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See detailState of Martian Upper Atmosphere as Observed by Imaging Ultraviolet Spectroscope Onboard MAVEN
Jain; Stewart; Deighan et al

Conference (2017, August 09)

NASA’s MAVEN spacecraft has taken more than two earth years (one Martian year) of observations of Mars to understand the process of Martian atmospheric evolution. The Imaging Ultraviolet Spectrograph ... [more ▼]

NASA’s MAVEN spacecraft has taken more than two earth years (one Martian year) of observations of Mars to understand the process of Martian atmospheric evolution. The Imaging Ultraviolet Spectrograph (IUVS) on board MAVEN observes Mars in far and mid ultraviolet (110-340 nm) with unique scanning and pointing capabilities, which are optimized for airglow studies. Dayglow emissions observed on Mars are a perfect tracer for the processes occurring in the emitting region of the atmosphere (100-200 km) and provide basic information about atmospheric composition (and its structure), and give insight into the dynamics, energetics, and physics and chemistry of the thermosphere. With its wide spatial and temporal coverage, IUVS observations of Martian dayglow has contributed immensely to our understanding of the Martian upper atmosphere and its response to incoming solar flux (EUV/FUV) and coupling between lower and upper atmosphere through tides and waves. In this presentation, I will talk about an overview of scientific results obtained by IUVS dayglow measurements, including (1) spatial/temporal distribution of major MUV and FUV emissions and their seasonal variability; (2) the seasonal variation of thermosphere temperatures inferred from dayglow measurements; (3) the effect of solar EUV flux (including the ~27-day solar rotation) and heliocentric distance on upper atmosphere temperature structure. We will present an overview of these results and a discussion of their implications for the state of the Martian upper atmosphere. [less ▲]

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See detailHydrogen Loss from Mars: Seasonal and Sourced from Upper Atmospheric Water
Chaffin; Deighan; Stewart et al

Conference (2017, August 09)

Mars has lost a significant fraction of its initial water inventory to space over its history. This loss proceeds via a chemical chain initiated in the lower and middle atmosphere below 100 km altitude ... [more ▼]

Mars has lost a significant fraction of its initial water inventory to space over its history. This loss proceeds via a chemical chain initiated in the lower and middle atmosphere below 100 km altitude, which results in H escape to space in the collisionless corona above about 200 km altitude. Hydrogen loss from Mars is tracked via brigtness measurements of this corona in Lyman alpha light at 121.6 nm, which is scattered by neutral H orbiting and escaping the planet. Here we present observations of H escape variability made by the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission's Imaging Ultraviolet Spectrograph (IUVS) that demonstrate the seasonal dependence of H escape, adding to evidence initially gathered by Mars Express and the Hubble Space Telescope. We show that for two Mars years the atmosphere has exhibited enhanced H escape in Southern Summer near perihelion. We also present the result of photochemical model calculations which demonstrate that this variation can be explained as a result of high concentrations of water vapor in the upper atmosphere, consistent with Mars Express solar occultation measurements and several general circulation models. Our results demonstrate that the large variations in H escape at high altitudes can be driven by lower atmospheric dynamics, suggesting that Mars hydrogen escape may depend on climate, in addition to the long-term evolution of Martian climate depending on atmospheric escape. [less ▲]

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See detailScience Highlights from MAVEN/IUVS After Two Years in Mars Orbit
Jain; Schneider; Stiepen, Arnaud ULg et al

Conference (2017, August 08)

The Mars Atmosphere and Volatile EvolutioN (MAVEN) mission's Imaging Ultraviolet Spectrograph (IUVS) observes Mars in the far and mid ultraviolet (110-340 nm), investigating lower and upper atmospheric ... [more ▼]

The Mars Atmosphere and Volatile EvolutioN (MAVEN) mission's Imaging Ultraviolet Spectrograph (IUVS) observes Mars in the far and mid ultraviolet (110-340 nm), investigating lower and upper atmospheric structure and indirectly probing neutral atmospheric escape. The instrument is among the most powerful spectrographs sent to another planet, with several key capabilities: separate Far-UV & Mid-UV channels for stray light control; a high-resolution echelle mode to resolve deuterium and hydrogen emission; internal instrument pointing and scanning capabilities to allow complete mapping and nearly continuous operation; and optimization for airglow studies. After two Earth years in orbit (one Mars year), IUVS has assembled a large quantity of data and provided insights on present-day processes at Mars including dayglow, nightglow, aurora, meteor showers, clouds, and solar-planetary interactions. In this presentation, we will highlight several new discoveries made by IUVS. Among the key results obtained by IUVS are: (1) discovery of the widespread occurrence of a diffuse proton aurora representing a previously unknown source of energy deposition into the atmospheres of unmagnetized planets; (2) first spatial mapping of nitric oxide nightglow reveals regions of atmospheric downwelling necessitating substantial changes to global atmospheric circulation models; (3) a new high-spatial-resolution UV imaging mode allows detection of clouds from nadir to limb and their local time evolution, as well as unprecedented determinations of Mars’ low-altitude ozone; (4) discovery of a persistent meteoric metal layer in Martian atmosphere; (5) atmospheric structure, composition and dynamics from stellar occultation. We will present an overview of these results and a discussion of their implications for characterizing the state of the atmosphere and its evolution. [less ▲]

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See detailMAVEN/IUVS Observations of the Reflectance Spectrum of Phobos
Chaffin; Deighan; Schneider et al

Conference (2017, August 08)

The Mars Atmosphere and Volatile Evolution (MAVEN) spacecraft occasionally has close encounter seasons with Phobos as a consequence of its orbital precession and its apoapsis being near the orbit of the ... [more ▼]

The Mars Atmosphere and Volatile Evolution (MAVEN) spacecraft occasionally has close encounter seasons with Phobos as a consequence of its orbital precession and its apoapsis being near the orbit of the moon. During one encounter season in late 2015, MAVEN's Imaging Ultraviolet Spectrograph (IUVS) was able to gather the first ever spectral images of the moon in the mid-ultraviolet. During these flybys, IUVS was able to observe the trailing hemisphere of the moon, producing spectra useful for comparison with the Mariner 9 Ultraviolet Spectrometer measurements, which observed only the moon's leading side. The IUVS data reveal that the trailing side of the Moon is bluer than the leading side, indicating possible differences in the weathering history of the hemispheres. In addition, we see some evidence for an absorption feature longward of 300 nm, potentially produced by organic compounds, in accordance with Mariner 9 and SPICAM/UV observations. We will present an overview of our images and spectra and a discussion of their interpretation for the history and formation of Phobos. [less ▲]

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See detailImpact of canopy aerodynamic distance spatial and temporal variability on long term eddy covariance measurements
Hurdebise, Quentin ULg; Heinesch, Bernard ULg; De Ligne, Anne ULg et al

in Agricultural and Forest Meteorology (2017), 247(2017), 131-138

Understanding if and how the spatial and temporal variability of the surrounding environment affects turbulence is essential for long-term eddy covariance measurements. It requires characterizing the ... [more ▼]

Understanding if and how the spatial and temporal variability of the surrounding environment affects turbulence is essential for long-term eddy covariance measurements. It requires characterizing the surrounding environment. One way to achieve this is to analyse the canopy aerodynamic distance (Δ), which is the difference between measurement height (zm) and displacement height (d). In this work, an original method to estimate the canopy aerodynamic distance at a fine spatial (30° sectors) and temporal (one year) resolution was proposed. It was based on sensible heat cospectra analysis, calibrated on a measurement height change and validated using canopy height inventories. This method was applied to 20 years of eddy covariance measurements from the Vielsalm Terrestrial Observatory (VTO), a site located in a mixed temperate forest. The method allowed Δ spatio-temporal variability due to changes in canopy or measurement height to be detected. Relationships between Δ and turbulence statistics were then analysed: the momentum correlation coefficient (ruw) was found to be dependent on Δ, confirming that the measurements were made in the roughness sublayer of the atmospheric surface layer. In contrast, no such relationship was found sensible heat, CO2 or water vapour correlation coefficients, suggesting that the Δ variability did not affect significantly these fluxes. There were significant differences, however, between azimuthal directions, suggesting that these scalars were affected by forest heterogeneity in a different way. Various hypotheses were put forward to explain the differences and their relevance was evaluated. This study highlighted the need to consider the spatial and temporal variability of the surrounding environment in order to verify the consistency of long-term eddy covariance datasets. [less ▲]

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See detailImpact of Financial Assumptions on the Cost Optimality towards Nearly Zero Energy Buildings- A case study
Hamdy, Mohamed; Siren, Kai; Attia, Shady ULg

in Energy and Buildings (2017)

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See detailMild synthesis of poly(HEMA)-networks as well-defined nanoparticles in supercritical carbon dioxide
Parilti, Rahmet ULg; Alaimo, David; Grignard, Bruno ULg et al

in Journal of Materials Chemistry B (2017), 5(29), 5806-5815

Free-radical dispersion polymerisation of 2-hydroxyethyl methacrylate was carried out in supercritical carbon dioxide (scCO2) in the presence of stabilisers based on polyethylene oxide (PEO) and poly ... [more ▼]

Free-radical dispersion polymerisation of 2-hydroxyethyl methacrylate was carried out in supercritical carbon dioxide (scCO2) in the presence of stabilisers based on polyethylene oxide (PEO) and poly(heptadecafluorodecyl acrylate) (PFDA). Different architectures of copolymers (random, palm-tree and diblock) were tested for their surface tension, cloud point and as a stabilising agent. The diblock architecture was found to be the best candidate resulting in poly(HEMA) spherical particles with a size of 316 nm. Furthermore, the effect of the CO2-phobic block (PEO) in the diblock architecture was investigated by using three different chain lengths (1000, 2000, 5000 g mol−1). By optimizing the stabiliser composition and structure, mild reaction conditions have been identified allowing us to obtain well-defined spherical cross-linked poly(HEMA) particles with a mean diameter of unprecedented low size (216 nm) at a temperature as low as 35 °C. [less ▲]

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See detailOviposition deterrent activity of basil plants and their essentials oils against Tuta absoluta (Lepidoptera: Gelechiidae)
Yarou, Boni Barthélémy ULg; Bawin, Thomas; Boullis, Antoine ULg et al

in Environmental Science and Pollution Research (2017)

The leafminer Tuta absoluta Meyrick (Lepidoptera: Gelechiidae) is one of the most important pests of tomato, reducing crop yields by up to 100% in greenhouses and fields, in several countries globally ... [more ▼]

The leafminer Tuta absoluta Meyrick (Lepidoptera: Gelechiidae) is one of the most important pests of tomato, reducing crop yields by up to 100% in greenhouses and fields, in several countries globally. Because synthetic insecticides lead to resistance and have adverse effects on natural enemies and the health of producers, alternative control methods are needed. In this study, we assessed the oviposition-deterring effect of basil plants, Ocimum gratissimum L. and O. basilicum L. (Lamiaceae), using dual-choice behavioural assays performed in flight tunnels. We found that both plants significantly reduced T. absoluta oviposition behaviour on a tomato plant located nearby. To evaluate the potential effect of basil volatile organic compounds, we formulated essential oils of both plant species in paraffin oil, and observed a similar oviposition-deterring effect. Gas chromatography analyses detected 18 constituents in these essential oils which the major constituents included thymol (33.3%), p-cymene (20.4%), γ-terpinene (16.9%), myrcene (3.9%) in O. gratissimum and estragol (73.8%), linalool (8.6%), β-elemene (2.9%) and E-β-ocimene (2.6%) in O. basilicum. Twenty and 33 compounds were identified of the volatiles collected on O. gratissimum and O. basilicum plants, respectively. The main components include the following: p-cymene (33.5%), γ-terpinene (23.6%), α-terpinene (7.2%), α-thujene (6.7%) and E-α-bergamotene (38.9%) in O. gratissimum, and methyl eugenol (26.1%), E-β-ocimene (17.7%), and linalool (9.4%) in O. basilicum. Four compounds (α-pinene, β-pinene, Myrcene, Limonene) were common in essential oils and plants. Our results suggest the valuable potential of basil and associated essential oils as a component of integrated management strategies against the tomato leafminer. [less ▲]

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See detailEt si on se passait (complètement) des sciences humaines ?
Winand, Jean ULg

Conference (2017, August 06)

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See detailHistories of Comics by its Makers. Contemporary Graphic Novels and the Heritage of Comics
Crucifix, Benoît ULg

Conference (2017, August 03)

PhD project presentation

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See detailLos ingrávidos de Valeria Luiselli: entre fantástico y autoficción
Licata, Nicolas ULg

Conference (2017, August 03)

En 2011, la escritora mexicana Valeria Luiselli publica su primera novela, Los ingrávidos, cuyo título alude al proceso de afantasmamiento de los dos narradores: una narradora notablemente similar a la ... [more ▼]

En 2011, la escritora mexicana Valeria Luiselli publica su primera novela, Los ingrávidos, cuyo título alude al proceso de afantasmamiento de los dos narradores: una narradora notablemente similar a la propia Luiselli y el poeta mexicano Gilberto Owen. Narración en primera persona y parecidos con el autor por un lado, fenómenos indiscutiblemente inverosímiles por otro, el libro reúne todos los ingredientes de lo que el teórico francés Vincent Colonna llamó “autoficción fantástica”. Sin embargo, en una de sus entrevistas, Luiselli declara que “no quería escribir una novela fantástica”, y, más aún, “que [se] moriría si alguien dice que Los ingrávidos es una novela de ese estilo, estaría profundamente indignada” (Barbosa Vera, Scofaulos 2012). Aunque el efecto fantástico no siempre dependa de la intención de un autor, en este caso preciso Valeria Luiselli parece tener razón. De hecho, un examen detenido de la obra revela una antinomia: sin ser fantástica, Los ingrávidos es una autoficción “de ese estilo”. Es sobre esa antinomia que esta comunicación inclina la perspectiva. Después de un sucinto resumen, nos centremos en primer lugar en los indicios autoficcionales de la novela y luego en sus componentes fantásticos, examinando con más detenimiento los que impiden que el libro se adhiera a esa modalidad, a saber, los moduladores de duda, los comentarios metadiegéticos y la no fiabilidad de la narradora. [less ▲]

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See detailExergy analysis applied to performance of buildings in Europe
Sartor, Kevin ULg; Dewallef, Pierre ULg

in Energy and Buildings (2017), 148

Energy performance of buildings generally assesses the energy consumption of buildings such as heating, domestic heat water, ventilation systems, etc. However, this approach is based on the first law of ... [more ▼]

Energy performance of buildings generally assesses the energy consumption of buildings such as heating, domestic heat water, ventilation systems, etc. However, this approach is based on the first law of thermodynamics and considers only the quantity of energy used without considering its ‘quality’ and leads to a lack of information about the energy conversion processes. This is particularly true in the new low-energy buildings where sometimes high temperatures sources are used to meet low-temperature needs. The exergy analysis of a system, based on first and second thermodynamic laws, can be used to overcome this. In this work, it is proposed to compare the energy and the exergy consumption and the related CO2 emissions of several kinds of buildings to determine the best systems in terms of energy and exergy needs. The energy demand calculations are performed using the official software available in Belgium and some assumptions are implemented to consider the exergy approach. As exergy calculations require a reference state, some different climatic conditions are also investigated. Finally, some conclusions are discussed to rank the sources of energy and their related exergy losses. [less ▲]

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See detailThe inner structure of early-type galaxies in the Illustris simulation
Xu, Dandan; Springel, Volker; Sluse, Dominique ULg et al

in Monthly Notices of the Royal Astronomical Society (2017), 469

Early-type galaxies provide unique tests for the predictions of the cold dark matter cosmology and the baryonic physics assumptions entering models for galaxy formation. In this work, we use the Illustris ... [more ▼]

Early-type galaxies provide unique tests for the predictions of the cold dark matter cosmology and the baryonic physics assumptions entering models for galaxy formation. In this work, we use the Illustris simulation to study correlations of three main properties of early-type galaxies, namely the stellar orbital anisotropies, the central dark matter fractions and the central radial density slopes, as well as their redshift evolution since z = 1.0. We find that lower mass galaxies or galaxies at higher redshift tend to be bluer in rest-frame colour, have higher central gas fractions, and feature more tangentially anisotropic orbits and steeper central density slopes than their higher mass or lower redshift counterparts, respectively. The projected central dark matter fraction within the effective radius shows a very mild mass dependence but positively correlates with galaxy effective radii due to the aperture effect. The central density slopes obtained by combining strong lensing measurements with single-aperture kinematics are found to differ from the true density slopes. We identify systematic biases in this measurement to be due to two common modelling assumptions, isotropic stellar orbital distributions and power-law density profiles. We also compare the properties of early-type galaxies in Illustris to those from existing galaxy and strong lensing surveys; we find in general broad agreement but also some tension, which poses a potential challenge to the stellar formation and feedback models adopted by the simulation. [less ▲]

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See detailUniversally dispreferred structures through change. The diachrony of affix ordering in Egyptian-Coptic
Grossman, Eitan; Polis, Stéphane ULg

Conference (2017, August 01)

It has been repeatedly observed, on the basis of typological ‘big data,’ that there is a worldwide preference for suffixes as opposed to prefixes. This can be explained in several ways. A possible ... [more ▼]

It has been repeatedly observed, on the basis of typological ‘big data,’ that there is a worldwide preference for suffixes as opposed to prefixes. This can be explained in several ways. A possible explanation is that this feature is a world-wide retention from Proto-World, or is prone to diffusion through language contact. Another possible explanation is that suffixes are preferred for some reason in Universal Grammar or for hitherto unclear general cognitive reasons (Caballero et al. 2008). Yet another explanation is that suffixes are more prone to be created through regular processes of language change, e.g., grammaticalization (Bybee 1985), perhaps due to online usage factors (Himmelmann 2014). The explanation of this preference is directly relevant to a question highlighted in Good (2008), namely, the relationship between language universals and language change: do synchronic structural universals constrain change, or do diachronic universals, ultimately motivated by synchronic usage factors, give rise to synchronic universals? Kiparsky (2008) argues that the form of synchronic grammars constrains change, i.e., languages should not be able to change in such a way that they flout Universal Grammar. On the other hand, for Bybee (2008), the most robust universals are in fact universals of language change, and synchronic states are in a sense epiphenoma. For this question, apparently ‘counter-directional’ changes are crucial: why should language change lead to universally dispreferred distributions of linguistic structures? n this paper, we argue that universally dispreferred structures can and do arise as the result of regular language change, given the right background structures as the particular ‘ecology’ in which change takes place. Specifically, we show that Ancient Egyptian-Coptic (Afroasiatic), shows a long-term diachronic macro-change from mixed suffixing-prefixing to an overwhelming preference for prefixing. The empirical basis for this study is a comparison of ten typologically-significant parameters in which prefixing or affixing is at stake, based on Dryer’s (2013) 969-language sample. With its extremely high prefixing preference, Coptic belongs to the rare 6% or so of languages that are predominantly prefixing (Tables 1,2). Moreover, it has a higher prefixing index (11) than any other language in Dryer’s 969-language sample. The closest competitor is Hunde (Bantu; Democratic Republic of Congo), with a prefixing index of 9.5. In terms of areality, Coptic is an outlier: in mediterranean northern Africa, Coptic is the only language that is predominantly prefixing. We argue that each of the micro-changes implicated in this macro-change are better understood in terms of changes at the level of individual constructions, via grammaticalization, rather than in terms of a broad structural ‘drift.’ Crucially, there is nothing unusual about the actual processes of change themselves; what may be unusual, from a cross-linguistic point of view, is the length of uninterrupted documentation of a single language, which allows us to observe long-term changes with abundant evidence. In short, we argue that Ancient Egyptian-Coptic looks as though it is swimming against the typological tide, although it is constantly paddling along with the usual tides of language change. [less ▲]

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See detailSocial sustainability assessments in the biobased economy: Towards a systemic approach
Rafiaani, Parisa ULg; Kuppens, Tom; Van Dael, Miet et al

in Renewable & Sustainable Energy Reviews (2017)

The majority of impact assessments for the biobased economy are primarily focused on the environmental and (techno-)economic aspects, while social aspects are rarely considered. This study proposes a ... [more ▼]

The majority of impact assessments for the biobased economy are primarily focused on the environmental and (techno-)economic aspects, while social aspects are rarely considered. This study proposes a modified systemic approach for a social sustainability impact assessment of the biobased economy, based on a review on the common methodologies for assessing social impacts. Accordingly, the proposed approach follows the four general iterative steps of social life cycle analysis (SLCA) as it considers all life cycle phases of the biobased economy. The systemic approach considers the potential social impacts on local communities, workers, and consumers as the main three groups of the stakeholders. The review showed that the most common social indicators for inventory analysis within the biobased economy include health and safety, food security, income, employment, land- and worker-related concerns, energy security, profitability, and gender issues. Multi-criteria decision analysis (MCDA) was also highlighted as the broadly utilized methodology for aggregating the results of impact assessments within the biobased economy. Taking a life cycle perspective, this study provides a holistic view of the full sustainability of research, design, and innovation in the biobased economy by suggesting the integration of the social aspects with techno-economic and an environmental life cycle assessment. Our proposed systemic approach makes possible to integrate the social impacts that are highly valued by the affected stakeholders into the existing sustainability models that focus only on environmental and techno-economic aspects. We discuss the steps of the proposed systemic approach in order to identify the challenges of applying them within the biobased economy. These challenges refer mainly to the definition of the functional unit and system boundaries, the selection and the analysis of social indicators (inventory analysis), the aggregation of the inventory to impact categories, and the uncertainties associated with the social sustainability evaluation. The result of this review and the proposed systemic approach serve as a foundation for industry and policy makers to gain a better insight into the importance of social sustainability impacts assessment within the biobased economy. [less ▲]

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See detailThe Far Ultra-Violet Imager on the Icon Mission
Mende, Stephen; Frey, Harald; Rider, Kodi et al

in Space Science Reviews (2017)

ICON Far UltraViolet (FUV) imager contributes to the ICON science objectives by providing remote sensing measurements of the daytime and nighttime atmosphere/ ionosphere. During sunlit atmospheric ... [more ▼]

ICON Far UltraViolet (FUV) imager contributes to the ICON science objectives by providing remote sensing measurements of the daytime and nighttime atmosphere/ ionosphere. During sunlit atmospheric conditions, ICON FUV images the limb altitude profile in the shortwave (SW) band at 135.6 nm and the longwave (LW) band at 157 nm perpendicular to the satellite motion to retrieve the atmospheric O/N2 ratio. In conditions of atmospheric darkness, ICON FUV measures the 135.6 nm recombination emission of O+ ions used to compute the nighttime ionospheric altitude distribution. ICON Far Ultra- Violet (FUV) imager is a Czerny–Turner design Spectrographic Imager with two exit slits and corresponding back imager cameras that produce two independent images in separate wavelength bands on two detectors. All observations will be processed as limb altitude profiles. In addition, the ionospheric 135.6 nm data will be processed as longitude and latitude spatial maps to obtain images of ion distributions around regions of equatorial spread F. The ICON FUV optic axis is pointed 20 degrees below local horizontal and has a steering mirror that allows the field of view to be steered up to 30 degrees forward and aft, to keep the local magnetic meridian in the field of view. The detectors are micro channel plate (MCP) intensified FUV tubes with the phosphor fiber-optically coupled to Charge Coupled Devices (CCDs). The dual stack MCP-s amplify the photoelectron signals to overcome the CCD noise and the rapidly scanned frames are co-added to digitally create 12-second integrated images. Digital on-board signal processing is used to compensate for geometric distortion and satellite motion and to achieve data compression. The instrument was originally aligned in visible light by using a special grating and visible cameras. Final alignment, functional and environmental testing and calibration were performed in a large vacuum chamber with a UV source. The test and calibration program showed that ICON FUV meets its design requirements and is ready to be launched on the ICON spacecraft. [less ▲]

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See detailImpact of dependency on the distribution of p-value
Ernst, Marie ULg; Swan, Yvik ULg

Conference (2017, August 01)

We study the impact of dependence assumptions on the distribution of p-values and quantiles for repeated testing on dependent data. This leads us to considering the general problem of the quality of a ... [more ▼]

We study the impact of dependence assumptions on the distribution of p-values and quantiles for repeated testing on dependent data. This leads us to considering the general problem of the quality of a binomial approximation to the distribution of a sum of dependent indicator variables. Whenever possible we use classical and adhoc versions of Stein’s method to provide tight bounds on classical probability distances. In many cases, however, the relevant expressions are intractable and we resort to empirical analysis by extensive simulations. We apply our findings to a realistic real-life scenario. [less ▲]

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See detailMolecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria
Kurmayer, Rainer; Sivonen, Kaarina; Wilmotte, Annick ULg et al

Book published by John Wiley and sons LTD - This edition first published 2017 (2017)

A guide to state-of-the-art molecular tools for monitoring and managing the toxigenicity of cyanobacteria Runaway climate change has made the monitoring and management of toxigenic organisms in the ... [more ▼]

A guide to state-of-the-art molecular tools for monitoring and managing the toxigenicity of cyanobacteria Runaway climate change has made the monitoring and management of toxigenic organisms in the world’s bodies of water more urgent than ever. In order to influence public policy regarding the detection and quantification of those organisms, it is incumbent upon scientists to clearly demonstrate to policy makers the increase of toxigenic cyanobacteria and the threats they pose. As molecular methods can handle many samples in short time, they are the most reliable, cost-effective tools currently available for tracking cyanotoxicity worldwide. This volume arms scientists with the tools they need to track toxigenicity in surface waters and food supplies and, hopefully, to develop new techniques for managing the spread of toxic cyanobacteria. This book offers the first comprehensive treatment of molecular tools for monitoring cyanotoxicity. Growing out of the findings of the landmark European Cooperation in Science and Technology Cyanobacteria project (CYANOCOST), it provides detailed, practical coverage of the full array of available molecular tools and protocols, from water sampling, nucleic acid extraction, and downstream analysis—including PCR and qPCR based methods—to genotyping (DGGE), diagnostic microarrays, and community characterization using next-gen sequencing techniques. [less ▲]

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See detailBioinformatic Processing of Amplicon Sequencing Datasets
Sweetlove, Maxime; Obbels, Dagmar; Verleyen, Elie et al

in Kurmayer, Rainer; Sivonen, Kaarina; Wilmotte, Annick (Eds.) et al Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria (2017)

Amplicon sequencing can be a very powerful approach for detecting toxic cyanobacteria or any other kind of microorganism during monitoring programs. However, owing to the huge size of next-generation ... [more ▼]

Amplicon sequencing can be a very powerful approach for detecting toxic cyanobacteria or any other kind of microorganism during monitoring programs. However, owing to the huge size of next-generation sequencing (NGS) datasets (up to several Gb), there is an obvious need for semi-automatic data processing and statistical analysis, as well as visualization of the patterns found. Importantly, raw NGS data contain errors, some of which are easily detected (e.g. too short or low-quality reads), while others remain hidden even after the most stringent quality controls (e.g. chimeras, contaminations, reads with large insertions or deletions, referred to as “indels”). As a consequence, NGS data need to be interpreted with caution, and bioinformatics analysis implementing poor error identification can easily lead to erroneous conclusions. Hence, a crucial step in the analysis of NGS data is the detection and removal of as many erroneous reads as possible. Moreover, bioinformatics involve additional preprocessing steps, including demultiplexing (i.e. grouping reads to samples according to the barcode sequence), deleting non-biological tags together with the adaptors and primer sequences, and removing chimeric sequences. In addition, the bioinformatics pipelines enable the quality-filtered sequences to be clustered into biologically relevant operational taxonomic units (OTUs), which form the basis of the statistical analysis, including the calculation of alpha- and beta-diversity. [less ▲]

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See detailTaxonomic Identification of Cyanobacteria by a Polyphasic Approach
Wilmotte, Annick ULg; Laughinghouse, Dail Haywood IV; Capelli, Camilla et al

in Kurmayer, Rainer; Sivonen, Kaarina; Wilmotte, Annick (Eds.) et al Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria (2017)

In this chapter, we shall discuss the criteria and methods to be adopted for the taxonomic identification and classification of cyanobacteria. This includes a brief introduction of the two Codes of ... [more ▼]

In this chapter, we shall discuss the criteria and methods to be adopted for the taxonomic identification and classification of cyanobacteria. This includes a brief introduction of the two Codes of Nomenclature ruling in parallel on the valid naming of these organisms. We shall then present the major steps important for cyanobacterial taxa identification and their nomenclature. These include: 1) determination of morphology by light microscopy; 2) genetic characterization by single and/or multilocus sequence typing; 3) the assignment of the organism to a taxonomic entity (genus, species, eco- and/or genotype within a species) by reference to, and phylogenetic analysis of, cyanobacterial nucleotide sequences available in public repositories. Ideally, these methods should be accompanied by the determination of other relevant properties (ultrastructural, physiological, biochemical, and ecological characteristics) that may help to define/redefine and circumscribe the cyanobacterial taxon under study. [less ▲]

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