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Metatranscriptomic unigenes catalog of MICROSTORE project
<p><strong>Extracted from Monjot et al., 2023 </strong></p> <p><em>Sequencing data are archived at ENA under accession number PRJEB61527.</em></p> <p>The metatranscriptome derived unigene catalog and the assessment of their expression were obtained as described in Carradec <em>et al.</em> (2018). Paired-ends reads from each metatranscriptomic sample were assembled using velvet (v1.2.07) with a kmer size of 89 as described in Carradec <em>et al.</em> (2018). Isoform detection was performed using oases (v0.2.08). Contigs smaller than 150 bp were removed from further analysis. Contig redundancy was removed using CD-HIT-EST (v4.6.1), with the following parameters: <em>-id 95 -aS 90</em> (95% of nucleic identity over 90% of the length of the smallest sequence). For each cluster of contigs, the longest sequence was kept as reference for the unigene catalog. In order to estimate the expression of each unigene in each sample, cleaned reads were mapped against the reference catalog using the bwa tool (v0.7.15). The following parameters were used: <em>bwa aln -l 30 -O 11 -R 1; bwa sampe -a 20000 -n 1 –N; samtools; rmdup</em>. Low complexity reads were removed. Reads covering at least 80% of read length with at least 95% of identity were retained for further analysis. In the case of several possible best matches, a random one was picked.</p> <p>Proteins were predicted from all unigenes with <em>Transdecoder.LongOrfs</em> followed by <em>TransDecoder.Predict</em> (v5.5.0) using the default parameters. Then, unigenes without predicted protein were used for a second run with a minimum protein length of 70 <em>(-m</em>). Finally, the predicted proteins were tested against the AntiFam database (v7.0) (Eberhardt <em>et al.,</em> 2012) with <em>hmmsearch</em> using the <em>--cut_ga</em> parameter (Eddy, 2011).</p> <p>The KEGG Orthology (KO) identifiers were assigned by KoFamScan (v1.3.0) with the KO’s HMM profiles (2022-01-03 release). For proteins without significant hit, the best hit with an e-value <1e-5 was retained as described in Hu <em>et al.</em>(2018).</p> <p>Taxonomic affiliation was performed on proteins with the MMseqs2 suite (v407b315) (Steinegger & Söding, 2017), against the MetaEuk database (Levy Karin <em>et al.,</em> 2020). Taxonomy was assigned with mmseqs taxonomy and the parameters <em>--tax-lineage 1 --lca-mode 2 --max-seqs 100 -e 0.00001 -s 6 --max-accept 100</em>. The unigene catalog was cleaned of contaminants by excluding proteins and unigenes affiliated to Human, Bacteria, Archaea, Virus and Metazoans. </p> <p> </p> <p><strong>References</strong></p> <p>Carradec, Q., Pelletier, E., Da Silva, C., Alberti, A., Seeleuthner, Y., Blanc-Mathieu, R., et al. (2018) A global ocean atlas of eukaryotic genes. <em>Nat Commun</em> <strong>9</strong>: 373.</p> <p>Eddy, S.R. (2011) Accelerated Profile HMM Searches. <em>PLoS Comput Biol</em> <strong>7</strong>: e1002195.</p> <p>Hu, S.K., Liu, Z., Alexander, H., Campbell, V., Connell, P.E., Dyhrman, S.T., et al. (2018) Shifting metabolic priorities among key protistan taxa within and below the euphotic zone. <em>Environmental Microbiology</em> <strong>20</strong>: 2865–2879.</p> <p>Levy Karin, E., Mirdita, M., and Söding, J. (2020) MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. <em>Microbiome</em> <strong>8</strong>: 48.</p> <p>Steinegger, M. and Söding, J. (2017) MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. <em>Nat Biotechnol</em> <strong>35</strong>: 1026–1028.</p>
NEMARCO project: Dataset for the publication "Development of a new manufacturing route for NiCrSiFeB alloys by Direct Energy Deposition Laser Beam process (LMD)"
<p><strong>LMD dataset</strong></p> <p>This dataset gathers data from different parts of the Laser Metal Deposition metal Additive Manufacturing process (DED-LB). The dataset covers not only the process development data for samples manufacturing and monitored data of the melt pool size during the process, but also the metrics associated to the powder feedstock consumption, energy consumption and process efficiency.</p> <p><strong>Motivation</strong></p> <p>Nickel-based NiCrSiFeB alloy (Ni-Cr-Si-B self-fluxing family) are excellent candidates for replacing Cobalt-based alloys in aeronautical components such as sealing rings, valve seats, sliding bearing seats, etc. In this type of components, commonly manufactured by centrifugal casting and conventional processes, high temperature wear and stiffness under complex thermo-mechanical stresses cause lack of sealing and an increase in the wear rate. Metal additive manufacturing by direct laser metal deposition with powder (p-LMD) is presented as a potential manufacturing route for the complex processing of this type of alloys. This research work deals with the development of a new manufacturing route using p-LMD that ranges from the proper selection of the chemical composition for the starting powders, the development of the LMD process parameters to tackle the challenges associated to the wide solidification range and crack susceptibility of Ni-Cr-Si-B alloys, its monitoring and control, as well as the post- processing required to achieve the manufacture of aeronautical components.</p>
BQE WIM Data Year 6 Project (Evaluation of Integrated Overweight Enforcement System using High Accuracy WIM System and Non-Proprietary ALPR System)
<p>NEW BQE (Brooklyn-Queens Expressway) WIM Data for QB (Queens Bound) for Direct Overweight Enforcement</p>
NEMARCO project: Dataset for the publication "Solidification Path, Strengthening Mechanisms and Hardness of Ni-Cr-Si-Fe-B Self-Fluxing Alloys Obtained by Laser-Directed Energy Deposition (LMD)"
<p><strong>LMD dataset</strong></p> <p>This dataset gathers data from different parts of the Laser Metal Deposition metal Additive Manufacturing process (DED-LB). The dataset covers not only the process development data for samples manufacturing and monitored data of the melt pool size during the process, but also the metrics associated to the powder feedstock consumption, energy consumption and process efficiency.</p> <p><strong>Motivation</strong></p> <p>Nickel-based Ni-Cr-Si-B self-fluxing alloys are excellent candidates to replace Cobalt-based alloys in aeronautical components. In this work, metal additive manufacturing by directed energy deposition using a laser beam (DED-LB, also known as LMD) and gas-atomized powders as a material feedstock is presented as a potential manufacturing route for the complex processing of these alloys. This research deals with the advanced material characterization of these alloys obtained by LMD and the study and understanding of their solidification paths and strengthening mechanisms.</p>
META DATA FOR ENSEMBLE PROJECT
<p>### META DATA FOR ENSEMBLE PROJECT ###</p> <p>This dataset contains raw field measurements and laboratory results of field surveys and experiments performed in the ENSEMBLE project.</p> <p><br> For more information on the ENSEMBLE Project and related publications please see: https://www.epfl.ch/labs/river/ensemble/</p> <p>This dataset contains data and metadata for field surveys conducted in June and August 2019 (ENSEMBLE_2019_Campaign) and data and metadata on a global-change microbiology experiment performed during summer 2020 (ENSEMBLE_2020_Experiment).</p> <p>### ENSEMBLE Field Campaign ###<br> - Sensor data contains a continuous record of key environmental parameter (Temperature, Electrical Conductivity, pH, Turbidity) measured at the the three field sites (Val Sorey, Valroseg and Otemma)<br> - BA contains flow cytometric measurements of bacterial abundance (in cells g-1 dry sediment).<br> - BP contains measurements of bacterial carbon production measured as 3H Leucine incorporation.<br> - Chla-1 and Chla-2 contain data on the spectrophotometric measurement of chlorophyl-a (after extraction in EtOH).<br> - DOC contains data on the concentration of Dissolved Organic Carbon.<br> - EEA contains data on the measurements of Extracellular Enzyme Activities.<br> - EPS contains data on the quantification of Extracellular Polymeric Substances measured as carbohydrate equivalents (Dubois assay).<br> - Field Data contains metadata (ID, coordinates, sampling time, etc) for the field sites.<br> - NUT contains measurements of main water nutrients (NO3, NO2, NH4, and SRP)<br> - SI contains data on water stable isotopes<br> - Water Metadata contains measurements of key environmental data for a subset of sites.</p> <p><br> ### ENSEMBLE Experiment ###</p> <p>- The folder Pictures contains drone images and close-up pictures of the field experiment setup.<br> - CHLA_BA contains measurements of chl-a concentration and bacterial cell counts<br> - metadata contains measurements of key environmental parameter for each treatment over the course of the experiment<br> - NUT contains measurement of main water nutrients (NO3, NO2, NH4, and SRP)<br> </p>
Graphic representation of data set for the project "IRI model performance evaluation for the Mexican region"
<p>Here, we illustrate the modeling and experimental results for vertical Total Electron Content (TEC) over Mexico during the five year period 2018-2022. The results were obtained for the UCOE GNSS receiver station (geographic coordinates: 19.6°N; 101.68°W ). The calculations were made each two hours during the whole period under considerations. The modeling results were obtained using the "International Reference Ionosphere (IRI)" model, which is an empirical climatological model based on ground and space observations of the ionosphere [Bilitza et al., 2022].</p>
DATA of the RESOLVE Project (https://resolve.osug.fr/)
<p>The data set contains all data presented in the ''The RESOLVE project: a multi-physics experiment with a temporary dense seismic array on the Argentière Glacier, French Alps'' paper published in Seismological Research Letter <a href="https://doi.org/10.1785/0220200280">https://doi.org/10.1785/0220200280</a>.</p><p>Here we present a dense seismic array experiment made of 98 3-component seismic stations continuously recording during 35 days in early spring on the Argentière Glacier, French Alps. The seismic dataset is supplemented by a wide range of complementary observations obtained from ground penetrating radar, drone imagery, GNSS positioning and in-situ instrumentation of basal glacier sliding velocities and subglacial water discharge. Through applying multiple processing techniques including event detection from template matching and systematic beamforming, we demonstrate that the present dataset provides enhanced spatial resolution on basal stick slip and englacial fracturing sources as well as novel constraints on heterogeneous nature of the noise field generated by subglacial water flow and on the link between crevasse properties and englacial seismic velocities.</p><p> </p><p>This dataset is also linked to the following paper and dataset:</p><p><i>PNAS paper: </i><strong>Observing the subglacial hydrology network and its dynamics with a dense seismic array</strong></p><p><a href="https://doi.org/10.1073/pnas.2023757118">https://doi.org/10.1073/pnas.2023757118</a>.</p><p>GRL paper: <strong>Dynamic Imaging of Glacier Structures at High-Resolution Using Source Localization With a Dense Seismic Array</strong></p><p><a href="https://doi.org/10.1029/2021GL095996">https://doi.org/10.1029/2021GL095996</a></p><p><i>DATASET: </i><strong>Seismic source location with a match field processing approach during the RESOLVE dense seismic array experiment on the Glacier d'Argentiere</strong></p><p><a href="http://10.5281/zenodo.5645545">10.5281/zenodo.5645545</a></p><p> </p>
Transliterated Fragments of the Electronic Babylonian Literature Project (eBL)
<pre>Data from Paper "Transliterated Fragments of the Electronic Babylonian Literature Project (eBL, https://www.ebl.lmu.de/)</pre> <p>Use together with code https://github.com/ElectronicBabylonianLiterature/tansliterated-fragments</p>
Synthetic in-situ T/S data over 1993-2018 from a NEMO-based simulation of the IMHOTEP project
<p>"Synthetic observations" of in-situ Temperature and Salinity profiles as a function of depth have been extracted online during the production of the global, NEMO-based experiment ** IMHOTEP-GAIc**, at every single time and location (in x,y,z dimensions) where a true in-situ profile exists in the ENACT-4 database (Good et al 2013) over the simulation period: 1980-2018. This global ocean/sea-ice/iceberg simulation uses the NEMO model, and has a horizontal resolution of 1/4°. The atmospheric forcing applied at the surface is based on the JRA reanalysis (Kobayashi et al., 2015) and varies over the full range of time-scales from 6 hours to multi-decadal. The freshwater runoff forcing applied to the experiment is fully-variable (daily to multi-decadal) based on the ISBA-CTRIP hydrographic reanalysis for rivers (Decharme et al., 2019) and from altimeter data and regional GCM simulations for the liquid and solid discharges from the Greenland ice-sheet (Mouginot et al 2019). These runoffs are only climatological around Antarctica. The synthetic in-situ T/S dataset from the model is available over the period 1993-2018.</p><p>See the README file for more information. And online documentation is also available here: https://doc-imhotep.readthedocs.io/en/latest/6-Synthetic-Obs.html</p>
CO2SMOS Project_Clostridium autoethanogenum 2,3-BDO - zenodo
<p><span>CO2SMOS’ task 3.1.1 aims at optimizing syngas fermentation process parameters for 2,3-BDO production using improved Clostridium spp. This dataset compiles the fermentation conditions and growth and 2,3-BDO production parameters as well as the chromatograms used to quantify that production</span></p>
Examples of PET tracers synthesized via arene C-H radiofluorination (A) Maximum intensity projection (MIP) PET images of [18F]Fenoprofen (42) demonstrate higher uptake in TPA-treated mouse ear
<p>Examples of PET tracers synthesized via arene C-H radiofluorination (A) Maximum intensity projection (MIP) PET images of [18F]Fenoprofen (42) demonstrate higher uptake in TPA-treated mouse ear (A-1) compared with control (A-2) mouse ear. (B) PET/CT images demonstrate preferential tumor (MCF-7) accumulation of 39, compared with longer blood circulation and higher non-specific binding of 41 at 1 hour post-injection. (C) Structures of the tracers used in the preceding panels are shown.</p>
Photomedicine Project 14: PBMT for Performance Enhancement in SOF
ClinicalTrials.gov study NCT06380179. IPD Sharing: YES. Countries: 1. Publications: 22.
Project MIMIC (Maximizing Implementation of Motivational Incentives in Clinics)
ClinicalTrials.gov study NCT03931174. IPD Sharing: YES. Countries: 1. Publications: 5.
The UnProcessed Pantry Project (UP3)
ClinicalTrials.gov study NCT04241133. IPD Sharing: YES. Countries: 1. Publications: 2.
Project SMART Automated Pillbox Study
ClinicalTrials.gov study NCT04418076. IPD Sharing: NO. Countries: 1. Publications: 1.
The Digital Wellbeing Project
ClinicalTrials.gov study NCT05061966. IPD Sharing: YES. Countries: 1. Publications: 1.
The BE WITH Project: A Partially Nested Randomized Control Trial (PN-RCT)
ClinicalTrials.gov study NCT07204444. IPD Sharing: NO. Countries: 1. Publications: 26.
TYRO Couples Project Study
ClinicalTrials.gov study NCT05267236. IPD Sharing: NO. Countries: 1. Publications: 5.
Data: Applying stochastic and Bayesian integral projection modeling to amphibian population viability analysis
Open the record for dataset details and reuse information.
Biweekly soil-moisture in the 18 CARBONO Project plots, La Selva Biological Station, March 1998-October 2018
Open the record for dataset details and reuse information.
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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.