cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/rf6kfk74sc
title: Inherited CD4 deficiency: short-read single-cell RNA sequencing (scRNASeq) of stimulated TCRab+ memory T cells

description: To identify transcriptional modules perturbed by inherited CD4 deficiency, single-cell RNA sequencing was performed on isolated memory (defined as CD45RA-CCR7+/-) CD3+CD8-TCRαβ+ and/or CD3+CD4-CD8-TCRαβ+ double negative (DN) T cells from healthy donors (n=4), FAS deficient (n=1), STAT3GOF (n=1) and CD4 deficient (P1-P5) patients. Isolated cells were cultured with TAE beads + IL-2 (50 IU/mL, #IL002, Millipore) for 20h. Cells were washed 3 times in cold PBS + 2% HI FBS and incubated with TotalSeq anti human hashtag antibodies (A0251-A0256, #394601, #394603, #394605, #394607, #394609, #394611, BioLegend) for 30 min on ice. Hashtagged cells were washed 3 times in cold PBS + 2% HI FBS and passed through a 35µm nylon mesh cell strainer (#352235, Falcon) to remove aggregates. Cells were resuspended at a concentration of 1000 cells/µl in cold PBS + 2% HI FBS, pooled, and loaded onto a 10X Genomics Chromium B or G chips. Single-cell capture, reverse transcription, and library preparation were performed with the Chromium Single-Cell 3’ Reagent Kits (v3 or v3.1), in accordance with the manufacturer’s instructions. The quality of the cDNA and feature barcode library was assessed with a TapeStation (Agilent). Transcriptome sequencing was performed on the S4 flow cells of an Illumina NovaSeq 6000 sequencer, while hashtag library sequencing was performed on NextSeq 500/550 system with High Output Kit v2.5 (Illumina). Cells from P1/P2/P3 and P4/P5 were processed in two batches of experiments, along with cells from two healthy donors per batch. For comparison, CD3+CD4-CD8 TCRαβ+ double-negative T cells from two healthy donors, one FAS-deficient patient, and one patient with a STAT3 GOF mutation were isolated and processed similarly. 
 Hashtag demultiplexing was performed using Seurat with default parameter settings. Hash tag doublets were excluded from subsequent analyses. Cells were further filtered based on standard QC metrics. Batch correction, unsupervised clustering, pseudobulk PCA, differential expression (DE) analysis, and gene-set enrichment analysis (GSEA) were performed as described previously (Ogishi et al., 2022). All analyses were conducted in R (version 4.2.2, https://www.R-project.org/).
DOI: 10.17632/bnt8bthn8b
title: Data for: Structure of Income Inequality and Household Leverage: Theory and Cross-Country Evidence

description: Enclosed file allow the replication of the dataset and estimates for Bazillier, Hericourt and Ligonnière (2019).
DOI: 10.17632/h8hmkcf6gk
title: Host dysosmia in SARS-CoV-2 infection

description: The respiratory condition COVID-19 arises in a human host upon the infection with SARS-CoV-2, a coronavirus that was first acknowledged in Wuhan, China, at the end of December 2019 after its outbreak of viral pneumonia. The full-blown COVID-19 can lead, in susceptible individuals, to premature death because of the massive viral proliferation, hypoxia, misdirected host immunoresponse, microthrombosis, and drug toxicities. Alike other coronaviruses, SARS-CoV-2 has a neuroinvasive potential, which may be associated with early neurological symptoms. In the past, the nervous tissue of patients infected with other coronaviruses was shown to be heavily infiltrated. Patients with SARS-CoV-2 commonly report dysosmia, which has been related to the viral access in the olfactory bulb. However, this early symptom may reflect the nasal proliferation that should not be confused with the viral access in the central nervous system of the host, which can instead be allowed by means of other routes for spreading in most of the neuroanatomical districts. The dataset was used to write the hypothesis "Disentangling the Hypothesis of Host Dysosmia and SARS-CoV-2: The Bait Symptom That Hides Neglected Neurophysiological Routes", which was published by the Journal Frontiers in Physiology in 2020.
DOI: 10.17632/mx95kzj46z
title: Automated Evaluation Framework for Word Normalization Tasks

description: This Flask application provides a user-friendly interface for evaluating the normalization of words. Users can input original and normalized word pairs, assign ratings to each pair, and automatically compute evaluation metrics. The application streamlines the evaluation process and provides valuable insights into the performance of normalization techniques.

Introduction

Word normalization is a crucial preprocessing step in many natural language processing tasks. It involves transforming words into their canonical form to improve consistency and accuracy. To assess the effectiveness of normalization techniques, a reliable evaluation process is essential.

Functionality

User Interface:

A simple, intuitive interface allows users to input original and normalized word pairs.
Users can assign ratings to each pair, indicating the quality of the normalization.

Automated Evaluation:

The application automatically calculates the following evaluation metrics:
Precision: The proportion of correctly normalized words among all words predicted as normalized.
Recall: The proportion of correctly normalized words among all actual normalized words.
F1-Score: The harmonic mean of precision and recall, providing a balanced measure of performance.
Data Storage and Visualization:

The application stores evaluation data, enabling users to track progress and identify areas for improvement.
Visualization tools can be integrated to provide visual representations of evaluation results, such as confusion matrices or line charts.
Benefits

Efficiency: Automates the evaluation process, saving time and effort.
Objectivity: Provides quantitative metrics to assess normalization performance.
Transparency: Offers clear insights into the strengths and weaknesses of normalization techniques.
User-Friendliness: Intuitive interface simplifies the evaluation process.
Conclusion

This Flask application offers a valuable tool for researchers and practitioners to evaluate the quality of word normalization techniques. By automating the evaluation process and providing quantitative metrics, it empowers users to make informed decisions and improve the accuracy of their natural language processing systems.
DOI: 10.17632/6vrhk2tvcy
title: Supplemental material: Intercellular Pathways from the Vasculature to the Forming Bone in the Zebrafish Larval Caudal Fin: Possible Role in Bone Formation. JSB 2019

description: This dataset includes five videos and four raw data-sets that are part of the article “Intercellular Pathways from the Vasculature to the Forming Bone in the Zebrafish Larval Caudal Fin: Possible Role in Bone Formation”. The data set contains two large volume stacks, obtained by cryo FIB-SEM and three fluorescence images. Stack A contains 616 micrographs comprising a volume of x = 30.75 µm, y = 23.06 µm, z = 12.32 µm, with a voxel size of x = 10 nm, y = 10 nm, z = 20 nm. Stack B: contains 609 micrographs comprising a volume of x = 37.4 µm, y = 23.4 µm, z = 24.4 µm, with a voxel size of x = 20 nm, y = 20 nm, z = 40 nm. Please see the attached PDF file for detailed video captions
DOI: 10.17632/fm7gwd4rct
title: PPARγ controls ESCRT-dependent synoviocyte exosome biogenesis and Alleviates chondrocyte Osteoarthritis by Exosomal ANXA1

description: Osteoarthritis (OA) is characterized by synovitis, cartilage degeneration and exercise therapy has been recognized as first line therapy. The exercise related exosome involved in the interaction between fibroblast-like synoviocytes (FLSs) and chondrocytes could be a novel promising strategy for treating OA. In this study, PPARγ was upregulated in FLSs under exercise by single cell transcriptome sequencing. Then, we investigated the underlying mechanisms of PPARγ-treated FLSs derived exosome on OA in vivo and vitro. Our data revealed that overexpression PPARγ FLSs derived exosome could ameliorate the OA severity in vivo and vitro. But knockdown PPARγ FLSs derived exosome aggravate OA. Moreover, we found PPARγ controls the endosomal sorting complex required for the transport (ESCRT)-dependent exosome biogenesis pathway. Annexin A1 (ANXA1) was enriched in OE-PPARγ exosome by quantitative proteomics. By Chip-qPCR and Co-IP methods, PPARγ and its coactivator -1α (PGC-1α) acts with ESCRT subunits including HRS, STAM1, TSG101, CHMP7 and promotes their association to cargo ANXA1. As a therapeutic cargo, exosomal ANXA1 was confirmed be internalization by chondrocyte via exosome labeled experiment and ANXA1 could inhibit the phospharylation of ERK to activate the autophagy and decrease chondrocyte apoptosis. While the ANXA1 receptor blocker BOC-2 could reverse the therapic effect. In conclusion, PPARγ/ESCRT – FLSs exosomal ANXA1 – ERK axis provides a deeper theoretical basis for exercise therapy of OA and a new idea for the clinical transformation of exosomes into OA therapy.
DOI: 10.17632/hzrsn6sbxn
title: Data for: Paleomagnetism and rock magnetic cyclostratigraphy of the Ediacaran Doushantuo Formation, South China: Constraints on the remagnetization mechanism and the encoding process of Milankovitch cycles

description: Supplementary data for the manuscript titled "Paleomagnetism and rock magnetic cyclostratigraphy of the Ediacaran Doushantuo Formation, South China: Constraints on the remagnetization mechanism and the encoding process of Milankovitch cycles"
DOI: 10.17632/hpmvy7h4t9
title: Decentralized Government and Firm Pollution Discharges: Evidence from China’s Province-Managing-County Reform

description: Replication Folder for "Decentralized Government and Firm Pollution Discharges: Evidence from China’s Province-Managing-County Reform" by Xunyong Xiang, Wenjie Luo, Bin Li, and Wenquan Liang.
DOI: 10.17632/xpywbvs5zn
title: Data for: Development of the Sensitizer for Generating Higher-Energy Photons under Diluted Condition via the Triplet-Triplet Annihilation-Supported Upconversion

description: supporting information
DOI: 10.17632/w4mbjzm2md
title: Codes for the Article “Exposures to climate change's physical risks in Chile”, LAJCB

description: These codes use the original sources of data to add in replicating the article “Exposures to climate change's physical risks in Chile”, Latin American Journal of Central Banking, 2023, 4(2), 100090.

All data files (.dta and .do) are in either R or Stata format.
DOI: 10.17632/x2dy7pkwtf
title: Transition metal nanoparticles enclosed in carbon nanocages: microscopic images and X-Ray diffraction pattern

description: Image "Precursors" shows the dried crystals of Ni, Co and Fe precursors for synthesis of nanoparticles in carbon nanocages. Its preparation is described in related research article. SEM images present Ni, Co and Fe nanoparticles enclosed in carbon nanocages (CNCs). Sythesis is made at different temperatures between 500 °C and 850 °C during 10 min. The Ni@ CNCs formed at 500, 550 and 600 °C are seen as small white dots of ~10 nm. However, at 700 and 850 °C, the particle size is increased to ~50-100 nm. Image sequence for Ni shows rapid change of thermolysis rate with temperature. Also, the SEM images of Ni, Co and Fe synthesized at 600 °C is given. The Ni@CNCs and Co@CNCs seen as white dots are similar in size while the size of Fe@CNCs varies from few to a hundred nanometers. Table and image "XRD_FeSPN_in_CNC" shows the XRD pattern of Fe nanoparticles encapsulated in CNCs synthesized at 600 °C. It shows the presence of different phases, metallic α-Fe (red), F2O3 (blue) and Fe3C (green). Table gives the numerical data for these peaks and intensities for α-Fe, Fe2O3 and Fe3C correspondingly.
DOI: 10.17632/ygv49pb4dx
title: SINSO Ontology

description: Ontology created for: SinSO: An ontology of  Sustainability in Software.
DOI: 10.17632/cmddbrxc87
title: Lizards’ response to the sound of fire is modified by fire history

description: This dataset is composed of:

Location's data: habitat type (Site) and name of sampling location (Location). 
Lizards' individual data: individual code, sex, age, SVL (snout-vent length, in cm), mass (in grams), tail autotomy (yes or no), and body temperature. 
Climatic data: humidity (%RH), wind speed (km/h), soil temperature (°C), air temperature (°C). 
Data about experiment trials: height (from the ground to the lizard, in cm), distance to closest shelter (in cm), type of shelter, speaker distance to the lizard (in cm), lizard's initial head orientation before the sound trial (relative to the speaker, in degrees), sound treatment, rate of looks, rate of foraging, rate of push-ups, rate of locomotion, and binary variables (rate_forage_bin, rate, pushup_bin, rate_locomotion_bin), starting distance (SD, in cm), alert distance (AD, in cm), flight initiation distance (FID, in cm).
DOI: 10.17632/zp6kzvh986
title: Effects of ADI5529

description: Raw data of US-pharmaceutical patents filed in Brazil which were under effect of single paragraph of art 40 of LPI
DOI: 10.17632/rvyzmy88c5
title: Energy expenditure in children and adolescents during digging activities. Dataset from EVOBREATH 2016-2017

description: This dataset contains records of an experimental research project (BioE5-CEIC 1586) on energetic expenditure of a simulated extractive foraging activity (digging out wooden stakes which simulated underground food resources) in a sample of 40 urban children and adolescents of both sexes, aged 8-14 years.

The dataset also contains some anthropometrical and body composition data of the subjects. Metabolic rates were also recorded during the different tests, performed indoors, at the BioEnergy and Motion Lab (LabBioEM) of National Research Center on Human Evolution (CENIEH, Spain), and outdoors, in 2016 and 2017. 

The description of recorded variables are included in the data and document files.
DOI: 10.17632/5z9hs5k88h
title: Supplemental material : Milk replacer feeding once or twice a day did not change the ruminal metabolomic profile and the microbiota diversity of dairy calves from birth to weaning

description: Supplemental material : Milk replacer feeding once or twice a day did not change the ruminal metabolomic profile and the microbiota diversity of dairy calves from birth to weaning
DOI: 10.15468/dl.xvatc6
title: Occurrence Download

description: A dataset containing 69406 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lepidium didymum L.)",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation, Literature Occurrence)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 69406 records from 479 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001527-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/2537f6mpxh
title: Dataset for " Flexible synthesis of phosphorus(V)-substituted 1,3,4-thiadiazoles and pyridazines"

description: The raw 1H, 13C, 31P NMR FID files, copies of IR and HRMS spectra for representative compounds are available.
DOI: 10.17632/mhvzzh6ndv
title: Data for: Contrasting dynamics of soil fungal functional groups in the plant rhizosphere

description: Soil microbiomes, critical for plant productivity and ecosystem functioning, mediate essential functions such as pathogenesis, mutualism, and decomposition through different fungal functional groups. Yet, our understanding of the dynamics of co-existing soil fungal functional groups in the plant rhizosphere remains limited. By leveraging a ‘natural’ experiment in urban farming with fields of varying ages and multiple plant genotypes, we tracked the relative abundance, richness, and microbial networks of plant pathogens, mycorrhizal fungi, and saprotrophic fungi across fields over two years. We observed an increase in the relative abundance of plant pathogens in older fields relative to younger fields, supporting the prediction of pathogen accumulation over time. In contrast, there was a decrease in the relative abundance of mycorrhizal fungi in older fields. Unlike plant pathogens and mycorrhizal fungi, the relative abundance of saprotrophic fungi remained similar among fields. For fungal richness, the richness of plant pathogens and saprotrophic fungi showed no significant differences among fields. However, the richness of mycorrhizal fungi declined in older fields and over the two years. These dynamics led to distinct microbial networks, with decreased network links for mycorrhizal fungi and increased links for saprotrophic fungi in older fields, whereas the links for plant pathogens remained similar across fields. Our study reveals contrasting dynamics of essential soil fungal functional groups in the plant rhizosphere, and provides a predictive insight into the potential shifts in soil function and their impact on plant productivity.
DOI: 10.17632/wdv72kxgjg
title: Eomesodermin partners with MITF and PU.1 in myeloid precursors to modulate expression of osteoclast lineage determining transcription factors

description: Immunoprecipitation with FLAG-MITF, HA-PU.1, and V5-EOMES in HEK-293 cells.
DOI: 10.17632/54p84dj5jj
title: Eastern Greater Caucasus Thermochronometry

description: These are the data files for eastern Greater Caucasus thermochronometry, as described in the manuscript: Tye, A. R., Niemi, N. A., Cowgill, E., Kadirov, F. A., and Babayev, G. R. Diverse deformation mechanisms and lithologic controls in an active orogenic wedge: Structural geology and thermochronometry of the eastern Greater Caucasus. Tectonics (in revision).

The data include apatite and zircon (U-Th-Sm)/He age data, apatite fission track count data, and apatite fission track length data from samples collected throughout the eastern Greater Caucasus.
DOI: 10.17632/mdhdp8mdb6
title: Supplementary Data for: Geometric morphometric analysis and meristic variations of Philippine populations of the crescent perch Terapon jarbua (Centrarchiformes: Terapontidae)

description: Supplementary Data File 1 (.docx). Representative specimens from the nine Philippine sampling sites.
Supplementary Data File 1 (folder): All photographs of Terapon jarbua specimens from the nine Philippine sampling sites.
Supplementary Data File 2 (.xlsx). Measurements, meristic counts and metadata information of all Terapon jarbua specimens in the study.
DOI: 10.17632/m39bfzbzgc
title: DataSets Mobile Applications for Android (AHFE 2019)

description: Data set to reproduce the experiment in the evaluation of most used mobile applications for Android. The data are part of the paper at the AHFE 2019 Conference. Data is in MS Excel format.
DOI: 10.17632/hkkmjytcm3
title: Qi He NWA 6177 lunar olivine gabbro
DOI: 10.17632/k52tmp95p9
title: data to support Days with a maximum temperature of 40 C in 2100 with SSP5-8.5 pathway

description: The is the data used to produce the analysis of Days with a maximum temperature of 40 C in 2100 with SSP5-8.5 pathway.
DOI: 10.17632/3t2p7cjz2w
title: Santos_2020_sheep_bagstudy

description: Data referring to the doctoral thesis of Antônio Carneiro Santana dos Santos, in the Animal Science Postgraduate Program of Federal University of Bahia (UFBA) - Brazil
DOI: 10.17632/s6kdxyn3s7
title: Data for: Global Sourcing in Oil Markets

description: Replication files for "Global Sourcing in Oil Markets" for the publication in Journal of International Economics. Notes: I can make available only the non-confidential parts of the data I have used. The replication files that contain these non-confidential data together with my codes are available here and also from my personal website. See the "read me" file within the replication files for a detailed guideline.
DOI: 10.17632/7kbbbjcgyy
title: Data for: OPTICAL AND ELECTRICAL PROPERTIES OF Ti SUBOXIDES GROWN BY REACTIVE GRID-ASSISTED MAGNETRON SPUTTERING

description: Data of X-Ray diffraction (XRD), X-Ray photoelectron spectroscopy (XPS) and spectrofotmetry of TiOx films deposited onto glass substrates by magnetron sputtering at different O2 concentrations on working gas flow rate.
DOI: 10.17632/72hvpmctvg
title: Can large trade shocks cause crises

description: This dataset replicates the results for the paper "Can large trade shocks cause crises? The case of the Finnish-Soviet trade collapse", by Adam Gulan, Markus Haavio, Juha Kilponen
DOI: 10.17632/vm974fwcjz
title: A Cross-Sectional Study of Attitudes and Factors that Promote Medical Student Participation in Professional Medical Societies

description: Please see article for a full description of the methods: Rigby MJ, Bennett DD. A Cross-Sectional Study of Attitudes and Factors That Promote Medical Student Participation in Professional Medical Societies. WMJ 2020;119(4):263-269
DOI: 10.17632/f4bcz9bsp6
title: Data: Bibliometric Analysis on Motivation and Gamified Learning with the Use of Software HistCite
DOI: 10.17632/kwnd8h888f
title: Supplementary material - Increasing school building usage through adaptable building design: a quantitative sustainability assessment

description: These documents are supplementary material which belong to the publication entitled: "Increasing school building usage through adaptable building design: a quantitative sustainability assessment"
DOI: 10.17632/vvd6r9jpxt
title: Replication material for "Intangibles, Markups, and the Measurement of Productivity Growth"

description: This is replication code for "Intangibles, Markups, and the Measurement of Productivity Growth", Journal of Monetary Economics (2021), https://doi.org/10.1016/j.jmoneco.2021.09.005 . The zip contains a readme file outlining the steps to replicate the results of the paper.
DOI: 10.15468/dl.rxxus6
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (Royal Ontario Museum - Herpetology Collection, INSDC Sequences, Anfibios y reptiles del estado de Tamaulipas, México, Arizona State University Herpetology Collection, AMNH Herpetology Collections, Museum of Comparative Zoology, Harvard University, Digitalización y Sistematización de las Colecciones Biológicas Nacionales del Instituto de Biología, UNAM (vertebrados), UTA Reptiles, Formación de una base de datos y elaboración de un atlas de la herpetofauna de México (Anfibiosreptiles))",
 "TaxonKey is Crotalus morulus Klauber, 1952"
 ]
}

 The dataset includes 62 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001510-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/bxv78zszvc
title: Proteomic data (FCS files, mass cytometry) for expanded regulatory T cells in autoimmune polyendocrine syndrome type 1

description: The deposit contains mass cytometric (CyTOF) characterization data for the paper "Single cell characterization of blood and expanded regulatory T cells in autoimmune polyendocrine syndrome type 1", published in iScience in 2024. The dataset includes thawed expanded Tregs from 17 APS-1 patients and 17 healthy controls. Please see more details in the publication.
DOI: 10.17632/j7d837wn6d
title: Dataset for the publication entitled "Comparative Analysis of Mechanical and Thermal Characteristics of 3D-Printed Polyamide Using Material Extrusion and Powder Bed Fusion Process with Industrial and Desktop printers"

description: Dataset for the publication entitled "Comparative Analysis of Mechanical and Thermal Characteristics of 3D-Printed Polyamide Using Material Extrusion and Powder Bed Fusion Process with Industrial and Desktop printers". Upon citation, please refer to the original article as well.