cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7946648
title: Decaying Turbulence in Molecular Clouds

description: <strong>Introduction</strong> This data release contains a suite of 15 AREPO simulations of a spherical molecular clouds of mass \(M=10^4\text{M}_\odot\) and radius \(R \approx 9\text{pc}\) seeded with different types of decaying turbulence. The initial conditions for each simulation are different, with different turbulent modes: mixed turbulence, purely compressive, and purely solenoidal; and different Virial ratios: gravitationally underbound and overbound clouds. <strong>Simulations</strong> Each of the .zip archives contains a simulation. The simulation name is as follows: <em>&lt;Turbulent mode&gt;&lt;RNG seed&gt;&lt;Virial ratio&gt;</em> where: Turbulent mode can be: M = mixed, C = compressive, S = solenoidal. RNG seed used to generate the turbulence can be: 26, 57 and 90. The Virial ratio can be: <em>none</em> = Virial equilibrium (\(\alpha_\text{vir}=1.0 \)), O = overbound (\(\alpha_\text{vir}=0.6\)), U = underbound (\(\alpha_\text{vir}=2.0\)). Each simulation consists of: Four simulation snapshots, which are AREPO binary files, corresponding to the four epochs of interest: when total mass in sinks/stars is \(250\text{M}_\odot\), \(500\text{M}_\odot\), \(750\text{M}_\odot\), \(1000\text{M}_\odot\). Four density grids, corresponding to the four snapshots, which are ray-casted from the AREPO simulations. Four filament networks identified in the density grids using the tool DisPerSE. <strong>Reading in the files</strong> The simulations are easily read and analyzed using the code released as part of our study, called \(\texttt{fiesta}\): fiesta-astro.readthedocs.io. <strong>Supplementary content</strong> The data release also contains two animations: 2D_temporal_animation.mp4 and 3D_sinkepoch_animation.mp4, which are useful for visualizing the simulations.
DOI: 10.6084/m9.figshare.23734104
title: Microenvironment has little effect on the litter decomposition rate of temperate trees

description: Remaining total and ash-free dry mass, nitrogen (N) content, phosphorus (P) content, and carbon to nitrogen ratio (C/N) of the litter of eight tree species in the Arboretum of the Universidad Austral de Chile, expressed as % of the initial content. Initial values correspond to winter time (0). Harvests were performed in spring (4), summer (7) and autumn (9). Constants of decay are estimated.
DOI: 10.6084/m9.figshare.3761562.v2655
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.21227/85qk-q280
title: Synthetic Retail Dataset Machine Learning Evaluation

description: This study delves into the creation of a synthetic dataset, designed to emulate real-world retail scenarios for the purpose of machine learning (ML) evaluation. Utilizing Python, the dataset was generated with 39,500 unique product identities, with a total of approximately 70,000 samples. These samples were distributed across the product identities based on a chi-square distribution. Each product was assigned a set of attributes, including weight, aisle and shelf numbers, and a restocking threshold. In addition, the dataset incorporated the time elapsed since the last restocking for each product, providing a more comprehensive view of the retail environment.The preprocessing stage was a critical part of the dataset preparation. It involved feature engineering, where new variables were introduced to the dataset. These variables included a binary indicator of whether a product's weight on the shelf is below a certain threshold and the time elapsed since the last restock. These new features were designed to enhance the performance of the ML models by providing additional, relevant information.The initial dataset exhibited an imbalance with respect to the 'need_restock' label. To address this issue, the sklearn resample utility was used to undersample the majority class, aligning it with the minority class count. This process resulted in a balanced dataset, with each class containing 35,040 samples. The dataset was then randomized to ensure diversity and prevent any potential bias in the ML model evaluation.
DOI: 10.6084/m9.figshare.23290226
title: Figshare_data.xlsx

description: Raw data used to create figures in the manuscript " <strong>Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions" </strong>by Irby and Broddrick (https://doi.org/10.21203/rs.3.rs-2602810/v1) Updated 2023-7-23, data for Figure 4 was updated due to using an additional database for mapping prophage regions.
DOI: 10.6084/m9.figshare.23290226.v1
title: Figshare_data.xlsx

description: Raw data used to create figures in the manuscript " <strong>Microbial adaptation to spaceflight is correlated with bacteriophage-encoded functions" </strong>by Irby and Broddrick (https://doi.org/10.21203/rs.3.rs-2602810/v1)
DOI: 10.5281/zenodo.7843839
title: The relation among the ring current, subauroral polarization stream, and the geospace plume: MAGE Simulation of the March 31 2001 Super Storm

description: Open data for Figure 3 to Figure 11 in manuscript, "The relation among the ring current, subauroral polarization stream, and the geospace plume: MAGE Simulation of the March 31 2001 Super Storm". The data was generated by the Multiscale Atmosphere Geospace Environment model. The manuscript is submitted to JGR for review.
DOI: 10.5281/zenodo.8176174
title: Structural, electronic and mechanical properties of double core carbon nanothreads (Supplemental Files)

description: The structures shown here are examples of the double core nanothreads studied in the article entitled “Structural, electronic and mechanical properties of double core carbon nanothreads” submitted to Carbon and authored by Caio M. Miliante, J. P. Dotto de Matos and André R. Muniz.<br> While these structures are shared in the file format used with the VASP program (“.vasp” extension) all the calculations for this article were performed with the Quantum Espresso package, as described in the article. The choice for this file format was chosen because allows for an easier conveying of the atom coordinates alongside the cell parameters in which they were run in and can be visualized with the VESTA program (https://jp-minerals.org/vesta/en).
DOI: 10.5281/zenodo.8176173
title: Structural, electronic and mechanical properties of double core carbon nanothreads (Supplemental Files)

description: The structures shown here are examples of the double core nanothreads studied in the article entitled “Structural, electronic and mechanical properties of double core carbon nanothreads” submitted to Carbon and authored by Caio M. Miliante, J. P. Dotto de Matos and André R. Muniz.<br> While these structures are shared in the file format used with the VASP program (“.vasp” extension) all the calculations for this article were performed with the Quantum Espresso package, as described in the article. The choice for this file format was chosen because allows for an easier conveying of the atom coordinates alongside the cell parameters in which they were run in and can be visualized with the VESTA program (https://jp-minerals.org/vesta/en).
DOI: 10.17909/b92g-sp96
title: SDSSJ1608
DOI: 10.6084/m9.figshare.22105817
title: A tectonic reconstruction model for Aotearoa-New Zealand from the mid-Late Cretaceous to the present day - Supplementary data

description: This document contains descriptions of the data sources and background relating to the development of the tectonic crustal block reconstruction model in the paper ‘A tectonic reconstruction model for Aotearoa-New Zealand from the mid-Late Cretaceous to the present day’ published in the New Zealand Journal of Geology and Geophysics, available at: https://doi.org/10.1080/00288306.2023.2239175
DOI: 10.6084/m9.figshare.22105817.v3
title: A tectonic reconstruction model for Aotearoa-New Zealand from the mid-Late Cretaceous to the present day - Supplementary data

description: This document contains descriptions of the data sources and background relating to the development of the tectonic crustal block reconstruction model in the paper ‘A tectonic reconstruction model for Aotearoa-New Zealand from the mid-Late Cretaceous to the present day’ published in the New Zealand Journal of Geology and Geophysics, available at: https://doi.org/10.1080/00288306.2023.2239175
DOI: 10.15480/882.5960
title: Sediment samples from the weser estuary - lab generated time dependend density profiles and lutocline evolution

description: As part of the FAUST project, both field and laboratory investigations were conducted on the sediment exchange behavior of cohesive sediments in the Weser estuary. A particular focus of the work was the examination of vertical exchange processes at the interface between the water column and highly concentrated suspensions. Since the transitions between the sub-processes of sediment exchange are partially fluid or directly connected, investigations were carried out not only on the predominant aspects of settling and erosion behavior but also on consolidation behavior and rheology of cohesive sediments. The methodology to generate the density profiles is described in the corresponding publication, where the results were published and discussed first hand (https://doi.org/10.3389/feart.2022.916056). In general, an Anton Paar DMA Standard Densimeter has been used to measure the suspensions densities. For very high (approx. &gt;1300 kg/m³) densities a suspension balance has been used as alternative. Lutocline evolution curves are generated by digitization of photographic observations of the lutoclines evolution over time. Information on the composition (approximate fractions of sand, silt and clay) of the sediments used is also given in https://doi.org/10.3389/feart.2022.916056. Data abbreviations are location based: BB - Blexer Bogen, NH - Nordenham, H - Harbour, S - Ship, L - Laboratory, MW - Measurementtrip Weser; Numbers are sample and field trip specific. Natural profiles: e.g. MW-II, NH-13H: Sample number 3 from the second field trip (first 0, second 1,...) on the Weser (MW-II) collected at Position Nordenham. Density profile generated immediately after returning in the harbour (H). Lab generated development of density-depth-profiles: e.g. BB-05 rho_0 = 1065 kg/m³: Sample number 5 from the first field trip on the Weser collected at Position Blexer Bogen having an initially homogeneous density profile of rho_0 = 1065 kg/m³
DOI: 10.7910/dvn/fsq4tq
title: Replication Data for: Intercity relationships between 293 Chinese cities extracted and classified based on collocation analysis on Common Crawl April 2019 corpus

description: This dataset presents relationships between 293 Chinese cities, derived using a toponym co-occurrence method. By employing this toponym co-occurrence analysis method, the strength of an intercity relationship is determined by the frequency at which both city names appear on the same webpage. The data was sourced from the Common Crawl web archive's 2019 April Corpus, which contains approximately 2.5 billion web pages. The primary aim of this dataset is to provide a fresh perspective on intercity relationships, thereby facilitating studies on city network analysis. The dataset not only encourages further research into comparing this innovative city relationship with other established networks but is also a showcase that presents a straightforward methodology that can be applied to other archives within Common Crawl. As such, it paves the way for longitudinal studies that probe the evolution of city networks.
DOI: 10.5281/zenodo.7814499
title: Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing

description: <strong>Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing.</strong> Zhang, Annie, Massachusetts Institute of Technology, ORCID: 0000-0003-3939-2585 DOI: 10.5281/zenodo.7814499 Primary publication DOI: https://doi.org/10.1073/pnas.2305556120 <strong>Folder Structure</strong> Source data are organized based on the parent figures from the main text (Figs 1-6). Source data from supplementary figures associated are placed within the associated parent figure folder. All figures, their associated parent figures, and the experiment names from which these figures are derived are summarized in the 'Summary.xlsx' file. <strong>File Formats</strong> <strong> </strong> 1. Integrated trace files are saved as .dat files. - These trace files are obtained by integrating the fluorescence intensity contained within each DNA spot, or Area of Interest (AOI), over the range of the experimental time frame. They can be read and viewed in Matlab or the Matlab program imscroll, which is publicly available: https://github.com/gelles-brandeis/CoSMoS_Analysis. - Naming of files: The experiment name is specified at the beginning of the file name. The excitation and emission fields are specified using the following abbreviations. Gex: Green excited (Donor excited) Rex: Red excited (Acceptor excited) GexRex: Green and red excited (Donor and acceptor excited) Gem: Green emission (Donor emission) Rem: Red emission (Acceptor emission) To read the .dat integrated trace files in Matlab the user may type: &gt;&gt;[fn fp] = uigetfile % use the dialog box to mouse click on the appropriate *.dat file, then type: &gt;&gt;eval(['load ' [fp fn] ' -mat']) % This loads an aoifits structure array into the Matlab command environment The integrated trace data is stored in the aoifits.data matrix. A description of the columns is in the aoifits.dataDescription. The first five columns within aoifits.data are the most relevant to view fluorescence emission intensities at individual AOIs over time. Column 1: aoinumber Column 2: framenumber Column 3: amplitude (of fluorescence emission) Column 4: xcenter of the aoi Column 5: ycenter of the aoi 2. Time Intervals are stored as excel spreadsheet (.xlsx) files. These files contain the AOI numbers used for analysis and frame numbers that correspond to specific events, such as protein arrival and departure events. 3. For experiments with <em>E</em><sub>FRET</sub> analysis performed, <em>E</em><sub>FRET</sub> values are stored as .mat matrix files. Column 1: Time in seconds after protein colocalization with DNA Column 2: <em>E</em><sub>FRET </sub>values Column 3: AOI number Column 4: Frame number
DOI: 10.5281/zenodo.7814498
title: Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing

description: <strong>Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing.</strong> Zhang, Annie, Massachusetts Institute of Technology, ORCID: 0000-0003-3939-2585 DOI: 10.5281/zenodo.7814499 Primary publication DOI: https://doi.org/10.1073/pnas.2305556120 <strong>Folder Structure</strong> Source data are organized based on the parent figures from the main text (Figs 1-6). Source data from supplementary figures associated are placed within the associated parent figure folder. All figures, their associated parent figures, and the experiment names from which these figures are derived are summarized in the 'Summary.xlsx' file. <strong>File Formats</strong> <strong> </strong> 1. Integrated trace files are saved as .dat files. - These trace files are obtained by integrating the fluorescence intensity contained within each DNA spot, or Area of Interest (AOI), over the range of the experimental time frame. They can be read and viewed in Matlab or the Matlab program imscroll, which is publicly available: https://github.com/gelles-brandeis/CoSMoS_Analysis. - Naming of files: The experiment name is specified at the beginning of the file name. The excitation and emission fields are specified using the following abbreviations. Gex: Green excited (Donor excited) Rex: Red excited (Acceptor excited) GexRex: Green and red excited (Donor and acceptor excited) Gem: Green emission (Donor emission) Rem: Red emission (Acceptor emission) To read the .dat integrated trace files in Matlab the user may type: &gt;&gt;[fn fp] = uigetfile % use the dialog box to mouse click on the appropriate *.dat file, then type: &gt;&gt;eval(['load ' [fp fn] ' -mat']) % This loads an aoifits structure array into the Matlab command environment The integrated trace data is stored in the aoifits.data matrix. A description of the columns is in the aoifits.dataDescription. The first five columns within aoifits.data are the most relevant to view fluorescence emission intensities at individual AOIs over time. Column 1: aoinumber Column 2: framenumber Column 3: amplitude (of fluorescence emission) Column 4: xcenter of the aoi Column 5: ycenter of the aoi 2. Time Intervals are stored as excel spreadsheet (.xlsx) files. These files contain the AOI numbers used for analysis and frame numbers that correspond to specific events, such as protein arrival and departure events. 3. For experiments with <em>E</em><sub>FRET</sub> analysis performed, <em>E</em><sub>FRET</sub> values are stored as .mat matrix files. Column 1: Time in seconds after protein colocalization with DNA Column 2: <em>E</em><sub>FRET </sub>values Column 3: AOI number Column 4: Frame number
DOI: 10.5281/zenodo.8176254
title: Mars Thermal + Non-Thermal Modeling Data from figures

description: This folder contains all the values from all the figures present in the paper titled "Evidence of Non-thermal Hydrogen in the Exosphere of Mars Resulting in Enhanced Water Loss", by Bhattacharyya et al.
DOI: 10.6084/m9.figshare.23734188
title: Base COVID19_final+++.sav

description: data of all patients hospitalized for COID-19 in a tunisian center
DOI: 10.6084/m9.figshare.23734188.v1
title: Base COVID19_final+++.sav

description: data of all patients hospitalized for COID-19 in a tunisian center
DOI: 10.6084/m9.figshare.23734188.v2
title: Base COVID19_final+++.sav

description: data of all patients hospitalized for COID-19 in a tunisian center
DOI: 10.6084/m9.figshare.19128099
title: Identification and differential expression of cold-stress-responsive microRNAs in cold-tolerant and -susceptible <i>Hemerocallis fulva</i> varieties

description: Exploring microRNA (miRNA) expression patterns in <i>Hemerocallis</i> under low-temperature stress helps understanding the mechanisms of miRNA-mediated stress responses. Here, eight separate libraries were generated from the leaves and roots of two different varieties, cold-tolerant ‘Jinyan 7’ and cold-sensitive ‘Lucretius 4’, which were exposed to 20°C and −4°C for 8 h. In total, 333 cold-responsive miRNAs, including 85 putative novel and 248 conserved miRNAs, were identified during different temperature treatments. Under cold-stress conditions, two miRNAs were down-regulated and one was up-regulated in the roots, and no differentially expressed miRNAs were detected in the leaves in ‘Lucretius 4’. In ‘Jinyan 7’, there were two novel and one conserved differentially expressed miRNAs in leaves, whereas three conserved and two novel miRNAs were differentially expressed in roots. The target genes were mainly involved in metabolic processes and cellular components. The differential expression levels of 10 miRNAs were validated using quantitative RT–PCR. Some candidate miRNAs (e.g. ath-miR165a, ath-miR166a, ath-miR395a and novel-miR67) may be involved in plant response-related processes to low-temperature.
DOI: 10.6084/m9.figshare.19128099.v1
title: Identification and differential expression of cold-stress-responsive microRNAs in cold-tolerant and -susceptible <i>Hemerocallis fulva</i> varieties

description: Exploring microRNA (miRNA) expression patterns in <i>Hemerocallis</i> under low-temperature stress helps understanding the mechanisms of miRNA-mediated stress responses. Here, eight separate libraries were generated from the leaves and roots of two different varieties, cold-tolerant ‘Jinyan 7’ and cold-sensitive ‘Lucretius 4’, which were exposed to 20°C and −4°C for 8 h. In total, 333 cold-responsive miRNAs, including 85 putative novel and 248 conserved miRNAs, were identified during different temperature treatments. Under cold-stress conditions, two miRNAs were down-regulated and one was up-regulated in the roots, and no differentially expressed miRNAs were detected in the leaves in ‘Lucretius 4’. In ‘Jinyan 7’, there were two novel and one conserved differentially expressed miRNAs in leaves, whereas three conserved and two novel miRNAs were differentially expressed in roots. The target genes were mainly involved in metabolic processes and cellular components. The differential expression levels of 10 miRNAs were validated using quantitative RT–PCR. Some candidate miRNAs (e.g. ath-miR165a, ath-miR166a, ath-miR395a and novel-miR67) may be involved in plant response-related processes to low-temperature.
DOI: 10.6084/m9.figshare.16869651
title: Generation mean analysis for resistance to bacterial brown spot disease in dry bean

description: Dry bean (<i>Phaseolus vulgaris</i> L.) is a key protein and income source grown worldwide. This study determined gene effects influencing resistance to the bacterial brown spot (BBS) disease caused by <i>Pseudomonas syringae pv. syringae,</i> and estimated heritability in a dry bean cross between A55 (resistant) and cultivar RS7 (susceptible). Generations derived from the parents, namely F<sub>1</sub>, F<sub>2</sub>, two backcross generations, and the parents themselves were analysed. The six generations were cultivated in a randomised block design with two replications and inoculated with BBS isolates at two weeks after planting. Disease scoring was done at two weeks after inoculation using standard scale (1–9), where 1 represented highly resistant, and 9 represented highly susceptible. Generation means differed (<i>P </i>&lt; 0.001), and scaling test parameters A and C were significant (<i>P</i> &lt; 0.001) revealing that variation in data was not sufficiently explained by additive [d] and dominance [h] components. Five parameters <i>viz</i>. mean [m], [d], [h], additive × additive epistasis [i], and dominance × dominance epistasis [l] were significant (<i>P</i> &lt; 0.001). The [h] and [l] effects had contrasting signs, indicating duplicate epistasis. Significant non-additive gene effects, together with moderate heritability, suggested that phenotypic selection for resistance, especially in early segregating generations, would be ineffective in conventional breeding.
DOI: 10.6084/m9.figshare.16869651.v1
title: Generation mean analysis for resistance to bacterial brown spot disease in dry bean

description: Dry bean (<i>Phaseolus vulgaris</i> L.) is a key protein and income source grown worldwide. This study determined gene effects influencing resistance to the bacterial brown spot (BBS) disease caused by <i>Pseudomonas syringae pv. syringae,</i> and estimated heritability in a dry bean cross between A55 (resistant) and cultivar RS7 (susceptible). Generations derived from the parents, namely F<sub>1</sub>, F<sub>2</sub>, two backcross generations, and the parents themselves were analysed. The six generations were cultivated in a randomised block design with two replications and inoculated with BBS isolates at two weeks after planting. Disease scoring was done at two weeks after inoculation using standard scale (1–9), where 1 represented highly resistant, and 9 represented highly susceptible. Generation means differed (<i>P </i>&lt; 0.001), and scaling test parameters A and C were significant (<i>P</i> &lt; 0.001) revealing that variation in data was not sufficiently explained by additive [d] and dominance [h] components. Five parameters <i>viz</i>. mean [m], [d], [h], additive × additive epistasis [i], and dominance × dominance epistasis [l] were significant (<i>P</i> &lt; 0.001). The [h] and [l] effects had contrasting signs, indicating duplicate epistasis. Significant non-additive gene effects, together with moderate heritability, suggested that phenotypic selection for resistance, especially in early segregating generations, would be ineffective in conventional breeding.