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The selaginella genome identifies genetic changes associated with the evolution of vascular plants
(2011)
Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
A catalog of genetic loci associated with kidney function from analyses of a million individuals
(2019)
Chronic kidney disease (CKD) is responsible for a public health burden with multi-systemic complications. Through transancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n = 1,046,070), we identified 264 associated loci (166 new). Of these,147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n = 416,178). Pathway and enrichment analyses, including mouse models with renal phenotypes, support the kidney as the main target organ. A genetic risk score for lower eGFR was associated with clinically diagnosed CKD in 452,264 independent individuals. Colocalization analyses of associations with eGFR among 783,978 European-ancestry individuals and gene expression across 46 human tissues, including tubulo-interstitial and glomerular kidney compartments, identified 17 genes differentially expressed in kidney. Fine-mapping highlighted missense driver variants in 11 genes and kidney-specific regulatory variants. These results provide a comprehensive priority list of molecular targets for translational research.
This study pushes our understanding of research reliability by reproducing and replicating claims from 110 papers in leading economic and political science journals. The analysis involves computational reproducibility checks and robustness assessments. It reveals several patterns. First, we uncover a high rate of fully computationally reproducible results (over 85%). Second, excluding minor issues like missing packages or broken pathways, we uncover coding errors for about 25% of studies, with some studies containing multiple errors. Third, we test the robustness of the results to 5,511 re-analyses. We find a robustness reproducibility of about 70%. Robustness reproducibility rates are relatively higher for re-analyses that introduce new data and lower for re-analyses that change the sample or the definition of the dependent variable. Fourth, 52% of re-analysis effect size estimates are smaller than the original published estimates and the average statistical significance of a re-analysis is 77% of the original. Lastly, we rely on six teams of researchers working independently to answer eight additional research questions on the determinants of robustness reproducibility. Most teams find a negative relationship between replicators' experience and reproducibility, while finding no relationship between reproducibility and the provision of intermediate or even raw data combined with the necessary cleaning codes.
The results of follow-up observations of the TeV gamma-ray source HESS J1640-465 from 2004 to 2011 with the High Energy Stereoscopic System (HESS) are reported in this work. The spectrum is well described by an exponential cut-off power law with photon index Gamma = 2.11 +/- 0.09(stat) +/- 0.10(sys), and a cut-off energy of E-2 = 6.0(-1.2)(+2.0) TeV. The TeV emission is significantly extended and overlaps with the northwestern part of the shell of the SNR G338.3-0.0. The new HESS results, a re-analysis of archival XMM-Newton data and multiwavelength observations suggest that a significant part of the gamma-ray emission from HESS J1640-465 originates in the supernova remnant shell. In a hadronic scenario, as suggested by the smooth connection of the GeV and TeV spectra, the product of total proton energy and mean target density could be as high as W(p)n(H) similar to 4 x 10(52)(d/10kpc)(2) erg cm(-3).
An annihilation signal of dark matter is searched for from the central region of the Milky Way. Data acquired in dedicated on-off observations of the Galactic center region with H.E.S.S. are analyzed for this purpose. No significant signal is found in a total of similar to 9 h of on-off observations. Upper limits on the velocity averaged cross section, <sigma upsilon >, for the annihilation of dark matter particles with masses in the range of similar to 300 GeV to similar to 10 TeV are derived. In contrast to previous constraints derived from observations of the Galactic center region, the constraints that are derived here apply also under the assumption of a central core of constant dark matter density around the center of the Galaxy. Values of <sigma upsilon > that are larger than 3 x 10(-24) cm(3)/s are excluded for dark matter particles with masses between similar to 1 and similar to 4 TeV at 95% C.L. if the radius of the central dark matter density core does not exceed 500 pc. This is the strongest constraint that is derived on <sigma upsilon > for annihilating TeV mass dark matter without the assumption of a centrally cusped dark matter density distribution in the search region.
Diffuse gamma-ray emission is the most prominent observable signature of celestial cosmic-ray interactions at high energies. While already being investigated at GeVenergies over several decades, assessments of diffuse gamma-ray emission at TeVenergies remain sparse. After completion of the systematic survey of the inner Galaxy, the H.E.S.S. experiment is in a prime position to observe large-scale diffuse emission at TeVenergies. Data of the H.E.S.S. Galactic Plane Survey are investigated in regions off known gamma-ray sources. Corresponding gamma-ray flux measurements were made over an extensive grid of celestial locations. Longitudinal and latitudinal profiles of the observed gamma-ray fluxes show characteristic excess emission not attributable to known gamma-ray sources. For the first time large-scale gamma-ray emission along the Galactic plane using imaging atmospheric Cherenkov telescopes has been observed. While the background subtraction technique limits the ability to recover modest variation on the scale of the H.E.S.S. field of view or larger, which is characteristic of the inverse Compton scatter-induced Galactic diffuse emission, contributions of neutral pion decay as well as emission from unresolved gamma-ray sources can be recovered in the observed signal to a large fraction. Calculations show that the minimum gamma-ray emission from pi(0) decay represents a significant contribution to the total signal. This detection is interpreted as a mix of diffuse Galactic gamma-ray emission and unresolved sources.
Context. Puppis A is an interesting similar to 4 kyr-old supernova remnant (SNR) that shows strong evidence of interaction between the forward shock and a molecular cloud. It has been studied in detail from radio frequencies to high-energy (HE, 0.1-100 GeV) gamma-rays. An analysis of the Fermi-LAT data has shown extended HE gamma-ray emission with a 0.2-100 GeV spectrum exhibiting no significant deviation from a power law, unlike most of the GeV-emitting SNRs known to be interacting with molecular clouds. This makes it a promising target for imaging atmospheric Cherenkov telescopes (IACTs) to probe the gamma-ray emission above 100 GeV.
Aims. Very-high-energy (VHE, E >= 0.1 TeV) gamma-ray emission from Puppis A has been, for the first time, searched for with the High Energy Stereoscopic System (HESS.).
Methods. Stereoscopic imaging of Cherenkov radiation from extensive air showers is used to reconstruct the direction and energy of the incident gamma-rays in order to produce sky images and source spectra. The profile likelihood method is applied to find constraints on the existence of a potential break or cutoff in the photon spectrum.
Results. The analysis of the HESS. data does not reveal any significant emission towards Puppis A. The derived upper limits on the differential photon flux imply that its broadband gamma-ray spectrum must exhibit a spectral break or cutoff. By combining Fermi-LAT and HESS. measurements, the 99% confidence-level upper limits on such a cutoff are found to be 450 and 280 GeV, assuming a power law with a simple exponential and a sub-exponential cutoff, respectively. It is concluded that none of the standard limitations (age, size, radiative losses) on the particle acceleration mechanism, assumed to be continuing at present, can explain the lack of VHE signal. The scenario in which particle acceleration has ceased some time ago is considered as an alternative explanation. The HE/VHE spectrum of Puppis A could then exhibit a break of non-radiative origin (as observed in several other interacting SNRs, albeit at somewhat higher energies), owing to the interaction with dense and neutral material, in particular towards the NE region.
A comprehensive molecular analysis of a simple aqueous complexing system. U(VI) acetate. selected to be independently investigated by various spectroscopic (vibrational, luminescence, X-ray absorption, and nuclear magnetic resonance spectroscopy) and quantum chemical methods was achieved by an international round-robin test (RRT). Twenty laboratories from six different countries with a focus on actinide or geochemical research participated and contributed to this scientific endeavor. The outcomes of this RRT were considered on two levels of complexity: first, within each technical discipline, conformities as well as discrepancies of the results and their sources were evaluated. The raw data from the different experimental approaches were found to be generally consistent. In particular, for complex setups such as accelerator-based X-ray absorption spectroscopy, the agreement between the raw data was high. By contrast, luminescence spectroscopic data turned out to be strongly related to the chosen acquisition parameters. Second, the potentials and limitations of coupling various spectroscopic and theoretical approaches for the comprehensive study of actinide molecular complexes were assessed. Previous spectroscopic data from the literature were revised and the benchmark data on the U(VI) acetate system provided an unambiguous molecular interpretation based on the correlation of spectroscopic and theoretical results. The multimethodologic approach and the conclusions drawn address not only important aspects of actinide spectroscopy but particularly general aspects of modern molecular analytical chemistry.
Xenikoudakis et al. report a partial mitochondrial genome of the extinct giant beaver Castoroides and estimate the origin of aquatic behavior in beavers to approximately 20 million years. This time estimate coincides with the extinction of terrestrial beavers and raises the question whether the two events had a common cause.
For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks.
Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.
This Letter reports the discovery of a remarkably hard spectrum source, HESS J1641-463, by the High Energy Stereoscopic System (H.E.S.S.) in the very high energy (VHE) domain. HESS J1641-463 remained unnoticed by the usual analysis techniques due to confusion with the bright nearby source HESS J1640-465. It emerged at a significance level of 8.5 standard deviations after restricting the analysis to events with energies above 4 TeV. It shows a moderate flux level of phi(E > 1TeV) = (3.64 +/- 0.44(stat)+/- 0.73(sys)) x 10(-13) cm(-2) s(-1), corresponding to 1.8% of the Crab Nebula flux above the same energy, and a hard spectrum with a photon index of Gamma = 2.07 +/- 0.11(stat)+/- 0.20(sys). It is a point-like source, although an extension up to a Gaussian width of sigma = 3 arcmin cannot be discounted due to uncertainties in the H.E.S.S. point-spread function. The VHE gamma-ray flux of HESS J1641-463 is found to be constant over the observed period when checking time binnings from the year-by-year to the 28 minute exposure timescales. HESS J1641-463 is positionally coincident with the radio supernova remnant SNR G338.5+0.1. No X-ray candidate stands out as a clear association; however, Chandra and XMM-Newton data reveal some potential weak counterparts. Various VHE gamma-ray production scenarios are discussed. If the emission from HESS J1641-463 is produced by cosmic ray protons colliding with the ambient gas, then their spectrum must extend close to 1 PeV. This object may represent a source population contributing significantly to the galactic cosmic ray flux around the knee.
Search for dark matter annihilation signatures in HESS observations of
dwarf spheroidal galaxies
(2014)
Dwarf spheroidal galaxies of the Local Group are close satellites of the Milky Way characterized by a large mass-to-light ratio and are not expected to be the site of nonthermal high-energy gamma-ray emission or intense star formation. Therefore they are among the most promising candidates for indirect dark matter searches. During the last years the High Energy Stereoscopic System (H.E.S.S.) of imaging atmospheric Cherenkov telescopes observed five of these dwarf galaxies for more than 140 hours in total, searching for TeV gamma-ray emission from annihilation of dark matter particles. The new results of the deep exposure of the Sagittarius dwarf spheroidal galaxy, the first observations of the Coma Berenices and Fornax dwarves and the reanalysis of two more dwarf spheroidal galaxies already published by the H.E.S.S. Collaboration, Carina and Sculptor, are presented. In the absence of a significant signal new constraints on the annihilation cross section applicable to weakly interacting massive particles (WIMPs) are derived by combining the observations of the five dwarf galaxies. The combined exclusion limit depends on the WIMP mass and the best constraint is reached at 1-2 TeV masses with a cross-section upper bound of similar to 3.9 x 10(-24) cm(3) s(-1) at a 95% confidence level.
Aims. Previous observations with the High Energy Stereoscopic System (H.E.S.S.) have revealed an extended very-high-energy (VHE; E > 100 GeV) gamma-ray source, HESS J1834-087, coincident with the supernova remnant (SNR) W41. The origin of the gamma-ray emission was investigated in more detail with the H.E.S.S. array and the Large Area Telescope (LAT) onboard the Fermi Gamma-ray Space Telescope.
Methods. The gamma-ray data provided by 61 h of observations with H.E.S.S., and four years with the Fermi LAT were analyzed, covering over five decades in energy from 1.8 GeV up to 30 TeV. The morphology and spectrum of the TeV and GeV sources were studied and multiwavelength data were used to investigate the origin of the gamma-ray emission toward W41.
Results. The TeV source can be modeled with a sum of two components: one point-like and one significantly extended (sigma(TeV) = 0.17 degrees +/- 0.01 degrees), both centered on SNR W41 and exhibiting spectra described by a power law with index Gamma(TeV) similar or equal to 2.6. The GeV source detected with Fermi LAT is extended (sigma(GeV) = 0.15 degrees +/- 0.03 degrees) and morphologically matches the VHE emission. Its spectrum can be described by a power-law model with an index Gamma(GeV) = 2.15 +/- 0.12 and smoothly joins the spectrum of the whole TeV source. A break appears in the gamma-ray spectra around 100 GeV. No pulsations were found in the GeV range.
Conclusions. Two main scenarios are proposed to explain the observed emission: a pulsar wind nebula (PWN) or the interaction of SNR W41 with an associated molecular cloud. X-ray observations suggest the presence of a point-like source (a pulsar candidate) near the center of the remnant and nonthermal X-ray diffuse emission that could arise from the possibly associated PWN. The PWN scenario is supported by the compatible positions of the TeV and GeV sources with the putative pulsar. However, the spectral energy distribution from radio to gamma-rays is reproduced by a one-zone leptonic model only if an excess of low-energy electrons is injected following a Maxwellian distribution by a pulsar with a high spin-down power (> 10(37) erg s(-1)). This additional low-energy component is not needed if we consider that the point-like TeV source is unrelated to the extended GeV and TeV sources. The interacting SNR scenario is supported by the spatial coincidence between the gamma-ray sources, the detection of OH (1720 MHz) maser lines, and the hadronic modeling.
The Large Magellanic Cloud, a satellite galaxy of the Milky Way, has been observed with the High Energy Stereoscopic System (H.E.S.S.) above an energy of 100 billion electron volts for a deep exposure of 210 hours. Three sources of different types were detected: the pulsar wind nebula of the most energetic pulsar known, N 157B; the radio-loud supernova remnant N 132D; and the largest nonthermal x-ray shell, the superbubble 30 Dor C. The unique object SN 1987A is, unexpectedly, not detected, which constrains the theoretical framework of particle acceleration in very young supernova remnants. These detections reveal the most energetic tip of a g-ray source population in an external galaxy and provide via 30 Dor C the unambiguous detection of g-ray emission from a superbubble.
Context. Very-high-energy (VHE; E > 100 GeV) gamma-ray emission from blazars inevitably gives rise to electron-positron pair production through the interaction of these gamma-rays with the extragalactic background light (EBL). Depending on the magnetic fields in the proximity of the source, the cascade initiated from pair production can result in either an isotropic halo around an initially- beamed source or a magnetically- broadened cascade :aux.
Aims. Both extended pair-halo (PH) and magnetically broadened cascade (MBC) emission from regions surrounding the blazars 1ES 1101-232, IRS 0229+200, and PKS 2155-304 were searched for using VHE y-ray data taken with the High Energy Stereoscopic System (HESS.) and high-energy (HE; 100 MeV < E < 100 GeV) gamma-ray data with the Fermi Large Area Telescope (LAT).
Methods. By comparing the angular distributions of the reconstructed gamma-ray events to the angular profiles calculated from detailed theoretical models, the presence of PH and MBC was investigated.
Results. Upper limits on the extended emission around lES 1101-232, lES 0229+200, and PKS 2155-304 are found to be at a level of a few per cent of the Crab nebula flux above 1 TeV, depending on the assumed photon index of the cascade emission. Assuming strong extra-Galactic magnetic field (EGME) values, >10(-12) G, this limits the production of pair haloes developing from electromagnetic cascades. For weaker magnetic fields, in which electromagnetic cascades would result in MBCs. EGMF strengths in the range (0.3-3) x 10(-15) G were excluded for PKS 2155-304 at the 99% confidence level, under the assumption of a 1 Mpc coherence length.
Very high energy (VHE, E > 100 GeV)gamma-ray flaring activity of the high-frequency peaked BL Lac object PG 1553 + 113 has been detected by the H.E.S.S. telescopes. The flux of the source increased by a factor of 3 during the nights of 2012 April 26 and 27 with respect to the archival measurements with a hint of intra-night variability. No counterpart of this event has been detected in the Fermi-Large Area Telescope data. This pattern is consistent with VHE gamma(-)ray flaring being caused by the injection of ultrarelativistic particles, emitting.-rays at the highest energies. The dataset offers a unique opportunity to constrain the redshift of this source at z = 0.49 +/- 0.04 using a novel method based on Bayesian statistics. The indication of intra-night variability is used to introduce a novel method to probe for a possible Lorentz invariance violation (LIV), and to set limits on the energy scale at which Quantum Gravity (QG) effects causing LIV may arise. For the subluminal case, the derived limits are E-QG,E- 1 > 4.10 x 10(17) GeV and E-QG,E- 2 > 2.10 x 10(10) GeV for linear and quadratic LIV effects, respectively.
In this paper we report on the analysis of all the available optical and very high-energy gamma-ray (> 200 GeV) data for the BL Lac object PKS 2155-304, collected simultaneously with the ATOM and H.E.S.S. telescopes from 2007 until 2009. This study also includes X-ray (RXTE, Swift) and high-energy gamma-ray (Fermi-LAT) data. During the period analysed, the source was transitioning from its flaring to quiescent optical states, and was characterized by only moderate flux changes at different wavelengths on the timescales of days and months. A flattening of the optical continuum with an increasing optical flux can be noted in the collected dataset, but only occasionally and only at higher flux levels. We did not find any universal relation between the very high-energy gamma-ray and optical flux changes on the timescales from days and weeks up to several years. On the other hand, we noted that at higher flux levels the source can follow two distinct tracks in the optical flux-colour diagrams, which seem to be related to distinct gamma-ray states of the blazar. The obtained results therefore indicate a complex scaling between the optical and gamma-ray emission of PKS 2155 304, with different correlation patterns holding at different epochs, and a gamma-ray flux depending on the combination of an optical flux and colour rather than a flux alone.
The gamma-ray spectrum of the low-frequency-peaked BL Lac (LBL) object AP Librae is studied, following the discovery of very-high-energy (VHE; E > 100 GeV) gamma-ray emission up to the TeV range by the H.E.S.S. experiment. Thismakes AP Librae one of the few VHE emitters of the LBL type. The measured spectrum yields a flux of (8.8 +/- 1.5(stat) +/- 1.8(sys)) x 10(-12) cm(-2) s(-1) above 130 GeV and a spectral index of Gamma = 2.65 +/- 0.19(stat) +/- 0.20(sys). This study also makes use of Fermi-LAT observations in the high energy (HE, E > 100 MeV) range, providing the longest continuous light curve (5 years) ever published on this source. The source underwent a flaring event between MJD 56 306-56 376 in the HE range, with a flux increase of a factor of 3.5 in the 14 day bin light curve and no significant variation in spectral shape with respect to the low-flux state. While the H.E.S.S. and (low state) Fermi-LAT fluxes are in good agreement where they overlap, a spectral curvature between the steep VHE spectrum and the Fermi-LAT spectrum is observed. The maximum of the gamma-ray emission in the spectral energy distribution is located below the GeV energy range.