cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23047088.v1
title: <em>Haematococcus pluvialis genome annotation and protein sequences.</em>

description: The green microalga<em> Haematococcus pluvialis</em> can synthesize high amounts of astaxanthin, which is a valuable antioxidant that has been utilized in human health, cosmetics, and aquaculture. To illustrate detailed molecular clues to astaxanthin yield, we performed PacBio HIFI along with Hi-C sequencing to construct an improved chromosome-level haplotypic genome assembly with 32 chromosomes and a genome size of 316.0 Mb. Its scaffold N50 (942.6 kb) and contig N50 (304.8 kb) have been upgraded remarkably from our previous genome draft, and a total of 30,575 protein-coding genes were predicted. We also established a high-evidence phylogenetic tree from seven representative algae species, with the main aim to calculate their divergence times and identify expanded/contracted gene families. We also characterized genome-wide localizations on chromosomes of some important genes such as five <em>BKTs </em>(encoding beta-carotene ketolases) that are putatively involved in astaxanthin production. In summary, we reported the first chromosome-scale map of <em>H. pluvialis</em>, which provides a valuable genetic resource for in-depth biomedical investigations on this momentous green alga and commercial astaxanthin bioproduction.
DOI: 10.6084/m9.figshare.28318997.v1
title: A Multimodal Dataset of Cardiac, Electrodermal, and Environmental Signals

description: This dataset combines signals from two domains: ambient environmental conditions (e.g., temperature, humidity, light, sound, air quality) and physiological responses (e.g., cardiac and electrodermal activity). Data was collected individually over approximately 48 minutes per participant, totaling over 600 minutes, under varied indoor conditions. Ambient signals and electrodermal activity were sampled at 1 Hz, resulting in over 30,000 data points. Cardiac activity and sound were sampled at higher frequencies, generating significantly more data points. Machine Learning models were developed using this dataset to classify ambient environmental risks to cardiac health and estimate physiological responses based solely on environmental data. The dataset enables exploration of the links between indoor climates and health, paving the way for advancements in context-aware technology.
DOI: 10.6084/m9.figshare.22121171.v2
title: Code

description: Data processing and visualization code
DOI: 10.6084/m9.figshare.28120874.v5
title: China's City Level Expressions of Public Views Indices on Climate Risk and Government Responses on Climate Risk

description: A dataset on China's climate risk public opinion and government response indices in city Level, 2011-2023 (excluding data from Hong Kong, Macao, and Taiwan).
DOI: 10.6084/m9.figshare.7562510.v1
title: semen trait gwas

description: phenotype files of semen traits: VE.txt, SC.txt, MS.txt, NMSP.txt, NSP.txtpedigree file of all bulls: pedigree.txtgenotype files of 1508 bulls: mapfile, 1508chip_id.map
DOI: 10.6084/m9.figshare.24268510.v1
title: SLWise Data

description: Data for SLWise model training/evaluation
DOI: 10.6084/m9.figshare.28877618.v1
title: Supplemental Figs. S1 and S2

description: supplemental figures
DOI: 10.6084/m9.figshare.29036063.v1
title: <b>Stable isotope evidence for the </b><b>hydroclimatic</b><b> evolution of the Alagu planation surface and its </b><b>relationship with climate change and tectonic activity</b>

description: The carbon and oxygen isotope composition of carbonate obtained from Late Miocene sediment in Alagu planation surface of the Northeastern Tibetan Plateau.
DOI: 10.6084/m9.figshare.20454462.v4
title: Statistical Shape Model of the Tibia.

description: This project provides a freely accessible three-dimensional statistical shape model (SSM) of the tibia, the coded scripts for generating a SSM and the segmented surface models of the cortical and trabecular bone. Further, it provides three potential applications for the SSM. Please see the associated read-me files for further details. <br> Please cite our work if you use this code or data.<br> <em>Keast M, Bonacci J, Fox A. 2023. Geometric variation of the human tibia-fibula: a public dataset of tibia-fibula surface meshes and statistical shape model. PeerJ 11:e14708 https://doi.org/10.7717/peerj.14708 (2023)</em> <br>
DOI: 10.6084/m9.figshare.22825511.v1
title: RescueNet Semantic Segmentation Train Set

description: Train set of RescueNet semantic segmentation.
DOI: 10.6084/m9.figshare.11477946.v2
title: GFDL ocean pCO2 testbed

description: This dataset contains select variables from 25 randomly selected members from the GFDL large ensemble. Each variable is interpolated from the native grid to a 1x1 degree lat/lon grid. The variables are monthly over the 1982-2017 time frame. Each variable has been sampled as the SOCATv5 data product. RCP8.5 is used after 2005. <br> The intent of this testbed is to evaluate ocean pCO2 gap-filling methods. <br> <strong>Extracting variables</strong> <em>&gt;&gt; unzip file.tar.gz</em>
DOI: 10.6084/m9.figshare.6818681.v1
title: Experiment 5F-SubjectB-160316-5St-SGLHand

description: Experiment in which subject performed motor imagery of a single hand's 5 finger motions, recorded using standard sampling rate setting of 200 Hz.
DOI: 10.6084/m9.figshare.23939481.v1
title: BE1 10XGenomics count matrices

description: BE1 is a benchmark dataset for single cell RNAseq (10XGenomics platform) providing a controlled heterogeneity environment using lung cancer cell lines characterised by expressing seven different driver genes (EGFR, ALK, MET, ERBB2, KRAS, BRAF, ROS1).Fastq files will be soon available on GEO database.This dataset contains for each cell line:QC of the 10XGenomics runs (metrics_summary.csv, web_summary.html).The sparse matrices generated for each experiment by cellranger software.
DOI: 10.6084/m9.figshare.7144277.v2
title: Supplementary Tables SI-SVII

description: Supplementary Tables SI-SVII<br>
DOI: 10.17605/osf.io/s4j37
title: Reassessing the Influence of Experience-based and Resource-based Constraints on Comprehending Mixed-headed Relative Clause Sentences in Mandarin Chinese

description: This article examined the extent to which the processing of comprehending complex sentences in Mandarin Chinese is guided by an individual’s experience or resource limitations by focusing on the processing mechanism in the context of headedness differences (head-initial vs. head-final) in the relative clause configurations. Across three experiments, native Chinese speakers read Mandarin relative clause sentences with a “mixed-headed” configuration: i.e., the main clause is head-initial, whereas the relative clause is head-final. The “mixed-headed” structure provides a highly contrastive test case to disentangle the relative dominance of experience and resource constraints in producing the sentence complexity effect as the relative clause unfolds. Experiment 1 used a gated completion task to track the interpretation preferences at each position in the ambiguous relative clause string. Experiment 2 employed both self-paced reading and eye-tracking to validate the effect of the experience-based expectation cross-methodologically. Experiment 3 assessed the processing dynamics between experience and memory factors with the form of the relative clause noun varied in different types (i.e., descriptions vs. indexical pronouns), using self-paced reading. In contrast to previously predominant views that the relative clause comprehension difficulty results from various sources of the clause properties, not their ambiguities, the results indicate that the initial reading of the head-final relative clause components is highly ambiguous and that its moment-by-moment processing is also highly resource-taxing. The pattern provides insights into cross-linguistic examinations of the sentence complexity effects. Comprehension difficulty reflects the prominence of experience-driven predictions that preserve resource-based memory operations. The head noun’s directionality variation may affect the relative dominance of experience and memory factors over the time course of processing.
DOI: 10.6084/m9.figshare.25478704.v1
title: Mammalian Scratch Assay Measurements

description: Mammalian Scratch Assay Measurements
DOI: 10.6084/m9.figshare.9114485.v1
title: Social class and interpersonal trust: Partner’s warmth, external threats and interpretations of trust betrayal

description: The present research investigated the effects of social class on interpersonal trust. In a series of experiments, we showed how the contextualist socio-cognitive tendencies of the lower class and the solipsistic tendencies of the upper class were reflected in their trusting attitudes and behaviors. In Study 1 (N = 491), upper class individuals expressed the same levels of trust towards all partners, while lower class individuals adjusted their trust choices to the affect-rich information about their interaction partner and trusted warm partners more than cold partners. The results of Study 2 (N = 210) showed that when threatened, lower class individuals had generally less trusting attitudes, while upper class members were equally trusting as in a neutral situation. Study 3 (N = 200) revealed that upper class individuals explained a betrayal of their trust with dispositional factors to a higher degree than lower class individuals. We discuss how these differences contribute to perpetuating the disadvantage of the lower class.
DOI: 10.6084/m9.figshare.19146611.v5
title: Long-term ice phenology records for 78 lakes in the Northern Hemisphere

description: Lake ice is an important resource supporting water quality, local biodiversity, arctic transportation, and regional economies. Long-term surveys of lake ice collected in situ are the gold standard for monitoring in environmental science., Here, we present ice phenology records for 78 lakes in the Northern Hemisphere spanning up to 578 years. These surveys include 12 different countries across North America and Eurasia collected by researchers, community scientists, priests, and digital observations. This database includes information about ice phenology (ice-on dates, ice-off dates, ice cover duration), lake characteristics (e.g., size, location, names), and meta-data about each data source (e.g., how the data was collected). Our intention is that this database may be used to understand factors driving lake ice patterns and the biological or socio-economic consequences.
DOI: 10.25377/sussex.7613852.v1
title: Performance material and computer code 4th experiment

description: —Digital Appendix / Documentation of the PhD Study: IM-Medea: Posthumanism and Remediation in Music Theatre.—<br>These are the files of all the performance material and computer code generated and used during the 4th experiment of this PhD study (Kalamata Art Residency)
DOI: 10.6084/m9.figshare.25239427.v1
title: Genotype file of re-sequencing data-set from Meishan and Erhualian pigs

description: The pig teat number traits have significant economic importance. Meishan and Erhualian pigs in Chinese Taihu Lake region have the highest teat counts worldwide, with an average of 20 teats for Erhualian pig and 17 teats for Meishan pig. To unveil genetic basis of teat number variation in Meishan and Erhualian pigs, this study employed whole-population genome re-sequencing for total 1119 individuals. Subsequently, a genome-wide association study (GWAS), meta-analysis, and Bayesian fine mapping were conducted. Additionally RNA-seq was performed on mammary placodes of 26-day-old Erhualian pig embryos from sows with extremely high and low teat numbers. The GWAS results from two breeds revealed multiple significant QTLs for total teat number (TNT) mainly on SSC1, SSC5, SSC10, and others. Bayesian fine mapping was conducted for the most significant quantitative trait locus (QTL) in both Meishan pig GWAS and meta-analysis resulting in the mapping of SSC1:264293859bp-266080039bp. Similarly, Bayesian fine mapping was performed for the second most significant QTL in meta-analysis, which also was the most significant QTL in Erhualian pig GWAS. This led to the identification of the mapping of SSC5:58093547bp-59198414bp. A total of ninteen protein-coding genes were identified in SSC1:264293859bp-266080039bp and two protein-coding genes were identified in SSC5:58093547bp-59198414bp. In the integration of RNA-seq results from mammary placodes of extreme high and low 26-day-old Erhualian pig embryos, only OLFML2A showed a significant differential expression among these twenty-one candidate genes. OLFML2A was primarily enriched in the extracellular matrix and extracellular matrix organization pathways, which may play a role in the interaction between epithelial and stromal cells of mammary placodes. In addition, the utilization of pig FarmGTEx data for TWAS revealed a significant association between the expression level of OLFML2A in the placenta and TNT in Meishan pig. Furthermore, the results of pheWAS further validate the significant association of OLFML2A with teat number traits in Western commercial pigs. After integrating multiple omics, such as genomics and transcriptomics, we have tentatively identified the OLFML2A gene as a potential causal gene responsible for teat number variation in Meishan and Erhualian pigs. This gene could potentially play a role in the development of mammary placodes in Meishan and Erhualian pigs, consequently influencing the phenotype of teat number.
DOI: 10.6084/m9.figshare.9948179.v1
title: Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation

description: Background: Human embryonic stem cells (hESC) have are an invaluable research tool to study motor neuron development and disorders. However, transcriptional regulation of multiple temporal stages from ESCs to spinal motor neurons (MN) has not yet been fully elucidated. Thus, the goals of this study were to profile the time-course expression patterns of lncRNAs during MN differentiation of ESCs and to clarify the potential mechanisms of the lncRNAs that are related to MN differentiation.Methods: We utilized our previous protocol which can harvest motor neuron in more than 90% purity from hESCs. Then, differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) during MN differentiation were identified through RNA sequencing. Bioinformatic analyses were performed to assess potential biological functions of genes. We also performed qRT-PCR to validate the DElncRNAs and DEmRNAs. Results: Total 441 lncRNAs and 1068 mRNAs at day 6, 443 and 1175 at day 12, and 338 lncRNAs and 68 mRNAs at day 18 were differentially expressed compared with day 0. Bioinformatic analyses identified that several key regulatory genes including POU5F1, TDGF1, SOX17, LEFTY2 and ZSCAN10, which involved in the regulation of embryonic development. We also predict 283 target genes of DElncRNAs, in which 6 mRNAs were differentially expressed. Significant fold changes in lncRNAs (NCAM1-AS) and mRNAs (HOXA3) were confirmed by qRT-PCR. Then, through predicted overlapped miRNA verification, we construct lncRNA NCAM1-AS-miRNA-HOXA3 network.Conclusion: This study comprehensively identified lncRNAs and mRNAs during MN differentiation of hESCs, providing the theoretical basis for further study of the regulatory role of lncRNAs in MN differentiation.<br>
DOI: 10.6084/m9.figshare.20424028.v1
title: Additional file 1 of Multiple roles of apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B) in human tumors: a pan-cancer analysis

description: Additional file 1. Clinical prognostic significance of DNA methylation of APOBEC3B.
DOI: 10.6084/m9.figshare.19397627.v2
title: Hong Yuan Plots Data

description: observing data in the field experiment
DOI: 10.6084/m9.figshare.28925246.v1
title: <b>Segmentation and Classification from MRI Scans</b>

description: This research proposes a novel deep-learning framework for Glioblastoma diagnosis and enhanced survival prediction. The proposed workflow starts with the collection of data, which is then improved during pre-processing by applying a median filter.
DOI: 10.6084/m9.figshare.13055333.v2
title: JARVIS-ML-CFID-OQMD

description: CFID descriptors for OQMD dataset with ~460k materials
DOI: 10.6084/m9.figshare.27054940.v1
title: AIGenJan.xlsx

description: The data were generated during our empirical research <b>Generative AI as catalyst for HRM practices organizational commitment, employee engagement and performance: mediating effects of trust</b>. This study investigated the impact of generative AI tools on human resource management practices organizational commitment, employee engagement, and employee performance. The authors also investigated the mediating role of trust on the relationship between user perception and organizational commitment. A structured questionnaire was used to collect the data and to measure the 9 reflective constructs Optimism, Innovativeness, Ease of use, Usefulness, Trust, Organizational commitment, Vigor, Dedication, and Employee performance. Two constructs, ease of use and usefulness, are modeled as a higher-order construct, User Perception, whereas the Vigor and Dedication are modeled as another higher order construct, Employee Engagement.
DOI: 10.6084/m9.figshare.28171178.v3
title: Plant species loss reduces rare soil microbes through diversity effect amplified by multitrophic interactions

description: <b>Abstract</b>Evidence is mounting that plant diversity loss erodes ecosystem functioning by altering biochemical processes regulated by diverse organisms aboveground and belowground. However, we know little about how plant diversity loss influences soil biodiversity, especially whether loss of ecologically rare and/or functionally distinctive plants leads to a reduction in the rare soil microbes associated with soil multifunctionality. In plant species-rich alpine meadow communities on the Tibetan Plateau, we conducted a 12-year plant species removal experiment to reveal the effect of losing ecologically rare and functionally distinctive (many) forbs, versus the loss of (few) dominant sedges and (several) common forbs, on soil biodiversity. We found that the removal of rare forbs, rather than dominant species and common plants, significantly decreased the richness of soil bacteria and fungi by decreasing rare microbial taxa in later years. This decline in the richness of rare taxa was attributed not only to the decreased plant richness but also to increased soil nematodes, especially fungivores and omnivores-predators. The study revealed that the loss of rare plants induces the loss of rare soil microbes through the plant diversity effect amplified by belowground multitrophic interactions, triggering shifts in microbial community composition and soil food web structure.
DOI: 10.6084/m9.figshare.7312067.v2
title: processed mutational profiles

description: Collated and pre-processed profiles of insertions and deletions resulting from Cas9 mutations as collected for 2018 Nature Biotechnology paper Allen et al, "Predicting the mutations generated by repair of Cas9-induced double-strand breaks".<br>The high level directories are samples.The individual files are in the format:<br>@@@ oligo_id_1 indel1 read_count example_readindel2 read_count example_read<br>...@@@ oligo_id_2 <br>...<br>These files were generated by running the included collate_indels.py file on data pre-processed using code at github repository (https://github.com/felicityallen/selftarget) and code ocean module (https://codeocean.com/capsule/6bc7bcae-d736-475b-bae5-00ca0562d401)<br><br>
DOI: 10.6084/m9.figshare.24440860.v1
title: BraTS2023 challenge raw data_vol.2

description: Ample multi-institutional routine clinically-acquired multi-parametric MRI (mpMRI) scans of glioma.BraTS2023 challenge raw data_vol.2
DOI: 10.6084/m9.figshare.16664080.v1
title: scDRS_data_release_092121

description: Data files used for reproducing main results of the paper (initial submission).<br>- downstream_file.zip: scDRS gene-level correlation on the TMS FACS data for 74 diseases/traits.<br>- gold_standard_gs.zip: drug targets and Mendelian disease genes, consistent with Supp. Table.<br>- score_file.zip: (1) scDRS score files for TMS FACS + hepatocyte signatures, (2) scDRS score files for Zeisel et al. 2015 (brain traits + inferred spatial coordinates).<br><br>- gene_annotation.zip: (1) MAGMA p-values for all genes and the 74 diseases/traits, (2) mouse-human homologs.<br><br>- gs_file.zip: (1) .gs file for the 74 diseases/traits (magma_10kb_1000.74_traits.gs), (2) batch .gs files for the 74 diseases/traits (magma_10kb_1000.74_traits.gs.batch).<br><br>- single_cell_data.zip: (1) reprocessed TMS FACS T cell data (./tms_proc/tcell.facs.annot.h5ad), (2) reprocessed TMS FACS hepatocytes data (./tms_proc/hep.facs_annot.h5ad), (3) Zeisel et al. 2015 processed data ./zeisel_2015<br>- sumstats.zip: GWAS summary statistics of the 74 diseases/traits.<br>- tabula_muris_senis.zip: TMS FACS scRNA-seq data.<br>- supp_table.zip: disease information (trait_info.tsv), consistent with Supp. Table.
DOI: 10.6084/m9.figshare.19164893.v1
title: Global observation dataset for effects of non-continuous flooding practices in rice fields

description: Supplementary Data 1: Global observation dataset including observations of target variables (i.e., CH<sub>4</sub>, N<sub>2</sub>O emisssions, irrigation water use and rice yield) under continuously flooding (CK) and non-continuous flooding (T) and experimental conditions (location, climate and soil condisitons and other management information)<br>Supplementary Data 2: Treatment effects of non-continuous flooding practices on target variables<br><br>Supplementary Data 3: Ratio of GWP reduction due to practicing non-continuous flooding to national total emissions and agricultural emissions<br><br>Supplementary Data 4: Relative change in GWP, IRR and rice yield and ratio of irrigated areas that is feasible to adopt non-continuous flooding practices under SGWP and SIRR at national scale<br>
DOI: 10.6084/m9.figshare.26968489.v1
title: Genome assembly and annotation information of female <i>Clarias fuscus</i>

description: Genome assembly and annotation information of female <i>Clarias fuscus</i>
DOI: 10.6084/m9.figshare.3550299.v1
title: Appendix A. Comparison of best-fit survival curves for the five study species.

description: Comparison of best-fit survival curves for the five study species.
DOI: 10.6084/m9.figshare.27119196.v1
title: HEXACO and forgiveness data cleaned (10 pseudo removed).sav

description: We examined the relationships between HEXACO and three types of forgiveness: divine, self-, and victim forgiveness. All forgiveness scales were measured in the specific context of a relational hurt, and we examined their associations with HEXACO personality factors. Also, we examined which personality factors uniquely explain forgiveness.
DOI: 10.6084/m9.figshare.28872284.v1
title: Proteomics and RNAseq Data.xlsx

description: Proteomics and RNAseq Data for "Engineering pyroptotic vesicles as personalized cancer vaccines".
DOI: 10.6084/m9.figshare.20173208.v1
title: ELISA Plate IDs.xlsx

description: ELISA plate results from the 15 participants included in the study for salivary cortisol vs. occupational stress.
DOI: 10.6084/m9.figshare.26861077.v1
title: Multiomics features dataset for "A multiomics dataset of paired CT image and plasma cell-free DNA end motif profiles for patients with pulmonary nodules"

description: multiomics dataset for "A multiomics dataset of paired CT image and plasma cell-free DNA end motif profiles for patients with pulmonary nodules"
DOI: 10.6084/m9.figshare.4814647.v1
title: Genome-enabled prediction for feedlot average daily gain in Nelore cattle

description: Files used to produce the results in the paper "Genome-enable prediction of breeding values for feedlot average daily weight gain in Nelore cattle" published in G3.AdjustedADGs.txt - Animal ID,year of birth during the study and adjusted feedlot average daily weight gain.<br>Genotype files in Plink format after quality control - Three files (*.bed,*.bim and *.fam) for each of the four datasets used in the analysis. <br>