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1.
  • Birney, Ewan, et al. (författare)
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
  • 2007
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
  • Tidskriftsartikel (refereegranskat)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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2.
  • Abelev, Betty, et al. (författare)
  • Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
  • 2012
  • Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
  • Tidskriftsartikel (refereegranskat)abstract
    • The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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3.
  • Abelev, Betty, et al. (författare)
  • Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
  • 2012
  • Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7
  • Tidskriftsartikel (refereegranskat)abstract
    • We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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4.
  • Speakman, John R., et al. (författare)
  • Total daily energy expenditure has declined over the past three decades due to declining basal expenditure, not reduced activity expenditure
  • 2023
  • Ingår i: Nature Metabolism. - : NATURE PORTFOLIO. - 2522-5812. ; 5:4, s. 579-588
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • Obesity is caused by a prolonged positive energy balance(1,2). Whether reduced energy expenditure stemming from reduced activity levels contributes is debated(3,4). Here we show that in both sexes, total energy expenditure (TEE) adjusted for body composition and age declined since the late 1980s, while adjusted activity energy expenditure increased over time. We use the International Atomic Energy Agency Doubly Labelled Water database on energy expenditure of adults in the United States and Europe (n = 4,799) to explore patterns in total (TEE: n = 4,799), basal (BEE: n = 1,432) and physical activity energy expenditure (n = 1,432) over time. In males, adjusted BEE decreased significantly, but in females this did not reach significance. A larger dataset of basal metabolic rate (equivalent to BEE) measurements of 9,912 adults across 163 studies spanning 100 years replicates the decline in BEE in both sexes. We conclude that increasing obesity in the United States/Europe has probably not been fuelled by reduced physical activity leading to lowered TEE. We identify here a decline in adjusted BEE as a previously unrecognized factor.
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5.
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6.
  • Abdalla, H., et al. (författare)
  • A search for new supernova remnant shells in the Galactic plane with HESS
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 612
  • Tidskriftsartikel (refereegranskat)abstract
    • A search for new supernova remnants (SNRs) has been conducted using TeV gamma-ray data from the H.E.S.S. Galactic plane survey. As an identification criterion, shell morphologies that are characteristic for known resolved TeV SNRs have been used. Three new SNR candidates were identified in the H.E.S.S. data set with this method. Extensive multiwavelength searches for counterparts were conducted. A radio SNR candidate has been identified to be a counterpart to HESS J1534-571. The TeV source is therefore classified as a SNR. For the other two sources, HESS J1614-518 and HESS J1912 + 101, no identifying counterparts have been found, thus they remain SNR candidates for the time being. TeV-emitting SNRs are key objects in the context of identifying the accelerators of Galactic cosmic rays. The TeV emission of the relativistic particles in the new sources is examined in view of possible leptonic and hadronic emission scenarios, taking the current multiwavelength knowledge into account.
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7.
  • Abdalla, H., et al. (författare)
  • Characterising the VHE diffuse emission in the central 200 parsecs of our Galaxy with HESS
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 612
  • Tidskriftsartikel (refereegranskat)abstract
    • The diffuse very high-energy (VHE; > 100 GeV) gamma-ray emission observed in the central 200 pc of the Milky Way by H.E.S.S. was found to follow dense matter distribution in the central molecular zone (CMZ) up to a longitudinal distance of about 130 pc to the Galactic centre (GC), where the flux rapidly decreases. This was initially interpreted as the result of a burst-like injection of energetic particles 104 yr ago, but a recent more sensitive H.E.S.S. analysis revealed that the cosmic-ray (CR) density profile drops with the distance to the centre, making data compatible with a steady cosmic PeVatron at the GC. In this paper, we extend this analysis to obtain, for the first time, a detailed characterisation of the correlation with matter and to search for additional features and individual gamma-ray sources in the inner 200 pc. Taking advantage of 250 h of H.E.S.S. data and improved analysis techniques, we perform a detailed morphology study of the diffuse VHE emission observed from the GC ridge and reconstruct its total spectrum. To test the various contributions to the total gamma-ray emission, we used an iterative 2D maximum-likelihood approach that allows us to build a phenomenological model of the emission by summing a number of different spatial components. We show that the emission correlated with dense matter covers the full CMZ and that its flux is about half the total diffuse emission flux. We also detect some emission at higher latitude that is likely produced by hadronic collisions of CRs in less dense regions of the GC interstellar medium. We detect an additional emission component centred on the GC and extending over about 15 pc that is consistent with the existence of a strong CR density gradient and confirms the presence of a CR accelerator at the very centre of our Galaxy. We show that the spectrum of full ridge diffuse emission is compatible with that previously derived from the central regions, suggesting that a single population of particles fills the entire CMZ. Finally, we report the discovery of a VHE gamma-ray source near the GC radio arc and argue that it is produced by the pulsar wind nebula candidate G0.13-0.11.
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8.
  • Abdalla, H., et al. (författare)
  • Deeper HESS observations of Vela Junior (RX J0852.0-4622) : Morphology studies and resolved spectroscopy
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 612
  • Tidskriftsartikel (refereegranskat)abstract
    • Aims. We study gamma-ray emission from the shell-type supernova remnant (SNR) RXJ0852.0-4622 to better characterize its spectral properties and its distribution over the SNR. Methods. The analysis of an extended High Energy Spectroscopic System (H.E.S.S.) data set at very high energies (E > 100 GeV) permits detailed studies, as well as spatially resolved spectroscopy, of the morphology and spectrum of the whole RXJ0852.0-4622 region. The H.E.S.S. data are combined with archival data from other wavebands and interpreted in the framework of leptonic and hadronic models. The joint Fermi-LAT-H.E.S.S. spectrum allows the direct determination of the spectral characteristics of the parent particle population in leptonic and hadronic scenarios using only GeV-TeV data. Results. An updated analysis of the H.E.S.S. data shows that the spectrum of the entire SNR connects smoothly to the high-energy spectrum measured by Fermi-LAT. The increased data set makes it possible to demonstrate that the H.E.S.S. spectrum deviates significantly from a power law and is well described by both a curved power law and a power law with an exponential cutoff at an energy of E-cut = (6.7 +/- 1.2(stat) +/- 1.2(syst)) TeV. The joint Fermi-LAT-H.E.S.S. spectrum allows the unambiguous identification of the spectral shape as a power law with an exponential cutoff. No significant evidence is found for a variation of the spectral parameters across the SNR, suggesting similar conditions of particle acceleration across the remnant. A simple modeling using one particle population to model the SNR emission demonstrates that both leptonic and hadronic emission scenarios remain plausible. It is also shown that at least a part of the shell emission is likely due to the presence of a pulsar wind nebula around PSR J0855-4644.
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9.
  • Abdalla, H., et al. (författare)
  • Detection of variable VHE gamma-ray emission from the extra-galactic gamma-ray binary LMC P3
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 610
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. Recently, the high-energy (HE, 0.1-100 GeV) gamma-ray emission from the object LMC P3 in the Large Magellanic Cloud (LMC) has been discovered to be modulated with a 10.3-day period, making it the first extra-galactic gamma-ray binary. Aims. This work aims at the detection of very-high-energy (VHE, >100 GeV) gamma-ray emission and the search for modulation of the VHE signal with the orbital period of the binary system. Methods. LMC P3 has been observed with the High Energy Stereoscopic System (H.E.S.S.); the acceptance-corrected exposure time is 100 h. The data set has been folded with the known orbital period of the system in order to test for variability of the emission. Results. VHE gamma-ray emission is detected with a statistical significance of 6.4 sigma. The data clearly show variability which is phase-locked to the orbital period of the system. Periodicity cannot be deduced from the H.E.S.S. data set alone. The orbit-averaged luminosity in the 1-10 TeV energy range is (1.4 +/- 0.2) x 10(35) erg s(-1). A luminosity of (5 +/- 1) x 10(35) erg s(-1) is reached during 20% of the orbit. HE and VHE gamma-ray emissions are anti-correlated. LMC P3 is the most luminous gamma-ray binary known so far.
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10.
  • Abdalla, H., et al. (författare)
  • First ground-based measurement of sub-20 GeV to 100 GeV gamma-Rays from the Vela pulsar with HESS II
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 620
  • Tidskriftsartikel (refereegranskat)abstract
    • Aims. We report on the measurement and investigation of pulsed high-energy y-ray emission from the Vela pulsar, PSR B0833-45, based on observations with the largest telescope of H.E.S.S., CT5, in monoscopic mode, and on data obtained with the Fermi-LAT. Methods. Data from 40.3 h of observations carried out with the H.E.S.S. II array from 2013 to 2015 have been used. A dedicated very low-threshold event reconstruction and analysis pipeline was developed to achieve the lowest possible energy threshold. Eight years of Fermi-LAT data were analysed and also used as reference to validate the CT5 telescope response model and analysis methods. Results. A pulsed gamma-ray signal at a significance level of more than 15 sigma is detected from the P2 peak of the Vela pulsar light curve. Of a total of 15 835 events, more than 6000 lie at an energy below 20 GeV, implying a significant overlap between H.E.S.S. II-CT5 and the Fermi-LAT. While the investigation of the pulsar light curve with the LAT confirms characteristics previously known up to 20 GeV in the tens of GeV energy range, CT5 data show a change in the pulse morphology of P2, i.e. an extreme sharpening of its trailing edge, together with the possible onset of a new component at 3.4 sigma significance level. Assuming a power-law model for the P2 spectrum, an excellent agreement is found for the photon indices (Gamma similar or equal to 4.1) obtained with the two telescopes above 10 GeV and an upper bound of 8% is derived on the relative offset between their energy scales. Using data from both instruments, it is shown however that the spectrum of P2 in the 10-100 GeV has a pronounced curvature; this is a confirmation of the sub-exponential cut-off form found at lower energies with the LAT. This is further supported by weak evidence of an emission above 100 GeV obtained with CT5. In contrast, converging indications are found from both CT5 and LAT data for the emergence of a hard component above 50 GeV in the leading wing (LW2) of P2, which possibly extends beyond 100 GeV. Conclusions. The detection demonstrates the performance and understanding of CT5 from 100 GeV down to the sub-20 GeV domain, i.e. unprecedented low energy for ground-based gamma-ray astronomy. The extreme sharpening of the trailing edge of the P2 peak found in the H.E.S.S. II light curve of the Vela pulsar and the possible extension beyond 100 GeV of at least one of its features, LW2, provide further constraints to models of gamma-Ray emission from pulsars.
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11.
  • Abdalla, H., et al. (författare)
  • Gamma-ray blazar spectra with HESS II mono analysis : The case of PKS2155-304 and PG1553+113
  • 2017
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 600
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. The addition of a 28 m Cherenkov telescope (CT5) to the H.E.S.S. array extended the experiment's sensitivity to lower energies. The lowest energy threshold is obtained using monoscopic analysis of data taken with CT5, providing access to gamma-ray energies below 100 GeV for small zenith angle observations. Such an extension of the instrument's energy range is particularly beneficial for studies of active galactic nuclei with soft spectra, as expected for those at a redshift >= 0.5. The high-frequency peaked BL Lac objects PKS 2155-304 (z = 0.116) and PG 1553 + 113 (0.43 < z < 0.58) are among the brightest objects in the gamma-ray sky, both showing clear signatures of gamma-ray absorption at E > 100 GeV interpreted as being due to interactions with the extragalactic background light (EBL). Aims. The aims of this work are twofold: to demonstrate the monoscopic analysis of CT5 data with a low energy threshold, and to obtain accurate measurements of the spectral energy distributions (SED) of PKS 2155-304 and PG 1553 + 113 near their SED peaks at energies approximate to 100 GeV. Methods. Multiple observational campaigns of PKS 2155 304 and PG 1553 + 113 were conducted during 2013 and 2014 using the full H.E.S.S. II instrument (CT1-5). A monoscopic analysis of the data taken with the new CT5 telescope was developed along with an investigation into the systematic uncertainties on the spectral parameters which are derived from this analysis. Results. Using the data from CT5, the energy spectra of PKS 2155 304 and PG 1553 + 113 were reconstructed down to conservative threshold energies of 80 GeV for PKS 2155 304, which transits near zenith, and 110 GeV for the more northern PG 1553 + 113. The measured spectra, well fitted in both cases by a log-parabola spectral model ( with a 5.0 similar to statistical preference for non-zero curvature for PKS 2155 304 and 4.5 sigma for PG 1553+113), were found consistent with spectra derived from contemporaneous Fermi-LAT data, indicating a sharp break in the observed spectra of both sources at E approximate to 100 GeV. When corrected for EBL absorption, the intrinsic H.E.S.S. II mono and Fermi-LAT spectrum of PKS 2155 304 was found to show significant curvature. For PG 1553+113, however, no significant detection of curvature in the intrinsic spectrum could be found within statistical and systematic uncertainties.
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12.
  • Abdalla, H., et al. (författare)
  • H.E.S.S. observations of the flaring gravitationally lensed galaxy PKS 1830–211
  • 2019
  • Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 486:3, s. 3886-3891
  • Tidskriftsartikel (refereegranskat)abstract
    • PKS 1830-211 is a known macrolensed quasar located at a redshift of z = 2.5. Its highenergy gamma-ray emission has been detected with the Fermi-Large Area Telescope (LAT) instrument and evidence for lensing was obtained by several authors from its high-energy data. Observations of PKS 1830-211 were taken with the High Energy Stereoscopic System (H.E.S.S.) array of Imaging Atmospheric Cherenkov Telescopes in 2014 August, following a flare alert by the Fermi-LAT Collaboration. The H.E.S.S observations were aimed at detecting a gamma-ray flare delayed by 20-27 d from the alert flare, as expected from observations at other wavelengths. More than 12 h of good-quality data were taken with an analysis threshold of similar to 67 GeV. The significance of a potential signal is computed as a function of the date and the average significance over the whole period. Data are compared to simultaneous observations by Fermi-LAT. No photon excess or significant signal is detected. An upper limit on PKS 1830-211 flux above 67 GeV is computed and compared to the extrapolation of the Fermi-LAT flare spectrum.
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13.
  • Abdalla, H., et al. (författare)
  • HESS discovery of very high energy gamma-ray emission from PKS 0625-354
  • 2018
  • Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press. - 0035-8711 .- 1365-2966. ; 476:3, s. 4187-4198
  • Tidskriftsartikel (refereegranskat)abstract
    • PKS 0625-354 (z = 0.055) was observed with the four High Energy Stereoscopic System (H.E.S.S.) telescopes in 2012 during 5.5 h. The source was detected above an energy threshold of 200 GeV at a significance level of 6.1 sigma. No significant variability is found in these observations. The source is well described with a power-law spectrum with photon index Gamma = 2.84 +/- 0.50(stat) +/- 0.10(syst) and normalization (at E-0 = 1.0 TeV) N-0(E-0)=(0.58 +/- 0.22(stat) +/- 0.12(syst)) x 10(-12) TeV-1 cm(-2) s(-1). Multiwavelength data collected with Fermi-LAT, Swift-XRT, Swift-UVOT, ATOM and WISE are also analysed. Significant variability is observed only in the Fermi-LAT gamma-ray and Swift-XRT X-ray energy bands. Having a good multiwavelength coverage from radio to very high energy, we performed a broad-band modelling from two types of emission scenarios. The results from a one zone lepto-hadronic and a multizone leptonic models are compared and discussed. On the grounds of energetics, our analysis favours a leptonic multizone model. Models associated to the X-ray variability constraint support previous results, suggesting a BL Lac nature of PKS 0625-354 with, however, a large-scale jet structure typical of a radio galaxy.
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14.
  • Abdalla, H., et al. (författare)
  • HESS J1741-302 : a hidden accelerator in the Galactic plane
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 612
  • Tidskriftsartikel (refereegranskat)abstract
    • The H.E.S.S. Collaboration has discovered a new very high energy (VHE, E > 0.1 TeV) gamma-ray source, HESS J1741-302, located in the Galactic plane. Despite several attempts to constrain its nature, no plausible counterpart has been found so far at X-ray and MeV/GeV gamma-ray energies, and the source remains unidentified. An analysis of 145-h of observations of HESS J1741-302 at VHEs has revealed a steady and relatively weak TeV source (similar to 1% of the Crab Nebula flux), with a spectral index of Gamma = 2.3 +/- 0.2(stat) +/- 0.2(sys), extending to energies up to 10 TeV without any clear signature of a cut-off. In a hadronic scenario, such a spectrum implies an object with particle acceleration up to energies of several hundred TeV. Contrary to most H.E.S.S. unidentified sources, the angular size of HESS J1741-302 is compatible with the H.E.S.S. point spread function at VHEs, with an extension constrained to be below 0.068 degrees at a 99% confidence level. The gamma-ray emission detected by H.E.S.S. can be explained both within a hadronic scenario, due to collisions of protons with energies of hundreds of TeV with dense molecular clouds, and in a leptonic scenario, as a relic pulsar wind nebula, possibly powered by the middle-aged (20 kyr) pulsar PSR B1737-30. A binary scenario, related to the compact radio source 1LC 358.266+0.038 found to be spatially coincident with the best fit position of HESS J1741-302, is also envisaged.
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15.
  • Abdalla, H., et al. (författare)
  • HESS observations of RX J1713.7-3946 with improved angular and spectral resolution : Evidence for gamma-ray emission extending beyond the X-ray emitting shell
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 612
  • Tidskriftsartikel (refereegranskat)abstract
    • Supernova remnants exhibit shock fronts (shells) that can accelerate charged particles up to very high energies. In the past decade, measurements of a handful of shell-type supernova remnants in very high-energy gamma rays have provided unique insights into the acceleration process. Among those objects, RX J1713.7-3946 (also known as G347.3-0.5) has the largest surface brightness, allowing us in the past to perform the most comprehensive study of morphology and spatially resolved spectra of any such very high-energy gamma-ray source. Here we present extensive new H.E.S.S. measurements of RX J1713.7-3946, almost doubling the observation time compared to our previous publication. Combined with new improved analysis tools, the previous sensitivity is more than doubled. The H.E.S.S. angular resolution of 0.048 degrees (0.036 degrees above 2 TeV) is unprecedented in gamma-ray astronomy and probes physical scales of 0.8 (0.6) parsec at the remnant's location. The new H. E. S. S. image of RX J1713.7-3946 allows us to reveal clear morphological di ff erences between X-rays and gamma rays. In particular, for the outer edge of the brightest shell region, we find the first ever indication for particles in the process of leaving the acceleration shock region. By studying the broadband energy spectrum, we furthermore extract properties of the parent particle populations, providing new input to the discussion of the leptonic or hadronic nature of the gamma-ray emission mechanism.
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16.
  • Abdalla, H., et al. (författare)
  • Particle transport within the pulsar wind nebula HESS J1825-137
  • 2019
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 621
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. We present a detailed view of the pulsar wind nebula (PWN) HESS J1825-137. We aim to constrain the mechanisms dominating the particle transport within the nebula, accounting for its anomalously large size and spectral characteristics. Aims. The nebula was studied using a deep exposure from over 12 years of H.E.S.S. I operation, together with data from H.E.S.S. II that improve the low-energy sensitivity. Enhanced energy-dependent morphological and spatially resolved spectral analyses probe the very high energy (VHE, E > 0.1 TeV) gamma-ray properties of the nebula. Methods. The nebula emission is revealed to extend out to 1.5 degrees from the pulsar, similar to 1.5 times farther than previously seen, making HESS J1825-137, with an intrinsic diameter of similar to 100 pc, potentially the largest gamma-ray PWN currently known. Characterising the strongly energy-dependent morphology of the nebula enables us to constrain the particle transport mechanisms. A dependence of the nebula extent with energy of R proportional to E alpha with alpha = -0.29 +/- 0.04(stat) +/- 0.05(sys) disfavours a pure diffusion scenario for particle transport within the nebula. The total gamma-ray flux of the nebula above 1 TeV is found to be (1.12 +/- 0.03(stat) +/- 0.25(sys)) +/- 10(-11) cm(-2) s(-1), corresponding to similar to 64% of the flux of the Crab nebula. Results. HESS J1825-137 is a PWN with clearly energy-dependent morphology at VHE gamma-ray energies. This source is used as a laboratory to investigate particle transport within intermediate-age PWNe. Based on deep observations of this highly spatially extended PWN, we produce a spectral map of the region that provides insights into the spectral variation within the nebula.
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17.
  • Abdalla, H., et al. (författare)
  • Population study of Galactic supernova remnants at very high gamma-ray energies with HESS
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 612
  • Tidskriftsartikel (refereegranskat)abstract
    • Shell-type supernova remnants (SNRs) are considered prime candidates for the acceleration of Galactic cosmic rays (CRs) up to the knee of the CR spectrum at E approximate to 3 x 10(15) eV. Our MilkyWay galaxy hosts more than 350 SNRs discovered at radio wavelengths and at high energies, of which 220 fall into the H.E.S.S. Galactic Plane Survey (HGPS) region. Of those, only 50 SNRs are coincident with a H.E.S.S source and in 8 cases the very high-energy (VHE) emission is firmly identified as an SNR. The H.E.S.S. GPS provides us with a legacy for SNR population study in VHE gamma-rays and we use this rich data set to extract VHE flux upper limits from all undetected SNRs. Overall, the derived flux upper limits are not in contradiction with the canonical CR paradigm. Assuming this paradigm holds true, we can constrain typical ambient density values around shell-type SNRs to n <= 7 cm(-3) and electron-to-proton energy fractions above 10 TeV to epsilon(ep) <= 5 x 10(-3). Furthermore, comparisons of VHE with radio luminosities in non-interacting SNRs reveal a behaviour that is in agreement with the theory of magnetic field amplification at shell-type SNRs.
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18.
  • Abdalla, H., et al. (författare)
  • Resolving the Crab pulsar wind nebula at teraelectronvolt energies
  • 2020
  • Ingår i: Nature Astronomy. - : Nature Publishing Group. - 2397-3366. ; 4:2, s. 167-173
  • Tidskriftsartikel (refereegranskat)abstract
    • An angular extension at gamma-ray energies of 52 arcseconds is detected for the Crab nebula, revealing the emission region of the highest-energy gamma rays; simulations of the electromagnetic emission provide a non-trivial test of our understanding of particle acceleration in the Crab nebula. The Crab nebula is one of the most-studied cosmic particle accelerators, shining brightly across the entire electromagnetic spectrum up to very-high-energy gamma rays(1,2). It is known from observations in the radio to gamma-ray part of the spectrum that the nebula is powered by a pulsar, which converts most of its rotational energy losses into a highly relativistic outflow. This outflow powers a pulsar wind nebula, a region of up to ten light-years across, filled with relativistic electrons and positrons. These particles emit synchrotron photons in the ambient magnetic field and produce very-high-energy gamma rays by Compton up-scattering of ambient low-energy photons. Although the synchrotron morphology of the nebula is well established, it has not been known from which region the very-high-energy gamma rays are emitted(3-8). Here we report that the Crab nebula has an angular extension at gamma-ray energies of 52 arcseconds (assuming a Gaussian source width), much larger than at X-ray energies. This result closes a gap in the multi-wavelength coverage of the nebula, revealing the emission region of the highest-energy gamma rays. These gamma rays enable us to probe a previously inaccessible electron and positron energy range. We find that simulations of the electromagnetic emission reproduce our measurement, providing a non-trivial test of our understanding of particle acceleration in the Crab nebula.
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19.
  • Abdalla, H., et al. (författare)
  • Searches for gamma-ray lines and 'pure WIMP' spectra from Dark Matter annihilations in dwarf galaxies with HESS
  • 2018
  • Ingår i: Journal of Cosmology and Astroparticle Physics. - : Institute of Physics Publishing (IOPP). - 1475-7516. ; :11
  • Tidskriftsartikel (refereegranskat)abstract
    • Dwarf spheroidal galaxies are among the most promising targets for detecting signals of Dark Matter (DM) annihilations. The H.E.S.S. experiment has observed five of these systems for a total of about 130 hours. The data are re-analyzed here, and, in the absence of any detected signals, are interpreted in terms of limits on the DM annihilation cross section. Two scenarios are considered: i) DM annihilation into mono-energetic gamma-rays and ii) DM in the form of pure WIMP multiplets that, annihilating into all electroweak bosons, produce a distinctive gamma-ray spectral shape with a high-energy peak at the DM mass and a lower-energy continuum. For case i), upper limits at 95% confidence level of about less than or similar to 3 x 10(-25) cm(3) s(-1) are obtained in the mass range of 400 GeV to 1TeV. For case ii), the full spectral shape of the models is used and several excluded regions are identified, but the thermal masses of the candidates are not robustly ruled out.
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20.
  • Abdalla, H., et al. (författare)
  • Systematic search for very-high-energy gamma-ray emission from bow shocks of runaway stars
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 612
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. Runaway stars form bow shocks by ploughing through the interstellar medium at supersonic speeds and are promising sources of non-thermal emission of photons. One of these objects has been found to emit non-thermal radiation in the radio band. This triggered the development of theoretical models predicting non-thermal photons from radio up to very-high-energy (VHE, E >= 0.1 TeV) gamma rays. Subsequently, one bow shock was also detected in X-ray observations. However, the data did not allow discrimination between a hot thermal and a non-thermal origin. Further observations of different candidates at X-ray energies showed no evidence for emission at the position of the bow shocks either. A systematic search in the Fermi-LAT energy regime resulted in flux upper limits for 27 candidates listed in the E-BOSS catalogue. Aims. Here we perform the first systematic search for VHE gamma-ray emission from bow shocks of runaway stars. Methods. Using all available archival H.E.S.S. data we search for very-high-energy gamma-ray emission at the positions of bow shock candidates listed in the second E-BOSS catalogue release. Out of the 73 bow shock candidates in this catalogue, 32 have been observed with H.E.S.S. Results. None of the observed 32 bow shock candidates in this population study show significant emission in the H.E.S.S. energy range. Therefore, flux upper limits are calculated in five energy bins and the fraction of the kinetic wind power that is converted into VHE gamma rays is constrained. Conclusions. Emission from stellar bow shocks is not detected in the energy range between 0.14 and 18 TeV. The resulting upper limits constrain the level of VHE gamma-ray emission from these objects down to 0.1-1% of the kinetic wind energy.
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21.
  • Abdalla, H., et al. (författare)
  • The 2014 TeV γ-Ray Flare of Mrk 501 Seen with H.E.S.S. : Temporal and Spectral Constraints on Lorentz Invariance Violation
  • 2019
  • Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 870:2
  • Tidskriftsartikel (refereegranskat)abstract
    • The blazar Mrk 501 (z = 0.034) was observed at very-high-energy (VHE, E greater than or similar to 100 GeV) gamma-ray wavelengths during a bright flare on the night of 2014 June 23-24 (MJD 56832) with the H.E.S.S. phase-II array of Cherenkov telescopes. Data taken that night by H.E.S.S. at large zenith angle reveal an exceptional number of gamma-ray photons at multi-TeV energies, with rapid flux variability and an energy coverage extending significantly up to 20 TeV. This data set is used to constrain Lorentz invariance violation (LIV) using two independent channels: a temporal approach considers the possibility of an energy dependence in the arrival time of gamma-rays, whereas a spectral approach considers the possibility of modifications to the interaction of VHE gamma-rays with extragalactic background light (EBL) photons. The non-detection of energy-dependent time delays and the non-observation of deviations between the measured spectrum and that of a supposed power-law intrinsic spectrum with standard EBL attenuation are used independently to derive strong constraints on the energy scale of LIV (E-QG) in the subluminal scenario for linear and quadratic perturbations in the dispersion relation of photons. For the case of linear perturbations, the 95% confidence level limits obtained are E-QG,E-1 > 3.6 x 10(17) GeV using the temporal approach and E-QG,E-1 > 2.6 x 10(19) GeV using the spectral approach. For the case of quadratic perturbations, the limits obtained are E-QG,E-2 > 8.5 x 10(10) GeV using the temporal approach and E-QG,E-2 > 7.8 x 10(11) GeV using the spectral approach.
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22.
  • Abdalla, H., et al. (författare)
  • The gamma-ray spectrum of the core of Centaurus A as observed with HESS and Fermi-LAT
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 619
  • Tidskriftsartikel (refereegranskat)abstract
    • Centaurus A (Cen A) is the nearest radio galaxy discovered as a very-high-energy (VHE; 100 GeV-100 TeV) gamma-ray source by the High Energy Stereoscopic System (H.E.S.S.). It is a faint VHE gamma-ray emitter, though its VHE flux exceeds both the extrapolation from early Fermi-LAT observations as well as expectations from a (misaligned) single-zone synchrotron-self Compton (SSC) description. The latter satisfactorily reproduces the emission from Cen A at lower energies up to a few GeV. New observations with H.E.S.S., comparable in exposure time to those previously reported, were performed and eight years of Fermi-LAT data were accumulated to clarify the spectral characteristics of the gamma-ray emission from the core of Cen A. The results allow us for the first time to achieve the goal of constructing a representative, contemporaneous gamma-ray core spectrum of Cen A over almost five orders of magnitude in energy. Advanced analysis methods, including the template fitting method, allow detection in the VHE range of the core with a statistical significance of 12 sigma on the basis of 213 hours of total exposure time. The spectrum in the energy range of 250 GeV-6 TeV is compatible with a power-law function with a photon index Gamma = 2.52 +/- 0.13(stat) +/- 0.20(sys). An updated Fermi-LAT analysis provides evidence for spectral hardening by Delta Gamma similar or equal to 0.4 +/- 0.1 at gamma-ray energies above 2.8(-0.6)(+1.0) GeV at a level of 4.0 sigma. The fact that the spectrum hardens at GeV energies and extends into the VHE regime disfavour a single-zone SSC interpretation for the overall spectral energy distribution (SED) of the core and is suggestive of a new gamma-ray emitting component connecting the high-energy emission above the break energy to the one observed at VHE energies. The absence of significant variability at both GeV and TeV energies does not yet allow disentanglement of the physical nature of this component, though a jet-related origin is possible and a simple two-zone SED model fit is provided to this end.
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23.
  • Abdalla, H., et al. (författare)
  • The HESS Galactic plane survey
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 612
  • Tidskriftsartikel (refereegranskat)abstract
    • We present the results of the most comprehensive survey of the Galactic plane in very high-energy (VHE) gamma-rays, including a public release of Galactic sky maps, a catalog of VHE sources, and the discovery of 16 new sources of VHE gamma-rays. The High Energy Spectroscopic System (H.E.S.S.) Galactic plane survey (HGPS) was a decade-long observation program carried out by the H.E.S.S. I array of Cherenkov telescopes in Namibia from 2004 to 2013. The observations amount to nearly 2700 h of quality-selected data, covering the Galactic plane at longitudes from l = 250 degrees to 65 degrees and latitudes vertical bar b vertical bar <= 3 degrees. In addition to the unprecedented spatial coverage, the HGPS also features a relatively high angular resolution (0.08 degrees approximate to 5 arcmin mean point spread function 68% containment radius), sensitivity (less than or similar to 1.5% Crab flux for point-like sources), and energy range (0.2-100 TeV). We constructed a catalog of VHE gamma-ray sources from the HGPS data set with a systematic procedure for both source detection and characterization of morphology and spectrum. We present this likelihood-based method in detail, including the introduction of a model component to account for unresolved, large-scale emission along the Galactic plane. In total, the resulting HGPS catalog contains 78 VHE sources, of which 14 are not reanalyzed here, for example, due to their complex morphology, namely shell-like sources and the Galactic center region. Where possible, we provide a firm identification of the VHE source or plausible associations with sources in other astronomical catalogs. We also studied the characteristics of the VHE sources with source parameter distributions. 16 new sources were previously unknown or unpublished, and we individually discuss their identifications or possible associations. We firmly identified 31 sources as pulsar wind nebulae (PWNe), supernova remnants (SNRs), composite SNRs, or gamma-ray binaries. Among the 47 sources not yet identified, most of them (36) have possible associations with cataloged objects, notably PWNe and energetic pulsars that could power VHE PWNe.
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24.
  • Abdalla, H., et al. (författare)
  • The population of TeV pulsar wind nebulae in the HESS Galactic Plane Survey
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 612
  • Tidskriftsartikel (refereegranskat)abstract
    • The nine-year H.E.S.S. Galactic Plane Survey (HGPS) has yielded the most uniform observation scan of the inner Milky Way in the TeV gamma-ray band to date. The sky maps and source catalogue of the HGPS allow for a systematic study of the population of TeV pulsar wind nebulae found throughout the last decade. To investigate the nature and evolution of pulsar wind nebulae, for the first time we also present several upper limits for regions around pulsars without a detected TeV wind nebula. Our data exhibit a correlation of TeV surface brightness with pulsar spindown power (E) over dot. This seems to be caused both by an increase of extension with decreasing (E) over dot, and hence with time, compatible with a power law R-PWN((E) over dot) similar to(E) over dot(0.65 +/- 0.20), and by a mild decrease of TeV gamma-ray luminosity with decreasing (E) over dot, compatible with L-1 (10 TeV) similar to (E) over dot(0.59 +/- 0.21). We also find that the off sets of pulsars with respect to the wind nebula centre with ages around 10 kyr are frequently larger than can be plausibly explained by pulsar proper motion and could be due to an asymmetric environment. In the present data, it seems that a large pulsar off set is correlated with a high apparent TeV efficiency L1- 10 TeV / (E) over dot. In addition to 14 HGPS sources considered firmly identified pulsar wind nebulae and 5 additional pulsar wind nebulae taken from literature, we find 10 HGPS sources that are likely TeV pulsar wind nebula candidates. Using a model that subsumes the present common understanding of the very high-energy radiative evolution of pulsar wind nebulae, we find that the trends and variations of the TeV observables and limits can be reproduced to a good level, drawing a consistent picture of present-day TeV data and theory.
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25.
  • Abdalla, H., et al. (författare)
  • The starburst galaxy NGC 253 revisited by HESS and Fermi-LAT
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 617
  • Tidskriftsartikel (refereegranskat)abstract
    • Context. NGC 253 is one of only two starburst galaxies found to emit gamma-rays from hundreds of MeV to multi-TeV energies. Accurate measurements of the very-high-energy (VHE; E> 100 GeV) and high-energy (HE; E > 60 MeV) spectra are crucial to study the underlying particle accelerators, probe the dominant emission mechanism(s) and to study cosmic-ray interaction and transport. Aims. The measurement of the VHE gamma-ray emission of NGC 253 published in 2012 by H.E.S.S. was limited by large systematic uncertainties. Here, the most up to date measurement of the gamma-ray spectrum of NGC 253 is investigated in both HE and VHE gamma-rays. Assuming a hadronic origin of the gamma-ray emission, the measurement uncertainties are propagated into the interpretation of the accelerated particle population. Methods. The data of H.E.S.S. observations are reanalysed using an updated calibration and analysis chain. The improved Fermi-LAT analysis employs more than 8 yr of data processed using pass 8. The cosmic-ray particle population is evaluated from the combined HE-VHE gamma-ray spectrum using NAIMA in the optically thin case. Results. The VHE gamma-ray energy spectrum is best fit by a power-law distribution with a flux normalisation of (1.34 +/- 0.14(stat) +/- 0.27(sys)) x 10(-13) cm(-2) s(-1) TeV-1 at 1 TeV - about 40% above, but compatible with the value obtained in Abramowski et al. (2012). The spectral index Gamma = 2.39 +/- 0.14(stat) +/- 0.25(sys) is slightly softer than but consistent with the previous measurement within systematic errors. In the Fermi energy range an integral flux of F(E > 60 MeV) = (1.56 +/- 0.28(stat) +/- 0.15(sys)) x 10(-8) cm(-2) s(-1) is obtained. At energies above similar to 3 GeV the HE spectrum is consistent with a power-law ranging into the VHE part of the spectrum measured by H.E.S.S. with an overall spectral index Gamma = 2.22 +/- 0.06(stat). Conclusions. Two scenarios for the starburst nucleus are tested, in which the gas in the starburst nucleus acts as either a thin or a thick target for hadronic cosmic rays accelerated by the individual sources in the nucleus. In these two models, the level to which NGC 253 acts as a calorimeter is estimated to a range of f(cal) = 0.1 to 1 while accounting for the measurement uncertainties. The presented spectrum is likely to remain the most accurate measurements until the Cherenkov Telescope Array (CTA) has collected a substantial set of data towards NGC 253.
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26.
  • Abdalla, H., et al. (författare)
  • The supernova remnant W49B as seen with HESS and Fermi-LAT
  • 2018
  • Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 612
  • Tidskriftsartikel (refereegranskat)abstract
    • The supernova remnant (SNR) W49B originated from a core-collapse supernova that occurred between one and four thousand years ago, and subsequently evolved into a mixed-morphology remnant, which is interacting with molecular clouds (MC). Gamma-ray observations of SNR-MC associations are a powerful tool to constrain the origin of Galactic cosmic rays, as they can probe the acceleration of hadrons through their interaction with the surrounding medium and subsequent emission of non-thermal photons. We report the detection of a gamma-ray source coincident with W49B at very high energies (VHE; E > 100 GeV) with the H.E.S.S. Cherenkov telescopes together with a study of the source with five years of Fermi-LAT high-energy gamma-ray (0.06-300 GeV) data. The smoothly connected, combined source spectrum, measured from 60 MeV to multi-TeV energies, shows two significant spectral breaks at 304 +/- 20 MeV and 8.4(-2.5)(+2.5) GeV; the latter is constrained by the joint fit from the two instruments. The detected spectral features are similar to those observed in several other SNR-MC associations and are found to be indicative of gamma-ray emission produced through neutral-pion decay.
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27.
  • Abdalla, H., et al. (författare)
  • VHE γ-ray discovery and multiwavelength study of the blazar 1ES 2322−409 
  • 2019
  • Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 482:3, s. 3011-3022
  • Tidskriftsartikel (refereegranskat)abstract
    • A hotspot at a position compatible with the BL. Lac object 1ES 2322-409 was serendipitously detected with H.E.S.S. during observations performed in 2004 and 2006 on the blazar PKS 2316-423. Additional data on 1ES 2322-409 were taken in 2011 and 2012, leading to a total live-time of 22.3 h. Point-like very-high-energy (VHE; E > 100 GeV) gamma-ray emission is detected from a source centred on the IFS 2322-409 position, with an excess of 116.7 events at a significance of 6.0 sigma. The average VHE gamma-ray spectrum is well described with a power law with a photon index Gamma = 3.40 +/- 0.66(stat) +/- 0.20(sys) and an integral flux Phi(E > 200 GeV) = (3.11 +/- 0.71(stat) 0.62(sys)) x 10(-2)cm(-2)s(-1), which corresponds to 1.1 per cent of the Crab nebula flux above 200 GeV. Multiwavelength data obtained with Fermi LAT, Swift XRT and UVOT, RXTE PCA, ATOM, and additional data from WISE, GROND, and Catalina are also used to characterize the broad-band non-thermal emission of lES 2322-409. The multiwavelength behaviour indicates day-scale variability. Swift UVOT and XRT data show strong variability at longer scales. A spectral energy distribution (SED) is built from contemporaneous observations obtained around a high state identified in Swift data. A modelling of the SED is performed with a stationary homogeneous one-zone synchrotronself-Compton leptonic model. The redshift of the source being unknown, two plausible values were tested for the modelling. A systematic scan of the model parameters space is performed, resulting in a well-constrained combination of values providing a good description of the broad-band behaviour of 1ES 2322-409.
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28.
  • Abdallah, H., et al. (författare)
  • Search for gamma-Ray Line Signals from Dark Matter Annihilations in the Inner Galactic Halo from 10 Years of Observations with HESS
  • 2018
  • Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 120:20
  • Tidskriftsartikel (refereegranskat)abstract
    • Spectral lines are among the most powerful signatures for dark matter (DM) annihilation searches in very-high-energy gamma rays. The central region of the Milky Way halo is one of the most promising targets given its large amount of DM and proximity to Earth. We report on a search for a monoenergetic spectral line from self-annihilations of DM particles in the energy range from 300 GeV to 70 TeV using a two-dimensional maximum likelihood method taking advantage of both the spectral and spatial features of the signal versus background. The analysis makes use of Galactic center observations accumulated over ten years (2004-2014) with the H.E.S.S. array of ground-based Cherenkov telescopes. No significant gamma-ray excess above the background is found. We derive upper limits on the annihilation cross section (sigma v) for monoenergetic DM lines at the level of 4 x 10(-28) cm(3) s(-1) at 1 TeV, assuming an Einasto DM profile for the Milky Way halo. For a DM mass of 1 TeV, they improve over the previous ones by a factor of 6. The present constraints are the strongest obtained so far for DM particles in the mass range 300 GeV-70 TeV. Ground-based gamma-ray observations have reached sufficient sensitivity to explore relevant velocity-averaged cross sections for DM annihilation into two gamma-ray photons at the level expected from the thermal relic density for TeV DM particles.
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29.
  • Abel, I, et al. (författare)
  • Overview of the JET results with the ITER-like wall
  • 2013
  • Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 53:10, s. 104002-
  • Tidskriftsartikel (refereegranskat)abstract
    • Following the completion in May 2011 of the shutdown for the installation of the beryllium wall and the tungsten divertor, the first set of JET campaigns have addressed the investigation of the retention properties and the development of operational scenarios with the new plasma-facing materials. The large reduction in the carbon content (more than a factor ten) led to a much lower Z(eff) (1.2-1.4) during L- and H-mode plasmas, and radiation during the burn-through phase of the plasma initiation with the consequence that breakdown failures are almost absent. Gas balance experiments have shown that the fuel retention rate with the new wall is substantially reduced with respect to the C wall. The re-establishment of the baseline H-mode and hybrid scenarios compatible with the new wall has required an optimization of the control of metallic impurity sources and heat loads. Stable type-I ELMy H-mode regimes with H-98,H-y2 close to 1 and beta(N) similar to 1.6 have been achieved using gas injection. ELM frequency is a key factor for the control of the metallic impurity accumulation. Pedestal temperatures tend to be lower with the new wall, leading to reduced confinement, but nitrogen seeding restores high pedestal temperatures and confinement. Compared with the carbon wall, major disruptions with the new wall show a lower radiated power and a slower current quench. The higher heat loads on Be wall plasma-facing components due to lower radiation made the routine use of massive gas injection for disruption mitigation essential.
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30.
  • Acero, F., et al. (författare)
  • Prospects for Cherenkov Telescope Array Observations of the Young Supernova Remnant RX J1713.7-3946
  • 2017
  • Ingår i: Astrophysical Journal. - : Institute of Physics Publishing (IOPP). - 0004-637X .- 1538-4357. ; 840:2
  • Tidskriftsartikel (refereegranskat)abstract
    • We perform simulations for future Cherenkov Telescope Array (CTA) observations of RX J1713.7-3946, a young supernova remnant (SNR) and one of the brightest sources ever discovered in very high energy (VHE) gamma rays. Special attention is paid to exploring possible spatial (anti) correlations of gamma rays with emission at other wavelengths, in particular X-rays and CO/H I emission. We present a series of simulated images of RX J1713.7-3946 for CTA based on a set of observationally motivated models for the gamma-ray emission. In these models, VHE gamma rays produced by high-energy electrons are assumed to trace the nonthermal X-ray emission observed by XMM-Newton, whereas those originating from relativistic protons delineate the local gas distributions. The local atomic and molecular gas distributions are deduced by the NANTEN team from CO and H I observations. Our primary goal is to show how one can distinguish the emission mechanism(s) of the gamma rays (i.e., hadronic versus leptonic, or a mixture of the two) through information provided by their spatial distribution, spectra, and time variation. This work is the first attempt to quantitatively evaluate the capabilities of CTA to achieve various proposed scientific goals by observing this important cosmic particle accelerator.
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31.
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32.
  • Bassani, Carlos L., et al. (författare)
  • Nanocrystal Assemblies : Current Advances and Open Problems
  • 2024
  • Ingår i: ACS Nano. - 1936-0851. ; 18:23, s. 14791-14840
  • Forskningsöversikt (refereegranskat)abstract
    • We explore the potential of nanocrystals (a term used equivalently to nanoparticles) as building blocks for nanomaterials, and the current advances and open challenges for fundamental science developments and applications. Nanocrystal assemblies are inherently multiscale, and the generation of revolutionary material properties requires a precise understanding of the relationship between structure and function, the former being determined by classical effects and the latter often by quantum effects. With an emphasis on theory and computation, we discuss challenges that hamper current assembly strategies and to what extent nanocrystal assemblies represent thermodynamic equilibrium or kinetically trapped metastable states. We also examine dynamic effects and optimization of assembly protocols. Finally, we discuss promising material functions and examples of their realization with nanocrystal assemblies.
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33.
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34.
  • Chapman, Joanne R., et al. (författare)
  • The Evolution of Innate Immune Genes : Purifying and Balancing Selection on beta-Defensins in Waterfowl
  • 2016
  • Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 33:12, s. 3075-3087
  • Tidskriftsartikel (refereegranskat)abstract
    • In disease dynamics, high immune gene diversity can confer a selective advantage to hosts in the face of a rapidly evolving and diverse pathogen fauna. This is supported empirically for genes involved in pathogen recognition and signalling. In contrast, effector genes involved in pathogen clearance may be more constrained. beta-Defensins are innate immune effector genes; their main mode of action is via disruption of microbial membranes. Here, five beta-defensin genes were characterized in mallards (Anas platyrhynchos) and other waterfowl; key reservoir species for many zoonotic diseases. All five genes showed remarkably low diversity at the individual-, population-, and species-level. Furthermore, there was widespread sharing of identical alleles across species divides. Thus, specific beta-defensin alleles were maintained not only spatially but also over long temporal scales, with many amino acid residues being fixed across all species investigated. Purifying selection to maintain individual, highly efficacious alleles was the primary evolutionary driver of these genes in waterfowl. However, we also found evidence for balancing selection acting on the most recently duplicated beta-defensin gene (AvBD3b). For this gene, we found that amino acid replacements were more likely to be radical changes, suggesting that duplication of beta-defensin genes allows exploration of wider functional space. Structural conservation to maintain function appears to be crucial for avian beta-defensin effector molecules, resulting in low tolerance for new allelic variants. This contrasts with other types of innate immune genes, such as receptor and signalling molecules, where balancing selection to maintain allelic diversity has been shown to be a strong evolutionary force.
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35.
  • Dahn, Hollis A., et al. (författare)
  • Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
  • 2022
  • Ingår i: GigaScience. - : Oxford University Press. - 2047-217X. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types.Results: We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4 degrees C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4 degrees C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield.Conclusion: We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all similar to 70,000 extant vertebrate species.
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36.
  • Gschwendtner, Dda, et al. (författare)
  • The AWAKE Run 2 Programme and Beyond
  • 2022
  • Ingår i: Symmetry. - : MDPI AG. - 2073-8994. ; 14:8
  • Tidskriftsartikel (refereegranskat)abstract
    • Plasma wakefield acceleration is a promising technology to reduce the size of particle accelerators. The use of high energy protons to drive wakefields in plasma has been demonstrated during Run 1 of the AWAKE programme at CERN. Protons of energy 400 GeV drove wakefields that accelerated electrons to 2 GeV in under 10 m of plasma. The AWAKE collaboration is now embarking on Run 2 with the main aims to demonstrate stable accelerating gradients of 0.5-1 GV/m, preserve emittance of the electron bunches during acceleration and develop plasma sources scalable to 100s of metres and beyond. By the end of Run 2, the AWAKE scheme should be able to provide electron beams for particle physics experiments and several possible experiments have already been evaluated. This article summarises the programme of AWAKE Run 2 and how it will be achieved as well as the possible application of the AWAKE scheme to novel particle physics experiments.
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37.
  • Gusarova, Viktoria, et al. (författare)
  • Genetic inactivation of ANGPTL4 improves glucose homeostasis and is associated with reduced risk of diabetes
  • 2018
  • Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9, s. 1-11
  • Tidskriftsartikel (refereegranskat)abstract
    • Angiopoietin-like 4 (ANGPTL4) is an endogenous inhibitor of lipoprotein lipase that modulates lipid levels, coronary atherosclerosis risk, and nutrient partitioning. We hypothesize that loss of ANGPTL4 function might improve glucose homeostasis and decrease risk of type 2 diabetes (T2D). We investigate protein-altering variants in ANGPTL4 among 58,124 participants in the DiscovEHR human genetics study, with follow-up studies in 82,766 T2D cases and 498,761 controls. Carriers of p.E40K, a variant that abolishes ANGPTL4 ability to inhibit lipoprotein lipase, have lower odds of T2D (odds ratio 0.89, 95% confidence interval 0.85-0.92, p = 6.3 × 10-10), lower fasting glucose, and greater insulin sensitivity. Predicted loss-of-function variants are associated with lower odds of T2D among 32,015 cases and 84,006 controls (odds ratio 0.71, 95% confidence interval 0.49-0.99, p = 0.041). Functional studies in Angptl4-deficient mice confirm improved insulin sensitivity and glucose homeostasis. In conclusion, genetic inactivation of ANGPTL4 is associated with improved glucose homeostasis and reduced risk of T2D.
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38.
  • Gyepesi, Aron, et al. (författare)
  • Psychometric Properties of the Cannabis Abuse Screening Test in Hungarian Samples of Adolescents and Young Adults
  • 2014
  • Ingår i: European Addiction Research. - : S. Karger AG. - 1022-6877 .- 1421-9891. ; 20:3, s. 119-128
  • Tidskriftsartikel (refereegranskat)abstract
    • Aim: The aim of our study was to analyze psychometric properties of the Cannabis Abuse Screening Test (CAST). Methods: Our sample comprised Hungarian high school (n = 476; male 56.3%; mean age 19.0 years, SD = 0.65 years) and college students (n = 439; male 65.1%; mean age 23.9 years, SD = 1.56 years) who reported cannabis use in the past year. The sample covered the five biggest universities of Hungary. Besides the CAST, participants responded to the Munich-Composite International Diagnostic Interview. Factor structure was analyzed by a confirmatory factor analysis. Receiver operating characteristic curve analysis was made to assess cut-off scores. Data collection took place in 2010. Results: CAST proved to be a reliable (Cronbach's alpha 0.71 and 0.76) one-dimensional measure. Regarding both cannabis dependence and cannabis use disorders, a cut-off of 2 points proved to be ideal in both samples, resulting in optimal specificity, negative predictive values and accuracy, but less than optimal positive predictive values (dependence) and low sensitivity (cannabis use disorder). Discussion and Conclusions: In line with former results, the CAST proved to be an adequate measure for the screening of cannabis-related problems among adolescents and young adults in an Eastern European country where this scale has not been studied before. (C) 2013 S. Karger AG, Basel
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39.
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40.
  • Jax, Elinor, et al. (författare)
  • Comparative Genomics of the Waterfowl Innate Immune System
  • 2022
  • Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 39:8
  • Tidskriftsartikel (refereegranskat)abstract
    • Animal species differ considerably in their ability to fight off infections. Finding the genetic basis of these differences is not easy, as the immune response is comprised of a complex network of proteins that interact with one another to defend the body against infection. Here, we used population- and comparative genomics to study the evolutionary forces acting on the innate immune system in natural hosts of the avian influenza virus (AIV). For this purpose, we used a combination of hybrid capture, next- generation sequencing and published genomes to examine genetic diversity, divergence, and signatures of selection in 127 innate immune genes at a micro- and macroevolutionary time scale in 26 species of waterfowl. We show across multiple immune pathways (AIV-, toll-like-, and RIG-I -like receptors signalling pathways) that genes involved genes in pathogen detection (i.e., toll-like receptors) and direct pathogen inhibition (i.e., antimicrobial peptides and interferon-stimulated genes), as well as host proteins targeted by viral antagonist proteins (i.e., mitochondrial antiviral-signaling protein, [MAVS]) are more likely to be polymorphic, genetically divergent, and under positive selection than other innate immune genes. Our results demonstrate that selective forces vary across innate immune signaling signalling pathways in waterfowl, and we present candidate genes that may contribute to differences in susceptibility and resistance to infectious diseases in wild birds, and that may be manipulated by viruses. Our findings improve our understanding of the interplay between host genetics and pathogens, and offer the opportunity for new insights into pathogenesis and potential drug targets. 
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41.
  • Jax, Elinor, et al. (författare)
  • Evaluating Effects of AIV Infection Status on Ducks Using a Flow Cytometry-Based Differential Blood Count
  • 2023
  • Ingår i: Microbiology Spectrum. - : American Society for Microbiology. - 2165-0497. ; 11:4
  • Tidskriftsartikel (refereegranskat)abstract
    • Ducks have recently received a lot of attention from the research community due to their importance as natural reservoirs of avian influenza virus (AIV). Still, there is a lack of tools to efficiently determine the immune status of ducks. The purpose of this work was to develop an automated differential blood count for the mallard duck (Anas platyrhynchos), to assess reference values of white blood cell (WBC) counts in this species, and to apply the protocol in an AIV field study. We established a flow cytometry-based duck WBC differential based on a no-lyse no-wash single-step one-tube technique, applying a combination of newly generated monoclonal antibodies with available duck-specific as well as cross-reacting chicken markers. The blood cell count enables quantification of mallard thrombocytes, granulocytes, monocytes, B cells, CD4(+) T cells (T helper) and CD8(+) cytotoxic T cells. The technique is reproducible, accurate, and much faster than traditional evaluations of blood smears. Stabilization of blood samples enables analysis up to 1 week after sampling, thus allowing for evaluation of blood samples collected in the field. We used the new technique to investigate a possible influence of sex, age, and AIV infection status on WBC counts in wild mallards. We show that age has an effect on the WBC counts in mallards, as does sex in juvenile mallards. Interestingly, males naturally infected with low pathogenic AIV showed a reduction of lymphocytes (lymphocytopenia) and thrombocytes (thrombocytopenia), which are both common in influenza A infection in humans.IMPORTANCE Outbreaks of avian influenza in poultry and humans are a global public health concern. Aquatic birds are the primary natural reservoir of avian influenza viruses (AIVs), and strikingly, AIVs mainly cause asymptomatic or mild infection in these species. Hence, immunological studies in aquatic birds are important for investigating variation in disease outcome of different hosts to AIV and may aid in early recognition and a better understanding of zoonotic events. Unfortunately, immunological studies in these species were so far hampered by the lack of diagnostic tools. Here, we present a technique that enables high-throughput white blood cell (WBC) analysis in the mallard and report changes in WBC counts in wild mallards naturally infected with AIV. Our protocol permits large-scale immune status monitoring in a widespread wild and domesticated duck species and provides a tool to further investigate the immune response in an important reservoir host of zoonotic viruses. Outbreaks of avian influenza in poultry and humans are a global public health concern. Aquatic birds are the primary natural reservoir of avian influenza viruses (AIVs), and strikingly, AIVs mainly cause asymptomatic or mild infection in these species.
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42.
  • Jax, Elinor, et al. (författare)
  • Health monitoring in birds using bio-loggers and whole blood transcriptomics
  • 2021
  • Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Monitoring and early detection of emerging infectious diseases in wild animals is of crucial global importance, yet reliable ways to measure immune status and responses are lacking for animals in the wild. Here we assess the usefulness of bio-loggers for detecting disease outbreaks in free-living birds and confirm detailed responses using leukocyte composition and large-scale transcriptomics. We simulated natural infections by viral and bacterial pathogens in captive mallards (Anas platyrhynchos), an important natural vector for avian influenza virus. We show that body temperature, heart rate and leukocyte composition change reliably during an acute phase immune response. Using genome-wide gene expression profiling of whole blood across time points we confirm that immunostimulants activate pathogen-specific gene regulatory networks. By reporting immune response related changes in physiological and behavioural traits that can be studied in free-ranging populations, we provide baseline information with importance to the global monitoring of zoonotic diseases.
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43.
  • Karawita, Anjana C., et al. (författare)
  • The swan genome and transcriptome, it is not all black and white
  • 2023
  • Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundThe Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information.ResultsHere, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan.ConclusionTogether, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.
  •  
44.
  • Kluska, J., et al. (författare)
  • VLTI images of circumbinary disks around evolved stars
  • 2020
  • Ingår i: Proceedings of SPIE - The International Society for Optical Engineering. - : SPIE. - 0277-786X .- 1996-756X. ; 11446
  • Konferensbidrag (refereegranskat)abstract
    • The new generation of VLTI instruments (GRAVITY, MATISSE) aims to produce routinely interferometric images to uncover the morphological complexity of different objects at high angular resolution. Image reconstruction is, however, not a fully automated process. Here we focus on a specific science case, namely the complex circumbinary environments of a subset of evolved binaries, for which interferometric imaging provides the spatial resolution required to resolve the immediate circumbinary environment. Indeed, many binaries where the main star is in the post-asymptotic giant branch (post-AGB) phase are surrounded by circumbinary disks. Those disks were first inferred from the infrared excess produced by dust. Snapshot interferometric observations in the infrared confirmed disk-like morphology and revealed high spatial complexity of the emission that the use of geometrical models could not recover without being strongly biased. Arguably, the most convincing proof of the disk-like shape of the circumbinary environment came from the first interferometric image of such a system (IRAS08544-4431) using the PIONIER instrument at the VLTI. This image was obtained using the SPARCO image reconstruction approach that enables to subtract a model of a component of the image and reconstruct an image of its environment only. In the case of IRAS08544-4431, the model involved a binary and the image of the remaining signal revealed several unexpected features. Then, a second image revealed a different but also complex circumstellar morphology around HD101584 that was well studied by ALMA. To exploit the VLTI imaging capability to understand these targets, we started a large programme at the VLTI to image post-AGB binary systems using both PIONIER and GRAVITY instruments.
  •  
45.
  • Kraus, Jakub, et al. (författare)
  • Social support modulates subjective and neural responses to sad mental imagery
  • 2020
  • Ingår i: Behavioural Brain Research. - : Elsevier BV. - 0166-4328 .- 1872-7549. ; 380
  • Tidskriftsartikel (refereegranskat)abstract
    • Mental imagery related to the recent death of a loved one is associated with intense sadness and distress. Social relations, such as with one's significant other, can regulate negative emotions and provide comfort, but the neural correlates of social comfort are largely unknown. In this functional magnetic resonance imaging study, we examined brain responses to sad mental imagery and how these are modulated by holding hands with one's romantic partner. We found that mental imagery of a recently deceased loved one was associated with increased reactivity in the dorsal striatum, medial prefrontal cortex, anterior and posterior cingulate cortex, thalamus and cerebellum. Holding hands with one's partner as compared to being alone or holding hands with a stranger provided subjective comfort and reduced neural reactivity in the dorsal striatum without affecting the vividness of the imagery. Our findings indicate an important role for the dorsal striatum in sad mental imagery and social comfort and suggest that tactile social support by one's romantic partner regulates subjective distress through other processes than mere distraction from the mental imagery.
  •  
46.
  • Kraus, Jakub, et al. (författare)
  • Soothing the emotional brain : modulation of neural activity to personal emotional stimulation by social touch
  • 2019
  • Ingår i: Social Cognitive & Affective Neuroscience. - : Oxford University Press (OUP). - 1749-5016 .- 1749-5024. ; 14:11, s. 1179-1185
  • Tidskriftsartikel (refereegranskat)abstract
    • Social touch may modulate emotions, but the neurobehavioral correlates are poorly understood. Here, we investigated neural responses to a picture of a deceased close person and if neural activity and connectivity are modulated by social touch from one's romantic partner. Using functional magnetic resonance imaging (fMRI) we found altered reactivity in several brain areas including the anterior cingulate cortex (ACC) and the anterior insula in response to the personal picture compared to a picture of an unfamiliar person. Hand holding with the romantic partner, compared to being alone, reduced reactivity in the ACC and cerebellum and provided subjective comfort. To separate physical touch from the emotional effect of partner presence, we evaluated hand holding with the partner relative to a stranger, and found reduced reactivity in the anterior insula. Connectivity between the anterior insula and the ACC was reduced during partner touch, and the connectivity strength were negatively related to attachment security, with higher reported partner security associated with weaker connectivity. Overall, holding hands with one's partner attenuates reactivity in emotional brain areas and reduces between-region connectivity.
  •  
47.
  • Kraus, Robert H. S., et al. (författare)
  • Avian influenza surveillance with FTA cards : field methods, biosafety, and transportation issues solved
  • 2011
  • Ingår i: Journal of Visualized Experiments. - : MyJove Corporation. - 1940-087X. ; :54
  • Tidskriftsartikel (refereegranskat)abstract
    • Avian Influenza Viruses (AIVs) infect many mammals, including humans(1). These AIVs are diverse in their natural hosts, harboring almost all possible viral subtypes(2). Human pandemics of flu originally stem from AIVs(3). Many fatal human cases during the H5N1 outbreaks in recent years were reported. Lately, a new AIV related strain swept through the human population, causing the 'swine flu epidemic'(4). Although human trading and transportation activity seems to be responsible for the spread of highly pathogenic strains(5), dispersal can also partly be attributed to wild birds(6, 7). However, the actual reservoir of all AIV strains is wild birds. In reaction to this and in face of severe commercial losses in the poultry industry, large surveillance programs have been implemented globally to collect information on the ecology of AIVs, and to install early warning systems to detect certain highly pathogenic strains(8-12). Traditional virological methods require viruses to be intact and cultivated before analysis. This necessitates strict cold chains with deep freezers and heavy biosafety procedures to be in place during transport. Long-term surveillance is therefore usually restricted to a few field stations close to well equipped laboratories. Remote areas cannot be sampled unless logistically cumbersome procedures are implemented. These problems have been recognised(13, 14) and the use of alternative storage and transport strategies investigated (alcohols or guanidine)(15-17). Recently, Kraus et al.(18) introduced a method to collect, store and transport AIV samples, based on a special filter paper. FTA cards(19) preserve RNA on a dry storage basis(20) and render pathogens inactive upon contact(21). This study showed that FTA cards can be used to detect AIV RNA in reverse-transcription PCR and that the resulting cDNA could be sequenced and virus genes and determined. In the study of Kraus et al.(18) a laboratory isolate of AIV was used, and samples were handled individually. In the extension presented here, faecal samples from wild birds from the duck trap at the Ottenby Bird Observatory (SE Sweden) were tested directly to illustrate the usefulness of the methods under field conditions. Catching of ducks and sample collection by cloacal swabs is demonstrated. The current protocol includes up-scaling of the work flow from single tube handling to a 96-well design. Although less sensitive than the traditional methods, the method of FTA cards provides an excellent supplement to large surveillance schemes. It allows collection and analysis of samples from anywhere in the world, without the need to maintaining a cool chain or safety regulations with respect to shipping of hazardous reagents, such as alcohol or guanidine.
  •  
48.
  • Kraus, Robert H. S., et al. (författare)
  • Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)
  • 2011
  • Ingår i: BMC Genomics. - 1471-2164 .- 1471-2164. ; 12, s. 150-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl. Results: More than one billion base pairs of sequence information were generated resulting in a 16x coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72. Conclusion: We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, similar to 101,000 SNPs were detected within our wild mallard sequences and similar to 49,000 were detected between wild and domesticated duck data. In the similar to 101,000 SNPs we found a subset of similar to 20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (similar to 150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e. g. disentangling migratory connectivity) and industrial breeding programs.
  •  
49.
  • Kraus, Robert H. S., et al. (författare)
  • Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)
  • 2011
  • Ingår i: BMC Genomics. - : BioMed Central Ltd.. - 1471-2164. ; 12
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl. Results: More than one billion base pairs of sequence information were generated resulting in a 16x coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72. Conclusion: We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, similar to 101,000 SNPs were detected within our wild mallard sequences and similar to 49,000 were detected between wild and domesticated duck data. In the similar to 101,000 SNPs we found a subset of similar to 20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (similar to 150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e. g. disentangling migratory connectivity) and industrial breeding programs.
  •  
50.
  • Kraus, Robert, et al. (författare)
  • Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks
  • 2012
  • Ingår i: BMC Evolutionary Biology. - 1471-2148 .- 1471-2148. ; 12, s. 45-
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND:The study of speciation and maintenance of species barriers is at the core of evolutionary biology. During speciation the genome of one population becomes separated from other populations of the same species, which may lead to genomic incompatibility with time. This separation is complete when no fertile offspring is produced from inter-population matings, which is the basis of the biological species concept. Birds, in particular ducks, are recognised as a challenging and illustrative group of higher vertebrates for speciation studies. There are many sympatric and ecologically similar duck species, among which fertile hybrids occur relatively frequently in nature, yet these species remain distinct.RESULTS:We show that the degree of shared single nucleotide polymorphisms (SNPs) between five species of dabbling ducks (genus Anas) is an order of magnitude higher than that previously reported between any pair of eukaryotic species with comparable evolutionary distances. We demonstrate that hybridisation has led to sustained exchange of genetic material between duck species on an evolutionary time scale without disintegrating species boundaries. Even though behavioural, genetic and ecological factors uphold species boundaries in ducks, we detect opposing forces allowing for viable interspecific hybrids, with long-term evolutionary implications. Based on the superspecies concept we here introduce the novel term "supra-population" to explain the persistence of SNPs identical by descent within the studied ducks despite their history as distinct species dating back millions of years.CONCLUSIONS:By reviewing evidence from speciation theory, palaeogeography and palaeontology we propose a fundamentally new model of speciation to accommodate our genetic findings in dabbling ducks. This model, we argue, may also shed light on longstanding unresolved general speciation and hybridisation patterns in higher organisms, e.g. in other bird groups with unusually high hybridisation rates. Observed parallels to horizontal gene transfer in bacteria facilitate the understanding of why ducks have been such an evolutionarily successful group of animals. There is large evolutionary potential in the ability to exchange genes among species and the resulting dramatic increase of effective population size to counter selective constraints.
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