cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24204750.v1
title: EPI-Clone dataset: Single cell targeted DNA methylation profiling of hematopoietic stem and progenitor cells

description: This is the dataset supporting the EPI-Clone manuscript: Targeted single cell methylation profiling of hematopoietic stem and progenitor cells (HSPCs) was performed with the scTAMseq method. Three experiments are included: Two where HSCs were clonally labeled with the LARRY system, transplanted to recipient mouse and profiled 4-5 months later (post-transplant hematopoiesis), and one where HSPCs were profiled straight from an unperturbed mouse.<b>Remaining experiments are available under different DOIs:</b>Mature cell experiment: https://doi.org/10.6084/m9.figshare.25472467Unperturbed old vs young mouse experiment: https://doi.org/10.6084/m9.figshare.25472434Human total bone marrow: https://doi.org/10.6084/m9.figshare.25526899Dataset is a seurat (v4) object with the following assays, reductions and metadata:<br><b>ASSAYS:</b>AB: Antibody expression dataDNAm: DNA methylation data, containing binary observations (0: amplicon not observed, i.e. dropout or absence of DNA methylation, 1: amplicon observed, i.e. DNA methylation). See the paper on scTAMseqintegrated: Integration of DNA methylation data performed across experimental batches.<b>DIMENSIONALITY REDUCTION</b>pca: PCA performed on the integrated dataumap: UMAP computed on the integrated dataFor strategies how to obtain dimensionality reduction that reflect clonal identity, please see the github page accompanying the manuscript.<b>METADATA</b>Experiment: The experiment that the cell is from, values are "LARRY main experiment", "LARRY replicate" and "Native hematopoiesis"ProcessingBatch: Experiments were processed in several batches.CellType: Cell type annotationLARRY: Error corrected LARRY barcodeLARRYSize: Size of the cloneGFP.or.Saphire: Identity of the donor mousePseudotime: Differentiation pseudotimePerformanceNonHhaI: Performance of the control amplicons in that cell
DOI: 10.6084/m9.figshare.26511253.v1
title: DeepParticle dataset [MICRO, MESO, MACRO] (2022)

description: These are the datasets used to train the models described in our method paper:"Computer vision segmentation model—deep learning for categorizing microplastic debris"The image segmentation and classification models are designed to identify plastic particles from an image. Two types of models were built:Segmentation models which segment and label the particle found within an input image with a homogeneous backgroundClassification models that classify a particle image into a category (e.g. hard plastic, pellet, line, cap...)See our Gitlab page: https://gitlab.com/Grouumf/particle_detectEach folder: MICRO, MESO, and MACRO represents a different size category.MICRO: 0.05 cm–0.5 cmMESO: 0.5 cm–5.0 cmMACRO &gt; 5.0 cmThe VALIDATION dataset contains additional annotated images used for validation.Each folder is organized as follows:MICRO ├── annotation ├── foam ├── hard ├── line ├── noise ├── pellet ├── raw_img └── reference<br>`raw_img` contains the raw images that each display a variety of plastic particles.`annotation` contains the particle pixel coordinates within the raw images.The remaining folders represent particle categories (line, noise, pellet, foam, reference). Each of these folders contains the individual image of each particle annotated in the raw imagesFor example, the MICRO annotation folder contains a TSV file named `08_03_micro_line_only1.JPG.tsv`. This file contains the particle annotations and coordinates for the raw images labeled: `08_03_micro_line_only1.JPG`The beginning of the TSV file is as follows:ID minr minc maxr maxc classline/2022-03-28 07:18:39.577051_k0.jpg 2255 530 2329 601 lineline/2022-03-28 07:18:39.577051_k1.jpg 2185 754 2363 842 lineline/2022-03-28 07:18:39.577051_k2.jpg 2974 863 3079 921 lineEach line represents an annotated particle, with the four first columns its pixel coordinates. the last column is the annotated category.Also, the image of the first annotated particle `line/2022-03-28 07:18:39.577051_k0.jpg` can be found in the `line` folder.The MESO and MACRO folders contain different categories, e.g. cap_me, or butt_me, which are the bottle caps and the cigarette butt used for the MESO models.Finally, the noise folders contain noise "particles" or sections of the raw images that should not be identified as particles. These are useful when training the classifiers and removing the false positives from the annotations.<br>
DOI: 10.6084/m9.figshare.29206443
title: Additional file 1 of Identification of EPHB4 as a potential causal gene and therapeutic target for endometriosis using Mendelian randomization

description: Supplementary Material 1
DOI: 10.17632/98ywc24xv7
title: The histone acetyltransferase Mst2 protects active chromatin from epigenetic silencing by acetylating the ubiquitin ligase Brl1. Flury et al.

description: Raw data Flury et al, Molecular Cell, 2017
DOI: 10.6084/m9.figshare.20057066.v1
title: Single cell RNA sequencing analysis

description: The HB-EGF expression in difference cell types in lung cancer <br>
DOI: 10.6084/m9.figshare.8006204.v1
title: Critical appraisal checklist for analytical cross sectional studies

description: The critical appraisal tool, recommended by The Joanna Briggs Institute for cross sectional studies, was used to assess risk of bias in the reviewed studies. Here are the critical appraisal tools for each article analyzed in this systematic review.
DOI: 10.6084/m9.figshare.14290860.v1
title: Synergistic effect of ibuprofen with itraconazole and fluconazole against Cryptococcus neoformans

description: The present study investigated the association of the non-steroidal anti-inflammatory drug ibuprofen with itraconazole, fluconazole and amphotericin B against Cryptococcus neoformans isolates. The minimal inhibitory concentration (MIC) was found according to M27-A3 protocol and in vitro interactions were evaluated using checkerboard microdilution method. Synergism was demonstrated between azoles and ibuprofen for most isolates. However, no synergistic effects were seen when amphotericin B was combined with ibuprofen. Therefore, our results suggest that ibuprofen presents clinical potential when combined with azole drugs in the treatment of cryptococcosis.
DOI: 10.6084/m9.figshare.21257799.v1
title: The anti-tumor effects of caloric restriction are mediated by the gut microbiome

description: Calorie restriction（CR) as well as intermittent fasting (IF) without malnutrition have been shown to reduce the risk of cancer development. Separately, CR and IF can also lead to gut microbiota remodeling. However, whether the gut microbiota plays a role in the anti-tumor effect related to CR or IF is still unknown. Here we show that CR, but not IF, protects against subcutaneous MC38 tumor formation through a mechanism that is dependent on the gut microbiota in female mice. Following CR, we identify enrichment of Bifidobacterium through 16S rRNA sequencing of the gut microbiome. Moreover, B. bifidum administration is sufficient to rescue the anti-tumor effect of CR in microbiota-depleted mice. Mechanistically, B. bifidum mediates the CR-induced anti-tumor effect through acetate production, and is also dependent on the accumulation of IFNγ+CD8+T cells in the tumor microenvironment. Our results demonstrate that CR can modulate the gut taxonomic composition, which is of oncological significance in tumor growth kinetics and cancer immunosurveillance.
DOI: 10.6084/m9.figshare.21353222.v1
title: Biopsy of the olfactory epithelium from the superior nasal septum: is it possible to obtain neurons without damaging olfaction?

description: Abstract Introduction Olfactory epithelium biopsy has been useful for studying diverse otorhinolaryngological and neurological diseases, including the potential to better understand the pathophysiology behind COVID-19 olfactory manifestations. However, the safety and efficacy of the technique for obtaining human olfactory epithelium are still not fully established. Objective This study aimed to determine the safety and efficacy of harvesting olfactory epithelium cells, nerve bundles, and olfactory epithelium proper for morphological analysis from the superior nasal septum. Methods During nasal surgery, 22 individuals without olfactory complaints underwent olfactory epithelium biopsies from the superior nasal septum. The efficacy of obtaining olfactory epithelium, verification of intact olfactory epithelium and the presence of nerve bundles in biopsies were assessed using immunofluorescence. Safety for the olfactory function was tested psychophysically using both unilateral and bilateral tests before and 1 month after the operative procedure. Results Olfactory epithelium was found in 59.1% of the subjects. Of the samples, 50% were of the quality necessary for morphological characterization and 90.9% had nerve bundles. There was no difference in the psychophysical scores obtained in the bilateral olfactory test (University of Pennsylvania Smell Identification Test [UPSIT®]) between means before biopsy: 32.3 vs. postoperative: 32.5, p= 0.81. Also, no significant decrease occurred in unilateral testing (mean unilateral test scores 6 vs. 6.2, p= 0.46). None out of the 56 different odorant identification significantly diminished (p&gt; 0.05). Conclusion The technique depicted for olfactory epithelium biopsy is highly effective in obtaining neuronal olfactory tissue, but it has moderate efficacy in achieving samples useful for morphological analysis. Olfactory sensitivity remained intact.
DOI: 10.6084/m9.figshare.28915787.v1
title: Nucleus Ambiguus Histology data from doi 10.1113/JP287457 ; NIH Grant AG086136

description: F344 rats at 6, 18 and 24-months-old.Cyropreserved brainstem cut at 15 microns.Nissl Stain.10 section intervals.Read the readme for metadata.
DOI: 10.6084/m9.figshare.5127805.v1
title: Supplementary Material for: Association between Hypouricemia and Reduced Kidney Function: A Cross-Sectional Population-Based Study in Japan

description: <b><i>Background:</i></b> Hypouricemia, conventionally defined as a serum uric acid level of ≤2 mg/dl, is considered a biochemical disorder with no clinical significance. However, individuals with renal hypouricemia have a high risk of urolithiasis and exercise-induced acute kidney injury, both of which are risk factors for reduced kidney function. <b><i>Methods:</i></b> To test the hypothesis that individuals with hypouricemia would be at a higher risk of reduced kidney function, we conducted a population-based cross-sectional study using data from the Specific Health Checkups and Guidance System in Japan. Logistic analysis was used to examine the relationship between hypouricemia and reduced kidney function, defined as estimated glomerular filtration rate &lt;60 ml/min/1.73 m<sup>2</sup>. <b><i>Results:</i></b> Among 90,710 men (mean age, 63.8 years) and 136,935 women (63.7 years), 193 (0.2%) and 540 (0.4%) were identified as having hypouricemia, respectively. The prevalence of hypouricemia decreased with age in women (p for trend &lt;0.001), but not in men (p for trend = 0.24). Hypouricemia was associated with reduced kidney function in men (odds ratio, 1.83; 95% confidence interval, 1.23-2.74), but not in women (0.61; 0.43-0.86), relative to the reference category (i.e., serum uric acid levels of 4.1-5.0 mg/dl) after adjusting for age, drinking, smoking, diabetes, hypertension, hypercholesterolemia, obesity, and history of renal failure. Sensitivity analyses stratified by diabetic status yielded similar results. <b><i>Conclusions:</i></b> This study is the first to provide evidence that hypouricemia is associated with reduced kidney function in men. Further research will be needed to determine the long-term prognosis of individuals with hypouricemia.
DOI: 10.17632/pchm4c6369
title: Repositorio de tesis doctoral: Impacto de las emisiones naturales y antropogénicas sobre la calidad del aire regional en Argentina

description: Repositorio de la tesis doctoral Impacto de las emisiones naturales y antropogénicas sobre la calidad del aire regional en Argentina. 
Listado de archivos contenidos en este repositorio.
Capítulo 2: 
Configurar WPS:
● GEOG.TBL original 
● GEOG.TB modificada
● METGRID.TBL original 
● METGRID.TBL modificada
● Carpeta geog_geaa 

Configurar WRF-Chem
● Compile_wrf_and_deps_v1.sh
● flex_lib_modifications_kpp.txt
● variables.sh
● submit.job
● README.compile_wrf.docx

Capítulo 3:
● código fuente para anthro_emis_merge
● namelist.inp_anthro_emis_merge 
● htap_preprocesamiento.sh
● geaa-aei_preprocesamiento.ipynb
● edgarv5_preprocesamiento.ipynb

Capítulo 5:
● namelist.wps_sub-regional
● namelist.input_sub-regional
● namelist.inp_sub-regional

Capítulo 6:
● namelist.wps_regional 
● namelist.input_regional
● namelisst.inp_regional_category_profile.inp
DOI: 10.6084/m9.figshare.15109260.v2
title: Base de datos sobre "Selección de candidaturas presidenciales"

description: Esta base de datos sistematiza las reformas a los mecanismos de selección de la candidatura presidencial en América Latina entre 1978 y 2021.<br>
DOI: 10.6084/m9.figshare.22085627.v1
title: aamodt_signal_diversity_morning_sleep

description: <br>
Dream EEG and Mentation (DREAM) data set
<br>
<br>
---Data set information---
<br>
Common name: Aamodt_morning_sleep
Full name: (Optional, unwieldly full name)
Authors: Aamodt, A., Nilsen, A.S., Thürer, B., Moghadam, F.H., Kauppi, N., Juel, B.E. and Storm, J.F.
Location: Oslo, Norway
Year: 2020
Set ID: [SET BY DATABASE]
Amendment: [SET BY DATABASE]
Corresponding author ID: [SET BY DATABASE]
Download URL: [SET BY DATABASE]
<br>
Previous publications:
1) Aamodt, A., Nilsen, A.S., Thürer, B., Moghadam, F.H., Kauppi, N., Juel, B.E. and Storm, J.F. (2021) ‘EEG Signal Diversity Varies With Sleep Stage and Aspects of Dream Experience’, Frontiers in psychology, 12, p. 655884.
2) Aamodt, A., Sevenius Nilsen, A., Markhus, R., Kusztor, A., HasanzadehMoghadam, F., Kauppi, N., Thürer, B., Storm, J.F. and Juel, B.E. (2023) ‘EEG Lempel-Ziv complexity varies with sleep stage, but does not seem to track dream experience’, Frontiers in human neuroscience, 16. Available at: https://doi.org/10.3389/fnhum.2022.987714.
<br>
Correspondence:
Johan F Storm (j.f.storm@medisin.uio.no)
<br>
---Metadata---
<br>
Key ID: [SET BY DATABASE]
Date entered: [SET BY DATABASE]
Number of samples: [INFERRED BY DATABASE]
Number of subjects: [INFERRED BY DATABASE]
Proportion REM: [INFERRED BY DATABASE]
Proportion N1: [INFERRED BY DATABASE]
Proportion N2: [INFERRED BY DATABASE]
Proportion experience: [INFERRED BY DATABASE]
Proportion no-experience: [INFERRED BY DATABASE]
Proportion healthy: [INFERRED BY DATABASE]
Provoked awakening: Yes
Time of awakening: Morning
Form of response: Structured
Date approved: [SET BY DATABASE]
<br>
<br>
---How to decode data files---
<br>
The files in the PSG directory are named according to the subjectID and the CaseNumber for each awakening. For example the file 01_0103.edf is associated with the third awakening (case 0103) from subject 01. 
<br>
--Treatment group codes--
<br>
No treatment groups
<br>
<br>
---Experimental description---
<br>
See previous publications
<br>
--DREAM categorization procedure--
<br>
The original experiment categorized the dream reports according to the DREAM definitions.
<br>
<br>
---Technical details---
<br>
The data include a single EMG channel (called EMG1), which is a bipolar derivation of the standard LAT and RAT electrodes placed on the chin of the sleeping subject.
The data include two EOG channels (called EOGu and EOGl), which were placed in the American Academy of Sleep Medicine (AASM) recommended E1 and E2 positions below (l for lower) and above (u for upper) the lateral canthi. 
<br>
--Data acquisition--
<br>
See published manuscripts
<br>
--Data preprocessing--
<br>
Data were rereferenced to a common average reference and zero centered to adjust for the DC offset. Raw data can be requested in accordance with statements in published manuscripts. 
<br>
DOI: 10.6084/m9.figshare.19312205.v1
title: Support Data for "Target-Oriented Prioritization: targeted selection strategy by integrating organismal and molecular traits through predictive analytics in breeding"

description: Folder Data_TOP contains four sets of data, NCII, Maize 368 , Maize 282 and Rice 210, used in the article entitled "Target-Oriented Prioritization: targeted selection strategy by integrating organismal and molecular traits through predictive analytics in breeding".The maize NCII population consists of 5,820 F1 hybrids with 156,269 SNPs and 18 agronomic traits.Maize 368 was characterized with 100K SNPs, 20 agronomic traits and 749 metabolic traits.Maize 282 was genotyped with 50878 SNPs and phenotyped for 21 agronomic traits and 37127 transcriptomic traits from seven tissues.The Rice 210 dataset consists of 1619 bins, 4 agronomic traits, 24,994 gene expressions and 1000 metabolic traits.<br>
DOI: 10.6084/m9.figshare.28860935.v1
title: Datasets associated to "Unravelling water pathways and sources in leafless maples during early spring sap-ascent"

description: MetadataDataset dt.hw: Raw stable isotope and yields data<br>date: date of the samplingday: sap flow day<br>ID: Tree identifierdelta_2H: δ2H ‰ VSMOW<br>volume: maple sap volume (ml)<br>sc: maple sap sugar content (Brix %)cmvol: Cumulative volume (ml)<br>treatment: Treatment TB=Tree base, TR=Tree Trunk, CT=Control, S=Soil, CR=CrownDBH: Diameter at breast height (cm)<br>H: Total height (m)size_ratio: Ratio of DBH to height (cm/m)<br>hw_pres: Presence or absence of labelled water<br>Dataset dt.sc.fin: Processed data for sugar content model<br>date: date of the samplingday: sap flow day<br>ID: Tree identifier<br>sc: maple sap sugar content (Brix %)<br>treatment: Treatment TB=Tree base, TR=Tree Trunk, CT=Control, S=Soil, CR=CrownDBH: Diameter at breast height (cm)<br>H: Total height (m)SizeRatio: Ratio of DBH to height (cm/m)<br>minT: Minimum temperature of the freezing event<br>maxT: Maximum daily temperature<br>meanT: Mean daily temperature<br>FreezeHrs0: Total duration in hours of the freezing eventTR: Probability of detecting trunk water source<br>TB: Probability of detecting tree base water sourceS: Probability of detecting soil water source<br>Dataset dt.vol.fin: Processed data for sap volume model<br>date: date of the samplingday: sap flow day<br>ID: Tree identifier<br>vol: Daily sap volume (ml)<br>treatment: Treatment TB=Tree base, TR=Tree Trunk, CT=Control, S=Soil, CR=CrownDBH: Diameter at breast height (cm)<br>H: Total height (m)SizeRatio: Ratio of DBH to height (cm/m)<br>minT: Minimum temperature of the exothermic phase<br>maxT: Maximum daily temperature<br>meanT: Mean daily temperatureThawHrs0: Number of hours of the endothermic phase<br>TR: Probability of detecting trunk water source<br>TB: Probability of detecting tree base water sourceS: Probability of detecting soil water source<br><br>
DOI: 10.6084/m9.figshare.6121640.v1
title: ROS levels under various drugs treament

description: ROS levels under various drugs treament
DOI: 10.6084/m9.figshare.4522751.v1
title: Gene length as a biological timer to establish temporal transcriptional regulation

description: Transcriptional timing is inherently influenced by gene length, thus providing a mechanism for temporal regulation of gene expression. While gene size has been shown to be important for the expression timing of specific genes during early development, whether it plays a role in the timing of other global gene expression programs has not been extensively explored. Here, we investigate the role of gene length during the early transcriptional response of human fibroblasts to serum stimulation. Using the nascent sequencing techniques Bru-seq and BruUV-seq, we identified immediate genome-wide transcriptional changes following serum stimulation that were linked to rapid activation of enhancer elements. We identified 873 significantly induced and 209 significantly repressed genes. Variations in gene size allowed for a large group of genes to be simultaneously activated but produce full-length RNAs at different times. The median length of the group of serum-induced genes was significantly larger than the median length of all expressed genes, housekeeping genes, and serum-repressed genes. These gene length relationships were also observed in corresponding mouse orthologs, suggesting that relative gene size is evolutionarily conserved. The sizes of transcription factor and microRNA genes immediately induced after serum stimulation varied dramatically, setting up a cascade mechanism for temporal expression arising from a single activation event. The retention and expansion of large intronic sequences during evolution have likely played important roles in fine-tuning the temporal expression of target genes in various cellular response programs.
DOI: 10.17632/ygwrwtryz2
title: Remote sensing for cost-effective blue carbon accounting

description: This repository contains the data used to generate Figure 1 and 2 in the article "Remote sensing for cost-effective blue carbon accounting" (2023) in Earth-Science Review
DOI: 10.6084/m9.figshare.19700056.v2
title: DepMap 22Q2 Public

description: This DepMap release contains data from CRISPR knockout screens from project Achilles, as well as genomic characterization data from the CCLE project.<br>For more information, please see README.txt.
DOI: 10.6084/m9.figshare.28938791.v1
title: hcpaTemplateFA.nii.gz

description: HCP-Aging FA template
DOI: 10.17632/8ghyn6n6x8
title: Mechanism of MRX Inhibition by Rif2 at Telomeres

description: Specific proteins present at telomeres ensure chromosome end stability. In this work, we address how the Saccharomyces cerevisiae ORC-related Rif2 protein protects telomere.
DOI: 10.6084/m9.figshare.19499072.v1
title: Demographic Performa

description: this form described the socio demographic characteristics of the participants
DOI: 10.6084/m9.figshare.25222118.v3
title: Datos brutos de mensajes publicados en usuarios vinculados a medios informativos digitales españoles en X, FB y Web

description: Datos brutos recabados en el marco del proyecto Hatemedia (PID2020-114584GB-I00), financiado por <b>MCIN/ AEI /10.13039/501100011033.</b>Los datos recopilados corresponden a cinco medios informativos digitales, tomados como casos de estudio en el proyecto al que corresponde estos datos, tanto en la plataforma X, como en FB y en sus portales web; durante 2021-2022.El proceso de recolección de estos datos fueron recolectados, a partir del procedimiento expuesto en:Ruiz-Iniesta, Almudena; Blanco Valencia, Xiomara; Pérez, Daniel; De Gregorio Vicente, Oscar; José Cubillas, Juan; Julio Montero Díaz, https://orcid.org/0000-0002-4145-7424; et al. (2024). Informe final sobre el scrapeo de datos brutos obtenidos en medios informativos digitales españoles en X, FB y Web. figshare. Presentation. https://doi.org/10.6084/m9.figshare.25187591.v2Los datos fueron recolectados con el apoyo de la empresa colaboradora: Possible IncPara más información del proyecto, ingresar en: https://www.hatemedia.es/Si deseas tener acceso a estos datos, contactar con los IPs del proyecto, a traves de: elias.said@unir.net, en copia a julio.montero@unir.net
DOI: 10.6084/m9.figshare.28667525.v1
title: Urban vacant land of 36 major Chinese cities

description: The data include two parts: (1) urban vacant land of 36 major Chinese cities (in shapefile format), and (2) codes and data used for automatic vacant land identification.<br>Urban vacant land is a growing issue worldwide. The study is aimed to realize large-scale automatic identification of urban vacant land. A framework based on deep learning techniques is proposed to extract urban vacant land of 36 major Chinese cities through semantic segmentation of high-resolution remote sensing images. The automatic identification framework is proved to be accurate and efficient, with strong robustness. This method is expected to serve as a practical approach in various countries and regions. The data of urban vacant land of 36 cities can be used in further studies.