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2.
  • Molinaro, Antonio, et al. (author)
  • Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology
  • 2020
  • In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1
  • Journal article (peer-reviewed)abstract
    • Microbiota-host-diet interactions contribute to the development of metabolic diseases. Imidazole propionate is a novel microbially produced metabolite from histidine, which impairs glucose metabolism. Here, we show that subjects with prediabetes and diabetes in the MetaCardis cohort from three European countries have elevated serum imidazole propionate levels. Furthermore, imidazole propionate levels were increased in subjects with low bacterial gene richness and Bacteroides 2 enterotype, which have previously been associated with obesity. The Bacteroides 2 enterotype was also associated with increased abundance of the genes involved in imidazole propionate biosynthesis from dietary histidine. Since patients and controls did not differ in their histidine dietary intake, the elevated levels of imidazole propionate in type 2 diabetes likely reflects altered microbial metabolism of histidine, rather than histidine intake per se. Thus the microbiota may contribute to type 2 diabetes by generating imidazole propionate that can modulate host inflammation and metabolism.
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3.
  • Forslund, Sofia K., et al. (author)
  • Combinatorial, additive and dose-dependent drug–microbiome associations
  • 2021
  • In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 600:7889, s. 500-505
  • Journal article (peer-reviewed)abstract
    • During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery1–5. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the explanatory power of drugs for the variability in both host and gut microbiome features exceeds that of disease. We quantify inferred effects of single medications, their combinations as well as additive effects, and show that the latter shift the metabolome and microbiome towards a healthier state, exemplified in synergistic reduction in serum atherogenic lipoproteins by statins combined with aspirin, or enrichment of intestinal Roseburia by diuretic agents combined with beta-blockers. Several antibiotics exhibit a quantitative relationship between the number of courses prescribed and progression towards a microbiome state that is associated with the severity of cardiometabolic disease. We also report a relationship between cardiometabolic drug dosage, improvement in clinical markers and microbiome composition, supporting direct drug effects. Taken together, our computational framework and resulting resources enable the disentanglement of the effects of drugs and disease on host and microbiome features in multimedicated individuals. Furthermore, the robust signatures identified using our framework provide new hypotheses for drug–host–microbiome interactions in cardiometabolic disease.
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4.
  • Rodriguez, Sébastien, et al. (author)
  • Science goals and new mission concepts for future exploration of Titan's atmosphere, geology and habitability : titan POlar scout/orbitEr and in situ lake lander and DrONe explorer (POSEIDON)
  • 2022
  • In: Experimental astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 54:2-3, s. 911-973
  • Journal article (peer-reviewed)abstract
    • In response to ESA’s “Voyage 2050” announcement of opportunity, we propose an ambitious L-class mission to explore one of the most exciting bodies in the Solar System, Saturn’s largest moon Titan. Titan, a “world with two oceans”, is an organic-rich body with interior-surface-atmosphere interactions that are comparable in complexity to the Earth. Titan is also one of the few places in the Solar System with habitability potential. Titan’s remarkable nature was only partly revealed by the Cassini-Huygens mission and still holds mysteries requiring a complete exploration using a variety of vehicles and instruments. The proposed mission concept POSEIDON (Titan POlar Scout/orbitEr and In situ lake lander DrONe explorer) would perform joint orbital and in situ investigations of Titan. It is designed to build on and exceed the scope and scientific/technological accomplishments of Cassini-Huygens, exploring Titan in ways that were not previously possible, in particular through full close-up and in situ coverage over long periods of time. In the proposed mission architecture, POSEIDON consists of two major elements: a spacecraft with a large set of instruments that would orbit Titan, preferably in a low-eccentricity polar orbit, and a suite of in situ investigation components, i.e. a lake lander, a “heavy” drone (possibly amphibious) and/or a fleet of mini-drones, dedicated to the exploration of the polar regions. The ideal arrival time at Titan would be slightly before the next northern Spring equinox (2039), as equinoxes are the most active periods to monitor still largely unknown atmospheric and surface seasonal changes. The exploration of Titan’s northern latitudes with an orbiter and in situ element(s) would be highly complementary in terms of timing (with possible mission timing overlap), locations, and science goals with the upcoming NASA New Frontiers Dragonfly mission that will provide in situ exploration of Titan’s equatorial regions, in the mid-2030s. 
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5.
  • Vono, Maxime, et al. (author)
  • A Fully Bayesian Approach for Inferring Physical Properties with Credibility Intervals from Noisy Astronomical Data
  • 2019
  • In: 2019 10TH WORKSHOP ON HYPERSPECTRAL IMAGING AND SIGNAL PROCESSING - EVOLUTION IN REMOTE SENSING (WHISPERS). - 2158-6268. - 9781728152943
  • Conference paper (peer-reviewed)abstract
    • The atoms and molecules of interstellar clouds emit photons when passing from an excited state to a lower energy state. The resulting emission lines can be detected by telescopes in the different wavelength domains (radio, infrared, visible, UV...). Through the excitation and chemical conditions they reveal, these lines provide key constraints on the local physical conditions reigning in giant molecular clouds (GMCs), which constitute the birthplace of stars in galaxies. Inferring these physical conditions from observed maps of GMCs using complex astrophysical models of these regions remains a complicated challenge due to potentially degenerate solutions and widely varying signal-to-noise ratios over the map. We propose a Bayesian framework to infer the probability distributions associated to each of these physical parameters, taking a spatial smoothness prior into account to tackle the challenge of low signal-to-noise ratio regions of the observed maps. A numerical astrophysical model of the cloud is involved in the likelihood within an approximate Bayesian computation (ABC) method. This enables to both infer point-wise estimators (e.g., minimum mean square or maximum a posteriori) and quantify the uncertainty associated to the estimation process. The benefits of the proposed approach are illustrated based on noisy synthetic observation maps.
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6.
  • Andrikopoulos, Petros, et al. (author)
  • Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide
  • 2023
  • In: Nature Communications. - 2041-1723 .- 2041-1723. ; 14:1
  • Journal article (peer-reviewed)abstract
    • The host-microbiota co-metabolite trimethylamine N-oxide (TMAO) is linked to increased cardiovascular risk but how its circulating levels are regulated remains unclear. We applied "explainable" machine learning, univariate, multivariate and mediation analyses of fasting plasma TMAO concentration and a multitude of phenotypes in 1,741 adult Europeans of the MetaCardis study. Here we show that next to age, kidney function is the primary variable predicting circulating TMAO, with microbiota composition and diet playing minor, albeit significant, roles. Mediation analysis suggests a causal relationship between TMAO and kidney function that we corroborate in preclinical models where TMAO exposure increases kidney scarring. Consistent with our findings, patients receiving glucose-lowering drugs with reno-protective properties have significantly lower circulating TMAO when compared to propensity-score matched control individuals. Our analyses uncover a bidirectional relationship between kidney function and TMAO that can potentially be modified by reno-protective anti-diabetic drugs and suggest a clinically actionable intervention for decreasing TMAO-associated excess cardiovascular risk.
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7.
  • Bron, E., et al. (author)
  • Tracers of the ionization fraction in dense and translucent gas: I. Automated exploitation of massive astrochemical model grids
  • 2021
  • In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 645
  • Journal article (peer-reviewed)abstract
    • Context. The ionization fraction in the neutral interstellar medium (ISM) plays a key role in the physics and chemistry of the ISM, from controlling the coupling of the gas to the magnetic field to allowing fast ion-neutral reactions that drive interstellar chemistry. Most estimations of the ionization fraction have relied on deuterated species such as DCO+, whose detection is limited to dense cores representing an extremely small fraction of the volume of the giant molecular clouds that they are part of. As large field-of-view hyperspectral maps become available, new tracers may be found. The growth of observational datasets is paralleled by the growth of massive modeling datasets and new methods need to be devised to exploit the wealth of information they contain. Aims. We search for the best observable tracers of the ionization fraction based on a grid of astrochemical models, with the broader aim of finding a general automated method applicable to searching for tracers of any unobservable quantity based on grids of models. Methods. We built grids of models that randomly sample a large range of physical conditions (unobservable quantities such as gas density, temperature, elemental abundances, etc.) and computed the corresponding observables (line intensities, column densities) and the ionization fraction. We estimated the predictive power of each potential tracer by training a random forest model to predict the ionization fraction from that tracer, based on these model grids. Results. In both translucent medium and cold dense medium conditions, we found several observable tracers with very good predictive power for the ionization fraction. Many tracers in cold dense medium conditions are found to be better and more widely applicable than the traditional DCO+/HCO+ ratio. We also provide simpler analytical fits for estimating the ionization fraction from the best tracers, and for estimating the associated uncertainties. We discuss the limitations of the present study and select a few recommended tracers in both types of conditions. Conclusions. The method presented here is very general and can be applied to the measurement of any other quantity of interest (cosmic ray flux, elemental abundances, etc.) from any type of model (PDR models, time-dependent chemical models, etc.).
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8.
  • Einig, Lucas, et al. (author)
  • Deep learning denoising by dimension reduction: Application to the ORION-B line cubes
  • 2023
  • In: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 677
  • Journal article (peer-reviewed)abstract
    • Context. The availability of large bandwidth receivers for millimeter radio telescopes allows for the acquisition of position-position-frequency data cubes over a wide field of view and a broad frequency coverage. These cubes contain a lot of information on the physical, chemical, and kinematical properties of the emitting gas. However, their large size coupled with an inhomogenous signal-to-noise ratio (S/N) are major challenges for consistent analysis and interpretation. Aims. We searched for a denoising method of the low S/N regions of the studied data cubes that would allow the low S/N emission to be recovered without distorting the signals with a high S/N. Methods. We performed an in-depth data analysis of the 13CO and C17O (1-0) data cubes obtained as part of the ORION-B large program performed at the IRAM 30 m telescope. We analyzed the statistical properties of the noise and the evolution of the correlation of the signal in a given frequency channel with that of the adjacent channels. This has allowed us to propose significant improvements of typical autoassociative neural networks, often used to denoise hyperspectral Earth remote sensing data. Applying this method to the 13CO (1-0) cube, we were able to compare the denoised data with those derived with the multiple Gaussian fitting algorithm ROHSA, considered as the state-of-the-art procedure for data line cubes. Results. The nature of astronomical spectral data cubes is distinct from that of the hyperspectral data usually studied in the Earth remote sensing literature because the observed intensities become statistically independent beyond a short channel separation. This lack of redundancy in data has led us to adapt the method, notably by taking into account the sparsity of the signal along the spectral axis. The application of the proposed algorithm leads to an increase in the S/N in voxels with a weak signal, while preserving the spectral shape of the data in high S/N voxels. Conclusions. The proposed algorithm that combines a detailed analysis of the noise statistics with an innovative autoencoder architecture is a promising path to denoise radio-astronomy line data cubes. In the future, exploring whether a better use of the spatial correlations of the noise may further improve the denoising performances seems to be a promising avenue. In addition, dealing with the multiplicative noise associated with the calibration uncertainty at high S/N would also be beneficial for such large data cubes.
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9.
  • Gaudel, Mathilde, et al. (author)
  • Gas kinematics around filamentary structures in the Orion B cloud
  • 2023
  • In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 670
  • Journal article (peer-reviewed)abstract
    • Context. Understanding the initial properties of star-forming material and how they affect the star formation process is key. From an observational point of view, the feedback from young high-mass stars on future star formation properties is still poorly constrained. Aims. In the framework of the IRAM 30m ORION-B large program, we obtained observations of the translucent (2 ≤ AV < 6 mag) and moderately dense gas (6 ≤ AV < 15 mag), which we used to analyze the kinematics over a field of 5 deg2 around the filamentary structures. Methods. We used the Regularized Optimization for Hyper-Spectral Analysis (ROHSA) algorithm to decompose and de-noise the C 18 O(1−0) and 13CO(1−0) signals by taking the spatial coherence of the emission into account. We produced gas column density and mean velocity maps to estimate the relative orientation of their spatial gradients. Results. We identified three cloud velocity layers at different systemic velocities and extracted the filaments in each velocity layer. The filaments are preferentially located in regions of low centroid velocity gradients. By comparing the relative orientation between the column density and velocity gradients of each layer from the ORION-B observations and synthetic observations from 3D kinematic toy models, we distinguish two types of behavior in the dynamics around filaments: (i) radial flows perpendicular to the filament axis that can be either inflows (increasing the filament mass) or outflows and (ii) longitudinal flows along the filament axis. The former case is seen in the Orion B data, while the latter is not identified. We have also identified asymmetrical flow patterns, usually associated with filaments located at the edge of an H II region. Conclusions. This is the first observational study to highlight feedback from H II regions on filament formation and, thus, on star formation in the Orion B cloud. This simple statistical method can be used for any molecular cloud to obtain coherent information on the kinematics.
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10.
  • Gratier, Pierre, et al. (author)
  • Quantitative inference of the H2 column densities from 3mm molecular emission: case study towards Orion B
  • 2021
  • In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 645
  • Journal article (peer-reviewed)abstract
    • Context. Based on the finding that molecular hydrogen is unobservable in cold molecular clouds, the column density measurements of molecular gas currently rely either on dust emission observation in the far-infrared, which requires space telescopes, or on star counting, which is limited in angular resolution by the stellar density. The (sub)millimeter observations of numerous trace molecules can be effective using ground-based telescopes, but the relationship between the emission of one molecular line and the H-2 column density is non-linear and sensitive to excitation conditions, optical depths, and abundance variations due to the underlying physico- chemistry.Aims. We aim to use multi-molecule line emission to infer the H-2 molecular column density from radio observations.Methods. We propose a data-driven approach to determine the H-2 gas column densities from radio molecular line observations. We use supervised machine-learning methods (random forest) on wide-field hyperspectral IRAM-30m observations of the Orion B molecular cloud to train a predictor of the H-2 column density, using a limited set of molecular lines between 72 and 116 GHz as input, and the Herschel-based dust-derived column densities as "ground truth" output.Results. For conditions similar to those of the Orion B molecular cloud, we obtained predictions of the H-2 column density within a typical factor of 1.2 from the Herschel-based column density estimates. A global analysis of the contributions of the different lines to the predictions show that the most important lines are (CO)-C-13(1-0), (CO)-C-12(1-0), (CO)-O-18(1-0), and HCO+(1-0). A detailed analysis distinguishing between diffuse, translucent, filamentary, and dense core conditions show that the importance of these four lines depends on the regime, and that it is recommended that the N2H+(1-0) and CH3OH(2(0)-1(0)) lines be added for the prediction of the H-2 column density in dense core conditions.Conclusions. This article opens a promising avenue for advancing direct inferencing of important physical parameters from the molecular line emission in the millimeter domain. The next step will be to attempt to infer several parameters simultaneously (e.g., the column density and far-UV illumination field) to further test the method.
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11.
  • Klionsky, Daniel J., et al. (author)
  • Guidelines for the use and interpretation of assays for monitoring autophagy
  • 2012
  • In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
  • Research review (peer-reviewed)abstract
    • In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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12.
  • Martin, Francis, et al. (author)
  • The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
  • 2008
  • In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 452:7183, s. 7-88
  • Journal article (peer-reviewed)abstract
    • Mycorrhizal symbioses -- the union of roots and soil fungi -- are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants1,2. Boreal, temperate, and montane forests all depend upon ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of 2 ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here, we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-million-base genome assembly contains ~ 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features most notably a battery of effector-type small secreted proteins (SSP) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific proteins likely play a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell walls, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus which enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem in order to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
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13.
  • Plomion, Christophe, et al. (author)
  • Oak genome reveals facets of long lifespan
  • 2018
  • In: NATURE PLANTS. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 4:7, s. 440-452
  • Journal article (peer-reviewed)abstract
    • Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
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14.
  • Roueff, Antoine, et al. (author)
  • Bias versus variance when fitting multi-species molecular lines with a non-LTE radiative transfer model: Application to the estimation of the gas temperature and volume density
  • 2024
  • In: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 686
  • Journal article (peer-reviewed)abstract
    • Context. Robust radiative transfer techniques are requisite for efficiently extracting the physical and chemical information from molecular rotational lines. Aims. We study several hypotheses that enable robust estimations of the column densities and physical conditions when fitting one or two transitions per molecular species. We study the extent to which simplifying assumptions aimed at reducing the complexity of the problem introduce estimation biases and how to detect them. Methods. We focus on the CO and HCO+ isotopologues and analyze maps of a 50 square arcminutes field. We used the RADEX escape probability model to solve the statistical equilibrium equations and compute the emerging line profiles, assuming that all species coexist. Depending on the considered set of species, we also fixed the abundance ratio between some species and explored different values. We proposed a maximum likelihood estimator to infer the physical conditions and considered the effect of both the thermal noise and calibration uncertainty. We analyzed any potential biases induced by model misspecifications by comparing the results on the actual data for several sets of species and confirmed with Monte Carlo simulations. The variance of the estimations and the efficiency of the estimator were studied based on the Cramér-Rao lower bound. Results. Column densities can be estimated with 30% accuracy, while the best estimations of the volume density are found to be within a factor of two. Under the chosen model framework, the peak 12CO (1 -0) is useful for constraining the kinetic temperature. The thermal pressure is better and more robustly estimated than the volume density and kinetic temperature separately. Analyzing CO and HCO+ isotopologues and fitting the full line profile are recommended practices with respect to detecting possible biases. Conclusions. Combining a non-local thermodynamic equilibrium model with a rigorous analysis of the accuracy allows us to obtain an efficient estimator and identify where the model is misspecified. We note that other combinations of molecular lines could be studied in the future.
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15.
  • Roueff, Antoine, et al. (author)
  • C18O, 13CO, and 12CO abundances and excitation temperatures in the Orion B molecular cloud: Analysis of the achievable precision in modeling spectral lines within the approximation of the local thermodynamic equilibrium
  • 2021
  • In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 645
  • Journal article (peer-reviewed)abstract
    • Context. CO isotopologue transitions are routinely observed in molecular clouds for the purpose of probing the column density of the gas and the elemental ratios of carbon and oxygen, in addition to tracing the kinematics of the environment. Aims. Our study is aimed at estimating the abundances, excitation temperatures, velocity field, and velocity dispersions of the three main CO isotopologues towards a subset of the Orion B molecular cloud, which includes IC 434, NGC 2023, and the Horsehead pillar. Methods. We used the Cramer Rao bound (CRB) technique to analyze and estimate the precision of the physical parameters in the framework of local-thermodynamic-equilibrium (LTE) excitation and radiative transfer with added white Gaussian noise. We propose a maximum likelihood estimator to infer the physical conditions from the 1-0 and 2-1 transitions of CO isotopologues. Simulations show that this estimator is unbiased and proves efficient for a common range of excitation temperatures and column densities (Tex > 6 K, N > 1014-1015 cm-2). Results. Contrary to general assumptions, the various CO isotopologues have distinct excitation temperatures and the line intensity ratios between different isotopologues do not accurately reflect the column density ratios. We find mean fractional abundances that are consistent with previous determinations towards other molecular clouds. However, significant local deviations are inferred, not only in regions exposed to the UV radiation field, but also in shielded regions. These deviations result from the competition between selective photodissociation, chemical fractionation, and depletion on grain surfaces. We observe that the velocity dispersion of the C18O emission is 10% smaller than that of 13CO. The substantial gain resulting from the simultaneous analysis of two different rotational transitions of the same species is rigorously quantified. Conclusions. The CRB technique is a promising avenue for analyzing the estimation of physical parameters from the fit of spectral lines. Future works will generalize its application to non-LTE excitation and radiative transfer methods.
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16.
  • Santa-Maria, Miriam G., et al. (author)
  • HCN emission from translucent gas and UV-illuminated cloud edges revealed by wide-field IRAM 30 m maps of the Orion B GMC: Revisiting its role as a tracer of the dense gas reservoir for star formation
  • 2023
  • In: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 679
  • Journal article (peer-reviewed)abstract
    • Context. Massive stars form within dense clumps inside giant molecular clouds (GMCs). Finding appropriate chemical tracers of the dense gas (n(H2) > several 104 cm-3 or AV > 8 mag) and linking their line luminosity with the star formation rate is of critical importance. Aims. Our aim is to determine the origin and physical conditions of the HCN-emitting gas and study their relation to those of other molecules. Methods. In the context of the IRAM 30m ORION-B large program, we present 5 deg2 (~250 pc2) HCN, HNC, HCO+, and CO J =1-0 maps of the Orion B GMC, complemented with existing wide-field [CI] 492 GHz maps, as well as new pointed observations of rotationally excited HCN, HNC, H13CN, and HN13C lines. We compare the observed HCN line intensities with radiative transfer models including line overlap effects and electron excitation. Furthermore, we study the HCN/HNC isomeric abundance ratio with updated photochemical models. Results. We spectroscopically resolve the HCN J = 1-0 hyperfine structure (HFS) components (and partially resolved J = 2-1 and 3-2 components). We detect anomalous HFS line intensity (and line width) ratios almost everywhere in the cloud. About 70% of the total HCN J = 1-0 luminosity, L′(HCN J = 1-0) = 110 K km s-1 pc-2, arises from AV < 8 mag. The HCN/CO J = 1-0 line intensity ratio, widely used as a tracer of the dense gas fraction, shows a bimodal behavior with an inflection point at AV < 3 mag typical of translucent gas and illuminated cloud edges. We find that most of the HCN J = 1-0 emission arises from extended gas with n(H2) < 104 cm-3, and even lower density gas if the ionization fraction is χe ≥10-5 and electron excitation dominates. This result contrasts with the prevailing view of HCN J = 1-0 emission as a tracer of dense gas and explains the low-AV branch of the HCN/CO J = 1-0 intensity ratio distribution. Indeed, the highest HCN/CO ratios (~ 0.1) at AV < 3 mag correspond to regions of high [CI] 492 GHz/CO J = 1-0 intensity ratios (>1) characteristic of low-density photodissociation regions. The low surface brightness (≲ 1 K km s-1) and extended HCN and HCO+ J = 1-0 emission scale with IFIR -a proxy of the stellar far-ultraviolet (FUV) radiation field -in a similar way. Together with CO J = 1-0, these lines respond to increasing IFIR up to G0 ≅ 20. On the other hand, the bright HCN J = 1-0 emission (> 6 K km s-1) from dense gas in star-forming clumps weakly responds to IFIR once the FUV field becomes too intense (G0 > 1500). In contrast, HNC J = 1-0 and [CI] 492 GHz lines weakly respond to IFIR for all G0. The different power law scalings (produced by different chemistries, densities, and line excitation regimes) in a single but spatially resolved GMC resemble the variety of Kennicutt-Schmidt law indexes found in galaxy averages. Conclusions. Given the widespread and extended nature of the [CI] 492 GHz emission, as well as its spatial correlation with that of HCO+, HCN, and 13CO J = 1-0 lines (in this order), we argue that the edges of GMCs are porous to FUV radiation from nearby massive stars. Enhanced FUV radiation favors the formation and excitation of HCN on large scales, not only in dense star-forming clumps, and it leads to a relatively low value of the dense gas mass to total luminosity ratio, α (HCN) = 29 M⊙ /(K km s-1pc2) in Orion B. As a corollary for extragalactic studies, we conclude that high HCN/CO J = 1-0 line intensity ratios do not always imply the presence of dense gas, which may be better traced by HNC than by HCN.
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17.
  • Abelev, Betty, et al. (author)
  • Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
  • 2012
  • In: Journal of High Energy Physics. - 1029-8479. ; :11
  • Journal article (peer-reviewed)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.
  •  
18.
  • Abelev, Betty, et al. (author)
  • Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
  • 2012
  • In: Journal of High Energy Physics. - 1029-8479. ; :7
  • Journal article (peer-reviewed)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%.
  •  
19.
  • Abolfathi, Bela, et al. (author)
  • The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
  • 2018
  • In: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
  • Journal article (peer-reviewed)abstract
    • The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
  •  
20.
  • Ahmar, Yosser El, et al. (author)
  • Visual variables in UML: A first empirical assessment
  • 2017
  • In: CEUR Workshop Proceedings. - 1613-0073. ; 2019, s. 376-384
  • Conference paper (peer-reviewed)abstract
    • This paper presents results of an empirical research study of the Unified Modeling Language (UML) use in practice. We employed a selective range of research methodologies including in-depth semi structured interviews and quantitative analysis of > 3500 UML diagrams related to open source projects in GitHub. The aim of the study is to provide greater understanding about the use of UML and to particularly shed light on the use of the visual variables (i.e., color, size, brightness, texture/grain, shape and orientation) in practice. The theoretical perspective of the study is to explore the usefulness of the visual variables in UML. These latter are highly significant in reducing the cognitive load of human beings, when effectively employed. As with all qualitative study, findings should be carefully interpreted, they should be seen as providing better understanding about the aforementioned scopes. We conclude by discussions of the obtained results and lessons learned for future researches.
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21.
  • Archambault, Alexi N., et al. (author)
  • Cumulative Burden of Colorectal Cancer Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer
  • 2020
  • In: Gastroenterology. - : Elsevier BV. - 0016-5085 .- 1528-0012. ; 158:5, s. 1274-1286.e12
  • Journal article (peer-reviewed)abstract
    • BACKGROUND & AIMS: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC.METHODS: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants.RESULTS: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28-4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80-3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 x 10(-5)). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61-5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70-3.00). Sensitivity analyses were consistent with these findings.CONCLUSIONS: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.
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22.
  • Arun, K. G., et al. (author)
  • New horizons for fundamental physics with LISA
  • 2022
  • In: Living Reviews in Relativity. - : Springer Science and Business Media LLC. - 1433-8351 .- 2367-3613. ; 25:1
  • Research review (peer-reviewed)abstract
    • The Laser Interferometer Space Antenna (LISA) has the potential to reveal wonders about the fundamental theory of nature at play in the extreme gravity regime, where the gravitational interaction is both strong and dynamical. In this white paper, the Fundamental Physics Working Group of the LISA Consortium summarizes the current topics in fundamental physics where LISA observations of gravitational waves can be expected to provide key input. We provide the briefest of reviews to then delineate avenues for future research directions and to discuss connections between this working group, other working groups and the consortium work package teams. These connections must be developed for LISA to live up to its science potential in these areas.
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23.
  • Barkefors, Irmeli, et al. (author)
  • Endothelial cell migration in stable gradients of vascular endothelial growth factor A and fibroblast growth factor 2 : effects on chemotaxis and chemokinesis
  • 2008
  • In: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 283:20, s. 13905-13912
  • Journal article (peer-reviewed)abstract
    • Gradients of secreted signaling proteins guide growing blood vessels during both normal and pathological angiogenesis. However, the mechanisms by which endothelial cells integrate and respond to graded distributions of chemotactic factors are still poorly understood. We have in this study investigated endothelial cell migration in response to hill-shaped gradients of vascular endothelial growth factor A (VEGFA) and fibroblast growth factor 2 (FGF2) using a novel microfluidic chemotaxis chamber (MCC). Cell migration was scored at the level of individual cells using time-lapse microscopy. A stable gradient of VEGFA165 ranging from 0 to 50 ng/ml over a distance of 400 microm was shown to strongly induce chemotaxis of endothelial cells of different vascular origin. VEGFA121, unable to bind proteoglycan and neuropilin coreceptors, was also shown to induce chemotaxis in this setup. Furthermore, a gradient of FGF2 was able to attract venular but not arterial endothelial cells, albeit less efficiently than VEGFA165. Notably, constant levels of VEGFA165, but not of FGF2, were shown to efficiently reduce chemokinesis. Systematic exploration of different gradient shapes led to the identification of a minimal gradient steepness required for efficient cell guidance. Finally, analysis of cell migration in different regions of the applied gradients showed that chemotaxis is reduced when cells reach the high end of the gradient. Our findings suggest that chemotactic growth factor gradients may instruct endothelial cells to shift toward a nonmigratory phenotype when approaching the growth factor source.
  •  
24.
  • Bastard, Paul, et al. (author)
  • Preexisting autoantibodies to type I IFNs underlie critical COVID-19 pneumonia in patients with APS-1.
  • 2021
  • In: The Journal of experimental medicine. - 1540-9538. ; 218:7
  • Journal article (peer-reviewed)abstract
    • Patients with biallelic loss-of-function variants of AIRE suffer from autoimmune polyendocrine syndrome type-1 (APS-1) and produce a broad range of autoantibodies (auto-Abs), including circulating auto-Abs neutralizing most type I interferons (IFNs). These auto-Abs were recently reported to account for at least 10% of cases of life-threatening COVID-19 pneumonia in the general population. We report 22 APS-1 patients from 21 kindreds in seven countries, aged between 8 and 48 yr and infected with SARS-CoV-2 since February 2020. The 21 patients tested had auto-Abs neutralizing IFN-α subtypes and/or IFN-ω; one had anti-IFN-β and another anti-IFN-ε, but none had anti-IFN-κ. Strikingly, 19 patients (86%) were hospitalized for COVID-19 pneumonia, including 15 (68%) admitted to an intensive care unit, 11 (50%) who required mechanical ventilation, and four (18%) who died. Ambulatory disease in three patients (14%) was possibly accounted for by prior or early specific interventions. Preexisting auto-Abs neutralizing type I IFNs in APS-1 patients confer a very high risk of life-threatening COVID-19 pneumonia at any age.
  •  
25.
  • Benzinou, Michael, et al. (author)
  • Common nonsynonymous variants in PCSK1 confer risk of obesity.
  • 2008
  • In: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 40:8, s. 943-5
  • Journal article (peer-reviewed)abstract
    • Mutations in PCSK1 cause monogenic obesity. To assess the contribution of PCSK1 to polygenic obesity risk, we genotyped tag SNPs in a total of 13,659 individuals of European ancestry from eight independent case-control or family-based cohorts. The nonsynonymous variants rs6232, encoding N221D, and rs6234-rs6235, encoding the Q665E-S690T pair, were consistently associated with obesity in adults and children (P = 7.27 x 10(-8) and P = 2.31 x 10(-12), respectively). Functional analysis showed a significant impairment of the N221D-mutant PC1/3 protein catalytic activity.
  •  
26.
  • Bertrand, Lionel, et al. (author)
  • A multiscale analysis of a fracture pattern in granite : A case study of the Tamariu granite, Catalunya, Spain
  • 2015
  • In: Journal of Structural Geology. - : Elsevier BV. - 0191-8141 .- 1873-1201. ; 78, s. 52-66
  • Journal article (peer-reviewed)abstract
    • The in-depth investigation of fractured reservoirs is mainly limited to geophysical data that is in 3D and mostly on the scale of hundred meters to several kilometers or boreholes data that is in 1D and at meter to lower scale. The study of outcropping analogues of buried reservoirs is therefore a key tool for the characterization of the fault and fracture network at the reservoir scale. Tamariu granite has been the subject of this study with the aim to analyse faults and fractures from seismic to borehole scale. With the combination of satellite picture at different resolution and field study, we perform a statistical analysis focused of the length and orientation from infra centimeter crack to hundred kilometer length fault. On the whole range of scale studied, i.e. on 7 orders of magnitude, we have defined a length distribution following a power-law with an exponent a = -2. On the contrary to the length that can be modelled with a unique law, the orientation data shows a variation depending on the scale of observation: as the fault and fracture sets are suitable from the regional faults to the centimeter crack, the proportion of the sets varies at each scale of observation.
  •  
27.
  • Bien, Stephanie A., et al. (author)
  • Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
  • 2019
  • In: Human Genetics. - : Springer. - 0340-6717 .- 1432-1203. ; 138:4, s. 307-326
  • Journal article (peer-reviewed)abstract
    • Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n=169) and whole blood (n=922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P=2.2x10(-4), replication P=0.01), and PYGL (discovery P=2.3x10(-4), replication P=6.7x10(-4)). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P<0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
  •  
28.
  • Blanton, Michael R., et al. (author)
  • Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
  • 2017
  • In: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
  • Journal article (peer-reviewed)abstract
    • We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
  •  
29.
  • Boen, Rune, et al. (author)
  • Beyond the global brain differences : intraindividual variability differences in 1q21.1 distal and 15q11.2 bp1-bp2 deletion carriers
  • 2024
  • In: Biological Psychiatry. - 0006-3223 .- 1873-2402. ; 95:2, s. 147-160
  • Journal article (peer-reviewed)abstract
    • Background: Carriers of the 1q21.1 distal and 15q11.2 BP1-BP2 copy number variants exhibit regional and global brain differences compared with noncarriers. However, interpreting regional differences is challenging if a global difference drives the regional brain differences. Intraindividual variability measures can be used to test for regional differences beyond global differences in brain structure.Methods: Magnetic resonance imaging data were used to obtain regional brain values for 1q21.1 distal deletion (n = 30) and duplication (n = 27) and 15q11.2 BP1-BP2 deletion (n = 170) and duplication (n = 243) carriers and matched noncarriers (n = 2350). Regional intra-deviation scores, i.e., the standardized difference between an individual's regional difference and global difference, were used to test for regional differences that diverge from the global difference.Results: For the 1q21.1 distal deletion carriers, cortical surface area for regions in the medial visual cortex, posterior cingulate, and temporal pole differed less and regions in the prefrontal and superior temporal cortex differed more than the global difference in cortical surface area. For the 15q11.2 BP1-BP2 deletion carriers, cortical thickness in regions in the medial visual cortex, auditory cortex, and temporal pole differed less and the prefrontal and somatosensory cortex differed more than the global difference in cortical thickness.Conclusions: We find evidence for regional effects beyond differences in global brain measures in 1q21.1 distal and 15q11.2 BP1-BP2 copy number variants. The results provide new insight into brain profiling of the 1q21.1 distal and 15q11.2 BP1-BP2 copy number variants, with the potential to increase understanding of the mechanisms involved in altered neurodevelopment.
  •  
30.
  • Bucchiarone, Antonio, et al. (author)
  • Gamifying model-based engineering : The PapyGame tool
  • 2023
  • In: Science of Computer Programming. - : Elsevier. - 0167-6423 .- 1872-7964. ; 230
  • Journal article (peer-reviewed)abstract
    • Modeling is an essential and challenging activity in any engineering environment, and it requires some hard-to-train skills such as abstraction and communication. This makes it difficult for educators to teach or train their students, co-workers, or users. The audience of this paper is both educators and learners who struggle with modeling. To address this challenge, we present PapyGame, a gamified version of a robust modeling environment (Papyrus) that aims to improve the learner's motivation, make the learning process an enjoyable experience, and boost learning outcomes. Gamification is the exploitation of gaming mechanisms for serious purposes, such as promoting behavioral changes, soliciting participation and engagement in activities, and more. The paper presents PapyGame's functionalities, architectures, illustrative scenarios, and its potential impact on both educators and learners.
  •  
31.
  • Calvet, LE, et al. (author)
  • Who Are the Value and Growth Investors?
  • 2017
  • In: Journal of Finance. - : Wiley: No OnlineOpen. - 1540-6261 .- 0022-1082. ; 72:1, s. 5-46
  • Journal article (peer-reviewed)abstract
    • This paper investigates value and growth investing in a large administrative panel of Swedish residents. We show that, over the life cycle, households progressively shift from growth to value as they become older and their balance sheets improve. Furthermore, investors with high human capital and high exposure to macroeconomic risk tilt their portfolios away from value. While several behavioral biases seem evident in the data, the patterns we uncover are overall remarkably consistent with the portfolio implications of risk-based theories of the value premium.
  •  
32.
  • Chambault, Philippine, et al. (author)
  • The influence of oceanographic features on the foraging behavior of the olive ridley sea turtle Lepidochelys olivacea along the Guiana coast
  • 2016
  • In: Progress in Oceanography. - : Elsevier BV. - 0079-6611 .- 1873-4472. ; 142, s. 58-71
  • Research review (peer-reviewed)abstract
    • The circulation in the Western Equatorial Atlantic is characterized by a highly dynamic mesoscale activity that shapes the Guiana continental shelf. Olive ridley sea turtles (Lepidochelys olivacea) nesting in French Guiana cross this turbulent environment during their post-nesting migration. We studied how oceanographic and biological conditions drove the foraging behavior of 18 adult females, using satellite telemetry, remote sensing data (sea surface temperature, sea surface height, current velocity and euphotic depth), simulations of micronekton biomass (pelagic organisms) and in situ records (water temperature and salinity). The occurrence of foraging events throughout migration was located using Residence Time analysis, while an innovative proxy of the hunting time within a dive was used to identify and quantify foraging events during dives. Olive ridleys migrated northwestwards using the Guiana current and remained on the continental shelf at the edge of eddies formed by the North Brazil retroflection, an area characterized by low turbulence and high micronekton biomass. They performed mainly pelagic dives, hunting for an average 77% of their time. Hunting time within a dive increased with shallower euphotic depth and with lower water temperatures, and mean hunting depth increased with deeper thermocline. This is the first study to quantify foraging activity within dives in olive ridleys, and reveals the crucial role played by the thermocline on the foraging behavior of this carnivorous species. This study also provides novel and detailed data describing how turtles actively use oceanographic structures during post-nesting migration.
  •  
33.
  • Coley, Nicola, et al. (author)
  • Plasma p-tau181 as an outcome and predictor of multidomain intervention effects: a secondary analysis of a randomised, controlled, dementia prevention trial
  • 2024
  • In: The Lancet Healthy Longevity. - 2666-7568. ; 5:2
  • Journal article (peer-reviewed)abstract
    • Background: It is unknown whether multidomain interventions, which might preserve late-life cognition, affect Alzheimer's disease pathology. Previous studies measured cerebrospinal fluid and imaging Alzheimer's disease biomarkers in small subsamples of multidomain trial participants. Newly developed assays enable the measurement of blood-based Alzheimer's disease biomarkers in larger samples. We aimed to assess whether plasma tau phosphorylated at threonine 181 (p-tau181) was able to detect or predict 3-year multidomain intervention effects. Methods: This is a secondary analysis of the randomised, controlled, Multidomain Alzheimer Prevention Trial (MAPT) testing a 3-year multidomain intervention, omega-3 fatty acid supplementation, or both versus placebo, in individuals aged 70 years and older in 13 memory centres in France and Monaco. Plasma p-tau181 was measured in stored blood samples in a subsample of 527 participants on an intention-to-treat basis. Changes in cognitive score were calculated as a composite measure using the average of Z scores for the following tests: Mini Mental State Examination orientation items, Free and Cued Selective Reminding Test (sum of free and total recall scores), category fluency, and Digit Symbol Substitution Test. Intervention effects on 3-year change in p-tau181 concentration were estimated by use of a linear mixed model with centre-specific random intercepts. Findings: Recruitment took place between May 30, 2008, and Feb 24, 2011. Median baseline plasma p-tau181 was 8·8 pg/mL (IQR 6·7–11·9) in the total sample, and significantly higher in older individuals, men, APOE ε4 carriers, and participants with renal dysfunction or a positive PET amyloid scan. During 3-year follow-up, individuals with raised baseline p-tau181 underwent greater cognitive decline (eg, mean difference in 3-year change on the composite cognitive score between control group participants with normal and abnormal baseline levels of p-tau was −0·34 [effect size −0·52; 95% CI −0·61 to 0·07] in the fully adjusted model using a 12·4 pg/mL cutoff for abnormal baseline p-tau181), but there were no intervention effects on change in p-tau181 either in this subgroup or the total population, and no effect on cognitive change in individuals with raised baseline p-tau181 (eg, in the fully adjusted model using the 12·4 pg/mL cutoff for p-tau181 abnormality, the mean difference [95% CI] in this subgroup in 3-year decline on the composite cognitive score between the control group and the multidomain + omega-3 group, the omega-3 group, and the multidomain intervention group, was, respectively: 0·13 [−0·21 to 0·47], 0·03 [−0·30 to 0·36], and 0·10 [−0·26 to 0·46]). Surprisingly, individuals with raised baseline p-tau181 showed a decrease in p-tau181 during follow-up (eg, unadjusted mean [95% CI] 3-year change was −3·01 pg/mL (−4·45 to −1·56) in control group subjects with abnormal baseline p-tau181 [using the 12·4 pg/mL abnormal p-tau cutoff]). Interpretation: Our results support the utility of p-tau181 as a prognostic biomarker, but it did not predict or detect intervention effects in this study. Further investigation of its usefulness as a prevention trial outcome measure is required.
  •  
34.
  • Fallet, Manon, 1992-, et al. (author)
  • Early life microbial exposures shape the Crassostrea gigas immune system for lifelong and intergenerational disease protection
  • 2022
  • In: Microbiome. - : BioMed Central (BMC). - 2049-2618. ; 10:1
  • Journal article (peer-reviewed)abstract
    • Background: The interaction of organisms with their surrounding microbial communities influences many biological processes, a notable example of which is the shaping of the immune system in early life. In the Pacific oyster, Crassostrea gigas, the role of the environmental microbial community on immune system maturation — and, importantly, protection from infectious disease — is still an open question.Results: Here, we demonstrate that early life microbial exposure durably improves oyster survival when challenged with the pathogen causing Pacific oyster mortality syndrome (POMS), both in the exposed generation and in the subsequent one. Combining microbiota, transcriptomic, genetic, and epigenetic analyses, we show that the microbial exposure induced changes in epigenetic marks and a reprogramming of immune gene expression leading to long-term and intergenerational immune protection against POMS.Conclusions: We anticipate that this protection likely extends to additional pathogens and may prove to be an important new strategy for safeguarding oyster aquaculture efforts from infectious disease
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35.
  • Gal, R. Le, et al. (author)
  • The ortho-to-para ratio of H2Cl+: Quasi-classical trajectory calculations and new simulations in light of new observations
  • 2017
  • In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 608, s. A96-
  • Journal article (peer-reviewed)abstract
    • Multi-hydrogenated species with proper symmetry properties can present different spin configurations, and thus exist under different spin symmetry forms, labeled as para and ortho for two-hydrogen molecules. We investigated here the ortho-to-para ratio (OPR) of H2Cl+ in the light of new observations performed in the z = 0.89 absorber toward the lensed quasar PKS 1830−211 with the Atacama Large Millimeter/submillimeter Array (ALMA). Two independent lines of sight were observed, to the southwest (SW) and northeast (NE) images of the quasar, with OPR values found to be 3.15 ± 0.13 and 3.1 ± 0.5 in each region, respectively, in agreement with a spin statistical weight of 3:1. An OPR of 3:1 for a molecule containing two identical hydrogen nuclei can refer to either a statistical result or a high-temperature limit depending on the reaction mechanism leading to its formation. It is thus crucial to identify rigorously how OPRs are produced in order to constrain the information that these probes can provide. To understand the production of the H2Cl+ OPR, we undertook a careful theoretical study of the reaction mechanisms involved with the aid of quasi-classical trajectory calculations on a new global potential energy surface fit to a large number of high-level ab initio data. Our study shows that the major formation reaction for H2Cl+ produces this ion via a hydrogen abstraction rather than a scrambling mechanism. Such a mechanism leads to a 3:1 OPR, which is not changed by destruction and possible thermalization reactions for H2Cl+ and is thus likely to be the cause of observed 3:1 OPR ratios, contrary to the normal assumption of scrambling.
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36.
  • Galaup, Ariane, et al. (author)
  • Protection Against Myocardial Infarction and No-Reflow Through Preservation of Vascular Integrity by Angiopoietin-Like 4
  • 2012
  • In: Circulation. - 0009-7322 .- 1524-4539. ; 125:1, s. 140-149
  • Journal article (peer-reviewed)abstract
    • Background-Increased permeability, predominantly controlled by endothelial junction stability, is an early event in the deterioration of vascular integrity in ischemic disorders. Hemorrhage, edema, and inflammation are the main features of reperfusion injuries, as observed in acute myocardial infarction (AMI). Thus, preservation of vascular integrity is fundamental in ischemic heart disease. Angiopoietins are pivotal modulators of cell-cell junctions and vascular integrity. We hypothesized that hypoxic induction of angiopoietin-like protein 4 (ANGPTL4) might modulate vascular damage, infarct size, and no-reflow during AMI. Methods and Results-We showed that vascular permeability, hemorrhage, edema, inflammation, and infarct severity were increased in angptl4-deficient mice. We determined that decrease in vascular endothelial growth factor receptor 2 (VEGFR2) and VE-cadherin expression and increase in Src kinase phosphorylation downstream of VEGFR2 were accentuated after ischemia-reperfusion in the coronary microcirculation of angptl4-deficient mice. Both events led to altered VEGFR2/VE-cadherin complexes and to disrupted adherens junctions in the endothelial cells of angptl4-deficient mice that correlated with increased no-reflow. In vivo injection of recombinant human ANGPTL4 protected VEGF-driven dissociation of the VEGFR2/VE-cadherin complex, reduced myocardial infarct size, and the extent of no-reflow in mice and rabbits. Conclusions-These data showed that ANGPTL4 might constitute a relevant target for therapeutic vasculoprotection aimed at counteracting the effects of VEGF, thus being crucial for preventing no-reflow and conferring secondary cardioprotection during AMI.
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37.
  • Haïssaguerre, Michel, et al. (author)
  • Sudden cardiac arrest associated with early repolarization
  • 2008
  • In: New England Journal of Medicine. - 0028-4793 .- 1533-4406. ; 358:19, s. 2016-2023
  • Journal article (peer-reviewed)abstract
    • BACKGROUND: Early repolarization is a common electrocardiographic finding that is generally considered to be benign. Its potential to cause cardiac arrhythmias has been hypothesized from experimental studies, but it is not known whether there is a clinical association with sudden cardiac arrest.METHODS: We reviewed data from 206 case subjects at 22 centers who were resuscitated after cardiac arrest due to idiopathic ventricular fibrillation and assessed the prevalence of electrocardiographic early repolarization. The latter was defined as an elevation of the QRS-ST junction of at least 0.1 mV from baseline in the inferior or lateral lead, manifested as QRS slurring or notching. The control group comprised 412 subjects without heart disease who were matched for age, sex, race, and level of physical activity. Follow-up data that included the results of monitoring with an implantable defibrillator were obtained for all case subjects.RESULTS: Early repolarization was more frequent in case subjects with idiopathic ventricular fibrillation than in control subjects (31% vs. 5%, P<0.001). Among case subjects, those with early repolarization were more likely to be male and to have a history of syncope or sudden cardiac arrest during sleep than those without early repolarization. In eight subjects, the origin of ectopy that initiated ventricular arrhythmias was mapped to sites concordant with the localization of repolarization abnormalities. During a mean (+/-SD) follow-up of 61+/-50 months, defibrillator monitoring showed a higher incidence of recurrent ventricular fibrillation in case subjects with a repolarization abnormality than in those without such an abnormality (hazard ratio, 2.1; 95% confidence interval, 1.2 to 3.5; P=0.008).CONCLUSIONS: Among patients with a history of idiopathic ventricular fibrillation, there is an increased prevalence of early repolarization.
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38.
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39.
  • Huyghe, Jeroen R., et al. (author)
  • Discovery of common and rare genetic risk variants for colorectal cancer
  • 2019
  • In: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 51:1, s. 76-
  • Journal article (peer-reviewed)abstract
    • To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 x 10(-8), bringing the number of known independent signals for CRC to similar to 100. New signals implicate lower-frequency variants, Kruppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
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40.
  • Huyghe, Jeroen R, et al. (author)
  • Genetic architectures of proximal and distal colorectal cancer are partly distinct
  • 2021
  • In: Gut. - : BMJ Publishing Group Ltd. - 0017-5749 .- 1468-3288. ; 70:7, s. 1325-1334
  • Journal article (peer-reviewed)abstract
    • Objective: An understanding of the etiologic heterogeneity of colorectal cancer (CRC) is critical for improving precision prevention, including individualized screening recommendations and the discovery of novel drug targets and repurposable drug candidates for chemoprevention. Known differences in molecular characteristics and environmental risk factors among tumors arising in different locations of the colorectum suggest partly distinct mechanisms of carcinogenesis. The extent to which the contribution of inherited genetic risk factors for CRC differs by anatomical subsite of the primary tumor has not been examined.Design: To identify new anatomical subsite-specific risk loci, we performed genome-wide association study (GWAS) meta-analyses including data of 48 214 CRC cases and 64 159 controls of European ancestry. We characterised effect heterogeneity at CRC risk loci using multinomial modelling.Results: We identified 13 loci that reached genome-wide significance (p<5×10-8) and that were not reported by previous GWASs for overall CRC risk. Multiple lines of evidence support candidate genes at several of these loci. We detected substantial heterogeneity between anatomical subsites. Just over half (61) of 109 known and new risk variants showed no evidence for heterogeneity. In contrast, 22 variants showed association with distal CRC (including rectal cancer), but no evidence for association or an attenuated association with proximal CRC. For two loci, there was strong evidence for effects confined to proximal colon cancer.Conclusion: Genetic architectures of proximal and distal CRC are partly distinct. Studies of risk factors and mechanisms of carcinogenesis, and precision prevention strategies should take into consideration the anatomical subsite of the tumour.
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41.
  • Jolak, Rodi, 1985, et al. (author)
  • The influence of software design representation on the design communication of teams with diverse personalities
  • 2022
  • In: Proceedings - 25th ACM/IEEE International Conference on Model Driven Engineering Languages and Systems, MODELS 2022. - New York, NY, USA : ACM. ; , s. 255-265
  • Conference paper (peer-reviewed)abstract
    • Software is the main driver of added-value in many of the systems that surround us. While its complexity is increasing, so is the diversity of systems driven by software. To meet the challenges emerging from this combination, it is necessary to mobilize increasingly large and heterogeneous multidisciplinary teams, comprising software experts, as well as experts from various domains related to the systems driven by software. Hence, the quality of communication about software between stakeholders of different domains and with different personalities is becoming a key issue for successfully engineering software-intensive systems. The goal of this study, thus, is to investigate the effect of the representation of software design models on the communication of design decisions between stakeholders with diverse personality traits. As a result, this study finds that graphical representations of software design models are better than textual representations in enhancing the communication and increasing the productivity of stakeholders with diverse personalities.
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42.
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43.
  • Kergoat, Laurent, et al. (author)
  • Nitrogen controls plant canopy light-use efficiency in temperate and boreal ecosystems
  • 2008
  • In: Journal of Geophysical Research. - 2156-2202. ; 113:G4, s. 04017-04017
  • Research review (peer-reviewed)abstract
    • Optimum daily light-use efficiency (LUE) and normalized canopy photosynthesis (GEE*) rate, a proxy for LUE, have been derived from eddy covariance CO2 flux measurements obtained at a range of sites located in the mid to high latitudes. These two variables were analyzed with respect to environmental conditions, plant functional types (PFT) and leaf nitrogen concentration, in an attempt to characterize their variability and their potential drivers. LUE averaged 0.0182 mol/mol with a coefficient of variation of 37% (42% for GEE*). Foliar nitrogen N of the dominant plant species was found to explain 71% of LUE (n = 26) and 62% of GEE* (n = 44) variance, across all PFTs and sites. Mean Annual Temperature, MAT, explained 27% of LUE variance, and the two factors (MAT and N) combined in a simple linear model explain 80% of LUE and 76% GEE* variance. These results showed that plant canopies in the temperate, boreal and arctic zones fit into a general scheme closely related to the one, which had been established for plant leaves worldwide. The N-MAT- LUE relationships offer perspectives for LUE-based models of terrestrial photosynthesis based on remote sensing. On a continental scale, the decrease of LUE from the temperate to the arctic zone found in the data derived from flux measurements is not in line with LUE resulting from inversion of atmospheric CO2.
  •  
44.
  • Koch, Sina, et al. (author)
  • NRP1 Presented in trans to the Endothelium Arrests VEGFR2 Endocytosis, Preventing Angiogenic Signaling and Tumor Initiation
  • 2014
  • In: Developmental Cell. - : Elsevier BV. - 1534-5807 .- 1878-1551. ; 28:6, s. 633-646
  • Journal article (peer-reviewed)abstract
    • Neuropilin 1 (NRP1) modulates angiogenesis by binding vascular endothelial growth factor (VEGF) and its receptor, VEGFR2. We examined the consequences when VEGFR2 and NRP1 were expressed on the same cell (cis) or on different cells (trans). In cis, VEGF induced rapid VEGFR2/NRP1 complex formation and internalization. In trans, complex formation was delayed and phosphorylation of phospholipase C gamma (PLC gamma) and extracellular regulated kinase 2 (ERK2) was prolonged, whereas ERK1 phosphorylation was reduced. Trans complex formation suppressed initiation and vascularization of NRP1-expressing mouse fibrosarcoma and melanoma. Suppression in trans required high-affinity, steady-state binding of VEGF to NRP1, which was dependent on the NRP1 C-terminal domain. Compatible with a trans effect of NRP1, quiescent vasculature in the developing retina showed continuous high NRP1 expression, whereas angiogenic sprouting occurred where NRP1 levels fluctuated between adjacent endothelial cells. Therefore, through communication in trans, NRP1 can modulate VEGFR2 signaling and suppress angiogenesis.
  •  
45.
  • Laban, Guy, et al. (author)
  • Robo-Identity : Exploring Artificial Identity and Emotion via Speech Interactions
  • 2022
  • In: PROCEEDINGS OF THE 2022 17TH ACM/IEEE INTERNATIONAL CONFERENCE ON HUMAN-ROBOT INTERACTION (HRI '22). - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 1265-1268
  • Conference paper (peer-reviewed)abstract
    • Following the success of the first edition of Robo-Identity, the second edition will provide an opportunity to expand the discussion about artificial identity. This year, we are focusing on emotions that are expressed through speech and voice. Synthetic voices of robots can resemble and are becoming indistinguishable from expressive human voices. This can be an opportunity and a constraint in expressing emotional speech that can (falsely) convey a human-like identity that can mislead people, leading to ethical issues. How should we envision an agent's artificial identity? In what ways should we have robots that maintain a machine-like stance, e.g., through robotic speech, and should emotional expressions that are increasingly human-like be seen as design opportunities? These are not mutually exclusive concerns. As this discussion needs to be conducted in a multidisciplinary manner, we welcome perspectives on challenges and opportunities from variety of fields. For this year's edition, the special theme will be "speech, emotion and artificial identity".
  •  
46.
  • LAURENT, Marion, et al. (author)
  • Novel indices reveal that pollinator exposure to pesticides varies across biological compartments and crop surroundings
  • 2024
  • In: Science of the Total Environment. - 0048-9697. ; 927
  • Journal article (peer-reviewed)abstract
    • Declines in insect pollinators have been linked to a range of causative factors such as disease, loss of habitats, the quality and availability of food, and exposure to pesticides. Here, we analysed an extensive dataset generated from pesticide screening of foraging insects, pollen-nectar stores/beebread, pollen and ingested nectar across three species of bees collected at 128 European sites set in two types of crop. In this paper, we aimed to (i) derive a new index to summarise key aspects of complex pesticide exposure data and (ii) understand the links between pesticide exposures depicted by the different matrices, bee species and apple orchards versus oilseed rape crops. We found that summary indices were highly correlated with the number of pesticides detected in the related matrix but not with which pesticides were present. Matrices collected from apple orchards generally contained a higher number of pesticides (7.6 pesticides per site) than matrices from sites collected from oilseed rape crops (3.5 pesticides), with fungicides being highly represented in apple crops. A greater number of pesticides were found in pollen-nectar stores/beebread and pollen matrices compared with nectar and bee body matrices. Our results show that for a complete assessment of pollinator pesticide exposure, it is necessary to consider several different exposure routes and multiple species of bees across different agricultural systems.
  •  
47.
  • Le-Bail, Alain, et al. (author)
  • Review on the impact of electrical and magnetic disturbances during freezing
  • 2018
  • In: Refrigeration Science and Technology. - 9782362150241 ; , s. 225-232
  • Conference paper (peer-reviewed)abstract
    • Phase change in biological tissues may be affected by electrical and magnetic disturbances. This presentation proposes a review based on existing literature as well as some very recent results on freezing under static electric field (SEF), magnetic field (MF) and electromagnetic radiations. Freezing under static electric field of water, aqueous solution and pork meat has been investigated by the authors, showing the ability of this process to refine ice crystals in frozen matrices. SEF permits to lower the supercooling and to trigger the phase change of water to ice. Radiofrequencies and microwaves havebeen used recently by researchers to promote refined ice crystallization in food systems. Even though the energy optimization of the process is still in debate, the benefit in terms of size of ice crystals has been evidenced. © 2018 International Institute of Refrigeration. All rights reserved.
  •  
48.
  • Le Jan, Sébastien, et al. (author)
  • Functional Overlap Between Chondroitin and Heparan Sulfate Proteoglycans During VEGF-Induced Sprouting Angiogenesis
  • 2012
  • In: Arteriosclerosis, Thrombosis and Vascular Biology. - 1079-5642 .- 1524-4636. ; 32:5, s. 1255-1263
  • Journal article (peer-reviewed)abstract
    • OBJECTIVE: Heparan sulfate proteoglycans regulate key steps of blood vessel formation. The present study was undertaken to investigate if there is a functional overlap between heparan sulfate proteoglycans and chondroitin sulfate proteoglycans during sprouting angiogenesis.METHODS AND RESULTS: Using cultures of genetically engineered mouse embryonic stem cells, we show that angiogenic sprouting occurs also in the absence of heparan sulfate biosynthesis. Cells unable to produce heparan sulfate instead increase their production of chondroitin sulfate that binds key angiogenic growth factors such as vascular endothelial growth factor A, TGFβ, and platelet-derived growth factor B. Lack of heparan sulfate proteoglycan production however leads to increased pericyte numbers and reduced adhesion of pericytes to nascent sprouts, likely due to dysregulation of TGFβ and platelet-derived growth factor B signal transduction.CONCLUSIONS: The present study provides direct evidence for a previously undefined functional overlap between chondroitin sulfate proteoglycans and heparan sulfate proteoglycans during sprouting angiogenesis. Our findings provide information relevant for potential future drug design efforts that involve targeting of proteoglycans in the vasculature.
  •  
49.
  • Luo, Tao, et al. (author)
  • Goethite-bound copper controls the fate of antibiotics in aquatic environments
  • 2024
  • In: ACS - ES & T Water. - : American Chemical Society (ACS). - 2690-0637. ; 4:2, s. 638-647
  • Journal article (peer-reviewed)abstract
    • Ciprofloxacin (CIP), a commonly used antibiotic, is today found in natural waterways and terrestrial environments alongside trace heavy metal contaminants. CIP however has a weak affinity for iron (oxy)hydroxide minerals, which often control contaminant transport in nature. This weak affinity is caused by the electrostatic repulsion between positively charged mineral surfaces and the CIP piperazine ring. Using goethite (α-FeOOH), a representative iron (oxy)hydroxide nanomineral, we show that the presence of Cu(II) greatly enhances CIP adsorption while at the same time catalyzes CIP oxidation to byproducts, which are new to nature. The CIP uptake was greatest at circumneutral pH and in saline conditions, where Cu(II), CIP, and mineral surface charges were the least repulsive. Vibrational spectroscopy and molecular simulations revealed that the enhanced uptake of CIP was caused by the the coordination of metal-bonded Cu(II)-CIP surface complexes on goethite. The inner-sphere Cu(II)-CIP complex also facilitated CIP oxidation into a series of new products, which we identified by mass spectrometry. Finally, to predict Cu(II) and quinolone loadings prior to redox-driven reactions, we propose a multisite surface complexation model using Cu(II)-CIP ternary surface complexes, alongside an ion pair to account for the ionic strength dependence on loadings. The information developed in this work will help tracking the fate of CIP in contaminated aquatic environments.
  •  
50.
  • Marquer, Laurent, et al. (author)
  • Pollen-based reconstruction of Holocene land-cover in mountain regions : Evaluation of the Landscape Reconstruction Algorithm in the Vicdessos valley, northern Pyrenees, France
  • 2020
  • In: Quaternary Science Reviews. - : Elsevier. - 0277-3791 .- 1873-457X. ; 228, s. 1-15
  • Research review (peer-reviewed)abstract
    • Long-term perspectives on climate- and human-induced shifts in plant communities and tree line in mountains are often inferred from fossil pollen records. However, various factors, such as complex patterns of orographic wind fields and abundant insect-pollinated plants in higher altitudes, make pollen-based reconstruction in mountain regions difficult. Over the last decade the Landscape Reconstruction Algorithm (LRA) - a model-based approach in reconstruction of vegetation - has been successfully applied in various parts of the globe. However, evaluation of its effectiveness in mountain ranges is still limited. The present study assesses the extent to which the LRA approach helps quantify the local changes in vegetation cover at Vicdessos valley in northern French Pyrenees as a case study. In the study area well-dated sediment cores are available from eight bogs and ponds, 6-113 m in radius, located above the current tree line. We first use a simple simulation experiment to evaluate the way how pollen records from "landscape islands" (mountain tops and plateaus) would represent local vegetation and to clarify important factors affecting the LRA-based reconstruction in a mountainous region. This study then uses pollen records from these sites and vegetation and land-cover data both within a 50-km radius around the Vicdessos valley and within a 2-km radius from each site for evaluation of the REVEALS- and LOVE-based reconstruction of the regional and local plant cover, respectively, in the LRA approach. The land-cover data are complied for coniferous trees, broadleaved trees and non-forested areas from the CORINE and historical maps in three time windows: 1960-1970, 1990-2000 and 2000-2013. Major findings are as follows. (1) Accuracy of the regional vegetation estimates affects the reliability of the LRA-based reconstruction of vegetation within a 2-km radius; use of the CORINE data as input to the LOVE model improves reliability of the results over the use of the REVEALS-based estimates of regional vegetation. This implies that a systematic selection of pollen data only from sites above the tree line is problematic for estimating regional vegetation, and thus the entire LRA process. (2) Selection of the dispersal models for pollen transport (i.e. the Langrangian Stochastic Model vs. Gaussian Plume Model) does not affect significantly the LRA-based estimates at both the regional and local scales in the study area. (3) The LRA approach improves the pollen-based reconstruction of local vegetation compared to pollen percentage alone in northern Pyrenees. Although further empirical and simulation studies are necessary, our results emphasize the importance of site selection for the LRA-based reconstruction of vegetation in mountain regions. (C) 2019 Elsevier Ltd. All rights reserved.
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