1. |
- Schael, S, et al.
(author)
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Precision electroweak measurements on the Z resonance
- 2006
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In: Physics Reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 427:5-6, s. 257-454
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Research review (peer-reviewed)abstract
- We report on the final electroweak measurements performed with data taken at the Z resonance by the experiments operating at the electron-positron colliders SLC and LEP. The data consist of 17 million Z decays accumulated by the ALEPH, DELPHI, L3 and OPAL experiments at LEP, and 600 thousand Z decays by the SLID experiment using a polarised beam at SLC. The measurements include cross-sections, forward-backward asymmetries and polarised asymmetries. The mass and width of the Z boson, m(Z) and Gamma(Z), and its couplings to fermions, for example the p parameter and the effective electroweak mixing angle for leptons, are precisely measured: m(Z) = 91.1875 +/- 0.0021 GeV, Gamma(Z) = 2.4952 +/- 0.0023 GeV, rho(l) = 1.0050 +/- 0.0010, sin(2)theta(eff)(lept) = 0.23153 +/- 0.00016. The number of light neutrino species is determined to be 2.9840 +/- 0.0082, in agreement with the three observed generations of fundamental fermions. The results are compared to the predictions of the Standard Model (SM). At the Z-pole, electroweak radiative corrections beyond the running of the QED and QCD coupling constants are observed with a significance of five standard deviations, and in agreement with the Standard Model. Of the many Z-pole measurements, the forward-backward asymmetry in b-quark production shows the largest difference with respect to its SM expectation, at the level of 2.8 standard deviations. Through radiative corrections evaluated in the framework of the Standard Model, the Z-pole data are also used to predict the mass of the top quark, m(t) = 173(+10)(+13) GeV, and the mass of the W boson, m(W) = 80.363 +/- 0.032 GeV. These indirect constraints are compared to the direct measurements, providing a stringent test of the SM. Using in addition the direct measurements of m(t) and m(W), the mass of the as yet unobserved SM Higgs boson is predicted with a relative uncertainty of about 50% and found to be less than 285 GeV at 95% confidence level. (c) 2006 Elsevier B.V. All rights reserved.
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3. |
- de Jong, R. S., et al.
(author)
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4MOST : Project overview and information for the First Call for Proposals
- 2019
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In: The Messenger. - : European Southern Observatory. - 0722-6691. ; 175, s. 3-11
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Journal article (other academic/artistic)abstract
- We introduce the 4-metre Multi-Object Spectroscopic Telescope (4MOST), a new high-multiplex, wide-field spectroscopic survey facility under development for the four-metre-class Visible and Infrared Survey Telescope for Astronomy (VISTA) at Paranal. Its key specifications are: a large field of view (FoV) of 4.2 square degrees and a high multiplex capability, with 1624 fibres feeding two low-resolution spectrographs (R = λ/Δλ ~ 6500), and 812 fibres transferring light to the high-resolution spectrograph (R ~ 20 000). After a description of the instrument and its expected performance, a short overview is given of its operational scheme and planned 4MOST Consortium science; these aspects are covered in more detail in other articles in this edition of The Messenger. Finally, the processes, schedules, and policies concerning the selection of ESO Community Surveys are presented, commencing with a singular opportunity to submit Letters of Intent for Public Surveys during the first five years of 4MOST operations.
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4. |
- Ade, P. A. R., et al.
(author)
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XXIV. Cosmology from Sunyaev-Zeldovich cluster counts
- 2016
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 594
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Journal article (peer-reviewed)abstract
- We present cluster counts and corresponding cosmological constraints from the Planck full mission data set. Our catalogue consists of 439 clusters detected via their Sunyaev-Zeldovich (SZ) signal down to a signal-to-noise ratio of 6, and is more than a factor of 2 larger than the 2013 Planck cluster cosmology sample. The counts are consistent with those from 2013 and yield compatible constraints under the same modelling assumptions. Taking advantage of the larger catalogue, we extend our analysis to the two-dimensional distribution in redshift and signal-to-noise. We use mass estimates from two recent studies of gravitational lensing of background galaxies by Planck clusters to provide priors on the hydrostatic bias parameter, (1 - b). In addition, we use lensing of cosmic microwave background (CMB) temperature fluctuations by Planck clusters as an independent constraint on this parameter. These various calibrations imply constraints on the present-day amplitude of matter fluctuations in varying degrees of tension with those from the Planck analysis of primary fluctuations in the CMB; for the lowest estimated values of (1 b) the tension is mild, only a little over one standard deviation, while it remains substantial (3.7 sigma) for the largest estimated value. We also examine constraints on extensions to the base flat Lambda CDM model by combining the cluster and CMB constraints. The combination appears to favour non-minimal neutrino masses, but this possibility does little to relieve the overall tension because it simultaneously lowers the implied value of the Hubble parameter, thereby exacerbating the discrepancy with most current astrophysical estimates. Improving the precision of cluster mass calibrations from the current 10%-level to 1% would significantly strengthen these combined analyses and provide a stringent test of the base Lambda CDM model.
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5. |
- Ade, P. A. R., et al.
(author)
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Planck 2015 results XIX. Constraints on primordial magnetic fields
- 2016
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 594
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Journal article (peer-reviewed)abstract
- We compute and investigate four types of imprint of a stochastic background of primordial magnetic fields (PMFs) on the cosmic microwave background (CMB) anisotropies: the impact of PMFs on the CMB temperature and polarization spectra, which is related to their contribution to cosmological perturbations; the effect on CMB polarization induced by Faraday rotation; the impact of PMFs on the ionization history; magnetically-induced non-Gaussianities and related non-zero bispectra; and the magnetically-induced breaking of statistical isotropy. We present constraints on the amplitude of PMFs that are derived from different Planck data products, depending on the specific effect that is being analysed. Overall, Planck data constrain the amplitude of PMFs to less than a few nanoGauss, with different bounds that depend on the considered model. In particular, individual limits coming from the analysis of the CMB angular power spectra, using the Planck likelihood, are B-1 (Mpc) < 4.4 nG (where B1 Mpc is the comoving field amplitude at a scale of 1 Mpc) at 95% confidence level, assuming zero helicity. By considering the Planck likelihood, based only on parity-even angular power spectra, we obtain B-1 (Mpc) < 5.6 nG for a maximally helical field. For nearly scale-invariant PMFs we obtain B-1 (Mpc) < 2.0 nG and B-1 (Mpc) < 0.9 nG if the impact of PMFs on the ionization history of the Universe is included in the analysis. From the analysis of magnetically-induced non-Gaussianity, we obtain three different values, corresponding to three applied methods, all below 5 nG. The constraint from the magnetically-induced passive-tensor bispectrum is B-1 (Mpc) < 2.8 nG. A search for preferred directions in the magnetically-induced passive bispectrum yields B-1 (Mpc) < 4.5 nG, whereas the compensated-scalar bispectrum gives B-1 (Mpc) < 3 nG. The analysis of the Faraday rotation of CMB polarization by PMFs uses the Planck power spectra in EE and BB at 70 GHz and gives B-1 (Mpc) < 1380 nG. In our final analysis, we consider the harmonic-space correlations produced by Alfven waves, finding no significant evidence for the presence of these waves. Together, these results comprise a comprehensive set of constraints on possible PMFs with Planck data.
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6. |
- Ade, P. A. R., et al.
(author)
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Planck 2015 results XV. Gravitational lensing
- 2016
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 594
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Journal article (peer-reviewed)abstract
- We present the most significant measurement of the cosmic microwave background (CMB) lensing potential to date (at a level of 40 sigma), using temperature and polarization data from the Planck 2015 full-mission release. Using a polarization-only estimator, we detect lensing at a significance of 5 sigma. We cross-check the accuracy of our measurement using the wide frequency coverage and complementarity of the temperature and polarization measurements. Public products based on this measurement include an estimate of the lensing potential over approximately 70% of the sky, an estimate of the lensing potential power spectrum in bandpowers for the multipole range 40 <= L <= 400, and an associated likelihood for cosmological parameter constraints. We find good agreement between our measurement of the lensing potential power spectrum and that found in the Lambda CDM model that best fits the Planck temperature and polarization power spectra. Using the lensing likelihood alone we obtain a percent-level measurement of the parameter combination sigma(8) Omega(0.25)(m) = 0.591 +/- 0.021. We combine our determination of the lensing potential with the E-mode polarization, also measured by Planck, to generate an estimate of the lensing B-mode. We show that this lensing B-mode estimate is correlated with the B-modes observed directly by Planck at the expected level and with a statistical significance of 10 sigma, confirming Planck's sensitivity to this known sky signal. We also correlate our lensing potential estimate with the large-scale temperature anisotropies, detecting a cross-correlation at the 3 sigma level, as expected because of dark energy in the concordance Lambda CDM model.
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7. |
- Ade, P. A. R., et al.
(author)
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Planck 2015 results XVII. Constraints on primordial non-Gaussianity
- 2016
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 594
-
Journal article (peer-reviewed)abstract
- The Planck full mission cosmic microwave background (CMB) temperature and E-mode polarization maps are analysed to obtain constraints on primordial non-Gaussianity (NG). Using three classes of optimal bispectrum estimators - separable template-fitting (KSW), binned, and modal we obtain consistent values for the primordial local, equilateral, and orthogonal bispectrum amplitudes, quoting as our final result from temperature alone f(NL)(local) = 2.5 +/- 5.7, f(NL)(equil) = 16 +/- 70, and f(NL)(ortho) = 34 +/- 33 (68% CL, statistical). Combining temperature and polarization data we obtain f(NL)(local) = 0.8 +/- 5.0, f(NL)(equil) = 4 +/- 43, and f(NL)(ortho) = 26 +/- 21 (68% CL, statistical). The results are based on comprehensive cross-validation of these estimators on Gaussian and non-Gaussian simulations, are stable across component separation techniques, pass an extensive suite of tests, and are consistent with estimators based on measuring the Minkowski functionals of the CMB. The effect of time-domain de-glitching systematics on the bispectrum is negligible. In spite of these test outcomes we conservatively label the results including polarization data as preliminary, owing to a known mismatch of the noise model in simulations and the data. Beyond estimates of individual shape amplitudes, we present model-independent, three-dimensional reconstructions of the Planck CMB bispectrum and derive constraints on early universe scenarios that generate primordial NG, including general single-field models of inflation, axion inflation, initial state modifications, models producing parity-violating tensor bispectra, and directionally dependent vector models. We present a wide survey of scale-dependent feature and resonance models, accounting for the look elsewhere effect in estimating the statistical significance of features. We also look for isocurvature NG, and find no signal, but we obtain constraints that improve significantly with the inclusion of polarization. The primordial trispectrum amplitude in the local model is constrained to be g(NL)(local) = (9.0 +/- 7.7) x 10(4) (68% CL statistical), and we perform an analysis of trispectrum shapes beyond the local case. The global picture that emerges is one of consistency with the premises of the Lambda CDM cosmology, namely that the structure we observe today was sourced by adiabatic, passive, Gaussian, and primordial seed perturbations.
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8. |
- Ade, P. A. R., et al.
(author)
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Planck 2015 results XIV. Dark energy and modified gravity
- 2016
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 594
-
Journal article (peer-reviewed)abstract
- We study the implications of Planck data for models of dark energy (DE) and modified gravity (MG) beyond the standard cosmological constant scenario. We start with cases where the DE only directly affects the background evolution, considering Taylor expansions of the equation of state w(a), as well as principal component analysis and parameterizations related to the potential of a minimally coupled DE scalar field. When estimating the density of DE at early times, we significantly improve present constraints and find that it has to be below similar to 2% (at 95% confidence) of the critical density, even when forced to play a role for z < 50 only. We then move to general parameterizations of the DE or MG perturbations that encompass both effective field theories and the phenomenology of gravitational potentials in MG models. Lastly, we test a range of specific models, such as k-essence, f(R) theories, and coupled DE. In addition to the latest Planck data, for our main analyses, we use background constraints from baryonic acoustic oscillations, type-Ia supernovae, and local measurements of the Hubble constant. We further show the impact of measurements of the cosmological perturbations, such as redshift-space distortions and weak gravitational lensing. These additional probes are important tools for testing MG models and for breaking degeneracies that are still present in the combination of Planck and background data sets. All results that include only background parameterizations (expansion of the equation of state, early DE, general potentials in minimally-coupled scalar fields or principal component analysis) are in agreement with ACDM. When testing models that also change perturbations (even when the background is fixed to ACDM), some tensions appear in a few scenarios: the maximum one found is similar to 2 sigma for Planck TT + lowP when parameterizing observables related to the gravitational potentials with a chosen time dependence; the tension increases to, at most, 3 sigma when external data sets are included. It however disappears when including CMB lensing.
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9. |
- Ade, P. A. R., et al.
(author)
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Planck 2015 results XVIII. Background geometry and topology of the Universe
- 2016
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 594
-
Journal article (peer-reviewed)abstract
- Maps of cosmic microwave background (CMB) temperature and polarization from the 2015 release of Planck data provide the highest quality full-sky view of the surface of last scattering available to date. This enables us to detect possible departures from a globally isotropic cosmology. We present the first searches using CMB polarization for correlations induced by a possible non-trivial topology with a fundamental domain that intersects, or nearly intersects, the last-scattering surface (at comoving distance chi(rec)), both via a direct scan for matched circular patterns at the intersections and by an optimal likelihood calculation for specific topologies. We specialize to flat spaces with cubic toroidal (T3) and slab (T1) topologies, finding that explicit searches for the latter are sensitive to other topologies with antipodal symmetry. These searches yield no detection of a compact topology with a scale below the diameter of the last-scattering surface. The limits on the radius R-i of the largest sphere inscribed in the fundamental domain (at log-likelihood ratio Delta ln L > -5 relative to a simply-connected flat Planck best-fit model) are: R-i > 0.97 chi(rec) for the T3 cubic torus; and R-i > 0.56 chi(rec) for the T1 slab. The limit for the T3 cubic torus from the matched-circles search is numerically equivalent, R-i > 0.97 chi(rec) at 99% confidence level from polarization data alone. We also perform a Bayesian search for an anisotropic global Bianchi VIIh geometry. In the non-physical setting, where the Bianchi cosmology is decoupled from the standard cosmology, Planck temperature data favour the inclusion of a Bianchi component with a Bayes factor of at least 2.3 units of log-evidence. However, the cosmological parameters that generate this pattern are in strong disagreement with those found from CMB anisotropy data alone. Fitting the induced polarization pattern for this model to the Planck data requires an amplitude of -0.10 +/- 0.04 compared to the value of + 1 if the model were to be correct. In the physically motivated setting, where the Bianchi parameters are coupled and fitted simultaneously with the standard cosmological parameters, we find no evidence for a Bianchi VIIh cosmology and constrain the vorticity of such models to (omega/H)(0) < 7.6 x 10(-10) (95% CL).
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10. |
- Ade, P. A. R., et al.
(author)
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XXI. The integrated Sachs-Wolfe effect
- 2016
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 594
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Journal article (peer-reviewed)abstract
- This paper presents a study of the integrated Sachs-Wolfe (ISW) effect from the Planck 2015 temperature and polarization data release. This secondary cosmic microwave background (CMB) anisotropy caused by the large-scale time-evolving gravitational potential is probed from different perspectives. The CMB is cross-correlated with different large-scale structure (LSS) tracers: radio sources from the NVSS catalogue; galaxies from the optical SDSS and the infrared WISE surveys; and the Planck 2015 convergence lensing map. The joint cross-correlation of the CMB with the tracers yields a detection at 4 sigma where most of the signal-to-noise is due to the Planck lensing and the NVSS radio catalogue. In fact, the ISW effect is detected from the Planck data only at approximate to 3 sigma (through the ISW-lensing bispectrum), which is similar to the detection level achieved by combining the cross-correlation signal coming from all the galaxy catalogues mentioned above. We study the ability of the ISW effect to place constraints on the dark-energy parameters; in particular, we show that Omega(Lambda) is detected at more than 3 sigma. This cross-correlation analysis is performed only with the Planck temperature data, since the polarization scales available in the 2015 release do not permit significant improvement of the CMB-LSS cross-correlation detectability. Nevertheless, the Planck polarization data are used to study the anomalously large ISW signal previously reported through the aperture photometry on stacked CMB features at the locations of known superclusters and supervoids, which is in conflict with Lambda CDM expectations. We find that the current Planck polarization data do not exclude that this signal could be caused by the ISW effect. In addition, the stacking of the Planck lensing map on the locations of superstructures exhibits a positive cross-correlation with these large-scale structures. Finally, we have improved our previous reconstruction of the ISW temperature fluctuations by combining the information encoded in all the previously mentioned LSS tracers. In particular, we construct a map of the ISW secondary anisotropies and the corresponding uncertainties map, obtained from simulations. We also explore the reconstruction of the ISW anisotropies caused by the large-scale structure traced by the 2MASS Photometric Redshift Survey (2MPZ) by directly inverting the density field into the gravitational potential field.
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11. |
- Rauer, H., et al.
(author)
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The PLATO 2.0 mission
- 2014
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In: Experimental astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 38:1-2, s. 249-330
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Journal article (peer-reviewed)abstract
- PLATO 2.0 has recently been selected for ESA's M3 launch opportunity (2022/24). Providing accurate key planet parameters (radius, mass, density and age) in statistical numbers, it addresses fundamental questions such as: How do planetary systems form and evolve? Are there other systems with planets like ours, including potentially habitable planets? The PLATO 2.0 instrument consists of 34 small aperture telescopes (32 with 25 s readout cadence and 2 with 2.5 s cadence) providing a wide field-of-view (2232 deg(2)) and a large photometric magnitude range (4-16 mag). It focuses on bright (4-11 mag) stars in wide fields to detect and characterize planets down to Earth-size by photometric transits, whose masses can then be determined by ground-based radial-velocity follow-up measurements. Asteroseismology will be performed for these bright stars to obtain highly accurate stellar parameters, including masses and ages. The combination of bright targets and asteroseismology results in high accuracy for the bulk planet parameters: 2 %, 4-10 % and 10 % for planet radii, masses and ages, respectively. The planned baseline observing strategy includes two long pointings (2-3 years) to detect and bulk characterize planets reaching into the habitable zone (HZ) of solar-like stars and an additional step-and-stare phase to cover in total about 50 % of the sky. PLATO 2.0 will observe up to 1,000,000 stars and detect and characterize hundreds of small planets, and thousands of planets in the Neptune to gas giant regime out to the HZ. It will therefore provide the first large-scale catalogue of bulk characterized planets with accurate radii, masses, mean densities and ages. This catalogue will include terrestrial planets at intermediate orbital distances, where surface temperatures are moderate. Coverage of this parameter range with statistical numbers of bulk characterized planets is unique to PLATO 2.0. The PLATO 2.0 catalogue allows us to e. g.: - complete our knowledge of planet diversity for low-mass objects, - correlate the planet mean density-orbital distance distribution with predictions from planet formation theories,- constrain the influence of planet migration and scattering on the architecture of multiple systems, and - specify how planet and system parameters change with host star characteristics, such as type, metallicity and age. The catalogue will allow us to study planets and planetary systems at different evolutionary phases. It will further provide a census for small, low-mass planets. This will serve to identify objects which retained their primordial hydrogen atmosphere and in general the typical characteristics of planets in such a low-mass, low-density range. Planets detected by PLATO 2.0 will orbit bright stars and many of them will be targets for future atmosphere spectroscopy exploring their atmospheres. Furthermore, the mission has the potential to detect exomoons, planetary rings, binary and Trojan planets. The planetary science possible with PLATO 2.0 is complemented by its impact on stellar and galactic science via asteroseismology as well as light curves of all kinds of variable stars, together with observations of stellar clusters of different ages. This will allow us to improve stellar models and study stellar activity. A large number of well-known ages from red giant stars will probe the structure and evolution of our Galaxy. Asteroseismic ages of bright stars for different phases of stellar evolution allow calibrating stellar age-rotation relationships. Together with the results of ESA's Gaia mission, the results of PLATO 2.0 will provide a huge legacy to planetary, stellar and galactic science.
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12. |
- Schmit, Stephanie L, et al.
(author)
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Novel Common Genetic Susceptibility Loci for Colorectal Cancer.
- 2019
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In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 111:2, s. 146-157
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Journal article (peer-reviewed)abstract
- Background: Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk.Methods: We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided.Results: The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0.Conclusions: This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.
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13. |
- Sumaila, U. Rashid, et al.
(author)
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WTO must ban harmful fisheries subsidies
- 2021
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 374:6567, s. 544-544
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Journal article (other academic/artistic)
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14. |
- Birney, Ewan, et al.
(author)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Journal article (peer-reviewed)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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15. |
- Luo, Y. -W, et al.
(author)
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Database of diazotrophs in global ocean : abundance, biomass and nitrogen fixation rates
- 2012
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In: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 4:1, s. 47-73
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Journal article (peer-reviewed)abstract
- Marine N-2 fixing microorganisms, termed di-azotrophs, are a key functional group in marine pelagic ecosystems. The biological fixation of dinitrogen ( N-2) to bioavailable nitrogen provides an important new source of nitrogen for pelagic marine ecosystems and influences primary productivity and organic matter export to the deep ocean. As one of a series of efforts to collect biomass and rates specific to different phytoplankton functional groups, we have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling about 12 000 direct field measurements of cyanobacterial diazotroph abundances (based on microscopic cell counts or qPCR assays targeting the nifH genes) and N-2 fixation rates. Biomass conversion factors are estimated based on cell sizes to convert abundance data to diazotrophic biomass. The database is limited spatially, lacking large regions of the ocean especially in the Indian Ocean. The data are approximately log-normal distributed, and large variances exist in most sub-databases with non-zero values differing 5 to 8 orders of magnitude. Reporting the geometric mean and the range of one geometric standard error below and above the geometric mean, the pelagic N-2 fixation rate in the global ocean is estimated to be 62 (52-73) Tg Nyr(-1) and the pelagic diazotrophic biomass in the global ocean is estimated to be 2.1 (1.4-3.1) Tg C from cell counts and to 89 (43-150) Tg C from nifH- based abundances. Reporting the arithmetic mean and one standard error instead, these three global estimates are 140 +/- 9.2 Tg Nyr(-1), 18 +/- 1.8 Tg C and 590 +/- 70 Tg C, respectively. Uncertainties related to biomass conversion factors can change the estimate of geometric mean pelagic diazotrophic biomass in the global ocean by about +/- 70 %. It was recently established that the most commonly applied method used to measure N-2 fixation has underestimated the true rates. As a result, one can expect that future rate measurements will shift the mean N-2 fixation rate upward and may result in significantly higher estimates for the global N-2 fixation. The evolving database can nevertheless be used to study spatial and temporal distributions and variations of marine N-2 fixation, to validate geochemical estimates and to parameterize and validate biogeochemical models, keeping in mind that future rate measurements may rise in the future.
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16. |
- Jabbari, E., et al.
(author)
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Diagnosis across the Spectrum of Progressive Supranuclear Palsy and Corticobasal Syndrome
- 2020
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In: JAMA Neurology. - : American Medical Association (AMA). - 2168-6149 .- 2168-6157. ; 77:3, s. 377-387
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Journal article (peer-reviewed)abstract
- Importance Atypical parkinsonian syndromes (APS), including progressive supranuclear palsy (PSP), corticobasal syndrome (CBS), and multiple system atrophy (MSA), may be difficult to distinguish in early stages and are often misdiagnosed as Parkinson disease (PD). The diagnostic criteria for PSP have been updated to encompass a range of clinical subtypes but have not been prospectively studied. Objective To define the distinguishing features of PSP and CBS subtypes and to assess their usefulness in facilitating early diagnosis and separation from PD. Design, Setting, Participants This cohort study recruited patients with APS and PD from movement disorder clinics across the United Kingdom from September 1, 2015, through December 1, 2018. Patients with APS were stratified into the following groups: those with Richardson syndrome (PSP-RS), PSP-subcortical (including PSP-parkinsonism and progressive gait freezing subtypes), PSP-cortical (including PSP-frontal and PSP-CBS overlap subtypes), MSA-parkinsonism, MSA-cerebellar, CBS–Alzheimer disease (CBS-AD), and CBS–non-AD. Data were analyzed from February 1, through May 1, 2019. Main Outcomes and Measures Baseline group comparisons used (1) clinical trajectory; (2) cognitive screening scales; (3) serum neurofilament light chain (NF-L) levels; (4) TRIM11, ApoE, and MAPT genotypes; and (5) volumetric magnetic resonance imaging measures. Results A total of 222 patients with APS (101 with PSP, 55 with MSA, 40 with CBS, and 26 indeterminate) were recruited (129 [58.1%] male; mean [SD] age at recruitment, 68.3 [8.7] years). Age-matched control participants (n=76) and patients with PD (n=1967) were included for comparison. Concordance between the antemortem clinical and pathologic diagnoses was achieved in 12 of 13 patients with PSP and CBS (92.3%) undergoing postmortem evaluation. Applying the Movement Disorder Society PSP diagnostic criteria almost doubled the number of patients diagnosed with PSP from 58 to 101. Forty-nine of 101 patients with reclassified PSP (48.5%) did not have the classic PSP-RS subtype. Patients in the PSP-subcortical group had a longer diagnostic latency and a more benign clinical trajectory than those in PSP-RS and PSP-cortical groups. The PSP-subcortical group was distinguished from PSP-cortical and PSP-RS groups by cortical volumetric magnetic resonance imaging measures (area under the curve [AUC], 0.84-0.89), cognitive profile (AUC, 0.80-0.83), serum NF-L level (AUC, 0.75-0.83), and TRIM11 rs564309 genotype. Midbrain atrophy was a common feature of all PSP groups. Eight of 17 patients with CBS (47.1%) undergoing cerebrospinal fluid analysis were identified as having the CBS-AD subtype. Patients in the CBS-AD group had a longer diagnostic latency, relatively benign clinical trajectory, greater cognitive impairment, and higher APOE-ε4 allele frequency than those in the CBS–non-AD group (AUC, 0.80-0.87; P<.05). Serum NF-L levels distinguished PD from all PSP and CBS cases combined (AUC, 0.80; P<.05). Conclusions and Relevance These findings suggest that studies focusing on the PSP-RS subtype are likely to miss a large number of patients with underlying PSP tau pathology. Analysis of cerebrospinal fluid defined a distinct CBS-AD subtype. The PSP and CBS subtypes have distinct characteristics that may enhance their early diagnosis.
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17. |
- Su, Zhan, et al.
(author)
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Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus.
- 2012
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 44:10
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Journal article (peer-reviewed)abstract
- Barrett's esophagus is an increasingly common disease that is strongly associated with reflux of stomach acid and usually a hiatus hernia, and it strongly predisposes to esophageal adenocarcinoma (EAC), a tumor with a very poor prognosis. We report the first genome-wide association study on Barrett's esophagus, comprising 1,852 UK cases and 5,172 UK controls in the discovery stage and 5,986 cases and 12,825 controls in the replication stage. Variants at two loci were associated with disease risk: chromosome 6p21, rs9257809 (Pcombined=4.09×10(-9); odds ratio (OR)=1.21, 95% confidence interval (CI)=1.13-1.28), within the major histocompatibility complex locus, and chromosome 16q24, rs9936833 (Pcombined=2.74×10(-10); OR=1.14, 95% CI=1.10-1.19), for which the closest protein-coding gene is FOXF1, which is implicated in esophageal development and structure. We found evidence that many common variants of small effect contribute to genetic susceptibility to Barrett's esophagus and that SNP alleles predisposing to obesity also increase risk for Barrett's esophagus.
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18. |
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19. |
- Smith, A., et al.
(author)
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LunarEX-a proposal to cosmic vision
- 2009
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In: Experimental Astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 23:3, s. 711-740
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Journal article (peer-reviewed)
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20. |
- Street, D., et al.
(author)
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Progression of atypical parkinsonian syndromes: PROSPECT-M-UK study implications for clinical trials
- 2023
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In: Brain. - : Oxford University Press (OUP). - 0006-8950 .- 1460-2156. ; 146:8, s. 3232-3242
-
Journal article (peer-reviewed)abstract
- Street et al. compare candidate clinical trial end points in progressive supranuclear palsy, multiple system atrophy, corticobasal syndrome and related disorders. Neuroimaging metrics generally enable lower sample sizes than cognitive and functional measures, although optimal outcome measures vary by disease and subtype. The advent of clinical trials of disease-modifying agents for neurodegenerative disease highlights the need for evidence-based end point selection. Here we report the longitudinal PROSPECT-M-UK study of progressive supranuclear palsy (PSP), corticobasal syndrome (CBS), multiple system atrophy (MSA) and related disorders, to compare candidate clinical trial end points. In this multicentre UK study, participants were assessed with serial questionnaires, motor examination, neuropsychiatric and MRI assessments at baseline, 6 and 12 months. Participants were classified by diagnosis at baseline and study end, into Richardson syndrome, PSP-subcortical (PSP-parkinsonism and progressive gait freezing subtypes), PSP-cortical (PSP-frontal, PSP-speech and language and PSP-CBS subtypes), MSA-parkinsonism, MSA-cerebellar, CBS with and without evidence of Alzheimer's disease pathology and indeterminate syndromes. We calculated annual rate of change, with linear mixed modelling and sample sizes for clinical trials of disease-modifying agents, according to group and assessment type. Two hundred forty-three people were recruited [117 PSP, 68 CBS, 42 MSA and 16 indeterminate; 138 (56.8%) male; age at recruitment 68.7 +/- 8.61 years]. One hundred and fifty-nine completed the 6-month assessment (82 PSP, 27 CBS, 40 MSA and 10 indeterminate) and 153 completed the 12-month assessment (80 PSP, 29 CBS, 35 MSA and nine indeterminate). Questionnaire, motor examination, neuropsychiatric and neuroimaging measures declined in all groups, with differences in longitudinal change between groups. Neuroimaging metrics would enable lower sample sizes to achieve equivalent power for clinical trials than cognitive and functional measures, often achieving N < 100 required for 1-year two-arm trials (with 80% power to detect 50% slowing). However, optimal outcome measures were disease-specific. In conclusion, phenotypic variance within PSP, CBS and MSA is a major challenge to clinical trial design. Our findings provide an evidence base for selection of clinical trial end points, from potential functional, cognitive, clinical or neuroimaging measures of disease progression.
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22. |
- Diez, S., et al.
(author)
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A double-sided, shield-less stave prototype for the ATLAS Upgrade strip tracker for the High Luminosity LHC
- 2014
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In: Journal of Instrumentation. - 1748-0221. ; 9, s. P03012-
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Journal article (peer-reviewed)abstract
- A detailed description of the integration structures for the barrel region of the silicon strips tracker of the ATLAS Phase-II upgrade for the upgrade of the Large Hadron Collider, the so-called High Luminosity LHC (HL-LHC), is presented. This paper focuses on one of the latest demonstrator prototypes recently assembled, with numerous unique features. It consists of a shortened, shield-less, and double sided stave, with two candidate power distributions implemented. Thermal and electrical performances of the prototype are presented, as well as a description of the assembly procedures and tools.
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23. |
- Gonzalez-Sevilla, S., et al.
(author)
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A double-sided silicon micro-strip Super-Module for the ATLAS Inner Detector upgrade in the High-Luminosity LHC
- 2014
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In: Journal of Instrumentation. - 1748-0221. ; 9, s. P02003-
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Journal article (peer-reviewed)abstract
- The ATLAS experiment is a general purpose detector aiming to fully exploit the discovery potential of the Large Hadron Collider (LHC) at CERN. It is foreseen that after several years of successful data-taking, the LHC physics programme will be extended in the so-called High-Luminosity LHC, where the instantaneous luminosity will be increased up to 5 x 10(34) cm(-2) s(-1). For ATLAS, an upgrade scenario will imply the complete replacement of its internal tracker, as the existing detector will not provide the required performance due to the cumulated radiation damage and the increase in the detector occupancy. The current baseline layout for the new ATLAS tracker is an all-silicon-based detector, with pixel sensors in the inner layers and silicon micro-strip detectors at intermediate and outer radii. The super-module is an integration concept proposed for the strip region of the future ATLAS tracker, where double-sided stereo silicon micro-strip modules are assembled into a low-mass local support structure. An electrical super-module prototype for eight double-sided strip modules has been constructed. The aim is to exercise the multi-module readout chain and to investigate the noise performance of such a system. In this paper, the main components of the current super-module prototype are described and its electrical performance is presented in detail.
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24. |
- Walcher, C.~J., et al.
(author)
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4MOST Scientific Operations
- 2019
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In: Messenger. - 0722-6691. ; 175, s. 12-16
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Journal article (other academic/artistic)abstract
- The 4MOST instrument is a multi-object spectrograph that will address Galactic and extragalactic science cases simultaneously by observing targets from a large number of different surveys within each science exposure. This parallel mode of operation and the survey nature of 4MOST require some distinct 4MOST- specific operational features within the overall operations model of ESO. The main feature is that the 4MOST Consortium will deliver, not only the instrument, but also contractual services to the user community, which is why 4MOST is also described as a facility. This white paper concentrates on information particularly useful to answering the forthcoming Call for Letters of Intent.
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25. |
- Chelban, V., et al.
(author)
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Neurofilament light levels predict clinical progression and death in multiple system atrophy
- 2022
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In: Brain. - : Oxford University Press (OUP). - 0006-8950 .- 1460-2156. ; 145:12, s. 4398-4408
-
Journal article (peer-reviewed)abstract
- In this large multiple system atrophy cohort, Chelban et al. show that plasma NfL correlates with clinical disease severity, progression and prognosis, and could help inform patient stratification and monitor treatment responses in future trials of putative disease-modifying agents. Disease-modifying treatments are currently being trialled in multiple system atrophy. Approaches based solely on clinical measures are challenged by heterogeneity of phenotype and pathogenic complexity. Neurofilament light chain protein has been explored as a reliable biomarker in several neurodegenerative disorders but data on multiple system atrophy have been limited. Therefore, neurofilament light chain is not yet routinely used as an outcome measure in multiple system atrophy. We aimed to comprehensively investigate the role and dynamics of neurofilament light chain in multiple system atrophy combined with cross-sectional and longitudinal clinical and imaging scales and for subject trial selection. In this cohort study, we recruited cross-sectional and longitudinal cases in a multicentre European set-up. Plasma and CSF neurofilament light chain concentrations were measured at baseline from 212 multiple system atrophy cases, annually for a mean period of 2 years in 44 multiple system atrophy patients in conjunction with clinical, neuropsychological and MRI brain assessments. Baseline neurofilament light chain characteristics were compared between groups. Cox regression was used to assess survival; receiver operating characteristic analysis to assess the ability of neurofilament light chain to distinguish between multiple system atrophy patients and healthy controls. Multivariate linear mixed-effects models were used to analyse longitudinal neurofilament light chain changes and correlated with clinical and imaging parameters. Polynomial models were used to determine the differential trajectories of neurofilament light chain in multiple system atrophy. We estimated sample sizes for trials aiming to decrease neurofilament light chain levels. We show that in multiple system atrophy, baseline plasma neurofilament light chain levels were better predictors of clinical progression, survival and degree of brain atrophy than the neurofilament light chain rate of change. Comparative analysis of multiple system atrophy progression over the course of disease, using plasma neurofilament light chain and clinical rating scales, indicated that neurofilament light chain levels rise as the motor symptoms progress, followed by deceleration in advanced stages. Sample size prediction suggested that significantly lower trial participant numbers would be needed to demonstrate treatment effects when incorporating plasma neurofilament light chain values into multiple system atrophy clinical trials in comparison to clinical measures alone. In conclusion, neurofilament light chain correlates with clinical disease severity, progression and prognosis in multiple system atrophy. Combined with clinical and imaging analysis, neurofilament light chain can inform patient stratification and serve as a reliable biomarker of treatment response in future multiple system atrophy trials of putative disease-modifying agents.
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26. |
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27. |
- Shapiro, M, et al.
(author)
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An Earth-system prediction initiative for the twenty-first century: An international interdisciplinary initiative to accelerate advances in knowledge, prediction, use and value of weather, climate and Earth-system information
- 2010
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In: BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY. - 0003-0007. ; 91:10, s. 1377-1388
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Journal article (peer-reviewed)abstract
- The necessity and benefits for establishing the international Earth-system Prediction Initiative (EPI) are discussed by scientists associated with the World Meteorological Organization (WMO) World Weather Research Programme (WWRP), World Climate Research Programme (WCRP), International Geosphere–Biosphere Programme (IGBP), Global Climate Observing System (GCOS), and natural-hazards and socioeconomic communities. The proposed initiative will provide research and services to accelerate advances in weather, climate, and Earth system prediction and the use of this information by global societies. It will build upon the WMO, the Group on Earth Observations (GEO), the Global Earth Observation System of Systems (GEOSS) and the International Council for Science (ICSU) to coordinate the effort across the weather, climate, Earth system, natural-hazards, and socioeconomic disciplines. It will require (i) advanced high-performance computing facilities, supporting a worldwide network of research and operational modeling centers, and early warning systems; (ii) science, technology, and education projects to enhance knowledge, awareness, and utilization of weather, climate, environmental, and socioeconomic information; (iii) investments in maintaining existing and developing new observational capabilities; and (iv) infrastructure to transition achievements into operational products and services.
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28. |
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29. |
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30. |
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32. |
- Traven, G., et al.
(author)
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The GALAH survey : multiple stars and our Galaxy: I. A comprehensive method for deriving properties of FGK binary stars?
- 2020
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 638
-
Journal article (peer-reviewed)abstract
- Context. Binary stellar systems form a large fraction of the Galaxy's stars. They are useful as laboratories for studying the physical processes taking place within stars, and must be correctly taken into account when observations of stars are used to study the structure and evolution of the Galaxy. The advent of large-scale spectroscopic and photometric surveys allows us to obtain large samples of binaries that permit characterising their populations.Aims. We aim to obtain a large sample of double-lined spectroscopic binaries (SB2s) by analysis of spectra from the GALAH survey in combination with photometric and astrometric data. A combined analysis will provide stellar parameters of thousands of binary stars that can be combined to form statistical observables of a given population. We aim to produce a catalogue of well-characterised systems, which can in turn be compared to models of populations of binary stars, or to follow-up individual systems of interest.Methods. We obtained a list of candidate SB2 systems from a t-distributed stochastic neighbour embedding (t-SNE) classification and a cross-correlation analysis of GALAH spectra. To compute parameters of the primary and secondary star, we used a Bayesian approach that includes a parallax prior from Gaia DR2, spectra from GALAH, and apparent magnitudes from APASS, Gaia DR2, 2MASS, and WISE. We used a Markov chain Monte Carlo approach to sample the posterior distributions of the following model parameters for the two stars: T-eff[1,T-2], logg([1,2]), [Fe/H], V-r[1,V-2], v(mic[1,2]), v(broad[1,2]), R-[1,R-2], and E(B-V).Results. We present results for 12 760 binary stars detected as SB2s. We construct the statistical observables T-1/T-2, Delta V-r, and R-1/R-2, which demonstrate that our sample mostly consists of dwarfs, with a significant fraction of evolved stars and several dozen members of the giant branch. The majority of these binary stars is concentrated at the lower boundary of the Delta V-r distribution, and the R-1/R-2 ratio is mostly close to unity. The derived metallicity of our binary stars is statistically lower than that of single dwarf stars from the same magnitude-limited sample.Conclusions. Our sample of binary stars represents a large population of well-characterised double-lined spectroscopic binaries that are appropriate for statistical studies of the binary populations. The derived stellar properties and their distributions show trends that are expected for a population of close binary stars (a < 10 AU) detected through double lines in their spectra. Our detection technique allows us to probe binary systems with mass ratios 0.5 q <= 1.
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33. |
- Balucinska-Church, M., et al.
(author)
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Dipping in Cygnus X-2 in a multi-wavelength campaign due to absorption of extended ADC emission
- 2011
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 530
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Journal article (peer-reviewed)abstract
- We report results of one-day simultaneous multiwavelength observations of Cygnus X-2 using XMM, Chandra, the European VLBI Network and the XMM Optical Monitor. During the observations, the source did not exhibit Z-track movement, but remained in the vicinity of the soft apex. It was in a radio quiescent/quiet state of 60 degrees these structures can still cover large parts of the extended ADC, without absorbing emission from the central neutral star.
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34. |
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35. |
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36. |
- Guiglion, G., et al.
(author)
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4MOST Survey Strategy Plan
- 2019
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In: Messenger. - 0722-6691. ; 175, s. 17-21
-
Journal article (other academic/artistic)abstract
- The current status of and motivation for the 4MOST survey strategy, as developed by the Consortium science team, are presented here. Key elements of the strategy are described, such as sky coverage, number of visits and total exposure times in different parts of the sky, and how to deal with different observing conditions. The task of organising the strategy is not simple, with many different surveys that have vastly different target brightnesses and densities, sample completeness levels, and signal-to-noise requirements. We introduce here a number of concepts that we will use to ensure all surveys are optimised. Astronomers who are planning to submit a Participating Survey proposal are strongly encouraged to read this article and any relevant 4MOST Survey articles in this issue of The Messenger such that they can optimally complement and benefit from the planned surveys of the 4MOST Consortium.
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37. |
- Jabbari, E., et al.
(author)
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Proximity extension assay testing reveals novel diagnostic biomarkers of atypical parkinsonian syndromes
- 2019
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In: Journal of Neurology Neurosurgery and Psychiatry. - : BMJ. - 0022-3050 .- 1468-330X. ; 90:7, s. 768-773
-
Journal article (peer-reviewed)abstract
- Objective The high degree of clinical overlap between atypical parkinsonian syndromes (APS) and Parkinson's disease (PD) makes diagnosis challenging. We aimed to identify novel diagnostic protein biomarkers of APS using multiplex proximity extension assay (PEA) testing. Methods Cerebrospinal fluid (CSF) samples from two independent cohorts, each consisting of APS and PD cases, and controls, were analysed for neurofilament light chain (NF-L) and Olink Neurology and Inflammation PEA biomarker panels. Whole-cohort comparisons of biomarker concentrations were made between APS (n=114), PD (n=37) and control (n=34) groups using logistic regression analyses that included gender, age and disease duration as covariates. Results APS versus controls analyses revealed 11 CSF markers with significantly different levels in cases and controls (p<0.002). Four of these markers also reached significance (p<0.05) in APS versus PD analyses. Disease-specific analyses revealed lower group levels of FGF-5, FGF-19 and SPOCK1 in multiple system atrophy compared with progressive supranuclear palsy and corticobasal syndrome. Receiver operating characteristic curve analyses suggested that the diagnostic accuracy of NF-L was superior to the significant PEA biomarkers in distinguishing APS, PD and controls. The biological processes regulated by the significant proteins include cell differentiation and immune cell migration. Delta and notch-like epidermal growth factor-related receptor (DNER) had the strongest effect size in APS versus controls and APS versus PD analyses. DNER is highly expressed in substantia nigra and is an activator of the NOTCH1 pathway which has been implicated in the aetiology of other neurodegenerative disorders including Alzheimer's disease. Conclusions PEA testing has identified potential novel diagnostic biomarkers of APS.
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38. |
- Li, W, et al.
(author)
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Predicting breast cancer response to neoadjuvant treatment using multi-feature MRI: results from the I-SPY 2 TRIAL
- 2020
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In: NPJ breast cancer. - : Springer Science and Business Media LLC. - 2374-4677. ; 6:1, s. 63-
-
Journal article (peer-reviewed)abstract
- Dynamic contrast-enhanced (DCE) MRI provides both morphological and functional information regarding breast tumor response to neoadjuvant chemotherapy (NAC). The purpose of this retrospective study is to test if prediction models combining multiple MRI features outperform models with single features. Four features were quantitatively calculated in each MRI exam: functional tumor volume, longest diameter, sphericity, and contralateral background parenchymal enhancement. Logistic regression analysis was used to study the relationship between MRI variables and pathologic complete response (pCR). Predictive performance was estimated using the area under the receiver operating characteristic curve (AUC). The full cohort was stratified by hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) status (positive or negative). A total of 384 patients (median age: 49 y/o) were included. Results showed analysis with combined features achieved higher AUCs than analysis with any feature alone. AUCs estimated for the combined versus highest AUCs among single features were 0.81 (95% confidence interval [CI]: 0.76, 0.86) versus 0.79 (95% CI: 0.73, 0.85) in the full cohort, 0.83 (95% CI: 0.77, 0.92) versus 0.73 (95% CI: 0.61, 0.84) in HR-positive/HER2-negative, 0.88 (95% CI: 0.79, 0.97) versus 0.78 (95% CI: 0.63, 0.89) in HR-positive/HER2-positive, 0.83 (95% CI not available) versus 0.75 (95% CI: 0.46, 0.81) in HR-negative/HER2-positive, and 0.82 (95% CI: 0.74, 0.91) versus 0.75 (95% CI: 0.64, 0.83) in triple negatives. Multi-feature MRI analysis improved pCR prediction over analysis of any individual feature that we examined. Additionally, the improvements in prediction were more notable when analysis was conducted according to cancer subtype.
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39. |
- Miller, David T., et al.
(author)
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Consensus Statement : Chromosomal Microarray Is a First-Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies
- 2010
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In: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 86:5, s. 749-764
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Journal article (peer-reviewed)abstract
- Chromosomal microarray (CMA) is increasingly utilized for genetic testing of individuals with unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), or multiple congenital anomalies (MCA). Performing CMA and G-banded karyotyping on every patient substantially increases the total cost of genetic testing. The International Standard Cytogenomic Array (ISCA) Consortium held two international workshops and conducted a literature review of 33 studies, including 21,698 patients tested by CMA. We provide an evidence-based summary of clinical cytogenetic testing comparing CMA to G-banded karyotyping with respect to technical advantages and limitations, diagnostic yield for various types of chromosomal aberrations, and issues that affect test interpretation. CMA offers a much higher diagnostic yield (15%-20%) for genetic testing of individuals with unexplained DD/ID, ASD, or MCA than a G-banded karyotype (similar to 3%, excluding Down syndrome and other recognizable chromosomal syndromes), primarily because of its higher sensitivity for submicroscopic deletions and duplications. Truly balanced rearrangements and low-level mosaicism are generally not detectable by arrays, but these are relatively infrequent causes of abnormal phenotypes in this population (<1%). Available evidence strongly supports the use of CMA in place of G-banded karyotyping as the first-tier cytogenetic diagnostic test for patients with DD/ID, ASD, or MCA. G-banded karyotype analysis should be reserved for patients with obvious chromosomal syndromes (e.g., Down syndrome), a family history of chromosomal rearrangement, or a history of multiple miscarriages.
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40. |
- Wilson, Samuel T., et al.
(author)
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Short-term variability in euphotic zone biogeochemistry and primary productivity at Station ALOHA : A case study of summer 2012
- 2015
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In: Global Biogeochemical Cycles. - 0886-6236 .- 1944-9224. ; 29:8, s. 1145-1164
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Journal article (peer-reviewed)abstract
- Time-series observations are critical to understand the structure, function, and dynamics of marine ecosystems. The Hawaii Ocean Time-series program has maintained near-monthly sampling at Station ALOHA (22°45′N, 158°00′W) in the oligotrophic North Pacific Subtropical Gyre (NPSG) since 1988 and has identified ecosystem variability over seasonal to interannual timescales. To further extend the temporal resolution of these near-monthly time-series observations, an extensive field campaign was conducted during July-September 2012 at Station ALOHA with near-daily sampling of upper water-column biogeochemistry, phytoplankton abundance, and activity. The resulting data set provided biogeochemical measurements at high temporal resolution and documents two important events at Station ALOHA: (1) a prolonged period of low productivity when net community production in the mixed layer shifted to a net heterotrophic state and (2) detection of a distinct sea-surface salinity minimum feature which was prominent in the upper water column (0-50 m) for a period of approximately 30 days. The shipboard observations during July-September 2012 were supplemented with in situ measurements provided by Seagliders, profiling floats, and remote satellite observations that together revealed the extent of the low productivity and the sea-surface salinity minimum feature in the NPSG.
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41. |
- Acciarri, R., et al.
(author)
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Demonstration of MeV-scale physics in liquid argon time projection chambers using ArgoNeuT
- 2019
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In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 99:1
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Journal article (peer-reviewed)abstract
- MeV-scale energy depositions by low-energy photons produced in neutrino-argon interactions have been identified and reconstructed in ArgoNeuT liquid argon time projection chamber (LArTPC) data. ArgoNeuT data collected on the NuMI beam at Fermilab were analyzed to select isolated low-energy depositions in the TPC volume. The total number, reconstructed energies, and positions of these depositions have been compared to those from simulations of neutrino-argon interactions using the FLUKA Monte Carlo generator. Measured features are consistent with energy depositions from photons produced by deexcitation of the neutrino's target nucleus and by inelastic scattering of primary neutrons produced by neutrino-argon interactions. This study represents a successful reconstruction of physics at the MeV scale in a LArTPC, a capability of crucial importance for detection and reconstruction of supernova and solar neutrino interactions in future large LArTPCs.
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42. |
- Christleib, Norbert, et al.
(author)
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4MOST Consortium Survey 2: The Milky Way Halo High-Resolution Survey
- 2019
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In: Messenger. - 0722-6691. ; 175, s. 26-29
-
Journal article (other academic/artistic)abstract
- We will study the formation history of the Milky Way, and the earliest phases of its chemical enrichment, with a sample of more than 1.5 million stars at high galactic latitude. Elemental abundances of up to 20 elements with a precision of better than 0.2 dex will be derived for these stars. The sample will include members of kinematically coherent substructures, which we will associate with their possible birthplaces by means of their abundance signatures and kinematics, allowing us to test models of galaxy formation. Our target catalogue is also expected to contain 30 000 stars at a metallicity of less than one hundredth that of the Sun. This sample will therefore be almost a factor of 100 larger than currently existing samples of metal-poor stars for which precise elemental abundances are available (determined from high-resolution spectroscopy), enabling us to study the early chemical evolution of the Milky Way in unprecedented detail.
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44. |
- Cornish, Alex J., et al.
(author)
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The genomic landscape of 2,023 colorectal cancers
- 2024
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In: Nature. - 0028-0836 .- 1476-4687. ; In Press
-
Journal article (peer-reviewed)abstract
- Colorectal carcinoma (CRC) is a common cause of mortality1, but a comprehensive description of its genomic landscape is lacking2–9. Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichiacolipks+ colibactin in rectal cancers10 and the importance of the SBS93 signature11–13, which suggests that diet or smoking is a risk factor. Immune-escape driver mutations14 are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care.
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45. |
- Eichner, Meri, et al.
(author)
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Chemical microenvironments and single-cell carbon and nitrogen uptake in field-collected colonies of Trichodesmium under different pCO2
- 2017
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In: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 11, s. 1305-1317
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Journal article (peer-reviewed)abstract
- © 2017 The Author(s)Gradients of oxygen (O2) and pH, as well as small-scale fluxes of carbon (C), nitrogen (N) and O2 were investigated under different partial pressures of carbon dioxide (pCO2) in field-collected colonies of the marine dinitrogen (N2)-fixing cyanobacterium Trichodesmium. Microsensor measurements indicated that cells within colonies experienced large fluctuations in O2, pH and CO2 concentrations over a day–night cycle. O2 concentrations varied with light intensity and time of day, yet colonies exposed to light were supersaturated with O2 (up to ~200%) throughout the light period and anoxia was not detected. Alternating between light and dark conditions caused a variation in pH levels by on average 0.5 units (equivalent to 15nmoll-1 proton concentration). Single-cell analyses of C and N assimilation using secondary ion mass spectrometry (SIMS; large geometry SIMS and nanoscale SIMS) revealed high variability in metabolic activity of single cells and trichomes of Trichodesmium, and indicated transfer of C and N to colony-associated non-photosynthetic bacteria. Neither O2 fluxes nor C fixation by Trichodesmium were significantly influenced by short-term incubations under different pCO2 levels, whereas N2 fixation increased with increasing pCO2. The large range of metabolic rates observed at the single-cell level may reflect a response by colony-forming microbial populations to highly variable microenvironments.The ISME Journal advance online publication, 11 April 2017; doi:10.1038/ismej.2017.15.
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48. |
- Frantz, Laurent A. F., et al.
(author)
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Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
- 2019
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:35, s. 17231-17238
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Journal article (peer-reviewed)abstract
- Archaeological evidence indicates that pig domestication had begun by similar to 10,500 y before the present ( BP) in the Near East, and mitochondrial DNA ( mtDNA) suggests that pigs arrived in Europe alongside farmers similar to 8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.
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49. |
- Gron, Kurt J., et al.
(author)
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Archaeological cereals as an isotope record of long-term soil health and anthropogenic amendment in southern Scandinavia
- 2021
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In: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791. ; 253
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Journal article (peer-reviewed)abstract
- Maintaining soil health is integral to agricultural production, and the archaeological record contains multiple lines of palaeoclimatic and palaeoenvironmental proxy evidence that can contribute to the understanding and analysis of long-term trajectories of change that are key for contextualizing 21st century global environmental challenges. Soil is a capital resource and its nutrient balance is modified by agricultural activities, making it necessary to ensure soil productivity is maintained and managed through human choices and actions. Since prehistory this has always been the case; soil is a non-renewable resource within a human lifetime. Here, we present and interpret carbon and nitrogen isotope analysis of charred cereals from southern Scandinavia. Anthropogenic effects on soils are evident from the initiation of farming 6000 years ago, as is amendment to counteract its effects. The earliest cereals were planted on pristine soils, and by the late Neolithic, agriculture extensified. By the Iron Age it was necessary to significantly amend depleted soils to maintain crop yields. We propose that these data provide a record of soil water retention, net precipitation and amendment. From the start of the Neolithic there is a concurrent decrease in both Δ13C and δ15N, mitigated only by the replacement of soil organic content in the form of manure in the Iron Age. The cereal isotopes provide a record of trajectories of agricultural sustainability and anthropogenic adaptation for nearly the entire history of farming in the region.
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- Gron, Kurt J., et al.
(author)
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Nitrogen isotope evidence for manuring of early Neolithic Funnel Beaker Culture cereals from Stensborg, Sweden
- 2017
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In: Journal of Archaeological Science: Reports. - : Elsevier BV. - 2352-409X. ; 14, s. 575-579
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Journal article (peer-reviewed)abstract
- Little is known about arable agriculture in the Early Neolithic (4000–3300 cal BC, Funnel Beaker Culture) of Southern Scandinavia. Archaeobotanical material is rare and few archaeological sites have yielded more than a small number of charred cereal grains. In this short communication, we present single-entity carbon and nitrogen isotope analyses of charred cereals from Stensborg, an early Funnel Beaker Culture site near Stockholm, Sweden. This cereal assemblage is important as it is large, well-preserved and consists of multiple crop species. Our isotopic results indicate that many of the Stensborg cereal crops had been manured and that there is intra- and inter-species variation in manuring. We interpret these data as evidence of an integrated regime of stock-keeping and small-scale agriculture in the early Funnel Beaker Culture near its northernmost limit.
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