cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6506678
title: SVAFotate supporting files and data

description: Here we provide input BED files for use with SVAFotate that are derived from the SV datasets generated by CCDG, gnomAD, and 1000G. These are provided for GRCh37 and GRCh38 reference builds and the files are named:<br> <br> SVAFotate_core_SV_popAFs.GRCh37.bed.gz<br> SVAFotate_core_SV_popAFs.GRCh38.bed.gz Additional data files are included that contain the information necessary to generate the NeoSeq analysis as described in the SVAFotate manuscript. These correspond to SV calls made by the variant callers Smoove and Manta and annotations provided by SVAFotate using the provisional BED files listed above and also a custom NeoSeq-specific BED file. These files are named:<br> <br> manta_proband_GTs_AFs_NeoSeq_BED.txt<br> manta_proband_GTs_AFs_provisional_BED.txt<br> smoove_proband_GTs_AFs_NeoSeq_BED.txt<br> smoove_proband_GTs_AFs_provisional_BED.txt
DOI: 10.17903/fk2/egxnwn
title: Industrial work and de-industrialization

description: At the class with study topic “Oral History” with the professor Antonis Antoniou collected 19 biographical narrative interviews from the students of I.A.K.A. during the winter semester of 2018 for the subject of deindustrialization. The aim of the research was to record the changes in working life and their meaning by men and women who worked in factories during the last decades and experienced the closure of their business, the deregulation of employment after 1990, unemployment or even forms of resistance. of employees in these changes. The narrators interviewed were born between 1944 and 1972 and their working lives cover most of the period from the 1980s to the present, while the older ones have worked in a factory during the junta and the post-colonial era. That means that the biographical narratives have a great interest in the study of deindustrialisation, as the narrators' experiences often cover both an era of "prosperity" with abundant employment opportunities in the mid-1980s and the personal and professional immersion that took place in the following decades, and especially in the years of the crisis. The rapid changes in the world of work are mainly due to the deregulation of labor relations in the 1990s and the closure of many factories due to competition with cheap products from China, Bulgaria, etc. and due to the relocation of Greek companies to neighboring countries during the crisis. The interviews mainly concern metal and clothing companies that closed after 2006. Most of them concern the industrial area of Volos, but there are also interviews for Thessaloniki (Coca-Cola). Larissa (Raptex, BIOTEXTIL, Olympus), Lamia (carpentry) and Xanthi (sugar factory). The sample includes 15 men and 4 women. The interviews were conducted on a guided basis.
DOI: 10.34740/kaggle/ds/2113411
title: Toronto Tree and Demographic Data
DOI: 10.6084/m9.figshare.19686723
title: H&N MM.xlsx

description: Head and neck melanoma patients
DOI: 10.6084/m9.figshare.19686723.v1
title: H&N MM.xlsx

description: Head and neck melanoma patients
DOI: 10.25345/c53r0px7s
title: MassIVE MSV000089340 - Untargeted LC-MS/MS dataset of Brachypodium distachyon leaves and roots under different environmental conditions
title: Brachypodium plants were grown to different ages and under different growth conditions in order to produce significant metabolome perturbations. Roots, leaves (young and mature combined), and in some cases, culms and spikelets were sampled. Overall, 17 organ-condition combinations were sampled, with plants grown across three major regimens: Hydroponics (Hydro), Symbiosis (Sym), and Tissue (Tis). Hydroponics samples were subjected to Control, NoCopper, NoCopper+Heat and Heat conditions. Symbiosis plants were subjected to Control (Regular Phosphate), SporeWash (Low Phosphate/Mock) and Spore (Low Phosphate + Rhizophagus irregularis spores). Tissue samples were grown to maturity and leaves, culm and spikelets were sampled. The efficacy of the spore treatment and copper deficiency was verified through RT-PCR of symbiosis and copper deficiency marker genes, respectively. All samples were analyzed via LC-MS/MS in both positive and negative mode to obtain a comprehensive snapshot of their metabolome. This work (10.46936/10.25585/60001229) was generated by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, which is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
DOI: 10.3886/e120462v1-116700
title: National Neighborhood Data Archive (NaNDA): Socioeconomic Status and Demographic Characteristics of ZIP Code Tabulation Areas, United States, 2008-2017

description: This dataset contains measures of socioeconomic and demographic characteristics by US ZIP code tabulation area (ZCTA) for the years 2008-2017. Example measures include population density; population distribution by race, ethnicity, age, and income; and proportion of population living below the poverty level, receiving public assistance, and female-headed families. The dataset also contains a set of index variables to represent neighborhood disadvantage and affluence.
description: ZCTAs in the United States. Smallest Geographic Unit: ZIP code tabulation area
description: A ZIP code to ZCTA crosswalk must be used to combine this dataset with ZIP code geocoded data. Such a crosswalk is available on the UDS Mapper website at https://udsmapper.org/zip-code-to-zcta-crosswalk/. Sample code for merging the UDS Mapper crosswalk with NaNDA datasets is available on the NaNDA repository at https://www.openicpsr.org/openicpsr/project/120088/.
DOI: 10.5281/zenodo.6506694
title: A meteorology and snow dataset from adjacent forested and meadow sites at Crested Butte, CO, USA

description: This dataset contains meteorology and snow observation data collected at sites in the southwestern Colorado Rocky Mountains during water years 2019-2021. Data collection had an emphasis on paired open-forest sites and included three forested elevations. In total, we present 270 snow pit observations, 4,019 snow depth measurements, and three years of meteorological forcing from two weather stations (one in a meadow, the other in an adjacent forest). The dataset is described in a forthcoming publication of the same name: <em>A meteorology and snow dataset from adjacent forested and meadow sites at Crested Butte, CO, USA</em> (Bonner et al., 2022).
description: Version 1.2: Added .nc versions of the .mat files
DOI: 10.25345/c50000428
title: MassIVE MSV000089341 - Characterization of Affinity Purifications of full length MST2 and exon 7 deleted MST2 by mass spectrometry
title: Hippo is a tumor suppressor pathway and is related to the regulation of cell proliferation, apoptosis, organ size and tumorigenesis. In mammals, the Hippo pathway core is composed of 4 serine-threonine kinases: Mammalian Ste-20-like Kinase 1 and 2 (MST1 and MST2) and large suppressive tumor 1 and 2 (LATS1 and LATS2). When Hippo is active, the transcription co-activators YAP and TAZ are phosphorylated and retained in the cytoplasm. However, when the pathway is inactive, YAP and TAZ are not phosphorylated and enter the cell nucleus, where they activate transcription factors, increasing proliferation and inducing malignant phenotype in epithelial cells. Preliminary results from our laboratory showed that in malignant cells (T4-2), STK3 mRNA (gene encoding MST2) is shorter, a result of an exon skipping splicing that excludes exon 7 from the transcript (STK3delexon7). Analysis of RNAseq data from The Cancer Genome Atlas (TCGA) revealed that the variant STK3delexon7 is also found in samples from patients with breast cancer. We observed that with the exclusion of exon 7 the transcript is translated into a protein that is more susceptible to degradation. Therefore, we wanted to characterize the protein complex of the exon 7 excluded transcript and the full-length protein. To this end, we transfected HEK293-T cells with flag tagged version of full length MST2 and MST2 with the deletion of exon-7. We performed affinity purification of these proteins and characterized their binding partners using mass spectrometry.
DOI: 10.25345/c5v698g7q
title: MassIVE MSV000089342 - Characterization of zymosan-modulated neutrophils with neuroregenerative properties
title: Recent studies using advanced techniques such as single cell RNA sequencing (scRNAseq), high parameter flow cytometry, and proteomics reveal that neutrophils are more heterogeneous than previously appreciated. Unique subsets have been identified in the context of bacterial and parasitic infections, cancer, and tissue injury and repair. The characteristics of infiltrating neutrophils differ depending on the nature of the inflammation-inciting stimulus, the stage of the inflammatory response, as well as the tissue microenvironment in which they accumulate. We previously described a new subpopulation of immature Ly6Glow neutrophils that accumulate in the peritoneal cavity 3 days following intraperitoneal (i.p.) administration of the fungal cell wall extract, zymosan. These neutrophils express markers of alternative activation and possess neuroprotective/regenerative properties. In addition to inducing neurite outgrowth of explanted neurons, they enhance neuronal survival and axon regeneration in vivo following traumatic injury to the optic nerve or spinal cord. In contrast, the majority of neutrophils that accumulate in the peritoneal fluid 4 hours following i.p. zymosan injection have features of conventional, mature Ly6Ghi neutrophils and lack neuroprotective or neuroregenerative properties. In the current study, we expand upon on our previously published observations by performing a granular, in-depth analysis of these i.p. zymosan-modulated neutrophil populations using scRNAseq and high parameter flow cytometry. We also analyze cell lysates of each neutrophil population by liquid chromatography/mass spectrometry. Circulating blood neutrophils, harvested from naive mice, are analyzed in parallel as a control. When samples were pooled from all three groups, scRNAseq revealed 11 distinct neutrophil clusters. Pathway analyses demonstrated that 3d neutrophils upregulate genes involved in tissue development and wound healing, while 4h neutrophils upregulate genes involved in cytokine production and perpetuation of the immune response. Proteomics analysis revealed that 3d neutrophils and 4h neutrophils also express distinct protein signatures. Adding to our earlier findings, 3d neutrophils expressed a number of neuroprotective/ neuroregenerative candidate proteins that may contribute to their biological functions. Collectively, the data generated by the current study add to the growing literature on neutrophil heterogeneity and functional sub-specialization and might provide new insights in elucidating the mechanisms of action of pro-regenerative, neuroprotective neutrophil subsets.
DOI: 10.6084/m9.figshare.19358585.v2
title: variable_metadata

description: See README
DOI: 10.25345/c5qj7825t
title: MassIVE MSV000089343 - RNF43 G659fs is an oncogenic colorectal cancer mutation and sensitizes tumor cells to PI3K/mTOR inhibition
title: Fang L, Ford-Roshon D, Russo M, O'Brien C, Xiong X, Gurjao C, Grandclaudon M, Raghavan S, Corsello SM, Carr SA, Udeshi ND, Berstler J, Sicinska E, Ng K, Giannakis M. 2022. The RNF43_p.G659fs mutation occurs frequently in colorectal cancer, but its function remains poorly understood and there are no specific therapies directed against this alteration. In this study, we find that RNF43_p.G659fs promotes cell growth independent of Wnt signaling. We perform a drug repurposing library screen and discover that cells with RNF43_G659 mutations are selectively killed by inhibition of PI3K signaling. PI3K/mTOR inhibitors yield promising antitumor activity in RNF43659mut isogenic cell lines and xenograft models, as well as in patient-derived organoids harboring RNF43_p.G659fs mutations. We find that RNF43659mut binds p85 leading to increased PI3K signaling through p85 ubiquitination and degradation. Additionally, RNA-sequencing of RNF43659mut isogenic cells reveals decreased interferon response gene expression, that is reversed by PI3K/mTOR inhibition, suggesting that RNF43659mut may alter tumor immunity. Our findings suggest a therapeutic application for PI3K/mTOR inhibitors in treating RNF43_p.G659fs mutant cancers.
DOI: 10.6084/m9.figshare.19655772
title: Supplementary table 3.pdf

description: Table 3: Comparison of microleakage values at the occlusal and gingival margin within each caries removing method group using Wilcoxon Signed Rank test.
DOI: 10.6084/m9.figshare.19655772.v1
title: Supplementary table 3.pdf

description: Table 3: Comparison of microleakage values at the occlusal and gingival margin within each caries removing method group using Wilcoxon Signed Rank test.
DOI: 10.6084/m9.figshare.19655751.v1
title: Supplementary table 2.pdf

description: Table 2: Comparison of microleakage values between the Brix3000 and CeraBur groups at the gingival margin using Independent t-test.
DOI: 10.6084/m9.figshare.19655751
title: Supplementary table 2.pdf

description: Table 2: Comparison of microleakage values between the Brix3000 and CeraBur groups at the gingival margin using Independent t-test.
DOI: 10.6084/m9.figshare.19655736
title: Supplementary table 1.pdf

description: Table 1: Comparison of microleakage values between Brix 3000 and CeraBur groups at the occlusal margin using Mann Whitney U test.
DOI: 10.6084/m9.figshare.19655736.v1
title: Supplementary table 1.pdf

description: Table 1: Comparison of microleakage values between Brix 3000 and CeraBur groups at the occlusal margin using Mann Whitney U test.
DOI: 10.17632/7bf279kgfg.2
title: Farmers' livelihood strategies and perceived constraints from the poor and non-poor households: A dataset from field survey in Nghe An, Vietnam

description: This article presents a dataset on trends and difficulties in forest land use in Chau Thai Commune, Nghe An Province - a rural mountainous area in Vietnam. A random sampling technique and a face-to-face interview method were employed to survey 215 households in the region in 2018. Overall, the dataset presents that economic growth in Chau Thai Commune largely depends on agriculture and forestry, and the main source of income derives from forest land that covers 90% of the region’s land area. It also shows that the government's growth-stimulating policies, in addition to the natural and human factors, play a key role in socio-economic development.
DOI: 10.17632/vh78xyy85f.1
title: Jupyter script for automatic polycrystalline generation with desired grain size and elongation.

description: This document is a jupyter notebook that generates polycrystals for MOOSE (EBSD format) with the desired grain size, elongation, texture. It saves the grain structure into the format of EBSD data. 
This python script is being published with the following paper:
P.-C. A. Simon, L. K. Aagesen, C. Jiang, W. Jiang, J.-H. Ke, Multiscale calculation of the effective silver diffusion coefficient in polycrystalline silicon carbide: application to silver release in AGR-1 TRISO particles, Journal of Nuclear Materials, Submitted (2022).

This work was funded by the Department of Energy Nuclear Energy Advanced Modeling and Simulation program. This manuscript has been authored by Battelle Energy Alliance, LLC under Contract No.~DE-AC07-05ID14517 with the U.S. Department of Energy. The United States Government retains, and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.
DOI: 10.17632/tdggxgygrw.1
title: Sequencing data from human brain metastases

description: Processed scRNA-seq and spatial transcriptomics for Sudmeier et al., Cell Reports Medicine 2022. "Metacluster signatures.xlsx" shows the gene expression profile for each metacluster of brain metastasis-infiltrating PD-1+ CD8+ T cell. "CellphoneDB output.xlsx" contains the CellphoneDB output from spatial transcriptomics experiments.
DOI: 10.17632/wkhswx3nf8.1
title: Poly(I:C) Enhances Mesenchymal Stem CellControl of Myeloid Cells and CorrectDysfunction in COVID-19. Souza-Moreira, L.et al.

description: Using a combination of ex vivo models (whole blood culture), we reveal that poly(I:C)-primed MSCs enhance the antiviral and modulatory ability of MSCs, leading to the recalibration of the dysregulated immune cellular response in COVID-19 patient whole blood samples. This study demonstrates that MSCs can be induced to upregulate antiviral protein expression while enhancing the ability to modulate patient immune cells, including direct evidence of MSCs and immune cells in the context of severe COVID-19. We establish a unique ex-vivo MSC co-culture system using whole blood from healthy donors and severe COVID-19 patients to examine the modulation of MSCs on acute inflammation, and severe COVID-19 immune responses. Deep profiling of the immune landscape using mass cytometry (CyTOF) reveals how viral mimic poly(I:C) enhanced MSCs’ influence on specific immune cell compositions, particularly on phenotypic and functional shifts on the myeloid-derived populations to the less inflammatory phenotypes. A SARS-CoV-2 pseudoviral system is utilized to demonstrate, for the first time, that poly(I:C)-priming enhances MSCs’ ability to block pseudoviral entry into lung epithelial cells.
DOI: 10.17632/4x27jjp9mv.1
title: Natural sleep electrophysiology: mPFC, thalamus, hippocampus

description: This data set includes local field potential recordings, obtained from the mPFC, midline thalamus and the hippocampus of head-fixed cats during natural sleep/wake cycles. Recordings were obtained using stainless-steel electrodes or high-impedance tetrodes constructed out of 12.5 micron wires. 
We observed high-amplitude bursts of gamma activity (~40 Hz), phase-locked to a 1-Hz respiration-related potential during wakefulness but not during NREM or REM sleep.  Gamma bursts were coherent across the mPFC-thal-hipp network.
DOI: 10.13026/qcpr-xg17
title: The CirCor DigiScope Phonocardiogram Dataset

description: A total number of 5272 heart sound recordings were collected from the main
four auscultation locations of 1568 subjects, aged between 0 and 21 years
(mean ± STD = 6.1 ± 4.3 years), with a duration between 4.8 to 80.4 seconds
(mean ± STD = 22.9 ± 7.4 s), totaling more than 33.5 hours of recording. Each
cardiac murmur in the dataset has been annotated in detail by a human
annotator, in terms of timing, shape, pitch, grading, quality and location.
Moreover, segmentation annotations regarding the location of fundamental heart
sounds (S1 and S2) in the recordings have been obtained using a semi-
supervised scheme. The segmentation annotations were performed by voting
between three state-of-the-art machine-based algorithms. An expert annotator
later studied the consensus and mismatches between the algorithms beat-by-beat
and performed a manual annotation whenever the algorithms had disagreed or
were not acceptable for the expert. To date, the dataset is the largest
publicly available pediatric heart sound dataset, supporting deeper research
on the topic of auscultation-based health recommendation systems. The dataset
is being used in the George B. Moody PhysioNet Challenge 2022 on Heart Murmur
Detection from Phonocardiogram Recordings.
DOI: 10.6084/m9.figshare.19686954
title: Labelled Hate Speech Detection Dataset.

description: This dataset contains 3000 labelled comments and posts scraped from the Reddit, Twitter and 4Chan social media websites in 2022. In this dataset, 2400 comments are labelled as non-hateful or '0', and 600 comments are labelled as hateful or '1', making an even 80/20 split. <br> This dataset's primary purpose is for the use in machine learning classifications of hateful speech in the online speher.
DOI: 10.34740/kaggle/dsv/3551534
title: Health insurance data set
DOI: 10.5519/qd.0gjiifs7
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (2496328 records)
DOI: 10.13139/ornlnccs/1797498
title: Machine Learning assisted optimization and parameter space exploration dataset of spin ice Hamiltonian

description: This repository contains both simulated and experimental structure factor data for the data challenge involving the inverse scattering problem. The simulated data were generated during a machine-learning-assisted optimization routine described in ref[1]. The experimental structure factor was measured on a rare-earth oxide, Dy2Ti2O7 using diffuse neutron scattering from time-of-flight techniques on the CORELLI instrument at the Spallation Neutron Source, Oak Ridge National Laboratory. A Metropolis Monte Carlo code implemented to run in a High-performance computing setting was used to calculated simulated structure factors for the spin-ice Hamiltonian at 680 mK, which is the same temperature as for the experimental data. The total size of all the files in this repository is 5.12 GB. A detailed description of the files is given below. ExperimentalData_630mK.dat â A linearized version of 3-dimensional experimental data of size 61Ã81Ã21. This data was processed to remove an estimation of non-magnetic background, including nuclear scattering signal and instrumentation background. Parameters.dat â 6700 samples were evaluated over the 4-dimensional parameter space (J_1, J_2, J_3 and J_(3^' )). There is an additional parameter, D in the spin Hamiltonian to mimic the dipolar interaction between magnetic ions. However, this parameter, D was fixed to a value determined by prior work. This file contains five columns for the parameters J_1, J_2, J_3, J_(3^' ) and D respectively. 3D_Simulation_Data.dat â The simulated structure factor, S(Q) data are included in this file. Each raw contains a linearized array of 3D volumes of S(Q) calculated for the parameter set given in the corresponding row of the file "Parameters.dat". The size of the volume data was matched to the experimental data. Qx(h,-h,0).dat, Qy(k,k,-2k).dat, Qz(l,l,l).dat â These files contain the h, k, and l values along with the reciprocal vectors [h,-h,0], [k,k,-2k] and [l,l,l] respectively.