cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100542
title: Supporting data for "EEG Dataset and OpenBMI Toolbox for Three BCI Paradigms: An Investigation into BCI Illiteracy"

description: Electroencephalography (EEG)-based brain-computer interface (BCI) systems are mainly divided into three major paradigms: motor-imagery (MI), event-related potential (ERP), and steady-state visually evoked potential (SSVEP). In this paper, we present a BCI dataset that includes the three major BCI paradigms with a large number of subjects over multiple sessions. In addition, information about the psychological and physiological conditions of BCI users was obtained using a questionnaire, and task-unrelated parameters such as resting state, artifacts, and electromyography of both arms were also recorded. We evaluated the decoding accuracies for the individual paradigms and determined performance variations across both, subjects and sessions. Furthermore, we looked for more general, severe cases of BCI illiteracy than have been previously reported in the literature.<br>
Average decoding accuracies across all subjects and sessions were 71.1% (±0.15), 96.7% (±0.05), and 95.1% (±0.09), and rates of BCI illiteracy were 53.7%, 11.1%, and 10.2% for MI, ERP, and SSVEP, respectively. Compared to the ERP and SSVEP paradigms, the MI paradigm exhibited large performance variations between both, subjects and sessions. Furthermore, we found that 27.8% (15 out of 54) of users were universally BCI literate, i.e. they were able to pro ciently perform all three paradigms. Interestingly, we found no universally illiterate BCI user, i.e. all participants were able able to control at least one type of BCI system. <br>Our EEG dataset can be utilized for a wide range of BCI-related research questions. All methods for the data analysis in this study are supported with fully open-source scripts that can aid in every step of BCI technology. Furthermore, our results support previous but disjointed ndings on the phenomenon of BCI illiteracy.
DOI: 10.5524/100543
title: Supporting data for "Modelling genotypes in their microenvironment to predict single- and multi-cellular behaviour"

description: A cells phenotype is the set of observable characteristics resulting from the interaction of the genotype with the surrounding environment, determining cell behaviour. Deciphering genotype-phenotype relationships has been crucial to understand normal and disease biology. Analysis of molecular pathways has provided an invaluable tool to such understanding; however, it does typically not consider the physical microenvironment, which is a key determinant of phenotype. In this study, we present a novel modelling framework that enables to study the link between genotype, signalling networks and cell behaviour in a 3D microenvironment. To achieve this we bring together Agent Based Modelling, a powerful computational modelling technique, and gene networks. This combination allows biological hypotheses to be tested in a controlled stepwise fashion, and it lends itself naturally to model a heterogeneous population of cells acting and evolving in a dynamic microenvironment, which is needed to predict the evolution of complex multi-cellular dynamics. Importantly, this enables modelling co-occurring intrinsic perturbations, such as mutations, and extrinsic perturbations, such as nutrients availability, and their interactions. Using cancer as a model system, we illustrate the how this framework delivers a unique opportunity to identify determinants of single-cell behaviour, while uncovering emerging properties of multi-cellular growth.
DOI: 10.5524/100546
title: Supporting data for "New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing"

description: High quality genomes are essential to resolve challenges in breeding, comparative biology, medicine and conservation planning. New library preparation techniques along with better assembly algorithms result in continued improvements in assemblies for non-model organisms, moving them toward reference quality genomes. We report on the latest genome assembly of the Atlantic bottlenose dolphin leveraging Illumina sequencing data coupled with a combination of several library preparation techniques. These include Linked-Reads (Chromium, 10x Genomics), mate pairs, long insert paired ends and standard paired ends. Data were assembled with the commercial DeNovoMAGICTM assembly software resulting in two assemblies, a traditional haploid assembly (Tur_tru_Illumina_hap_v1) that is a mosaic of the two parental haplotypes and a phased assembly (Tur_tru_Illumina_phased_v1) where each scaffold has sequence from a single homologous chromosome. We show that Tur_tru_Illumina_hap_v1 is more complete and accurate compared to the current best reference based on the amount and composition of sequence, the consistency of the mate pair alignments to the assembled scaffolds, and on the analysis of conserved single-copy mammalian orthologs. The phased de novo assembly Tur_tru_Illumina_phased_v1 is the first publicly available for this species and provides the community with novel and accurate ways to explore the heterozygous nature of the dolphin genome.
DOI: 10.5524/100549
title: Supporting data for "Genome sequence of Malania oleifera, a tree with great value for nervonic acid production"

description: Malania oleifera, a member of the Olacaceae family, is an IUCN Red Listed tree, endemic and restricted to the Karst region of southwest China. This trees seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic make-up, and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. We generated 51 Gigabases (Gb) and 135 Gb of raw DNA sequences, using PacBio Single-Molecule Real-Time (SMRT) and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Megabases (Mb) and a total length of 1.51 Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted ~82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long chain fatty acid were identified and studied in detail. Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology, and for the functional genomics of nervonic acid biosynthesis.
DOI: 10.5524/100552
title: Supporting data for "Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale"

description: In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community, but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies).<br> Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates.<br>Sequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost effective, portable and universal approach for eukaryote DNA barcoding. Although bulk community analyses using long-amplicon approaches may introduce biases, the long rDNA amplicons approach signifies a powerful tool for enabling the accurate recovery of taxonomic and phylogenetic diversity across biological communities.
DOI: 10.5524/100553
title: Supporting data for "Common Workflow Language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data"

description: Here, we created an automated pipeline for the de novo-assembly of genomes from PacBio long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (~100 Mb), Drosophila melanogaster (~138 Mb) and Plasmodium falciparum (~23 Mb) directly from publicly accessible nucleotide sequence data sets, and assessed the quality of the assemblies against curated reference genomes. We showed a dependency of the accuracy of assembly on sequencing technology and GC content, and repeatedly achieved assemblies that meet the high standards set by the National Human Genome Research Institute, being applicable to gene prediction and subsequent genomic analyses. This CWL pipeline overcomes current challenges of achieving repeatability and reproducibility of assembly results and offers a platform for the re-use of the workflow and the integration of diverse data sets. This workflow is publicly available via GitHub (https://github.com/vetscience/Assemblosis) and is currently applicable to the assembly of haploid and diploid genomes of eukaryotes.
DOI: 10.5524/100561
title: Supporting data for "Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks"

description: Advances in large scale tumor sequencing have lead to an understanding that there are combinations of genomic and transcriptomic alterations specific to tumor types, shared across many patients. Unfortunately, computational identification of functionally meaningful and recurrent alteration patterns within gene/protein interaction networks has proven to be challenging. We introduce a novel combinatorial method, cd-CAP, for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples. Our method differentiates distinct alteration types associated with each gene (rather than relying on binary information of a gene being altered or not), and simultaneously detects multiple alteration profile conserved subnetworks. In a number of The Cancer Genome Atlas (TCGA) data sets, cd-CAP identified large biologically significant subnetworks with conserved alteration patterns, shared across many tumor samples.
DOI: 10.5524/100564
title: A draft genome assembly of the acoel flatworm Praesagittifera naikaiensis

description: Acoels are primitive bilaterians with very simple soft-bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in formation of the basic bilaterian body-plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel,<i> Praesagittifera naikaiensis</i>.<br>To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired end and mate-pair libraries) and PacBio sequencing. RNA-seq and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ~17-kbp mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nucleargenome assembly was ~656-Mbp in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb, respectively. Although ~70% of the assembled sequences were likely comprised of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein coding genes, approximately 99% of which were substantiated by corresponding transcripts.
We could not find horizontally-transferred microalgal genes in the acoel genome. BUSCO analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules.<br> Our present sequencing and assembly of the <i>P. naikaiensis</i> nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.
DOI: 10.3535/36a-67c-7dd
title: †Gryphaea Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l5q-ptg-sdv
title: Nymphaea L.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x1c-8tx-jj9
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a3w-fm1-l1w
title: †Fusulinidae Möller, 1878

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d4h-mtk-5wm
title: Nummulitidae Blainville, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j7p-wxw-n6n
title: Chenopodium L.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/361-qj9-vev
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w3t-2s3-sz6
title: Lenticulina bowdenensis (Cushman, 1919)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/b1v-df6-ypz
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yyt-qvp-02a
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jes-r28-yah
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s02-xk6-qyk
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wt2-6y2-y4t
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wj8-lkn-wky
title: Ostracoda Latreille, 1802

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/71e-d7s-bap
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m53-3h4-lhr
title: Globobulimina perversa (Cushman, 1921)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4bb-cw5-zy8
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cwd-jhm-yc2
title: †Lepidocyclina Gümbel, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jqh-1dy-cys
title: †Lepidorbitoides Silvestri, 1907

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9c3-a6d-d55
title: †Archaeoglobigerina cretacea (d'Orbigny, 1840)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d6v-465-pfl
title: Lagenidae Reuss, 1862

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/azn-w6e-31m
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r2a-afz-plh
title: Bison C. H. Smith, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/452-phf-3fw
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kb5-cy4-36w
title: †Lepidocyclina Gümbel, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x6w-8df-19g
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.24403/jp.1383463
title: Kleine Anatomie des Buches : Aufkleber / von Felix Haenlein
DOI: 10.3535/jzk-7kw-sxr
title: Planorbulinella Cushman, 1927

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xgc-dv9-r9w
title: Ammotium cassis (Parker, 1870)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9wk-az0-xc7
title: Juncus L.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7f1-czr-qm6
title: †Pseudotextularia Rzehak, 1891

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gm2-lk6-3bx
title: Neogloboquadrina dutertrei (d'Orbigny, 1839)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l1s-khn-wb2
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pth-x2s-qrq
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3qe-t6y-z1h
title: †Assilina exponens (Sowerby, 1840)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m33-0c5-5sm
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jgh-v6p-hnn
title: Elphidium Montfort, 1808

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4kd-gr0-r6n
title: †Lepidocyclina Gümbel, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fp8-f9g-43y
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wbk-gjp-8z4
title: Trilobatus trilobus (Reuss, 1850)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wdg-fba-xmv
title: †Echinocorys Leske, 1778

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.s4mjd6
title: Occurrence Download

description: A dataset containing 5763 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is France",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Vipera berus",
 "Year 2000-2024"
 ]
}

 The dataset includes 5763 records from 231 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018254-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12558125
title: Dataset: IBEX Limited (IBEX) Stock Performance

description: This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
DOI: 10.5281/zenodo.12558126
title: Dataset: IBEX Limited (IBEX) Stock Performance

description: This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
DOI: 10.5281/zenodo.12558127
title: Dataset: iShares iBonds Dec 2044 Term Treasury ETF (IBGA) Stock Performance

description: This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
DOI: 10.5281/zenodo.12558128
title: Dataset: iShares iBonds Dec 2044 Term Treasury ETF (IBGA) Stock Performance

description: This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
DOI: 10.15468/dl.aevzvm
title: Occurrence Download

description: A dataset containing 1019 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Ulmus pumila L."
 ]
}

 The dataset includes 1019 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001045-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fsfdy6
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pyractonema bifenestrata (Fairmaire & Germain, 1862)"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001046-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12558129
title: Dataset: iShares iBonds Dec 2054 Term Treasury ETF (IBGK) Stock Performance

description: This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
DOI: 10.5281/zenodo.12558130
title: Dataset: iShares iBonds Dec 2054 Term Treasury ETF (IBGK) Stock Performance

description: This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
DOI: 10.15468/dl.b94sd3
title: Occurrence Download

description: A dataset listing the 157893 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 157893 records were derived from 3404 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000983-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.