cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/gn8rb3z846
title: Supplemental Materials to the Manuscript "Three-Dimensional Numerical Modeling of Coseismic Atmospheric Dynamics and Ionospheric Responses in Slant Total Electron Content Observations"

description: This collection hosts the datasets associated with the journal article, Three-Dimensional Numerical Modeling of Coseismic Atmospheric Dynamics and Ionospheric Responses in Slant Total Electron Content Observations.

Authors:
P.A. Inchin
Center for Space and Atmospheric Research, Embry-Riddle Aeronautical University, Daytona Beach, Florida, USA
Computational Physics, Inc., Springfield, Virginia, USA
Y. Kaneko
Department of Geophysics, Kyoto University, Kyoto, Japan
 A.-A. Gabriel
Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
Department of Earth and Environmental Sciences, Ludwig-Maximilians-University, Munich, Germany
T. Ulrich
Department of Earth and Environmental Sciences, Ludwig-Maximilians-University, Munich, Germany
L. Martire
Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
 A. Komjathy
Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
J. Aguilar Guerrero
Center for Space and Atmospheric Research, Embry-Riddle Aeronautical University, Daytona Beach, Florida, USA
M.D. Zettergren
Center for Space and Atmospheric Research, Embry-Riddle Aeronautical University, Daytona Beach, Florida, USA
J.B. Snively
Center for Space and Atmospheric Research, Embry-Riddle Aeronautical University, Daytona Beach, Florida, USA

Correspondence: P.A. Inchin, pinchin@cpi.com

The collection includes next datasets:
Dataset 1
Title: Sim #1. Electron density 3D fields
Description: 3D outputs of electron densities of GEMINI simulation #1 in HDF5 format, geographic coordinates and scripts for reading and plotting of the data.

Dataset 2
Title: Sim #1. Vertical fluid velocity 3D fields
Description: 3D outputs of vertical fluid velocities of MAGIC simulation #1 in mat format, geographic coordinates and scripts for reading and plotting of the data.

Dataset 3
Title: Sim #3. Vertical fluid velocity 3D fields
Description: 3D outputs of vertical fluid velocities of MAGIC simulation #3 in mat format, geographic coordinates and scripts for reading and plotting of the data.

Dataset 4
Title: DynamicVSKinematic model sTEC comparison
Description: The figures illustrating the comparison of sTEC signals from Simulation #1 and Simulation #3 and observations.
DOI: 10.17632/h4rf6wzjcr
title: Conceptual Design Exploration: EEG Dataset in Open-ended Loosely Controlled Design Experiments

description: In this dataset, 42 graduate students, aged 24 to 39, participated in conceptual design experiments where Electroencephalogram (EEG) signals were recorded while participants were performing the design tasks. Three, eleven, and one participant were excluded from the experiment due to not finishing all the experiments, some technical errors, and recorded biosignals with poor quality, respectively. Finally, EEG signals from 27 participants (8 women) were stored in the dataset. Before participating, all individuals signed a consent form after being informed about the experiments and procedures.
The EEG recording system used was the 64-channel BrainVision (Brain Vision Solutions, Montreal, Canada). Electrodes were placed according to the 10-10 international standard system over the participants' heads. EEGs were recorded throughout the experiments and later underwent preprocessing and segmentation. Each participant engaged in six design problems, each containing five open-ended, self-paced, and loosely controlled design tasks. These six design problems were designing: 1) a birthday cake (BDC), 2) a recycle bin (REB), 3) a toothbrush (TOB), 4) a wheelchair (WHC), 5) a workspace (WOS), and 6) a drinking fountain (DRF). Participants performed five design tasks within each design problem: understanding the problem (PU), idea generation (IG), rating generated ideas (RIG), evaluating ideas (IE), and rating idea evaluations (RIE). Additionally, each experiment included two 3-minute eye-closed rest periods, at the beginning and end of each session, represented by RST1 and RST2. To decrease the complexity of the whole design process, each design problem was divided into five open-ended tasks, providing structure without imposing excessive constraints. We aimed to replicate a real-world environment by allowing participants to work at their own pace, free from interruptions. It was the main and the only structure we placed in the whole experiment to help participants with the design problems.
The dataset is organized in a folder containing 27 .mat files for the 27 participants. Each file contains EEGs of one participant recorded during their performance of design problems. EEGs are represented as variables in these files. These variables are systematically named using the pattern [“Design”]_[participant number]_[design problem number]_[task name], with participant numbers ranging from 1 to 27, design problem numbers from 1 to 6, and task names as PU, IG, RIG, IE, and RIE.
To remove artifacts, recorded EEGs were referenced to Cz channel, which was later removed. This suggests that the dataset includes 63 channels of EEG signals. The recorded EEGs were preprocessed using EEGLAB and artifacts were removed. Subsequently, the preprocessed EEGs were then re-referenced to the average reference and downsampled to 250 Hz. Finally, the EEG signals were segmented using video recordings of the experiments. The preprocessed and segmented EEGs are stored in this dataset.
DOI: 10.6084/m9.figshare.22040393.v1
title: Enformer Celltyping training positions and cell types

description: The training positions and cell types for the Enformer Celltyping model. More on this here. <br> In detail: <br> When training Enformer Celltyping, we used the following approach to identify training positions: <br> 1. Bin genome based on predictive window 2. Filter bins to select training set based on DNA and cell type filters. * DNA filters: 1. Leave buffer at start/end of chromosome large enough for DNA and local chromatin accessibility windows 2. Not in blacklist regions * Cell type filters: 1. Coverage for the histone mark &gt; 12.5% of the returned window to prioritise training on regions with peaks. 3. Down sample resulting regions to equal the lowest count of regions for any histone mark so each hist mark has equal representation. This avoids the model biasing training on one mark. <br> This results in 67,007 training & validation positions (cell type and genomic region combinations) and 14,188 unique genomic positions which is similar to number of positions basenji & enformer trained on (14,533). The approach ensures model sees peaks for all histone marks. The validation set positons are randomly shifted by up to a quarter of the predictive window so the model's performance doesn't overfit to the initial genomic bins.
DOI: 10.6084/m9.figshare.1130849.v1
title: GEUVADIS Processed Data

description: These are processed files from the GEUVADIS study that were produced in the preparation of the paper: http://biorxiv.org/content/biorxiv/early/2014/03/30/003665.full.pdf
DOI: 10.6084/m9.figshare.24010383.v1
title: Research Proposal - Group 7 (updated).

description: The document contains the research proposal in Microsoft Word format.
DOI: 10.6084/m9.figshare.24632181.v6
title: Lifespan Disparity Dataset (LDD): An open repository on inequality and polarization in length of life (1950-2021)

description: This database includes a comprehensive set of estimates on lifespan inequality and polarization for 258 countries and areas for the period 1950–2021. These extensive series on the distribution of lifespans provide access to crucial information for researchers, policy-makers, and the general public, thus representing a fundamental step towards a better understanding of health differences within and between nations.
DOI: 10.6084/m9.figshare.28265126.v1
title: The Darwin Tree of Life (DToL) <i>Nematostella vectensis</i> reference genome jaNemVect1.1 with the addition of the mCherry transgene used in this study. GTF transcriptome annotation file is included.

description: We performed bulk RNA transcriptome analysis of a Nematostella vectensis transgenic reporter line expressing mCherry under the regulation of the RIG-I-like receptor (RLRb). We sorted gastrula stage embryo derived cells treated from zygotes injected with the viral mimic poly(I:C) using fluorescence-activated cell sorting (FACS). RNA was extracted from mCherry positive and negative cells and used for constructing libraries for RNA sequencing.Additionally, two-day-old wild-type animals were dissociated and subjected to intracellular immunofluorescence. RLRb cells with high (approximately 15%) and low expression levels were isolated using FACS and processed for RNA sequencing.
DOI: 10.6084/m9.figshare.5458696.v1
title: Dataset of aperture field created by dissolution experiment of fractured granite at 350 dgreeC

description: Data set of aperture fields which evolved during dissolution of fractured granite. Each aperture in a fracture is measured by X-ray CT (voxel size of 10 micron meters). The unit of data is micron meters.<br>Run ARun_A_initial.txt : Initial aperture distributionRun_A_after_A-1.txt : After stage A-1 (room T flow)Run_A_after_A-2.txt : After stage A-2 (350C batch)Run_A_after_A-3.txt : After stage A-3 (350 C flow)<br>Run BRun_B_initial.txt : Initial aperture distributionRun_B_after_B-1.txt : After stage B-1 (room T flow)Run_B_after_B-2.txt : After stage B-2 (350 C flow)
DOI: 10.6084/m9.figshare.7297202.v1
title: Atomic force microscopy indentation data of zebrafish spinal cord sections

description: The HDF5 file was created using the Python package nanite. It contains 1132 raw atomic force microscopy (AFM) force-indentation curves of zebrafish spinal cord sections, the preprocessed curves, and the corresponding fits to the approach part. In addition, a manual rating was assigned to each force-indentation curve. The intended use of this dataset is the application of machine-learning approaches to quantify AFM data quality for biological tissues.<br>
DOI: 10.17632/44khystv6t
title: Obesity Intensifies Sex-specific Interferon (IFN) Signaling to Selectively Worsen Central Nervous System Autoimmunity in Females

description: Human Blood Collection and Processing
For OLINK analysis, serum samples were collected in BD Vacutainer Serum tubes. Blood was allowed to clot for 60 minutes and then centrifuged at 1300 x g for 10 minutes. Serum was then aliquoted into tubes for storage at -80 °C. For naïve CD4+ T cell studies, peripheral blood was collected in BD Vacutainer tubes with sodium heparin. Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized blood using Ficoll-Paque density gradient centrifugation (GE Healthcare). Cells were washed in 1 x MACS buffer and were counted. 

Proteomic Analysis on Human Serum
Proteins were measured from serum samples using Olink Explore 1536 from Olink Proteomics which combines the proximity extension assay (PEA)78 with next-generation sequencing (NGS) technology79. The complete library contains antibodies targeting 1472 proteins, of which 1463 are unique proteins. Patient samples were randomized and incubated overnight with antibodies conjugated to oligonucleotide PEA probes at 4°C. After antibody binding, oligonucleotide annealing, and extension steps, the pre-amplification mix was added to the samples at room temperature. PCR amplification was performed, and PCR amplicons were then pooled and subjected to another PCR amplification step after addition of individual sample index sequences. After pooling of the samples, bead purification and quality control of the generated libraries were performed. Sequencing was carried out using Illumina’s NovaSeq 6000 instrument. Quality control and normalization processes were then performed to translate barcode sequence counts into normalized protein expression (NPX) units. Assays on the samples were performed blinded from the clinical data. Significant differences in individual protein levels (NPX units) between obese and non-obese was determined using T tests (two groups were compared) and adjusted for multiple comparisons by the Bonferroni and Hochberg method (R v4.2.3). Statistical comparisons of individual proteins between three or more groups were determined using one-way ANOVA (GraphPad Prism v9.5.0). For bioinformatic analysis, differentially abundant serum proteins were mapped to biological pathways using Ingenuity Pathway Analysis (IPA) (QIAGEN Inc.)80.
DOI: 10.17632/wd77gnrmxw
title: DNA polymorphisms in inflammatory and endocrine signals linked to frailty are also associated with obesity: data from the FRASNET cohort

description: Obesity and frailty are prevalent geriatric conditions that share some pathophysiological mechanisms and are associated with adverse clinical outcomes. The relationship between frailty, obesity, and polymorphism remains inadequately explored. Single nucleotide polymorphisms (SNPs) offer insights into genetic predispositions that may influence the development of both frailty and obesity. SNPs related to frailty and linked to the renin–angiotensin system
(CYP11B2 rs1799998, AGT rs5051, and AGTR1 rs2131127), apoptosis pathways (CASP8 rs6747918), growth hormone signaling (GHR rs6180), inflammation
(TLR4 rs5030717, CD33 rs3865444, and sFN1 rs7567647), adducin (ADD3 rs3731566), and the 9p21–23 region (rs518054) were found to be associated
with various measures of obesity in community-dwelling older adults.
DOI: 10.6084/m9.figshare.10248362.v1
title: Fig. S6C_RNA_JB1-WT_ESC.zip

description: RNA-FISH microscopy images related to Fig.S6C (Number of associated file: 1)<br><br>Manuscript: Lleres, David; Moindrot, Benoit; Noordermeer, Daan; Feil, Robert (2019), “CTCF modulates allele-specific sub-TAD organisation and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains”
DOI: 10.6084/m9.figshare.12034482.v1
title: firm-level trading data (Phase I).csv

description: firm-level emission trading data derived from the European Union Transaction Log.
DOI: 10.6084/m9.figshare.18972935.v2
title: RAAAP-2 Datasets (17 linked datasets)

description: This collection contains the 17 anonymised datasets from the RAAAP-2 international survey of research management and administration professional undertaken in 2019. To preserve anonymity the data are presented in 17 datasets linked only by <em>AnalysisRegionofEmployment</em>, as many of the textual responses, even though redacted to remove institutional affiliation could be used to identify some individuals if linked to the other data. Each dataset is presented in the original SPSS format, suitable for further analyses, as well as an Excel equivalent for ease of viewing. There are additional files in this collection showing the the questionnaire and the mappings to the datasets together with the SPSS scripts used to produce the datasets. These data follow on from, but re not directly linked to the first RAAAP survey undertaken in 2016, data from which can also be found in FigShare Errata (16/5/23) an error in v13 of the main Data Cleansing syntax file (now updated to v14) meant that two variables were missing their value labels (the underlying codes were correct) - a new version (SPSS & Excel) of the Main Dataset has been updated
DOI: 10.6084/m9.figshare.25965196.v1
title: <b>Identif</b><b>ication and characterization of a novel </b><b>prophage lysin</b><b> against </b><b><i>Streptococcus dysgalactiae</i></b>

description: <i>Streptococcus dysgalactiae</i> infection could cause bovine mastitis and lead to huge economic losses to dairy industry. The abuse of antibiotics has resulted in growing drug-resistance of <i>S. dysgalactiae</i> that<i> </i>cause hard-to-treat infections. Bacteriophage lysin, as a novel antibacterial agent, has great potential for application against drug-resistant gram-positive bacteria. However, few studies have been conducted on the prophage lysin of <i>S. dysgalactiae</i>. In this study, we mined a novel prophage lysin, named Lys1644, from a clinical <i>S. dysgalactiae </i>isolate, by genome sequencing and bioinformatic analysis. Lys1644 was expressed and purified, and the lytic activity, antibacterial spectrum, optimal pH and temperature, lytic activity in milk, synergistic bacteriostasis with antibiotics was assessed. The Lys1644 prophage lysin showed high bacteriolysis activity specifically on <i>S. dysgalactiae</i>, which results in CFU 100-fold reduction in milk. Moreover, Lys1644 maintained high activity over a wide pH range (pH 5–10) and a wide temperature range (4–42 ℃). Synergistic bacteriostatic experiments showed that the combination of low dose Lys1644 (50 μg/mL) and subinhibitory concentration of aminoglycoside antibiotics (kanamycin or spectinomycin) can completely inhibit bacterial growth, suggesting that the combination of Lys1644 and antibiotics could be an effective therapeutic strategy against <i>S. dysgalactiae </i>infection.
DOI: 10.6084/m9.figshare.27302142.v1
title: A. Datasets

description: The comprehensive list of lncRNAs dysregulated in diverse human cancers, their expression patterns, methodologies of their identification, and references to research articles (PubMed ID) used to gather these details were obtained from the Lnc2Cancer 3.0 dataset. The aliases of all these lncRNAs were manually compiled from the GeneCards dataset. The nucleotide sequences and the corresponding NCBI accession numbers of all the identified lncRNAs, including their functional transcript variants, with “validated” or “reviewed” RefSeq status, were retrieved from NCBI Nucleotide.For identification of Putative Quadruplex-forming Sequences (PQS) within these lncRNAs, their FASTA sequences are imported to the QGRS mapper, a tool that presents data on the constitution and distribution of Quadruplex-forming G-rich sequences (QGRS). The PQS within these lncRNAs are also identified using G4Hunter, a tool for identifying putative G4-forming motifs based on the G-richness and G-skewness of the query sequence.The details of experimentally-validated RNA and protein interacting partners of catalogued lncRNAs were sourced from NPInter v4.0 and LncTarD 2.0 datasets. The data obtained from LncTarD 2.0 was filtered to present the data exclusively in the context of human cancers. The information on the experimentally-validated RNA G4-binding proteins (RGBPs) interacting with the catalogued lncRNAs was obtained from QUADRatlas and G4IPDB datasets, supplemented by scientific literature mining.
DOI: 10.6084/m9.figshare.28414973.v1
title: <b>RNA-Seq of Bos taurus:adult male</b>

description: Twelve Huaxi cattle with the highest LMA (loin eye muscle, H-LMA) and the lowest LMA (L-LMA) were selected for transcriptome analysis to identify candidate genes regulating the LMA trait.At the time of slaughter, Samples of the left longissimus dorsi muscle from all male individuals were collected and placed into 5 mL freezing tubes, which were immediately frozen in liquid nitrogen and subsequently transferred to a liquid nitrogen tank for long-term storage. These samples will be used for transcriptome sequencing. Illumina NovaSeq 6000 paired end sequencing for LD muscle.
DOI: 10.17632/d35tjjgjnx
title: 2D Geometric shapes with properties

description: The presented data is a set of 3,80,000 black and white images of a fixed resolution of 200 x 200 pixels Each image consists of one of the geometric shapes: Circle, Triangle, square, Rectangle, Rhombus, Parallelogram, Trapezium with one of the properties: diagonal, perpendicular, chord, radius, diameter., symbol showing sides are equal. In total 76 such classes are created. The background color is white and the foreground color when the shape is drawn is black. o A random rotation angle between -180° and 180°. A random shape perimeter. A random shape position inside the containing image. This dataset can be used for identification of shape using classification approach with deep learning. Choosing a 2D geometrical form dataset also helps understand the number of patterns in each class of particular shape.
DOI: 10.6084/m9.figshare.20010179.v1
title: Bee communities net collected from New Jersey blueberry crop flowers

description: Wild bee communities were sampled at highbush blueberry (<em>Vaccinium corymbosum</em> L., cultivars Duke and Bluecrop) farms in the eastern USA. We netted all bees visiting crop flowers within a predefined 50- to 200-m2 transect. Netting was repeated in three 20-minute periods each sampling day. Specimens were identified to species using published taxonomic keys and assistance by expert taxonomists. <br> Data collection methods are further described in Lemanski et al, 2022, Greater bee diversity is needed to maintain crop pollination over time, Nature Ecology and Evolution. <br> Both files contain the same data, but the file "blueberry_visit_table.csv" is formatted for the main analysis in the manuscript, while the file "blue_obs.csv" is formatted for use in a null model analysis.
DOI: 10.6084/m9.figshare.26334697.v2
title: Urban cooling data and codes used for collection and analysis.

description: This study presents urban cooling data and the codes used for their collection and analysis. Remote sensing data was collected using Google Earth Engine (GEE) and analyzed with R.
DOI: 10.17632/78gbtkv78v
title: Avian Biodiversity Dataset: Bird Species of Bangladesh

description: This dataset offers a curated collection of images from eight bird species commonly found in Bangladesh, aimed at advancing machine learning and ecological research in avian detection and classification.

Bird Species Included:
 Cassowary: 697 images
 Chukar Partridge: 375 images
 Crested Serpent Eagle: 640 images
 Emerald Dove: 524 images
 Indian Peacock: 611 images
 Ostrich: 439 images
 Paradise Shelduck: 511 images
 Sarus Crane: 595 images
#Dataset Features:
 1.Diverse postures and environmental backgrounds
 2.Supports machine learning model development for bird recognition
 3.Aids in conservation, ecological education, and biodiversity protection efforts in Bangladesh.
DOI: 10.17632/cx9zbfvdx4
title: Feeling touch through a mirror: the role of vision and body ownership in generating non-veridical tactile experiences_DATA

description: This dataset is linked to the study "Feeling touch through a mirror: the role of vision and body ownership in generating non-veridical tactile experiences." 
It includes behavioral and electrodermal activity (EDA) data from an experiment using the Tactile Quadrant Stimulation (TQS) protocol combined with a mirror box illusion paradigm. 
This study explores synchiric errors and mislocalization errors under three experimental conditions: Baseline, Mirror Condition Vision, and Mirror Condition Blind.

The dataset is divided into three files:

VTQS_COMPLETE_DATA: Full dataset with all collected data, including unprocessed variables and outliers.
VTQS_MAIN_ANALYSIS_DATA: Preprocessed dataset excluding outliers, focusing on variables relevant to the main findings, such as error types and their distribution across conditions.
VTQS_SUPPLEMENTARY_DATA: Preprocessed dataset excluding outliers, containing variables detailed in the supplementary materials.
These files enable replication of the analyses in the main paper and supplementary materials and provide additional opportunities for secondary analyses.
DOI: 10.6084/m9.figshare.15173451.v1
title: Cookies Rich in Iron (Fe), Folic Acid and Cobalamin : A Novel Functional Food for Adolescent with Anemia

description: The data uploaded in this repository is RAW Data for: Cookies Rich in Iron (Fe), Folic Acid and Cobalamin : A Novel Functional Food for Adolescent with Anemia