cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/ryr859j6pr
title: Viral fitness landscapes in diverse host species reveal multiple evolutionary lines for the NS1 gene of influenza A viruses - Supplemental Data (Part 2)

description: IAV NS1 protein is a multifunctional virulence factor that inhibits the type-I interferon host response through a myriad of mechanisms. How NS1 has evolved to enable this remarkable property across species and its specific impact in the overall replication, pathogenicity and host preference, remains unknown. We analyzed the NS1 evolutionary landscape and host tropism through the use of a barcoded library of recombinant IAV. We designed a barcoded viral library of recombinant influenza A viruses expressing a selection of NS1 from different strains, hosts, countries and years. Each virus was individually rescued and deep-sequenced using the Illumina MiSeq platform to verify viral genome integrity and sequence. Results showed diverse and apparently random evolutionary pathways taken by IAV NS1 according to its multiple phylogenetic lineages. In summary, the high evolutionary plasticity of this viral protein underscores the ability of IAV to adapt to multiple hosts and aids in our understanding of its global prevalence. This dataset contains the following: 1. Illumina deep-sequencing raw data of each virus included in the final library (barcodes 124-128). 2. Illumina deep-sequencing raw data of the barcode analysis in infection experiments. 3-6. Custom scripts for different data analysis in the manuscript. 7. Segment sequences of WT Influenza A viruses (A/Puerto Rico/08/1934 and A/Vietnam/1203/04) used in this work. 8. Full sequences of empty vectors (pCAGGS, pPolI and pDZ) used in this work.
DOI: 10.17632/zgytmbrnr2
title: Long-term follow-up data on three siblings with a novel NNT duplication mutation causing primary adrenal insuficiency

description: We performed a long-term follow-up of three sibling that were found to be homozygous for a novel duplication mutation in the NNT gene, encoding nicotinamide nucleotide transhydrogenase (NNT). Lack of a functional NNT protein results in primary adrenal insuficiency and also some other extra-adrenal manifestations.

All three brothers were managed as out- and in-patients at the University Children's Hospital, University Medical Centre Ljubljana. They presented to us at the age of 1.4, 1.1 years and 2 monts. Their age at last follow-up was 21.6, 20.2 and 4.2 years. Patients 1 and 2 presented with Addisonian crisis.

In this dataset, we provide the raw data on:
- Laboratory values at first presentation,
- Laboratory values through follow-up,
- Bone mineral density,
- Growth (height, weight, BMI),
- Hydrocortisone treatment,
- ACTH stimulation test,
- GnRH stimulation test.

The main findings were:
- all three brothers who were homozygous for a novel mutation in NNT gene developed isolated glucocorticoid deficiency,
- acute adrenal crisis developed in patients 1 and 2 after the first year of life,
- patient 3 was identified at the age of 2 months in the asymptomatic stage,
- none had mineralocorticoid deficiency,
- thyroid function was normal,
- testicular volume was somewhat lower than expected for their age, but testosteron, inhibin B and GnRH test results were appropriate,
- low bone mineral density was observed in patients 1 and 2.
DOI: 10.3535/7pf-f5t-px0
title: Granite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/87l-vls-tr7
title: Phlogopite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14979879.v1
title: K-Means Cluster Analysis Syntax.R

description: K-Means Cluster Analysis Syntax RStudio
DOI: 10.6084/m9.figshare.24191133.v1
title: Means_PNG results 280618_FORMATTED_MV.xlsx

description: The raw trait data for the species included in the manuscript alongside additional species sampled as part of the wider project.
DOI: 10.3535/7rc-vkw-chh
title: Lava

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vc3-3tc-wbe
title: Conochitina iklaensis

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/31p-nh9-all
title: Pinite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wf3-fw9-v8r
title: Eisenackitina elongata

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/9bw-j8n-twd
title: Melaphyre

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/2m4-sdl-xn2
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v3s-cha-jdc
title: Hemimorphite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.21652340.v1
title: Refined Phylogenetic Results

description: clean.full.reduced.aln - the snippy-generated genome alignment parsnp-tree.newick - phylogenetic tree generated by parsnp and FastTree in the Harvest suite snippy-genome-tree.newick - phylogenetic tree generated by fasttree using the snippy alignment TeNT-alignment-aa.fst - TeNT amino acid alignment TeNT-alignment-nt.fst - TeNT nucleotide alignment TeNT-tree.newick - TeNT phylogenetic tree
DOI: 10.6084/m9.figshare.24498484.v1
title: Data and analysis scripts from the global bacterial growth potential study

description: Soil properties, climate variables, and metagenomic traits for global soil bacterial communities, including maximum growth rates estimated using codon usage bias statistics.
DOI: 10.3535/2m6-bj7-n39
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/rp9-q1q-3wz
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.7308695.v1
title: Dataset - Inferential false memory for emotional events in older adults

description: Dataset and R code for the analysis on "Inferential False Memory for Emotional Events in Older Adults"<br>The analysis in R employs MCMC estimation methods that may take long (from a few minutes for fitting a single model to serveral hours--or days--for cycles computing sensitivity analyses).<br>The dataset reports observations on 76 healthy older adults.<br>The dataset is presented in the long form, i.e., there is one row per single response (each participant gave 90 responses). This allows to fit mixed-effects logistic regressions on recognition data. If any statistics is to be computed at the participant level, averaging data by participant (column "ID") is recommended first.<br><br>Recognition responses are reported in column "Response" (1 refers to "yes", 0 refers to "no"). CWMS is Verbal Working Memory. GDS is Geriatric Depression Scale. In column "Type", "trg_inco" and "fa_inco" refers to items presented at the very beginning and end of the encoding procedure only to avoid primacy or recency effects; "gapfilling" refers to gap-filling distractors, "causal" refers to causal antecedent distractors, "target" refers to target (or "hit") items.
DOI: 10.3535/8z5-dne-l7s
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/d43-865-jw2
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.c.3866416_d4.v1
title: Additional file 4: Table S3. of Differential gene expression in Anopheles stephensi following infection with drug-resistant Plasmodium yoelii

description: KEGG analysis of differentially expressed genes: (A) R-As24h vs S-As24h; (B) R-As13d vs S-As13d; (C) R-As19d vs S-As19d. (XLS 34 kb)
DOI: 10.3535/f9e-ce4-08a
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xcm-z13-nry
title: Eisenackitina sp. 1

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.22548124.v1
title: 1. Genome annotation file for Neixiu blood orange 2. Supplementary Tables 3. Supplementary Figures

description: 1. Genome annotaton file for Neixiu Blood orange 2. Supplementary Tables are as follows: Supplementary Table 1. Genome estimatiion for Neixiu blood orange Supplementary Table 2. Statistics of assembled genome sequences for Neixiu blood orange Supplementary Table 3. Integrated function annotation of Neixiu blood genome Supplementary Table 4. Statistics of gene family clustering among Neixiu blood orange and other 11 representative plant species Supplementary Table 5. List of the expanded and constracted gene families 3. Supplementary Figures are as follows: Supplementary Figure 1. GO enrichment analysis for the specific genes of Neixiu blood orange Supplementary Figure 2. GO enrichment analysis for the contracted gene families of Neixiu blood orange Supplementary Figure 3. GO enrichment analysis for the expanded gene families of Neixiu blood orange Supplementary Figure 4. KEGG enrichment analysis for the contracted gene families of Neixiu blood orange Supplementary Figure 5. KEGG enrichment analysis for the expanded gene families of Neixiu blood orange Supplementary Figure 6. GO enrichment analysis for the SNPs between Neixiu blood orange and sweet orange Supplementary Figure 7. KEGG enrichment analysis for the SNPs between Neixiu blood orange and sweet orange Supplementary Figure 8. GO enrichment analysis for the InDels between Neixiu blood orange and sweet orange Supplementary Figure 9. KEGG enrichment analysis for the InDels between Neixiu blood orange and sweet orange Supplementary Figure 10. GO enrichment analysis for the SVs between Neixiu blood orange and sweet orange Supplementary Figure 11. KEGG enrichment analysis for the SVs between Neixiu blood orange and sweet orange Supplementary Figure 12. GO enrichment analysis for the Presence variations between Neixiu blood orange and sweet orange Supplementary Figure 13. KEGG enrichment analysis for the Presence variations between Neixiu blood orange and sweet orange Supplementary Figure 14. GO enrichment analysis for the Absence variations between Neixiu blood orange and sweet orange Supplementary Figure 15. KEGG enrichment analysis for the Absence variations between Neixiu blood orange and sweet orange Supplementary Figure 16. GO enrichment analysis for the CNVs between Neixiu blood orange and sweet orange Supplementary Figure 17. KEGG enrichment analysis for the CNVs between Neixiu blood orange and sweet orange
DOI: 10.3535/fws-vc2-ez0
title: Specimen from Tallinn University of Technology

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/sav-n8s-7b9
title: Cyathochitina calix

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.16441608.v1
title: CLM output for "A Comparison of Land Surface Phenology in the Northern Hemisphere Derived from Satellite Remote Sensing and the Community Land Model"

description: This data set includes the Leaf Area Index (LAI) and net primary production (NPP) outputs from two data atmosphere forced CLM-only simulations. The manuscript titled "A Comparison of Land Surface Phenology in the Northern Hemisphere Derived from Satellite Remote Sensing and the Community Land Model" has been accepted by the Journal of Hydrometeorology for publication (doi: 10.1175/JHM-D-21-0169.1).
DOI: 10.3535/d2d-bqp-z46
title: Pyrite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/klh-wvt-qrq
title: Conochitina sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.19248626.v1
title: Prince Edward Islands geospatial database

description: This database contains vector files, raster datasets, and maps of topographical and hydrological parameters of the sub-Antarctic Prince Edward Islands. Data production procedures are described in the associated paper (see references below) and the metadata are described in the "README" word document. The data is intended for scientific and/or educational use. Marion Island = "mi" and Prince Edward Island = "pe".<br>
DOI: 10.6084/m9.figshare.c.3662366_d702.v1
title: CT scan of the head of a Cetorhinus maximus (BMNH 2004.4.15.30)

description: This file includes 1654 DICOM files of the head of a Cetorhinus maximus specimen housed in the spirit collection of the British Natural History Museum, London with registrationnumber BMNH 2004.4.15.30. The specimen is scanned in a medical CT scanner (Siemens Sensation 64) at the Royal Brompton Hospital, London at 100 kV and 210 mAs with a slice thickness of 1.00 mm.
DOI: 10.3535/3cr-6pf-cmq
title: Sphaerochitina? sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14546346.v1
title: China’s monthly BC emissions during COVID-19 in 2020

description: China’s monthly BC emissions by source sector and by province
DOI: 10.3535/dt7-j7g-h09
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/qzv-a70-8e2
title: Aegirine

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.19614315.v1
title: Anolis allogus draft genome (repeat-softmasked)

description: Repeatitive elements annotated by RepeatMasker were softmasked.
DOI: 10.3535/m5y-619-b83
title: †Plectambonitoidea Jones, 1928

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/sa1-fbz-9t1
title: †Subulites Emmons, 1842

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.5497903.v1
title: Classification of mosasaurs - using networks

description: The file set contains figures (orginal and additional) and data relating to my post on mosasaur matrix used by Madzia & Cau (2017: <i>Inferring `weak spots' in phylogenetic trees: application to mosasauroid nomenclature. PeerJ 5:e3782</i>). The post outlines why networks and not trees should be used to identify weak spots in the phylogenies based on morphological data sets.<br> <br><b>Method:</b> Neighbour-nets were computed with SplitsTree 4 based on simple (Hamming) mean pairwise morphological distances; consensus networks are either based on a sample of equally (most) parsimonious trees (MPT) or 10,000 non-parametric bootstrap pseudoreplicates (generated with PAUP* under the least-squares and parsimony optimality criteria; and RAxML 8 under maximum likelihood.<br><br><b>Main result: </b>The networks allow straightforward identification of unambiguous or unchallengend phylogenetic hypothesis and general signal issues in the data. Thus, providing a much more comprehensive analytical framework for defining systematic groups using 'cladistic' (clade-, node-based), 'phylogenetic' (monophyly) or 'evolutionary' (overall similarity + monophyla and paraphyla) classification philosophies. See provided links for further details on the data and the graphs.<br><br><b>Content</b>: Figures 1–5 refer to the according figures in the blogpost. Fig. 2 shows several consensus graphs of the MPT sample, Figs 3 and 4 neighbour-nets, Fig. 5 parsimony bootstrap (BS) support networks (consensus networks in which the edge-lengths reflect the frequency of a split in the BS replicate sample)<br><i>Mosauroidea.nex</i><b> </b>is the NEXUS-formatted character matrix including the code-lines for parsimony and distance analysis.<br><i>PairwiseDistanceHeatMap.xlsx</i> is an EXCEL-formatted spread-sheet file with the distance matrix re-ordered according to proposed systematic groups, with the cells gradually (auto-)coloured green (no difference, morphological distance, MD, of 0) to red (differing in all characters covered in both taxa, MD = 1) <br><br>The complete analysis files are included in an archive hosted at www.palaeogrimm.org/data (see ReadMe.txt in the archive for file naming conventions).<br><br><br>
DOI: 10.21253/dmu.28287596.v1
title: Whole genome sequencing laundry detergent tolerance assay

description: Whole genome sequence of five isolates. Three <i>Staphyloccocus aureus</i> isolates, the original background strain NCTC 10788 before the induction of laundry detergent tolerance, one isolate after 15 passage on powder domestic laundry detergent and one isolate after 15 passages on liquid domestic laundry detergent. Two <i>Klebsiella pneumoniae</i> isolates, the original background strain NCIMB 10341 before the induction and one isolate after 15 passages on powder domestic laundry detergent.
DOI: 10.3535/8vn-r1f-sn0
title: Kyanite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/kc1-rb9-yln
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.19151016.v1
title: Additional file 9 of An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development

description: Additional file 9: Table S8. A summary of fusion transcripts identified in this study.
DOI: 10.3535/d31-6ey-bq0
title: Lava

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/g18-st0-dsk
title: Lava

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/k80-aa5-26g
title: Ramochitina sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.28615325.v1
title: <b>Receptive Field Properties and Functional Organization of the Entopallium Region in Pigeons</b>

description: In this study, we systematically investigated the receptive field properties and functional organization of the entopallium (ENTO) by recording the activity of 558 neurons in anesthetized pigeons. We demonstrate that ENTO neurons exhibit significant encoding capabilities for color, shape, and motion, with distinct spatial clustering of functional properties.
DOI: 10.3535/zyx-cwl-d2v
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/nbx-3cg-h36
title: Quartz

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/z54-8lq-774
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.c.3810205_d1.v1
title: Additional file 1: of Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus

description: List and position of CGIs found across the goat reference genome. (XLSX 3401 kb)
DOI: 10.3535/41j-sb4-e64
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/k1k-h37-n5g
title: Specimen from Tallinn University of Technology

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/aye-6wc-87w
title: Ramochitina? sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/erb-vad-bkv
title: Conochitina sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.15113106.v1
title: Datasets from: "Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō"

description: Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (<i>Strigops habroptilus</i>), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (F<sub>H</sub>), the diagonal elements of a genomic-relatedness matrix (F<sub>GRM</sub>), and runs of homozygosity (RoH, F<sub>RoH</sub>). Additionally, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry were found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between diverse lineages. <br><b>Datasets:</b>kākāpō_all_unfiltered.vcf: genotypes for all individuals, no filteringkākāpō_all_filtered_md80.vcf: genotypes for all individuals, filtered for depth and missing datakākāpō_noRHF1_filtered_md80.vcf: genotypes without Richard-Henry (sole mainland founder) and his three offspring, filtered for depth and missing datakākāpō_nomainland_filtered_md80.vcf: genotypes without any mainland ancestrykākāpō_inbreeding_alldatasets.xlsx: inbreeding metrics for all datasets<br><b>For more details of the data subsets and filtering, see methods section:</b>Foster et al. 2021. Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō. G3: Genes|Genomes|Genetics.<b><br></b><b>For any questions, please email: y.al.foster@gmail.com</b><b><br></b><b><br></b>
DOI: 10.6084/m9.figshare.5522059.v2
title: Multifunctional Smart Polymer Coatings

description: Monomer feed rate regulates the chemical structure of smart plasma copolymer coating and its surface wettability in various pH environment. The combined effect of surface chemical compositions and surface roughness causes tunable wettability from superhydrophobicity to superhydrophilicity of smart plasma copolymer coatings. Further on, the presence of the carboxylic acid functional group in plasma copolymer coatings made this surface wettability switchable for different pH environment.
DOI: 10.3535/nex-vpk-g0q
title: Vinnalochitina sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xdh-4fm-6wd
title: Vinnalochitina sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/467-kae-pxb
title: Sphaerochitina sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ezx-1fa-zt8
title: Conochitina n. sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.