cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26075857.v1
title: Russian university student comments in VKontakte online communities according to their migration status

description: The dataset in this research includes data collected from student online communities on VKontakte, spanning from September 2021 to July 2022. This data encompasses posts and comments from 297 groups where students from 208 Russian universities engaged. Initially, 10,099 unique comments were collected. After filtering out bots and fake profiles, the dataset was refined to 1,595 relevant comments.Each comment in the dataset is accompanied by metadata, including the number of likes, shares, views, user IDs, hometown, and current residence of the users. The user verification process involved analyzing publication activity, reactions to content (likes and shares), time spent on the social network, and validating location data through the analysis of internet groups and regional community subscriptions.The comments were classified into six key themes using text classification tools. Since some comments pertained to multiple themes, a separate row was added for each combination, ensuring comprehensive coverage of the topics. Thus, the final number of rows included in the dataset is 2,351.In addition to thematic classification, the dataset includes information on the migration status of students. If a student's city of origin matched the city of their university, the comment was identified as from a local student (374 comments, 23%). Conversely, if the city of origin differed, the comment was from a visiting student (1,221 comments, 77%).The data is presented in Russian. Please note that the texts have not been censored, posts and comments may contain inappropriate language.
DOI: 10.6084/m9.figshare.28531982.v4
title: genome fasta and gff files of 15 Agaricus bisporus

description: 15 Agaricus bisporus genome assemblies: 6 <i>de novo</i> assemblies (A10_9, A13_20, A33_49, A33_62, A58_19, A7_31) with GFF files, and 9 scaffold public genomes（AB58, ARP23, gfAgaBisp1, gfAgaBisp1_AH, H119, H39, H97, JB137, KMCC00540） with new annotation files.
DOI: 10.6084/m9.figshare.3863361.v1
title: Correlation in the Abundance and Variety of Insects Found Between Slightly Different Micro- Climates in a Grassland Ecosystem at York University

description: Study corresponds the relationship of insects and three micro- climates at a grassland ecosystem at York University<br>Methods:Set six deep plates, two blues, two yellows and two whites, in a hexagonal configuration, each with it's own color opposite of itself, at three different locations within a grassland ecosystem at York University, for a total of 18 plates usedChose all three locations to be near a tree, approximately 13 meters apart from one another, in a triangle formatOne location to be exposed to a substantial amount of sunlight, the other to be in the shade, and the third to be exposed to intermediate sunlight Pour about an inch high's worth of soapy water into each containerLet sit for approximately one and a half to two hoursRecord the total number of insects in each individual container and the number of different insect species in those containers<br>Hypothesis:There will be more insects in the colored containers, compared to the non colored, and more insects will be present at locations abundant with sunlight<br>Prediction:The colored containers, especially the yellow will contain the most average insects, as well as variety of insects due to the abundance of yellow flowering plants in the grassland ecosystem, followed by blue and then white being the least, regardless of sun exposure.The location with the most sun exposure will have the most insects, and variety, followed by the intermediate exposure and then the shade being last, due to the insects converging in areas where light is abundant, where there would presumably be more flowering plants <br>Metadata:Hexagonal configuration of two of each color was used to eliminate coincidences in results, reassuring the notion of color preference from insectsEqual distance and triangle format was used to set plates to ensure evenness of proximity between each locationEvery individual insect was countedAll different species were sectioned as a seperate species, regardless of family group, ex. large ants and small ants were counted as different species<br><br><br><br>
DOI: 10.6084/m9.figshare.5759823.v1
title: Individual human non-click data

description: These are the individual human data sets for non-click trials. Run the script EMREO_STATS_PNAS to re-create the summary statistics file using various processing options.
DOI: 10.6084/m9.figshare.5982340.v1
title: Data_YoungOld_LexicalBundleProcessing

description: Eye-tracking data of two groups of participants: people in their twenties and people in their late sixties / beginning seventies, consisting of 25 and 27 people respectively.<br>Participants had to read through a list of frequent Dutch trigrams which were presented one by one on a computer screen for 1,200 ms, with an interstimulus interval of 1,000 ms. <br><br>- dat_firstFixations.rda contains a dataframe with information on the durations of the first fixations. <br>- dat_secondFixations.rda contains a dataframe with information on the durations of the second fixations. <br>- firstFixX.rda contains information on the horizontal location of the first fixations on the screen in pixels.<br>- secondFixX.rda contains information on the horizontal location of the second fixations on the screen in pixels. <br>- ngrams.csv contains all trigrams used and their frequencies as found in the OpenSoNaR corpus (https://portal.clarin.nl/node/4195). <br>- plot_NumberFix, plot_FF, plot_SF: plots of the models of the number of fixations, the first fixations durations, and the second fixation durations<br>- OldYoung_Analyses *: R markdown files with the whole analysis process documented for analyses of the first fixation duration, second fixation durations, and the number of fixations.<br> <br>
DOI: 10.6084/m9.figshare.7305905.v1
title: Additional file 3: of SyNDI: synchronous network data integration framework

description: Source code and data files of the example presented in Additional file 2. This additional file is a zip package that contains all source code data files used in Additional file 2. Detailed descriptions of each of these files are presented in a README file included in this zip package (ZIP 16.2 MB)
DOI: 10.6084/m9.figshare.25822609.v1
title: Assembled transcriptomes from two <i>Hanseniaspora </i>species:<i> H. occidentalis</i> var. <i>occidentalis </i>and<i> H. uvarum</i>

description: Triplicate cultures of <i>Hanseniaspora occidentals</i> var. <i>occidentals </i>and <i>Hanseniaspora uvarum </i>were grown for 18 hours in 20 ml rich YPD medium (yeast extract, peptone, 2% glucose) in a room-temperature shaker at 250 rpm. Cell pellets were flash-frozen and stored at -80oC. mRNA was isolated using the NEBNext Poly(A) mRNA Magentic Isolation Module (NEB) with the NEBNext Ultra II Directional RNA Library Prep kit (NEB). One of the three <i>H. occidental</i>s var. <i>occidentals </i>libraries failed, leaving only two replicates for sequencing. Sequencing was performed at the University of Wisconsin-Madison Biotechnology Center. Paired-end reads were trimmed and deduplicated using fastp v.0.20.1. A guided assembly was conducted using HISAT2 v2.2.1 to align the sequence reads against their respective reference draft genomes, both of which were retrieved from the Y1000+ Project. The resulting alignment files were processed through Stringtie v2.2.1 for transcript annotation from their respective reference species annotation files, followed by extracting the protein-coding sequences from the reference genomes of each replicate annotation file into FASTA files using TransDecoder v5.5.0.Codon usage data was calculated using DAMBE v7.3.32FilesH_occ-YPD-replicate-1.CDS.fasta - <i>Hanseniaspora occidentals</i> var. <i>occidentals </i>assembled transcriptome replicate 1H_occ-YPD-replicate-2.CDS.fasta - <i>Hanseniaspora occidentals</i> var. <i>occidentals </i>assembled transcriptome replicate 2H_uv-YPD-replicate-1.CDS.fasta - <i>Hanseniaspora uvarum</i> assembled transcriptome replicate 1H_uv-YPD-replicate-2.CDS.fasta - <i>Hanseniaspora uvarum</i> assembled transcriptome replicate 2H_uv-YPD-replicate-3.CDS.fasta - <i>Hanseniaspora uvarum</i> assembled transcriptome replicate 3H_occ-YPD-replicate-1.CDS.count.out - <i>Hanseniaspora occidentals</i> var. <i>occidentals </i>transcriptome codon counts replicate 1H_occ-YPD-replicate-2.CDS.count.out - <i>Hanseniaspora occidentals</i> var. <i>occidentals </i>transcriptome codon counts replicate 2H_uv-YPD-replicate-1.CDS.count.out - <i>Hanseniaspora uvarum</i> transcriptome codon counts replicate 1H_uv-YPD-replicate-2.CDS.count.out - <i>Hanseniaspora uvarum</i> transcriptome codon counts replicate 2H_uv-YPD-replicate-3.CDS.count.out - <i>Hanseniaspora uvarum</i> transcriptome codon counts replicate 3The codon transcriptome counts have 1 transcript per row and 1 codon per column. The numbers are the raw counts for each codon in that transcript
DOI: 10.6084/m9.figshare.25874374.v1
title: EH23b.tar.gz

description: Genome assembly and annotation
DOI: 10.17632/7mt9cf89ws
title: Dataset: Composition of Ichthyocarbonate and Associated Organic Coatings

description: The datasets available here include measurements of dissolution rate on natural and bleach-treated ichthyocarbonate produced by the Gulf toadfish (Opsanus beta) and the Olive flounder (Paralichthys olivaceus) reported in the first tab. In addition, a second tab reports the C/N ratios and stable carbon isotope values of organic matter associated with ichthyocarbonate produced by the Gulf toadfish and Olive flounder. Stable carbon isotope values of organic matter associated with ichthyocarbonate produced by the Gulf toadfish were previously reported in Oehlert et al., (2024), but reported again here to enable statistical comparison between the composition of ichthyocarbonate produced by different species. Finally, volumetric analyses of carbonate and organic matter associated with ichthyocarbonate assessed via microCT analyses are presented in the third tab of this dataset. 

References:
Oehlert, A.M., Garza, J., Nixon, S., Frank, L., Folkerts, E.J., Heuer, R.M., Benetti, D.D., del Campo, J., Gomez, F., Grosell, M. (2024). Implications of dietary carbon incorporation in fish carbonates for the global carbon cycle. Science of the Total Environment, 916, 169895.
DOI: 10.6084/m9.figshare.19944383.v1
title: Annealing of polycrystalline Al

description: After shear deformation, the loading was removed, and the system was annealed at 300K for 220 ps to monitor post-shear defect evolution.
DOI: 10.6084/m9.figshare.28924775.v1
title: Tabela S2_DIAMOND.xlsx

description: <br><b>Tabela S2.</b> Melhores correspondências (hits) obtidas para cada contig com base na comparação das sequências traduzidas (a nível de aminoácidos) contra bancos de dados de proteínas, utilizando o algoritmo DIAMOND.
DOI: 10.6084/m9.figshare.4910576.v1
title: II.5 - Agrogenom genomic blocks of evolutionary events (first pass)

description: Blocks of evolutionary events ( gene duplication, D, or transfer, T) involving several neighbour genes ; this is a first pass of running the script getblockevents.py to find congruent neighbouring events across gene family trees.This will allow (at the next step) to pick the optimal events amongst the set of mutually exclusive events retained as possible for a gene tree node at the previous step (see item #II.4).<br><br>getblockevents_out.<b>l.</b>*/ folders are results of parallel jobs searching for neighbouring genes in extant ("leaf") genomes involved in similar events, i.e. <b>leaf blocks</b>; each job searched separately within a set of replicon (or contigs). This search is performed with a greedy algorithm covering chromosome; "gap" genes without signal for a congruent event are first allowed, and then tested for compatibility and eventually rejected if negative.<br>getblockevents_out.<b>a</b>.*/ folder is the result of the single job that searched for leaf blocks linking to the same events in gene trees, to reconstruct the one <b>ancestral block</b> of genes from which descend the extant blocks of co-evolved gene.<br><br>The file structure in <i>getblockevents_out.</i><i>l.</i><i>*/</i> folders is similar:- <i>blocks/</i> folder: one file per replicon listing genes involved in a block- <i>before_split_blocks.stats</i> file: stats on blocks generated by the greedy algorithm recognizing similar events based on their event characteristics, i.e. the sets of possible recipient and donor species;- <i>transferred_blocks.stats</i> file: stats on blocks after the compatibility of common events with gap gene trees was checked and incopatibility resolved by splitting the initial blocks into several blocks.<br>[omitted here for space sake, several Gb altogether]:- <i>block_trees/</i> folder: the gene trees associated to the block events - <i>replicon.shelve</i> file: the serialized Python objects containing all the genes borne by a replicon/contig and the event block that link them.<br> file structure in <i>getblockevents_out.a</i><i>.</i><i>*/:</i>- <i>ancestral_blocks</i> file: list of all ancestral blocks and the leaf blocks they link to;<br>[similar files as described above for leaf blocks]- <i>blocks_events.mat</i> file: summary of block events recorded between donor and recipient (ancestral) species pairs[omitted here for space sake, several Gb for 1 file]:- <i>ancblocks.shelve</i> file:the serialized Python objects containing all the ancestral blocks and the leaf blocks linked to them
DOI: 10.6084/m9.figshare.9925097.v1
title: Supplementary data, Horgby et al.

description: Supplementary data for: Unexpected large evasion fluxes of carbon dioxide from turbulent streams draining the world’s mountains by Horgby et al.<br>
DOI: 10.6084/m9.figshare.12947240.v1
title: Real Light Source SPDs and Color Data for Use in Research

description: This set of 1,529 SPDs for real light sources (many of which are commercially available) is intended for research purposes. The spectral data is accompanied by chromaticity and color rendition data. This is not a representative sample of light sources from any population.
DOI: 10.6084/m9.figshare.18183185.v1
title: Supplemental Table 1

description: ASVs that varied in differential abundance, as detected by DESeq2, across rhizosphere communities grouped categorically by treatment, block, treatment x time (growth stage or specific day), or treatment x block.
DOI: 10.6084/m9.figshare.21856309.v1
title: Development and optimization of metoclopramide containing polymeric patches: impact of permeation enhancers

description: Abstract The study is aimed to develop a monolithic controlled matrix transdermal patches containing Metoclopramide as a model drug by solvent casting method. Eudragit L100, Polyvinylpyrrolidone K-30, and Methylcellulose were used in different ratios and Polyethylene glycol 400 added as a plasticizer. Resulting patches were evaluated for their physicochemical characters like organoleptic characters, weight variation, folding endurance, thickness, swelling index, flatness, drug content, swelling index, percentage erosion, moisture content, water vapor transmission rate and moisture uptake. Formed patches were also evaluated through Fourier transform spectroscopy (FT-IR), X-ray diffraction (XRD), Differential Scanning calorimetry (DSC) and Scanning Electron Microscopy (SEM). Results of SEM unveiled smooth surface of drug-loaded patches. In-vitro dissolution studies were conducted by using dissolution medium phosphate buffer saline pH 7.4. Effect of natural permeation enhancers was elucidated on two optimized formulations (Z4 and Z9). Different concentrations (5%-10 %) of permeation enhancers i.e. Olive oil, Castor oil and Eucalyptus oil were evaluated on Franz diffusion cell using excised abdominal rat skin. Z4-O2 (Olive oil 10%) had enhanced sustain effect and flux value (310.72) close to the desired flux value. Z4-O2 followed Higuchi release model (R2= 0.9833) with non-fickian diffusion release mechanism (n=0.612).
DOI: 10.6084/m9.figshare.23846982.v1
title: Aquaculture farmer group survey indicator data

description: Social-ecological indicator data underlying archetype analysis of coastal pond aquaculture farmer groups. Some data omitted (e.g., demographic, location) to preserve anonymity.
DOI: 10.6084/m9.figshare.14912868.v1
title: Farm and field information

description: Information on the ages, cover types, and paired conventional sites of each farm field.
DOI: 10.6084/m9.figshare.26888665.v1
title: Annotation files for two haplotype genomes of Rosa chinensis 'Chilong Hanzhu'

description: Annotation files for two haplotype genomes of Rosa chinensis 'Chilong Hanzhu'The two haplotype genomes of Rosa chinensis 'Chilong Hanzhu' can be downloaded from NCBI(PRJNA932466 and PRJNA1130681)
DOI: 10.17632/zp9yxjtsfb
title: Data for MS# 2020JB020730

description: This dataset include the whole rock major and trace element compositions of harzburgite from the Xigaze ophiolites in southern Tibet. It also includes the major and trace element compositions of olivine, orthopyroxene, clinopyroxene, spinel, tremolite and carbonate minerals in the harzburgites, and the structrual hydroxyl of orthopyroxene and clinopyroxene. These data show that the harzburgite reflect high degrees of melt extraction at mid-ocean ridge, but experience fluid metasomatism during ophiolite emplacement. This metasomatic process greatly affects the whole rock and mineral compositions of the harzburgite.
DOI: 10.6084/m9.figshare.14525880.v1
title: Gene database of Oryza sativa

description: <i>Oryza sativa</i> is an important food crop that feeds half of the world’s population. Thus, much interest exists in understanding genes-phenotype correlation for developing higher yield and better varieties able to handle drought and salt intrusion in rice fields. This work sought to provide foundational information about the genetic repertoire of the rice genome by parsing its annotated genome sequence downloaded from GenBank. Comprising gene name, gene function, and gene sequence, the resource should be useful as initial information for understanding genetic repertoire of rice, and serve as guide for molecular cloning and genome editing workflows.
DOI: 10.6084/m9.figshare.14669952.v1
title: AHP Result.csv

description: AHP result from expert assessment related to solid waste management strategy in university
DOI: 10.6084/m9.figshare.14743317.v1
title: Figure3 - WholeGenomeSequencingAtlanticPuffin(71)

description: Files needed to recreate Figure 3 in the publication - Kersten et al. 2021 - DOI: <b>10.1038/s42003-021-02415-4</b><br> (https://www.biorxiv.org/content/10.1101/2020.11.05.351874v2.full)<br>1. F_RoH values for 71 Atlantic puffin nuclear genomes 2. RoH Lengths for 71 Atlantic puffin nuclear genomes3. Global heterozygosity values for 71 Atlantic puffin nuclear genomes4. Window-based heterozygosity values for 71 Atlantic puffin nuclear genomes.<br>Detailed methods can be found in the manuscript.<br>
DOI: 10.6084/m9.figshare.21178468.v1
title: Data presented in Multi-trial analysis of HIV-1 envelope gp41-reactive antibodies among global recipients of candidate HIV-1 vaccines

description: This folder contains datasets analyzed in the manuscript: <br> Multi-trial analysis of HIV-1 envelope gp41-reactive antibodies among global recipients of candidate HIV-1 vaccines. <br> Frontiers in Immunology<br> Sec. Vaccines and Molecular Therapeutics<br> doi: 10.3389/fimmu.2022.983313
DOI: 10.6084/m9.figshare.3547209.v1
title: Data Paper. Data Paper

description: File List Files are ASCII text, tab delimited. No compression schemes were used. TGPP_pres.csv -- for the species occurrences from 1998 to 2009. TGPP_cover.csv -- for the species cover classes from 1998 to 2009. TGPP_rich.csv -- contains species richness for each corner and each level (spatial scale) of each sample. TGPP_specodes.csv -- for the species names. TGPP_env.csv -- contains all environmental variables including management and climate information for the study period. TGPP_clim.csv -- contains monthly total rainfall and average temperature for all years of available Mesnet data, including years prior to the origination of sampling (1994–1997). Description We present data that were collected as part of a monitoring project on vascular plant composition at the Tallgrass Prairie Preserve in Osage County, Oklahoma, USA. The purpose of these data are to promote the study of multi-scale patterns of species composition for both theoretical and applied questions. Furthermore, these data will provide a reference point for tallgrass prairie restoration projects in the Flint Hills. Over the course of the 12-year period, we sampled 20 permanent plots annually. The permanent plots were selected semi-randomly from a UTM grid using the criteria that they contain less than 20% of woody cover, standing water, or exposed rock. Plant species presence was recorded at five spatial scales: 0.01, 0.1, 1.0, 10, and 100 m<sup>2</sup> in each of the four corners of a 100-m<sup>2</sup> square quadrat. Plant species were assigned to a percent cover class at the 100-m<sup>2</sup> grain. In addition to information on plant composition, we provide data on topography, soil variables, monthly total rainfall, monthly average temperature, and management records related to fire and grazing history. We hope this data set will stimulate further research into the scaling of biodiversity and insight into the functioning and conservation of tallgrass prairie plant communities. <i>Key words: bison; Flint Hills; restoration; spatial scale; species-time-area relationship; tallgrass prairie; vascular plants; vegetation monitoring.</i>
DOI: 10.6084/m9.figshare.3556668.v1
title: Appendix A. Supplementary information about study sites and communities of fleshy-fruited plants and frugivorous birds.

description: Supplementary information about study sites and communities of fleshy-fruited plants and frugivorous birds.
DOI: 10.17632/8gngr6tphf
title: Neural Geometry from Mixed Sensorimotor Selectivity for Predictive Sensorimotor Control

description: Sorted spike data recorded from the primary motor cortex (M1) of three monkeys , with Utah-array (Blackrock Microsystems), and example code to reproduce the major results.
More details could be found in this article: 
Zhang Yiheng, Chen Yun, Wang Tianwei, Cui He (2024) Neural Geometry from Mixed Sensorimotor Selectivity for Predictive Sensorimotor Control, eLife, 13:RP100064
https://doi.org/10.7554/eLife.100064.1
DOI: 10.17632/wzf2f59hbz
title: Supplemental Tables I-IV

description: Supplemental Tables I-IV
DOI: 10.6084/m9.figshare.13204118.v1
title: Predicting pathogenicity of missense variants by deep learning

description: Accurate pathogenicity prediction of missense variants is critically important in genetic studies and clinical diagnosis. Previously published prediction methods have facilitated the interpretation of missense variants but have limited performance. Here we describe MVP (Missense Variant Pathogenicity prediction), a new prediction method that uses deep residual network to leverage large training data sets and many correlated predictors. We train the model separately in genes that are intolerant of loss of function variants and the ones that are tolerant, in order to take account of potentially different genetic effect size and mode of action. We compile cancer mutation hotspots and <i>de novo</i> variants from developmental disorders for benchmarking. Overall, MVP achieves better performance in prioritizing pathogenic missense variants than previous methods, especially in genes tolerant of loss of function variants. Finally, using MVP, we estimate that <i>de novo</i> coding variants contribute to 7.8% of isolated congenital heart disease, nearly doubling previous estimates.