cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25452/figshare.plus.21632564.v1
title: "Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq" Replogle et al. 2022 - commonly requested supplemental files

description: Commonly requested supplemental files supporting the publication: Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq, Replogle, Joseph M. et al. Cell, Volume 185, Issue 14, 2559 - 2575.e28 https://doi.org/10.1016/j.cell.2022.05.013: <br> 1) All Anderson-Darling p-values for differential expression analysis <br> 2) Embedding coordinates for Figure 2D <br> 3) Downloadable interactive scatter plot of Fig. 2D <br> 4) Z-normalized expression data used to make Figs. 2 and 4, annotated with the cluster identities from Supplementary Table 3 <br> See related datasets at: https://doi.org/10.25452/figshare.plus.20029387 https://doi.org/10.25452/figshare.plus.20127869 https://doi.org/10.25452/figshare.plus.20022944
DOI: 10.6084/m9.figshare.14442314.v1
title: GSE121861

description: Multiple tumour types sequenced from mice.<br>
DOI: 10.6084/m9.figshare.23607735.v1
title: patient42.rar

description: A Patient with fundus images that taken by Ret-cam.
DOI: 10.6084/m9.figshare.1581499.v2
title: A new species of baenid turtle from the Kaiparowits Formation (Upper Cretaceous, Campanian) of southern Utah

description: ABSTRACTNewly discovered baenid turtle specimens from the middle Campanian Kaiparowits Formation of southern Utah are described herein as a new taxon, <i>Arvinachelys goldeni</i>, gen. et sp. nov. The holotype consists of a nearly complete articulated skeleton and shell. The skull was scanned using micro-computed tomography (μCT) to gain a better understanding of its internal anatomy. This baenid possesses two distinct external nares almost completely separated by a dorsal projection of the premaxillae and a ventral extension of the nasals, an autapomorphic feature among known baenid taxa. The skull is wedge-shaped with a broad rostrum and laterally expanded nasals. The importance of skull/shell associations is exemplified by <i>Arvinachelys goldeni</i>, because isolated shells attributable to this taxon had previously been assigned to the genus <i>Plesiobaena</i>, whereas phylogenetic analysis of more complete material supports a sister relationship with the Maastrichtian taxon <i>Hayemys latifrons</i>. These taxa are relatively basal within the Baenodda, a nested clade within Baenidae. The general shell morphology exhibited by <i>Plesiobaena antiqua</i>, <i>Peckemys brinkman</i>, and <i>Palatobaena cohen</i> was previously hypothesized to support a monophyletic clade that included those three taxa, along with <i>Cedrobaena putorius</i>, <i>Gamerabaena sonsalla</i>, <i>Palatobaena bairdi</i>, and <i>Palatobaena gaffneyi</i>. However, the inclusion of <i>Arvinachelys goldeni</i>, gen. et sp. nov., in a phylogenetic analysis of Baenidae indicates that the character states exhibited by those taxa are representative of plesiomorphic states within Baenodda, and the phylogenetic relationships within this clade are in need of reevaluation.http://zoobank.org/urn:lsid:zoobank.org:pub:A5C5717C-4962-4056-8563-2C90C3276FDFSUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPCitation for this article: Lively, J. R. 2015. A new species of baenid turtle from the Kaiparowits Formation (Upper Cretaceous, Campanian) of southern Utah. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2015.1009084.
DOI: 10.6084/m9.figshare.11869548.v2
title: WN18

description: This WORDNET TENSOR DATA consists of a collection of triplets (synset, relation_type, triplet) extracted from WordNet 3.0 (http://wordnet.princeton.edu). This data set can be seen as a 3-mode tensor depicting ternary relationships between synsets.<br><br>The definitions file (wordnet-mlj12-definitions.txt) contains one synset per line with the following format: synset_id (a 8-digit unique identifier) intelligible name (word+POS_tag+sense_index), definition. The previous 3 pieces of information are separated by a tab ('\t').<br>All wordnet-mlj12-*.txt files contain one triplet per line, with 2 synset_ids and relation type identifier in a tab separated format. The first element is the synset_id of the left hand side of the relation triple, the third one is the synset_id of the right hand side and the second element is the name of the type of relations between them.<br>There are 40,943 synsets and 18 relation types among them. The training set contains 141,442 triplets, the validation set 5,000 and the test set 5,000.<br>All triplets are unique and we made sure that all synsets appearing in the validation or test sets were occurring in the training set.<br>The WN18.zip file contains the other files, with more compression than the default "download all".<br>
DOI: 10.6084/m9.figshare.26819455.v2
title: Chromosome-level haplotype-resolved genome assembly and annotation of the genetically highly structured loach (<i>Oreonectes plathycephalus</i>)

description: This genome consists of two haplotypes (24 pseudo-chromosomes in each), with sizes of 565.68 Mb (haplotype A) and 521.13 Mb (haplotype B), containing 27,127 protein-coding genes in haplotype A and 25,576 in haplotype B, respectively.
DOI: 10.6084/m9.figshare.12765902.v1
title: Data --- Magnetic Gradient-Curvature Drift

description: Data --- Magnetic Gradient-Curvature Drift
DOI: 10.25375/uct.28925711.v1
title: Code and data for "Emerging topics and new directions in statistical ecology"

description: The dataset and accompanying R code provided in the R Markdown file linked to the following manuscript submitted for review: Altwegg et al. <i>"Emerging topics and new directions in statistical ecology"</i><i>.</i><b>Abstract of linked material:</b>Ecological science relies on robust estimates of the abundance, diversity, and spatial distribution of individuals and species, but these quantities are notoriously difficult to observe directly. Data collected on these quantities not only reflect the ecological processes giving rise to them but also the observation process, which is often biased by factors such as uneven sampling effort or imperfect detection. Furthermore, collecting data according to standard sampling designs is often not possible. Statistical ecology as a research field specialises in developing statistical methods for analysing such complex ecological data. Here, we apply text analysis tools to the abstracts submitted to eight International Statistical Ecology Conferences between 2008 and 2022 to guide a review of recent topics in statistical ecology. Results show that estimating various aspects of demography (including survival, recruitment, abundance, density and movement) and spatial distribution remains a key area of research. The field has benefited from and embraced new data collection methods such as automated recorders and rapidly developing remote sensing techniques. How to integrate data from different sources is a central challenge that spans multiple areas of statistical ecology. The statistical ecology community strives to be inclusive. It also promotes robust data analysis strategies that underpin reproducible research and transparent conservation decisions. With the increasing pressure of human society on nature, we feel statistical ecology is becoming an ever more important research field. <b>Files:</b>Data_Altwegg_et_al_JSTP_2025.csvData_Altwegg_et_al_JSTP_2025.rmd
DOI: 10.6084/m9.figshare.24891633.v1
title: Sample Datasets For VR-Omics Cross Platform Comparison

description: Sample datasets based on and processed using the VR-Omics AW to be visualised in VR-Omics including:S1R1 from the "MERFISH Mouse Brain Receptor Map" (https://info.vizgen.com/mouse-brain-map) SS200000135TL_D1.tissue.gef from the "Stereopy Demo Data" (http://116.6.21.110:8090/share/dd965cba-7c1f-40b2-a275-0150890e005f)SS15 - Zebrafish Junker et al. Cell, https://www.sciencedirect.com/science/article/pii/S0092867414012264Mouse Brain Section (Coronal)" dataset (https://www.10xgenomics.com/resources/datasets/mouse-brain-section-coronal-1-standard)Replicate 1 from the "Fresh Frozen Mouse Brain Replicates" (https://www.10xgenomics.com/resources/datasets/fresh-frozen-mouse-brain-replicates-1-standard)<br>
DOI: 10.6084/m9.figshare.25757292.v1
title: apple.xlsx

description: The apple dataset comprised 220 spectral samples and corresponding soluble solid content (SSC) measurements. The spectral data were measured using the Ocean Optics QE Pro high-sensitivity fiber-optic spectrometer, with a wavelength measurement range of 185–1100 nm (the range of 380–1100 nm was selected). SSC measurements were obtained using a PAL-HIKARi apple non-destructive saccharimeter with a measurement accuracy of ±1% Brix.
DOI: 10.6084/m9.figshare.12163569.v2
title: Anger makes fake news viral online

description: The data set is used in our working paper entitled "Anger makes fake news viral online", which can be cited as: <br> Yuwei Chuai and <strong>Jichang Zhao*</strong>. Anger Can Make Fake News Viral Online. <em><strong>Frontiers in Physics</strong></em>, 10:970174, 2022, doi:10.3389/fphy.2022.970174. <br> 1. Details of the data set and code can be found in Readme.png. <br> 2. Any issues please feel free to contact jichang@buaa.edu.cn for information.
DOI: 10.6084/m9.figshare.1612225.v3
title: Vegetation cover data

description: Pin point data from the MS "Large increases in arctic biogenic VOC emissions are a direct effect of warming". See Kramshøj et al. 2016 (in prep)
DOI: 10.6084/m9.figshare.25050554.v1
title: A machine-learning based alternative to phylogenetic bootstrap

description: A data-driven approach to estimate branch support values with a probabilistic interpretation
DOI: 10.6084/m9.figshare.1552037.v1
title: Shema Iudin

description: Lab 2, Dataset 3
DOI: 10.6084/m9.figshare.24598638.v2
title: Data for "Intraspecific variability of leaf form and function across habitat types"

description: Files in the folder:1 - dbReady.csvIt contains:standName: species binomial according to the World Flora Online (https://www.worldfloraonline.org/).EUNIS_1L: habitat classification according to the first level of EUNIS habitat classification (Chytrý et al., 2020, Applied Vegetation Science, 23, 648-675).LMA: log10-transformed leaf dry mass per unit leaf area (original unit: g m-2).LA: log10-transformed individual projected leaf area (original unit: mm2).2 - dbReady_reorderedThis dataset is needed to reproduce the phylogenetic analysis.It contains:standName: species binomial according to the World Flora Online (https://www.worldfloraonline.org/).<i>Note that species order follows the order in the phylogenetic tree (</i><i>Phylo_dbReady.tree</i><i>)</i>LMA: log10-transformed leaf dry mass per unit leaf area (original unit: g m-2).LA: log10-transformed individual projected leaf area (original unit: mm2).3 - Phylo_dbReady.treeThe phylogenetic tree for the species list in dbReady.csv. <br>
DOI: 10.6084/m9.figshare.24999359.v1
title: Supplementary Material Alignment 1.fas

description: Dataset 1 (<i>Agaricales</i>) - 5.8S, LSU, SSU, <i>RPB</i><i>1</i>-exons, <i>RPB</i><i>2</i>-exons, <i>TEF1</i>-exons
DOI: 10.6084/m9.figshare.28659218.v2
title: Zemax files contain design results

description: high polarization-maintaining refractive-metasurface hybrid laser communication optical system
DOI: 10.6084/m9.figshare.24145485.v1
title: Supplementary Material for: Two distinct characteristics of immune microenvironment in human hepatocellular carcinoma with Wnt/β-catenin mutations

description: Introduction Immunotherapy is becoming a promising approach for unresectable-hepatocellular carcinoma (HCC); the anti-tumor response is affected by the tumor microenvironment (TME). Although Wnt/β-catenin mutations are reported to cause non-inflamed phenotype, their role on TME remains controversial. We aimed to clarify the heterogeneity of immunophenotype in HCC with Wnt/β-catenin mutations. Methods This study includes 152 resected HCCs; mutations in the catenin beta-1, adenomatous polyposis coli, or AXIN1, or AXIN2 genes were defined as Wnt/β-catenin mutations. With hierarchical cluster analyses, TME were classified into inflamed or non-inflamed classes based on the gene expressions associated with T-cell activation. Expression profiles of molecules related to cell differentiation and biliary-stem cell markers were compared between the TME classes to investigate whether differences in tumor traits were associated with TME. Results Forty of 152 (26.3%) HCCs carried the Wnt/β-catenin mutations. Of these, 33 were classified as non-inflamed (33/40, 82.5%) and 7 as inflamed (7/40, 17.5%). Non-inflamed class was characterized by low number of CD3+, CD4+, and CD8+ cells on immunostaining, and high mRNA expressions of AXIN2 and GLUL, which are involved in the canonical Wnt/β-catenin signaling and hepatocyte differentiation, respectively. Non-inflamed tumors showed higher enhancement on the hepatobiliary-phase of gadolinium-ethoxybenzyl-diethylenetriamine (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI) compared to inflamed tumors. HCCs classified as inflamed class are revealed to have high numbers of CD3+, CD4+, and CD8+ tumor infiltrating lymphocytes on immunostaining. This class is associated with increased expression of anti-epithelial cell adhesion molecule (EpCAM) and FOXM1 accompanied by upregulation of genes related to interferon-gamma signaling, dendritic cell migration, regulatory T cells and MDSC activation and recognized as low enhancement nodule on Gd-EOB-DTPA-enhanced MRI. Conclusion Heterogeneity of tumor traits and TME was observed in HCC with Wnt/β-catenin mutation. The potential was indicated that tumor traits and TME are determined not only by the activation of the HNF4A but also by FOXM1, both of which are downstream transcription factor of the Wnt/β-catenin signaling pathway.
DOI: 10.6084/m9.figshare.12198471.v1
title: Meta-Analysis Results for Any MSDP

description: Results from our meta-analysis of maternal smoking during pregnancy and placental DNA methylation; models were adjusted for maternal age, parity, education, putative cellular heterogeneity, and residual bias. This file includes the following:CPG_ID = Name of the CpG site,Meta_BETA = Difference in DNA methylation (proportion between 0.0 and 1.0) between placental tissue exposed to any smoking during pregnancy versus no smoking during pregnancy,Meta_ZVAL = Test-statistics for regression coefficients,Meta_PVAL = Raw p-values,Meta_CI_lb = Lower bound of 95% confidence intervals,Meta_CI_ub = Upper bound of 95% confidence intervals,Meta_I2 = I-squared for the meta-analysis test of heterogeneity,Meta_Het_PVAL = p-values for the meta-analysis test of heterogeneity.<br>
DOI: 10.6084/m9.figshare.22227547.v1
title: A new hybrid credit scoring ensemble model with feature enhancement and soft voting weight optimization

description: The raw data are divided into five parts: the Australian credit dataset (Australian.csv), the German credit dataset (German.csv), the Polish credit dataset (Polish.csv), the Taiwan credit dataset (Taiwan.csv), and the Creator credit dataset (Creator.csv).
DOI: 10.6084/m9.figshare.14903061.v1
title: ghg-emissions.csv

description: Climate Watch Historical Emission data contains sector-level greenhouse gas (GHG) emissions data for 194 countries and the European Union (EU) for the period 1990-2018, including emissions of the six major GHGs from most major sources and sinks. Non-CO2 emissions are expressed in CO2 equivalents using 100-year global warming potential values from IPCC Fourth Assessment Report. See http://cait.wri.org/docs/CAIT2.0_CountryGHG_Methods.pdf for details regarding data source and methodology.
DOI: 10.6084/m9.figshare.21249516.v1
title: LUMIERE dataset - MRI data and automated segmentations

description: This zip files contains the anonymized MRI data for 91 Glioblastoma patients. 599 of a total of 638 studies include the complete set of four MRI sequences (pre- and post-contrast T1-weighted, T2-weighted and fluid-attenuated inversion recovery). The remaining studies consist of three of fewer MRI images. The dataset contains a total of 2487 MRI images. For the time points with all four MRI sequences, we additionally provide automated tumor segmentation by DeepBraTumIA and HD-GLIO-AUTO.
DOI: 10.6084/m9.figshare.21769493.v1
title: Microsatellite and SNP datasets of the Critically Endangered Swift Parrot (Lathamus discolor)

description: GenAlEx data file of 3761 SNPs for 781 individuals of Swift Parrot <i>Lathamus discolor</i>.The SNP data file follows the structure of GenAlEx input file. Columns indicate:SNP_ID: individual ID of the specimens genotyped in this project, based on SNPsmicrosat_ID: individual ID of the specimens genotyped in a previous project (Olah <i>et al.</i>, 2021), based on microsatellitesmicrosat_YN: whether the sample was genotyped based on the microsatellite study (Olah <i>et al.</i>, 2021)Lat: latitude of the sample locationLong: longitude of the sample locationPop: <i>a priori</i> assigned population nameage: whether the sample is from adult or chickyear: sampling yearsex: whether the individual is male (M) or female (F)The microsatellite data file follows the structure of GenAlEx input file. Columns indicate:Pop: <i>a priori</i> assigned population nameUTM Easting of the sample locationUTM Northing of the sample locationSNP_ID: individual ID of the specimens genotyped in this project, based on SNPsmicrosat_ID: individual ID of the specimens genotyped in a previous project (Olah <i>et al.</i>, 2021), based on microsatellitesSeason: sampling seasonDate Samples: exact date when the sample was collectedAge: whether the sample is from adult or chick
DOI: 10.15468/dl.f43zh5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Holtbyrnia innesi (Fowler, 1934)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((17.9648 28.8496,8.9648 28.8496,8.9648 19.8496,17.9648 19.8496,17.9648 28.8496))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013510-250525065834625/datasets/export for details.
DOI: 10.6084/m9.figshare.1460716.v1
title: Example SAM file

description: This is a subset of the reads aligning to the first 100kb of the chromosome 1 of from sample Col0_C1 of experiment MTAB-3279 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3279). Full data can be found here: http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-3279/E-MTAB-3279.Col0_C1.snp.concordant_uniq.sorted.bam
DOI: 10.6084/m9.figshare.23511828.v1
title: Quinone-mediated hydrogen anode for non-aqueous reductive electrosynthesis - NMR Spectra

description: Quinone-mediated hydrogen anode for non-aqueous reductive electrosynthesis - NMR Spectra
DOI: 10.6084/m9.figshare.28879697.v1
title: TableS10.xlsx

description: Significantly expanded and contracted gene families in Cerceris sabulosa.
DOI: 10.6084/m9.figshare.21822225.v1
title: dpmd_data

description: We provided the deep potential model and training data for LYC/LYBC system in our publication: xxxxxxx The frozen_model.pb are the trained model using the Deepmd_kit (v2.0) based on the training database in the same folder. <br> More details about the Deepmd_kit methods and the usage of DP potential can be found here: https://github.com/deepmodeling/deepmd-kit <br>
DOI: 10.6084/m9.figshare.16853350.v1
title: Data of a Manipulator Size Optimization Method Based on Dexterous Workspace Volume

description: Data of a Manipulator Size Optimization Method Based on Dexterous Workspace Volume
DOI: 10.6084/m9.figshare.28396166.v1
title: Data and Code for "Pseudo-linear Summation explains Neural Geometry of Multi-finger Movements in Human Premotor Cortex", Nishal P. Shah, Donald Avansino, Foram Kamdar, Claire Nicolas, Anastasia Kapitonava, Carlos Vargas-Irwin, Leigh R. Hochberg, Chethan Pandarinath, Krishna V Shenoy, Francis R Willett, Jaimie M. Henderson

description: <b>Abstract</b>How does the motor cortex combine simple movements (such as single finger flexion/extension) into complex movements (such as hand gestures, or playing the piano)? To address this question, motor cortical activity was recorded using intracortical multi-electrode arrays in two male people with tetraplegia as they attempted single, pairwise and higher-order finger movements. Neural activity for simultaneous movements was largely aligned with linear summation of corresponding single finger movement activities, with two violations. First, the neural activity exhibited normalization, preventing a large magnitude with an increasing number of moving fingers. Second, the neural tuning direction of weakly represented fingers changed significantly as a result of the movement of more strongly represented fingers. These deviations from linearity resulted in non-linear methods outperforming linear methods for neural decoding. Simultaneous finger movements are thus represented by the combination of individual finger movements by pseudo-linear summation.<br>Please refer to README for details.
DOI: 10.6084/m9.figshare.28676180.v1
title: Research Data - Does noise pollution influence modal choices?A random forest application.

description: This work investigates the relationship between noise pollution and modal choices exploring and comparing two different urban contexts: Greater London and Brisbane. To achieve this, data on commuting flows by mode of transport and estimated noise pollution have been obtained and combined with measures to characterise the built environment which demonstrated to have an influence on modal choices. Random forest models have shown very good performances in solving classification problems to predict transport modes and allow the exploration of non-linear relationships between the predicted classes and explanatory variables. Two random forest models have been tuned, trained and tested to investigate the association between modal choices and contextual variables, including noise pollution, in Greater London and Brisbane. Results have shown that noise levels play a role in predicting modal choices in Greater London, while the characteristics of the built environment are more relevant when predicting modal choices in Brisbane. Furthermore, we find that walking and cycling, despite being both active travel modes, are influenced by very different factors, with cycling displaying patterns more similar to those characterising driving. Evidence showing the varying relationships between walking and cycling with contextual variables, e.g. noise levels, building and street density, presence of amenities can inform more targeted policies to encourage active travel.
DOI: 10.7910/dvn/jjvbwt
title: Replication Data for: What unaligned voters are (not): covert partisanship and anti-establishment voting patterns in Taiwan in 2024

description: Ecological inference produces estimates, so it will not be possible to exactly replicate my results. However, it should be possible to produce very similar results.
DOI: 10.6084/m9.figshare.12674372.v1
title: Data to run the analyses in the paper "Tropical and Mediterranean biodiversity is disproportionately sensitive to land-use and climate change"

description: This dataset contains an archive of all the data needed to replicate the main analyses in the paper.
DOI: 10.6084/m9.figshare.5047666.v1
title: Face Research Lab London Set

description: Images are of 102 adult faces 1350x1350 pixels in full colour. Template files mark out 189 coordinates delineating face shape, for use with Psychomorph or WebMorph.org.<br><br>All individuals gave signed consent for their images to be "<i>used in lab-based and web-based studies in their original or altered forms and to illustrate research (e.g., in scientific journals, news media or presentations).</i>" Images were taken in London, UK, in April 2012.