cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/101999
title: Image data of Nanmaohu Park vascular plant specimen, RL0936

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains images from the plant vouchered as not provided. Preliminary identification is that it is of the family uncharacterized vascular plant. <br>Unforuntaly insufficient DNA was extracted from the sample to make suquencing possible at this time.
DOI: 10.5524/102004
title: Image data of Nanmaohu Park Cleidion brevipetiolatum plant specimen, RL0941

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains images from the plant vouchered as HCNGB:RUILI:HCNGB_00002295. Preliminary identification is that of a Cleidion brevipetiolatum plant. <br>Unforuntaly insufficient DNA was extracted from the sample to make suquencing possible at this time.
DOI: 10.5524/102006
title: Image data of Nanmaohu Park vascular plant specimen, RL0943

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains images from the plant vouchered as not provided. Preliminary identification is that it is of the family uncharacterized vascular plant. <br>Unforuntaly insufficient DNA was extracted from the sample to make suquencing possible at this time.
DOI: 10.5524/102017
title: Image data of Nanmaohu Park vascular plant specimen, RL0954

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains images from the plant vouchered as not provided. Preliminary identification is that it is of the family uncharacterized vascular plant. <br>Unforuntaly insufficient DNA was extracted from the sample to make suquencing possible at this time.
DOI: 10.5524/102031
title: Image data of Nanmaohu Park vascular plant specimen, RL0968

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains images from the plant vouchered as not provided. Preliminary identification is that it is of the family uncharacterized vascular plant. <br>Unforuntaly insufficient DNA was extracted from the sample to make suquencing possible at this time.
DOI: 10.5524/102032
title: Genomic data of Nanmaohu Park vascular plant specimen, RL0969

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00002304. Preliminary identification is that it is of the family Pyrrosia costata. <br>The K-mer distribution of the sequencing predicted the genome size to be Not recordedbp. We have generated 83520000000bp of data, which gives a theoretical coverage of x.
DOI: 10.5524/101983
title: Image data of Nanmaohu Park Helixanthera pulchra plant specimen, RL0920

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains images from the plant vouchered as HCNGB:RUILI:HCNGB_00002285. Preliminary identification is that of a Helixanthera pulchra plant. <br>Unforuntaly insufficient DNA was extracted from the sample to make suquencing possible at this time.
DOI: 10.5524/101993
title: Image data of Nanmaohu Park vascular plant specimen, RL0930

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains images from the plant vouchered as not provided. Preliminary identification is that it is of the family uncharacterized vascular plant. <br>Unforuntaly insufficient DNA was extracted from the sample to make suquencing possible at this time.
DOI: 10.5524/101994
title: Genomic data of Nanmaohu Park Dysoxylum binectariferum plant specimen, RL0931

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains genomic data and images from the plant vouchered as HCNGB:RUILI:HCNGB_00002347. Preliminary identification is that it is Dysoxylum binectariferum. <br>The K-mer distribution of the sequencing predicted the genome size to be 642653000bp. We have generated 63180000000bp of data, which gives a theoretical coverage of 98.3x.
DOI: 10.5524/102008
title: Image data of Nanmaohu Park vascular plant specimen, RL0945

description: We sampled vascular plants from Ruili Botanical Garden,Yunnan, China. All the samples were collected within the geographical region Longitude 97.646389 to 98.099167, Latitude 23.878333 to 24.155556, altitudes ranging from 740 meters to 1,200 meters above sea level. In total, we collected 1,093 vascular plants, from which we used the young leaves for sequencing, and at the same time the specimens were vouchered. The specimens are maintained at the Herbarium of China National GeneBank (HCNGB).<br>Of these, 761 specimens yielded DNA suitable for sequencing. The other 332 samples are vouchered and images of those plants are available in those datasets. The 761 samples represented 689 vascular plant species from 137 families belonging to 49 different orders.<br>There is an ongoing effort to formally identify all specimens, but at time of publication only a very small number had been identified beyond family level. <br>This dataset contains images from the plant vouchered as not provided. Preliminary identification is that it is of the family uncharacterized vascular plant. <br>Unforuntaly insufficient DNA was extracted from the sample to make suquencing possible at this time.
DOI: 10.5524/102207
title: Supporting data for "NuCLS: A scalable crowdsourcing approach & dataset for nucleus classification and segmentation in breast cancer"

description: Deep learning enables accurate high-resolution mapping of cells and tissue structures that can serve as the foundation of interpretable machine-learning models for computational pathology. However, generating adequate labels for these structures is a critical barrier, given the time and effort required from pathologists. <br>This paper describes a novel collaborative framework for engaging crowds of medical students and pathologists to produce quality labels for cell nuclei. We used this approach to produce the NuCLS dataset, containing over 220,000 annotations of cell nuclei in breast cancers. This builds on prior work labeling tissue regions to produce an integrated tissue region- and cell-level annotation dataset for training that is the largest such resource for multi-scale analysis of breast cancer histology. This paper presents data and analysis results for single and multi-rater annotations from both non-experts and pathologists. We present a novel method for suggesting annotations that allows us to collect accurate segmentation data without the need for laborious manual tracing of cells. Our results indicate that even noisy algorithmic suggestions do not adversely affect pathologist accuracy, and can help non-experts improve annotation quality. We also present a new approach for inferring truth from multiple raters, and show that non-experts can produce accurate annotations for visually distinctive classes. <br>This study is the most extensive systematic exploration of the large-scale use of wisdom-of-the-crowd approaches to generate data for computational pathology applications.<br>The NuCLS study utilises TCGA data. The TCGA group established informed consent guidelines for effective and fair use of cancer genomic information. The following link details TCGA Ethics & Policies, including TCGA informed consent policy, data access policy and information about HIPAA Privacy Rule compliance: https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga/history/policies
DOI: 10.5524/102209
title: Supporting data for"Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans"

description: SARS-CoV-2 has a complex strategy for the transcription of viral subgenomic mRNAs (sgmRNAs), which are targets for nucleic acid diagnostics. Each of these sgmRNAs has a unique 5 sequence, the leader-transcriptional regulatory sequence gene junction (leader-TRS-junction), that can be identified using sequencing. High resolution sequencing has been used to investigate the biology of SARS-CoV-2 and the host response in cell culture and animal models and from clinical samples.<br> LeTRS, a bioinformatics tool, was developed to identify leader-TRS-junctions and be used as a proxy to quantify sgmRNAs for understanding virus biology. LeTRS is readily adaptable for other coronaviruses such as Middle East respiratory syndrome coronavirus (MERS-CoV) or a future newly discovered coronavirus. LeTRS accepts FASTQ files derived from Illumina paired-end or Oxford Nanopore sequencing (amplicon or direct RNA) and showed greater sensitivity and F-measure score than the other currently available tools for processing the Nanopore sequencing reads. 
LeTRS was tested on published datasets and novel clinical samples from patients and longitudinal samples from animal models with COVID-19. LeTRS identified known leader-TRS-junctions and identified putative novel sgmRNAs that were common across different mammalian species. This may be indicative of an evolutionary mechanism where plasticity in transcription generates novel open reading frames, that can then subject to selection pressure. The data indicated multi-phasic abundance of sgmRNAs in two different animal models. This recapitulates the relative sgmRNA abundance observed in cells at early points in infection, but not at late points. This pattern is reflected in some human nasopharyngeal samples, and therefore has implications for transmission models and nucleic acid-based diagnostics. <br> LeTRS provides a quantitative measure of sgmRNA abundance from sequencing data. This can be used to assess the biology of SARS-CoV-2 (or other coronaviruses) in clinical and non-clinical samples, especially to evaluate different variants and medical countermeasures that may influence viral RNA synthesis.
DOI: 10.5524/102220
title: Supporting data for "A novel ground truth multispectral image dataset with weight, anthocyanins and Brix index measures of grape berries tested for its utility in machine learning pipelines"

description: The combination of computer vision devices such as multispectral cameras coupled with Artificial Intelligence has provided a major leap forward in image-based analysis of biological processes. Supervised Artificial Intelligence algorithms require large ground truth image datasets for model training, which allows to validate or refute research hypotheses and to carry out comparisons between models. However, public datasets of images are scarce and ground truth images are surprisingly few considering the numbers required for training algorithms. <br>We created a dataset of 1283 multidimensional arrays, using berries from five different grape varieties. Each array has 37 images of wavelengths between 488.38nm and 952.76nm obtained from single berries. Coupled to each multispectral image we added a dataset with measurements including, weight, anthocyanin content and Brix index for each independent grape. Thus, the images have paired measures creating a ground truth dataset. We tested the dataset with two neural network algorithms: multilayer perceptron (MLP), three-dimensional convolutional neural network (3D-CNN). A perfect (100% accuracy) classification model was fit with either the MLP or 3D-CNN algorithms. <br>This is the first public dataset of grape ground truth multispectral images. Associated with each multispectral image there are measures of the weight, anthocyanins, and Brix index. The dataset should be useful to develop deep learning algorithms for classification, dimensionality reduction, regression, and prediction analysis.
DOI: 10.5524/102229
title: Supporting data for "Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes"

description: Insect silk is an incredibly versatile biomaterial. Lepidoptera and their sister lineage, Trichoptera, display some of the most diverse uses of silk with varying strength, adhesive qualities and elastic properties. It is well known that silk fibroin genes are long (&gt; 20 kb) and have many repetitive motifs. These features make these genes challenging to sequence. Most research thus far has focused on conserved N- and C-terminal regions of fibroin genes because a full comparison of repetitive regions across taxa has not been possible. Using the PacBio Sequel II system and SMRT sequencing, we generated high fidelity (HiFi) long-read genomic and transcriptomic sequences for the Indianmeal moth (<i>Plodia interpunctella</i>) and genomic sequences for the caddisfly, <i>Eubasilissa regina</i>. Both genomes were highly contiguous (N50 = 9.7 Mbp/32.4 Mbp, L50 = 13/11) and complete (BUSCO Complete = 99.3%/95.5%), with complete and contiguous recovery of silk <i>heavy fibroin</i> gene sequences. This study demonstrates that HiFi long-read sequencing can significantly help our understanding of genes with highly contiguous, repetitive regions.
DOI: 10.5524/102233
title: Supporting data for "Chromosome-level assembly and annotation of the blue catfish <i>Ictalurus furcatus</i>, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies"

description: The blue catfish is of great value in aquaculture and recreational fisheries. The F1 hybrids of female channel catfish (<i>Ictalurus punctatus</i>) x male blue catfish (<i>I. furcatus</i>) have been the primary driver of US catfish production in recent years because of superior growth, survival, and carcass yield. The channel-blue hybrid also provides an excellent model to investigate molecular mechanisms of environment-dependent heterosis. However, transcriptome and methylome studies suffered from low alignment rates to the channel catfish genome due to divergence, and the genome resources for blue catfish are not publicly available. <br>The blue catfish genome assembly is 841.86 Mbp in length with excellent continuity (8.6 Mbp contig N50, 28.2 Mbp scaffold N50) and completeness (98.6% BUSCO). A total of 30,971 protein-coding genes were predicted, of which 21,781 were supported by RNA-seq evidence. Phylogenomic analyses revealed that it diverged from channel catfish approximately 9 million years ago with 15.7 million fixed nucleotide differences. The within-species SNP density is 0.32% between the most agriculturally important blue catfish strains (D&B and Rio Grande). Gene family analysis discovered significant expansion of immune-related families in the blue catfish lineage, which may contribute to disease resistance in blue catfish. <br>We reported the first high-quality, chromosome-level assembly of the blue catfish genome, which provides the necessary genomic tool kit for transcriptome and methylome analysis, SNP discovery and marker-assisted selection, gene editing and genome engineering, as well as reproductive enhancement of the blue catfish and hybrid catfish.