Publications by authors named "Daniel Jacob"

84 Publications

Description of the NASA GEOS Composition Forecast Modeling System GEOS-CF v1.0.

J Adv Model Earth Syst 2021 Apr 7;13(4):e2020MS002413. Epub 2021 Apr 7.

NASA Goddard Space Flight Center Greenbelt MD USA.

The Goddard Earth Observing System composition forecast (GEOS-CF) system is a high-resolution (0.25°) global constituent prediction system from NASA's Global Modeling and Assimilation Office (GMAO). GEOS-CF offers a new tool for atmospheric chemistry research, with the goal to supplement NASA's broad range of space-based and in-situ observations. GEOS-CF expands on the GEOS weather and aerosol modeling system by introducing the GEOS-Chem chemistry module to provide hindcasts and 5-days forecasts of atmospheric constituents including ozone (O), carbon monoxide (CO), nitrogen dioxide (NO), sulfur dioxide (SO), and fine particulate matter (PM). The chemistry module integrated in GEOS-CF is identical to the offline GEOS-Chem model and readily benefits from the innovations provided by the GEOS-Chem community. Evaluation of GEOS-CF against satellite, ozonesonde and surface observations for years 2018-2019 show realistic simulated concentrations of O, NO, and CO, with normalized mean biases of -0.1 to 0.3, normalized root mean square errors between 0.1-0.4, and correlations between 0.3-0.8. Comparisons against surface observations highlight the successful representation of air pollutants in many regions of the world and during all seasons, yet also highlight current limitations, such as a global high bias in SO and an overprediction of summertime O over the Southeast United States. GEOS-CF v1.0 generally overestimates aerosols by 20%-50% due to known issues in GEOS-Chem v12.0.1 that have been addressed in later versions. The 5-days forecasts have skill scores comparable to the 1-day hindcast. Model skills can be improved significantly by applying a bias-correction to the surface model output using a machine-learning approach.
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http://dx.doi.org/10.1029/2020MS002413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8244029PMC
April 2021

Satellite-based survey of extreme methane emissions in the Permian basin.

Sci Adv 2021 Jun 30;7(27). Epub 2021 Jun 30.

School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.

Industrial emissions play a major role in the global methane budget. The Permian basin is thought to be responsible for almost half of the methane emissions from all U.S. oil- and gas-producing regions, but little is known about individual contributors, a prerequisite for mitigation. We use a new class of satellite measurements acquired during several days in 2019 and 2020 to perform the first regional-scale and high-resolution survey of methane sources in the Permian. We find an unexpectedly large number of extreme point sources (37 plumes with emission rates >500 kg hour), which account for a range between 31 and 53% of the estimated emissions in the sampled area. Our analysis reveals that new facilities are major emitters in the area, often due to inefficient flaring operations (20% of detections). These results put current practices into question and are relevant to guide emission reduction efforts.
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http://dx.doi.org/10.1126/sciadv.abf4507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8245034PMC
June 2021

US COVID-19 Shutdown Demonstrates Importance of Background NO in Inferring NO Emissions From Satellite NO Observations.

Geophys Res Lett 2021 May 18;48(10):e2021GL092783. Epub 2021 May 18.

Department of Earth and Environmental Sciences University of Rochester Rochester NY USA.

Satellite nitrogen dioxide (NO) measurements are used extensively to infer nitrogen oxide emissions and their trends, but interpretation can be complicated by background contributions to the NO column sensed from space. We use the step decrease of US anthropogenic emissions from the COVID-19 shutdown to compare the responses of NO concentrations observed at surface network sites and from satellites (Ozone Monitoring Instrument [OMI], Tropospheric Ozone Monitoring Instrument [TROPOMI]). After correcting for differences in meteorology, surface NO measurements for 2020 show decreases of 20% in March-April and 10% in May-August compared to 2019. The satellites show much weaker responses in March-June and no decrease in July-August, consistent with a large background contribution to the NO column. Inspection of the long-term OMI trend over remote US regions shows a rising summertime NO background from 2010 to 2019 potentially attributable to wildfires.
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http://dx.doi.org/10.1029/2021GL092783DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8206743PMC
May 2021

Putative imbalanced amino acid metabolism in rainbow trout long term fed a plant-based diet as revealed by H-NMR metabolomics.

J Nutr Sci 2021 24;10:e13. Epub 2021 Feb 24.

INRAE, Univ. Pau Pays Adour, UMR Nutrition Metabolism Aquaculture, Centre INRAE Nouvelle Aquitaine Bordeaux, F-64310 Saint Pée-sur-Nivelle, France.

The long-term effect of a plant (P)-based diet was assessed by proton nuclear magnetic resonance (H-NMR) metabolomics in rainbow trout fed a marine fish meal (FM)-fish oil (FO) diet (M), a P-based diet and a control commercial-like diet (C) starting with the first feeding. Growth performances were not heavily altered by long-term feeding on the P-based diet. An H-NMR metabolomic analysis of the feed revealed significantly different soluble chemical compound profiles between the diets. A set of soluble chemical compounds was found to be specific either to the P-based diet or to the M diet. Pterin, a biomarker of plant feedstuffs, was identified both in the P-based diet and in the plasma of fish fed the P-based diet. H-NMR metabolomic analysis on fish plasma and liver and muscle tissues at 6 and 48 h post feeding revealed significantly different profiles between the P-based diet and the M diet, while the C diet showed intermediate results. A higher amino acid content was found in the plasma of fish fed the P-based diet compared with the M diet after 48 h, suggesting either a delayed delivery of the amino acids or a lower amino acid utilisation in the P-based diet. This was associated with an accumulation of essential amino acids and the depletion of glutamine in the muscle, together with an accumulation of choline in the liver. Combined with an anticipated absorption of methionine and lysine supplemented in free form, the present results suggest an imbalanced essential amino acid supply for protein metabolism in the muscle and for specific functions of the liver.
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http://dx.doi.org/10.1017/jns.2021.3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8057518PMC
February 2021

Ozone pollution in the North China Plain spreading into the late-winter haze season.

Proc Natl Acad Sci U S A 2021 03;118(10)

Samsung Advance Institute of Technology, Suwon-si, Gyeonggi-do, 16678, Republic of Korea.

Surface ozone is a severe air pollution problem in the North China Plain, which is home to 300 million people. Ozone concentrations are highest in summer, driven by fast photochemical production of hydrogen oxide radicals (HO) that can overcome the radical titration caused by high emissions of nitrogen oxides (NO) from fuel combustion. Ozone has been very low during winter haze (particulate) pollution episodes. However, the abrupt decrease of NO emissions following the COVID-19 lockdown in January 2020 reveals a switch to fast ozone production during winter haze episodes with maximum daily 8-h average (MDA8) ozone concentrations of 60 to 70 parts per billion. We reproduce this switch with the GEOS-Chem model, where the fast production of ozone is driven by HO radicals from photolysis of formaldehyde, overcoming radical titration from the decreased NO emissions. Formaldehyde is produced by oxidation of reactive volatile organic compounds (VOCs), which have very high emissions in the North China Plain. This remarkable switch to an ozone-producing regime in January-February following the lockdown illustrates a more general tendency from 2013 to 2019 of increasing winter-spring ozone in the North China Plain and increasing association of high ozone with winter haze events, as pollution control efforts have targeted NO emissions (30% decrease) while VOC emissions have remained constant. Decreasing VOC emissions would avoid further spreading of severe ozone pollution events into the winter-spring season.
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http://dx.doi.org/10.1073/pnas.2015797118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7958175PMC
March 2021

Aqueous production of secondary organic aerosol from fossil-fuel emissions in winter Beijing haze.

Proc Natl Acad Sci U S A 2021 02;118(8)

John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138;

Secondary organic aerosol (SOA) produced by atmospheric oxidation of primary emitted precursors is a major contributor to fine particulate matter (PM) air pollution worldwide. Observations during winter haze pollution episodes in urban China show that most of this SOA originates from fossil-fuel combustion but the chemical mechanisms involved are unclear. Here we report field observations in a Beijing winter haze event that reveal fast aqueous-phase conversion of fossil-fuel primary organic aerosol (POA) to SOA at high relative humidity. Analyses of aerosol mass spectra and elemental ratios indicate that ring-breaking oxidation of POA aromatic species, leading to functionalization as carbonyls and carboxylic acids, may serve as the dominant mechanism for this SOA formation. A POA origin for SOA could explain why SOA has been decreasing over the 2013-2018 period in response to POA emission controls even as emissions of volatile organic compounds (VOCs) have remained flat.
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http://dx.doi.org/10.1073/pnas.2022179118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7923588PMC
February 2021

Maize metabolome and proteome responses to controlled cold stress partly mimic early-sowing effects in the field and differ from those of Arabidopsis.

Plant Cell Environ 2021 May 25;44(5):1504-1521. Epub 2021 Jan 25.

Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine-Bordeaux, INRAE, Univ., Villenave d'Ornon, France.

In Northern Europe, sowing maize one-month earlier than current agricultural practices may lead to moderate chilling damage. However, studies of the metabolic responses to low, non-freezing, temperatures remain scarce. Here, genetically-diverse maize hybrids (Zea mays, dent inbred lines crossed with a flint inbred line) were cultivated in a growth chamber at optimal temperature and then three decreasing temperatures for 2 days each, as well as in the field. Leaf metabolomic and proteomic profiles were determined. In the growth chamber, 50% of metabolites and 18% of proteins changed between 20 and 16°C. These maize responses, partly differing from those of Arabidopsis to short-term chilling, were mapped on genome-wide metabolic maps. Several metabolites and proteins showed similar variation for all temperature decreases: seven MS-based metabolite signatures and two proteins involved in photosynthesis decreased continuously. Several increasing metabolites or proteins in the growth-chamber chilling conditions showed similar trends in the early-sowing field experiment, including trans-aconitate, three hydroxycinnamate derivatives, a benzoxazinoid, a sucrose synthase, lethal leaf-spot 1 protein, an allene oxide synthase, several glutathione transferases and peroxidases. Hybrid groups based on field biomass were used to search for the metabolite or protein responses differentiating them in growth-chamber conditions, which could be of interest for breeding.
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http://dx.doi.org/10.1111/pce.13993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8248070PMC
May 2021

Making experimental data tables in the life sciences more FAIR: a pragmatic approach.

Gigascience 2020 12;9(12)

INRAE, Université de Bordeaux, UMR BFP, 71 av E Bourlaux, 33140 Villenave d'Ornon, France.

Making data compliant with the FAIR Data principles (Findable, Accessible, Interoperable, Reusable) is still a challenge for many researchers, who are not sure which criteria should be met first and how. Illustrated with experimental data tables associated with a Design of Experiments, we propose an approach that can serve as a model for research data management that allows researchers to disseminate their data by satisfying the main FAIR criteria without insurmountable efforts. More importantly, this approach aims to facilitate the FAIR compliance process by providing researchers with tools to improve their data management practices.
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http://dx.doi.org/10.1093/gigascience/giaa144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7736789PMC
December 2020

Global Importance of Hydroxymethanesulfonate in Ambient Particulate Matter: Implications for Air Quality.

J Geophys Res Atmos 2020 Sep 11;125(18):e2020JD032706. Epub 2020 Sep 11.

Department of Earth and Planetary Sciences Harvard University Cambridge MA USA.

Sulfur compounds are an important constituent of particulate matter, with impacts on climate and public health. While most sulfur observed in particulate matter has been assumed to be sulfate, laboratory experiments reveal that hydroxymethanesulfonate (HMS), an adduct formed by aqueous phase chemical reaction of dissolved HCHO and SO, may be easily misinterpreted in measurements as sulfate. Here we present observational and modeling evidence for a ubiquitous global presence of HMS. We find that filter samples collected in Shijiazhuang, China, and examined with ion chromatography within 9 days show as much as 7.6 μg m of HMS, while samples from Singapore examined 9-18 months after collection reveal ~0.6 μg m of HMS. The Shijiazhuang samples show only minor traces of HMS 4 months later, suggesting that HMS had decomposed over time during sample storage. In contrast, the Singapore samples do not clearly show a decline in HMS concentration over 2 months of monitoring. Measurements from over 150 sites, primarily derived from the IMPROVE network across the United States, suggest the ubiquitous presence of HMS in at least trace amounts as much as 60 days after collection. The degree of possible HMS decomposition in the IMPROVE observations is unknown. Using the GEOS-Chem chemical transport model, we estimate that HMS may account for 10% of global particulate sulfur in continental surface air and over 25% in many polluted regions. Our results suggest that reducing emissions of HCHO and other volatile organic compounds may have a co-benefit of decreasing particulate sulfur.
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http://dx.doi.org/10.1029/2020JD032706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685164PMC
September 2020

Photochemistry of oxidized Hg(I) and Hg(II) species suggests missing mercury oxidation in the troposphere.

Proc Natl Acad Sci U S A 2020 12 23;117(49):30949-30956. Epub 2020 Nov 23.

Department of Earth and Environmental Science,University of Pennsylvania, Philadelphia, PA 19104;

Mercury (Hg), a global contaminant, is emitted mainly in its elemental form Hg to the atmosphere where it is oxidized to reactive Hg compounds, which efficiently deposit to surface ecosystems. Therefore, the chemical cycling between the elemental and oxidized Hg forms in the atmosphere determines the scale and geographical pattern of global Hg deposition. Recent advances in the photochemistry of gas-phase oxidized Hg and Hg species postulate their photodissociation back to Hg as a crucial step in the atmospheric Hg redox cycle. However, the significance of these photodissociation mechanisms on atmospheric Hg chemistry, lifetime, and surface deposition remains uncertain. Here we implement a comprehensive and quantitative mechanism of the photochemical and thermal atmospheric reactions between Hg, Hg, and Hg species in a global model and evaluate the results against atmospheric Hg observations. We find that the photochemistry of Hg and Hg leads to insufficient Hg oxidation globally. The combined efficient photoreduction of Hg and Hg to Hg competes with thermal oxidation of Hg, resulting in a large model overestimation of 99% of measured Hg and underestimation of 51% of oxidized Hg and ∼66% of Hg wet deposition. This in turn leads to a significant increase in the calculated global atmospheric Hg lifetime of 20 mo, which is unrealistically longer than the 3-6-mo range based on observed atmospheric Hg variability. These results show that the Hg and Hg photoreduction processes largely offset the efficiency of bromine-initiated Hg oxidation and reveal missing Hg oxidation processes in the troposphere.
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http://dx.doi.org/10.1073/pnas.1922486117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7733835PMC
December 2020

Hyperpolarized NMR Metabolomics at Natural C Abundance.

Anal Chem 2020 11 2;92(22):14867-14871. Epub 2020 Nov 2.

Université de Nantes, CNRS, CEISAM UMR 6230, F-44000 Nantes, France.

Metabolomics plays a pivotal role in systems biology, and NMR is a central tool with high precision and exceptional resolution of chemical information. Most NMR metabolomic studies are based on H 1D spectroscopy, severely limited by peak overlap. C NMR benefits from a larger signal dispersion but is barely used in metabolomics due to ca. 6000-fold lower sensitivity. We introduce a new approach, based on hyperpolarized C NMR at natural abundance, that circumvents this limitation. A new untargeted NMR-based metabolomic workflow based on dissolution dynamic nuclear polarization (d-DNP) for the first time enabled hyperpolarized natural abundance C metabolomics. Statistical analysis of resulting hyperpolarized C data distinguishes two groups of plant (tomato) extracts and highlights biomarkers, in full agreement with previous results on the same biological model. We also optimize parameters of the semiautomated d-DNP system suitable for high-throughput studies.
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http://dx.doi.org/10.1021/acs.analchem.0c03510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7705890PMC
November 2020

Mapping Human Monoclonal IgE Epitopes on the Major Dust Mite Allergen Der p 2.

J Immunol 2020 10 9;205(8):1999-2007. Epub 2020 Sep 9.

Basic Research, Indoor Biotechnologies, Inc., Charlottesville, VA 22903.

IgE Abs drive the symptoms of allergic disease upon cross-linking allergens on mast cells or basophils. If the IgE binding sites on the allergens could be identified, it may be useful for creating new forms of immunotherapy. However, direct knowledge of the human IgE (hIgE) epitopes is limited because of the very low frequency of IgE-producing B cells in blood. A new hybridoma technology using human B cells from house dust mite-allergic patients was used to identify four Der p 2-specific hIgE mAbs. Their relative binding sites were assessed and compared by immunoassays with three previously studied murine IgG mAbs. Immunoassays showed that the recognition of Der p 2 by the first three hIgE was inhibited by a single murine IgG, but the fourth hIgE recognized a different epitope from all the other mAbs. The functional ability of the hIgE that bind different epitopes to cross-link Der p 2 was demonstrated in a mouse model of passive systemic anaphylaxis. Nuclear magnetic resonance analyses of Der p 2 in complex with IgG and IgE Abs were used to identify specific residues in the epitopes. To our knowledge, the combination of immunoassays to distinguish overlapping epitopes and nuclear magnetic resonance analyses to identify specific residues involved in Ab binding provided the first epitope mapping of hIgE mAbs to an allergen. The technologies developed in this study will be useful in high-resolution mapping of human epitopes on other Ags and the design of improved therapeutics.
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http://dx.doi.org/10.4049/jimmunol.2000295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7541722PMC
October 2020

Quantifying Time-Averaged Methane Emissions from Individual Coal Mine Vents with GHGSat-D Satellite Observations.

Environ Sci Technol 2020 08 28;54(16):10246-10253. Epub 2020 Jul 28.

GHGSat Inc., Montréal, Québec H2W 1Y5, Canada.

Satellite observations of atmospheric methane plumes offer a means for global mapping of methane point sources. Here we use the GHGSat-D satellite instrument with 50 m effective spatial resolution and 9-18% single-pass column precision to quantify mean source rates for three coal mine vents (San Juan, United States; Appin, Australia; and Bulianta, China) over a two-year period (2016-2018). This involves averaging wind-rotated observations from 14 to 24 overpasses to achieve satisfactory signal-to-noise. Our wind rotation method optimizes the wind direction information for individual plumes to account for error in meteorological databases. We derive source rates from the time-averaged plumes using integrated mass enhancement (IME) and cross-sectional flux (CSF) methods calibrated with large eddy simulations. We find time-averaged source rates ranging from 2320 to 5850 kg h for the three coal mine vents, with 40-45% precision (1σ), and generally consistent with previous estimates. The IME and CSF methods agree within 15%. Our results demonstrate the potential of space-based monitoring for annual reporting of methane emissions from point sources and suggest that future satellite instruments with similar pixel resolution but better precision should be able to constrain a wide range of point sources.
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http://dx.doi.org/10.1021/acs.est.0c01213DOI Listing
August 2020

Effects of Anthropogenic Chlorine on PM and Ozone Air Quality in China.

Environ Sci Technol 2020 08 27;54(16):9908-9916. Epub 2020 Jul 27.

School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing, China.

China has large anthropogenic chlorine emissions from agricultural fires, residential biofuel, waste incineration, coal combustion, and industrial processes. Here we quantify the effects of chlorine on fine particulate matter (PM) and ozone air quality across China by using the GEOS-Chem chemical transport model with comprehensive anthropogenic emissions and detailed representation of gas-phase and heterogeneous chlorine chemistry. Comparison of the model to observed ClNO, HCl, and particulate Cl concentrations shows that reactive chlorine in China is mainly anthropogenic, unlike in other continental regions where it is mostly of marine origin. The model is successful in reproducing observed concentrations and their distributions, lending confidence in the anthropogenic chlorine emission estimates and the resulting chemistry. We find that anthropogenic chlorine emissions increase total inorganic PM by as much as 3.2 μg m on an annual mean basis through the formation of ammonium chloride, partly compensated by a decrease of nitrate because ClNO formation competes with NO hydrolysis. Annual mean MDA8 surface ozone increases by up to 1.9 ppb, mainly from ClNO chemistry, while reactivities of volatile organic compounds increase (by up to 48% for ethane). We find that a sufficient representation of chlorine chemistry in air quality models can be obtained from consideration of HCl/Cl thermodynamics and ClNO chemistry, because other more complicated aspects of chlorine chemistry have a relatively minor effect.
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http://dx.doi.org/10.1021/acs.est.0c02296DOI Listing
August 2020

Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species.

J Exp Bot 2020 10;71(19):5823-5836

UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine - Bordeaux, Avenue Edouard Bourlaux, Villenave d'Ornon, France.

Fleshy fruits are very varied, whether in terms of their composition, physiology, or rate and duration of growth. To understand the mechanisms that link metabolism to phenotypes, which would help the targeting of breeding strategies, we compared eight fleshy fruit species during development and ripening. Three herbaceous (eggplant, pepper, and cucumber), three tree (apple, peach, and clementine) and two vine (kiwifruit and grape) species were selected for their diversity. Fruit fresh weight and biomass composition, including the major soluble and insoluble components, were determined throughout fruit development and ripening. Best-fitting models of fruit weight were used to estimate relative growth rate (RGR), which was significantly correlated with several biomass components, especially protein content (R=84), stearate (R=0.72), palmitate (R=0.72), and lignocerate (R=0.68). The strong link between biomass composition and RGR was further evidenced by generalized linear models that predicted RGR with R-values exceeding 0.9. Comparison of the fruit also showed that climacteric fruit (apple, peach, kiwifruit) contained more non-cellulosic cell-wall glucose and fucose, and more starch, than non-climacteric fruit. The rate of starch net accumulation was also higher in climacteric fruit. These results suggest that the way biomass is constructed has a major influence on performance, especially growth rate.
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http://dx.doi.org/10.1093/jxb/eraa302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7540837PMC
October 2020

Fast sulfate formation from oxidation of SO by NO and HONO observed in Beijing haze.

Nat Commun 2020 06 5;11(1):2844. Epub 2020 Jun 5.

John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.

Severe events of wintertime particulate air pollution in Beijing (winter haze) are associated with high relative humidity (RH) and fast production of particulate sulfate from the oxidation of sulfur dioxide (SO) emitted by coal combustion. There has been considerable debate regarding the mechanism for SO oxidation. Here we show evidence from field observations of a haze event that rapid oxidation of SO by nitrogen dioxide (NO) and nitrous acid (HONO) takes place, the latter producing nitrous oxide (NO). Sulfate shifts to larger particle sizes during the event, indicative of fog/cloud processing. Fog and cloud readily form under winter haze conditions, leading to high liquid water contents with high pH (>5.5) from elevated ammonia. Such conditions enable fast aqueous-phase oxidation of SO by NO, producing HONO which can in turn oxidize SO to yield NO.This mechanism could provide an explanation for sulfate formation under some winter haze conditions.
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http://dx.doi.org/10.1038/s41467-020-16683-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7275061PMC
June 2020

Quantifying methane emissions from the largest oil-producing basin in the United States from space.

Sci Adv 2020 Apr 22;6(17):eaaz5120. Epub 2020 Apr 22.

School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.

Using new satellite observations and atmospheric inverse modeling, we report methane emissions from the Permian Basin, which is among the world's most prolific oil-producing regions and accounts for >30% of total U.S. oil production. Based on satellite measurements from May 2018 to March 2019, Permian methane emissions from oil and natural gas production are estimated to be 2.7 ± 0.5 Tg a, representing the largest methane flux ever reported from a U.S. oil/gas-producing region and are more than two times higher than bottom-up inventory-based estimates. This magnitude of emissions is 3.7% of the gross gas extracted in the Permian, i.e., ~60% higher than the national average leakage rate. The high methane leakage rate is likely contributed by extensive venting and flaring, resulting from insufficient infrastructure to process and transport natural gas. This work demonstrates a high-resolution satellite data-based atmospheric inversion framework, providing a robust top-down analytical tool for quantifying and evaluating subregional methane emissions.
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http://dx.doi.org/10.1126/sciadv.aaz5120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176423PMC
April 2020

Comparative Metabolomics and Molecular Phylogenetics of Melon (, Cucurbitaceae) Biodiversity.

Metabolites 2020 Mar 24;10(3). Epub 2020 Mar 24.

Newe Ya'ar Research Center, Agricultural Research Organization, P. O. Box 1021, Ramat Yishay 3009500, Israel.

The broad variability of (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within , we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of "metabolomic/elemental distance" and its correlation with the genetic GBS distance of melon accessions. This study indicates that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.
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http://dx.doi.org/10.3390/metabo10030121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143154PMC
March 2020

Fires, Smoke Exposure, and Public Health: An Integrative Framework to Maximize Health Benefits From Peatland Restoration.

Geohealth 2019 Jul 24;3(7):178-189. Epub 2019 Jul 24.

Harvard T.H. Chan School of Public Health Harvard University Boston MA USA.

Emissions of particulate matter from fires associated with land management practices in Indonesia contribute to regional air pollution and mortality. We assess the public health benefits in Indonesia, Malaysia, and Singapore from policies to reduce fires by integrating information on fire emissions, atmospheric transport patterns, and population exposure to fine particulate matter (PM). We use adjoint sensitivities to relate fire emissions to PM for a range of meteorological conditions and find that a Business-As-Usual scenario of land use change leads, on average, to 36,000 excess deaths per year into the foreseeable future (the next several decades) across the region. These deaths are largely preventable with fire reduction strategies, such as blocking fires in peatlands, industrial concessions, or protected areas, which reduce the health burden by 66, 45, and 14%, respectively. The effectiveness of these different strategies in mitigating human health impacts depends on the location of fires relative to the population distribution. For example, protecting peatlands through eliminating all fires on such lands would prevent on average 24,000 excess deaths per year into the foreseeable future across the region because, in addition to storing large amounts of fuel, many peatlands are located directly upwind of densely populated areas. We also demonstrate how this framework can be used to prioritize restoration locations for the Indonesian Peatland Restoration Agency based on their ability to reduce pollution exposure and health burden. This scientific framework is publicly available through an online decision support tool that allows stakeholders to readily determine the public health benefits of different land management strategies.
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http://dx.doi.org/10.1029/2019GH000191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7007093PMC
July 2019

Integrative Metabolomics for Assessing the Effect of Insect () Protein Extract on Rainbow Trout Metabolism.

Metabolites 2020 Feb 27;10(3). Epub 2020 Feb 27.

INRAE, University Pau & Pays Adour, E2S UPPA, UMR NuMeA Nutrition, Metabolism and Aquaculture, F-64310 Saint Pée sur Nivelle, France.

Nutrition of high trophic species in aquaculture is faced with the development of sustainable plant-based diets. Insects seem particularly promising for supplementing plant-based diets. However, the complex effect of whole insect meal on fish metabolism is not well understood, and even less is known about insect meal extracts. The purpose of this work was to decipher the metabolic utilization of a plant-based diet supplemented with the gradual addition of an insect protein extract (insect hydrolysate at 0%, 5%, 10% and 15%). H-NMR profiling was used to assess metabolites in experimental diets and in fish plasma, liver and muscle. A significant dose-dependent increase in growth and feed efficiency with increasing insect extract amounts was observed. The incremental incorporation of the insect extract in diet had a significant and progressive impact on the profile of dietary soluble compounds and trout metabolome. The metabolites modulated by dietary insect extracts in plasma and tissues were involved in protein and energy metabolism. This was associated with the efficient metabolic use of dietary free amino acids toward protein synthesis through the concomitant supply of balanced free amino acids and energy substrates in muscle. The findings provide new insights into how the dietary food metabolome affects fish metabolism.
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http://dx.doi.org/10.3390/metabo10030083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143670PMC
February 2020

Modeling the OH-Initiated Oxidation of Mercury in the Global Atmosphere without Violating Physical Laws.

J Phys Chem A 2020 Jan 6;124(2):444-453. Epub 2020 Jan 6.

Department of Chemistry , State University of New York, College of Environmental Science and Forestry , 1 Forestry Drive , Syracuse , New York 13210 , United States.

In 2005, Calvert and Lindberg (Calvert, J. G.; Lindberg, S. E. 3355-3367) wrote that the use of laboratory-derived rate constants for OH + Hg(0) "...to determine the extent of Hg removal by OH in the troposphere will greatly overestimate the importance of Hg removal by this reaction." The HOHg intermediate formed from OH + Hg will mostly fall apart in the atmosphere before it can react. By contrast, in laboratory experiments, Calvert and Lindberg expected HOHg to react with radicals (whose concentrations are much higher than in the atmosphere). Yet, almost all models of oxidation of Hg(0) ignore the argument of Calvert and Lindberg. We present a way for modelers to include the OH + Hg reaction while accounting quantitatively for the dissociation of HOHg. We use high levels of quantum chemistry to establish the HO-Hg bond energy as 11.0 kcal/mol and calculate the equilibrium constant for OH + Hg = HOHg. Using the measured rate constant for the association of OH with Hg, we determine the rate constant for HOHg dissociation. Theory is also used to demonstrate that HOHg forms stable compounds, HOHgY, with atmospheric radicals (Y = NO, HOO, CHOO, and BrO). We then present rate constants for use in modeling OH-initiated oxidation of Hg(0). We use this mechanism to model the global oxidation of Hg(0) in the period 2013-2015 using the GEOS-Chem 3D model of atmospheric chemistry. Because of the rapid dissociation of HOHg, OH accounts for <1% of the global oxidation of Hg(0) to Hg(II), while Br atoms account for 97%.
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http://dx.doi.org/10.1021/acs.jpca.9b10121DOI Listing
January 2020

NMR-Based Tissular and Developmental Metabolomics of Tomato Fruit.

Metabolites 2019 May 9;9(5). Epub 2019 May 9.

UMR1332 Biologie du Fruit et Pathologie, INRA, University Bordeaux, Centre INRA de Nouvelle Aquitaine-Bordeaux, 71 av Edouard Bourlaux, 33140 Villenave d'Ornon, France.

Fruit is a complex organ containing seeds and several interconnected tissues with dedicated roles. However, most biochemical or molecular studies about fleshy fruit development concern the entire fruit, the fruit without seeds, or pericarp only. We studied tomato () fruit at four stages of development (12, 20, 35, and 45 days post-anthesis). We separated the seeds and the other tissues, exocarp, mesocarp, columella with placenta and locular tissue, and analyzed them individually using proton NMR metabolomic profiling for the quantification of major polar metabolites, enzymatic analysis of starch, and LC-DAD analysis of isoprenoids. Pericarp tissue represented about half of the entire fruit mass only. The composition of each fruit tissue changed during fruit development. An ANOVA-PCA highlighted common, and specific metabolite trends between tissues e.g., higher contents of chlorogenate in locular tissue and of starch in columella. Euclidian distances based on compositional data showed proximities within and between tissues. Several metabolic regulations differed between tissues as revealed by the comparison of metabolite networks based on correlations between compounds. This work stressed the role of specific tissues less studied than pericarp but that impact fruit organoleptic quality including its shape and taste, and fruit processing quality.
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http://dx.doi.org/10.3390/metabo9050093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6571556PMC
May 2019

Being Parent Caregivers for Adult Children with Schizophrenia.

Issues Ment Health Nurs 2019 Apr 14;40(4):297-303. Epub 2019 Jan 14.

a Schizophrenia Program , Royal Ottawa Mental Health Centre , Ottawa , Ontario , Canada.

Parent caregivers support the health and well-being of their adult children with schizophrenia. As a result, parent caregivers spend vast amounts of time providing care, which necessitates changes to their relationships and lives. In this qualitative study, the experiences of parent caregivers for adult children with schizophrenia were explored. Interpretive Description guided the study design, and data were collected through interviews with 12 English-speaking participants. Data were analyzed according to conventional content analysis. The themes "Uncertainty, Change, and Challenges" and "The Meaning of It All" help to articulate the participants' experiences. Overall, the participants reported tremendous distress in their roles. This was compounded by difficulties accessing and navigating the healthcare system and interactions with police. Effective strategies are needed to help parent caregivers cope within their role and gain access to timely and appropriate care.
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http://dx.doi.org/10.1080/01612840.2018.1524531DOI Listing
April 2019

Metabolomic characterization of sunflower leaf allows discriminating genotype groups or stress levels with a minimal set of metabolic markers.

Metabolomics 2019 03 30;15(4):56. Epub 2019 Mar 30.

UMR1332 Biologie du Fruit et Pathologie, INRA, Centre INRA de Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France.

Introduction: Plant and crop metabolomic analyses may be used to study metabolism across genetic and environmental diversity. Complementary analytical strategies are useful for investigating metabolic changes and searching for biomarkers of response or performance.

Methods And Objectives: The experimental material consisted in eight sunflower lines with two line status, four restorers (R, used as males) and four maintainers (B, corresponding to females) routinely used for sunflower hybrid varietal production, respectively to complement or maintain the cytoplasmic male sterility PET1. These lines were either irrigated at full soil capacity (WW) or submitted to drought stress (DS). Our aim was to combine targeted and non-targeted metabolomics to characterize sunflower leaf composition in order to investigate the effect of line status genotypes and environmental conditions and to find the best and smallest set of biomarkers for line status and stress response using a custom-made process of variables selection.

Results: Five hundred and eighty-eight metabolic variables were measured by using complementary analytical methods such as H-NMR, MS-based profiles and targeted analyses of major metabolites. Based on statistical analyses, a limited number of markers were able to separate WW and DS samples in a more discriminant manner than previously published physiological data. Another metabolic marker set was able to discriminate line status.

Conclusion: This study underlines the potential of metabolic markers for discriminating genotype groups and environmental conditions. Their potential use for prediction is discussed.
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http://dx.doi.org/10.1007/s11306-019-1515-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441456PMC
March 2019

Optimizing 1D H-NMR profiling of plant samples for high throughput analysis: extract preparation, standardization, automation and spectra processing.

Metabolomics 2019 02 26;15(3):28. Epub 2019 Feb 26.

BIOPI - EA 3900, Univ. Picardie Jules Verne, 1, rue des Louvels, 80037, Amiens Cedex, France.

Introduction: Proton nuclear magnetic resonance spectroscopy (H-NMR)-based metabolomic profiling has a range of applications in plant sciences.

Objectives: The aim of the present work is to provide advice for minimizing uncontrolled variability in plant sample preparation before and during NMR metabolomic profiling, taking into account sample composition, including its specificity in terms of pH and paramagnetic ion concentrations, and NMR spectrometer performances.

Methods: An automation of spectrometer preparation routine standardization before NMR acquisition campaign was implemented and tested on three plant sample sets (extracts of durum wheat spikelet, Arabidopsis leaf and root, and flax leaf, root and stem). We performed H-NMR spectroscopy in three different sites on the wheat sample set utilizing instruments from two manufacturers with different probes and magnetic field strengths. The three collections of spectra were processed separately with the NMRProcFlow web tool using intelligent bucketing, and the resulting buckets were subjected to multivariate analysis.

Results: Comparability of large- (Arabidopsis) and medium-size (flax) datasets measured at 600 MHz and from the wheat sample set recorded at the three sites (400, 500 and 600 MHz) was exceptionally good in terms of spectral quality. The coefficient of variation of the full width at half maximum (FWHM) and the signal-to-noise ratio (S/N) of two selected peaks was comprised between 5 and 10% depending on the size of sample set and the spectrometer field. EDTA addition improved citrate and malate resonance patterns for wheat sample sets. A collection of 22 samples of wheat spikelet extracts was used as a proof of concept and showed that the data collected at the three sites on instruments of different field strengths and manufacturers yielded the same discrimination pattern of the biological groups.

Conclusion: Standardization or automation of several steps from extract preparation to data reduction improves data quality for small to large collections of plant samples of different origins.
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http://dx.doi.org/10.1007/s11306-019-1488-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394467PMC
February 2019

Metabotyping of 30 maize hybrids under early-sowing conditions reveals potential marker-metabolites for breeding.

Metabolomics 2018 09 26;14(10):132. Epub 2018 Sep 26.

UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France.

Introduction: In Northern Europe, maize early-sowing used to maximize yield may lead to moderate damages of seedlings due to chilling without visual phenotypes. Genetic studies and breeding for chilling tolerance remain necessary, and metabolic markers would be particularly useful in this context.

Objectives: Using an untargeted metabolomic approach on a collection of maize hybrids, our aim was to identify metabolite signatures and/or metabolites associated with chilling responses at the vegetative stage, to search for metabolites differentiating groups of hybrids based on silage-earliness, and to search for marker-metabolites correlated with aerial biomass.

Methods: Thirty genetically-diverse maize dent inbred-lines (Zea mays) crossed to a flint inbred-line were sown in a field to assess metabolite profiles upon cold treatment induced by a modification of sowing date, and characterized with climatic measurements and phenotyping.

Results: NMR- and LC-MS-based metabolomic profiling revealed the biological variation of primary and specialized metabolites in young leaves of plants before flowering-stage. The effect of early-sowing on leaf composition was larger than that of genotype, and several metabolites were associated to sowing response. The metabolic distances between genotypes based on leaf compositional data were not related to the genotype admixture groups, and their variability was lower under early-sowing than normal-sowing. Several metabolites or metabolite-features were related to silage-earliness groups in the normal-sowing condition, some of which were confirmed the following year. Correlation networks involving metabolites and aerial biomass suggested marker-metabolites for breeding for chilling tolerance.

Conclusion: After validation in other experiments and larger genotype panels, these marker-metabolites can contribute to breeding.
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http://dx.doi.org/10.1007/s11306-018-1427-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208756PMC
September 2018

Characterization of GMO or glyphosate effects on the composition of maize grain and maize-based diet for rat feeding.

Metabolomics 2018 02 17;14(3):36. Epub 2018 Feb 17.

UMR1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Centre INRA de Nouvelle Aquitaine - Bordeaux, 71 av Edouard Bourlaux, 33140, Villenave d'Ornon, France.

Introduction: In addition to classical targeted biochemical analyses, metabolomic analyses seem pertinent to reveal expected as well as unexpected compositional differences between plant genetically modified organisms (GMO) and non-GMO samples. Data previously published in the existing literature led to divergent conclusions on the effect of maize transgenes on grain compositional changes and feeding effects. Therefore, a new study examining field-grown harvested products and feeds derived from them remains useful.

Objectives: Our aim was to use a metabolomics approach to characterize grain and grain-based diet compositional changes for two GMO events, one involving Bacillus thuringiensis toxin to provide insect resistance and the other one conferring herbicide tolerance by detoxification of glyphosate. We also investigated the potential compositional modifications induced by the use of a glyphosate-based herbicide on the transgenic line conferring glyphosate tolerance.

Results: The majority of statistically significant differences in grain composition, evidenced by the use of H-NMR profiling of polar extracts and LC-ESI-QTOF-MS profiling of semi-polar extracts, could be attributed to the combined effect of genotype and environment. In comparison, transgene and glyphosate effects remained limited in grain for the compound families studied. Some but not all compositional changes observed in grain were also detected in grain-based diets formulated for rats.

Conclusion: Only part of the data previously published in the existing literature on maize grains of plants with the same GMO events could be reproduced in our experiment. All spectra have been deposited in a repository freely accessible to the public. Our grain and diet characterization opened the way for an in depth study of the effects of these diets on rat health.
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http://dx.doi.org/10.1007/s11306-018-1329-9DOI Listing
February 2018

SCOPE11 Method for Estimating Aircraft Black Carbon Mass and Particle Number Emissions.

Environ Sci Technol 2019 02 8;53(3):1364-1373. Epub 2019 Jan 8.

Laboratory for Aviation and the Environment, Department of Aeronautics and Astronautics , Massachusetts Institute of Technology , Cambridge , Massachusetts 02140 , United States.

Black carbon (BC) emissions from aircraft engines lead to an increase in the atmospheric burden of fine particulate matter (PM). Exposure to PM from sources, including aviation, is associated with an increased risk of premature mortality, and BC suspended in the atmosphere has a warming impact on the climate. BC particles emitted from aircraft also serve as nuclei for contrail ice particles, which are a major component of aviation's climate impact. To facilitate the evaluation of these impacts, we have developed a method to estimate BC mass and number emissions at the engine exit plane, referred to as the Smoke Correlation for Particle Emissions-CAEP11 (SCOPE11). We use a data set consisting of SN-BC mass concentration pairs, collected using certification-compliant measurement systems, to develop a new relationship between smoke number (SN) and BC mass concentration. In addition, we use a complementary data set to estimate measurement system loss correction factors and particle geometric mean diameters to estimate BC number emissions at the engine exit plane. Using this method, we estimate global BC emissions from aircraft landing and takeoff (LTO) operations for 2015 to be 0.74 Gg/year (95% CI = 0.64-0.84) and 2.85 × 10 particles/year (95% CI = 1.86-4.49 × 10).
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http://dx.doi.org/10.1021/acs.est.8b04060DOI Listing
February 2019

Anthropogenic drivers of 2013-2017 trends in summer surface ozone in China.

Proc Natl Acad Sci U S A 2019 01 31;116(2):422-427. Epub 2018 Dec 31.

John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138.

Observations of surface ozone available from ∼1,000 sites across China for the past 5 years (2013-2017) show severe summertime pollution and regionally variable trends. We resolve the effect of meteorological variability on the ozone trends by using a multiple linear regression model. The residual of this regression shows increasing ozone trends of 1-3 ppbv a in megacity clusters of eastern China that we attribute to changes in anthropogenic emissions. By contrast, ozone decreased in some areas of southern China. Anthropogenic NO emissions in China are estimated to have decreased by 21% during 2013-2017, whereas volatile organic compounds (VOCs) emissions changed little. Decreasing NO would increase ozone under the VOC-limited conditions thought to prevail in urban China while decreasing ozone under rural NO-limited conditions. However, simulations with the Goddard Earth Observing System Chemical Transport Model (GEOS-Chem) indicate that a more important factor for ozone trends in the North China Plain is the ∼40% decrease of fine particulate matter (PM) over the 2013-2017 period, slowing down the aerosol sink of hydroperoxy (HO) radicals and thus stimulating ozone production.
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http://dx.doi.org/10.1073/pnas.1812168116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329973PMC
January 2019

PhenoMeNal: processing and analysis of metabolomics data in the cloud.

Gigascience 2019 02;8(2)

Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.

Background: Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution.

Findings: PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm.

Conclusions: PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and 'omics research domains.
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http://dx.doi.org/10.1093/gigascience/giy149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377398PMC
February 2019