cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5441/001/1.mn019k4d/2
title: Movements of the Christmas Island flying fox Australia-reference-data

description: Todd CM, Westcott DA, Martin JM, Rose K, McKeown A, Hall J, Welbergen JA. 2022. Body-size dependent foraging strategies in the Christmas Island flying-fox: implications for seed and pollen dispersal within a threatened island ecosystem. Mov Ecol. 10:19. doi:10.1186/s40462-022-00315-8
description: Background: Animals are important vectors for the dispersal of a wide variety of plant species, and thus play a key role in maintaining the health and biodiversity of natural ecosystems. On oceanic islands, flying-foxes are often the only seed dispersers or pollinators. However, many flying-fox populations are currently in decline, particularly those of insular species, and this has consequences for the ecological services they provide. Knowledge of the drivers and the scale of flying-fox movements is important in determining the ecological roles that flying-foxes play on islands. This information is also useful for understanding the potential long-term consequences for forest dynamics resulting from population declines or extinction, and so can aid in the development of evidence-based ecological management strategies. To these ends, we examined the foraging movements, floral resource use, and social interactions of the Critically Endangered Christmas Island flying-fox (Pteropus natalis). Methods: Utilization distributions, using movement-based kernel estimates (MBKE) were generated to determine nightly foraging movements of GPS-tracked P. natalis (n = 24). Generalized linear models (GLMs), linear mixed-effect models (LMMs), and Generalized linear mixed-effects model (GLMMs) were constructed to explain how intrinsic factors (body mass, skeletal size, and sex) affected the extent of foraging movements. In addition, we identified pollen collected from facial and body swabs of P. natalis (n = 216) to determine foraging resource use. Direct observations (n = 272) of foraging P. natalis enabled us to assess the various behaviors used to defend foraging resources. Results: Larger P. natalis individuals spent more time foraging and less time traveling between foraging patches, traveled shorter nightly distances, and had smaller overall foraging ranges than smaller conspecifics. Additionally, larger individuals visited a lower diversity of floral resources. Conclusions: Our findings suggest that smaller P. natalis individuals are the primary vectors of long-distance dispersal of pollen and digested seeds in this species, providing a vital mechanism for maintaining the flow of plant genetic diversity across Christmas Island. Overall, our study highlights the need for more holistic research approaches that incorporate population demographics when assessing a species’ ecological services.
DOI: 10.5281/zenodo.7388344
title: Differences in visual-field sensitivity in the inferior hemifield between the eyes affect three-dimensional shape perception in glaucoma

description: <strong>Raw data repository for the article:</strong> <strong>Differences in visual-field sensitivity in the inferior hemifield between the eyes affect three-dimensional shape perception in glaucoma</strong> <strong>Hiromasa Sawamura<sup>1</sup>, Ryo Asaoka<sup>1,2,3,4,5</sup>, Hiroshi Murata<sup>1</sup>, Eriko Ando<sup>1</sup>, Céline R. Gillebert<sup>6</sup>, James T. Todd<sup>7</sup>, Guy A. Orban<sup>8</sup></strong> <sup>1</sup> Department of Ophthalmology, University of Tokyo Graduate School of Medicine, Tokyo, Japan. <sup>2</sup> Department of Ophthalmology, Seirei Hamamatsu General Hospital, Hamamatsu, Shizuoka, Japan. Seirei Christopher University, Hamamatsu, Shizuoka, Japan. <sup>4</sup> Nanovision Research Division, Research Institute of Electronics, Shizuoka University, Shizuoka Japan. <sup>5</sup> The Graduate School for the Creation of New Photonics Industries, Shizuoka Japan. Department of Brain and Cognition, KU Leuven, Leuven, Belgium. Department of Psychology, The Ohio State University, Columbus, OH, USA. Department of Medicine and Surgery, Neuroscience Unit, University of Parma, Parma, Italy. Excel data: Binocular Visual-filed sensitivity for 20 subjects: BinocularHFAData.xlsx Visual filed sensitivity in the right eye: OD_HFA_data.xlsx Visual filed sensitivity in the left eye: OS_HFA_data.xlsx Error-in-depth for 20 subjects: ErrorinDepth_20subj.xlsx Results of Simple feature discrimination: Result_SinpleFeatureDiscrimination.xlsx
DOI: 10.5281/zenodo.7388343
title: Differences in visual-field sensitivity in the inferior hemifield between the eyes affect three-dimensional shape perception in glaucoma

description: <strong>Raw data repository for the article:</strong> <strong>Differences in visual-field sensitivity in the inferior hemifield between the eyes affect three-dimensional shape perception in glaucoma</strong> <strong>Hiromasa Sawamura<sup>1</sup>, Ryo Asaoka<sup>1,2,3,4,5</sup>, Hiroshi Murata<sup>1</sup>, Eriko Ando<sup>1</sup>, Céline R. Gillebert<sup>6</sup>, James T. Todd<sup>7</sup>, Guy A. Orban<sup>8</sup></strong> <sup>1</sup> Department of Ophthalmology, University of Tokyo Graduate School of Medicine, Tokyo, Japan. <sup>2</sup> Department of Ophthalmology, Seirei Hamamatsu General Hospital, Hamamatsu, Shizuoka, Japan. Seirei Christopher University, Hamamatsu, Shizuoka, Japan. <sup>4</sup> Nanovision Research Division, Research Institute of Electronics, Shizuoka University, Shizuoka Japan. <sup>5</sup> The Graduate School for the Creation of New Photonics Industries, Shizuoka Japan. Department of Brain and Cognition, KU Leuven, Leuven, Belgium. Department of Psychology, The Ohio State University, Columbus, OH, USA. Department of Medicine and Surgery, Neuroscience Unit, University of Parma, Parma, Italy. Excel data: Binocular Visual-filed sensitivity for 20 subjects: BinocularHFAData.xlsx Visual filed sensitivity in the right eye: OD_HFA_data.xlsx Visual filed sensitivity in the left eye: OS_HFA_data.xlsx Error-in-depth for 20 subjects: ErrorinDepth_20subj.xlsx Results of Simple feature discrimination: Result_SinpleFeatureDiscrimination.xlsx
DOI: 10.26036/cnp0002864
title: Multi-Omics Research of Trichonephila clavata spider

description: Trichonephila clavata is a spider that produces golden orb-weaving. The spider has seven silk glands with different functions, among which the major ampulla gland can secrete the dragline silk of high-strength mechanical properties. This dataset includes multiple omics data for the major ampulla gland.
DOI: 10.26036/cnp0003776
title: Whole genome sequencing of 4 genomes in Characiformes

description: We sequenced 125.5 Gb (132-fold), 118.6 Gb (137-fold), 125.1 Gb (154-fold) and 120.7 Gb (102-fold) stLFR data of Acestrorhynchus altus (Aal), Hepsetus odoe (Hod), Distichodus sexfasciatus (Dse) and Semaprochilodus insignis (Sin), respectively. With a combination of stLFR, Nanopore and Hi-C reads, we assembled the genomes of them with total length of 952.8 Mb, 864.4 Mb, 813.5 Mb and 1.18 Gb, representatively.
DOI: 10.26036/cnp0002481
title: longan sRNA and degradome sequencing

description: 32 small RNA libraries and 2 degradome libraries were sequenced on an Illumina HiSeq 2500 platform. The sRNA-seq data were collected from different tissues of longan, including leaf, root, shoot, different stages of flower buds, female flower, and male flower. The degradome data included mixed vegetative tissues and mixed reproductive tissues.
DOI: 10.6084/m9.figshare.21714548
title: Olmsted Thesis Chapter 2 Supplementary Tables

description: SUPPLEMENTARY TABLE LEGENDS <strong>Supplementary Table 1.</strong> Lake-wide information. This table includes lake characteristics, lake-wide EET protein values and METABOLIC protein values and standard deviations when available. <strong>Supplementary Table 2.</strong> Abbreviations and descriptions. In addition to abbreviations, this table lists the names of proteins for which HMMs were used in METABOLIC for each category. <strong>Supplementary Table 3.</strong> Information unique to each metagenome assembled genome (MAG). This includes to what lake, sample, and mOTU each MAG belongs, its GTDB-tk taxonomy, genetic characteristics, and FEET and METBOLIC proteins. <strong>Supplementary Table 4.</strong> Bit scores for FeGenie Hidden Markov Models and observed redox association. This table also includes additional conditionals for whether each HMM was considered as promising evidence of EET capability. <strong>Supplementary Table 5. </strong>Unique taxa characteristics and references. This table includes average EET protein values for each unique taxa. It also contains our designation of the quality of evidence that each unique taxa contains members suspected capable of EET. These designations occur under the header “EET Evidence Quality” with following category keywords “obviously” (some members contain several promising EET genes as defined in Supplementary Table 2), “likely” (highest suspect members contain one or two promising EET genes), “possibly” (highest suspect members contain two or three DFE variants or FoxABCYZ proteins but no other more promising EET genes), and “unknown” (contains just one of such “possible” EET genes). This table also contains whether each unique taxa has been found in a previous study to have or likely have EET capabilities under the header “Previous EET evidence” with the following keyword meanings: “yes” (we found studies that show EET in organisms in the genus or species), “no” (we did not find studies including genus or species doing EET; or taxonomic level is not defined enough to know), and “related”(organisms in the same order or family but not the particular genus or species were found in a previous study with EET). <strong>Supplementary Table 6. </strong>Novel cluster information. This table includes each unique novel cluster sequence, its percent identity to the reference sequence, and its number of heme motifs. Also included is which open reading frame the sequence represents, and what taxa it was found in. <strong>Supplementary Table 7. </strong>Expression values for EET genes and METABOLIC oxidoreductases from Trout Bog Lake MAG metatranscriptomics dataset, averaged per timepoint (in hours) and integrated sampling layer. Timepoint zero is at 5:00 am CST, July 19th 2016. “NormAveTPM” is the TPM of the transcripts that mapped to the listed open reading frame normalized by the average of all open reading frames’ TPM values of the given MAG. “NormRefTPM” is normalized by the reference gene TPM value for the given MAG.
DOI: 10.6084/m9.figshare.21714548.v1
title: Olmsted Thesis Chapter 2 Supplementary Tables

description: SUPPLEMENTARY TABLE LEGENDS <strong>Supplementary Table 1.</strong> Lake-wide information. This table includes lake characteristics, lake-wide EET protein values and METABOLIC protein values and standard deviations when available. <strong>Supplementary Table 2.</strong> Abbreviations and descriptions. In addition to abbreviations, this table lists the names of proteins for which HMMs were used in METABOLIC for each category. <strong>Supplementary Table 3.</strong> Information unique to each metagenome assembled genome (MAG). This includes to what lake, sample, and mOTU each MAG belongs, its GTDB-tk taxonomy, genetic characteristics, and FEET and METBOLIC proteins. <strong>Supplementary Table 4.</strong> Bit scores for FeGenie Hidden Markov Models and observed redox association. This table also includes additional conditionals for whether each HMM was considered as promising evidence of EET capability. <strong>Supplementary Table 5. </strong>Unique taxa characteristics and references. This table includes average EET protein values for each unique taxa. It also contains our designation of the quality of evidence that each unique taxa contains members suspected capable of EET. These designations occur under the header “EET Evidence Quality” with following category keywords “obviously” (some members contain several promising EET genes as defined in Supplementary Table 2), “likely” (highest suspect members contain one or two promising EET genes), “possibly” (highest suspect members contain two or three DFE variants or FoxABCYZ proteins but no other more promising EET genes), and “unknown” (contains just one of such “possible” EET genes). This table also contains whether each unique taxa has been found in a previous study to have or likely have EET capabilities under the header “Previous EET evidence” with the following keyword meanings: “yes” (we found studies that show EET in organisms in the genus or species), “no” (we did not find studies including genus or species doing EET; or taxonomic level is not defined enough to know), and “related”(organisms in the same order or family but not the particular genus or species were found in a previous study with EET). <strong>Supplementary Table 6. </strong>Novel cluster information. This table includes each unique novel cluster sequence, its percent identity to the reference sequence, and its number of heme motifs. Also included is which open reading frame the sequence represents, and what taxa it was found in. <strong>Supplementary Table 7. </strong>Expression values for EET genes and METABOLIC oxidoreductases from Trout Bog Lake MAG metatranscriptomics dataset, averaged per timepoint (in hours) and integrated sampling layer. Timepoint zero is at 5:00 am CST, July 19th 2016. “NormAveTPM” is the TPM of the transcripts that mapped to the listed open reading frame normalized by the average of all open reading frames’ TPM values of the given MAG. “NormRefTPM” is normalized by the reference gene TPM value for the given MAG.
DOI: 10.5281/zenodo.7429113
title: Historical Plant Collections Card Catalog

description: TREC began operations in 1930 with development of the land and planting of the first crops. The digitized card catalog documents the earliest plants collected and cultivated at TREC including ornamental and fruit crops. Native and rare plants are also included with conservation focus. Most of the cards document activity from the 1930's to the 1960's with fewer entries from the 1970's and 1980's. The catalog for this collection is contained as `_CardCatalogFiles2021.xlsx` with the collection as the accompanying 468 image files that digitize 4,170 cards.
description: Funding provided by the UF Libraries digital initiatives endowment.
DOI: 10.5281/zenodo.7429114
title: Historical Plant Collections Card Catalog

description: TREC began operations in 1930 with development of the land and planting of the first crops. The digitized card catalog documents the earliest plants collected and cultivated at TREC including ornamental and fruit crops. Native and rare plants are also included with conservation focus. Most of the cards document activity from the 1930's to the 1960's with fewer entries from the 1970's and 1980's. The catalog for this collection is contained as `_CardCatalogFiles2021.xlsx` with the collection as the accompanying 468 image files that digitize 4,170 cards.
description: Funding provided by the UF Libraries digital initiatives endowment.
DOI: 10.25919/1842-k647
title: HI absorption associated to Norma's brightest cluster galaxy

description: Continuum and HI spectral cubes and multi-frequency synthesis continuum map towards the Norma cluster's brightest cluster galaxy, ESO137-G006. Cubes contain HI flux as a function of position and velocity. HI absorption has been detected to be associated to ESO137-G006. Telescope: The Australian Telescope Compact Array (ATCA) Centre RA: 16:15:04 Centre Dec: -60:54:26 Radius of cubes: 1 arcmin Radius of continuum map: 0.5 deg Synthesised Beam: 9 arcsec by 7 arcsec at 31 degrees Pixel Size: 2 arcsec RMS noise: 9 mJy/beam Frequency: 1396 MHz Velocity Resolution: 6.6 km/s Detection centre: 5460 km/s Detection width: 192 km/s Spectral noise: 9 mJy For more detailed information refer to Saraf, M et al 2022 (submitted to MNRAS)
DOI: 10.18112/openneuro.ds003764.v1.0.2
title: Neural dynamics underlying the acquisition of distinct auditory category structures
DOI: 10.6069/r5we-6z85
title: Global Burden of Disease (GBD) Cardiovascular Burden Estimates 1990 and 2021

description: This dataset includes total cardiovascular disease burden estimates globally for multiple cardiovascular diseases for 7 Global Burden of Disease Study (GBD) super regions, 21 GBD regions, 204 countries and territories, and select subnational locations. The following are reported: mortality by age and sex for the years 1990 and 2021; age-standardized mortality in 2021 by Socio-Demographic Index (SDI), a composite indicator of fertility, income, and education; all ages and age-standardized prevalence for 2021; and age-standardized disability-adjusted life years (DALYs) for 2021. The dataset also includes burden attributable to selected risk factors for each GBD region in 2021, as measured by DALYs. These data are custom calculated for publication in the Journal of the American College of Cardiology and will not be available in the GBD 2021 Results Tool.
DOI: 10.18112/openneuro.ds003764.v1.0.3
title: Neural dynamics underlying the acquisition of distinct auditory category structures
DOI: 10.6084/m9.figshare.21714605
title: Olmsted Thesis Chapter 3 Supplementary Tables

description: SUPPLEMENTARY TABLE LEGENDS <strong>Supplementary Table 1. </strong>Metagenome assembled genome (MAG)-specific information. This dataset lists all MAGs for all included samples and to which MetaMAG each belongs. No MAGs were removed, even poor-quality ones, but CheckM completeness and contamination values are given. MetaMagRelAbund is the relative abundance of the listed MetaMAG based on read mapping of the given sample to all MetaMAGs while RelAbund is the relative abundance based on read mapping to MAGs derived from that sample. TotEET, RedEET, OxiEET, PutEET, MtrB are values generated by the FEET pipeline on every MAG, respectively total, reductive, oxidative, putative, and MtrB EET genes. MtrB is a porin that can be involved in either OxiEET or RedEET. The values to the right of these are for each listed MetaMAG, and are from on the METABOLIC pipeline with the added hidden Markov models for EET genes from the FEET pipeline, but these may not always be counted as an EET gene by FEET rules. <strong>Supplementary Table 2. </strong>Sample-specific information. Sample DNA was sequenced by cited efforts, RTSF Genomics Core at Michigan State University (MSU), or California Institute for Quantitative Biosciences (QB3). All data is available for open access at [insert something]. <strong>Supplementary Table 3. </strong>Electroactive chemical species in Trout Bog Lake. Data are averages from all available samples during 2016–2021.
DOI: 10.6084/m9.figshare.21714605.v2
title: Olmsted Thesis Chapter 3 Supplementary Tables

description: SUPPLEMENTARY TABLE LEGENDS <strong>Supplementary Table 1. </strong>Metagenome assembled genome (MAG)-specific information. This dataset lists all MAGs for all included samples and to which MetaMAG each belongs. No MAGs were removed, even poor-quality ones, but CheckM completeness and contamination values are given. MetaMagRelAbund is the relative abundance of the listed MetaMAG based on read mapping of the given sample to all MetaMAGs while RelAbund is the relative abundance based on read mapping to MAGs derived from that sample. TotEET, RedEET, OxiEET, PutEET, MtrB are values generated by the FEET pipeline on every MAG, respectively total, reductive, oxidative, putative, and MtrB EET genes. MtrB is a porin that can be involved in either OxiEET or RedEET. The values to the right of these are for each listed MetaMAG, and are from on the METABOLIC pipeline with the added hidden Markov models for EET genes from the FEET pipeline, but these may not always be counted as an EET gene by FEET rules. <strong>Supplementary Table 2. </strong>Sample-specific information. Sample DNA was sequenced by cited efforts, RTSF Genomics Core at Michigan State University (MSU), or California Institute for Quantitative Biosciences (QB3). All data is available for open access at [insert something]. <strong>Supplementary Table 3. </strong>Electroactive chemical species in Trout Bog Lake. Data are averages from all available samples during 2016–2021.
DOI: 10.6084/m9.figshare.21714605.v1
title: Olmsted Thesis Chapter 4 Supplementary Tables

description: SUPPLEMENTARY TABLE LEGENDS <strong>Supplementary Table 1. </strong>Metagenome assembled genome (MAG)-specific information. This dataset lists all MAGs for all included samples and to which MetaMAG each belongs. No MAGs were removed, even poor-quality ones, but CheckM completeness and contamination values are given. MetaMagRelAbund is the relative abundance of the listed MetaMAG based on read mapping of the given sample to all MetaMAGs while RelAbund is the relative abundance based on read mapping to MAGs derived from that sample. TotEET, RedEET, OxiEET, PutEET, MtrB are values generated by the FEET pipeline on every MAG, respectively total, reductive, oxidative, putative, and MtrB EET genes. MtrB is a porin that can be involved in either OxiEET or RedEET. The values to the right of these are for each listed MetaMAG, and are from on the METABOLIC pipeline with the added hidden Markov models for EET genes from the FEET pipeline, but these may not always be counted as an EET gene by FEET rules. <strong>Supplementary Table 2. </strong>Sample-specific information. Sample DNA was sequenced by cited efforts, RTSF Genomics Core at Michigan State University (MSU), or California Institute for Quantitative Biosciences (QB3). All data is available for open access at [insert something]. <strong>Supplementary Table 3. </strong>Electroactive chemical species in Trout Bog Lake. Data are averages from all available samples during 2016–2021.
DOI: 10.6084/m9.figshare.21714602
title: supplemental table 1.docx

description: Associations Between Serum Metabolites and T2D Among Participants Without a Cancer Diagnosis During Follow-Up Period in the ATBC Study
DOI: 10.6084/m9.figshare.21714296
title: Dub-seq Dataset for Adler et al., Multicopy-suppressor screens reveal convergent evolution of single gene lysis proteins

description: Dub-seq dataset for: <br> "Multicopy-suppressor screens reveal convergent evolution of single gene lysis proteins" Adler, BA, Chamakura K, Carion H, Krog J, Deutschbauer AM, Young R, Mutalik VK*, Arkin AP*
DOI: 10.6084/m9.figshare.21714296.v2
title: Dub-seq Dataset for Adler et al., Multicopy-suppressor screens reveal convergent evolution of single gene lysis proteins

description: Dub-seq dataset for: <br> "Multicopy-suppressor screens reveal convergent evolution of single gene lysis proteins" Adler, BA, Chamakura K, Carion H, Krog J, Deutschbauer AM, Young R, Mutalik VK*, Arkin AP*
DOI: 10.6084/m9.figshare.21714296.v1
title: Dub-seq Dataset for Adler et al., Multicopy-suppressor screens reveal convergent evolution of single gene lysis proteins

description: Dub-seq dataset for: <br> "Multicopy-suppressor screens reveal convergent evolution of single gene lysis proteins" Adler, BA, Chamakura K, Carion H, Krog J, Deutschbauer AM, Young R, Mutalik VK*, Arkin AP*
DOI: 10.6084/m9.figshare.21714617
title: Phylogeny of concatenated mtaABC genes

description: Phylogenetic tree of concatenated mtaABC genes in newick format.
DOI: 10.6084/m9.figshare.21714617.v1
title: Phylogeny of concatenated mtaABC genes

description: Phylogenetic tree of concatenated mtaABC genes in newick format.
DOI: 10.6084/m9.figshare.21714608
title: Phylogeny of concatenated mcrABG genes

description: Phylogenetic tree of concatenated mcrABG genes in newick format.
DOI: 10.6084/m9.figshare.21714608.v1
title: Phylogeny of concatenated mcrABG genes

description: Phylogenetic tree of concatenated mcrABG genes in newick format.
DOI: 10.5281/zenodo.7430621
title: Spatiotemporal variability of current and future sub-daily rainfall in Japan using state-of-the-art high-quality datasets

description: Attached are the rainfall return levels based on peaks-over-threshold.
DOI: 10.5281/zenodo.7430620
title: Spatiotemporal variability of current and future sub-daily rainfall in Japan using state-of-the-art high-quality datasets

description: Attached are the rainfall return levels based on peaks-over-threshold.