ATOCA: an algorithm to treat order contamination. Application to the NIRISS SOSS mode

After a successful launch, the James Webb Space Telescope is preparing to undertake one of its principal missions, the characterization of the atmospheres of exoplanets. The Single Object Slitless Spectroscopy (SOSS) mode of the Near Infrared Imager and Slitless Spectrograph (NIRISS) is the only observing mode that has been specifically designed for this objective. It features a wide simultaneous spectral range (0.6--2.8\,\micron) through two spectral diffraction orders. However, due to mechanical constraints, these two orders overlap slightly over a short range, potentially introducing a ``contamination'' signal in the extracted spectrum. We show that for a typical box extraction, this contaminating signal amounts to 1\% or less over the 1.6--2.8\,\micron\ range (order 1), and up to 1\% over the 0.85--0.95\,\micron\ range (order 2). For observations of exoplanet atmospheres (transits, eclipses or phase curves) where only temporal variations in flux matter, the contamination signal typically biases the results by order of 1\% of the planetary atmosphere spectral features strength. To address this problem, we developed the Algorithm to Treat Order ContAmination (ATOCA). By constructing a linear model of each pixel on the detector, treating the underlying incident spectrum as a free variable, ATOCA is able to perform a simultaneous extraction of both orders. We show that, given appropriate estimates of the spatial trace profiles, the throughputs, the wavelength solutions, as well as the spectral resolution kernels for each order, it is possible to obtain an extracted spectrum accurate to within 10\,ppm over the full spectral range.Comment: Submitted to PASP. 22 pages, 12 figure

Characterizing the Near-infrared Spectra of Flares from TRAPPIST-1 During JWST Transit Spectroscopy Observations

We present the first analysis of JWST near-infrared spectroscopy of stellar flares from TRAPPIST-1 during transits of rocky exoplanets. Four flares were observed from 0.6--2.8 $\mu$m with NIRISS and 0.6--3.5 $\mu$m with NIRSpec during transits of TRAPPIST-1b, f, and g. We discover P$\alpha$ and Br$\beta$ line emission and characterize flare continuum at wavelengths from 1--3.5 $\mu$m for the first time. Observed lines include H$\alpha$, P$\alpha$-P$\epsilon$, Br$\beta$, He I $\lambda$0.7062$\mu$m, two Ca II infrared triplet (IRT) lines, and the He I IRT. We observe a reversed Paschen decrement from P$\alpha$-P$\gamma$ alongside changes in the light curve shapes of these lines. The continuum of all four flares is well-described by blackbody emission with an effective temperature below 5300 K, lower than temperatures typically observed at optical wavelengths. The 0.6--1 $\mu$m spectra were convolved with the TESS response, enabling us to measure the flare rate of TRAPPIST-1 in the TESS bandpass. We find flares of 10$^{30}$ erg large enough to impact transit spectra occur at a rate of 3.6$\substack{+2.1 \\ -1.3}$ flare d$^{-1}$, $\sim$10$\times$ higher than previous predictions from K2. We measure the amount of flare contamination at 2 $\mu$m for the TRAPPIST-1b and f transits to be 500$\pm$450 and 2100$\pm$400 ppm, respectively. We find up to 80% of flare contamination can be removed, with mitigation most effective from 1.0--2.4 $\mu$m. These results suggest transits affected by flares may still be useful for atmospheric characterization efforts.Comment: 29 pages, 17 figures, 3 tables, accepted to The Astrophysical Journa

Atmospheric Reconnaissance of TRAPPIST-1 b with JWST/NIRISS: Evidence for Strong Stellar Contamination in the Transmission Spectra

TRAPPIST-1 is a nearby system of seven Earth-sized, temperate, rocky exoplanets transiting a Jupiter-sized M8.5V star, ideally suited for in-depth atmospheric studies. Each TRAPPIST-1 planet has been observed in transmission both from space and from the ground, confidently rejecting cloud-free, hydrogen-rich atmospheres. Secondary eclipse observations of TRAPPIST-1 b with JWST/MIRI are consistent with little to no atmosphere given the lack of heat redistribution. Here we present the first transmission spectra of TRAPPIST-1 b obtained with JWST/NIRISS over two visits. The two transmission spectra show moderate to strong evidence of contamination from unocculted stellar heterogeneities, which dominates the signal in both visits. The transmission spectrum of the first visit is consistent with unocculted starspots and the second visit exhibits signatures of unocculted faculae. Fitting the stellar contamination and planetary atmosphere either sequentially or simultaneously, we confirm the absence of cloud-free hydrogen-rich atmospheres, but cannot assess the presence of secondary atmospheres. We find that the uncertainties associated with the lack of stellar model fidelity are one order of magnitude above the observation precision of 89 ppm (combining the two visits). Without affecting the conclusion regarding the atmosphere of TRAPPIST-1 b, this highlights an important caveat for future explorations, which calls for additional observations to characterize stellar heterogeneities empirically and/or theoretical works to improve model fidelity for such cool stars. This need is all the more justified as stellar contamination can affect the search for atmospheres around the outer, cooler TRAPPIST-1 planets for which transmission spectroscopy is currently the most efficient technique.Comment: 26 pages, 11 figures, accepted for publication in The Astrophysical Journal Letter

LC‐IMPACT: A regionalized life cycle damage assessment method

Life cycle impact assessment (LCIA) is a lively field of research, and data and models are continuously improved in terms of impact pathways covered, reliability, and spatial detail. However, many of these advancements are scattered throughout the scientific literature, making it difficult for practitioners to apply the new models. Here, we present the LC‐IMPACT method that provides characterization factors at the damage level for 11 impact categories related to three areas of protection (human health, ecosystem quality, natural resources). Human health damage is quantified as disability adjusted life years, damage to ecosystem quality as global species extinction equivalents (based on potentially disappeared fraction of species), and damage to mineral resources as kilogram of extra ore extracted. Seven of the impact categories include spatial differentiation at various levels of spatial scale. The influence of value choices related to the time horizon and the level of scientific evidence of the impacts considered is quantified with four distinct sets of characterization factors. We demonstrate the applicability of the proposed method with an illustrative life cycle assessment example of different fuel options in Europe (petrol or biofuel). Differences between generic and regionalized impacts vary up to two orders of magnitude for some of the selected impact categories, highlighting the importance of spatial detail in LCIA. This article met the requirements for a gold – gold JIE data openness badge described at http://jie.click/badges.info:eu-repo/semantics/publishedVersio

Awesome SOSS: Transmission Spectroscopy of WASP-96b with NIRISS/SOSS

The future is now - after its long-awaited launch in December 2021, JWST began science operations in July 2022 and is already revolutionizing exoplanet astronomy. The Early Release Observations (ERO) program was designed to provide the first images and spectra from JWST, covering a multitude of science cases and using multiple modes of each on-board instrument. Here, we present transmission spectroscopy observations of the hot-Saturn WASP-96b with the Single Object Slitless Spectroscopy (SOSS) mode of the Near Infrared Imager and Slitless Spectrograph, observed as part of the ERO program. As the SOSS mode presents some unique data reduction challenges, we provide an in-depth walk-through of the major steps necessary for the reduction of SOSS data: including background subtraction, correction of 1/f noise, and treatment of the trace order overlap. We furthermore offer potential routes to correct for field star contamination, which can occur due to the SOSS mode's slitless nature. By comparing our extracted transmission spectrum with grids of atmosphere models, we find an atmosphere metallicity between 1x and 5x solar, and a solar carbon-to-oxygen ratio. Moreover, our models indicate that no grey cloud deck is required to fit WASP-96b's transmission spectrum, but find evidence for a slope shortward of 0.9$\mu$m, which could either be caused by enhanced Rayleigh scattering or the red wing of a pressure-broadened Na feature. Our work demonstrates the unique capabilities of the SOSS mode for exoplanet transmission spectroscopy and presents a step-by-step reduction guide for this new and exciting instrument.Comment: MNRAS, in press. Updated to reflect published versio

Modern Approaches to the Monitoring of Biоdiversity (MAMBO)

EU policies, such as the EU biodiversity strategy 2030 and the Birds and Habitats Directives, demand unbiased, integrated and regularly updated biodiversity and ecosystem service data. However, efforts to monitor wildlife and other species groups are spatially and temporally fragmented, taxonomically biased, and lack integration in Europe. To bridge this gap, the MAMBO project will develop, test and implement enabling tools for monitoring conservation status and ecological requirements of species and habitats for which knowledge gaps still exist. MAMBO brings together the technical expertise of computer science, remote sensing, social science expertise on human-technology interactions, environmental economy, and citizen science, with the biological expertise on species, ecology, and conservation biology. MAMBO is built around stakeholder engagement and knowledge exchange (WP1) and the integration of new technology with existing research infrastructures (WP2). MAMBO will develop, test, and demonstrate new tools for monitoring species (WP3) and habitats (WP4) in a co-design process to create novel standards for species and habitat monitoring across the EU and beyond. MAMBO will work with stakeholders to identify user and policy needs for biodiversity monitoring and investigate the requirements for setting up a virtual lab to automate workflow deployment and efficient computing of the vast data streams (from on the ground sensors, and remote sensing) required to improve monitoring activities across Europe (WP4). Together with stakeholders, MAMBO will assess these new tools at demonstration sites distributed across Europe (WP5) to identify bottlenecks, analyze the cost-effectiveness of different tools, integrate data streams and upscale results (WP6). This will feed into the co-design of future, improved and more cost-effective monitoring schemes for species and habitats using novel technologies (WP7), and thus lead to a better management of protected sites and species

IMPACT World+: a globally regionalized life cycle impact assessment method

Purpose This paper addresses the need for a globally regionalized method for life cycle impact assessment (LCIA), integrating multiple state-of-the-art developments as well as damages on water and carbon areas of concern within a consistent LCIA framework. This method, named IMPACT World+, is the update of the IMPACT 2002+, LUCAS, and EDIP methods. This paper first presents the IMPACT World+ novelties and results and then analyzes the spatial variability for each regionalized impact category. Methods With IMPACT World+, we propose a midpoint-damage framework with four distinct complementary viewpoints to present an LCIA profile: (1) midpoint impacts, (2) damage impacts, (3) damages on human health, ecosystem quality, and resources & ecosystem service areas of protection, and (4) damages on water and carbon areas of concerns. Most of the regional impact categories have been spatially resolved and all the long-term impact categories have been subdivided between shorterterm damages (over the 100 years after the emission) and long-term damages. The IMPACT World+ method integrates developments in the following categories, all structured according to fate (or competition/scarcity), exposure, exposure response, and severity: (a) Complementary to the global warming potential (GWP100), the IPCC Global Temperature Potentials (GTP100) are used as a proxy for climate change long-term impacts at midpoint. At damage level, shorter-term damages (over the first 100 years after emission) are also differentiated from long-term damages. (b) Marine acidification impact is based on the same fate model as climate change, combined with the H+ concentration affecting 50% of the exposed species. (c) For mineral resources depletion impact, the material competition scarcity index is applied as a midpoint indicator. (d) Terrestrial and freshwater acidification impact assessment combines, at a resolution of 2° × 2.5° (latitude × longitude), global atmospheric source-deposition relationships with soil and water ecosystems’sensitivity. (e) Freshwater eutrophication impact is spatially assessed at a resolution grid of 0.5° × 0.5°, based on a global hydrological dataset. (f) Ecotoxicity and human toxicity impact are based on the parameterized version of USEtox for continents. We consider indoor emissions and differentiate the impacts of metals and persistent organic pollutants for the first 100 years from longer-term impacts. (g) Impacts on human health related to particulate matter formation are modeled using the USEtox regional archetypes to calculate intake fractions and epidemiologically derived exposure response factors. (h) Water consumption impacts are modeled using the consensus-based scarcity indicator AWARE as a proxy midpoint, whereas damages account for competition and adaptation capacity. (i) Impacts on ecosystem quality from land transformation and occupation are empirically characterized at the biome level. Results and discussion We analyze the magnitude of global potential damages for each impact indicator, based on an estimation of the total annual anthropogenic emissions and extractions at the global scale (i.e., Bdoing the LCA of the world^). Similarly with ReCiPe and IMPACT 2002+, IMPACT World+ finds that (a) climate change and impacts of particulate matter formation have a dominant contribution to global human health impacts whereas ionizing radiation, ozone layer depletion, and photochemical oxidant formation have a low contribution and (b) climate change and land use have a dominant contribution to global ecosystem quality impact. (c) New impact indicators introduced in IMPACT World+ and not considered in ReCiPe or IMPACT 2002+, in particular water consumption impacts on human health and the long-term impacts of marine acidification on ecosystem quality, are significant contributors to the overall global potential damage. According to the areas of concern version of IMPACT World+ applied to the total annual world emissions and extractions, damages on the water area of concern, carbon area of concern, and the remaining damages (not considered in those two areas of concern) are of the same order of magnitude, highlighting the need to consider all the impact categories. The spatial variability of human health impacts related to exposure to toxic substances and particulate matter is well reflected by using outdoor rural, outdoor urban, and indoor environment archetypes. For Bhuman toxicity cancer^ impact of substances emitted to continental air, the variability between continents is of two orders of magnitude, which is substantially lower than the 13 orders of magnitude total variability across substances. For impacts of water consumption on human health, the spatial variability across extraction locations is substantially higher than the variations between different water qualities. For regionalized impact categories affecting ecosystem quality (acidification, eutrophication, and land use), the characterization factors of half of the regions (25th to 75th percentiles) are within one to two orders of magnitude and the 95th percentile within three to four orders of magnitude, which is higher than the variability between substances, highlighting the relevance of regionalizing. Conclusions IMPACT World+ provides characterization factors within a consistent impact assessment framework for all regionalized impacts at four complementary resolutions: global default, continental, country, and native (i.e., original and non-aggregated) resolutions. IMPACT World+ enables the practitioner to parsimoniously account for spatial variability and to identify the elementary flows to be regionalized in priority to increase the discriminating power of LCA

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin