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8,924 results for “formation”
Quenching of star formation from a lack of inflowing gas to galaxies
<p>This dataset provides HST and ALMA mosaics of the REQUIEM-ALMA survey of six strong gravitationally lensed quiescent galaxies at z=1.6 to z=3.2 (MRG-M1341, MRG-M0138, MRG-M2129, MRG-M0150, MRG-M0454, MRG-M1423) from Whitaker et al. (2021). The HST mosaics were produced with the <a href="https://github.com/gbrammer/grizli">grizli</a> software module. The ALMA data products include the full spectrally-averaged continuum data weighted for optimum sensitivity (with MRG-M2129 and MRG-M0138 including a correction for the primary beam response).</p>
Data for "Formation of very large 'blocky alpha' grains in Zircaloy-4" by V. Tong and T.B. Britton published in Acta Materialia (2017)
<p>Data for "Formation of very large ‘blocky alpha’ grains in Zircaloy-4"</p> <p>Vivian S Tong, T Ben Britton<br> Department of Materials, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK</p> <p>For more information please contact: b.britton@imperial.ac.uk (Ben Britton)</p> <p>---</p> <p>Figures_data.xlsx contains the data for line graphs in the following figures on separate labelled sheets:<br> Figure 2(a)<br> Figure 2(b)<br> Figure 4(c)<br> Figure 6.</p> <p>Figures_data.xlsx also contains the HR-EBSD GND density data in Figures 3(b) and 3(d), which have been plotted on a log10 colour scale in the published figure.</p> <p>The EBSD orientation data have been exported as text files (.ctf) directly from Bruker Esprit 2.1 software.</p> <p>Orientations are described using Bruker EBSD software conventions, described in the paper "Tutorial: Crystal orientations and EBSD — Or which way is up?" by Britton et al.(http://dx.doi.org/10.1016/j.matchar.2016.04.008).</p> <p><br> EBSD data is provided for the following figures:<br> Figure 3(a)<br> Figure 3(c)<br> Figure 4(b), Figure 5(c), Figure 7(c) -- these are all the same dataset<br> Figure 5(b)<br> Figure 6 - EBSD maps of these two datsets were not shown, but this is the raw data from which twin fractions were calculated.<br> Figure 7(a)<br> Figure 7(b)</p>
Archaeological Survey of India Collections: Burma Circle, 1907-13. Photo 1004/2 : 1907-1913 (.jpg format)
<p>This is a digitized collections of photos held by the British Library (catalog record photo 1004/2). These photos were taken by the Archeological Survey of India (Burma Circle) between 1907-1913. The digitization was conducted by the photography lab of the British Library as part of the Pyu epigraphy sub-project (PI, Nathan W. Hill of SOAS University of London) of the ERC synergy grant "Beyond Boundaries: Religion, Region, Language and the State" (Identifier: ASIA 609823). The original photographs are under crown copyright, which means that sufficient time has past for them to be distributed to the public. Here is the record from the BL--</p> <ul> <li><strong>Title:</strong> <p>Archaeological Survey of India Collections: Burma Circle, 1907-13. Photographer(s): Archaeological Survey of India</p> </li> <li><strong>Collection Area: </strong> Visual Arts</li> <li><strong>Reference: </strong> Photo 1004/2</li> <li><strong>Creation Date: </strong> 1907-1913</li> <li><strong>Extent and Access: </strong><br> <strong>Extent: </strong>321 items<br> <strong>Conditions of Use: </strong>Appointment Required to view these records. Please consult Asian and African Studies Print Room staff.</li> <li><strong>Language: </strong> Not applicable</li> <li><strong>Contents and Scope: </strong><br> <strong>Contents: </strong> <p>Blue half-leather album, 385x322mm, containing prints mounted on pages interleaved with tissue. The photographs were taken by the Archaeological Survey, Burma, between 1907-13, and listed in the annual Report of the Superintendent... Copies of each year's report precede the photographs for that year, as follows:</p> <p>Year Photo no</p> <p>1907-08 510-609</p> <p>1908-09 610-750</p> <p>1909-10 751-859</p> <p>1910-11 860-962</p> <p>1911-12 963-1053</p> <p>1912-13 1054-1182</p> <p>The photographs, including views of Burmese architecture, sculpture and relics, were taken under the direction of the Superintendent, a post held at the time by Taw Sein Ko.</p> <p>Process = Collodio-chloride and gelatine silver prints</p> <p>Photographers = Archaeological Survey of India., ;</p> </li> <li><strong>History: </strong><br> <strong>Immediate Source of Acquisition: </strong> <p>Official Deposit</p> </li> </ul>
Archaeological Survey of India Collections: Burma Circle, 1913-1916. Photo 1004/3 : 1913-1916 (.jpg format)
<p>This is a digitized collections of photos held by the British Library (catalog record photo 1004/3). These photos were taken by the Archeological Survey of India (Burma Circle) between 1913-1916. The digitization was conducted by the photography lab of the British Library as part of the Pyu epigraphy sub-project (PI, Nathan W. Hill of SOAS University of London) of the ERC synergy grant "Beyond Boundaries: Religion, Region, Language and the State" (Identifier: ASIA 609823). The original photographs are under crown copyright, which means that sufficient time has past for them to be distributed to the public. Here is the record from the BL--</p> <ul> <li><strong>Title:</strong> <p>Archaeological Survey of India Collections: Burma Circle, 1913-16. Photographer(s): Archaeological Survey of India</p> </li> <li><strong>Collection Area: </strong> Visual Arts</li> <li><strong>Reference: </strong> Photo 1004/3</li> <li><strong>Creation Date: </strong> 1913-1916</li> <li><strong>Extent and Access: </strong><br> <strong>Extent: </strong>265 items<br> <strong>Conditions of Use: </strong>Appointment Required to view these records. Please consult Asian and African Studies Print Room staff.</li> <li><strong>Language: </strong> Not applicable</li> <li><strong>Contents and Scope: </strong><br> <strong>Contents: </strong> <p>Blue half-leather album, 385x322mm, containing prints mounted on pages interleaved with tissue. The photographs were taken by the Archaeological Survey, Burma, between 1913-16, and listed in the annual Report of the Superintendent... Copies of each year's report precede the photographs for that year, as follows:</p> <p>Year Photo no</p> <p>1913-14 1183-1317</p> <p>1914-15 1318-1490</p> <p>1915-16 1491-1593</p> <p>The photographs, including views of Burmese architecture, sculpture and relics, were taken under the direction of the Superintendent, a post held at the time by Taw Sein Ko.</p> <p>Process = Gelatine silver prints</p> <p>Photographers = Archaeological Survey of India., ;</p> </li> <li><strong>History: </strong><br> <strong>Immediate Source of Acquisition: </strong> <p>Official Deposit</p> </li> </ul>
Archaeological Survey of India Collections: Burma Circle, 1916-22. Photo 1004/4 : 1916-22 (.jpg format)
<p>This is a digitized collections of photos held by the British Library (catalog record photo 1004/4). These photos were taken by the Archeological Survey of India (Burma Circle) between 1916-22. The digitization was conducted by the photography lab of the British Library as part of the Pyu epigraphy sub-project (PI, Nathan W. Hill of SOAS University of London) of the ERC synergy grant "Beyond Boundaries: Religion, Region, Language and the State" (Identifier: ASIA 609823). The original photographs are under crown copyright, which means that sufficient time has past for them to be distributed to the public. Here is the record from the BL--</p> <ul> <li><strong>Title:</strong> <p>Archaeological Survey of India Collections: Burma Circle, 1916-22. Photographer(s): Archaeological Survey of India</p> </li> <li><strong>Collection Area: </strong> Visual Arts</li> <li><strong>Reference: </strong> Photo 1004/4</li> <li><strong>Creation Date: </strong> 1916-1922</li> <li><strong>Extent and Access: </strong><br> <strong>Extent: </strong>238 items<br> <strong>Conditions of Use: </strong>Appointment Required to view these records. Please consult Asian and African Studies Print Room staff.</li> <li><strong>Language: </strong> Not applicable</li> <li><strong>Contents and Scope: </strong><br> <strong>Contents: </strong> <p>Blue half-leather album, 385x335mm, containing prints mounted on pages interleaved with tissue. The photographs were taken by the Archaeological Survey, Burma, between 1916-22 (except for 1917-18 and 1918-19), and listed in the annual Report of the Superintendent ... Copies of each year's report precede the photographs for that year, as follows:</p> <p>Year Photo no</p> <p>1916-17 1594-1743</p> <p>1917-18 No prints</p> <p>1918-19 No prints</p> <p>1919-20 1991-2094</p> <p>1920-21 2095-2203</p> <p>1921-22 2204-2280</p> <p>The photographs, including views of Burmese architecture, sculpture and relics, were taken under the direction of the Superintendent, a post held until 1919 by Taw Sein Ko, and thereafter by his successor Charles Duroiselle.</p> <p>Process = Gelatine silver prints</p> <p>Photographers = Archaeological Survey of India., ;</p> </li> <li><strong>History: </strong><br> <strong>Immediate Source of Acquisition: </strong> <p>Official Deposit</p> </li> </ul> <p> </p>
GO-SHIP Easy Ocean: Formatted and gridded ship-based hydrographic section data
<p><a href="https://www.go-ship.org">GO-SHIP</a> (The Global Ocean Ship-based Hydrographic Investigations Program) has developed the protocols and methods to generate a data product that concatenates all occupations of individual sections into a time-series; the GO-SHIP Easy Ocean. Here we provide access to the analysis-ready gridded GO-SHIP Easy Ocean product that enhances the accessibility of this unique data set that spans four decades, comprised of more than 40 cross-ocean transects, many with multiple repeats.</p> <p>This product, of uniformly calibrated CTD (temperature, salinity and oxygen) data, provides easy access to and use of the high-quality hydrographic temperature and salinity data that span more than 40 years. The GO-SHIP Easy Ocean product will underpin the quality control of autonomous platforms, provide a ready assessment of ocean-only and coupled climate model simulations, and be used in specific research projects. The GO-SHIP Easy Oceanis a companion to the GLODAP inorganic and carbon product. The section data are available from Zenodo in two standard arrangements: Uninterpolated (reported) and interpolated (gridded). For both arrangements, five quantities are recorded; in situ temperature in ITS-90 scale, in situ salinity in PSS-78 scale, the dissolved oxygen concentration in μmol/kg, Conservative Temperature in °C, and Absolute Salinity in g/kg. The data are available in various formats.</p> <p>Cite <a href="https://doi.org/10.1038/s41597-022-01212-w">Katsumata et al (2022)</a> when using this product and include the following acknowledgment statement in any publication or derived product:</p> <p><em>Data were collected and made publicly available by the International Global Ship-based Hydrographic Investigations Program GO-SHIP (https://www.go-ship.org/) and the national programs that contribute to it.</em></p>
Dataset for "Heatwave reveals potential for enhanced aerosol formation in Siberian boreal forest"
<p>This dataset supplements the manuscript "Heatwave reveals potential for enhanced aerosol formation in Siberian boreal forest", Environmental Research Letters, 2023. </p>
Unraveling a synthetic rescue process involved in persisters formation
<p>A common strategy that bacteria utilize to increase their survival under stressful conditions in their natural environments, including antibiotic treatment, is the entry into quiescence, a state of reversible cell growth arrest that offers protection against many environmental insults. Understanding quiescence is an important fundamental question, with relevance in the medical and environmental fields. Little is known about the molecular and physiological determinants that orchestrate survival during this temporary arrest of proliferation, or those that allow a rapid transition back to the proliferating state when conditions again become favorable. In the wide host-range pathogen <em>Salmonella enterica</em> serovar Typhimurium (<em>S</em>. Typhimurium) and other Gram-negative bacteria, this temporary arrest of proliferation induces the expression of the alternative sigma subunit of RNA polymerase, sigma S/RpoS, which remodels global gene expression to reshape the cell physiology and ensure survival under starvation and various stress conditions (<em>i.e. </em>the general stress response).</p> <p>In <em>S</em>. Typhimurium, sigma S is required for stress resistance, biofilm formation and virulence. The incidence of human infections by non-typhoidal <em>Salmonella </em>such as <em>S.</em> Typhimurium increases. These serovars can infect farm animals, thus contaminating animal products, and can be transferred from animal carriers to the environment through fecal matter where they contaminate vegetables, fruits, nuts, and roots. Foodborne diseases caused by <em>Salmonella </em>represent a severe problem to the food supply as well as the public health. <em>S</em>. Typhimurium actively cycles through host and nonhost environments, where it is exposed to a wide variety of stresses, and where sigma S likely plays a crucial role in its persistence.</p> <p>One important aspect of persistence is the phenotypic differentiation of quiescent populations into sub-population(s) of "persisters" that survive in the presence of lethal concentrations of antibiotics. This phenomenon is worsening the worldwide antibiotic crisis, by causing therapy failure and chronic infections and potentially favoring the development of antibiotic resistance. Understanding mechanisms governing bacterial persisters is thus an important topic and a key issue for drug developments. However, despites many studies, the physiological and molecular mechanisms controlling the formation of persisters are poorly understood and controversial. <strong>In the present study we explore the recently discovered and unexpected functional interaction between sigma S and succinate dehydrogenase (Sdh), in the formation of persisters. </strong></p> <p>Persisters are phenotypic variants within a population that survive in the presence of lethal concentrations of antibiotics. When a bacterial population is diluted into fresh medium containing bactericidal antibiotics, a biphasic killing is observed. The bulk of the population, consisting of sensitive cells, dies rapidly and the surviving persisters are killed much more slowly, or do not die during the time course of the experiment. Their regrowth after antibiotic removal yields a new population that has the same sensibility to the antibiotics, as did the parental one. Persisters formation is critically dependent on the growth phase. Despite the identification of a number of genes and pathways involved in persisters formation (toxin-antitoxin modules, SOS and stringent responses, efflux systems, metabolic functions and global regulators), the underlying molecular mechanisms are still poorly understood and controversial. In particular, persisters formation in <em>Escherichia coli</em> K-12 has been reported to be increased, decreased or not affected by a <em>rpoS</em> deletion. A better understanding of physiological parameters favoring persisters formation is critical to develop antipersisters strategies.</p> <p>Succinate dehydrogenase (Sdh), a membrane bound complex that connects the TCA cycle and respiratory chain, is one major target down regulated by sigma S. Negative regulation by sigma S likely targets housekeeping genes that might be deleterious when fully expressed in quiescent cells. Understanding why full expression of those genes has a fitness cost might provide insights into survival mechanisms and weaknesses of quiescent cells, with potential application for antibacterial strategies. To tackle this issue, we used Sdh as a model system. <strong>Our study led us to unravel a synthetic rescue process of a </strong><em><strong>sdh</strong></em><strong> mutation in the formation of persisters. </strong></p> <p>Stationary-phase <em>Salmonella </em>form persisters with a higher frequency than actively growing bacteria, after transfer to fresh medium in the presence of lethal concentrations of ampicillin and ciprofloxacin, but not significant effect of the <em>rpoS</em> deletion on this phenomenon was observed. Surprisingly however, the <em>rpoS</em> deletion suppressed the defect in persister formation of a <em>sdh</em> deletion mutant. Similar results were obtained with independent <em>sdh</em> and <em>sdhrpoS</em> constructs and the mutations did not significantly affect the minimum inhibitory concentration (MIC) of <em>Salmonella</em> for ampicillin and ciprofloxacin. <strong>It is very likely that the </strong><em><strong>rpoS</strong></em><strong> deletion compensates for a metabolic perturbation provoked by the </strong><em><strong>sdh</strong></em><strong> deletion, and key for persister formation. </strong>Since a <em>sdh</em> mutation also decreases persister formation by <em>E. coli </em>and <em>Staphylococcus aureus</em>, the underlying physiological effect might be common to Gram-negative and Gram-positive bacteria. Understanding the molecular and physiological bases of this phenomenon should provide insights into key features driving persisters formation and revival. </p> <p>For references , see the <strong>STUDY</strong> pdf file. </p> <p>The persister assay is described in the <strong>PROTOCOL</strong> pdf file.</p> <p>Strains used are described in the <strong>STRAINS AND PRIMERS</strong> .xlsx file.</p> <p>Results are summarized in the <strong>STUDY</strong> pdf file </p> <p>For detailed data, see the <strong>M1 to M101 persisters</strong> .xlsx files. </p> <p><strong>This work was supported by the French National Research Agency (ANR-19-CE44-0005-01, PERIOMET project).</strong></p> <p>See also:</p> <p>NOREL Francoise, MONTEIL Veronique, DOUCHE Thibaut, & MATONDO Mariette. (2023). Global effects of deletion of the <em>sdh</em> genes, encoding succinate dehydrogenase, and of cobalt on protein abundance in stationary phase <em>Salmonella enterica</em> serovar Typhimurium. [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.8279681">https://doi.org/10.5281/zenodo.8279681</a>. </p> <p>Phégnon, L., Uttenweiler-Joseph, S., & Létisse, F. (2024). <span>Key physiological and metabolic characteristics for the differentiation of quiescent Salmonella's cells into persisters [Data set]. </span>Zenodo. <a href="https://doi.org/10.5281/zenodo.10885905" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10885905</a></p> <p> </p>
IODP Expedition 383 Formation temperature
Formation temperature was measured by the advanced piston corer temperature tool (APCT-3), Sediment Temperature Tool (SET), or sediment temperature pressure tool (SETP) and reduced to in situ temperature and (for SETP) pressure estimates. These data are compiled per instrument run and assigned to a core (the core cut with the APCT-3 cutting shoe or the core following the SET deployment).
Growing Diamonds in the Laboratory to investigate Growth, Dissolution, and Inclusions Formation processes
<p>Dataset for the manuscript : <strong>Growing Diamonds in the Laboratory to investigate Growth, Dissolution, and Inclusions Formation processes</strong></p><p><strong>after </strong>Hélène Bureau, Imène Estève, Caroline Raepsaet, Geeth Manthilake</p><p>It comprises one excel file containing raw SEM EDX data and 10 SEM images of the samples</p>
IODP Expedition 378 Formation temperature
Formation temperature was measured by the advanced piston corer temperature tool (APCT-3), Sediment Temperature Tool (SET), or sediment temperature pressure tool (SETP) and reduced to in situ temperature and (for SETP) pressure estimates. These data are compiled per instrument run and assigned to a core (the core cut with the APCT-3 cutting shoe or the core following the SET deployment).
User study data: Nudges to Mitigate Confirmation Bias during Web Search for Opinion Formation, automatic vs. reflective study
<p>Data of two user studies (282 and 307 participants), investigating the risks and benefits of warning labels with and without obfuscations to mitigate confirmation bias during web search on debated topics.</p> <p> </p> <p>Study Variables (study 1 and study 2)</p> <p> </p> <p> display_con: Search result display<br> - Study 1<br> - 1: targeted warning label with obfuscation<br> - 2: random warning label with obfuscation<br> - 3: regular (no intervention)<br> - Study 2<br> - 1: targeted warning label with obfuscation<br> - 2: targeted warning label without obfuscation<br> - 3: random warning label with obfuscation<br> - 4: random warning label without obfuscation<br> - 5: regular (no intervention)<br>- CRT_cat: Cognitive reflection<br> - 1: intuitive<br> - 2: analytic<br>- topic: Assigned debated topic<br> - 1: Is drinking milk healthy for humans? <br> - 2: Is homework beneficial?<br> - 3: Should people become vegetarian?<br> - 4: Should students have to wear school uniforms?<br>- clicksup_prop: Clicks on attitude-confirming (AC) search results (proportion of all clicks)<br>- clickwarn_prop: Clicks on warning label (WL) search results (proportion of all clicks)<br>- show_clicked: Clicks on show-button (number of clicks, only in conditions with obfuscation)<br>- accuracy_bias: Accuracy bias estimation (Difference between a) observed bias (as the proportion of attitude-confirming clicks) and b) perceived bias (reported in the post-interaction questionnaire and re-coded into values from 0 to 1), positive values indicate an overestimation of bias)<br>- att_change: Attitude change (Difference between attitude reported in the pre-interaction questionnaire and the post-interaction questionnaire. Negative values indicate an attitude change in the attitude-opposing direction, while positive values indicate an attitude strengthening in the attitude-supporting direction.)<br>- knowledge_1: Self-reported prior knowledge (Reported on a seven-point Likert scale ranging from non-existent to excellent as a response to how they would describe their knowledge on the topic they were assigned to)<br>- N_clicks: Cumulative clicks (Number of all clicks on search results)<br>- NFC: Need for Cognition (Mean response to 4-item subset of the NFC questionnaire)<br>- UX_usability: Usability (Mean of responses on a seven-point Likert scale to the module "usability"from the meCUE 2.0 questionnaire)<br>- UX_usefulness: Usefulness (Mean of responses on a seven-point Likert scale to the module "usefulness"from the meCUE 2.0 questionnaire)</p>
Source data for publication "Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation"
<p><strong>This dataset contains the source data for the figures in the following publication: </strong></p> <p><strong>Title: </strong>Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation</p> <p><strong>Authors: </strong>Sanika Vaidya, Dibya Saha, Daniel K.H. Rode, Gabriel Torrens, Mads F. Hansen, Praveen K. Singh, Eric Jelli, Kazuki Nosho, Hannah Jeckel, Stephan Göttig, Felipe Cava, Knut Drescher</p> <p><strong>Journal: </strong>Nature Microbiology, 2025</p> <p> </p> <p><strong>Description of the dataset: </strong></p> <p>The data is organized by figures in the publication receferenced above. For each figure, there is a XLSX-file that contains the processed data and a ZIP-archive that contains the raw image data. The ZIP-archive also contains readme documents with more detailed descriptions for every set of raw image data. </p> <p>Example: For Figure 1 in the main text of the publication, there following data are available:</p> <ul> <li>raw data: Figure_01.zip</li> <li>processed data: Processed_Source_Data_Figure1.xlsx</li> </ul> <p>Similarly, XLSX-files and ZIP-archives are available for the main text Figures 1-6. For the Extended Data (ED) Figures 1-10, there are XLSX-files available that present the data shown in each figure. Only some of the Extended Data Figures present results based on image data - therefore raw image data ZIP-archives are only available for ED Figures 3, 6, 7, 8, 9, 10.</p>
IODP Expedition 367 Formation temperature
Formation temperature was measured by the advanced piston corer temperature tool (APCT-3), Sediment Temperature Tool (SET), or sediment temperature pressure tool (SETP) and reduced to in situ temperature and (for SETP) pressure estimates. These data are compiled per instrument run and assigned to a core (the core cut with the APCT-3 cutting shoe or the core following the SET deployment).
Imputation panel for low-pass whole genome sequencing (GLIMPSE2 format)
<p>This dataset includes autosomal genotypes from the 1000 Genomes +HGDP project (<a href="https://doi.org/10.1101/2023.01.23.525248" target="_blank" rel="noopener">10.1101/2023.01.23.525248 </a>) as well as X chromosome genotypes from the NY Genome Center (as of yet, a comparable dataset that includes HGDP is not available for the X; see 10.1016/j.cell.2022.08.004). The genotypes were down-sampled so as to be appropriate for low-pass imputation; uncertain phase calls were removed (any PP tags), and individuals deemed to be outliers or relatives (based on autosomal data, as per the first citation) were also removed. Similarly, singleton polymorphisms were also excluded. Hemizygous genotypes on the X were converted into (quasi) diploid genotypes.</p> <p>These data were then converted into a binary imputation panel format using glimpse v2 (https://odelaneau.github.io/GLIMPSE/; using the static binaries provided). The "chunk" size was doubled from the defaults (which considers a minimum number of snps, genetic length and physical length) so as to be more performant.</p>
Dataset for: Oxygen isotope fractionation of O2 consumption through abiotic photochemical singlet oxygen formation pathways
<p>Dataset containing raw and treated isotope-ratio mass spectrometry data as well as O2 concentration data, accompanying the manuscript "Oxygen isotope fractionation of O2 consumption through abiotic photochemical singlet oxygen formation pathways".</p>
Simulated datasets for detector and particle flow reconstruction: CLIC detector, machine learning format
<p><strong>Synopsis</strong></p> <p>Machine-learning friendly format of tracks, clusters and target particles in electron-positron events, simulated with the CLIC detector. Ready to be used with <a href="https://zenodo.org/records/14930299">jpata/particleflow:v2.3.0</a>. Derived from the EDM4HEP ROOT files in <a href="https://zenodo.org/record/8260741">https://zenodo.org/record/8260741</a>.</p> <ul> <li>clic_edm_ttbar_pf.zip: e+e- -> ttbar, center of mass energy at 380 GeV</li> <li>clic_edm_qq_pf.zip: e+e- -> Z* -> qqbar, center of mass energy at 380 GeV</li> <li>clic_edm_ww_fullhad_pf.zip: e+e- -> WW -> W decaying hadronically, center of mass energy at 380 GeV</li> <li>clic-tfds.ipynb: an example notebook on how to load the files</li> </ul> <p><strong>Contents</strong></p> <p>Each .zip file contains the dataset in the <a href="https://github.com/tensorflow/datasets">tensorflow-datasets</a>, <a href="https://github.com/google/array_record">array_record</a> format. We have split the full datasets into 10 subsets, due to space considerations on zenodo, two subsets from each dataset are uploaded. Each dataset contains a train and test split of events.</p> <p><strong>Dataset semantics (to be updated)</strong></p> <p>Each dataset consists of events that can be iterated over using the tensorflow-datasets library and used in either tensorflow or pytorch. Each event has the following information available:</p> <ul> <li>X: the reconstruction input features, i.e. tracks and clusters</li> <li>ytarget: the ground truth particles with the features ["PDG", "charge", "pt", "eta", "sin_phi", "cos_phi", "energy", "jet_idx"], with "jet_idx" corresponding to the gen-jet assignment of this particle</li> <li>ycand: the baseline Pandora PF particles with the features ["PDG", "charge", "pt", "eta", "sin_phi", "cos_phi", "energy", "jet_idx"], with "jet_idx" corresponding to the gen-jet assignment of this particle</li> </ul> <p>The full semantics, including the list of features for X, are available at https://github.com/jpata/particleflow/blob/v2.3.0/mlpf/heptfds/clic_pf_edm4hep/utils_edm.py and https://github.com/jpata/particleflow/blob/v2.3.0/mlpf/data/key4hep/postprocessing.py.</p>
SARS-CoV-2 wastewater surveillance data and metadata in the Open Data Model format. Part 1: Québec City
<p>SARS-CoV-2 wastewater surveillance data and metadata in the Open Data Model format. Part 1: Québec City Authors</p> <ul> <li>Therrien, J-D<sup>1</sup></li> <li>Maere, T.<sup>1</sup></li> <li>Sanchez-Quete, F.<sup>2</sup></li> <li>Tsitouras, A.<sup>2</sup></li> <li>Goitom, E.<sup>3</sup></li> <li>Cloutier, F.<sup>4</sup></li> <li>Dufour, D.<sup>4</sup></li> <li>Proulx, F. <sup>4</sup></li> <li>Nicolaï, N.<sup>1</sup></li> <li>Philippe, R.<sup>1</sup></li> <li>Tohidi, M.<sup>1</sup></li> <li>Dorner, S.<sup>3</sup></li> <li>Frigon, D.<sup>2</sup></li> <li>Vanrolleghem, P.A.<sup>1</sup></li> </ul> <p>Affiliations</p> <ul> <li><sup>1</sup> model<em>EAU</em>, Département de génie civil et de génie des eaux, Université Laval</li> <li><sup>2</sup> Microbial Community Engineering Lab (MiCEL), Department of Civil Engineering, McGill University</li> <li><sup>3</sup> Polytechnique Montréal</li> <li><sup>4</sup> Ville de Québec</li> </ul> <p>General Remarks</p> <p>Wastewater-based surveillance of SARS-CoV-2 virus can detect between 1 and 30 infected individuals per 100,000 (including asymptomatic ones) by analyzing the population's sewage. As such, this method is very attractive since it costs only a fraction of clinical testing (as low as 1%). Human faeces may contain the virus a few days before a person becomes ill. Thus, this approach allows for detection of outbreaks 2-7 days before the increase in reported cases stemming from clinical screening tests (Bibby et al., 2021). Wastewater-based surveillance complements clinical testing by geolocating outbreaks, which may help targeting intensive screening programs. Moreover, it provides a quick indication of whether new public health measures (e.g., masks, social distancing, confinement, and curfew) are effective.</p> <p>Sampling</p> <p>The reported dataset contains open data collected in the province of Québec as part of the SARS-CoV-2 wastewater-based surveillance program <a href="https://www.centreau.ulaval.ca/en/covid/">CentrEau</a>-COVID. Four of the largest cities in the province (Montréal, Laval, Québec City, and Trois-Rivières), as well as the municipalities of four rural regions (Mauricie, Centre-du-Québec, Bas-St-Laurent, and Gaspésie) participated in the program. The entire dataset includes 31 sampling sites covering approximately half the population of the province of Québec (population size of 8.5 million). The timeframe covered by the dataset varies for each site. The earliest surveillance program was launched in March 2020, others followed soon after. Samples were collected using various methods, such as 24h composite samples, grab samples, and passive sampling using variations on the Moore swab method (Schang et al., 2020)</p> <p>Analysis</p> <p>Prior to the analysis of the samples for SARS-CoV-2, physiochemical parameters such as total suspended solids (TSS), turbidity, conductivity, ammonium concentration, and pH were measured. The samples were subsequently concentred by filtration using a MEC filter (0.45 um), followed by total RNA extraction using the Qiagen AllPrep PowerViral DNA/RNA Kit (Qiagen, USA) with some modifications (beta-mercaptoethanol concentration raised to 10% and lysis performed at 55 °C for 30 minutes) (Ahmed et al., 2020). SARS-CoV-2 viral RNA was detected by a one-step RT-qPCR. To assess the RNA recovery rate of the procedure, samples were spiked before extraction with a known concentration of Bovine Respiratory Syncytial Virus (BRSV) using the Zoetis INFORCE 3 vaccine (Zoetis, USA). In addition to SARS-CoV-2, samples were assessed for Pepper Mild Mottle Virus (PMMoV), the daily load of which is hypothesized to represent the fecal load contributions to the samples at a given site and time. PCR conditions and primer used to collect viral data are described in the files <code>primers.md</code> and <code>PCR conditions.md</code>.</p> <p>Compilation</p> <p>The measurements on wastewater samples carried out by the participating laboratories of this study are found in the <code>WWMeasure</code> table. The values provided by municipalities come from laboratories accredited by the Centre d'expertise en analyse environnementale du Québec (CEAEQ), in compliance with the latter's quality assurance protocols. The COVID-19-related public health data found in the <code>CPHD</code> table were collected from the Institut National de Santé Publique du Québec (INSPQ)'s public reports. Wastewater data taken in-situ at the sampling sites (e.g., the flow at pumping stations or water resource recovery facilities (WRRFs)) are found in the <code>SiteMeasure</code> table and were taken by the institutions responsible for managing the sites. All of the data, stemming from multiple sources, were combined into the <a href="https://github.com/Big-Life-Lab/ODM">Open Data Model (ODM)</a> standard format using the <a href="https://github.com/modelEAU/ODM-Import">ODM-Import python package</a> (see also Structure).</p> <p>Validation</p> <p>Wastewater and sample data were manually assessed for quality by our research collaborators. Data points for which the quality appeared to be uncertain were tagged with the value <code>True</code> in the <code>qualityFlag</code> column. Conversely, data deemed of good quality have a quality flag of <code>False</code>. Data that were not checked have a quality flag of <code>NA</code>. Textual comments describing the issues with the data points in more detail are also included in the dataset using the <code>notes</code> column of the relevant tables. Note that data validation was carried out by the data custodians responsible for each city in the dataset according to available resources. As the project continues and data validation is undertaken on more sections of the dataset, data may be re-analyzed, flagged, or commented as needed. Revisions to the dataset will be reported to the best of our ability.</p> <p>Structure</p> <p>The data contained in this dataset has been structured according to the <a href="https://github.com/Big-Life-Lab/ODM">Open Data Model (ODM) for Wastewater-Based Surveillance</a>. This model provides a standardized dictionary to collect and share data and metadata stemming from wastewater-based surveillance programs. By convention, it splits all data into 10+ thematic tables with each record representing a unique measurement, i.e., long format. For convenience, the <code>wide</code> folder presents the data found in all the other tables in a wide format, i.e., multiple measurements are aligned by <code>timestamp</code>, with each column representing a different parameter.</p> <p>Acknowledgements</p> <p>The authors would like to acknowledge that this dataset was collected thanks to the financial support of the Fonds de Recherche du Québec, the Molson Foundation, the Trottier Family Foundation, CentrEau and NSERC. The authors would also like to acknowledge the efforts of Douglas Manuel (Ottawa Hospital) and Howard Swerdfeger (Public Health Agency of Canada) for their original idea for the Open Data Model and continued development.</p> <p>References</p> <ol> <li> <p>Ahmed, W., Bertsch, P.M., Bivins, A., Bibby, K., Farkas, K., Gathercole, A., Haramoto, E., Gyawali, P., Korajkic, A., McMinn, B.R., Mueller, J.F., Simpson, S.L., Smith, W.J.M., Symonds, E.M., Thomas, K. v., Verhagen, R., Kitajima, M., 2020. Comparison of virus concentration methods for the RT-qPCR-based recovery of murine hepatitis virus, a surrogate for SARS-CoV-2 from untreated wastewater. Science of the Total Environment 739. <a href="https://doi.org/10.1016/j.scitotenv.2020.139960">https://doi.org/10.1016/j.scitotenv.2020.139960</a></p> </li> <li> <p>Bibby, K., Bivins, A., Wu, Z., North, D., 2021. Making waves: Plausible lead time for wastewater based epidemiology as an early warning system for COVID-19. Water Research 202, 117438. <a href="https://doi.org/10.1016/j.watres.2021.117438">https://doi.org/10.1016/j.watres.2021.117438</a></p> </li> <li> <p>Schang, C., Crosbie, N., Nolan, M., Poon, R., Wang, M., Jex, A., Scales, P., Schmidt, J., Thorley, B.R., Henry, R., Kolotelo, P., Langeveld, J., Schilperoort, R., Shi, B., Einsiedel, S., Thomas, M., Black, J., Wilson, S., McCarthy, D.T., 2020. Passive sampling of viruses for wastewater-based epidemiology: a case-study of SARS-CoV-2 [WWW Document]. URL <a href="https://www.researchgate.net/publication/347103410\_Passive\_sampling\_of\_viruses\_for\_wastewater-based\_epidemiology\_a\_case-study\_of\_SARS-CoV-2?channel=doi&linkId=5fd800f392851c13fe892393&showFulltext=true">https://www.researchgate.net/publication/347103410\_Passive\_sampling\_of\_viruses\_for\_wastewater-based\_epidemiology\_a\_case-study\_of\_SARS-CoV-2?channel=doi&linkId=5fd800f392851c13fe892393&showFulltext=true</a> (accessed 1.18.21).</p> </li> </ol>
Formatted TCGA clinical and RNA-Seq data for colon adenocarcinoma (COAD) and rectum adenocarcinoma (READ)
<p>COAD/READ/COADREAD_rnaseq_fpkm.txt files contain TCGA RNA-Seq data in FPKM normalisation for colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD).</p> <p>COAD/READ/COADREAD_rnaseq_tpm.txt files contain TCGA RNA-Seq data in TPM normalisation for colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD).</p> <p>COAD/READ/COADREAD_clinical_raw.xlsx files contain TCGA clinical data for patients with colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD).</p> <p>COAD/READ/COADREAD_rnaseq_clinical_raw.xlsx files contain corresponding information of TCGA clinical data and RNA-Seq data for patients with colorectal adenocarcinoma (COAD), rectum adenocarcinoma (READ) or combined (COADREAD).</p>
Supporting Data - Double Ridge Formation over Shallow Water Sills on Jupiter's Moon Europa
<p>This archive contains data produced in support of R. Culberg, D. M. Schroeder, G. Steinbrügge, Double Ridge Formation Over Shallow Water Sills on Jupiter’s Moon Europa, <em>Nature Communications</em>, 2022. This includes the WorldView imagery in Figure 1, the reprocessed radargrams underlying the radar analysis and inversion, and outputs of all inversion and sensitivity test runs. See the README file for a complete description of the files available in this archive.</p>
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