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1.	Abdellaoui, G., et al. (author) Meteor studies in the framework of the JEM-EUSO program 2017 In: Planetary and Space Science. - : Elsevier. - 0032-0633 .- 1873-5088. ; 143, s. 245-255 Journal article (peer-reviewed)abstract We summarize the state of the art of a program of UV observations from space of meteor phenomena, a secondary objective of the JEM-EUSO international collaboration. Our preliminary analysis indicates that JEM-EUSO, taking advantage of its large FOV and good sensitivity, should be able to detect meteors down to absolute magnitude close to 7. This means that JEM-EUSO should be able to record a statistically significant flux of meteors, including both sporadic ones, and events produced by different meteor streams. Being unaffected by adverse weather conditions, JEM-EUSO can also be a very important facility for the detection of bright meteors and fireballs, as these events can be detected even in conditions of very high sky background. In the case of bright events, moreover, exhibiting some persistence of the meteor train, preliminary simulations show that it should be possible to exploit the motion of the ISS itself and derive at least a rough 3D reconstruction of the meteor trajectory. Moreover, the observing strategy developed to detect meteors may also be applied to the detection of nuclearites, exotic particles whose existence has been suggested by some theoretical investigations. Nuclearites are expected to move at higher velocities than meteoroids, and to exhibit a wider range of possible trajectories, including particles moving upward after crossing the Earth. Some pilot studies, including the approved Mini-EUSO mission, a precursor of JEM-EUSO, are currently operational or in preparation. We are doing simulations to assess the performance of Mini-EUSO for meteor studies, while a few meteor events have been already detected using the ground-based facility EUSO-TA.
2.	Ederle, Joerg, et al. (author) Carotid artery stenting compared with endarterectomy in patients with symptomatic carotid stenosis (International Carotid Stenting Study): an interim analysis of a randomised controlled trial 2010 In: The Lancet. - 1474-547X. ; 375:9719, s. 985-997 Journal article (peer-reviewed)abstract Background Stents are an alternative treatment to carotid endarterectomy for symptomatic carotid stenosis, but previous trials have not established equivalent safety and efficacy. We compared the safety of carotid artery stenting with that of carotid endarterectomy. Methods The International Carotid Stenting Study (ICSS) is a multicentre, international, randomised controlled trial with blinded adjudication of outcomes. Patients with recently symptomatic carotid artery stenosis were randomly assigned in a 1:1 ratio to receive carotid artery stenting or carotid endarterectomy. Randomisation was by telephone call or fax to a central computerised service and was stratified by centre with minimisation for sex, age, contralateral occlusion, and side of the randomised artery. Patients and investigators were not masked to treatment assignment. Patients were followed up by independent clinicians not directly involved in delivering the randomised treatment. The primary outcome measure of the trial is the 3-year rate of fatal or disabling stroke in any territory, which has not been analysed yet. The main outcome measure for the interim safety analysis was the 120-day rate of stroke, death, or procedural myocardial infarction. Analysis was by intention to treat (ITT). This study is registered, number ISRCTN25337470. Findings The trial enrolled 1713 patients (stenting group, n=855; endarterectomy group, n=858). Two patients in the stenting group and one in the endarterectomy group withdrew immediately after randomisation, and were not included in the ITT analysis. Between randomisation and 120 days, there were 34 (Kaplan-Meier estimate 4.0%) events of disabling stroke or death in the stenting group compared with 27 (3.2%) events in the endarterectomy group (hazard ratio [HR] 1.28, 95% CI 0.77-2.11). The incidence of stroke, death, or procedural myocardial infarction was 8.5% in the stenting group compared with 5.2% in the endarterectomy group (72 vs 44 events; HR 1.69, 1.16-2.45, p=0.006), Risks of any stroke (65 vs 35 events; HR 1.92, 1.27-2.89) and all-cause death (19 vs seven events; HR 2.76, 1.16-6.56) were higher in the stenting group than in the endarterectomy group. Three procedural myocardial infarctions were recorded in the stenting group, all of which were fatal, compared with four, all non-fatal, in the endarterectomy group. There was one event of cranial nerve palsy in the stenting group compared with 45 in the endarterectomy group. There were also fewer haematomas of any severity in the stenting group than in the endarterectomy group (31 vs 50 events; p=0.0197). Interpretation Completion of long-term follow-up is needed to establish the efficacy of carotid artery stenting compared with endarterectomy. In the meantime, carotid endarterectomy should remain the treatment of choice for patients suitable for surgery.
3.	Abdellaoui, G., et al. (author) First observations of speed of light tracks by a fluorescence detector looking down on the atmosphere 2018 In: Journal of Instrumentation. - : IOP PUBLISHING LTD. - 1748-0221. ; 13 Journal article (peer-reviewed)abstract EUSO-Balloon is a pathfinder mission for the Extreme Universe Space Observatory onboard the Japanese Experiment Module (JEM-EUSO). It was launched on the moonless night of the 25(th) of August 2014 from Timmins, Canada. The flight ended successfully after maintaining the target altitude of 38 km for five hours. One part of the mission was a 2.5 hour underflight using a helicopter equipped with three UV light sources (LED, xenon flasher and laser) to perform an inflight calibration and examine the detectors capability to measure tracks moving at the speed of light. We describe the helicopter laser system and details of the underflight as well as how the laser tracks were recorded and found in the data. These are the first recorded laser tracks measured from a fluorescence detector looking down on the atmosphere. Finally, we present a first reconstruction of the direction of the laser tracks relative to the detector.
4.	Tinetti, Giovanna, et al. (author) The EChO science case 2015 In: Experimental astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 40:2-3, s. 329-391 Journal article (peer-reviewed)abstract The discovery of almost two thousand exoplanets has revealed an unexpectedly diverse planet population. We see gas giants in few-day orbits, whole multi-planet systems within the orbit of Mercury, and new populations of planets with masses between that of the Earth and Neptune-all unknown in the Solar System. Observations to date have shown that our Solar System is certainly not representative of the general population of planets in our Milky Way. The key science questions that urgently need addressing are therefore: What are exoplanets made of? Why are planets as they are? How do planetary systems work and what causes the exceptional diversity observed as compared to the Solar System? The EChO (Exoplanet Characterisation Observatory) space mission was conceived to take up the challenge to explain this diversity in terms of formation, evolution, internal structure and planet and atmospheric composition. This requires in-depth spectroscopic knowledge of the atmospheres of a large and well-defined planet sample for which precise physical, chemical and dynamical information can be obtained. In order to fulfil this ambitious scientific program, EChO was designed as a dedicated survey mission for transit and eclipse spectroscopy capable of observing a large, diverse and well-defined planet sample within its 4-year mission lifetime. The transit and eclipse spectroscopy method, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allows us to measure atmospheric signals from the planet at levels of at least 10(-4) relative to the star. This can only be achieved in conjunction with a carefully designed stable payload and satellite platform. It is also necessary to provide broad instantaneous wavelength coverage to detect as many molecular species as possible, to probe the thermal structure of the planetary atmospheres and to correct for the contaminating effects of the stellar photosphere. This requires wavelength coverage of at least 0.55 to 11 mu m with a goal of covering from 0.4 to 16 mu m. Only modest spectral resolving power is needed, with R similar to 300 for wavelengths less than 5 mu m and R similar to 30 for wavelengths greater than this. The transit spectroscopy technique means that no spatial resolution is required. A telescope collecting area of about 1 m(2) is sufficiently large to achieve the necessary spectro-photometric precision: for the Phase A study a 1.13 m(2) telescope, diffraction limited at 3 mu m has been adopted. Placing the satellite at L2 provides a cold and stable thermal environment as well as a large field of regard to allow efficient time-critical observation of targets randomly distributed over the sky. EChO has been conceived to achieve a single goal: exoplanet spectroscopy. The spectral coverage and signal-to-noise to be achieved by EChO, thanks to its high stability and dedicated design, would be a game changer by allowing atmospheric composition to be measured with unparalleled exactness: at least a factor 10 more precise and a factor 10 to 1000 more accurate than current observations. This would enable the detection of molecular abundances three orders of magnitude lower than currently possible and a fourfold increase from the handful of molecules detected to date. Combining these data with estimates of planetary bulk compositions from accurate measurements of their radii and masses would allow degeneracies associated with planetary interior modelling to be broken, giving unique insight into the interior structure and elemental abundances of these alien worlds. EChO would allow scientists to study exoplanets both as a population and as individuals. The mission can target super-Earths, Neptune-like, and Jupiter-like planets, in the very hot to temperate zones (planet temperatures of 300-3000 K) of F to M-type host stars. The EChO core science would be delivered by a three-tier survey. The EChO Chemical Census: This is a broad survey of a few-hundred exoplanets, which allows us to explore the spectroscopic and chemical diversity of the exoplanet population as a whole. The EChO Origin: This is a deep survey of a subsample of tens of exoplanets for which significantly higher signal to noise and spectral resolution spectra can be obtained to explain the origin of the exoplanet diversity (such as formation mechanisms, chemical processes, atmospheric escape). The EChO Rosetta Stones: This is an ultra-high accuracy survey targeting a subsample of select exoplanets. These will be the bright "benchmark" cases for which a large number of measurements would be taken to explore temporal variations, and to obtain two and three dimensional spatial information on the atmospheric conditions through eclipse-mapping techniques. If EChO were launched today, the exoplanets currently observed are sufficient to provide a large and diverse sample. The Chemical Census survey would consist of > 160 exoplanets with a range of planetary sizes, temperatures, orbital parameters and stellar host properties. Additionally, over the next 10 years, several new ground- and space-based transit photometric surveys and missions will come on-line (e.g. NGTS, CHEOPS, TESS, PLATO), which will specifically focus on finding bright, nearby systems. The current rapid rate of discovery would allow the target list to be further optimised in the years prior to EChO's launch and enable the atmospheric characterisation of hundreds of planets.
5.	Bonnefoy, M., et al. (author) First light of the VLT planet finder SPHERE IV. Physical and chemical properties of the planets around HR8799 2016 In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 587 Journal article (peer-reviewed)abstract Context. The system of four planets discovered around the intermediate-mass star HR8799 offers a unique opportunity to test planet formation theories at large orbital radii and to probe the physics and chemistry at play in the atmospheres of self-luminous young (similar to 30 Myr) planets. We recently obtained new photometry of the four planets and low-resolution (R similar to 30) spectra of HR8799 d and e with the SPHERE instrument (Paper III).Aims. In this paper (Paper IV), we aim to use these spectra and available photometry to determine how they compare to known objects, what the planet physical properties are, and how their atmospheres work.Methods. We compare the available spectra, photometry, and spectral energy distribution (SED) of the planets to field dwarfs and young companions. In addition, we use the extinction from corundum, silicate (enstatite and forsterite), or iron grains likely to form in the atmosphere of the planets to try to better understand empirically the peculiarity of their spectrophotometric properties. To conclude, we use three sets of atmospheric models (BT-SETTL14, Cloud-AE60, Exo-REM) to determine which ingredients are critically needed in the models to represent the SED of the objects, and to constrain their atmospheric parameters (T-eff, log g, M/H).Results. We find that HR8799d and e properties are well reproduced by those of L6-L8 dusty dwarfs discovered in the field, among which some are candidate members of young nearby associations. No known object reproduces well the properties of planets b and c. Nevertheless, we find that the spectra and WISE photometry of peculiar and/or young early-T dwarfs reddened by submicron grains made of corundum, iron, enstatite, or forsterite successfully reproduce the SED of these planets. Our analysis confirms that only the Exo-REM models with thick clouds fit (within 2 sigma) the whole set of spectrophotometric datapoints available for HR8799 d and e for T-eff = 1200 K, log g in the range 3.0-4.5, and M/H = +0.5. The models still fail to reproduce the SED of HR8799c and b. The determination of the metallicity, log g, and cloud thickness are degenerate.Conclusions. Our empirical analysis and atmospheric modelling show that an enhanced content in dust and decreased CIA of H-2 is certainly responsible for the deviation of the properties of the planet with respect to field dwarfs. The analysis suggests in addition that HR8799c and b have later spectral types than the two other planets, and therefore could both have lower masses.
6.	Langlois, M., et al. (author) The SPHERE infrared survey for exoplanets (SHINE) : II. Observations, data reduction and analysis, detection performances, and initial results 2021 In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 651 Journal article (peer-reviewed)abstract Context. In recent decades, direct imaging has confirmed the existence of substellar companions (exoplanets or brown dwarfs) on wide orbits (>10 au) around their host stars. In striving to understand their formation and evolution mechanisms, in 2015 we initiated the SPHERE infrared survey for exoplanets (SHINE), a systematic direct imaging survey of young, nearby stars that is targeted at exploring their demographics.Aims. We aim to detect and characterize the population of giant planets and brown dwarfs beyond the snow line around young, nearby stars. Combined with the survey completeness, our observations offer the opportunity to constrain the statistical properties (occurrence, mass and orbital distributions, dependency on the stellar mass) of these young giant planets.Methods. In this study, we present the observing and data analysis strategy, the ranking process of the detected candidates, and the survey performances for a subsample of 150 stars that are representative of the full SHINE sample. Observations were conducted in a homogeneous way between February 2015 and February 2017 with the dedicated ground-based VLT/SPHERE instrument equipped with the IFS integral field spectrograph and the IRDIS dual-band imager, covering a spectral range between 0.9 and 2.3 μm. We used coronographic, angular, and spectral differential imaging techniques to achieve the best detection performances for this study, down to the planetary mass regime.Results. We processed, in a uniform manner, more than 300 SHINE observations and datasets to assess the survey typical sensitivity as a function of the host star and of the observing conditions. The median detection performance reached 5σ-contrasts of 13 mag at 200 mas and 14.2 mag at 800 mas with the IFS (YJ and YJH bands), and of 11.8 mag at 200 mas, 13.1 mag at 800 mas, and 15.8 mag at 3 as with IRDIS in H band, delivering one of the deepest sensitivity surveys thus far for young, nearby stars. A total of sixteen substellar companions were imaged in this first part of SHINE: seven brown dwarf companions and ten planetary-mass companions.These include two new discoveries, HIP 65426 b and HIP 64892 B, but not the planets around PDS70 that had not been originally selected for the SHINE core sample. A total of 1483 candidates were detected, mainly in the large field of view that characterizes IRDIS. The color-magnitude diagrams, low-resolution spectrum (when available with IFS), and follow-up observations enabled us to identify the nature (background contaminant or comoving companion) of about 86% of our subsample. The remaining cases are often connected to crowded-field follow-up observations that were missing. Finally, even though SHINE was not initially designed for disk searches, we imaged twelve circumstellar disks, including three new detections around the HIP 73145, HIP 86598, and HD 106906 systems.Conclusions. Nowadays, direct imaging provides a unique opportunity to probe the outer part of exoplanetary systems beyond 10 au to explore planetary architectures, as highlighted by the discoveries of: one new exoplanet, one new brown dwarf companion, and three new debris disks during this early phase of SHINE. It also offers the opportunity to explore and revisit the physical and orbital properties of these young, giant planets and brown dwarf companions (relative position, photometry, and low-resolution spectrum in near-infrared, predicted masses, and contrast in order to search for additional companions). Finally, these results highlight the importance of finalizing the SHINE systematic observation of about 500 young, nearby stars for a full exploration of their outer part to explore the demographics of young giant planets beyond 10 au and to identify the most interesting systems for the next generation of high-contrast imagers on very large and extremely large telescopes.
7.	Fresard, Laure, et al. (author) Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts 2019 In: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919 Journal article (peer-reviewed)abstract It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
8.	Bonnefoy, M., et al. (author) The GJ 504 system revisited Combining interferometric, radial velocity, and high contrast imaging data 2018 In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 618 Journal article (peer-reviewed)abstract Context. The G-type star GJ504A is known to host a 3-35 M-Jup companion whose temperature, mass, and projected separation all contribute to making it a test case for planet formation theories and atmospheric models of giant planets and light brown dwarfs. Aims. We aim at revisiting the system age, architecture, and companion physical and chemical properties using new complementary interferometric, radial-velocity, and high-contrast imaging data. Methods. We used the CHARA interferometer to measure GJ504A's angular diameter and obtained an estimation of its radius in combination with the HIPPARCOS parallax. The radius was compared to evolutionary tracks to infer a new independent age range for the system. We collected dual imaging data with IRDIS on VLT/SPHERE to sample the near-infrared (1.02-2.25 mu m) spectral energy distribution (SED) of the companion. The SED was compared to five independent grids of atmospheric models (petitCODE, Exo-REM, BT-SETTL, Morley et al., and ATMO) to infer the atmospheric parameters of GJ 504b and evaluate model-to-model systematic errors. In addition, we used a specific model grid exploring the effect of different C/O ratios. Contrast limits from 2011 to 2017 were combined with radial velocity data of the host star through the MESS2 tool to define upper limits on the mass of additional companions in the system from 0.01 to 100 au. We used an MCMC fitting tool to constrain the companion's orbital parameters based on the measured astrometry, and dedicated formation models to investigate its origin. Results. We report a radius of 1.35 +/- 0.04 R-circle dot for GJ504A. The radius yields isochronal ages of 21 +/- 2 Myr or 4.0 +/- 1.8 Gyr for the system and line-of-sight stellar rotation axis inclination of 162.4(-4.3)(+3.8) degrees or 18.6(-3.8)(+4.3) degrees. We re-detect the companion in the Y2, Y3, J3, H2, and K1 dual-band images. The complete 1-4 mu m SED shape of GJ504b is best reproduced by T8-T9.5 objects with intermediate ages (<= 1.5Gyr), and/or unusual dusty atmospheres and/or super-solar metallicities. All atmospheric models yield T-eff = 550 +/- 50 K for GJ504b and point toward a low surface gravity (3.5-4.0 dex). The accuracy on the metallicity value is limited by model-to-model systematics; it is not degenerate with the C/O ratio. We derive log L/L-circle dot = 6.15 +/- 0.15 dex for the companion from the empirical analysis and spectral synthesis. The luminosity and T-eff yield masses of M = 1.3(-0.3)(+0.6) M-Jup and M = 23(-9)(+10) M-Jup for the young and old age ranges, respectively. The semi-major axis (sma) is above 27.8 au and the eccentricity is lower than 0.55. The posterior on GJ 504b's orbital inclination suggests a misalignment with the rotation axis of GJ 504A. We exclude additional objects (90% prob.) more massive than 2.5 and 30 M-Jup with semi-major axes in the range 0.01-80 au for the young and old isochronal ages, respectively. Conclusions. The mass and semi-major axis of GJ 504b are marginally compatible with a formation by disk-instability if the system is 4 Gyr old. The companion is in the envelope of the population of planets synthesized with our core-accretion model. Additional deep imaging and spectroscopic data with SPHERE and JWST should help to confirm the possible spin-orbit misalignment and refine the estimates on the companion temperature, luminosity, and atmospheric composition.
9.	Lopez-Garcia, SC, et al. (author) Treatment and long-term outcome in primary distal renal tubular acidosis 2019 In: Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association. - : Oxford University Press (OUP). - 1460-2385. ; 34:6, s. 981-991 Journal article (peer-reviewed)
10.	Warrington, N M, et al. (author) Maternal and fetal genetic contribution to gestational weight gain. 2018 In: International journal of obesity. - : Springer Science and Business Media LLC. - 1476-5497 .- 0307-0565. ; 42:4, s. 775-84 Journal article (peer-reviewed)abstract Clinical recommendations to limit gestational weight gain (GWG) imply high GWG is causally related to adverse outcomes in mother or offspring, but GWG is the sum of several inter-related complex phenotypes (maternal fat deposition and vascular expansion, placenta, amniotic fluid and fetal growth). Understanding the genetic contribution to GWG could help clarify the potential effect of its different components on maternal and offspring health. Here we explore the genetic contribution to total, early and late GWG.A genome-wide association study was used to identify maternal and fetal variants contributing to GWG in up to 10543 mothers and 16317 offspring of European origin, with replication in 10660 mothers and 7561 offspring. Additional analyses determined the proportion of variability in GWG from maternal and fetal common genetic variants and the overlap of established genome-wide significant variants for phenotypes relevant to GWG (for example, maternal body mass index (BMI) and glucose, birth weight).Approximately 20% of the variability in GWG was tagged by common maternal genetic variants, and the fetal genome made a surprisingly minor contribution to explain variation in GWG. Variants near the pregnancy-specific beta-1 glycoprotein 5 (PSG5) gene reached genome-wide significance (P=1.71 × 10-8) for total GWG in the offspring genome, but did not replicate. Some established variants associated with increased BMI, fasting glucose and type 2 diabetes were associated with lower early, and higher later GWG. Maternal variants related to higher systolic blood pressure were related to lower late GWG. Established maternal and fetal birth weight variants were largely unrelated to GWG.We found a modest contribution of maternal common variants to GWG and some overlap of maternal BMI, glucose and type 2 diabetes variants with GWG. These findings suggest that associations between GWG and later offspring/maternal outcomes may be due to the relationship of maternal BMI and diabetes with GWG.International Journal of Obesity advance online publication, 21 November 2017; doi:10.1038/ijo.2017.248.
11.	Sordo, Rosanna, et al. (author) Stellar libraries for Gaia 2011 In: Journal of Physics, Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 328:Conference 1, s. 012006- Journal article (peer-reviewed)abstract Gaia will observe up to a billion stellar sources. Automated algorithms are under development to derive the atmospheric parameters of all observed spectra, from low resolution optical spectra alone or in synergy with high resolution spectra in the near-IR Ca II triplet region. To do so, a large database of state-of-the-art stellar libraries has been produced for the Gaia community, computed using different codes optimized for specific purposes. The choice to use different spectral codes in different regions of the H-R diagram raises the problem of the coherence of the different spectra, specifically in the transition zones. We present a comparison between the libraries from the point of view of spectra simulations for training the Gaia algorithms. We also present the implementation of these libraries into a Simple Stellar Population code.
12.	Tinetti, G., et al. (author) A chemical survey of exoplanets with ARIEL 2018 In: Experimental Astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 46:1, s. 135-209 Journal article (peer-reviewed)abstract Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.
13.	Vogel, Jacob W., et al. (author) Four distinct trajectories of tau deposition identified in Alzheimer’s disease 2021 In: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:5, s. 871-881 Journal article (peer-reviewed)abstract Alzheimer’s disease (AD) is characterized by the spread of tau pathology throughout the cerebral cortex. This spreading pattern was thought to be fairly consistent across individuals, although recent work has demonstrated substantial variability in the population with AD. Using tau-positron emission tomography scans from 1,612 individuals, we identified 4 distinct spatiotemporal trajectories of tau pathology, ranging in prevalence from 18 to 33%. We replicated previously described limbic-predominant and medial temporal lobe-sparing patterns, while also discovering posterior and lateral temporal patterns resembling atypical clinical variants of AD. These ‘subtypes’ were stable during longitudinal follow-up and were replicated in a separate sample using a different radiotracer. The subtypes presented with distinct demographic and cognitive profiles and differing longitudinal outcomes. Additionally, network diffusion models implied that pathology originates and spreads through distinct corticolimbic networks in the different subtypes. Together, our results suggest that variation in tau pathology is common and systematic, perhaps warranting a re-examination of the notion of ‘typical AD’ and a revisiting of tau pathological staging. © 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.
14.	Zhou, XP, et al. (author) Non-coding variability at the APOE locus contributes to the Alzheimer's risk 2019 In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 3310- Journal article (peer-reviewed)abstract Alzheimer’s disease (AD) is a leading cause of mortality in the elderly. While the coding change of APOE-ε4 is a key risk factor for late-onset AD and has been believed to be the only risk factor in the APOE locus, it does not fully explain the risk effect conferred by the locus. Here, we report the identification of AD causal variants in PVRL2 and APOC1 regions in proximity to APOE and define common risk haplotypes independent of APOE-ε4 coding change. These risk haplotypes are associated with changes of AD-related endophenotypes including cognitive performance, and altered expression of APOE and its nearby genes in the human brain and blood. High-throughput genome-wide chromosome conformation capture analysis further supports the roles of these risk haplotypes in modulating chromatin states and gene expression in the brain. Our findings provide compelling evidence for additional risk factors in the APOE locus that contribute to AD pathogenesis.
15.	Formiga-Cruz, M, et al. (author) Evaluation of potential indicators of viral contamination in shellfish and their applicability to diverse geographical areas. 2003 In: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 69:3, s. 1556-63 Journal article (peer-reviewed)abstract The distribution of the concentration of potential indicators of fecal viral pollution in shellfish was analyzed under diverse conditions over 18 months in diverse geographical areas. These microorganisms have been evaluated in relation to contamination by human viral pathogens detected in parallel in the analyzed shellfish samples. Thus, significant shellfish-growing areas from diverse countries in the north and south of Europe (Greece, Spain, Sweden, and the United Kingdom) were defined and studied by analyzing different physicochemical parameters in the water and the levels of Escherichia coli, F-specific RNA bacteriophages, and phages infecting Bacteroides fragilis strain RYC2056 in the shellfish produced, before and after depuration treatments. A total of 475 shellfish samples were studied, and the results were statistically analyzed. According to statistical analysis, the presence of human viruses seems to be related to the presence of all potential indicators in the heavily contaminated areas, where E. coli would probably be suitable as a fecal indicator. The F-RNA phages, which are present in higher numbers in Northern Europe, seem to be significantly related to the presence of viral contamination in shellfish, with a very weak predictive value for hepatitis A virus, human adenovirus, and enterovirus and a stronger one for Norwalk-like virus. However, it is important to note that shellfish produced in A or clean B areas can sporadically contain human viruses even in the absence of E. coli or F-RNA phages. The data presented here will be useful in defining microbiological parameters for improving the sanitary control of shellfish consumed raw or barely cooked.
16.	Muller, X, et al. (author) Defining Benchmarks in Liver Transplantation: A Multicenter Outcome Analysis Determining Best Achievable Results 2018 In: Annals of surgery. - 1528-1140. ; 267:3, s. 419-425 Journal article (peer-reviewed)
17.	Muller, X, et al. (author) Novel Benchmarking in a Large Multicentric Cohort of "Ideal" Liver Transplantation to Quantify Increased Risk of Re-transplantation of the Liver 2017 In: TRANSPLANTATION. - 0041-1337. ; 101:5, s. 58-59 Conference paper (other academic/artistic)
18.	Rodet, L., et al. (author) Dynamical masses of M-dwarf binaries in young moving groups I. The case of TWA22 and GJ2060 2018 In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 618 Journal article (peer-reviewed)abstract Context. Evolutionary models are widely used to infer the mass of stars, brown dwarfs, and giant planets. Their predictions are thought to be less reliable at young ages (<200 Myr) and in the low-mass regime (< 1 M-circle dot). GJ 2060AB and TWA22AB are two rare astrometric M-dwarf binaries, respectively members of the AB Doradus (AB Dor) and Beta Pictoris (beta Pic) moving groups. As their dynamical mass can be measured to within a few years, they can be used to calibrate the evolutionary tracks and set new constraints on the age of young moving groups.Aims. We provide the first dynamical mass measurement of GJ 2060 and a refined measurement of the total mass of TWA22. We also characterize the atmospheric properties of the individual components of GJ 2060 that can be used as inputs to the evolutionary models.Methods. We used NaCo and SPHERE observations at VLT and archival Keck/NIRC2 data to complement the astrometric monitoring of the binaries. We combined the astrometry with new HARPS radial velocities (RVs) and FEROS RVs of GJ 2060. We used a Markov chain MonteCarlo (MCMC) module to estimate posteriors on the orbital parameters and dynamical masses of GJ 2060AB and TWA22AB from the astrometry and RVs. Complementary data obtained with the integral field spectrograph VLT /SINFONI were gathered to extract the individual near-infrared (1.1-2.5 mu m) medium-resolution (R similar to 1500 2000) spectra of GJ 2060A and B. We compared the spectra to those of known objects and to grids of BT-SETTL model spectra to infer the spectral type, bolometric luminosities, and temperatures of those objects.Results. We find a total mass of 0 : 18 +/- 0 : 02 M-circle dot for TWA22, which is in good agreement with model predictions at the age of the fi Pic moving group. We obtain a total mass of 1 : 09 +/- 0 : 10 M-circle dot for GJ 2060. We estimate a spectral type of M1 +/- 0.5, L/L-circle dot = -1.20 +/- 0.05 dex, and T-eff = 3700 +/- 100 K for GJ 2060 A. The B component is a M3 +/- 0 : 5 dwarf with L/L-circle dot = 1.63 +/- 0.05 dex and T-eff = 3400 +/- 100 K. The dynamical mass of GJ 2060AB is inconsistent with the most recent models predictions (BCAH15, PARSEC) for an AB Dor age in the range 50-150 Myr. It is 10%-20% (1-2 sigma, depending on the assumed age) above the model's predictions, corresponding to an underestimation of 0.10-0.20 M fi. Coevality suggests a young age for the system (similar to 50 Myr) according to most evolutionary models.Conclusions. TWA22 validates the predictions of recent evolutionary tracks at similar to 20 Myr. On the other hand, we evidence a 1-2 sigma mismatch between the predicted and observed mass of GJ 2060 AB. This slight departure may indicate that one of the stars hosts a tight companion. Alternatively, this would confirm the model's tendency to underestimate the mass of young low-mass stars.
19.	Solé Navais, Pol, et al. (author) Genetic effects on the timing of parturition and links to fetal birth weight. 2023 In: Nature genetics. - 1546-1718. ; 55:4, s. 559-567 Journal article (peer-reviewed)abstract The timing of parturition is crucial for neonatal survival and infant health. Yet, its genetic basis remains largely unresolved. We present a maternal genome-wide meta-analysis of gestational duration (n=195,555), identifying 22 associated loci (24 independent variants) and an enrichment in genes differentially expressed during labor. A meta-analysis of preterm delivery (18,797 cases, 260,246 controls) revealed six associated loci and large genetic similarities with gestational duration. Analysis of the parental transmitted and nontransmitted alleles (n=136,833) shows that 15 of the gestational duration genetic variants act through the maternal genome, whereas 7 act both through the maternal and fetal genomes and 2 act only via the fetal genome. Finally, the maternal effects on gestational duration show signs of antagonistic pleiotropy with the fetal effects on birth weight: maternal alleles that increase gestational duration have negative fetal effects on birth weight. The present study provides insights into the genetic effects on the timing of parturition and the complex maternal-fetal relationship between gestational duration and birth weight.
20.	Tyrrell, Jessica, et al. (author) Genetic Evidence for Causal Relationships Between Maternal Obesity-Related Traits and Birth Weight. 2016 In: JAMA. - : American Medical Association (AMA). - 1538-3598 .- 0098-7484. ; 315:11, s. 1129-40 Journal article (peer-reviewed)abstract Neonates born to overweight or obese women are larger and at higher risk of birth complications. Many maternal obesity-related traits are observationally associated with birth weight, but the causal nature of these associations is uncertain.To test for genetic evidence of causal associations of maternal body mass index (BMI) and related traits with birth weight.Mendelian randomization to test whether maternal BMI and obesity-related traits are potentially causally related to offspring birth weight. Data from 30,487 women in 18 studies were analyzed. Participants were of European ancestry from population- or community-based studies in Europe, North America, or Australia and were part of the Early Growth Genetics Consortium. Live, term, singleton offspring born between 1929 and 2013 were included.Genetic scores for BMI, fasting glucose level, type 2 diabetes, systolic blood pressure (SBP), triglyceride level, high-density lipoprotein cholesterol (HDL-C) level, vitamin D status, and adiponectin level.Offspring birth weight from 18 studies.Among the 30,487 newborns the mean birth weight in the various cohorts ranged from 3325 g to 3679 g. The maternal genetic score for BMI was associated with a 2-g (95% CI, 0 to 3 g) higher offspring birth weight per maternal BMI-raising allele (P=.008). The maternal genetic scores for fasting glucose and SBP were also associated with birth weight with effect sizes of 8 g (95% CI, 6 to 10 g) per glucose-raising allele (P=7×10(-14)) and -4 g (95% CI, -6 to -2 g) per SBP-raising allele (P=1×10(-5)), respectively. A 1-SD (≈4 points) genetically higher maternal BMI was associated with a 55-g higher offspring birth weight (95% CI, 17 to 93 g). A 1-SD (≈7.2 mg/dL) genetically higher maternal fasting glucose concentration was associated with 114-g higher offspring birth weight (95% CI, 80 to 147 g). However, a 1-SD (≈10 mm Hg) genetically higher maternal SBP was associated with a 208-g lower offspring birth weight (95% CI, -394 to -21 g). For BMI and fasting glucose, genetic associations were consistent with the observational associations, but for systolic blood pressure, the genetic and observational associations were in opposite directions.In this mendelian randomization study, genetically elevated maternal BMI and blood glucose levels were potentially causally associated with higher offspring birth weight, whereas genetically elevated maternal SBP was potentially causally related to lower birth weight. If replicated, these findings may have implications for counseling and managing pregnancies to avoid adverse weight-related birth outcomes.
21.	Allard, Bert, 1945-, et al. (author) Shale gas extraction : issues of particular relevance to the European Union 2014 Reports (other academic/artistic)
22.	Allard, F, et al. (author) Model atmospheres and spectra: The role of dust 2003 In: Proceedings of the International Astronomical Union (Brown Dwarfs). - 0074-1809. - 158381132X ; 211, s. 325-332 Conference paper (peer-reviewed)abstract Brown dwarf atmospheres form molecules, then high temperature condensates (corundum, titanates, silicates, and iron compounds), and then low temperature condensates (ices) as they cool down over time. These produce large opacities which govern entirely their spectral energy distribution. Just as it is important to know molecular opacities (TiO, H2O, CH4, etc.) with accuracy, it is imperative to understand the interplay of processes (e.g. condensation, sedimentation, coagulation, convection) that determines the radial and size distribution of grains. Limiting case models have shown that young, hot brown (L) dwarfs form dust mostly in equilibrium, while at much cooler stages (late T dwarfs) all high temperature condensates have sedimented out of their photospheres. But this process is gradual and all intermediate classes of brown dwarfs can partly be understood in terms of partial sedimentation of dust. With new models accounting for these processes, we describe the effects they may have upon brown dwarf spectral properties.
23.	Baraffe, I, et al. (author) Atmosphere models for very low mass stars, brown dwarfs and exoplanets 1997 In: FUNDAMENTAL STELLAR PROPERTIES: THE INTERACTION BETWEEN OBSERVATION AND THEORY. - : KLUWER ACADEMIC PUBL. - 0074-1809. ; :189, s. 227-233 Journal article (other academic/artistic)
24.	Beaumont, Robin N, et al. (author) Genome-wide association study of offspring birth weight in 86,577 women identifies five novel loci and highlights maternal genetic effects that are independent of fetal genetics. 2018 In: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 1460-2083 .- 0964-6906. ; 27:4, s. 742-756 Journal article (peer-reviewed)abstract Genome-wide association studies (GWAS) of birth weight have focused on fetal genetics, while relatively little is known about the role of maternal genetic variation. We aimed to identify maternal genetic variants associated with birth weight that could highlight potentially relevant maternal determinants of fetal growth. We meta-analysed data on up to 8.7 million SNPs in up to 86,577 women of European descent from the Early Growth Genetics (EGG) Consortium and the UK Biobank. We used structural equation modelling (SEM) and analyses of mother-child pairs to quantify the separate maternal and fetal genetic effects. Maternal SNPs at 10 loci (MTNR1B, HMGA2, SH2B3, KCNAB1, L3MBTL3, GCK, EBF1, TCF7L2, ACTL9, CYP3A7) were associated with offspring birth weight at P<5x10-8. In SEM analyses, at least 7 of the 10 associations were consistent with effects of the maternal genotype acting via the intrauterine environment, rather than via effects of shared alleles with the fetus. Variants, or correlated proxies, at many of the loci had been previously associated with adult traits, including fasting glucose (MTNR1B, GCK and TCF7L2) and sex hormone levels (CYP3A7), and one (EBF1) with gestational duration. The identified associations indicate genetic effects on maternal glucose, cytochrome P450 activity and gestational duration, and potentially on maternal blood pressure and immune function, are relevant for fetal growth. Further characterization of these associations in mechanistic and causal analyses will enhance understanding of the potentially modifiable maternal determinants of fetal growth, with the goal of reducing the morbidity and mortality associated with low and high birth weights.
25.	Beaumont, Robin N, et al. (author) Genome-wide association study of placental weight identifies distinct and shared genetic influences between placental and fetal growth. 2023 In: Nature genetics. - 1546-1718 .- 1061-4036. ; 55:11, s. 1807-19 Journal article (peer-reviewed)abstract A well-functioning placenta is essential for fetal and maternal health throughout pregnancy. Using placental weight as a proxy for placental growth, we report genome-wide association analyses in the fetal (n=65,405), maternal (n=61,228) and paternal (n=52,392) genomes, yielding 40 independent association signals. Twenty-six signals are classified as fetal, four maternal and three fetal and maternal. A maternal parent-of-origin effect is seen near KCNQ1. Genetic correlation and colocalization analyses reveal overlap with birth weight genetics, but 12 loci are classified as predominantly or only affecting placental weight, with connections to placental development and morphology, and transport of antibodies and amino acids. Mendelian randomization analyses indicate that fetal genetically mediated higher placental weight is causally associated with preeclampsia risk and shorter gestational duration. Moreover, these analyses support the role of fetal insulin in regulating placental weight, providing a key link between fetal and placental growth.
26.	Dalton, A. S., et al. (author) An updated radiocarbon-based ice margin chronology for the last deglaciation of the North American Ice Sheet Complex 2020 In: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791. ; 234 Journal article (peer-reviewed)abstract The North American Ice Sheet Complex (NAISC; consisting of the Laurentide, Cordilleran and Innuitian ice sheets) was the largest ice mass to repeatedly grow and decay in the Northern Hemisphere during the Quaternary. Understanding its pattern of retreat following the Last Glacial Maximum is critical for studying many facets of the Late Quaternary, including ice sheet behaviour, the evolution of Holocene landscapes, sea level, atmospheric circulation, and the peopling of the Americas. Currently, the most up-to-date and authoritative margin chronology for the entire ice sheet complex is featured in two publications (Geological Survey of Canada Open File 1574 [Dyke et al., 2003]; 'Quaternary Glaciations - Extent and Chronology, Part II' [Dyke, 2004]). These often-cited datasets track ice margin recession in 36 time slices spanning 18 ka to 1 ka (all ages in uncalibrated radiocarbon years) using a combination of geomorphology, stratigraphy and radiocarbon dating. However, by virtue of being over 15 years old, the ice margin chronology requires updating to reflect new work and important revisions. This paper updates the aforementioned 36 ice margin maps to reflect new data from regional studies. We also update the original radiocarbon dataset from the 2003/2004 papers with 1541 new ages to reflect work up to and including 2018. A major revision is made to the 18 ka ice margin, where Banks and Eglinton islands (once considered to be glacial refugia) are now shown to be fully glaciated. Our updated 18 ka ice sheet increased in areal extent from 17.81 to 18.37 million km(2), which is an increase of 3.1% in spatial coverage of the NAISC at that time. Elsewhere, we also summarize, region-by-region, significant changes to the deglaciation sequence. This paper integrates new information provided by regional experts and radiocarbon data into the deglaciation sequence while maintaining consistency with the original ice margin positions of Dyke et al. (2003) and Dyke (2004) where new information is lacking; this is a pragmatic solution to satisfy the needs of a Quaternary research community that requires up-to-date knowledge of the pattern of ice margin recession of what was once the world's largest ice mass. The 36 updated isochrones are available in PDF and shapefile format, together with a spreadsheet of the expanded radiocarbon dataset (n = 5195 ages) and estimates of uncertainty for each interval. (C) 2020 Elsevier Ltd. All rights reserved.
27.	Edin, Alicia, 1985- (author) Improved diagnosis and prediction of community-acquired pneumonia 2018 Doctoral thesis (other academic/artistic)abstract Community-acquired pneumonia (CAP) is a major cause of morbidity and mortality worldwide. Although there is wide variation in the microbial etiology, CAP may manifest with similar symptoms, making institution of proper treatment challenging. Therefore, etiological diagnosis is important to ensure that correct treatment and necessary infection control measures are instituted. This provides a challenge for conventional microbial diagnostic methods, typically based on culture and direct antigen tests. Moreover, existing molecular biomarkers have poor prognostic value. Few studies have investigated the global metabolic response during infection and virtually nothing is known about early responses after the start of antimicrobial treatment. The aim of this work was to improve diagnostic and predictive methods for CAP.In paper I, a qPCR panel targeting 15 pathogens known to cause CAP was developed and evaluated. It combined identification of bacterial pathogens and viruses in the same diagnostic platform. The method proved to be robust and the results consistent with those obtained by standard methods. The panel approach, compared to conventional, selective diagnostics, detected a larger number of pathogens. In Paper II, whole blood samples from 65 patients with bacteremic sepsis were analyzed for metabolite profiles. Forty-nine patients with symptoms of sepsis, but later attributed to other diagnoses, were matched according to age and sex and served as a control group. Six metabolites were identified, all of which predicted growth of bacteria in blood culture. One of the metabolites, myristic acid, alone predicted bacteremic sepsis with a sensitivity of 100% and a specificity of 95%. Paper III and IV were based on a clinical study enrolling 35 patients with suspected CAP in need of hospital care. The aim was to study the metabolic response during the early phase of acute infection. The qPCR panel developed in Paper I was used to obtain the microbial etiological diagnosis. Paper IV focused on the global metabolic response and highlighted the dynamics of changes in major metabolic pathways during early recovery. A specific metabolite pattern for M. pneumoniae etiology was found. Four metabolites accurately predicted all but one patient as either M. pneumoniae etiology or not. Paper III looked at phospholipid levels during the first 48 hours after hospital admission. It was found that all major phospholipid species, especially the lysophosphatidyl-cholines, were pronouncedly decreased during acute infection. Levels started to increase the day after admission, reaching statistical significance at 48 hours. Paper II-IV showed that metabolomics might be used to study a number of different aspects of infection, such as etiology, disease progress and recovery. Knowledge of the metabolic profiles of patients may not only be utilized for biomarker discovery, as proposed in this work, but also for the future development of targeted therapies and supportive treatment.
28.	Formiga-Cruz, M, et al. (author) Evaluation of potential indicators of viral contamination in shellfish and their applicability to diverse geographical areas 2003 In: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 69:3, s. 1556-1563 Journal article (peer-reviewed)abstract The distribution of the concentration of potential indicators of fecal viral pollution in shellfish was analyzed under diverse conditions over 18 months in diverse geographical areas. These microorganisms have been evaluated in relation to contamination by human viral pathogens detected in parallel in the analyzed shellfish samples. Thus, significant shellfish-growing areas from diverse countries in the north and south of Europe (Greece, Spain, Sweden, and the United Kingdom) were defined and studied by analyzing different physicochemical parameters in the water and the levels of Escherichia coli, F-specific RNA bacteriophages, and phages infecting Bacteroides fragilis strain RYC2056 in the shellfish produced, before and after depuration treatments. A total of 475 shellfish samples were studied, and the results were statistically analyzed. According to statistical analysis, the presence of human viruses seems to be related to the presence of all potential indicators in the heavily contaminated areas, where E. coli would probably be suitable as a fecal indicator. The F-RNA phages, which are present in higher numbers in Northern Europe, seem to be significantly related to the presence of viral contamination in shellfish, with a very weak predictive value for hepatitis A virus, human adenovirus, and enterovirus and a stronger one for Norwalk-like virus. However, it is important to note that shellfish produced in A or clean B areas can sporadically contain human viruses even in the absence of E. coli or F-RNA phages. The data presented here will be useful in defining microbiological parameters for improving the sanitary control of shellfish consumed raw or barely cooked.
29.	Jones, HRA, et al. (author) Status of the physics of substellar objects project 2005 In: Astronomical Notes - Astronomische Nachrichten. - : Wiley. - 0004-6337. ; 326:10, s. 920-924 Journal article (peer-reviewed)abstract A full understanding of the properties of substellar objects is one of the major challenges facing astrophysics. Since their discovery in 1995, hundreds of brown dwarfs and extrasolar planets have been discovered. While these discoveries have enabled important comparisons with theory, observational progress has been much more rapid than the theoretical understanding of cool atmospheres. The reliable determination of mass, abundances, gravities and temperatures is not yet possible. The key problem is that substellar objects emit their observable radiation in the infrared region of the spectrum where our knowledge of atomic, molecular and line broadening data is poor. Here we report on the status of our PoSSO (Physics of SubStellar Objects) project. In order to understand brown dwarfs and extrasolar planets increasing more like those in our solar system, we are studying a wide range of processes. Here we give an update on the project and sketch an outline of atoms, molecules and processes requiring study.
30.	Kadalayil, L, et al. (author) Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude 2023 In: Clinical epigenetics. - 1868-7083. ; 15:1, s. 148- Journal article (peer-reviewed)
31.	Kucinskas, Arunas, et al. (author) Broad-band photometric colors and effective temperature calibrations for late-type giants - I. Z=0.02 2005 In: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 442:1, s. 281-308 Journal article (peer-reviewed)abstract We present new synthetic broad-band photometric colors for late-type giants based on synthetic spectra calculated with the PHOENIX model atmosphere code. The grid covers effective temperatures T-eff = 3000... 5000 K, gravities log g = - 0.5... + 3.5, and metallicities [M/H] = + 0.5... - 4.0. We show that individual broad-band photometric colors are strongly affected by model parameters such as molecular opacities, gravity, microturbulent velocity, and stellar mass. Our exploratory 3D modeling of a prototypical late-type giant shows that convection has a noticeable effect on the photometric colors too, as it alters significantly both the vertical and horizontal thermal structures in the outer atmosphere. The differences between colors calculated with full 3D hydrodynamical and 1D model atmospheres are significant (e.g.,. (V- K) similar to 0.2 mag), translating into offsets in effective temperature of up to similar to 70 K. For a sample of 74 late-type giants in the Solar neighborhood, with interferometric effective temperatures and broad-band photometry available in the literature, we compare observed colors with a new PHOENIX grid of synthetic photometric colors, as well as with photometric colors calculated with the MARCS and ATLAS model atmosphere codes. We find good agreement of the new synthetic colors with observations and published T-eff-color and color - color relations, especially in the T-eff ( V - K), T-eff-(J - K) and (J - K) -(V - K) planes. Deviations from the observed trends in the T-eff-color planes are generally within +/- 100 K for T-eff = 3500 to 4800 K. Synthetic colors calculated with different stellar atmosphere models agree to +/- 100 K, within a large range of effective temperatures and gravities. The comparison of the observed and synthetic spectra of late-type giants shows that discrepancies result from the differences both in the strengths of various spectral lines/bands ( especially those of molecular bands, such as TiO, H2O, CO) and the continuum level. Finally, we derive several new T-eff - log g - color relations for late-type giants at solar-metallicity (valid for T-eff = 3500 to 4800 K), based both on the observed effective temperatures and colors of the nearby giants, and synthetic colors produced with PHOENIX, MARCS and ATLAS model atmospheres.
32.	Kucinskas, Arunas, et al. (author) Broad-band photometric colors and effective temperature calibrations for late-type giants - II. Z <0.02 2006 In: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 452:3, s. 1021-1038 Journal article (peer-reviewed)abstract We investigate the effects of metallicity on the broad-band photometric colors of late-type giants, and make a comparison of synthetic colors with observed photometric properties of late-type giants over a wide range of effective temperatures (T-eff = 3500- 4800K) and gravities (log g = 0.0-2.5), at [M/H] = -1.0 and -2.0. The influence of metallicity on the synthetic photometric colors is small at effective temperatures above similar to 3800K, but the effects grow larger at lower T-eff,T- due to the changing effciency of molecule formation which reduces molecular opacities at lower [M/H]. To make a detailed comparison of the synthetic and observed photometric colors of late type giants in the T-eff-color and color-color planes (which is done at two metallicities, [M/H] = -1.0 and -2.0), we derive a set of new T-eff-log g-color relations based on synthetic photometric colors, at [M/H] = -0.5, -1.0, -1.5, and -2.0. These relations are based on the T-eff- log g scales that we derive employing literature data for 178 late-type giants in 10 Galactic globular clusters (with metallicities of the individual stars between [M/H] = -0.7 and -2.5), and synthetic colors produced with the PHOENIX, MARCS and ATLAS stellar atmosphere codes. Combined with the T-eff- log g-color relations at [M/H] = 0.0 (Kucinskas et al. 2005), the set of new relations covers metallicities [M/H] = 0.0... -2.0 ([M/H] = 0.5), effective temperatures T-eff = 3500... 4800 K (T-eff = 100K), and gravities log g = - 0.5... 3.0. The new T-eff- log g-color relations are in good agreement with published T-eff-color relations based on observed properties of late-type giants, both at [M/H] = -1.0 and -2.0. The differences in all T-eff- color planes are typically well within similar to 100K. We find, however, that effective temperatures predicted by the scales based on synthetic colors tend to be slightly higher than those resulting from the T-eff- color relations based on observations, with the offsets up to similar to 100 K. This is clearly seen both at [M/H] = -1.0 and -2.0, especially in the T-eff-(B - V) and T-eff-(V - K) planes. The consistency between T-eff- log g-color scales based on synthetic colors calculated with different stellar atmosphere codes is very good, with typical differences being well within. Delta T-eff similar to 70 K at [M/H] = - 1.0 and. T-eff similar to 40 K at [M/H] = -2.0.
33.	Kucinskas, A., et al. (author) Photometric colors of late-type giants: theory versus observations 2006 In: Proceedings of the International Astronomical Union. ; 232, s. 276-277 Conference paper (peer-reviewed)
34.	Kupers, LK, et al. (author) Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight 2019 In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 1893- Journal article (peer-reviewed)abstract Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from −183 to 178 grams per 10% increase in methylation (PBonferroni < 1.06 x 10−7). In additional analyses in 7,278 participants, <1.3% of birthweight-associated differential methylation is also observed in childhood and adolescence, but not adulthood. Birthweight-related CpGs overlap with some Bonferroni-significant CpGs that were previously reported to be related to maternal smoking (55/914, p = 6.12 x 10−74) and BMI in pregnancy (3/914, p = 1.13x10−3), but not with those related to folate levels in pregnancy. Whether the associations that we observe are causal or explained by confounding or fetal growth influencing DNA methylation (i.e. reverse causality) requires further research.
35.	Lifvergren, Thomas, et al. (author) Mercury speciation and mobility in two contaminated soils Other publication (other academic/artistic)
36.	Lindahl, Lina, 1984, et al. (author) Alcohols enhance the rate of acetic acid diffusion in S. cerevisiae: biophysical mechanisms and implications for acetic acid tolerance 2018 In: Microbial Cell. - : Shared Science Publishers OG. - 2311-2638. ; 5:1, s. 42-55 Journal article (peer-reviewed)abstract Microbial cell factories with the ability to maintain high productivity in the presence of weak organic acids, such as acetic acid, are required in many industrial processes. For example, fermentation media derived from lignocellulosic biomass are rich in acetic acid and other weak acids. The rate of diffusional entry of acetic acid is one parameter determining the ability of microorganisms to tolerance the acid. The present study demonstrates that the rate of acetic acid diffusion in S. cerevisiae is strongly affected by the alcohols ethanol and n-butanol. Ethanol of 40 g/L and n-butanol of 8 g/L both caused a 65% increase in the rate of acetic acid diffusion, and higher alcohol concentrations caused even greater increases. Molecular dynamics simulations of membrane dynamics in the presence of alcohols demonstrated that the partitioning of alcohols to the head group region of the lipid bilayer causes a considerable increase in the membrane area, together with reduced membrane thickness and lipid order. These changes in physiochemical membrane properties lead to an increased number of water molecules in the membrane interior, providing biophysical mechanisms for the alcohol-induced increase in acetic acid diffusion rate. nbutanol affected S. cerevisiae and the cell membrane properties at lower concentrations than ethanol, due to greater and deeper partitioning in the membrane. This study demonstrates that the rate of acetic acid diffusion can be strongly affected by compounds that partition into the cell membrane, and highlights the need for considering interaction effects between compounds in the design of microbial processes.
37.	Ludwig, Hans-Günter, et al. (author) Energy transport, overshoot, and mixing in the atmospheres of M-type main- and pre-main-sequence objects 2006 In: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 459:2, s. 599-612 Journal article (peer-reviewed)abstract We constructed hydrodynamical model atmospheres for mid M-type main-,as well as pre-main-sequence (PMS) objects. Despite the complex chemistry encountered in these cool atmospheres a reasonably accurate representation of the radiative transfer is possible, even in the context of time-dependent and three-dimensional models. The models provide detailed information about the morphology of M-type granulation and statistical properties of the convective surface flows. In particular, we determined the efficiency of the convective energy transport, and the efficiency of mixing by convective overshoot. The convective transport efficiency was expressed in terms of an equivalent mixing-length parameter alpha(MLT) in the formulation of mixing-length theory (MLT) given by Mihalas (1978). aMLT amounts to values around approximate to 2 for matching the entropy of the deep, adiabatically stratified regions of the convective envelope, and lies between 2.5 and 3.0 for matching the thermal structure of the deep photosphere. For current spectral analysis of PMS objects this implies that MLT models based on alpha(MLT) = 2.0 overestimate the effective temperature by 100 K and surface gravities by 0.25 dex. The average thermal structure of the formally convectively stable layers is little affected by convective overshoot and wave heating, i.e., stays close to radiative equilibrium conditions. Our models suggest that the rate of mixing by convective overshoot declines exponentially with geometrical distance to the Schwarzschild stability boundary. It increases at given effective temperature with decreasing gravitational acceleration.
38.	Ludwig, Hans-Günter, et al. (author) Numerical simulations of surface convection in a late M-dwarf 2002 In: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 395:1, s. 99-115 Journal article (peer-reviewed)abstract Based on detailed 2D and 3D numerical radiation-hydrodynamics (RHD)simulations of time-dependent compressible convection, we have studiedthe dynamics and thermal structure of the convective surface layers of aprototypical late-type M-dwarf (Teffapprox 2800 K, log g=5.0,solar chemical composition). The RHD models predict stellar granulationqualitatively similar to the familiar solar pattern. Quantitatively, thegranular cells show a convective turn-over time scale of ~100 s, and ahorizontal scale of 80 km; the relative intensity contrast of thegranular pattern amounts to 1.1%, and root-mean-square verticalvelocities reach 240 m s-1 at maximum. Deviations fromradiative equilibrium in the higher, formally convectively stableatmospheric layers are found to be insignificant allowing a reliablemodeling of the atmosphere with 1D standard model atmospheres. Amixing-length parameter of alphaMLT = 2.1 provides the bestrepresentation of the average thermal structure of the RHD modelatmosphere while alternative values are found when fitting theasymptotic entropy encountered in deeper layers of the stellar envelope(alphaMLT = 1.5), or when matching the vertical velocity(alphaMLT = 3.5). The close correspondence between RHD andstandard model atmospheres implies that presently existing discrepanciesbetween observed and predicted stellar colors in the M-dwarf regimecannot be traced back to an inadequate treatment of convection in the 1Dstandard models. The RHD models predict a modest extension of theconvectively mixed region beyond the formal Schwarzschild stabilityboundary which provides hints for the distribution of dust grains incooler (brown dwarf) atmospheres.
39.	Merid, Simon Kebede, et al. (author) Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age 2020 In: Genome Medicine. - Stockholm : Karolinska Institutet, Dept of Clinical Science and Education, Södersjukhuset. - 1756-994X. Journal article (peer-reviewed)abstract Background: Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods: We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung. Results: We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10- 7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. Conclusions: We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.
40.	Peletier, R. F., et al. (author) Stars and gas in the inner parts of galaxies seen in SAURON integral field observations 2007 In: New Astronomy Reviews. - : Elsevier BV. - 1387-6473. ; 51:1-2, s. 29-33 Journal article (peer-reviewed)abstract We give two examples of spiral galaxies that show non-circular gas motions in the inner kiloparsecs, from SAURON integral field spectroscopy. We use harmonic decomposition of the velocity field of the ionized gas to study the underlying mass distribution, employing linear theory. The higher order harmonic terms and the main kinematic features of the observed data are consistent with an analytically constructed simple bar model. We also present maps of a number of strong absorption lines in M 100, derive simple stellar populations and correlate them with features in the gas kinematics.
41.	Rajpurohit, A. S., et al. (author) The very low mass multiple system LHS 1070. A testbed for model atmospheres for the lower end of the main sequence 2012 In: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 545 Journal article (peer-reviewed)abstract Context. LHS 1070 is a nearby multiple system of low mass stars. It is an important source of information for probing the low mass end of the main sequence, down to the hydrogen-burning limit. The primary of the system is a mid-M dwarf and two components are late-M to early L dwarfs, at the star-brown dwarf transition. Hence LHS 1070 is a valuable object to understand the onset of dust formation in cool stellar atmospheres. Aims. This work aims at determining the fundamental stellar parameters of LHS 1070 and to test recent model atmospheres: BT-Dusty, BT-Settl, DRIFT, and MARCS models. Methods. Unlike in previous studies, we have performed a chi(2)-minimization comparing well calibrated optical and infrared (IR) spectra with recent cool star synthetic spectra leading to the determination of the physical stellar parameters T-eff, radius, and log g for each of the three components of LHS 1070. Results. With exception of the MARCS models which do not include dust formation, the models are able to reproduce the observations and describe the main features of the visible to IR spectra. This is consistent with the fact that dust formation prevails in the B and C component atmospheres. The parameters obtained with the DRIFT models confirm the values determined in earlier studies. But important differences between models are observed, where the MARCS model is too bright in the H and K bands, and the BT-Settl and BT-Dusty models systematically yield up to 100 K higher T-eff in the case of the B and C components. This confirms a trend for models without, or with less efficient cloud formation, to predict higher T-eff than models richer in dust (DRIFT). Even models including cloud physics however still produce slightly too bright J band flux, showing as too blue J - K colors. The onset of dust formation remains therefore a particularly challenging regime to understand.
42.	Sharp, GC, et al. (author) Maternal BMI at the start of pregnancy and offspring epigenome-wide DNA methylation: findings from the pregnancy and childhood epigenetics (PACE) consortium 2017 In: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 0964-6906. ; 26:20, s. 4067-4085 Journal article (peer-reviewed)
43.	Stenman, U H, et al. (author) Summary report of the TD-3 workshop: characterization of 83 antibodies against prostate-specific antigen 1999 In: Tumor Biology. - : Springer Science and Business Media LLC. - 1423-0380 .- 1010-4283. ; 20:Suppl. 1, s. 1-12 Journal article (peer-reviewed)abstract Twelve research groups participated in the ISOBM TD-3 Workshop in which the reactivity and specificity of 83 antibodies against prostate-specific antigen (PSA) were investigated. Using a variety of techniques including cross-inhibition assays, Western blotting, BIAcore, immunoradiometric assays and immunohistochemistry, the antibodies were categorized into six major groups which formed the basis for mapping onto two- and three-dimensional (2-D and 3-D) models of PSA. The overall findings of the TD-3 Workshop are summarized in this report. In agreement with all participating groups, three main antigenic domains were identified: free PSA-specific epitopes located in or close to amino acids 86-91; discontinuous epitopes specific for PSA without human kallikrein (hK2) cross-reactivity located at or close to amino acids 158-163; and continuous or linear epitopes shared between PSA and hK2 located close to amino acids 3-11. In addition, several minor and partly overlapping domains were also identified. Clearly, the characterization of antibodies from this workshop and the location of their epitopes on the 3-D model of PSA illustrate the importance of selecting appropriate antibody pairs for use in immunoassays. It is hoped that these findings and the epitope nomenclature described in this TD-3 Workshop are used as a standard for future evaluation of anti-PSA antibodies.
44.	Strand, M., et al. (author) 2- 4,5-Difluoro-2-(2-Fluorobenzoylamino)-Benzoylamino Benzoic Acid, an Antiviral Compound with Activity against Acyclovir-Resistant Isolates of Herpes Simplex Virus Types 1 and 2 2012 In: Antimicrobial Agents and Chemotherapy. - : American Society for Microbiology. - 0066-4804 .- 1098-6596. ; 56:11, s. 5735-5743 Journal article (peer-reviewed)abstract Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are responsible for lifelong latent infections in humans, with periods of viral reactivation associated with recurring ulcerations in the orofacial and genital tracts. In immunosuppressed patients and neonates, HSV infections are associated with severe morbidity and, in some cases, even mortality. Today, acyclovir is the standard therapy for the management of HSV infections. However, the need for novel antiviral agents is apparent, since HSV isolates resistant to acyclovir therapy are frequently isolated in immunosuppressed patients. In this study, we assessed the anti-HSV activity of the antiadenoviral compounds 2-[2-(2- benzoylamino)-benzoylamino]benzoic acid (benzavir-1) and 2-[4,5-difluoro-2-(2-fluorobenzoylamino)-benzoylamino]benzoic acid (benzavir-2) on HSV-1 and HSV-2. Both compounds were active against both viruses. Importantly, benzavir-2 had potency similar to that of acyclovir against both HSV types, and it was active against clinical acyclovir-resistant HSV isolates.
45.	Vallenari, A., et al. (author) Synthetic stellar libraries and SSP simulations in the Gaia Era 2009 In: Proceedings of the International Astronomical Union. ; , s. 444-445 Conference paper (peer-reviewed)abstract The Gaia mission will obtain accurate positions, parallaxes and proper motions for 109 object all over the sky. In addition, it will collect low resolution spectroscopy in the optical range for ∼ 109 objects, stars, galaxies, and QSOs. Parameters of those objects are expected to be part of the final Catalog. Complete and up-to-date libraries of synthetic stellar spectra are needed to train the algorithms to classify this huge amount of data. Here we focus on the use of the synthetic libraries of spectra calculated by the Gaia community to derive grids of Single Stellar Populations as building blocks of population synthesis models. © International Astronomical Union 2010.
46.	Wang, Hsiu-Wen, et al. (author) Multi-scale characterization of pore evolution in a combustion metamorphic complex, Hatrurim basin, Israel: Combining (ultra) small-angle neutron scattering and image analysis 2013 In: Geochimica et Cosmochimica Acta. - : Elsevier BV. - 0016-7037. ; 121, s. 339-362 Journal article (peer-reviewed)abstract Backscattered scanning electron micrograph and ultra small- and small-angle neutron scattering data have been combined to provide statistically meaningful data on the pore/grain structure and pore evolution of combustion metamorphic complexes from the Hatrurim basin, Israel. Three processes, anti-sintering roughening, alteration of protolith (dehydration, decarbonation, and oxidation) and crystallization of high-temperature minerals, occurred simultaneously, leading to significant changes in observed pore/grain structures. Pore structures in the protoliths, and in low- and high-grade metamorphic rocks show surface (D-s) and mass (D-m) pore fractal geometries with gradual increases in both Ds and Dm values as a function of metamorphic grade. This suggests that increases in pore volume and formation of less branching pore networks are accompanied by a roughening of pore/grain interfaces. Additionally, pore evolution during combustion metamorphism is also characterized by reduced contributions from small-scale pores to the cumulative porosity in the high-grade rocks. At high temperatures, small-scale pores may be preferentially closed by the formation of high-temperature minerals, producing a rougher morphology with increasing temperature. Alternatively, large-scale pores may develop at the expense of small-scale pores. These observations (pore fractal geometry and cumulative porosity) indicate that the evolution of pore/grain structures is correlated with the growth of high-temperature phases and is a consequence of the energy balance between pore/grain surface energy and energy arising from heterogeneous phase contacts. The apparent pore volume density further suggests that the localized time/temperature development of the high-grade Hatrurim rocks is not simply an extension of that of the low-grade rocks. The former likely represents the "hot spots (burning foci)" in the overall metamorphic terrain while the latter may represent contact aureoles. (c) 2013 Elsevier Ltd. All rights reserved.
47.	Yeung, Edwina, et al. (author) Maternal age is related to offspring DNA methylation : a meta-analysis of results from the pace consortium 2024 In: Aging Cell. - : John Wiley & Sons. - 1474-9718 .- 1474-9726. Journal article (peer-reviewed)abstract Worldwide trends to delay childbearing have increased parental ages at birth. Older parental age may harm offspring health, but mechanisms remain unclear. Alterations in offspring DNA methylation (DNAm) patterns could play a role as aging has been associated with methylation changes in gametes of older individuals. We meta-analyzed epigenome-wide associations of parental age with offspring blood DNAm of over 9500 newborns and 2000 children (5–10 years old) from the Pregnancy and Childhood Epigenetics consortium. In newborns, we identified 33 CpG sites in 13 loci with DNAm associated with maternal age (PFDR < 0.05). Eight of these CpGs were located near/in the MTNR1B gene, coding for a melatonin receptor. Regional analysis identified them together as a differentially methylated region consisting of 9 CpGs in/near MTNR1B, at which higher DNAm was associated with greater maternal age (PFDR = 6.92 × 10−8) in newborns. In childhood blood samples, these differences in blood DNAm of MTNR1B CpGs were nominally significant (p < 0.05) and retained the same positive direction, suggesting persistence of associations. Maternal age was also positively associated with higher DNA methylation at three CpGs in RTEL1-TNFRSF6B at birth (PFDR < 0.05) and nominally in childhood (p < 0.0001). Of the remaining 10 CpGs also persistent in childhood, methylation at cg26709300 in YPEL3/BOLA2B in external data was associated with expression of ITGAL, an immune regulator. While further study is needed to establish causality, particularly due to the small effect sizes observed, our results potentially support offspring DNAm as a mechanism underlying associations of maternal age with child health.

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