cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100425
title: Supporting data for "Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning"

description: Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology which offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling: directly translating the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4000 reads, we show that our model provides state-of-the-art basecalling accuracy even on previously unseen species. Chiron achieves basecalling speeds of over 2000 bases per second using desktop computer graphics processing units, making it competitive with other deep-learning basecalling algorithms.
DOI: 10.5524/100441
title: Supporting data for “Population genomic data reveal genes related to important traits of quail”

description: Japanese quail (<em>Coturnix japonica</em>), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution and functional studies. Here, we present a quail genome assembly spanning 1.04Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and two sex chromosomes Z/W). Our genomic data has resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey) and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (<em>FSH</em>), which is correlated with different <em>FSH </em>levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs. This study provided a high-quality quail reference genome, identified quail-specific genes and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary process within the Phasianidae family.
DOI: 10.5524/100575
title: Supporting data for "GenPipes: an open-source framework for distributed and scalable genomic analyses"

description: With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing. Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for High Performance Computing clusters and the cloud. GenPipes already implements 12 benchmarked and scalable pipelines for various genomics applications, including RNA-Seq, ChIP-Seq, DNA-Seq, Methyl-Seq, Hi-C, capture Hi-C, metagenomics and PacBio long read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has been already configured on several servers and a docker image is also available to facilitate additional installations. In summary, GenPipes offers genomic researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.
DOI: 10.5281/zenodo.1219810
title: Divergent Evolution Between Sister Species Of European Green Lizards

description: Annotation and variant calling files (VCFs, heffas) for <em>L. viridis </em>and<em> L. bilineata.</em> The variants have been called with <em>L. viridis</em> genome as reference.
DOI: 10.5281/zenodo.7254994
title: Divergent evolution between sister species of European green lizards

description: Annotation and variant calling files (VCFs, heffas) for <em>L. viridis </em>and<em> L. bilineata.</em> The variants have been called with <em>L. viridis</em> genome as reference.
DOI: 10.5524/100533
title: Supporting data for 'Divergent evolution in the genomes of closely-related lacertids, <i>Lacerta viridis</i> and <i>L. bilineata</i> and implications for speciation'.

description: <i>Lacerta viridis</i> and <i>L. bilineata</i> are sister species of European green lizards (eastern and western clades respectively), which until recently were grouped together as the <i>L. viridis</i>complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the <i>L. viridis</i> complex. The population history of these sister species and processes driving divergence are unknown. We constructed high quality de novo genome assemblies for both <i>L. viridis</i> and <i>L. bilineata</i> through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signature of selection on non-coding RNA and protein-coding genes. <br>Here we show that the gene flow was primarily unidirectional from <i>L. bilineata</i> to <i>L. viridis</i> after their split at least 1.15 Mya. We detected positive selection of the noncoding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction and behaviour, as well as in UV-response possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species need to be further evaluated. <br>The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation related issue in lacertids.
DOI: 10.5524/100558
title: Supporting data for "Linking genetic, metabolic and phenotypic diversity among S. cerevisiae strains using multi-omics associations"

description: The selection of bioengineering platform strains and engineering strategies to improve the stress resistance of Saccharomyces cerevisiae remains a pressing need in biobased chemical production. Thus, a systematic effort to exploit the genotypic and phenotypic diversity to boost yeasts industrial value is still urgently needed. Here, we analyzed 5400 growth curves obtained from 36 <i>S. cerevisiae</i> strains and comprehensively profiled their resistances against 13 industrially relevant stresses. <br>We observed that bioethanol and brewing strains exhibit higher resistance against acidic conditions, however, plant isolates tend to have wider range of resistance, which may be associated with their metabolome and fluxome signatures in TCA cycle and fatty acid metabolism. By deep genomic sequencing we found that industrial strains have more genomic duplications especially affecting transcription factors, presenting disparate evolutionary paths in comparison to the environmental strains which have more InDels, gene deletions and strain-specific genes. Genome-wide association studies coupled with protein-protein interaction networks uncovered novel genetic determinants of stress resistances. These resistance-related engineering targets and strain rankings provide a valuable source for engineering significantly improved industrial platform strains.
DOI: 10.6084/m9.figshare.29149586
title: CNSW 1.0: Prefectural Reconstruction of China's Surface Water Resources Using Machine Learning Methods

description: A comprehensive and long-term dataset of prefectural surface water resources is crucial for effective water resource management in China. However, there has been a significant gap in the availability of such datasets, with no existing datasets providing comprehensive long-term coverage. To address this gap, we have developed CNSW 1.0, the first long-term (2000-2020) dataset of prefectural surface water resources in China. Utilizing surface water resource data from official water resource bulletins, we employed 14 advanced machine learning models to reconstruct the CNSW 1.0 dataset. The resulting dataset exhibits high accuracy, with an R² of 0.978 for total surface water resources and acceptable level of bias across China. CNSW 1.0 not only outperforms existing datasets like CNRD v1.0, GRUN, and ISIMIP in terms of simulation accuracy and spatial distribution but also fills a critical gap in water resource data for China. This dataset is expected to be an invaluable tool for developing more informed water resource management strategies at the administrative level in China, particularly in the context of climate change. The CNSW 1.0 encompasses surface water resource data for 341 prefectural-level administrative units in mainland China over a period from 2000 to 2020, comprising a total of 16 surface water datasets. The data are stored in both CSV and shapefile (SHP) formats. The naming convention for annual spatial distribution shapefiles follows the structure "CNSW_1.0_YYY_ZZZZ.shp," where "YYY" represents the model’s name, and "ZZZZ" denotes the year. The naming convention for multi-year average spatial distribution shapefiles is "CNSW_1.0_mean_YYY.shp," and for the spatial evolution trend shapefiles, it is "CNSW_1.0_trend_YYY.shp." A total of 368 shapefiles are provided, which approximately take up 4.26GB of disk space. Additional information, such as region, province, and prefecture area, is also stored in the files.
DOI: 10.5524/100467
title: Supporting data for "Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye"

description: Yeonsan Ogye (YO), an indigenous Korean chicken breed (Gallus gallus domesticus), has entirely black external features and internal organs. In this study, the draft genome of YO was assembled using a hybrid de novo assembly method that takes advantage of high-depth Illumina short-reads (376.6X) and low-depth PacBio long-reads (9.7X). The contig and scaffold NG50s of the hybrid de novo assembly were 362.3Kbp and 16.8Mbp, respectively. The completeness (97.6%) of the draft genome (Ogye_1.1) was evaluated with single copy orthologous genes using BUSCO, and found to be comparable to the current chicken reference genome (galGal5; 97.4%; contigs were assembled with high-depth PacBio long-reads (50X) and scaffolded with short-reads), and superior to other avian genomes (92~93%; assembled with short-read-only or hybrid methods). Compared to galGal4 and 5, the draft genome included 551 structural variations including the Fibromelanosis (FM) locus duplication, related to hyperpigmentation. To comprehensively reconstruct transcriptome maps, RNA sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS) data were analyzed from twenty different tissues, including four black tissues (skin, shank, comb, and fascia). The maps included 15,766 protein-coding and 6,900 long non-coding RNA genes, many of which were tissue-specifically expressed and displayed tissue-specific DNA methylation patterns in the promoter regions. We expect that the resulting genome sequence and transcriptome maps will be valuable resources for studying domestic chicken breeds, including black-skinned chickens, as well as for understanding genomic differences between breeds and the evolution of hyperpigmented chickens and functional elements related to hyperpigmentation.
DOI: 10.15468/dl.bjq4za
title: Occurrence Download

description: A dataset containing 5573674 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Annelida)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 5573674 records from 3019 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002016-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/412-jc1-ag8
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ehg-b5e-aee
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/225-yem-1sm
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5g4-prm-8py
title: †Lepidorbitoides Silvestri, 1907

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t7g-26v-bnn
title: †Globorotalites lobata Brotzen, 1948

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f1q-r8r-xv6
title: †Gyroidinoides nitida (Reuss, 1844)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z23-4bq-7xv
title: Cervus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a9f-j3c-cvp
title: Bolivina alata (Seguenza, 1862)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/be3-5pg-3n2
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4bh-gks-212
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/s70-8k7-3ln
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8ms-q38-11n
title: †Gryphaea Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nt4-3h4-n6h
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fjp-94s-qsx
title: †Lepidorbitoides Silvestri, 1907

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tdk-ykn-mvf
title: †Lepidorbitoides Silvestri, 1907

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.29930033
title: VI_image.mat

description: radar,radar,radar,radar,radar,radar,radar,radar,radar,radar,
DOI: 10.6084/m9.figshare.29930033.v1
title: VI_image.mat

description: radar,radar,radar,radar,radar,radar,radar,radar,radar,radar,
DOI: 10.3535/m3r-xw8-pd6
title: †Lepidocyclina Gümbel, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4ht-9p3-15e
title: †Gryphaea Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bxh-zsx-zvz
title: Reteporella Busk, 1884

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7wd-wnp-cax
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t2f-3kk-3sl
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/k3w-5m2-ka4
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rvm-tdn-dg8
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yx6-ba6-2tq
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/b33-qwe-v1k
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tgz-hsj-7qp
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0fa-q5x-3c2
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zap-egr-v35
title: Calcarina spengleri (Gmelin, 1791)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4nv-d7x-w2n
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1wb-pvl-z5g
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ayd-p8w-bl4
title: Operculina d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8d1-xb0-bqh
title: Protelphidium Haynes, 1956

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vwa-ghe-tj0
title: †Fusulinidae Möller, 1878

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5281/zenodo.16812609
title: Data for Completing the Hierarchy of Rotational Defects in Monolayer MoS₂ through Symmetry-Aware Evolutionary Search

description: The archive "supplementary_data.zip" contains trained models, data set splits and structure files obtained and reported in the study:

"Completing the Hierarchy of Rotational Defects in Monolayer MoS₂ through Symmetry-Aware Evolutionary Search".

 


See README for more information on the archive content.
DOI: 10.5281/zenodo.16812610
title: Data for Completing the Hierarchy of Rotational Defects in Monolayer MoS₂ through Symmetry-Aware Evolutionary Search

description: The archive "supplementary_data.zip" contains trained models, data set splits and structure files obtained and reported in the study:

"Completing the Hierarchy of Rotational Defects in Monolayer MoS₂ through Symmetry-Aware Evolutionary Search".

 


See README for more information on the archive content.
DOI: 10.3535/2jv-584-h2b
title: †Fusulinidae Möller, 1878

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/amn-gc2-6p0
title: Cellaria sinuosa (Hassall, 1840)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/31p-38f-q3j
title: †Nummofallotia cretacea (Schlumberger, 1900)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yy8-2y8-153
title: †Pseudouvigerina seligi (Cushman, 1925)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hjd-7m1-maq
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/62r-0xz-ykd
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t3j-w8w-y2q
title: Sphincterochila Ancey, 1887

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.fs5dv8
title: Occurrence Download

description: A dataset containing 585 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Urosalpinx cinerea",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 585 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018255-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/nzj-g05-fwc
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cyq-kv0-adl
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/v6m-1d5-evw
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.6084/m9.figshare.14276360.v1
title: “The pen is the blade, my skin the paper”: risk factors for self-injury in adolescents

description: ABSTRACT Objective: to describe the risk factors that influence the self-injury behavior of adolescents assisted at a Psychosocial Care Center for Children and Adolescents, according to subjects’ own perceptions. Method: a descriptive, exploratory, qualitative study carried out through medical records and a focus group with 07 adolescents. The statements were submitted to thematic content analysis. Results: in the risk factors category, four subcategories emerged: Family adversity factors; Social contagion; Adverse life events; Personal characteristics. Conflicts, lack of support, drug use in the family, meeting someone who cuts themselves, social networks, religiosity, history of sexual violence and bullying were identified as risk factors that influence self-injury. Final Considerations: adolescents pointed out the need for prejudice-free dialogues in schools, in health and family devices, configuring protective factors to avoid this practice that comes from several negative events throughout life.
DOI: 10.6084/m9.figshare.9808472.v2
title: Supplementary Data description

description: This file contains details of Supplementary Data 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 & 12 and should be read for full descriptions of these files.<br>
DOI: 10.6084/m9.figshare.28765952.v1
title: DSJ_Datasets_RDM in Environmental Studies_Rosini et.al.

description: This research attempts to analyse and reveal the scientific trends in research data management (RDM) related to environmental studies through the scoping review and bibliometric analysis. The investigation was conducted on five databases, including one journal, Scopus, EBSCO, Science Direct, Sage Journals, Emerald, and Nature. The search results on RDM topics in environmental studies discovered 248 papers that met the requirements. The Scoping Review framework and bibliometric analysis were used as a methodology, and VOSviewer and Bibliometrix were used as analytical tools.
DOI: 10.6084/m9.figshare.12401168.v21
title: The Brain Hierarchy Score

description: Here we provide data used in Nonaka, Majima, Aoki, & Kamitani (2021) Brain hierarchy score: Which deep neural networks are hierarchically brain-like? <i>iScience</i>.<br><br>See also https://github.com/KamitaniLab/BHscore.<br><br>History:<br><br>2022-01-25 Add DNN features of all units (features_all-*)<br><br>Note that version 4-20 are temporally released due to figshare upload limits and do not contain the full dataset.<br><br>2021-12-24 Add encoding accuracy data (encoding_accuracy.zip)<br><br>2020-08-08 Add DNN unit activation data (features-*.zip)<br><br>2020-08-03 Update directory organization in decoding_accuracy.zip<br>