, P = 0.042]. Increased expression of THBS2 and TAGLN was associated with shorter OS in MOC patients (HR, 1.25; 95% CI, 1.04-1.51, P = 0.016) and (HR, 1.21; 95% CI, 1.01-1.45, P = 0.043), respectively. ERBB2 (HER2) amplification or high mRNA expression was evident in 64 of 243 (26%) of MOCs, but only 8 of 243 (3%) were also infiltrative (4/39, 10%) or stage III/IV (4/31, 13%). Conclusions: An infiltrative growth pattern infers poor prognosis within 2 years from diagnosis and may help select stage I patients for adjuvant therapy. High expression of THBS2 and TAGLN in MOC confers an adverse prognosis and is upregulated in the infiltrative subtype, which warrants further investigation. Anti-HER2 therapy should be investigated in a subset of patients. MOC samples clustered with upper GI, yet markers to differentiate these entities remain elusive, suggesting similar underlying biology and shared treatment strategies.
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| 18. |
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| 19. |
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| 20. |
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| 21. |
- Hosseinzadeh, Griffin, et al.
(författare)
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Constraining the Progenitor System of the Type Ia Supernova 2021aefx
- 2022
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Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8205 .- 2041-8213. ; 933:2
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Tidskriftsartikel (refereegranskat)abstract
- We present high-cadence optical and ultraviolet light curves of the normal Type Ia supernova (SN) 2021aefx, which shows an early bump during the first two days of observation. This bump may be a signature of interaction between the exploding white dwarf and a nondegenerate binary companion, or it may be intrinsic to the white dwarf explosion mechanism. In the case of the former, the short duration of the bump implies a relatively compact main-sequence companion star, although this conclusion is viewing-angle dependent. Our best-fit companion-shocking and double-detonation models both overpredict the UV luminosity during the bump, and existing nickel-shell models do not match the strength and timescale of the bump. We also present nebular spectra of SN 2021aefx, which do not show the hydrogen or helium emission expected from a nondegenerate companion, as well as a radio nondetection that rules out all symbiotic progenitor systems and most accretion disk winds. Our analysis places strong but conflicting constraints on the progenitor of SN 2021aefx; no current model can explain all of our observations.
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| 22. |
- Hosseinzadeh, Griffin, et al.
(författare)
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The Early Light Curve of SN 2023bee : Constraining Type Ia Supernova Progenitors the Apian Way
- 2023
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Ingår i: Astrophysical Journal Letters. - 2041-8205 .- 2041-8213. ; 953:1
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Tidskriftsartikel (refereegranskat)abstract
- We present very early photometric and spectroscopic observations of the Type Ia supernova (SN Ia) 2023bee, starting about 8 hr after the explosion, which reveal a strong excess in the optical and nearest UV (U and UVW1) bands during the first several days of explosion. This data set allows us to probe the nature of the binary companion of the exploding white dwarf and the conditions leading to its ignition. We find a good match to the Kasen model in which a main-sequence companion star stings the ejecta with a shock as they buzz past. Models of double detonations, shells of radioactive nickel near the surface, interaction with circumstellar material, and pulsational delayed detonations do not provide good matches to our light curves. We also observe signatures of unburned material, in the form of carbon absorption, in our earliest spectra. Our radio nondetections place a limit on the mass-loss rate from the putative companion that rules out a red giant but allows a main-sequence star. We discuss our results in the context of other similar SNe Ia in the literature.
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| 23. |
- Naumov, V., et al.
(författare)
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COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity
- 2021
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Ingår i: Plos Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 17:7
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Tidskriftsartikel (refereegranskat)abstract
- Author summary This article introduces COVIDomic, a new integrative multi-omics online platform designed to facilitate the analysis of the large amount of health data collected from COVID-19 patients. The COVIDomic platform includes a user-friendly interface and provides a set of bioinformatics tools for the analysis of multi-modal metatranscriptomic data to determine the origin of the coronavirus strain and the expected severity of the disease. An analytical workflow includes microbial pathogens community analysis, COVID-19 genetic epidemiology and patient stratification. These features allow studying the presence of common microbial organisms, their antibiotic resistance and the severity of the infection, as well as obtaining insights on the geographical locations from which the strain could have originated. Such openly distributed multi-modal platform will greatly accelerate the ongoing COVID-19 research and improve our readiness to respond to other infectious outbreaks. Coronavirus disease 2019 (COVID-19) is an acute infection of the respiratory tract that emerged in December 2019 in Wuhan, China. It was quickly established that both the symptoms and the disease severity may vary from one case to another and several strains of SARS-CoV-2 have been identified. To gain a better understanding of the wide variety of SARS-CoV-2 strains and their associated symptoms, thousands of SARS-CoV-2 genomes have been sequenced in dozens of countries. In this article, we introduce COVIDomic, a multi-omics online platform designed to facilitate the analysis and interpretation of the large amount of health data collected from patients with COVID-19. The COVIDomic platform provides a comprehensive set of bioinformatic tools for the multi-modal metatranscriptomic data analysis of COVID-19 patients to determine the origin of the coronavirus strain and the expected severity of the disease. An integrative analytical workflow, which includes microbial pathogens community analysis, COVID-19 genetic epidemiology and patient stratification, allows to analyze the presence of the most common microbial organisms, their antibiotic resistance, the severity of the infection and the set of the most probable geographical locations from which the studied strain could have originated. The online platform integrates a user friendly interface which allows easy visualization of the results. We envision this tool will not only have immediate implications for management of the ongoing COVID-19 pandemic, but will also improve our readiness to respond to other infectious outbreaks.
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| 24. |
- Rheinbay, E, et al.
(författare)
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 102-
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Tidskriftsartikel (refereegranskat)abstract
- The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5′ region of TP53, in the 3′ untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
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| 25. |
- Ambros, I. M., et al.
(författare)
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Age Dependency of the Prognostic Impact of Tumor Genomics in Localized Resectable MYCN-Nonamplified Neuroblastomas. Report From the SIOPEN Biology Group on the LNESG Trials and a COG Validation Group
- 2020
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Ingår i: Journal of Clinical Oncology. - : American Society of Clinical Oncology (ASCO). - 0732-183X .- 1527-7755. ; 38:31
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSEFor localized, resectable neuroblastoma without MYCN amplification, surgery only is recommended even if incomplete. However, it is not known whether the genomic background of these tumors may influence outcome.PATIENTS AND METHODSDiagnostic samples were obtained from 317 tumors, International Neuroblastoma Staging System stages 1/2A/2B, from 3 cohorts: Localized Neuroblastoma European Study Group I/II and Children's Oncology Group. Genomic data were analyzed using multi- and pangenomic techniques and fluorescence in-situ hybridization in 2 age groups (cutoff age, 18 months) and were quality controlled by the International Society of Pediatric Oncology European Neuroblastoma (SIOPEN) Biology Group.RESULTSPatients with stage 1 tumors had an excellent outcome (5-year event-free survival [EFS] standard deviation [SD], 95% +/- 2%; 5-year overall survival [OS], 99% +/- 1%). In contrast, patients with stage 2 tumors had a reduced EFS in both age groups (5-year EFS +/- SD, 84% +/- 3% in patients < 18 months of age and 75% 7% in patients >= 18 months of age). However, OS was significantly decreased only in the latter group (5-year OS +/- SD in < 18months and 18months, 96% +/- 2% and 81% +/- 7%, respectively; P = .001). In < 18months, relapses occurred independent of segmental chromosome aberrations (SCAs); only 1p loss decreased EFS (5-year EFS SD in patients 1p loss and no 1p loss, 62% +/- 13% and 87% +/- 3%, respectively; P = .019) but not OS (5-year OS +/- SD, 92% +/- 8% and 97% +/- 2%, respectively). In patients >= 18 months, only SCAs led to relapse and death, with 11q loss as the strongest marker (11q loss and no 11q loss: 5-year EFS +/- SD, 48% +/- 16% and 85% +/- 7%, P = .033; 5-year OS +/- SD, 46% +/- 22% and 92% +/- 6%, P = .038).CONCLUSIONGenomic aberrations of resectable non-MYCN-amplified stage 2 neuroblastomas have a distinct age-dependent prognostic impact. Chromosome 1p loss is a risk factor for relapse but not for diminished OS in patients < 18 months, SCAs (especially 11q loss) are risk factors for reduced EFS and OS in those > 18months. In older patients with SCA, a randomized trial of postoperative chemotherapy compared with observation alone may be indicated.
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| 26. |
- Blinov, D., et al.
(författare)
-
The RoboPol sample of optical polarimetric standards
- 2023
-
Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 677
-
Tidskriftsartikel (refereegranskat)abstract
- Context. Optical polarimeters are typically calibrated using measurements of stars with known and stable polarization parameters. However, there is a lack of such stars available across the sky. Many of the currently available standards are not suitable for medium and large telescopes due to their high brightness. Moreover, as we find, some of the polarimetric standards used are in fact variable or have polarization parameters that differ from their cataloged values. Aims. Our goal is to establish a sample of stable standards suitable for calibrating linear optical polarimeters with an accuracy down to 10-3 in fractional polarization. Methods. For 4 yr, we have been running a monitoring campaign of a sample of standard candidates comprised of 107 stars distributed across the northern sky. We analyzed the variability of the linear polarization of these stars, taking into account the non-Gaussian nature of fractional polarization measurements. For a subsample of nine stars, we also performed multiband polarization measurements. Results. We created a new catalog of 65 stars (see Table 2) that are stable, have small uncertainties of measured polarimetric parameters, and can be used as calibrators of polarimeters at medium and large telescopes.
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| 27. |
- Galbany, L., et al.
(författare)
-
An updated measurement of the Hubble constant from near-infrared observations of Type Ia supernovae
- 2023
-
Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 679
-
Tidskriftsartikel (refereegranskat)abstract
- We present a measurement of the Hubble constant (H0) using type Ia supernovae (SNe Ia) in the near-infrared (NIR) from the recently updated sample of SNe Ia in nearby galaxies with distances measured via Cepheid period-luminosity relations by the SH0ES project. We collected public near-infrared photometry of up to 19 calibrator SNe Ia and 57 SNe Ia in the Hubble flow (z > 0.01), and directly measured their peak magnitudes in the J- and H-band by Gaussian processes and spline interpolation. Calibrator peak magnitudes together with Cepheid-based distances were used to estimate the average absolute magnitude in each band, while Hubble-flow SNe were used to constrain the zero-point intercept of the magnitude–redshift relation. Our baseline result of H0 is 72.3 ± 1.4 (stat) ±1.4 (syst) km s−1 Mpc−1 in the J-band and 72.3 ± 1.3 (stat) ±1.4 (syst) km s−1 Mpc−1 in the H-band, where the systematic uncertainties include the standard deviation of up to 21 variations of the analysis, the 0.7% distance scale systematic from SH0ES Cepheid anchors, a photometric zero-point systematic, and a cosmic variance systematic. Our final measurement represents a measurement with a precision of 2.8% in both bands. Among all the analysis variants, the largest change in H0 comes from limiting the sample to those SNe from the CSP and CfA programs; they are noteworthy because they are the best calibrated, yielding H0 ∼ 75 km s−1 Mpc−1 in both bands. We explore applying stretch and reddening corrections to standardize SN Ia NIR peak magnitudes, and we demonstrate that they are still useful to reduce the absolute magnitude scatter and, which improves its standardization, at least up to the H-band. Based on our results, in order to improve the precision of the H0 measurement with SNe Ia in the NIR in the future, we would need to increase the number of calibrator SNe Ia, to be able to extend the Hubble–Lemaître diagram to higher redshift, and to include standardization procedures to help reduce the NIR intrinsic scatter.
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| 28. |
- Koivula, Robert W., et al.
(författare)
-
The role of physical activity in metabolic homeostasis before and after the onset of type 2 diabetes : an IMI DIRECT study
- 2020
-
Ingår i: Diabetologia. - : Springer Nature. - 0012-186X .- 1432-0428. ; 63:4, s. 744-756
-
Tidskriftsartikel (refereegranskat)abstract
- Aims/hypothesis: It is well established that physical activity, abdominal ectopic fat and glycaemic regulation are related but the underlying structure of these relationships is unclear. The previously proposed twin-cycle hypothesis (TC) provides a mechanistic basis for impairment in glycaemic control through the interactions of substrate availability, substrate metabolism and abdominal ectopic fat accumulation. Here, we hypothesise that the effect of physical activity in glucose regulation is mediated by the twin-cycle. We aimed to examine this notion in the Innovative Medicines Initiative Diabetes Research on Patient Stratification (IMI DIRECT) Consortium cohorts comprised of participants with normal or impaired glucose regulation (cohort 1: N ≤ 920) or with recently diagnosed type 2 diabetes (cohort 2: N ≤ 435). Methods: We defined a structural equation model that describes the TC and fitted this within the IMI DIRECT dataset. A second model, twin-cycle plus physical activity (TC-PA), to assess the extent to which the effects of physical activity in glycaemic regulation are mediated by components in the twin-cycle, was also fitted. Beta cell function, insulin sensitivity and glycaemic control were modelled from frequently sampled 75 g OGTTs (fsOGTTs) and mixed-meal tolerance tests (MMTTs) in participants without and with diabetes, respectively. Abdominal fat distribution was assessed using MRI, and physical activity through wrist-worn triaxial accelerometry. Results are presented as standardised beta coefficients, SE and p values, respectively. Results: The TC and TC-PA models showed better fit than null models (TC: χ2 = 242, p = 0.004 and χ2 = 63, p = 0.001 in cohort 1 and 2, respectively; TC-PA: χ2 = 180, p = 0.041 and χ2 = 60, p = 0.008 in cohort 1 and 2, respectively). The association of physical activity with glycaemic control was primarily mediated by variables in the liver fat cycle. Conclusions/interpretation: These analyses partially support the mechanisms proposed in the twin-cycle model and highlight mechanistic pathways through which insulin sensitivity and liver fat mediate the association between physical activity and glycaemic control.
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| 29. |
- Muxlow, T. W. B., et al.
(författare)
-
The e-MERGE Survey (e-MERLIN Galaxy Evolution Survey): overview and survey description
- 2020
-
Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 495:1, s. 1188-1208
-
Tidskriftsartikel (refereegranskat)abstract
- We present an overview and description of the e-MERGE Survey (e-MERLIN Galaxy Evolution Survey) Data Release 1 (DR1), a large program of high-resolution 1.5-GHz radio observations of the GOODS-N field comprising similar to 140 h of observations with enhanced-Multi-Element Remotely Linked Interferometer Network (e-MERLIN) and similar to 40 h with the Very Large Array (VLA). We combine the long baselines of e-MERLIN (providing high angular resolution) with the relatively closely packed antennas of the VLA (providing excellent surface brightness sensitivity) to produce a deep 1.5-GHz radio survey with the sensitivity (similar to 1.5 mu Jy beam(-1)), angular resolution (0.2-0.7 arcsec) and field-of-view (similar to 15x15 arcmin(2)) to detect and spatially resolve star-forming galaxies and active galactic nucleus (AGN) at z greater than or similar to 1. The goal of e-MERGE is to provide new constraints on the deep, sub-arcsecond radio sky which will be surveyed by SKA1-mid. In this initial publication, we discuss our data analysis techniques, including steps taken to model in-beam source variability over an similar to 20-yr baseline and the development of newpoint spread function/primary beam models to seamlessly merge e-MERLIN and VLA data in the uv plane. We present early science results, including measurements of the luminosities and/or linear sizes of similar to 500 galaxies selected at 1.5 GHz. In combination with deep Hubble Space Telescope observations, we measure a mean radio-to-optical size ratio of r(e-MERGE)/r(HST) similar to 1.02 +/- 0.03, suggesting that in most high-redshift galaxies, the similar to GHz continuum emission traces the stellar light seen in optical imaging. This is the first in a series of papers that will explore the similar to kpc-scale radio properties of star-forming galaxies and AGN in the GOODS-N field observed by e-MERGE DR1.
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| 30. |
- Pearson, A. D. J., et al.
(författare)
-
Paediatric Strategy Forum for medicinal product development for acute myeloid leukaemia in children and adolescents ACCELERATE in collaboration with the European Medicines Agency with participation of the Food and Drug Administration
- 2020
-
Ingår i: European Journal of Cancer. - : Elsevier BV. - 0959-8049. ; 136, s. 116-129
-
Tidskriftsartikel (refereegranskat)abstract
- Purpose: The current standard-of-care for front-line therapy for acute myeloid leukaemia (AML) results in short-term and long-term toxicity, but still approximately 40% of children relapse. Therefore, there is a major need to accelerate the evaluation of innovative medicines, yet drug development continues to be adult-focused. Furthermore, the large number of competing agents in rare patient populations requires coordinated prioritisation, within the global regulatory framework and cooperative group initiatives. Methods: The fourth multi-stakeholder Paediatric Strategy Forum focused on AML in children and adolescents. Results: CD123 is a high priority target and the paediatric development should be accelerated as a proof-of-concept. Efforts must be coordinated, however, as there are a limited number of studies that can be delivered. Studies of FLT3 inhibitors in agreed paediatric investigation plans present challenges to be completed because they require enrolment of a larger number of patients than actually exist. A consensus was developed by industry and academia of optimised clinical trials. For AML with rare mutations that are more frequent in adolescents than in children, adult trials should enrol adolescents and when scientifically justified, efficacy data could be extrapolated. Methodologies and definitions of minimal residual disease need to be standardised internationally and validated as a new response criterion. Industry supported, academic sponsored platform trials could identify products to be further developed. The Leukaemia and Lymphoma Society PedAL/EUpAL initiative has the potential to be a major advance in the field. Conclusion: These initiatives continue to accelerate drug development for children with AML and ultimately improve clinical outcomes. (C) 2020 Elsevier Ltd. All rights reserved.
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| 31. |
- Steinthorsdottir, Margret, et al.
(författare)
-
The Miocene: The Future of the Past
- 2021
-
Ingår i: Paleoceanography and Paleoclimatology. - : American Geophysical Union (AGU). - 2572-4517 .- 2572-4525. ; 36:4
-
Tidskriftsartikel (refereegranskat)abstract
- The Miocene epoch (23.03–5.33 Ma) was a time interval of global warmth, relative to today. Continental configurations and mountain topography transitioned toward modern conditions, and many flora and fauna evolved into the same taxa that exist today. Miocene climate was dynamic: long periods of early and late glaciation bracketed a ∼2 Myr greenhouse interval—the Miocene Climatic Optimum (MCO). Floras, faunas, ice sheets, precipitation, pCO2, and ocean and atmospheric circulation mostly (but not ubiquitously) covaried with these large changes in climate. With higher temperatures and moderately higher pCO2 (∼400–600 ppm), the MCO has been suggested as a particularly appropriate analog for future climate scenarios, and for assessing the predictive accuracy of numerical climate models—the same models that are used to simulate future climate. Yet, Miocene conditions have proved difficult to reconcile with models. This implies either missing positive feedbacks in the models, a lack of knowledge of past climate forcings, or the need for re-interpretation of proxies, which might mitigate the model-data discrepancy. Our understanding of Miocene climatic, biogeochemical, and oceanic changes on broad spatial and temporal scales is still developing. New records documenting the physical, chemical, and biotic aspects of the Earth system are emerging, and together provide a more comprehensive understanding of this important time interval. Here, we review the state-of-the-art in Miocene climate, ocean circulation, biogeochemical cycling, ice sheet dynamics, and biotic adaptation research as inferred through proxy observations and modeling studies.
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| 32. |
- Stritzinger, M. D., et al.
(författare)
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The carbon-rich type Ic supernova 2016adj in the iconic dust lane of Centaurus A : Potential signatures of an interaction with circumstellar hydrogen
- 2024
-
Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 686
-
Tidskriftsartikel (refereegranskat)abstract
- We present a comprehensive data set of supernova (SN) 2016adj located within the central dust lane of Centaurus A. SN 2016adj is significantly reddened and after correcting the peak apparent B-band magnitude (mB = 17.48 ± 0.05) for Milky Way reddening and our inferred host-galaxy reddening parameters (i.e., RVhost = 5.7±0.7 and AVhost = 6.3 ± 0.2 mag), we estimated it reached a peak absolute magnitude of MB ∼ −18. A detailed inspection of the optical and near-infrared (NIR) spectroscopic time series reveals a carbon-rich SN Ic and not a SN Ib/IIb as previously suggested in the literature. The NIR spectra show prevalent carbon-monoxide formation occurring already by +41 days past B-band maximum, which is ≈11 days earlier than previously reported in the literature for this object. Interestingly, around two months past maximum, the NIR spectrum of SN 2016adj begins to exhibit H features, with a +97 days medium resolution spectrum revealing both Paschen and Bracket lines with absorption minima of ∼2000 km s−1, full-width-half-maximum emission velocities of ∼1000 km s−1, and emission line ratios consistent with a dense emission region. We speculate that these attributes are due to a circumstellar interaction (CSI) between the rapidly expanding SN ejecta and a H-rich shell of material that formed during the pre-SN phase. A bolometric light curve was constructed and a semi-analytical model fit suggests the SN synthesized 0.5 M⊙ of 56Ni and ejected 4.7 M⊙ of material, though these values should be approached with caution given the large uncertainties associated with the adopted reddening parameters and known light echo emission. Finally, inspection of the Hubble Space Telescope archival data yielded no progenitor detection.
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| 33. |
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| 34. |
- Barrie, William, et al.
(författare)
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Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations
- 2024
-
Ingår i: NATURE. - 0028-0836 .- 1476-4687. ; 625:7994
-
Tidskriftsartikel (refereegranskat)abstract
- Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated1. Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age2, along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune responses and their subsequent effect on the risk of developing MS in a changing environment. Analysis of a large ancient genome dataset shows that genetic risk for multiple sclerosis rose in steppe pastoralists, providing insight into how genetic ancestry from the Neolithic and Bronze Age has shaped modern immune responses.
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| 35. |
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| 36. |
- Camacho-Neves, Yssavo, et al.
(författare)
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Over 500 Days in the Life of the Photosphere of the Type Iax Supernova SN 2014dt
- 2023
-
Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 951:1
-
Tidskriftsartikel (refereegranskat)abstract
- Type Iax supernovae (SNe Iax) are the largest known class of peculiar white dwarf SNe, distinct from normal Type Ia supernovae (SNe Ia). The unique properties of SNe Iax, especially their strong photospheric lines out to extremely late times, allow us to model their optical spectra and derive the physical parameters of the long-lasting photosphere. We present an extensive spectral timeseries, including 21 new spectra, of SN Iax 2014dt from +11 to +562 days after maximum light. We are able to reproduce the entire timeseries with a self-consistent, nearly unaltered deflagration explosion model from Fink et al. using TARDIS, an open source radiative-transfer code. We find that the photospheric velocity of SN 2014dt slows its evolution between +64 and +148 days, which closely overlaps the phase when we see SN 2014dt diverge from the normal spectral evolution of SNe Ia (+90 to +150 days). The photospheric velocity at these epochs, ∼400–1000 km s−1, may demarcate a boundary within the ejecta below which the physics of SNe Iax and normal SNe Ia differ. Our results suggest that SN 2014dt is consistent with a weak deflagration explosion model that leaves behind a bound remnant and drives an optically thick, quasi-steady-state wind creating the photospheric lines at late times. The data also suggest that this wind may weaken at epochs past +450 days, perhaps indicating a radioactive power source that has decayed away.
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| 37. |
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| 38. |
- Chapai, R., et al.
(författare)
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Superconducting properties of the spin Hall candidate Ta3Sb with eightfold degeneracy
- 2022
-
Ingår i: Physical Review B. - 2469-9950 .- 2469-9969. ; 105:18
-
Tidskriftsartikel (refereegranskat)abstract
- We report the synthesis and characterization of phase pure Ta3Sb, a material predicted to be topological with eightfold degenerate fermionic states [Bradlyn et al., Science 353, aaf5037 (2016)] and to exhibit a large spin Hall effect [Derunova et al., Sci. Adv. 5, eaav8575 (2019)]. We observe superconductivity in Ta3Sb with Tc∼0.67 K in both electrical resistivity ρ(T) and specific heat c(T) measurements. Field-dependent measurements yield the superconducting phase diagram with an upper critical field of Hc2(0)∼ 0.95 T, corresponding to a superconducting coherence length of ξ≈18.6nm. The gap ratio deduced from specific heat anomaly 2Δ0/kBTc is 3.46, a value close to the Bardeen-Cooper-Schrieffer value of 3.53. From a detailed analysis of both the transport and thermodynamic data within the Ginsburg-Landau (GL) framework, a GL parameter of κ≈90 is obtained, identifying Ta3Sb as an extreme type-II superconductor. The observation of superconductivity in an eightfold degenerate fermionic compound with topological surface states and predicted large spin Hall conductance positions Ta3Sb as an appealing platform to further explore exotic quantum states in multifold degenerate systems.
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| 39. |
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| 40. |
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| 41. |
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| 42. |
- Maharana, S., et al.
(författare)
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Bright-Moon sky as a wide-field linear Polarimetric flat source for calibration
- 2023
-
Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 679
-
Tidskriftsartikel (refereegranskat)abstract
- Context. Next-generation wide-field optical polarimeters such as Wide-Area Linear Optical Polarimeters (WALOPs) have a field of view (FoV) of tens of arcminutes. Wide-field polarimetric flat sources are essential to the efficient and accurate calibration of these instruments. However, no established wide-field polarimetric standard or flat sources exist at present. Aims. This study tests the feasibility of using the polarized sky patches of the size of around 10 × 10 arcminutes2, at a distance of up to 20 from the Moon, on bright-Moon nights as a wide-field linear polarimetric flat source. Methods. We observed 19 patches of the sky adjacent to the bright-Moon with the RoboPol instrument in the SDSS-r broadband filter. These patches were observed on five nights within two days of the full-Moon across two RoboPol observing seasons. Results. We find that for 18 of the 19 patches, the uniformity in the measured normalized Stokes parameters q and u is within 0.2%, with 12 patches exhibiting uniformity within 0.07% or better for both q and u simultaneously, making them reliable and stable wide-field linear polarization flats. Conclusions. We demonstrate that the sky on bright-Moon nights is an excellent wide-field linear polarization flat source. Various combinations of the normalized Stokes parameters q and u can be obtained by choosing suitable locations of the sky patch with respect to the Moon.
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| 43. |
- N, Eernstman, et al.
(författare)
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Designing Collective Artist Residencies. Cultivating imaginative disruptions and light-heartedness in times of gravity
- 2021
-
Ingår i: Airea: Arts and Interdisciplinary Research. - : Edinburgh University Library. - 2516-8061. ; :3, s. 17-34
-
Tidskriftsartikel (refereegranskat)abstract
- Starting with an argument for a humanistic approach to climate change, this paper discusses the concept of the ‘Collective Artist Residency’ as a practicable means for engaging with complex socio-ecological issues that require collective answers. Through our analysis of the research project ‘Imaginative Disruptions,’ we propose that there is a need for creative spaces that include artists and non-artists alike, and which engender aimless play, inquisitive making and dialogic contemplation in the face of issues which are too painful, overwhelming and complex to rationally comprehend. We further argue that such residencies can generate comfortable, and even light-hearted, spaces in which people can be uncomfortable together. In other words, environments that feel safe and caring but that also encourage us to challenge status quos and experiment with alternatives via emotional, aesthetic, cognitive, somatic and social processing. The paper closes with five (suggested) guiding principles for designing a Collective Art Residency that supportsgroupsof people to co-reflect upon their fragility whilst re-imagining present and future possibilities for being in the world: deeply participatory, balancedbetween comfortable /uncomfortable emotions, highly experiential, cross-sectoral andintergenerational, place-based.
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| 44. |
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| 45. |
- Pelgrims, Vincent, et al.
(författare)
-
Starlight-polarization-based tomography of the magnetized ISM: PASIPHAE's line-of-sight inversion method
- 2023
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 670
-
Tidskriftsartikel (refereegranskat)abstract
- We present the first Bayesian method for tomographic decomposition of the plane-of-sky orientation of the magnetic field with the use of stellar polarimetry and distance. This standalone tomographic inversion method presents an important step forward in reconstructing the magnetized interstellar medium (ISM) in three dimensions within dusty regions. We develop a model in which the polarization signal from the magnetized and dusty ISM is described by thin layers at various distances, a working assumption which should be satisfied in small-angular circular apertures. Our modeling makes it possible to infer the mean polarization (amplitude and orientation) induced by individual dusty clouds and to account for the turbulence-induced scatter in a generic way. We present a likelihood function that explicitly accounts for uncertainties in polarization and parallax. We develop a framework for reconstructing the magnetized ISM through the maximization of the log-likelihood using a nested sampling method. We test our Bayesian inversion method on mock data, representative of the high Galactic latitude sky, taking into account realistic uncertainties from Gaia and as expected for the optical polarization survey PASIPHAE according to the currently planned observing strategy. We demonstrate that our method is effective at recovering the cloud properties as soon as the polarization induced by a cloud to its background stars is higher than ~0.1% for the adopted survey exposure time and level of systematic uncertainty. The larger the induced polarization is, the better the method's performance, and the lower the number of required stars. Our method makes it possible to recover not only the mean polarization properties but also to characterize the intrinsic scatter, thus creating new ways to characterize ISM turbulence and the magnetic field strength. Finally, we apply our method to an existing data set of starlight polarization with known line-of-sight decomposition, demonstrating agreement with previous results and an improved quantification of uncertainties in cloud properties.
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| 46. |
- Pelgrims, V., et al.
(författare)
-
The first degree-scale starlight-polarization-based tomography map of the magnetized interstellar medium
- 2024
-
Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 684
-
Tidskriftsartikel (refereegranskat)abstract
- We present the first degree-scale tomography map of the dusty magnetized interstellar medium (ISM) from stellar polarimetry and distance measurements. We used the RoboPol polarimeter at Skinakas Observatory to conduct a survey of the polarization of starlight in a region of the sky of about four square degrees. We propose a Bayesian method to decompose the stellar-polarization source field along the distance to invert the three-dimensional (3D) volume occupied by the observed stars. We used this method to obtain the first 3D map of the dusty magnetized ISM. Specifically, we produced a tomography map of the orientation of the plane-of-sky component of the magnetic field threading the diffuse, dusty regions responsible for the stellar polarization. For the targeted region centered on Galactic coordinates (l, b) (103.3, 22.3), we identified several ISM clouds. Most of the lines of sight intersect more than one cloud. A very nearby component was detected in the foreground of a dominant component from which most of the polarization signal comes and which we identified as being an intersection of the wall of the Local Bubble and the Cepheus Flare. Farther clouds, with a distance of up to 2 kpc, were similarly detected. Some of them likely correspond to intermediate-velocity clouds seen in H I spectra in this region of the sky. We found that the orientation of the plane-of-sky component of the magnetic field changes along distance for most of the lines of sight. Our study demonstrates that starlight polarization data coupled to distance measures have the power to reveal the great complexity of the dusty magnetized ISM in 3D and, in particular, to provide local measurements of the plane-of-sky component of the magnetic field in dusty regions. This demonstrates that the inversion of large data volumes, as expected from the PASIPHAE survey, will provide the necessary means to move forward in the modeling of the Galactic magnetic field and of the dusty magnetized ISM as a contaminant in observations of the cosmic microwave background polarization.
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| 47. |
- Reimer, Paula J., et al.
(författare)
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The IntCal20 Northern Hemisphere Radiocarbon Age Calibration Curve (0-55 cal kBP)
- 2020
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Ingår i: Radiocarbon. - 0033-8222. ; 62:4, s. 725-757
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Tidskriftsartikel (refereegranskat)abstract
- Radiocarbon (C) ages cannot provide absolutely dated chronologies for archaeological or paleoenvironmental studies directly but must be converted to calendar age equivalents using a calibration curve compensating for fluctuations in atmospheric C concentration. Although calibration curves are constructed from independently dated archives, they invariably require revision as new data become available and our understanding of the Earth system improves. In this volume the international C calibration curves for both the Northern and Southern Hemispheres, as well as for the ocean surface layer, have been updated to include a wealth of new data and extended to 55,000 cal BP. Based on tree rings, IntCal20 now extends as a fully atmospheric record to ca. 13,900 cal BP. For the older part of the timescale, IntCal20 comprises statistically integrated evidence from floating tree-ring chronologies, lacustrine and marine sediments, speleothems, and corals. We utilized improved evaluation of the timescales and location variable C offsets from the atmosphere (reservoir age, dead carbon fraction) for each dataset. New statistical methods have refined the structure of the calibration curves while maintaining a robust treatment of uncertainties in the C ages, the calendar ages and other corrections. The inclusion of modeled marine reservoir ages derived from a three-dimensional ocean circulation model has allowed us to apply more appropriate reservoir corrections to the marine C data rather than the previous use of constant regional offsets from the atmosphere. Here we provide an overview of the new and revised datasets and the associated methods used for the construction of the IntCal20 curve and explore potential regional offsets for tree-ring data. We discuss the main differences with respect to the previous calibration curve, IntCal13, and some of the implications for archaeology and geosciences ranging from the recent past to the time of the extinction of the Neanderthals.
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| 48. |
- Steinthorsdottir, Margret, et al.
(författare)
-
The Miocene : the Future of the Past
- 2021
-
Ingår i: Paleoceanography and Paleoclimatology. - : American Geophysical Union (AGU). - 2572-4517 .- 2572-4525. ; 36:4
-
Tidskriftsartikel (refereegranskat)abstract
- The Miocene epoch (23.03–5.33 Ma) was a time interval of global warmth, relative to today. Continental configurations and mountain topography transitioned towards modern conditions, and many flora and fauna evolved into the same taxa that exist today. Miocene climate was dynamic: long periods of early and late glaciation bracketed a ∼2 Myr greenhouse interval – the Miocene Climatic Optimum (MCO). Floras, faunas, ice sheets, precipitation, pCO2, and ocean and atmospheric circulation mostly (but not ubiquitously) covaried with these large changes in climate. With higher temperatures and moderately higher pCO2 (∼400–600 ppm), the MCO has been suggested as a particularly appropriate analogue for future climate scenarios, and for assessing the predictive accuracy of numerical climate models – the same models that are used to simulate future climate. Yet, Miocene conditions have proved difficult to reconcile with models. This implies either missing positive feedbacks in the models, a lack of knowledge of past climate forcings, or the need for re‐interpretation of proxies, which might mitigate the model‐data discrepancy. Our understanding of Miocene climatic, biogeochemical, and oceanic changes on broad spatial and temporal scales is still developing. New records documenting the physical, chemical, and biotic aspects of the Earth system are emerging, and together provide a more comprehensive understanding of this important time interval. Here we review the state‐of‐the‐art in Miocene climate, ocean circulation, biogeochemical cycling, ice sheet dynamics, and biotic adaptation research as inferred through proxy observations and modelling studies.
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| 49. |
- Watson, Hunna J., et al.
(författare)
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Common Genetic Variation and Age of Onset of Anorexia Nervosa
- 2022
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Ingår i: BIOLOGICAL PSYCHIATRY: GLOBAL OPEN SCIENCE. - : Elsevier BV. - 2667-1743. ; 2:4, s. 368-378
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Genetics and biology may influence the age of onset of anorexia nervosa (AN). The aims of this study were to determine whether common genetic variation contributes to age of onset of AN and to investigate the genetic associations between age of onset of AN and age at menarche.METHODS: A secondary analysis of the Psychiatric Genomics Consortium genome-wide association study (GWAS) of AN was performed, which included 9335 cases and 31,981 screened controls, all from European ancestries. We conducted GWASs of age of onset, early-onset AN (,13 years), and typical-onset AN, and genetic correlation, genetic risk score, and Mendelian randomization analyses.RESULTS: Two loci were genome-wide significant in the typical-onset AN GWAS. Heritability estimates (single nucleotide polymorphism-h2) were 0.01-0.04 for age of onset, 0.16-0.25 for early-onset AN, and 0.17-0.25 for typical-onset AN. Early-and typical-onset AN showed distinct genetic correlation patterns with putative risk factors for AN. Specifically, early-onset AN was significantly genetically correlated with younger age at menarche, and typical-onset AN was significantly negatively genetically correlated with anthropometric traits. Genetic risk scores for age of onset and early-onset AN estimated from independent GWASs significantly predicted age of onset. Mendelian randomization analysis suggested a causal link between younger age at menarche and early -onset AN.CONCLUSIONS: Our results provide evidence consistent with a common variant genetic basis for age of onset and implicate biological pathways regulating menarche and reproduction.
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| 50. |
- Abbott, Benjamin W., et al.
(författare)
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We Must Stop Fossil Fuel Emissions to Protect Permafrost Ecosystems
- 2022
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Ingår i: Frontiers in Environmental Science. - : Frontiers Media SA. - 2296-665X. ; 10
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Forskningsöversikt (refereegranskat)abstract
- Climate change is an existential threat to the vast global permafrost domain. The diverse human cultures, ecological communities, and biogeochemical cycles of this tenth of the planet depend on the persistence of frozen conditions. The complexity, immensity, and remoteness of permafrost ecosystems make it difficult to grasp how quickly things are changing and what can be done about it. Here, we summarize terrestrial and marine changes in the permafrost domain with an eye toward global policy. While many questions remain, we know that continued fossil fuel burning is incompatible with the continued existence of the permafrost domain as we know it. If we fail to protect permafrost ecosystems, the consequences for human rights, biosphere integrity, and global climate will be severe. The policy implications are clear: the faster we reduce human emissions and draw down atmospheric CO2, the more of the permafrost domain we can save. Emissions reduction targets must be strengthened and accompanied by support for local peoples to protect intact ecological communities and natural carbon sinks within the permafrost domain. Some proposed geoengineering interventions such as solar shading, surface albedo modification, and vegetation manipulations are unproven and may exacerbate environmental injustice without providing lasting protection. Conversely, astounding advances in renewable energy have reopened viable pathways to halve human greenhouse gas emissions by 2030 and effectively stop them well before 2050. We call on leaders, corporations, researchers, and citizens everywhere to acknowledge the global importance of the permafrost domain and work towards climate restoration and empowerment of Indigenous and immigrant communities in these regions.
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