| 1. |
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| 2. |
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| 3. |
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| 4. |
- Abat, E., et al.
(author)
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The ATLAS Transition Radiation Tracker (TRT) proportional drift tube: design and performance
- 2008
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In: Journal of Instrumentation. - 1748-0221. ; 3:2
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Journal article (peer-reviewed)abstract
- A straw proportional counter is the basic element of the ATLAS Transition Radiation Tracker (TRT). Its detailed properties as well as the main properties of a few TRT operating gas mixtures are described. Particular attention is paid to straw tube performance in high radiation conditions and to its operational stability.
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| 5. |
- Abat, E., et al.
(author)
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The ATLAS TRT barrel detector
- 2008
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In: Journal of Instrumentation. - 1748-0221. ; 3
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Journal article (peer-reviewed)abstract
- The ATLAS TRT barrel is a tracking drift chamber using 52,544 individual tubular drift tubes. It is one part of the ATLAS Inner Detector, which consists of three sub-systems: the pixel detector spanning the radius range 4 to 20 cm, the semiconductor tracker (SCT) from 30 to 52 cm, and the transition radiation tracker ( TRT) from 56 to 108 cm. The TRT barrel covers the central pseudo-rapidity region |eta| < 1, while the TRT endcaps cover the forward and backward eta regions. These TRT systems provide a combination of continuous tracking with many measurements in individual drift tubes ( or straws) and of electron identification based on transition radiation from fibers or foils interleaved between the straws themselves. This paper describes the recently-completed construction of the TRT Barrel detector, including the quality control procedures used in the fabrication of the detector.
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| 6. |
- Abat, E., et al.
(author)
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The ATLAS TRT electronics
- 2008
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In: Journal of Instrumentation. - 1748-0221. ; 3:6
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Journal article (peer-reviewed)abstract
- The ATLAS inner detector consists of three sub-systems: the pixel detector spanning the radius range 4cm-20cm, the semiconductor tracker at radii from 30 to 52 cm, and the transition radiation tracker (TRT), tracking from 56 to 107 cm. The TRT provides a combination of continuous tracking with many projective measurements based on individual drift tubes (or straws) and of electron identification based on transition radiation from fibres or foils interleaved between the straws themselves. This paper describes the on and off detector electronics for the TRT as well as the TRT portion of the data acquisition (DAQ) system.
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| 7. |
- Abat, E., et al.
(author)
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The ATLAS TRT end-cap detectors
- 2008
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In: Journal of Instrumentation. - 1748-0221. ; 3
-
Journal article (peer-reviewed)abstract
- The ATLAS TRT end-cap is a tracking drift chamber using 245,760 individual tubular drift tubes. It is a part of the TRT tracker which consist of the barrel and two end-caps. The TRT end-caps cover the forward and backward pseudo-rapidity region 1.0 < vertical bar eta vertical bar < 2.0, while the TRT barrel central eta region vertical bar eta vertical bar < 1.0. The TRT system provides a combination of continuous tracking with many measurements in individual drift tubes ( or straws) and of electron identification based on transition radiation from fibers or foils interleaved between the straws themselves. Along with other two sub-systems, namely the Pixel detector and Semi Conductor Tracker (SCT), the TRT constitutes the ATLAS Inner Detector. This paper describes the recently completed and installed TRT end-cap detectors, their design, assembly, integration and the acceptance tests applied during the construction.
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| 8. |
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| 9. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
-
Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 12. |
- Adiels, Lars, 1952-, et al.
(author)
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Test of CP violation with K0 and K‾0 at LEAR
- 1985
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In: Physics with antiprotons at LEAR in the ACOL era. - Gif sur Yvette : Editions Frontières. - 2863320351 ; , s. 467-482
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Conference paper (other academic/artistic)
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| 13. |
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| 14. |
- Sartelli, Massimo, et al.
(author)
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Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action
- 2023
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In: WORLD JOURNAL OF EMERGENCY SURGERY. - 1749-7922. ; 18:1
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Research review (peer-reviewed)abstract
- Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or "golden rules," for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice.
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| 15. |
- Tsiligiannis, Epameinondas, et al.
(author)
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A Four Carbon Organonitrate as a Significant Product of Secondary Isoprene Chemistry
- 2022
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In: Geophysical Research Letters. - : American Geophysical Union (AGU). - 0094-8276 .- 1944-8007. ; 49:11
-
Journal article (peer-reviewed)abstract
- Oxidation of isoprene by nitrate radicals (NO3) or by hydroxyl radicals (OH) under high NOx conditions forms a substantial amount of organonitrates (ONs). ONs impact NOx concentrations and consequently ozone formation while also contributing to secondary organic aerosol. Here we show that the ONs with the chemical formula C4H7NO5 are a significant fraction of isoprene-derived ONs, based on chamber experiments and ambient measurements from different sites around the globe. From chamber experiments we found that C4H7NO5 isomers contribute 5%-17% of all measured ONs formed during nighttime and constitute more than 40% of the measured ONs after further daytime oxidation. In ambient measurements C4H7NO5 isomers usually dominate both nighttime and daytime, implying a long residence time compared to C-5 ONs which are removed more rapidly. We propose potential nighttime sources and secondary formation pathways, and test them using a box model with an updated isoprene oxidation scheme.
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| 16. |
- Wu, R. R., et al.
(author)
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Molecular composition and volatility of multi-generation products formed from isoprene oxidation by nitrate radical
- 2021
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In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 21:13, s. 10799-10824
-
Journal article (peer-reviewed)abstract
- Isoprene oxidation by nitrate radical (NO3) is a potentially important source of secondary organic aerosol (SOA). It is suggested that the second or later-generation products are the more substantial contributors to SOA. However, there are few studies investigating the multi-generation chemistry of isoprene-NO3 reaction, and information about the volatility of different isoprene nitrates, which is essential to evaluate their potential to form SOA and determine their atmospheric fate, is rare. In this work, we studied the reaction between isoprene and NO3 in the SAPHIR chamber (Julich) under near-atmospheric conditions. Various oxidation products were measured by a high-resolution time-offlight chemical ionization mass spectrometer using Br as the reagent ion. Most of the products detected are organic nitrates, and they are grouped into monomers (C-4 and C-5 products) and dimers (C-10 products) with 1-3 nitrate groups according to their chemical composition. Most of the observed products match expected termination products observed in previous studies, but some compounds such as monomers and dimers with three nitrogen atoms were rarely reported in the literature as gas-phase products from isoprene oxidation by NO3. Possible formation mechanisms for these compounds are proposed. The multi-generation chemistry of isoprene and NO3 is characterized by taking advantage of the time behavior of different products. In addition, the vapor pressures of diverse isoprene nitrates are calculated by different parametrization methods. An estimation of the vapor pressure is also derived from their condensation behavior. According to our results, isoprene monomers belong to intermediate-volatility or semi-volatile organic compounds and thus have little effect on SOA formation. In contrast, the dimers are expected to have low or extremely low volatility, indicating that they are potentially substantial contributors to SOA. However, the monomers constitute 80% of the total explained signals on average, while the dimers contribute less than 2 %, suggesting that the contribution of isoprene NO3 oxidation to SOA by condensation should be low under atmospheric conditions. We expect a SOA mass yield of about 5% from the wall-loss- and dilution-corrected mass concentrations, assuming that all of the isoprene dimers in the low- or extremely low-volatility organic compound (LVOC or ELVOC) range will condense completely.
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| 17. |
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| 18. |
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| 19. |
- Bockelee-Morvan, D., et al.
(author)
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Composition and thermal properties of Ganymede's surface from JWST/NIRSpec and MIRI observations
- 2024
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 681, s. A27-
-
Journal article (peer-reviewed)abstract
- Context. We present the first spectroscopic observations of Ganymede by the James Webb Space Telescope undertaken in August 2022 as part of the proposal "ERS observations of the Jovian system as a demonstration of JWST's capabilities for Solar System science".Aims. We aimed to investigate the composition and thermal properties of the surface, and to study the relationships of ice and non-water-ice materials and their distribution.Methods. NIRSpec IFU (2.9-5.3 mu m) and MIRI MRS (4.9-28.5 mu m) observations were performed on both the leading and trailing hemispheres of Ganymede, with a spectral resolution of similar to 2700 and a spatial sampling of 0.1 to 0.17 '' (while the Ganymede size was similar to 1.68 ''). We characterized the spectral signatures and their spatial distribution on the surface. The distribution of brightness temperatures was analyzed with standard thermophysical modeling including surface roughness.Results. Reflectance spectra show signatures of water ice, CO2, and H2O2. An absorption feature at 5.9 mu m, with a shoulder at 6.5 mu m, is revealed, and is tentatively assigned to sulfuric acid hydrates. The CO2 4.26-mu m band shows latitudinal and longitudinal variations in depth, shape, and position over the two hemispheres, unveiling different CO2 physical states. In the ice-rich polar regions, which are the most exposed to Jupiter's plasma irradiation, the CO2 band is redshifted with respect to other terrains. In the boreal region of the leading hemisphere, the CO2 band is dominated by a high wavelength component at similar to 4.27 mu m, consistent with CO2 trapped in amorphous water ice. At equatorial latitudes (and especially on dark terrains), the observed band is broader and shifted toward the blue, suggesting CO2 adsorbed on non-icy materials, such as minerals or salts. Maps of the H2O Fresnel peak area correlate with Bond albedo maps and follow the distribution of water ice inferred from H2O absorption bands. Amorphous ice is detected in the ice-rich polar regions, and is especially abundant on the northern polar cap of the leading hemisphere. Leading and trailing polar regions exhibit different H2O, CO2, and H2O2 spectral properties. However, in both hemispheres the north polar cap ice appears to be more processed than the south polar cap. A longitudinal modification of the H2O ice molecular structure and/or nanometer- and micrometer-scale texture, of diurnal or geographic origin, is observed in both hemispheres. Ice frost is tentatively observed on the morning limb of the trailing hemisphere, which possibly formed during the night from the recondensation of water subliming from the warmer subsurface. Reflectance spectra of the dark terrains are compatible with the presence of Na- and Mg-sulfate salts, sulfuric acid hydrates, and possibly phyllosilicates mixed with fine-grained opaque minerals, with a highly porous texture. Latitude and local time variations of the brightness temperatures indicate a rough surface with mean slope angles of 15 degrees-25 degrees and a low thermal inertia Gamma = 20 - 40 J m(-2) s(-0.5) K-1, consistent with a porous surface, with no obvious difference between the leading and trailing sides.
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| 20. |
- Brownwood, B., et al.
(author)
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Gas-Particle Partitioning and SOA Yields of Organonitrate Products from NO3-Initiated Oxidation of Isoprene under Varied Chemical Regimes
- 2021
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In: Acs Earth and Space Chemistry. - : American Chemical Society (ACS). - 2472-3452. ; 5:4, s. 785-800
-
Journal article (peer-reviewed)abstract
- Alkyl nitrate (AN) and secondary organic aerosol (SOA) from the reaction of nitrate radicals (NO3) with isoprene were observed in the Simulation of Atmospheric PHotochemistry In a large Reaction (SAPHIR) chamber during the NO(3)Isop campaign in August 2018. Based on 15 day-long experiments under various reaction conditions, we conclude that the reaction has a nominally unity molar AN yield (observed range 90 +/- 40%) and an SOA mass yield of OA + organic nitrate aerosol of 13-15% (with similar to 50 mu g m(-3) inorganic seed aerosol and 2-5 mu g m-3 total organic aerosol). Isoprene (5-25 ppb) and oxidant (typically similar to 100 ppb O-3 and 5-25 ppb NO2) concentrations and aerosol composition (inorganic and organic coating) were varied while remaining close to ambient conditions, producing similar AN and SOA yields under all regimes. We observe the formation of dinitrates upon oxidation of the second double bond only once the isoprene precursor is fully consumed. We determine the bulk partitioning coefficient for ANs (K-p similar to 10(-3) m(3) mu g(-1)), indicating an average volatility corresponding to a C-5 hydroxy hydroperoxy nitrate.
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| 21. |
- Carlsson, P. T. M., et al.
(author)
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Comparison of isoprene chemical mechanisms under atmospheric night-time conditions in chamber experiments: evidence of hydroperoxy aldehydes and epoxy products from NO3 oxidation
- 2023
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In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 23:5, s. 3147-3180
-
Journal article (peer-reviewed)abstract
- The gas-phase reaction of isoprene with the nitrate radical (NO3) was investigated in experiments in the outdoor SAPHIR chamber under atmospherically relevant conditions specifically with respect to the chemical lifetime and fate of nitrato-organic peroxy radicals (RO2). Observations of organic products were compared to concentrations expected from different chemical mechanisms: (1) the Master Chemical Mechanism, which simplifies the NO3 isoprene chemistry by only considering one RO2 isomer; (2) the chemical mechanism derived from experiments in the Caltech chamber, which considers different RO2 isomers; and (3) the FZJ-NO3 isoprene mechanism derived from quantum chemical calculations, which in addition to the Caltech mechanism includes equilibrium reactions of RO(2 )isomers, unimolecular reactions of nitrate RO(2 )radicals and epoxidation reactions of nitrate alkoxy radicals. Measurements using mass spectrometer instruments give evidence that the new reactions pathways predicted by quantum chemical calculations play a role in the NO3 oxidation of isoprene. Hydroperoxy aldehyde (HPALD) species, which are specific to unimolecular reactions of nitrate RO2, were detected even in the presence of an OH scavenger, excluding the possibility that concurrent oxidation by hydroxyl radicals (OH) is responsible for their formation. In addition, ion signals at masses that can be attributed to epoxy compounds, which are specific to the epoxidation reaction of nitrate alkoxy radicals, were detected. Measurements of methyl vinyl ketone (MVK) and methacrolein (MACR) concentrations confirm that the decomposition of nitrate alkoxy radicals implemented in the Caltech mechanism cannot compete with the ring-closure reactions predicted by quantum chemical calculations. The validity of the FZJ-NO3 isoprene mechanism is further supported by a good agreement between measured and simulated hydroxyl radical (OH) reactivity. Nevertheless, the FZJ-NO3 isoprene mechanism needs further investigations with respect to the absolute importance of unimolecular reactions of nitrate RO2 and epoxidation reactions of nitrate alkoxy radicals. Absolute concentrations of specific organic nitrates such as nitrate hydroperoxides would be required to experimentally determine product yields and branching ratios of reactions but could not be measured in the chamber experiments due to the lack of calibration standards for these compounds. The temporal evolution of mass traces attributed to product species such as nitrate hydroperoxides, nitrate carbonyl and nitrate alcohols as well as hydroperoxy aldehydes observed by the mass spectrometer instruments demonstrates that further oxidation by the nitrate radical and ozone at atmospheric concentrations is small on the timescale of one night (12 h) for typical oxidant concentrations. However, oxidation by hydroxyl radicals present at night and potentially also produced from the decomposition of nitrate alkoxy radicals can contribute to their nocturnal chemical loss.
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| 22. |
- Agate, B, et al.
(author)
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Efficient frequency-doubling of femtosecond pulses in waveguide and bulk nonlinear crystals - Design, fabrication, theory and experiment
- 2006
-
In: FRONTIERS IN PLANAR LIGHTWAVE CIRCUIT TECHNOLOGY DESIGN, SIMULATION, AND FABRICATION. - : Springer Nature. ; , s. 189-
-
Conference paper (peer-reviewed)abstract
- We investigate efficient frequency-doubling of low energy femtosecond pulses in bulk and waveguide nonlinear crystals, thereby demonstrating how to achieve a compact and portable ultrafast blue light Source. Using a femtosecond Cr:LiSAF laser (fundamental wavelength 860 nm) we examine the relative merits of the process of second harmonic generation (SHG) using bulk potassium niobate, bulk aperiodically-poled KTP, periodically-poled and aperiodically-poled KTP waveguide crystals. While SHG conversion efficiencies LIP to 37% were achieved using the waveguides, non-traditional strong focusing in the bulk samples yielded efficiencies of 30%. We have developed several theoretical models to accurately describe the temporal and spectral properties of the generated blue light, as well as the observed saturation behavior of the conversion process in the waveguide structures.
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| 23. |
- de Pater, Imke, et al.
(author)
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An Energetic Eruption With Associated SO 1.707 Micron Emissions at Io's Kanehekili Fluctus and a Brightening Event at Loki Patera Observed by JWST
- 2023
-
In: Journal of Geophysical Research - Planets. - : American Geophysical Union (AGU). - 2169-9097 .- 2169-9100. ; 128:8
-
Journal article (peer-reviewed)abstract
- We observed Io with the James Webb Space Telescope (JWST) while the satellite was in eclipse, and detected thermal emission from several volcanoes. The data were taken as part of our JWST-ERS program #1373 on 15 November 2022. Kanehekili Fluctus was exceptionally bright, and Loki Patera had most likely entered a new brightening phase. Spectra were taken with NIRSpec/IFU at a resolving power R ≈ 2,700 between 1.65 and 5.3 µm. The spectra were matched by a combination of blackbody curves that showed that the highest temperature, ∼1,200 K, for Kanehekili Fluctus originated from an area ∼0.25 km2 in size, and for Loki Patera this high temperature was confined to an area of ∼0.06 km2. Lower temperatures, down to 300 K, cover areas of ∼2,000 km2 for Kanehekili Fluctus, and ∼5,000 km2 for Loki Patera. We further detected the a1Δ ⇒ X3Σ− 1.707 µm rovibronic forbidden SO emission band complex over the southern hemisphere, which peaked at the location of Kanehekili Fluctus. This is the first time this emission has been seen above an active volcano, and suggests that the origin of such emissions is ejection of SO molecules directly from the vent in an excited state, after having been equilibrated at temperatures of ∼1,500 K below the surface, as was previously hypothesized.
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| 28. |
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| 29. |
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| 30. |
- Milner-Gulland, E. J., et al.
(author)
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Accounting for the Impact of Conservation on Human Well-Being
- 2014
-
In: Conservation Biology. - : Wiley. - 0888-8892 .- 1523-1739. ; 28:5, s. 1160-1166
-
Journal article (peer-reviewed)abstract
- Conservationists are increasingly engaging with the concept of human well-being to improve the design and evaluation of their interventions. Since the convening of the influential Sarkozy Commission in 2009, development researchers have been refining conceptualizations and frameworks to understand and measure human well-being and are starting to converge on a common understanding of how best to do this. In conservation, the term human well-being is in widespread use, but there is a need for guidance on operationalizing it to measure the impacts of conservation interventions on people. We present a framework for understanding human well-being, which could be particularly useful in conservation. The framework includes 3 conditions; meeting needs, pursuing goals, and experiencing a satisfactory quality of life. We outline some of the complexities involved in evaluating the well-being effects of conservation interventions, with the understanding that well-being varies between people and over time and with the priorities of the evaluator. Key challenges for research into the well-being impacts of conservation interventions include the need to build up a collection of case studies so as to draw out generalizable lessons; harness the potential of modern technology to support well-being research; and contextualize evaluations of conservation impacts on well-being spatially and temporally within the wider landscape of social change. Pathways through the smog of confusion around the term well-being exist, and existing frameworks such as the Well-being in Developing Countries approach can help conservationists negotiate the challenges of operationalizing the concept. Conservationists have the opportunity to benefit from the recent flurry of research in the development field so as to carry out more nuanced and locally relevant evaluations of the effects of their interventions on human well-being. Consideracion del Impacto de la Conservacion sobre el Bienestar Humano
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| 31. |
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| 32. |
- Muyldermans, G, et al.
(author)
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External quality assessment for molecular detection of Bordetella pertussis in European laboratories.
- 2005
-
In: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 43:1, s. 30-35
-
Journal article (peer-reviewed)abstract
- Although the PCR for the detection of Bordetella pertussis is routinely performed in diagnostic laboratories, no quality assessment program has so far been described. We report on the results obtained with two external quality assessment proficiency panels sent to European laboratories. The first proficiency panel contained a series of dilutions of three previously characterized B. pertussis clinical isolates and two negative controls. No false-positive results were reported by six laboratories providing seven data sets. The reported limits of detection of the three B. pertussis strains varied between 4 and 4,000, 9 and 9,000, and 3 and 30,000 CFU/ml, respectively. The second proficiency panel, composed of a series of dilutions of reference strains of B. pertussis, B. holmesii, B. hinzii, and B. bronchiseptica, as well as negative controls, was sent to nine laboratories. One laboratory reported a negative result for a sample and reported a B. parapertussis-positive sample to be positive for B. pertussis. By using the B. pertussis-specific target gene pertactin, one laboratory detected B. pertussis with 100% specificity. All other laboratories, which used IS481-based assays, reported positive results for the samples containing B. holmesii and B. bronchiseptica, species that have occasionally been recovered from human respiratory samples. These data show that the choice of the target gene is particularly critical for the species specificity of B. pertussis PCR assays.
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| 33. |
- Agate, B., et al.
(author)
-
Portable ultrafast blue light sources
- 2004
-
In: OSA Trends Opt. Photonics Series. - 1557527709 ; , s. 651-652
-
Conference paper (peer-reviewed)abstract
- An effective means of achieving a portable, ultrafast blue-light source using a variety of nonlinear media is demonstrated. We investigate the relative merits of aperiodically-poled bulk and waveguide nonlinear crystals in comparison to periodically-poled structures.
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| 34. |
- Agate, B., et al.
(author)
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Portable ultrafast blue light sources designed with frequency doubling in KTP and KNbO3
- 2004
-
In: IEEE Journal of Selected Topics in Quantum Electronics. - : Institute of Electrical and Electronics Engineers (IEEE). - 1077-260X .- 1558-4542. ; 10:6, s. 1268-1276
-
Journal article (peer-reviewed)abstract
- We demonstrate an effective means of achieving compact, truly portable, and entirely self-contained ultrafast blue light sources. Using a variety of nonlinear media to achieve simple second-harmonic generation of a femtosecond Cr:LiSAF laser, we investigate the relative merits of aperiodically poled bulk and waveguide nonlinear crystals in comparison to periodically poled structures. Such a compact and convenient source of ultrashort laser pulses in the blue spectral region could be of great interest for on-site applications spanning a host of disciplines, such as biomedical imaging, optical micromanipulation, and high-resolution spectroscopy.
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| 35. |
- Ameen, Carly, et al.
(author)
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Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic
- 2019
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In: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 286:1916
-
Journal article (peer-reviewed)abstract
- Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.
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| 36. |
- Casewell, Nicholas R, et al.
(author)
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Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals.
- 2019
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:51, s. 25745-25755
-
Journal article (peer-reviewed)abstract
- Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon (Solenodon paradoxus). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 (KLK1) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions.
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| 37. |
- Clamp, Michele, et al.
(author)
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Distinguishing protein-coding and noncoding genes in the human genome
- 2007
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 104:49, s. 19428-19433
-
Journal article (peer-reviewed)abstract
- Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding genes remains a matter of controversy. Current catalogs list a total of ≈24,500 putative protein-coding genes. It is broadly suspected that a large fraction of these entries are functionally meaningless ORFs present by chance in RNA transcripts, because they show no evidence of evolutionary conservation with mouse or dog. However, there is currently no scientific justification for excluding ORFs simply because they fail to show evolutionary conservation: the alternative hypothesis is that most of these ORFs are actually valid human genes that reflect gene innovation in the primate lineage or gene loss in the other lineages. Here, we reject this hypothesis by carefully analyzing the nonconserved ORFs—specifically, their properties in other primates. We show that the vast majority of these ORFs are random occurrences. The analysis yields, as a by-product, a major revision of the current human catalogs, cutting the number of protein-coding genes to ≈20,500. Specifically, it suggests that nonconserved ORFs should be added to the human gene catalog only if there is clear evidence of an encoded protein. It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes.
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| 38. |
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| 39. |
- Gephart, Jessica A., et al.
(author)
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Scenarios for Global Aquaculture and Its Role in Human Nutrition
- 2021
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In: Reviews in Fisheries Science & Aquaculture. - : Informa UK Limited. - 2330-8249 .- 2330-8257. ; 29:1, s. 122-138
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Research review (peer-reviewed)abstract
- Global demand for freshwater and marine foods (i.e., seafood) is rising and an increasing proportion is farmed. Aquaculture encompasses a range of species and cultivation methods, resulting in diverse social, economic, nutritional, and environmental outcomes. As a result, how aquaculture develops will influence human wellbeing and environmental health outcomes. Recognition of this has spurred a push for nutrition-sensitive aquaculture, which aims to benefit public health through the production of diverse, nutrient-rich seafood and enabling equitable access. This article explores plausible aquaculture futures and their role in nutrition security using a qualitative scenario approach. Two dimensions of economic development - the degree of globalization and the predominant economic development philosophy - bound four scenarios representing systems that are either localized or globalized, and orientated toward maximizing sectoral economic growth or to meeting environmental and equity dimensions of sustainability. The potential contribution of aquaculture in improving nutrition security is then evaluated within each scenario. While aquaculture could be nutrition-sensitive under any of the scenarios, its contribution to addressing health inequities is more likely in the economic and political context of a more globally harmonized trade environment and where economic policies are oriented toward social equity and environmental sustainability.
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| 40. |
- Haas, Brian J., et al.
(author)
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Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
- 2009
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 461:7262, s. 393-398
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Journal article (peer-reviewed)abstract
- Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
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| 41. |
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| 42. |
- Hattne, Johan, et al.
(author)
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Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
- 2014
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In: Nature Methods. - 1548-7091 .- 1548-7105. ; 11:5, s. 545-548
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Journal article (peer-reviewed)abstract
- X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.
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| 43. |
- Hattne, Johan, et al.
(author)
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Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
- 2014
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In: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 11:5, s. 545-548
-
Journal article (peer-reviewed)abstract
- X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.
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| 44. |
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| 45. |
- Jallow, Muminatou, et al.
(author)
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Genome-wide and fine-resolution association analysis of malaria in West Africa.
- 2009
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; , s. 657-665
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Journal article (peer-reviewed)abstract
- We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 x 10(-7) to P = 4 x 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations.
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| 46. |
- Kainu, Kati, et al.
(author)
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Association of psoriasis to PGLYRP and SPRR genes at PSORS4 locus on 1q shows heterogeneity between Finnish, Swedish and Irish families.
- 2009
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In: Experimental dermatology. - : Wiley. - 1600-0625 .- 0906-6705. ; 18:2, s. 109-15
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Journal article (peer-reviewed)abstract
- A susceptibility locus for psoriasis, PSORS4, has been mapped to chromosome 1q21 in the region of the epidermal differentiation complex. The region has been refined to a 115 kb interval around the loricrin (LOR) gene. However, no evidence of association between polymorphisms in the LOR gene and psoriasis has been found. Therefore, we have analysed association to three candidate gene clusters of the region, the S100, small proline-rich protein (SPRR) and PGLYRP (peptidoglycan recognition protein) genes, which all contain functionally interesting psoriasis candidate genes. In previous studies, the SPRR and S100 genes have shown altered expression in psoriasis. Also polymorphisms in the PGLYRP genes have shown to be associated with psoriasis. We genotyped altogether 29 single nucleotide polymorphisms (SNPs) in 255 Finnish psoriasis families and analysed association with psoriasis using transmission disequilibrium test. A five-SNP haplotype of PGLYRP SNPs associated significantly with psoriasis. There was also suggestive evidence of association to SPRR gene locus in Finnish families. To confirm the putative associations, selected SNPs were genotyped also in a family collection of Swedish and Irish patients. The families supported association to the two gene regions, but there was also evidence of allelic heterogeneity.
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| 47. |
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| 48. |
- Kern, Jan, et al.
(author)
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Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy
- 2014
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 4371-
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Journal article (peer-reviewed)abstract
- The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O-2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 mu s after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 mu s after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 angstrom. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.
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| 49. |
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| 50. |
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