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PICASO 3.0 Atmospheric Models of WASP-39 b for the JWST Transiting Exoplanet Community Early Release Science Program
<p><strong>OVERVIEW</strong></p> <p>The exoplanetary atmospheric models used in the recent <a href="https://www.nature.com/articles/s41586-022-05269-w">discovery of CO<sub>2 </sub>in WASP- 39 b's atmosphere</a> by the JWST transiting exoplanet community early release science program are presented here. These models are also being used to analyze multiple observations of WASP 39-b obtained using various JWST instruments and observational modes by the transiting exoplanet ERS team. The 1D Radiative-Convective-Thermochemical Equilibrium (RCTE) atmospheric models were computed using the open-source 1D climate model <a href="https://natashabatalha.github.io/picaso/">PICASO 3.0</a> (<a href="https://ui.adsabs.harvard.edu/abs/2022arXiv220807836M/abstract">Mukherjee et al. (2022)</a>). These atmospheric models were then post-processed with condensation clouds using the open-source cloud model <a href="https://natashabatalha.github.io/virga/">VIRGA</a> (<a href="https://ui.adsabs.harvard.edu/abs/2022ApJ...925...33R/abstract">Rooney et al. (2022)</a>). The atmospheric models were also post-processed with the 1D photochemical network code <a href="https://github.com/exoclime/VULCAN">VULCAN</a> (<a href="https://arxiv.org/abs/2108.01790">Tsai et al. (2021)</a>) to explore photochemistry in WASP-39 b's atmosphere.</p> <p><strong>1D RCTE CLOUD-FREE MODELS</strong></p> <p>The base 1D RCTE grid includes atmospheric metallicity points at 0.1, 0.3, 1.0, 3.0, 10.0, 30.0, 50.0, and 100.0x solar values. The Carbon-to-Oxygen (C/O) ratio value is varied between four values - 0.23, 0.46, 0.69, and 0.92. The intrinsic temperature of the planet has been varied across 100, 200, and 300 K, whereas two values of the heat redistribution factor - 0.4 and 0.5 are included. A heat redistribution factor of 0.5 corresponds to the case of full heat redistribution. With these grid points, the grid includes a total of 8x4x3x2= 192 different models.</p> <p>These models are in the "RCTE_cloud_free.zip" folder. The naming scheme of these files is "profile_eq_planet_[T_int]_grav_4.5_mh_[MH]_CO_[CtoO]_sm_0.0486_v_[rfacv]_.nc" where [T_int] represents the intrinsic temperature of the planet, [MH] is the log<sub>10 </sub>of the atmospheric metallicity relative to solar, [CtoO] is the C/O ratio relative to solar, and [rfacv] is the heat-redistribution factor. So, a metallicity value of 0.3xsolar will have a [MH] value of -0.5, and a C/O 0.46 is considered 1xsolar and will correspond to [CtoO]=1. [T_int] and [rfacv] can assume values described in the previous paragraph.</p> <p><strong>1D RCTE CLOUDY MODELS</strong></p> <p>The base 1D RCTE cloud-free models were post-processed to include condensation cloud species Na<sub>2</sub>S, MnS, and MgSiO<sub>3</sub>. The cloud structure and optical property calculations were performed using the VIRGA model where the sedimentation efficiency <em>f<sub>sed </sub></em>and the vertical eddy diffusion coefficient (<em>K<sub>zz</sub></em>) are free parameters. For the cloudy models, 5 <em>f<sub>sed </sub></em> values - 0.6, 1, 3, 6, and 10 were used along with 3 different values of log<sub>10</sub><em>K<sub>zz </sub></em>- 5, 7, 9, and 11, where <em>K<sub>zz </sub></em>is in cm<sup>2</sup>/s. These models are included in the "RCTE_cloudy.zip" folder following the naming structure "profile_eq_planet_[T_int]_grav_4.5_mh_[MH]_CO_[CtoO]_sm_0.0486_v_[rfacv]_kzz_1e[log10Kzz]_fsed_[fsed].cld.nc" where two other variables are added in the name - [log10Kzz] and [fsed]. Both of these variables can take values listed here.</p> <p><strong>PHOTOCHEMICAL CLOUD-FREE MODELS</strong></p> <p>A much smaller subset of the base 1D RCTE models were post-processed with the 1D photochemical network code VULCAN to simulate the effects of vertical mixing and photochemistry in WASP-39 b's atmosphere. log<sub>10</sub><em>K<sub>zz </sub></em>was varied again between the 5, 7, 9, and 11 for this purpose. These files are named as "profile_diseq_planet_[T_int]_grav_4.5_mh_[MH]_CO_[CtoO]_sm_0.0486_v_[rfacv]_kzz_1e[log10Kzz].nc" and can be found in the "photochem_cloud_free.zip" folder.<br> <br> <strong>PHOTOCHEMICAL CLOUDY MODELS</strong></p> <p>The photochemical models were post-processed with clouds to simulate a cloudy atmosphere with disequilibrium chemistry. The <em>f<sub>sed </sub></em> and log<sub>10</sub><em>K<sub>zz </sub></em> grid system for the RCTE cloudy models has been used again for these models as well. These files are in the "photochem_cloudy.zip" folder and are named according to the format "profile_diseq_planet_[T_int]_grav_4.5_mh_[MH]_CO_[CtoO]_sm_0.0486_v_[rfacv]_kzz_1e[log10Kzz]_fsed_[fsed].cld.nc".</p> <p><strong>FILE FORMATTING AND USAGE</strong></p> <p>All the files are released in the <a href="https://docs.xarray.dev/en/stable/">xarray</a> format. Each model has one single xarray file containing all metadata of that model. This metadata includes the input parameters used to compute the model, for example, the metallicity, C/O ratio, and intrinsic temperature. The temperature-pressure (<em>T(P)</em>) profile and the volume mixing ratio profiles of all the different gases in each model is also included in the metadata. The computed transmission spectrum of the model planet from 0.3-6 microns is included in the same file as well. The spectrum is calculated with resampled opacities at a spectral resolution of 60,000, but they should be re-binned at a spectral resolution of 3000 or less for comparison with observed data. For cloudy models, the wavelength dependant optical depth, asymmetry parameter, and single scattering albedo for each atmospheric layer are included in these xarray files.</p> <p>We refer to this <a href="https://natashabatalha.github.io/picaso/notebooks/codehelp/data_uniformity_tutorial.html#Reading/interpreting-an-xarray-file">PICASO tutorial</a> for reading/writing these xarray files. The spectrum from these xarray files can be easily extracted using the following code.</p> <pre><code class="language-python">import xarray as xr path = "path/to/files" ds_sm = xr.open_dataset(path+"profile_eq_planet_300_grav_4.5_mh_+2.0_CO_2.0_sm_0.0486_v_0.5_.nc") # for spectrum wavelength = ds_sm['wavelength'].values transit_depth = ds_sm['transit_depth'].values # for T(P) profile temperature = ds_sm['temperature'].values pressure = ds_sm['pressure'].values</code></pre> <p><a href="https://github.com/natashabatalha/picaso/blob/master/docs/notebooks/fitdata/GridSearch.ipynb">This tutorial</a> shows how to use these models to analyze the NIRSpec Prism observations of WASP-39 b, which led to <a href="http://www.nature.com/articles/s41586-022-05269-w">CO<sub>2 </sub>detection</a>. Please note that the folders must be unzipped before using them with this notebook.</p> <p><strong>CREDITS</strong></p> <p>If you use these modeling products in your work, please cite this zenodo repository along with the following papers depending on the part of the grid being used:</p> <p>1) RCTE_cloud_free.zip</p> <p> <a href="https://ui.adsabs.harvard.edu/abs/2022arXiv220807836M/abstract">Mukherjee et al. (2022)</a>, <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...878...70B/abstract">Batalha et al. (2019)</a> </p> <p>2) RCTE_cloudy.zip</p> <p><a href="https://ui.adsabs.harvard.edu/abs/2022ApJ...925...33R/abstract">Rooney et al. (2022)</a>, <a href="https://ui.adsabs.harvard.edu/abs/2022arXiv220807836M/abstract">Mukherjee et al. (2022)</a>, <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...878...70B/abstract">Batalha et al. (2019)</a> </p> <p>3) photochem_cloud_free.zip</p> <p> <a href="https://arxiv.org/abs/2108.01790">Tsai et al. (2021)</a> , <a href="https://ui.adsabs.harvard.edu/abs/2022arXiv220807836M/abstract">Mukherjee et al. (2022)</a>, <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...878...70B/abstract">Batalha et al. (2019)</a> </p> <p>4) photochem_cloudy.zip</p> <p> <a href="https://arxiv.org/abs/2108.01790">Tsai et al. (2021)</a> , <a href="https://ui.adsabs.harvard.edu/abs/2022arXiv220807836M/abstract">Mukherjee et al. (2022)</a>, <a href="https://ui.adsabs.harvard.edu/abs/2019ApJ...878...70B/abstract">Batalha et al. (2019)</a>, <a href="https://ui.adsabs.harvard.edu/abs/2022ApJ...925...33R/abstract">Rooney et al. (2022)</a></p> <p> </p>
Supporting data: Land-use change alters the mechanisms assembling rainforest mammal communities in Borneo
<p>These supporting data files were used in the analyses for a forthcoming<em> </em>paper (DOI to be confirmed). The two files consist of: </p> <p>1. Combined camera trap and live trap species-abundance matrix. Each row corresponds to a separate location, with species in different columns. Old-growth forest, logged forest and oil palm plantation locations have the prefixes "Old", "Log" and "Palm", respectively. Values in each cell are the number of independent captures (as defined in the paper) per seven days summed over the camera- and live-trapping protocols.</p> <p>2. Covariate data for each location, covering habitat structure, topography and local landscape context (covariates as defined in the paper). </p>
Triggering Sustainable Biogas Energy Communities through Social Innovation- ISABEL ---- Social Innovation and Community energy best preactices, methods and tools across Europe ----Semi-structured interviews from communities
<p>Having identified through the literature review various success and failure factors for social innovation applied to community energy projects, ISABEL has further conducted 18 semi-structured interviews of a range of stakeholders. The interviewee sample was a convenience sample of participants in existing projects and thus, inevitably, they are able to speak more to successful than unsuccessful projects and they likely have had less exposure to obstacles to the success of their projects. T The interviews have focused on identifying answers to the questions: <em>What were the key success factors? What obstacles were overcome? How? Participants were also asked to specify the type of renewable energy and community energy model. </em></p>
Supplementary material 1 from: Spafford R, Lortie C, Butterfield B (2013) A systematic review of arthropod community diversity in association with invasive plants. NeoBiota 16: 81-102. https://doi.org/10.3897/neobiota.16.4190
Supplementary material 1 from: Spafford R, Lortie C, Butterfield B (2013) A systematic review of arthropod community diversity in association with invasive plants. NeoBiota 16: 81-102. https://doi.org/10.3897/neobiota.16.4190
Supplementary material 2 from: Spafford R, Lortie C, Butterfield B (2013) A systematic review of arthropod community diversity in association with invasive plants. NeoBiota 16: 81-102. https://doi.org/10.3897/neobiota.16.4190
Supplementary material 2 from: Spafford R, Lortie C, Butterfield B (2013) A systematic review of arthropod community diversity in association with invasive plants. NeoBiota 16: 81-102. https://doi.org/10.3897/neobiota.16.4190
Data archive: Trophic structure of cold-water coral communities revealed from the analysis of tissue isotopes and fatty acid composition
<p>Data belonging to the paper: </p> <p>Dick van Oevelen, Gerard C. A. Duineveld, Marc S. S. Lavaleye, Tina Kutti and Karline Soetaert (2017) Trophic structure of cold-water coral communities revealed from the analysis of 55 tissue isotopes and fatty acid composition. Marine Biology Research, DOI: https://doi.org/10.1080/17451000.2017.1398404</p> <p>Abstract:</p> <p>The trophic structure of cold-water coral reef communities at two contrasting locations, the 800-<br> m deep Belgica Mounds (Irish margin) and 300-m deep Træna reefs (Norwegian Shelf), was<br> investigated using stable isotope (δ13C and δ15N) and fatty-acid composition analysis. A<br> broad range of specimens, with emphasis on (commercial) fish species, and organic matter<br> sources were sampled using a variety of tools. Irrespective of the environmental and<br> geographical setting, the δ15N values indicated that the food web encompasses roughly 1.5<br> to 3 trophic levels. Mobile echinoderms, i.e. sea urchins and sea stars, had highest δ15N<br> values, indicative of a high trophic position in the food web. The fraction of bacterial fatty<br> acids in reef fauna was generally low (<5%), indicating that enhanced bacterial production in<br> the water column through seafloor seepage of nutrients (‘hydraulic theory’) does not form a<br> significant energy pathway into the food web. The high fraction of algal and essential fatty<br> acids in reef fauna and fish at both locations indicates a close coupling with surface<br> productivity, but the transport mechanism depends on the hydrographic setting. At Træna,<br> Calanus copepods and euphausiids form an additional link between primary production and<br> fish, which is largely absent at Belgica Mounds. At Belgica Mounds, the reef community is<br> primarily supported by phytodetritus, as evidenced by the high contribution of algal fatty<br> acids in faunal tissue and seasonal chlorophyll a deposition and marine snow at the reef. The<br> environmental setting of cold-water coral reefs influences the structure of the associated<br> food web.</p>
Dataset for 'Different in the dark: The effect of habitat characteristics on community composition and beta diversity in bromeliad microfauna'
<p>The file contains counting data for bromeliad-inhabiting microfauna (including, heterotrophic nanoflagellates, ciliates, amoeba and rotifers) from samples taken on Ilha do Cardoso, Brazil.</p> <p>Also included are additional Information on abiotic and biotic factors measured (e.g. pH, dissolved oxygen concentration etc.).</p>
R code and data for: How much is enough? Minimum sample sizes in community ecology
<p>minimum_sample_sizes_code.R includes the complete set of instructions used to carry out the analyses in the related manuscript, plus save the computed data files and generate the text figures. data_files.tar.gz includes all of the files generated by the R code.</p>
Data for: Community assembly of the human piercing microbiome
<p>Predicting how biological communities respond to disturbance requires understanding the forces that govern their assembly. We propose using human skin piercings as a model system for studying community assembly after rapid environmental change. Local skin sterilization provides a 'clean slate' within the novel ecological niche created by the piercing. Stochastic assembly processes can dominate skin microbiomes due to the influence of environmental exposure on local dispersal, but deterministic processes might play a greater role within occluded skin piercings if piercing habitats impose strong selection pressures on colonizing species. Here we explore the human ear-piercing microbiome and demonstrate that community assembly is predominantly stochastic but becomes significantly more deterministic with time, producing increasingly diverse and ecologically complex communities. We also observed changes in two dominant and medically relevant antagonists (<em>Cutibacterium acnes </em>and <em>Staphylococcus epidermidis</em>), consistent with competitive exclusion induced by a transition from sebaceous to moist environments. By exploiting this common yet uniquely human practice, we show that skin piercings are not just culturally significant but also represent ecosystem engineering on the human body. The novel habitats and communities that skin piercing produce may provide general insights into biological responses to environmental disturbance with implications for both ecosystem and human health.</p>
MJFF Data Community - Creative Commons Training: Copyright and Open Licensing
<p>This training, provided by Shanna Hollich, the Learning and Training Manager of Creative Commons (CC), was hosted by the Michael J. Fox Foundation's Data Community of Practice (DCOP). For more information on the DCOP, please contact: researchcommunity@michaeljfox.org.</p> <p>In the ever-evolving digital landscape, the management of research outputs, including data licensing and copyright, is of utmost importance. This 1.5-hour training provided a forum for participants to learn more about open licensing and copyright. It also aimed to equip participants with the knowledge and best practices they need to effectively navigate the complexities of CC licensing and copyright when using and generating research outputs such as scholarly publications, datasets, and white papers.<br><br>By the end of the workshop, participants developed an understanding of the basic principles of copyright, how it works, and where it applies. Participants are now able to describe the benefits of open licensing and the basics of how Creative Commons licenses work, have a deeper understanding of how research outputs interact with copyright and open licensing, and know where to find additional information and resources.</p> <p>To access a stream of this video with variable resolution, please <a href="https://share.vidyard.com/watch/5vMMsxsZK6q48yNHsDTkPe" target="_blank" rel="noopener">visit this link</a>.</p>
Assessment of microphytobenthos communities in the Kinzig catchment using photosynthesis-related traits, digital light microscopy and 18S-V9 amplicon sequencing
<p>This folder contains the datasets used in the article submitted to Frontiers in Ecology and Evolution in which we investigated the functional and compositional responses of microphytobenthos communities to surrounding land uses in the Kinzig River catchment, central Germany. We measured photosynthetic biomass using a Benthotorch, and analysed the diatom community using a newly developed digital light microscopy approach and 18S-V9 amplicon sequencing to characterise the whole protistan assemblages at sampling sites located in rural vs. urban areas.</p> <p>The folder contain the following datasets:</p> <p>kinzig2021_18SV9_filtered.csv # microphytobenthos 18SV9 amplicon sequencing data</p> <p>kinzig_paper.csv # OMNIDIA output of diatom data from microscopy and diatom subset from 18SV9 amplicon sequencing (including 4 letters OMINIDIA taxa codes for diatoms)</p> <p>kinzig2021_benthotorch.csv # Photosynthetic biomass (BenthoTorch data)</p> <p>Kinzig2021_fieldData.csv # environmental data</p> <p>env_dataKinz2021.csv # environment dataset</p> <p>Kinzig2021_diatDM&18S.R # Rscript used for analysis</p>
Free Open Source Communities Sustainability: Does It Make a Difference in Software Quality?
<p><strong>Context:</strong> Free and Open Source Software (FOSS) communities' ability to stay viable and productive over time is pivotal for society as they maintain the building blocks that digital infrastructure, products, and services depend on. Sustainability may, however, be characterized from multiple aspects, and less is known how these aspects interplay and impact community outputs, and software quality specifically.</p> <p><strong>Objective: </strong>This study, therefore, aims to empirically explore how the different aspects of FOSS sustainability impact software quality.</p> <p><strong>Method: </strong>16 sustainability metrics across four categories were sampled and applied to a set of 217 OSS projects sourced from the Apache Software Foundation Incubator program. The impact of a decline in the sustainability metrics was analyzed against eight software quality metrics using Bayesian data analysis, which incorporates probability distributions to represent the regression coefficients and intercepts.</p> <p><strong>Results: </strong>Findings suggest that selected sustainability metrics do not significantly affect defect density or code coverage. However, a positive impact of community age was observed on specific code quality metrics, such as risk complexity, number of very large files, and code duplication percentage. Interestingly, findings show that even when communities are experiencing sustainability, certain code quality metrics are negatively impacted.</p> <p><strong>Conclusion:</strong> Findings imply that code quality practices are not consistently linked to sustainability, and defect management and prevention may be prioritized over the former. Results suggest that growth, resulting in a more complex and large codebase, combined with a probable lack of understanding of code quality standards, may explain the degradation in certain aspects of code quality.</p>
Fig. 5 in ONCHOCERCA VOLVULUS transmission in the Mbam valley of Cameroon following 16 years of annual community-directed treatment with ivermectin, and the description of a new cytotype of SIMULIUM SQUAMOSUM
Fig. 5 Mean daily biting rates ± 1 standard error (SE) at the four collection sites based on three collection days each month. Biting rates were highest at the two riverside sites (Bayomen and Nyamongo I) and decreased with increasing distance from the river
Fig. 1 in ONCHOCERCA VOLVULUS transmission in the Mbam valley of Cameroon following 16 years of annual community-directed treatment with ivermectin, and the description of a new cytotype of SIMULIUM SQUAMOSUM
Fig. 1 Map of the study area showing adult and larval blackfly collection sites and dissection stations in relation to the Mbam river. Grey arrows show the direction of river flow and the inset map shows the location of the study area (black star) in Cameroon
Fig. 2 in ONCHOCERCA VOLVULUS transmission in the Mbam valley of Cameroon following 16 years of annual community-directed treatment with ivermectin, and the description of a new cytotype of SIMULIUM SQUAMOSUM
Fig. 2 Historical rainfall and river discharge for Bafia and the lower Mbam river. Bars show mean monthly rainfall (mm) ± 1 standard error (SE) at Bafia for years 1930–1994 [26]; dashed line shows mean monthly river discharge (m3/s) ± 1 standard error (SE) for years 1952–80 for the Goura gauge located on the Mbam river ≈25 km SE of Bafia (4.56703°N, 11.36740°E) [27]
Fig. 4 in ONCHOCERCA VOLVULUS transmission in the Mbam valley of Cameroon following 16 years of annual community-directed treatment with ivermectin, and the description of a new cytotype of SIMULIUM SQUAMOSUM
Fig. 4 Polytene chromosomes of S. squamosum E2 and S. mengense showing a chromosome 1 of S. squamosum E2 with fixed inversions 1S-1 and 1L-3, and inversion 1L-57 which was fixed in the specimens examined, b part of chromosome 3 of S. squamosum E2 male showing sex-linked band dimorphism 3C-Sp and sex-linked heterozygous inversion 3L/82 present in 19/20 male specimens examined,'b'= blister, and c chromosome 1 of S. mengense showing expanded centromere 1CER
Fig. 7 in ONCHOCERCA VOLVULUS transmission in the Mbam valley of Cameroon following 16 years of annual community-directed treatment with ivermectin, and the description of a new cytotype of SIMULIUM SQUAMOSUM
Fig. 7 Results of pool screening showing maximum likelihood estimate of the percentage of S. damnosum s.l. possessing L3 larvae in their heads (± 95% CI) based on black flies collected over the 12-month sampling period. The number above the bar denotes the maximum likelihood point estimate for each site
Fig. 3 in ONCHOCERCA VOLVULUS transmission in the Mbam valley of Cameroon following 16 years of annual community-directed treatment with ivermectin, and the description of a new cytotype of SIMULIUM SQUAMOSUM
Fig. 3 Head and thorax of late-instar larvae showing a S. squamosum E2, and b S. mengense with arrow pointing to tuft of hair-like scales on the anterior dorsum of the thorax
Fig. 6 Seasonal parasite transmission along the lower Mbam river showing a in ONCHOCERCA VOLVULUS transmission in the Mbam valley of Cameroon following 16 years of annual community-directed treatment with ivermectin, and the description of a new cytotype of SIMULIUM SQUAMOSUM
Fig. 6 Seasonal parasite transmission along the lower Mbam river showing a combined parity and infection rates for flies dissected at Bayomen and Nyamongo I riverside sites (L1–L2 = percentage of flies infected with developing parasite stages only, L3H = percentage of flies containing L3 stages in the head), and b monthly transmission potentials at Bayomen, Nyamongo I, and Egona II estimated based on dissection data only. Ondouano not shown since no larvae were found in dissected flies
Figure 5 in Evaluation of vertical and horizontal changes in community structure of zooplankton in a deep dam lake
Figure 5. Tree diagram resulting from average linkage clustering using UPGMA method on the zooplankton community data reported during study period.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.