cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12853584.v1
title: Expanding the molecular toolbox for Zygnematophyceae – transient genetic transformation of the desmid <i>Micrasterias radians</i> var. <i>evoluta</i>

description: In the past, various species of the unicellular algal genus <i>Micrasterias</i> (Zygnematophyceae) have been used for research in the fields of cell biology and physiology. Relatively large cell size, highly differentiated cell shape and a remarkable evolutionary position make <i>Micrasterias</i> interesting, especially for cytomorphogenetic studies. However, within this genus a model organism enabling molecular research has not yet been established. <i>Micrasterias radians</i> var. <i>evoluta</i> (W.B.Turner) Krieger allows easy culturing under axenic conditions and performs its whole life cycle <i>in vitro</i> thus fulfilling two important prerequisites for a model organism. In this work resources allowing transient expression of transgenes were developed. First, axenic lines were obtained by the treatment of zygospores with a cocktail of antibiotics followed by germination and regeneration. In order to allow transgene expression we isolated the 5′ -flanking region of the <i>M. radians</i> var. <i>evoluta Actin1</i> gene (<i>MrACT1</i>) and fused it to the green fluorescent protein (GFP). A higher promoter activity compared with various heterologous promoters regarding GFP expression was observed. Transient transgene expression was achieved by polyethylene glycol (PEG)-mediated protoplast transformation, yielding a rate of 3.9% transformed cells per surviving protoplasts. Transgene expression was also achieved by particle bombardment of vegetative cells. Employing the established protocol, a Lifeact-GFP fusion protein for labelling F-actin was expressed, allowing visualization of the actin cytoskeleton in <i>M. radians</i> var. <i>evoluta</i>.
DOI: 10.6084/m9.figshare.19382867.v1
title: Carlyle Olink Input data.xlsx

description: This dataset contains Olink NPX values plus basic demographics to accompany and reproduce the data in the Carlyle et al. manuscript entitled "Technical Performance Evaluation of Olink Proximity Extension Assay for Blood-based Biomarker Discovery in Longitudinal Studies of Alzheimer’s Disease". Ages over 90 years old have been capped to protect the identities of study volunteers. Individuals seeking to link these values back to more extensive demographic data should apply to searnold@mgh.harvard.edu. <b></b>
DOI: 10.6084/m9.figshare.25908841.v1
title: <b>Experimentally Supported siRNA Efficacy Dataset</b>

description: Small interfering RNA (siRNA) has revolutionized biomedical research and drug development through precise post-transcriptional gene silencing technology. Despite its immense potential, siRNA therapy still faces technical challenges, such as delivery efficiency, targeting specificity, and molecular stability. To address these challenges and facilitate siRNA drug development, we have developed siRNAEfficacyDB, a comprehensive database that integrates experimentally validated siRNA efficacy data. This database contains 3544 siRNA records, covering 42 target genes and seven cell lines. It provides detailed information on siRNA sequences, target genes, inhibition efficiencies, experimental techniques, cell lines, siRNA concentrations, and incubation times. siRNAEfficacyDB offers a user-friendly web interface that makes it easy to query, browse and analyze data, enabling efficient access to siRNA-related information. In summary, siRNAEfficacyDB provides a useful data foundation for siRNA drug design and optimization, serving as a valuable resource for advancing computer-aided siRNA design research and nucleic acid drug development. siRNAEfficacyDB is freely available at https://cellknowledge.com.cn/siRNAEfficacy.
DOI: 10.6084/m9.figshare.28914281.v1
title: Data generated in the study titled "Endolysosomal processing of neuron-derived signaling lipids regulates autophagy and lipid droplet degradation in astrocytes".

description: Endolysosomal processing of neuron-derived signaling lipids regulates autophagy and lipid droplet degradation in astrocytesJagannatham Naidu Bhupana <sup>1</sup>, Angelid Pabon <sup>1</sup>, Ho Hang Leung <sup>1</sup>, Mohamed Asik Rajmohamed <sup>1</sup>, Sang Hoon Kim <sup>2</sup>, Yan Tong <sup>1</sup>, Mi-Hyeon Jang <sup>2</sup>, Ching-On Wong <sup>1,3</sup><sup>1</sup> Department of Biological Sciences, School of Arts and Sciences-Newark, Rutgers University<sup>2</sup> Department of Neurosurgery, Robert Wood Johnson Medical School, Rutgers University<sup>3</sup> Correspondence: chingon.wong@rutgers.eduAstrocytes support brain metabolism by processing, storing, and distributing metabolites. Dynamic regulation of metabolic activities in astrocytes is critical to meeting the demands of other brain cells. During neuronal stress, lipid metabolites are transferred from neurons to astrocytes, where they are stored in lipid droplets (LDs). However, it is not clear whether and how neuron-derived lipids trigger metabolic adaptation in astrocytes. Here, we uncover an endolysosomal function that mediates a neuron-astrocyte transcellular lipid signaling paradigm. We identify Tweety homolog 1 (TTYH1) as an astrocyte-enriched transmembrane protein localized to endolysosomes, where it facilitates autophagic flux and lipid droplet (LD) degradation. Astrocyte-specific deletion of <i>Ttyh1</i> in mice and loss of TTYH1 ortholog in <i>Drosophila</i> lead to brain accumulation of neutral lipids. Computational and experimental evidence suggests that TTYH1 mediates endolysosomal clearance of ceramide 1-phosphate (C1P), a sphingolipid that dampens autophagic flux and LD breakdown in mouse and human astrocytes. We found that the inflammatory cytokine IL-1β induces neuronal upregulation of C1P biosynthesis. Concurrently, lipids secreted by neurons cause autophagic flux impairment and LD accumulation in astrocytes. Whereas TTYH1 deficiency in astrocytes exacerbates the catabolic blockage, inhibiting C1P synthesis in neurons restores autophagic flux and normalizes LD contents in astrocytes. Thus, astrocytes rely on the endolysosomal function of TTYH1 to mitigate the metabolic effects of neuron-derived lipids. Taken together, our findings reveal a neuron-initiated signaling paradigm that culminates in the regulation of catabolic activities in astrocytes.<br>
DOI: 10.6084/m9.figshare.5126821.v1
title: Supplementary Material for: Somatic Mutations Are Not Observed by Exome Sequencing of Lymphocyte DNA from Monozygotic Twins Discordant for Congenital Hypothyroidism due to Thyroid Dysgenesis

description: <b><i>Background/Aims:</i></b> Congenital primary hypothyroidism (CH) is a rare pediatric disorder estimated to occur in about 1:2,500 live births. Approximately half of these cases entail ectopic thyroid tissue, which is believed to result from a migration defect during embryogenesis. Approximately 3% of CH cases are explained by mutation(s) in known genes, most of which are transcription factors implicated in the embryology of the thyroid gland. Surprisingly, monozygotic (MZ) twins are usually discordant for CH due to thyroid dysgenesis, suggesting that most cases are not caused by transmitted genetic variation. One possible explanation is somatic mutation in genes involved in thyroid migration occurring after zygotic twinning. Such mutations should be observed only in the affected twin. <b><i>Methods:</i></b> To test the hypothesis of somatic mutation, we performed whole exome sequencing of DNA from three pairs of MZ twins discordant for CH with ectopic glands. <b><i>Results:</i></b> We found no somatic mutations exclusive to any of the three affected twins or in any of the unaffected twins. <b><i>Conclusion:</i></b> Either somatic mutations are not significant for the etiology of CH or else such mutations lie outside regions of the genome accessible by exome sequencing technology.
DOI: 10.6084/m9.figshare.7764014.v6
title: PEST-CHEMGRIDS_v1.01

description: PEST-CHEMGRIDS is a comprehensive database of the 20 most used pesticide active ingredients on 6 dominant crops and 4 aggregated crop classes at 5 arc-min resolution (about 10 km at the equator) projected from 2015 to 2025.<br>See attached metadata file for details on this release
DOI: 10.6084/m9.figshare.12409181.v1
title: Genome-Wide Association Study and Gene Specific Markers Identified a Large Number of Genes or QTL for Resistance to Stripe Rust in U.S. Winter Wheat Cultivars and Breeding Lines

description: To determine stripe rust resistance genes in U.S. winter wheat cultivars and breeding lines, we analyzed a winter wheat panel of 857 cultivars and breeding lines in a genome-wide association study (GWAS) using genotyping by multiplexed sequencing (GMS) and by genotyping with molecular markers of 18 important stripe rust resistance genes or quantitative trait loci (QTL).The 31 markers for the 18 previously reported <i>Yr</i> genes or QTL were successfully tested in the 857 winter wheat accessions and/or reference genotypes. The presence and absence of the markers are provided in Supplementary Table S3. The GMS-GWAS analysis identified 36 loci on 15 chromosomes (1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 5A, 5B, 5D, 6A, 6B, 7A, and 7B) significantly associated with stripe rust resistance in Supplementary Table S4.
DOI: 10.6084/m9.figshare.14044199.v2
title: lymph gland

description: A Seurat R object of Drosophila lymph gland, WT, 72~120h AEL
DOI: 10.6084/m9.figshare.1601891.v1
title: Gaussian Job Archive for C6H16ClNO5

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.19426994.v1
title: Alligator Original Cartilage Model

description: This is the simulation file (Adams MSC) for our model of the alligator elbow with its original cartilage (as acquired by 3D scanning).
DOI: 10.6084/m9.figshare.25664622.v1
title: The effects of servitization, digitalization, and digital learning orientation on sustainable performance: a hybrid PLS-SEM-ANN model

description: This is the experimental data of the manuscript entitled "The effects of servitization, digitalization, and digital learning orientation on sustainable performance: a hybrid PLS-SEM-ANN model"
DOI: 10.6084/m9.figshare.28087925.v3
title: Supplementary Information and Files for Tucker et al., (2024), a study on SAR11 metabolic and ecological diversification

description: This folder contains Supplementary Information for Tucker et al., (2024), a study entitled "Habitat-specificity in SAR11 is associated with a handful of genes under high selection". <br>
DOI: 10.6084/m9.figshare.28409153.v1
title: Sequence And Structural Information Used For Physicochemical, Molecular, And Biological Characterization of Two Novel Alternating Polarity Peptides Used As Gene Delivery Vector

description: pGL4.17.fastaThe sequence of the modified pGL4.17 plasmid that was used to assess peptide-DNA co-assembly and biological properties of the formed co-assemblies.DNA_fragment.pdbStructure of the DNA fragment that was used as an input in the coarse-grained MD simulations RFH.pdbStructure of RFH (RFRHRHRFR) peptide that was used as an input in the coarse-grained MD simulations RHF.pdbStructure of RHF (RHRFRFRHR) peptide that was used as an input in the coarse-grained MD simulations <br><br>
DOI: 10.6084/m9.figshare.28935134.v1
title: g12a2.gff3

description: The annotation file of the chromosomal-level genome assembled based on a small number of Giardia duodenalis trophozoites.
DOI: 10.6084/m9.figshare.7403777.v3
title: Plant cell division

description: Schematic drawing of plant cell division#plantillustrations
DOI: 10.6084/m9.figshare.9466511.v1
title: Table S3. Cross-analysis between the spatial and cell type specific RNA-seqs

description: See manuscript for details<br>
DOI: 10.17632/2vvjv5nvvn
title: Soil properties in different land-uses across various agroecological zones in India

description: The present data set obtained from field sampling and laboratory analysis was utilized to gain insights into the impact of available and total nitrogen dynamics on soil carbon sequestration across various land use systems including wheat-rice cropping (agriculture); wheat-poplar (agroforestry); mango orchards; Eucalyptus plantations; mixed forests within different agroecological zones (AZ’s).
DOI: 10.17632/xjtv62ncwr
title: Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues: Supplementary Data

description: Supplementary data for the study "Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues". The data.tar.gz archive contains: processed data files from 10x Visium experiments, immunofluorescence images and cell type proportion estimates generated with stereoscope. Scripts and rmarkdown files are available in the doc.tar.gz archive to run computational analyses related to the manuscript.

data:
1	annotation/ - files used for gene symbol conversion
2	archivalcancer/ - spatially resolved transcriptomics data from FFPE archival soft tissue carcinoma (generated with spaceranger v1.0.0)
3	HGSC/ - spatially resolved transcriptomics data from FFPE High Grade Serous Carcinosarcoma, HGSC (generated with spaceranger v1.0.0)
4	immunofluorescence/ - raw images (TIF format) of immunostaining with a SARS-CoV-1 antibody and DAPI staining
5	kidneyorganoid/ - spatially resolved transcriptomics data from PFA fixed kidney organoids (generated with spaceranger v1.0.0)
6	lung_SARS-CoV-2/- spatially resolved transcriptomics data from FFPE lung tissue infected with SARS-CoV-2 (generated with spaceranger v1.0.0)
7	lungcellmarkers/ - table of DE genes from Lung cell atlas
8	lungorganoid/ - spatially resolved transcriptomics data from PFA fixed lung organoids (generated with spaceranger v1.0.0)
9	mousebrain/- spatially resolved transcriptomics data from FFPE mousebrain (generated with spaceranger v1.0.0)
10	registration/ - image registration related data objects generated with the wholebrain workflow
11	stereoscope/ - cell type proportions estimates through cell type mapping with stereoscope


doc:
1	archival.Rmd - code for QC of archival samples
2	biotype_content_mouse_brain_data.Rmd - code for calculating and visualizing biotype content
3	fromHE_extended_FF.R - script to register FF coronal brain ection to the Allen Mouse Brain Atlas using the wholebrain workflow
4	fromHE_extended_FFPE.R - script to register FFPE coronal brain section to the Allen Mouse Brain Atlas using the wholebrain workflow
5	global_functions_segmentation.R - functions required for nuclei segmentation
6	global_functions.R - functions required for registration
7	HGSC.Rmd - analysis of FFPE High Grade Serous Carcinosarcoma (HGSC) tissue data 
8	Kidney_organoids.Rmd - analysis of PFA Kidney organoids Visium data
9	Lung_organoids.Rmd - analysis of PFA Lung organoids Visium data
10	Lung_tissue_Covid19.Rmd - analysis of FFPE Lung tissue infected with Covid19 Visium data
11	mouse_brain_multiple_sections.Rmd - joint analysis of 7 FFPE mouse brain (coronal) tissue sections Visium data
12	mouse_FFPE_vs_FF.Rmd - comparison of Visium data obtained from FFPE and FF tissue (coronal mouse brain tissue sections)
13	QC_metrics_by_age.Rmd - analysis and visualization of QC over storage time
14	segmentation_of_SARS-Cov-1.Rmd - simple nuclei segmentation of DAPI stain

images:
High resolution Hematoxylin and Eosin stained bright field images in JPG format.
DOI: 10.25422/azu.data.23272220.v1
title: Data and Code for "Photogrammetric monitoring of rock glacier motion using high-resolution cross-platform datasets: formation age estimation and modern thinning rates"

description: This directory contains the supporting information for "Photogrammetric monitoring of rock glacier motion using high-resolution cross-platform datasets: formation age estimation and modern thinning rates"Directory descriptions:boulder: Surface boulder position measurements and spreadsheets used to calculate displacements based on prior boulder position measurements provided by Potter (personal communication).cias: Processed change detection input images and corresponding results for Galena Creek (GCRG), Sulphur Creek (SCRG), Sourdough (SRG), and McCarthy Creek (MCRG).dem: Photogrammetrically generated digital elevation models and resulting elevation difference maps.code: Analysis code used to generate the results reported in the study.docs: PDF copies of the main manuscript and supplementary figures documents, along with the photogrammetric processing documentation.ortho: Full extents of the processed orthomosaics using the parameters listed in the docs directory. These orthomosaics have not been processed for ingestion into CIAS.photo: Raw photogrammetry data and relevant positioning files.<br><i>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</i><br><br><br><br>
DOI: 10.6084/m9.figshare.1094642.v2
title: Unedited Gephi file - set of 44 dissertations on electronic literature 2002-2013 with links to creative works cited

description: This is the "clean", unedited Gephi file I used to visualise the conncetions between 44 dissertations about electronic literature and the creative works they cite. This file is perfect if you want to download it, load it into Gephi and try visualising the data yourself. I provide a tutorial here: http://jilltxt.net/?p=3730 For more information, see my paper in ebr: electronic book review: http://electronicbookreview.com/thread/electropoetics/analyzing The data is from the ELMCIP Electronic Literature Knowledge Base (http://elmcip.net/category/publication-type/book-dissertation) and includes all dissertations published between 2002 and 2013 that we had registered in the Knowledge Base as of March 2014, with certain exceptions as explained in the full paper. A complete list of included dissertations can be found at the end of the paper. Because I did not initially export years of publication and titles from the Knowledge Base, only some of the creative works have publication year and title information. This file is shared under a CC-BY licence (http://creativecommons.org/licenses/by/4.0/).
DOI: 10.6084/m9.figshare.24920823.v1
title: DATA - Sport injuries in elite Paralympic judokas. Findings from the 2018 World Championship

description: Data on Sport injuries in elite Paralympic judokas. Findings from the 2018 World Championship
DOI: 10.6084/m9.figshare.3567054.v1
title: Appendix A. Ecosystems and references used in meta-analysis to assess dreissenid impacts.

description: Ecosystems and references used in meta-analysis to assess dreissenid impacts.
DOI: 10.17632/53tddmryhb
title: IBD colonoscopy

description: IBD colonoscopy
DOI: 10.6084/m9.figshare.26305225.v1
title: Code and Data

description: code and data for the paper "Lane-level identifying and map updating for road-restricted access areas based on driving record data"
DOI: 10.6084/m9.figshare.27433092.v1
title: IncucyteS3.zip

description: SLiMIA (Spheroid Light Microscope Image Atlas) provides light microscopy images (and manual segmentations/ground truths) of spheroids from 50 cell lines, 9 culture media, 4 formation methods and multiple seeding densities.This folder contains specifically the images obtained with an Incucyte S3 light microscope.
DOI: 10.6084/m9.figshare.3554583.v1
title: Appendix C. Vulnerability curves for study species.

description: Vulnerability curves for study species.
DOI: 10.11583/dtu.16940590.v1
title: COVID-19 Effects on the Energy System of Cape Verde

description: Set of xcel files presenting the data employed in the paper titled: "Effects of the COVID-19 Pandemic on the Isolated Energy System of Cape Verde" summited to Elsevier's Joint Special Issue on "COVID-19 Energy Impacts: Lockdown impact on Electricity Demand, Power Systems Operation and Pollution Levels".<br>The original sources of the data are all Open Access and cited in the paper.
DOI: 10.15468/dl.2k5e3m
title: Occurrence Download

description: A dataset containing 6652 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ipomoea hederacea Jacq.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 6652 records from 252 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013226-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.12206651.v1
title: Heat-Hardening Manuscript Lizard Data

description: Raw data collected for A. carolinesis & A. sagrei<br>Key:<br>Hour: The hour interval that each specific lizard was tested at.Species: Anolis sagrei represented as "sag" and Anolis caroliensis represented as "car"Lizard ID: Unique Identifier of each lizard, a combination of letters and numbers.Date: the date on which the CTmax1 value was measuredCTmax1: The initial critical thermal maximum value of each lizardCTmax2: The second time that the critical thermal maximum value was tested.SVL: Snout vent length (cm)Mass: mass of each lizard (g)Delta: ΔCTmax value for each lizard, calculated by subtracting CTmax1 from CTmax 2.<br>
DOI: 10.6084/m9.figshare.1281094.v2
title: Quizoola24 Twitter Capture

description: Performance of "Quizoola24!" by Forced Entertainment, 22 Nov 2014, Millenium Muesum, Sheffield. Raw tweets captured over the period 21 Nov - 23 Nov 2014, filtered using the hashtags #quizoola24 and #quizoola
DOI: 10.6084/m9.figshare.24160836.v1
title: New data-9.19.docx

description: Hydrogeochemical and isotopic characteristics of karst groundwater and Quaternary groundwater collected in Jinci spring in 2018
DOI: 10.6084/m9.figshare.25847368.v1
title: BII QES - Supplemental online material

description: Supplementary material for the article: <i>Experiences of women who self-report Breast Implant Illness (BII): A qualitative evidence synthesis</i>
DOI: 10.6084/m9.figshare.27625698.v1
title: Mouse Schistosome Microbiome Data

description: This is the master dataset used for the manuscript, titled “Does schistosome infection affect behavior through the gut-brain axis?”. Includes excel spreadsheets with sample data, descriptions, r-code, and phyloseq objects (.rds files).
DOI: 10.6084/m9.figshare.28758878.v1
title: SleepHygiene.xlsx

description: In this project we aim to investigate how adult attachment might be associated with sleep hygiene and if sleep hygiene might mediate the relationship between adult attachment and sleep quality. Daytime fatigue and an anxious and depressed mood will be entered as covariates.
DOI: 10.17632/65g4np9stj
title: Data for: "BARTOLUZZIO, A. I. S. S. Emendas Parlamentares e Domínio sobre o Orçamento Público: uma Análise da Relação Legislativo-Executivo no Brasil. Rio de Janeiro, 2024. Tese (Doutorado em Ciências Contábeis) – PPGCC/UFRJ, Rio de Janeiro, 2024"

description: Arquivos analisados para a Tese de Doutorado do discente Alann Inaldo Silva de Sá Bartoluzzio, defendida no Programa de Pós-Graduação em Ciências Contábeis da Universidade Federal do Rio de Janeiro. 

BARTOLUZZIO, Alann Inaldo Silva de Sá. Emendas parlamentares e domínio sobre o orçamento público: uma análise da relação Legislativo-Executivo no Brasil. Rio de Janeiro, 2024. Tese (Doutorado em Ciências Contábeis) – Programa de Pós-Graduação em Ciências Contábeis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 2024.