Validity of a self-administered food frequency questionnaire (FFQ) and its generalizability to the estimation of dietary folate intake in Japan

BACKGROUND: In an epidemiological study, it is essential to test the validity of the food frequency questionnaire (FFQ) for its ability to estimate dietary intake. The objectives of our study were to 1) validate a FFQ for estimating folate intake, and to identify the foods that contribute to inter-individual variation of folate intake in the Japanese population. METHODS: Validity of the FFQ was evaluated using 28-day weighed dietary records (DRs) as gold standard in the two groups independently. In the group for which the FFQ was developed, validity was evaluated by Spearman's correlation coefficients (CCs), and linear regression analysis was used to identify foods with large inter-individual variation. The cumulative mean intake of these foods was compared with total intake estimated by the DR. The external validity of the FFQ and intake from foods on the same list were evaluated in the other group to verify generalizability. Subjects were a subsample from the Japan Public Health Center-based prospective Study who volunteered to participate in the FFQ validation study. RESULTS: CCs for the internal validity of the FFQ were 0.49 for men and 0.29 and women, while CCs for external validity were 0.33 for men and 0.42 for women. CCs for cumulative folate intake from 33 foods selected by regression analysis were also applicable to an external population. CONCLUSION: Our FFQ was valid for and generalizable to the estimation of folate intake. Foods identified as predictors of inter-individual variation in folate intake were also generalizable in Japanese populations. The FFQ with 138 foods was valid for the estimation of folate intake, while that with 33 foods might be useful for estimating inter-individual variation and ranking of individual folate intake

Identification of carbon dioxide in an exoplanet atmosphere

Carbon dioxide (CO2) is a key chemical species that is found in a wide range of planetary atmospheres. In the context of exoplanets, CO2 is an indicator of the metal enrichment (that is, elements heavier than helium, also called ‘metallicity’)1–3, and thus the formation processes of the primary atmospheres of hot gas giants4–6. It is also one of the most promising species to detect in the secondary atmospheres of terrestrial exoplanets7–9. Previous photometric measurements of transiting planets with the Spitzer Space Telescope have given hints of the presence of CO2, but have not yielded definitive detections owing to the lack of unambiguous spectroscopic identification10–12. Here we present the detection of CO2 in the atmosphere of the gas giant exoplanet WASP-39b from transmission spectroscopy observations obtained with JWST as part of the Early Release Science programme13,14. The data used in this study span 3.0–5.5 micrometres in wavelength and show a prominent CO2 absorption feature at 4.3 micrometres (26-sigma significance). The overall spectrum is well matched by one-dimensional, ten-times solar metallicity models that assume radiative–convective–thermochemical equilibrium and have moderate cloud opacity. These models predict that the atmosphere should have water, carbon monoxide and hydrogen sulfide in addition to CO2, but little methane. Furthermore, we also tentatively detect a small absorption feature near 4.0 micrometres that is not reproduced by these models

Early Release Science of the Exoplanet WASP-39b with JWST NIRSpec G395H

Measuring the abundances of carbon and oxygen in exoplanet atmospheres is considered a crucial avenue for unlocking the formation and evolution of exoplanetary systems. Access to an exoplanet's chemical inventory requires high-precision observations, often inferred from individual molecular detections with low-resolution space-based and high-resolution ground-based facilities. Here we report the medium-resolution (R$\sim$600) transmission spectrum of an exoplanet atmosphere between 3-5 $\mu$m covering multiple absorption features for the Saturn-mass exoplanet WASP-39b, obtained with JWST NIRSpec G395H. Our observations achieve 1.46x photon precision, providing an average transit depth uncertainty of 221 ppm per spectroscopic bin, and present minimal impacts from systematic effects. We detect significant absorption from CO$_2$ (28.5$\sigma$) and H$_2$O (21.5$\sigma$), and identify SO$_2$ as the source of absorption at 4.1 $\mu$m (4.8$\sigma$). Best-fit atmospheric models range between 3 and 10x solar metallicity, with sub-solar to solar C/O ratios. These results, including the detection of SO$_2$, underscore the importance of characterising the chemistry in exoplanet atmospheres, and showcase NIRSpec G395H as an excellent mode for time series observations over this critical wavelength range.Comment: 44 pages, 11 figures, 3 tables. Resubmitted after revision to Natur

Early Release Science of the exoplanet WASP-39b with JWST NIRSpec PRISM

Transmission spectroscopy of exoplanets has revealed signatures of water vapor, aerosols, and alkali metals in a few dozen exoplanet atmospheres. However, these previous inferences with the Hubble and Spitzer Space Telescopes were hindered by the observations' relatively narrow wavelength range and spectral resolving power, which precluded the unambiguous identification of other chemical species$-$in particular the primary carbon-bearing molecules. Here we report a broad-wavelength 0.5-5.5 $\mu$m atmospheric transmission spectrum of WASP-39 b, a 1200 K, roughly Saturn-mass, Jupiter-radius exoplanet, measured with JWST NIRSpec's PRISM mode as part of the JWST Transiting Exoplanet Community Early Release Science Team program. We robustly detect multiple chemical species at high significance, including Na (19$\sigma$), H$_2$O (33$\sigma$), CO$_2$ (28$\sigma$), and CO (7$\sigma$). The non-detection of CH$_4$, combined with a strong CO$_2$ feature, favours atmospheric models with a super-solar atmospheric metallicity. An unanticipated absorption feature at 4$\mu$m is best explained by SO$_2$ (2.7$\sigma$), which could be a tracer of atmospheric photochemistry. These observations demonstrate JWST's sensitivity to a rich diversity of exoplanet compositions and chemical processes.Comment: 41 pages, 4 main figures, 10 extended data figures, 4 tables. Under review in Natur

Early Release Science of the exoplanet WASP-39b with JWST NIRCam

Measuring the metallicity and carbon-to-oxygen (C/O) ratio in exoplanet atmospheres is a fundamental step towards constraining the dominant chemical processes at work and, if in equilibrium, revealing planet formation histories. Transmission spectroscopy provides the necessary means by constraining the abundances of oxygen- and carbon-bearing species; however, this requires broad wavelength coverage, moderate spectral resolution, and high precision that, together, are not achievable with previous observatories. Now that JWST has commenced science operations, we are able to observe exoplanets at previously uncharted wavelengths and spectral resolutions. Here we report time-series observations of the transiting exoplanet WASP-39b using JWST's Near InfraRed Camera (NIRCam). The long-wavelength spectroscopic and short-wavelength photometric light curves span 2.0 - 4.0 $\mu$m, exhibit minimal systematics, and reveal well-defined molecular absorption features in the planet's spectrum. Specifically, we detect gaseous H$_2$O in the atmosphere and place an upper limit on the abundance of CH$_4$. The otherwise prominent CO$_2$ feature at 2.8 $\mu$m is largely masked by H$_2$O. The best-fit chemical equilibrium models favour an atmospheric metallicity of 1-100$\times$ solar (i.e., an enrichment of elements heavier than helium relative to the Sun) and a sub-stellar carbon-to-oxygen (C/O) ratio. The inferred high metallicity and low C/O ratio may indicate significant accretion of solid materials during planet formation or disequilibrium processes in the upper atmosphere.Comment: 35 pages, 13 figures, 3 tables, Nature, accepte

Identification of carbon dioxide in an exoplanet atmosphere

Carbon dioxide (CO2) is a key chemical species that is found in a wide range of planetary atmospheres. In the context of exoplanets, CO2 is an indicator of the metal enrichment (that is, elements heavier than helium, also called 'metallicity')1-3, and thus the formation processes of the primary atmospheres of hot gas giants4-6. It is also one of the most promising species to detect in the secondary atmospheres of terrestrial exoplanets7-9. Previous photometric measurements of transiting planets with the Spitzer Space Telescope have given hints of the presence of CO2, but have not yielded definitive detections owing to the lack of unambiguous spectroscopic identification10-12. Here we present the detection of CO2 in the atmosphere of the gas giant exoplanet WASP-39b from transmission spectroscopy observations obtained with JWST as part of the Early Release Science programme13,14. The data used in this study span 3.0-5.5 micrometres in wavelength and show a prominent CO2 absorption feature at 4.3 micrometres (26-sigma significance). The overall spectrum is well matched by one-dimensional, ten-times solar metallicity models that assume radiative-convective-thermochemical equilibrium and have moderate cloud opacity. These models predict that the atmosphere should have water, carbon monoxide and hydrogen sulfide in addition to CO2, but little methane. Furthermore, we also tentatively detect a small absorption feature near 4.0 micrometres that is not reproduced by these models

A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants.

This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/ng.3448Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 × 10(-8)) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 × 10(-10)). Very rare coding variants (frequency <0.1%) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.We thank all participants of all the studies included for enabling this research by their participation in these studies. Computer resources for this project have been provided by the high-performance computing centers of the University of Michigan and the University of Regensburg. Group-specific acknowledgments can be found in the Supplementary Note. The Center for Inherited Diseases Research (CIDR) Program contract number is HHSN268201200008I. This and the main consortium work were predominantly funded by 1X01HG006934-01 to G.R.A. and R01 EY022310 to J.L.H

Early Release Science of the exoplanet WASP-39b with JWST NIRSpec G395H

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this recordData Availability: The data used in this paper are associated with JWST program ERS 1366 (observation #4) and are available from the Mikulski Archive for Space Telescopes (https://mast.stsci.edu). Science data processing version (SDP_VER) 2022_2a generated the uncalibrated data that we downloaded from MAST. We used JWST Calibration Pipeline software version (CAL_VER) 1.5.3 with modifications described in the text. We used calibration reference data from context (CRDS_CTX) 0916, except as noted in the text. All the data and models presented in this publication can be found at 10.5281/zenodo.7185300.Code Availability: The codes used in this publication to extract, reduce and analyze the data are as follows; STScI JWST Calibration pipeline45 (https://github.com/spacetelescope/jwst), Eureka!53 (https://eurekadocs.readthedocs.io/en/latest/), ExoTiC-JEDI47 (https://github.com/ExoTiC/ExoTiC-JEDI), juliet71 (https://juliet.readthedocs.io/en/latest/), Tiberius15,49,50, transitspectroscopy51 (https://github.com/nespinoza/transitspectroscopy). In addition, these made use of batman65 (http://lkreidberg.github.io/batman/docs/html/index.html), celerite86 (https://celerite.readthedocs.io/en/stable/), chromatic (https://zkbt.github.io/chromatic/), Dynesty72 (https://dynesty.readthedocs.io/en/stable/index.html), emcee69 (https://emcee.readthedocs.io/en/stable/), exoplanet83 (https://docs.exoplanet.codes/en/latest/), ExoTEP75–77, ExoTHETyS79 (https://github.com/ucl-exoplanets/ExoTETHyS), ExoTiCISM57 (https://github.com/Exo-TiC/ExoTiC-ISM), ExoTiC-LD58 (https://exoticld.readthedocs.io/en/latest/), george68 (https://george.readthedocs.io/en/latest/) JAX82 (https://jax.readthedocs.io/en/latest/), LMFIT70 (https://lmfit.github.io/lmfit-py/), Pylightcurve78 (https://github.com/ucl-exoplanets/pylightcurve), Pymc3138 (https://docs.pymc.io/en/v3/index.html) and Starry84 (https://starry.readthedocs.io/en/latest/), each of which use the standard python libraries astropy139,140, matplotlib141, numpy142, pandas143, scipy64 and xarray144. The atmospheric models used to fit the data can be found at ATMO[Tremblin2015,Drummond2016,Goyal2018,Goyal2020]88–91, PHOENIX92–94, PICASO98,99 (https://natashabatalha.github.io/picaso/), Virga98,107 (https://natashabatalha.github.io/virga/), and gCMCRT115 (https://github.com/ELeeAstro/gCMCRT).Measuring the abundances of carbon and oxygen in exoplanet atmospheres is considered a crucial avenue for unlocking the formation and evolution of exoplanetary systems. Access to an exoplanet’s chemical inventory requires high precision observations, often inferred from individual molecular detections with low-resolution space-based and high-resolution ground-based facilities. Here we report the medium-resolution (R≈600) transmission spectrum of an exoplanet atmosphere between 3–5 μm covering multiple absorption features for the Saturn-mass exoplanet WASP-39b, obtained with JWST NIRSpec G395H. Our observations achieve 1.46× photon precision, providing an average transit depth uncertainty of 221 ppm per spectroscopic bin, and present minimal impacts from systematic effects. We detect significant absorption from CO2 (28.5σ ) and H2O (21.5σ ), and identify SO2 as the source of absorption at 4.1 μ m (4.8σ ). Best-fit atmospheric models range between 3× and 10× solar metallicity, with sub-solar to solar C/O ratios. These results, including the detection of SO2, underscore the importance of characterising the chemistry in exoplanet atmospheres, and showcase NIRSpec G395H as an excellent mode for time series observations over this critical wavelength range.Science and Technology Facilities Council (STFC)UKR