cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/pjtyzgxwwp.3
title: Heavy Sulfur Isotopes at Etinde, Cameroon Volcanic Line

description: We present a sulfur isotope dataset for lavas from Etinde, a volcano of the Cameroon Volcanic Line. We measured sulfur isotope compositions with an aim to characterise the geochemical reservoir the sulfur came from. We also provide some whole rock geochemical data for context.

Major-element compositions were determined by X-Ray Fluorescence (XRF) spectrometry at the University of Edinburgh, and trace element concentrations were determined by Inductively-Coupled Plasma Mass Spectrometry (ICP-MS) at the Scottish Universities Environmental Research Centre (SUERC). Sulfur concentrations were measured using combustion ion-chromatography at Universität Tübingen. Sulfate phases were dissolved in cold HCl at the University of Edinburgh using a method proposed by Renzulli et al., (1998) and solutions were analysed at the stable isotope facility at SUERC. Sulfide samples were prepared and analysed at the University of St Andrews following Canfield et al., 1986. Sulfide δ34S was calculated by mass-balance from measured acid-volatile and chromium-reducible sulfide components. Mass balance was also used to calculate bulk δ34S from sulfide and sulfate δ34S. 

Bulk δ34S which best represents Etinde magmatic values ranges from +3.7‰ to +6.3‰, a heavier signature than MORB and most other alkaline igneous rocks. We show that the most mafic Etinde samples are highly degassed, a process which affected their S-isotope composition. We suggest that assimilation of evaporite in shallow magma reservoirs or the involvement of a metasomatic carbonate component in the mantle source may explain these positive values.
DOI: 10.17632/d2kvsgym55.1
title: Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer

description: Hypoxia plays a critical role in tumor progression, including invasion and metastasis. Epithelial-mesenchymal transition (EMT) is one of the first steps in a metastatic cascade that hypoxic cells achieve through modulating the chromatin structure, epigenetics, and, importantly, alternative splicing. Recently, we reported hypoxia-driven CTCF induction through HIF1α that promotes EMT in hypoxic breast cancer cells. Nevertheless, it is still unknown how the HIF1α-CTCF axis promotes the invasiveness of hypoxic breast cancer cells. In the present study, we investigated the molecular mechanism of CTCF-mediated EMT under hypoxia. We observed a significant gain in CTCF occupancy throughout the genome, correlating with the increased CTCF expression under hypoxia. Many of these CTCF gain sites are observed at the promoter of the genes associated with cancer and hypoxia. Here, we put forward an intricate mechanism regulated by CTCF to promote EMT where CTCF modulates both gene expression and alternative splicing of an EMT gene, COL5A1. Mechanistically, the hypoxia-mediated CTCF binding to the COL5A1 promoter is an integral part of the mechanism of CTCF-HIF1α mediated transcriptional upregulation of COL5A1. Our data further demonstrates hypoxia-driven inclusion of exon 64A in the mutually exclusive alternative splicing event of COL5A1exon 64 (exon 64A or 64B). Notably, in the COL5A1 gene, CTCF mediates promoter-exon upstream looping, regulates DNA demethylation at distal alternatively spliced exon 64, and regulates RNA Pol II pausing at COL5A1 exon64A that decides the outcome of splicing to favor EMT under hypoxia. Further, we observed that hypoxia-induced differential CTCF occupancy across the genome is associated with gene expression and alternative splicing of other cancer-related genes, similar to the proposed model. Finally, specifically disrupting the HIF1α-CTCF-COL5A1 exon64A axis through the dCas9-DNMT3A system alleviates the EMT potential of hypoxic breast cancer cells and may represent a novel therapeutic target in breast cancer.
DOI: 10.17632/d2kvsgym55.2
title: Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer

description: Hypoxia plays a critical role in tumor progression, including invasion and metastasis. Epithelial-mesenchymal transition (EMT) is one of the first steps in a metastatic cascade that hypoxic cells achieve through modulating the chromatin structure, epigenetics, and, importantly, alternative splicing. Recently, we reported hypoxia-driven CTCF induction through HIF1α that promotes EMT in hypoxic breast cancer cells. Nevertheless, it is still unknown how the HIF1α-CTCF axis promotes the invasiveness of hypoxic breast cancer cells. In the present study, we investigated the molecular mechanism of CTCF-mediated EMT under hypoxia. We observed a significant gain in CTCF occupancy throughout the genome, correlating with the increased CTCF expression under hypoxia. Many of these CTCF gain sites are observed at the promoter of the genes associated with cancer and hypoxia. Here, we put forward an intricate mechanism regulated by CTCF to promote EMT where CTCF modulates both gene expression and alternative splicing of an EMT gene, COL5A1. Mechanistically, the hypoxia-mediated CTCF binding to the COL5A1 promoter is an integral part of the mechanism of CTCF-HIF1α mediated transcriptional upregulation of COL5A1. Our data further demonstrates hypoxia-driven inclusion of exon 64A in the mutually exclusive alternative splicing event of COL5A1exon 64 (exon 64A or 64B). Notably, in the COL5A1 gene, CTCF mediates promoter-exon upstream looping, regulates DNA demethylation at distal alternatively spliced exon 64, and regulates RNA Pol II pausing at COL5A1 exon64A that decides the outcome of splicing to favor EMT under hypoxia. Further, we observed that hypoxia-induced differential CTCF occupancy across the genome is associated with gene expression and alternative splicing of other cancer-related genes, similar to the proposed model. Finally, specifically disrupting the HIF1α-CTCF-COL5A1 exon64A axis through the dCas9-DNMT3A system alleviates the EMT potential of hypoxic breast cancer cells and may represent a novel therapeutic target in breast cancer.
DOI: 10.17632/92bzbwc2ss.1
title: LDHU3_14.1160

description: Calpain-like cysteine peptidase; Leishmania donovani (HU3 strain)
DOI: 10.17632/sxxghbrn63.1
title: supporting_material of Exploring the Performance of Ethanolamine-Based Ionic Liquid Composite Membranes for CO2/CH4 Separation

description: This is a supporting material for a study entitled as "Exploring the Performance of Ethanolamine-Based Ionic Liquid Composite Membranes for CO2/CH4 Separation". The data used on this study contains:
 S1. Materials, suppliers, purities, and molecular structures 
S2. NMR spectra 
S3. Membrane thickness and gas permeation experiments
S4. FT-IR_data - (MS Excel file)
DOI: 10.17632/f667jzmx8s.1
title: LDHU3_14.1240

description: Glutathione synthetase; Leishmania donovani (HU3 strain)
DOI: 10.17632/khkchmdpd7.1
title: Benefits of Cooperative Breeding for Acorn Woodpecker in a Human-Modified landscape of West Mexico

description: With database we tested causal relationships among territory quality, group size, and reproductive success in two habitats: native forests with low human disturbance and highly modified agricultural areas.
DOI: 10.17632/khkchmdpd7.2
title: Benefits of Cooperative Breeding for Acorn Woodpecker in a Human-Modified landscape of West Mexico

description: With database we tested causal relationships among territory quality, group size, and reproductive success in two habitats: native forests with low human disturbance and highly modified agricultural areas.
DOI: 10.15468/dl.dkwrzu
title: Occurrence Download

description: A dataset containing 3321 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Material citation, Material sample, Specimen)",
 "Country is India",
 "OccurrenceStatus is Present",
 "TaxonKey is Lantana camara L."
 ]
}

 The dataset includes 3321 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004510-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/rx4zj473rk.1
title: LDHU3_14.1290

description: RNA editing 3' terminal uridylyl transferase 1 | 3'TUTASE | KRET1; Leishmania donovani (HU3 strain)
DOI: 10.17632/sbfcrrrx2j.1
title: LDHU3_14.1280

description: Mitoribosomal protein uL16m; Leishmania donovani (HU3 strain)
DOI: 10.17632/kg4ytkwwzm.1
title: High selectivity fluorescence-based CQDs@cellulose membrane sensor for detection of hazardous gas

description: This file contains the data of all images and is real. Including some list of Gly / Bet @ CMC film and the detection of toluene gas, the reliability of fluorescence spectroscopy for the detection of harmful gases was confirmed.
DOI: 10.17632/dkxw36vzgx.1
title: LINF_100019000

description: small GTP-binding protein Rab7; Leishmania infantum (strain JPCM5)
DOI: 10.17632/kkmm72k2n3.1
title: LINF_100017200

description: nucleoside phosphorylase-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.15468/dl.p6yhad
title: Occurrence Download

description: A dataset containing 3321 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Material citation, Material sample, Specimen)",
 "Country is India",
 "OccurrenceStatus is Present",
 "TaxonKey is Lantana camara L."
 ]
}

 The dataset includes 3321 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004509-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/4xyt372py7.1
title: Capturing the Conversion of the Pathogenic Alpha-1 Antitrypsin Fold by ATF6 Enhanced Proteostasis

description: The excel file includes all the phenotype measurements for AAT variants with or without the treatment of AA-147 and AA-263.
The folder includes the input source data, R-code scripts and output files for the phenotype landscapes, phenotype barcodes and functional structures in response to ATF6 activators.
DOI: 10.17632/xvpg556mbs.1
title: Soil carbon, nitrogen and physicochemical factors

description: This database includes carbon and nitrogen stocks and physico-chemical factors in mangrove soils adjacent to coastal aquaculture, and also includes a description of the contribution of region-specific carbon sources to the soil carbon pool.
DOI: 10.15468/dl.3nw4h5
title: Occurrence Download

description: A dataset containing 1763 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "Country is Portugal",
 "Geometry POLYGON((-9.85528 36.17961,-6.06032 36.17961,-6.06032 42.52032,-9.85528 42.52032,-9.85528 36.17961))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Juniperus oxycedrus L."
 ]
}

 The dataset includes 1763 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004511-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2mp53j
title: Occurrence Download

description: A dataset containing 2429 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "OccurrenceStatus is Present",
 "TaxonKey is Graellsia isabellae Graëlls, 1849"
 ]
}

 The dataset includes 2429 records from 116 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004506-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/34jwycycdc.1
title: Wheel_squeal_AE_data_processed

description: Contains processed data from acoustic emission measurement on the full scale twin disk device. There are processed RMS values and calculated Kurtosis and Shannon entropy. Additionaly data from measurement of the Sound pressure levels and Coefficient of adhesion are also included in the set.
DOI: 10.17632/h7pgxb78db.1
title: LINF_100018600

description: protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/8wgf5sj7nk.2
title: Replication Package for "Financial Inclusion Across the United States"

description: Finclusion_Programs.zip is a replication package in Stata that creates and analyzes pseudo-microdata with the same variables as the actual tax microdata used in “Financial Inclusion Across the United States” by Yogo, Whitten, and Cox (Journal of Financial Economics, 2025).

Finclusion_Excel.zip (Excel format) and Finclusion_Stata.zip (Stata format) contain aggregate datasets, based on the actual tax microdata, on financial participation by year, ZCTA, and income quintile. These datasets are intended to facilitate future research.
DOI: 10.17632/byjrp4xns7.2
title: Sterechinus neumayeri v1 genome annotation

description: Genome annotation was performed using the BRAKER3 pipeline (Gabriel et al., 2023). A repeat library was generated with RepeatModeler (Smit & Hubley, 2010). The repeat families were compared to known echinoderm protein coding gene models using BLAST and any repeat with a significant hit (e-value &lt; 5e-5) were removed. The resulting repeat library was used to identify and mask repeats using RepeatMasker prior to annotation (Smit et al., 2010). BRAKER was run using protein models from S. purpuratus (available on echinobase https://download.xenbase.org/echinobase/Genomics/Spur5.0/sp5_0_GCF.gff3.gz ; last accessed 2/15/24), L.variegatus (available from echinobase https://download.xenbase.org/echinobase/Genomics/Lvar3.0/Lvar3_0_GCF_proteins.fa.gz ; last accessed 2/15/24), and L.pictus (available from echinobase https://download.xenbase.org/echinobase/Genomics/Lpic2.1/Lpic2_1_GCF_proteins.fa.gz ; last accessed 2/15/24) along with publicly available transcriptomic data on NCBI sequencing read archive and in house RNAseq dataset spanning embryogenesis. The gene models were annotated using the notation SNE_XXXXXX and analyzed for ‘completeness’ with BUSCO version 4 using the metazoan gene set (Simão et al., 2015). GRN gene curation was first carried out by curating a list of gene regulatory network genes (supplemental file X). Then, orthofinder2 (Emms & Kelly, 2019) was used to identify orthologs between S.neumayeri, L.variegatus, S.purupratus, and recently published genome annotation for P.lividus (Emms & Kelly, 2019; Marlétaz et al., 2023).
DOI: 10.17632/z4dn952ckj.1
title: Part 14 of data for Elizondo et al Adipose Tissue Macrophage Transglutaminase 2 and the Inflammation of Diet-Induced Obese Male Mice. RNAseq analysis data, continued

description: Part 14 of data for Elizondo et al Adipose Tissue Macrophage Transglutaminase 2 and the Inflammation of Diet-Induced Obese Male Mice. RNAseq analysis data, continued
DOI: 10.17632/xj8mpsdt6k.1
title: Raw data from: Effectiveness of the production of tissue-engineered living bone graft – a comparative study using perfusion and rotating bioreactor systems

description: The primary goal of the research was to compare the effectiveness of 2 bioreactors: (1) perfusion (Lazar Arrow-MTM Micro Bioreactor System) and rotating (Rotary Cell Culture System) in the generation of a living bone construct to select the system that is more favorable for cell cultivation and their differentiation towards mature bone cells. For this purpose bone marrow-derived mesenchymal stem cells (BMDSCs) were seeded on the surfaces of hydroxyapatite-based scaffolds and cultured in three different conditions: (1) static 3D culture – a test control (mat_S), (2) 3D culture in a perfusion bioreactor (mat_P), and (3) dynamic 3D culture in a rotating bioreactor (mat_R). Cell growth on the scaffolds was assessed quantitatively by LDH total assay and qualitatively by live/dead staining, cytoskeleton staining, and SEM imaging. Osteogenic differentiation was compared by ELISAs and immunofluorescent staining, whereas ECM mineralization was determined using Raman spectroscopy. 

Folders: ‘cytoskeleton_staining 1d’ and ‘cytoskeleton_staining 21d’ contain raw CLSM images after cytoskeleton staining after 1 day (before placing the samples into the bioreactors) and 21 days of culture, respectively. 

Folder ‘live dead” contains raw CLSM images of the cells on the scaffold after live/dead staining (before placing the samples into the bioreactors).

Folder ‘IF osteonectin_collagen” contains CLSM images after immunofluorescent staining of osteogenic markers.

Folder ‘SEM’ contains raw SEM images after 21 days of culture.

The name of the CLSM or SEM images indicates the specific sample and culture conditions, i.e. mat_S means static 3D culture, (2) mat_P means 3D culture in a perfusion bioreactor, and (3) mat_R means dynamic 3D culture in a rotating bioreactor.

Folder ‘Raman_maps’ contains various Microsoft Excel (.csv) files. Each Microsoft Excel file contains the raw data for Raman mapping.

Folder ‘Raman_spectra’ contains various Microsoft Excel (.csv) files. Each Microsoft Excel file contains the raw data for Raman spectra.

For Raman data, file name indicates the type of the sample, i.e. mat_S, mat_P, mat_R, mat_control that means non-seeded biomaterial incubated in the culture medium, and native that means untreated biomaterial.

Folder ‘ELISA_osteogenic markers’ contains various Microsoft Excel (.xlsx) files. Each Microsoft Excel file contains the raw results of ELISA for osteogenic marker (file name indicates the type of osteogenic marker). ELISA results are shown as concentration of specific osteogenic marker. Column B shows the name of the sample (mat_S, mat_P or mat_R).

The Microsoft Excel (.xlsx) file named ‘LDH_proliferation’ contains the raw results of LDH total proliferation assay performed after 1 day of culture (before placing the samples into the bioreactors) and after 21 days of culture in specific conditions.
DOI: 10.15468/dl.gs863s
title: Occurrence Download

description: A dataset containing 225 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-78.69336 0.44281,-76.81533 0.44281,-76.81533 1.19442,-78.69336 1.19442,-78.69336 0.44281))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Atelopus coynei Miyata, 1980",
 "Year 2016-2020"
 ]
}

 The dataset includes 225 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004513-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/kpjp3gnwbt.1
title: Mental Health Symptom Profiles Over Time: A Three-step Latent Transition Cognitive Diagnosis Modeling Analysis with Covariates

description: This data repository contains the companion data and R code files for Liang, de la Torre, Larimer, and Mun (2024). Mental health symptom profiles over time: A three-step latent transition cognitive diagnosis modeling analysis with covariates. In M. Stemmler, W. Wiedermann, & F. Huang (Eds.), Dependent data in social sciences research: Forms, issues, and methods of analysis (2nd ed.). New York: Springer.

Abstract 

Cognitive diagnostic modeling (CDM) is an item-level analysis that accounts for attribute co-occurrences when characterizing attributes and classifying individuals’ attribute profiles. Tan et al. (2023) provided an application for mental health symptom profiles. The current study extends Tan et al. (2023) to demonstrate how intervention and gender affect transition probabilities from one state to another in a three-step latent transition CDM. The sample used in this study consisted of 2,005 college students (34.5% men) who answered 40 items assessing four mental health symptoms (i.e., alcohol-related problems, anxiety, hostility, and depression) at baseline immediately before being randomly allocated to a brief alcohol intervention or control group (pre-test) and at a 12-month follow-up following the intervention (post-test). Participants in the intervention group received personalized feedback on their alcohol use and alcohol-related problems, along with descriptive drinking norms of peers and other personalized and general information aimed at motivating students to change. Results indicated that the selected models showed adequate fit and classification outcomes. Latent logistic regression analysis showed that the intervention helped improve participants’ anxiety and depression. Those in the intervention group were more likely to transition from having anxiety and depression attribute profiles at pre-test to not having them at post-test. In addition, male students were more likely to improve anxiety. Although the intervention was not associated with the transition probability from presence to absence for alcohol-related problems, it helped suppress the transition to having the attributes of alcohol-related problems (among men) and hostility (among women) at post-test. However, male students in the intervention were more likely to transition from absence to presence in their depression attribute profile state. The three-step latent transition CDM with covariates showcased in the current study may be an appealing analytical tool for examining and explaining change in mental health symptoms with informative covariates.
DOI: 10.17632/jdrx42jds9.3
title: Database for comparing two algorithms that classified eucalyptus in Landsat image time series

description: Data used in the development of the research entitled: "Comparison between machine learning classification and trajectory-based change detection for identifying eucalyptus areas in Landsat time series"
DOI: 10.15468/dl.jwfbux
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cyrtophora citricola (Forsskål, 1775)",
 "Year 1000-1900"
 ]
}

 The dataset includes 18 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004514-250117142028555/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/njwr8mn6wd.1
title: Supplementary Material for Manuscript ID ANIMAL-24-30118

description: Supplementary material for the manuscript "Milk Transcriptome Biomarker Identification to Enhance Feed Efficiency and Reduce Nutritional Costs in Dairy Ewes"
DOI: 10.17632/kjtdgk3f25.3
title: CDKN2A Deletion Remodels Lipid Metabolism to Prime Glioblastoma for Ferroptosis

description: Lipidomic abundance data (percent of total, percent of class) for 84 bulk patient tumors, 29 mouse xenografts, 43 gliomasphere cultures, and 27 biological replicates of genetically manipulated gliomasphere cultures. Further details on the data provided are described here https://youtu.be/PjUbVt968co

Data related to Figure 1C including lipid species - gene correlation values and clusters can be found in the "Correlation Analysis" folder.
DOI: 10.17632/cj96vvw329.1
title: LINF_110005800

description: protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/p5pdkzjr3r.1
title: LINF_110005000

description: protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/jywyhjgm3z.1
title: Eye tracking data for website design of Ecotourism related SMEs

description: The data set includes Time from First Fixation to Click and Click Count data from particpants who viewed a beta-version website that promotes ecotourism in Greece. A Tobii Nano eye tracker was used for the data collection.
DOI: 10.17632/wz4f2bpkbb.1
title: LINF_110005100

description: Endoplasmic reticulum vesicle transporter; Leishmania infantum (strain JPCM5)