cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5670268
title: Dataset from paper "Canopy palm cover across the Brazilian Amazon forests mapped with airborne LiDAR data and deep learning"

description: <strong>Data and code from the paper:</strong> Dalagnol, R., Wagner, F. H., Emilio, T., Streher, A. S., Galvão, L. S., Ometto, J. P. H. B., & Aragão, L. E. O. C. (2022). Canopy palm cover across the Brazilian Amazon forests mapped with airborne LiDAR data and deep learning. Remote Sensing in Ecology and Conservation, 1–14. https://doi.org/10.1002/rse2.264 <strong>Link:</strong> https://doi.org/10.1002/rse2.264 <strong>This repository contains:</strong> <strong>1) model_train.R:</strong> This is the code to run the U-Net model in R language. <strong>2) input.rar:</strong> Dataset of lidar canopy height model (CHM) images and masks (labels) patches of canopy palms obtained from four sites in the Brazilian Amazon. The images/masks have 128 x 128 pixels, where each pixel represents 0.5 m in the terrain. The dataset contains 2,269 images and masks, with close to 7,000 palms manually labelled. <strong>3) unet_weights_best.h5:</strong> These are the best weights for the U-Net architecture achieved in the paper. <strong>4) palm_stats.RData:</strong> Data frame with the lat/lon coordinates and palm metrics extracted for the 610 lidar sites in the Brazilian Amazon. (i) n_total is the number of palms, (ii) n_ha is the density of palms per hectare, (iii) crown_ metrics are based on the area of palm segments (in square meters), (iv) cover_total is the total area occupied by palms in the forest canopy (in square meters), (v) cover_rel is the relative cover of palms in the forest canopy (in percentage), (vi) height_ metrics are based on the height of palm segments (in meters), (vii) palm_height_dif_mean is the mean difference between palm height and local canopy height, and (viii) palm_height_dif_pvalue is the p-value assessing the statistical difference between the palm and canopy heights where 0 means no difference and -1/+1 means a negative/positive difference. If you need anything else, please contact the corresponding author: Ricardo Dalagnol (ricds@hotmail.com). <strong>If you use these data, please cite the paper:</strong> Dalagnol, R., Wagner, F. H., Emilio, T., Streher, A. S., Galvão, L. S., Ometto, J. P. H. B., & Aragão, L. E. O. C. (2022). Canopy palm cover across the Brazilian Amazon forests mapped with airborne LiDAR data and deep learning. Remote Sensing in Ecology and Conservation, 1–14. https://doi.org/10.1002/rse2.264
DOI: 10.5281/zenodo.5670267
title: Dataset from paper "Canopy palm cover across the Brazilian Amazon forests mapped with airborne LiDAR data and deep learning"

description: <strong>Data and code from the paper:</strong> Dalagnol, R., Wagner, F. H., Emilio, T., Streher, A. S., Galvão, L. S., Ometto, J. P. H. B., & Aragão, L. E. O. C. (2022). Canopy palm cover across the Brazilian Amazon forests mapped with airborne LiDAR data and deep learning. Remote Sensing in Ecology and Conservation, 1–14. https://doi.org/10.1002/rse2.264 <strong>Link:</strong> https://doi.org/10.1002/rse2.264 <strong>This repository contains:</strong> <strong>1) model_train.R:</strong> This is the code to run the U-Net model in R language. <strong>2) input.rar:</strong> Dataset of lidar canopy height model (CHM) images and masks (labels) patches of canopy palms obtained from four sites in the Brazilian Amazon. The images/masks have 128 x 128 pixels, where each pixel represents 0.5 m in the terrain. The dataset contains 2,269 images and masks, with close to 7,000 palms manually labelled. <strong>3) unet_weights_best.h5:</strong> These are the best weights for the U-Net architecture achieved in the paper. <strong>4) palm_stats.RData:</strong> Data frame with the lat/lon coordinates and palm metrics extracted for the 610 lidar sites in the Brazilian Amazon. (i) n_total is the number of palms, (ii) n_ha is the density of palms per hectare, (iii) crown_ metrics are based on the area of palm segments (in square meters), (iv) cover_total is the total area occupied by palms in the forest canopy (in square meters), (v) cover_rel is the relative cover of palms in the forest canopy (in percentage), (vi) height_ metrics are based on the height of palm segments (in meters), (vii) palm_height_dif_mean is the mean difference between palm height and local canopy height, and (viii) palm_height_dif_pvalue is the p-value assessing the statistical difference between the palm and canopy heights where 0 means no difference and -1/+1 means a negative/positive difference. If you need anything else, please contact the corresponding author: Ricardo Dalagnol (ricds@hotmail.com). <strong>If you use these data, please cite the paper:</strong> Dalagnol, R., Wagner, F. H., Emilio, T., Streher, A. S., Galvão, L. S., Ometto, J. P. H. B., & Aragão, L. E. O. C. (2022). Canopy palm cover across the Brazilian Amazon forests mapped with airborne LiDAR data and deep learning. Remote Sensing in Ecology and Conservation, 1–14. https://doi.org/10.1002/rse2.264
DOI: 10.5203/41y3-8k25
title: canada-and-lake-winnipeg-watershed-basemap-layers
DOI: 10.5203/883p-ts43
title: aafc-crop-type-map-of-canada-ag-canada-crop-inventory
DOI: 10.6084/m9.figshare.16451625
title: Object classification on video data of meteors and meteor-like phenomena: algorithm and data (NightSkyUCP Dataset)

description: Every moment, countless meteoroids enter our atmosphere unseen. The detection and measurement of meteors offer the unique opportunity to gain insights into the composition of our solar systems' celestial bodies. Researchers, therefore, carry out a wide-area-sky-monitoring to secure 360-degree video material, saving every single entry of a meteor. Existing machine intelligence cannot accurately recognize events of meteors intersecting the earth's atmosphere due to a lack of high-quality training data publicly available. This work presents four reusable open source solutions for researchers trained on data we collected due to the lack of available labeled high-quality training data. We refer to the proposed dataset as the NightSkyUCP dataset, consisting \hl{of 10,000 meteor- and 10,000 non-meteor-events summing up to} 20,000 events. Our solutions apply various machine learning techniques, namely classification, feature learning, anomaly detection, and extrapolation. For the balanced classification task, a mean accuracy of 99.1% is achieved..
DOI: 10.5258/soton/d1636
title: Retrospective Study of MED-EL Cochlear Implant Electrode Impedance from the University of Southampton Auditory Implant Service

description: This dataset supports the thesis entitled: Translational Approaches to Measurement and Analysis of the Cochlear Implant-Tissue Interface. Dataset includes electrode impedance measurements and electrode activation status made by telemetry during routine clinic sessions with cochlear implant patients at the University of Southampton Auditory Implant Service Data was exported from Med-El Maestro as a database file. The database was opened using Microsoft Access A custom MS Access query was used to output the ‘electrode impedance’ and the ‘electrode activation status’ This raw data is contained in the below files within the worksheets titled ‘Arranging’ The data is separated into different worksheets corresponding to 12 electrodes The data can be viewed in MS Excel Processing and plotting of the data described in Sanderson et al, 2019 (https://doi.org/10.3389/fnins.2018.01048) was performed using Mathworks Matlab
DOI: 10.6084/m9.figshare.20403023.v1
title: Eletronic_supp_mat.zip from Climate, immigration and speciation shape terrestrial and aquatic biodiversity in the European Alps

description: Quaternary climate fluctuations can affect speciation in regional biodiversity assembly in two non-mutually exclusive ways: a glacial species pump, where isolation in glacial refugia accelerates allopatric speciation, and adaptive radiation in underused adaptive zones during ice-free periods. We detected biogeographic and genetic signatures associated with both mechanisms in the assembly of the biota of the European Alps. Age distributions of endemic and widespread species within aquatic and terrestrial taxa (amphipods, fishes, amphibians, butterflies and flowering plants) revealed that endemic fish evolved only in lakes, are highly sympatric, and mainly of Holocene age, consistent with adaptive radiation. Endemic amphipods are ancient, suggesting preglacial radiation with limited range expansion and local Pleistocene survival, perhaps facilitated by a groundwater-dwelling lifestyle. Terrestrial endemics are mostly of Pleistocene age and are thus more consistent with the glacial species pump. The lack of evidence for Holocene adaptive radiation in the terrestrial biome is consistent with faster recolonization through range expansion of these taxa after glacial retreats. More stable and less seasonal ecological conditions in lakes during the Holocene may also have contributed to Holocene speciation in lakes. The high proportion of young, endemic species makes the Alpine biota vulnerable to climate change, but the mechanisms and consequences of species loss will likely differ between biomes because of their distinct evolutionary histories.
DOI: 10.6084/m9.figshare.20403023
title: Eletronic_supp_mat.zip from Climate, immigration and speciation shape terrestrial and aquatic biodiversity in the European Alps

description: Quaternary climate fluctuations can affect speciation in regional biodiversity assembly in two non-mutually exclusive ways: a glacial species pump, where isolation in glacial refugia accelerates allopatric speciation, and adaptive radiation in underused adaptive zones during ice-free periods. We detected biogeographic and genetic signatures associated with both mechanisms in the assembly of the biota of the European Alps. Age distributions of endemic and widespread species within aquatic and terrestrial taxa (amphipods, fishes, amphibians, butterflies and flowering plants) revealed that endemic fish evolved only in lakes, are highly sympatric, and mainly of Holocene age, consistent with adaptive radiation. Endemic amphipods are ancient, suggesting preglacial radiation with limited range expansion and local Pleistocene survival, perhaps facilitated by a groundwater-dwelling lifestyle. Terrestrial endemics are mostly of Pleistocene age and are thus more consistent with the glacial species pump. The lack of evidence for Holocene adaptive radiation in the terrestrial biome is consistent with faster recolonization through range expansion of these taxa after glacial retreats. More stable and less seasonal ecological conditions in lakes during the Holocene may also have contributed to Holocene speciation in lakes. The high proportion of young, endemic species makes the Alpine biota vulnerable to climate change, but the mechanisms and consequences of species loss will likely differ between biomes because of their distinct evolutionary histories.
DOI: 10.6084/m9.figshare.20403099
title: Results of the proteomic analysys V. coccineum;Results of the proteomic analysys V. vulpecula;Proteomic search database V. coccineum;Proteomic search database V. vulpecula from Vexitoxins: conotoxin-like venom peptides from predatory gastropods of the genus <i>Vexillum</i>

description: peptides predicted from monoisotopic masses aligned to the database entries;peptides predicted from monoisotopic masses aligned to the database entries;fasta file with transcripts of interest used for proteomic search;fasta file with transcripts of interest used for proteomic search
DOI: 10.6084/m9.figshare.20403099.v1
title: Results of the proteomic analysys V. coccineum;Results of the proteomic analysys V. vulpecula;Proteomic search database V. coccineum;Proteomic search database V. vulpecula from Vexitoxins: conotoxin-like venom peptides from predatory gastropods of the genus <i>Vexillum</i>

description: peptides predicted from monoisotopic masses aligned to the database entries;peptides predicted from monoisotopic masses aligned to the database entries;fasta file with transcripts of interest used for proteomic search;fasta file with transcripts of interest used for proteomic search
DOI: 10.5258/soton/d1650
title: Dataset supporting the thesis entitled "Developing a Framework for an Adaptive Transtibial Prosthetic Socket using FEA-based Tissue Injury Risk Estimation and Generalised Predictive Control"

description: Raw data behind simulations and figures for the thesis entitled "Developing a Framework for an Adaptive Transtibial Prosthetic Socket using FEA-based Tissue Injury Risk Estimation and Generalised Predictive Control", University of Southampton, 2020
DOI: 10.6084/m9.figshare.16955531
title: Runs of homozygosity analysis reveals population characteristics of yellow-feathered chickens using re-sequencing data

description: 1. To evaluate the inbreeding of yellow-feathered chickens (YFCs) and identify genes related to their unique characteristics, whole-genome re-sequencing data were applied to detect runs of homozygosity (ROH) in the genomes of 10 YFC chickens from each of 10 different YFC breeds. The number, length, distribution of ROH, and inbreeding coefficient in different YFC populations were calculated. Genomic regions with high frequency in ROH were annotated. 2. In total, 25,547 ROH with an average length of 335 kb were detected, with most being &lt;1 Mb. The domination of short ROH reflected the long breeding history of this chicken. The number, length, frequency, and distribution of ROH varied among chicken populations, and high genetic diversity was maintained. 3. Numerous genes related to YFC characteristics were identified in the high-frequency ROH regions. Among these, <i>IFNA, IFNB, IL11 RA, IL22 RA1, IFNLR1</i>, and <i>TRIF</i> genes were involved in disease resistance. The <i>AMY, G6PC, SDHB, GCNT4</i>, and <i>ACO</i> genes were associated with energy material metabolism; and <i>FABPL, AQP7, ACAA2</i>, and <i>RYR2</i> were related to meat quality and flavour. The <i>KITLG, CREB3, RYR2</i>, and <i>LGR4</i> genes, related to pigmentation, were detected. 4. This ROH-based inbreeding evaluation lays the foundation for breeding and conservation of YFC populations, and the candidate genes identified can be used for marker-assisted selection.
DOI: 10.6084/m9.figshare.16955531.v2
title: Runs of homozygosity analysis reveals population characteristics of yellow-feathered chickens using re-sequencing data

description: 1. To evaluate the inbreeding of yellow-feathered chickens (YFCs) and identify genes related to their unique characteristics, whole-genome re-sequencing data were applied to detect runs of homozygosity (ROH) in the genomes of 10 YFC chickens from each of 10 different YFC breeds. The number, length, distribution of ROH, and inbreeding coefficient in different YFC populations were calculated. Genomic regions with high frequency in ROH were annotated. 2. In total, 25,547 ROH with an average length of 335 kb were detected, with most being &lt;1 Mb. The domination of short ROH reflected the long breeding history of this chicken. The number, length, frequency, and distribution of ROH varied among chicken populations, and high genetic diversity was maintained. 3. Numerous genes related to YFC characteristics were identified in the high-frequency ROH regions. Among these, <i>IFNA, IFNB, IL11 RA, IL22 RA1, IFNLR1</i>, and <i>TRIF</i> genes were involved in disease resistance. The <i>AMY, G6PC, SDHB, GCNT4</i>, and <i>ACO</i> genes were associated with energy material metabolism; and <i>FABPL, AQP7, ACAA2</i>, and <i>RYR2</i> were related to meat quality and flavour. The <i>KITLG, CREB3, RYR2</i>, and <i>LGR4</i> genes, related to pigmentation, were detected. 4. This ROH-based inbreeding evaluation lays the foundation for breeding and conservation of YFC populations, and the candidate genes identified can be used for marker-assisted selection.
DOI: 10.6084/m9.figshare.16955534
title: The potential effect of microbiota in predicting the freshness of chilled chicken

description: 1. The goals of this study were to analyse the changes in microbiota composition of chilled chicken during storage and identify microbial biomarkers related to meat freshness. 2. The study used 16S rDNA sequencing to track the microbiota shift in chilled chicken during storage. Associations between microbiota composition and storage time were analysed and microbial biomarkers were identified. 3. The results showed that microbial diversity of chilled chicken decreased with the storage time. A total of 27 and 24 microbial biomarkers were identified by using orthogonal partial least squares (OPLS) and the random forest regression approach, respectively. The receiver operating characteristic (ROC) curve analysis indicated that the OPLS regression approach had better performance in identifying freshness-related biomarkers. The multiple stepwise regression analysis identified four key microbial biomarkers, including <i>Streptococcus, Carnobacterium, Serratia</i> and <i>Photobacterium</i> genera and constructed a predictive model. 4. The study provided microbial biomarkers and a model related to the freshness of chilled chicken. These findings provide a basis for developing detection methods of the freshness of chilled chicken.
DOI: 10.6084/m9.figshare.16661108.v2
title: Transcriptome analysis of oviduct in laying ducks under different stocking densities

description: 1. High stocking densities can lead to animal stress responses and lead to changes in bird behaviour, egg production and the fertility of laying birds. The oviduct plays a crucial role during the process of laying eggs. Therefore, it is essential to know how high stocking density affects oviduct function. 2. In this study, a total of 2,115 differentially expressed genes (DEGs) were identified in duck oviduct tissues between different stocking density groups. These genes are mainly enriched in membrane components, calcium ion binding, cytokine-cytokine receptor interaction and focal adhesion. These pathways were closely related to the formation of eggs. This indicated that secretion and material transport functions of the oviduct are affected under high-density stocking. Further analysis showed that a total of 408 genes related to the transportation process were expressed in the oviduct, of which 96 genes were differentially expressed (LogFC≥1, P &lt; 0.05). Forty-two of these DEGs belonged to the solute carrier family. The data showed that the expression of 31 transcripts was different between the two density groups. Expression of <i>KCNJ15, SLC26A8</i>, and <i>TRPM5</i> was only seen in the high-density group (8/m<sup>2</sup>), while <i>ATP13A3</i> and <i>KCNIP2</i> were only expressed in the low-density group (4/m<sup>2</sup>). 3. Consequently, high stocking density may affect the expression and splicing of genes related to molecular transport in the oviduct.
DOI: 10.6084/m9.figshare.16955534.v2
title: The potential effect of microbiota in predicting the freshness of chilled chicken

description: 1. The goals of this study were to analyse the changes in microbiota composition of chilled chicken during storage and identify microbial biomarkers related to meat freshness. 2. The study used 16S rDNA sequencing to track the microbiota shift in chilled chicken during storage. Associations between microbiota composition and storage time were analysed and microbial biomarkers were identified. 3. The results showed that microbial diversity of chilled chicken decreased with the storage time. A total of 27 and 24 microbial biomarkers were identified by using orthogonal partial least squares (OPLS) and the random forest regression approach, respectively. The receiver operating characteristic (ROC) curve analysis indicated that the OPLS regression approach had better performance in identifying freshness-related biomarkers. The multiple stepwise regression analysis identified four key microbial biomarkers, including <i>Streptococcus, Carnobacterium, Serratia</i> and <i>Photobacterium</i> genera and constructed a predictive model. 4. The study provided microbial biomarkers and a model related to the freshness of chilled chicken. These findings provide a basis for developing detection methods of the freshness of chilled chicken.
DOI: 10.6084/m9.figshare.16661108
title: Transcriptome analysis of oviduct in laying ducks under different stocking densities

description: 1. High stocking densities can lead to animal stress responses and lead to changes in bird behaviour, egg production and the fertility of laying birds. The oviduct plays a crucial role during the process of laying eggs. Therefore, it is essential to know how high stocking density affects oviduct function. 2. In this study, a total of 2,115 differentially expressed genes (DEGs) were identified in duck oviduct tissues between different stocking density groups. These genes are mainly enriched in membrane components, calcium ion binding, cytokine-cytokine receptor interaction and focal adhesion. These pathways were closely related to the formation of eggs. This indicated that secretion and material transport functions of the oviduct are affected under high-density stocking. Further analysis showed that a total of 408 genes related to the transportation process were expressed in the oviduct, of which 96 genes were differentially expressed (LogFC≥1, P &lt; 0.05). Forty-two of these DEGs belonged to the solute carrier family. The data showed that the expression of 31 transcripts was different between the two density groups. Expression of <i>KCNJ15, SLC26A8</i>, and <i>TRPM5</i> was only seen in the high-density group (8/m<sup>2</sup>), while <i>ATP13A3</i> and <i>KCNIP2</i> were only expressed in the low-density group (4/m<sup>2</sup>). 3. Consequently, high stocking density may affect the expression and splicing of genes related to molecular transport in the oviduct.
DOI: 10.6084/m9.figshare.9119975
title: The Optimal Packing of Eight Points in the Real Projective Plane

description: How can we arrange <i>n</i> lines through the origin in three-dimensional Euclidean space in a way that maximizes the minimum interior angle between pairs of lines? Conway, Hardin, and Sloane (1996) produced line packings for n≤55 that they conjectured to be within numerical precision of optimal in this sense, but until now only the cases n≤7 have been solved. In this paper, we resolve the case <i>n</i> = 8. Drawing inspiration from recent work on the Tammes problem, we enumerate contact graph candidates for an optimal configuration and eliminate those that violate various combinatorial and geometric necessary conditions. The contact graph of the putatively optimal numerical packing of Conway, Hardin, and Sloane is the only graph that survives, and we recover from this graph an exact expression for the minimum distance of eight optimally packed points in the real projective plane.
DOI: 10.5281/zenodo.6918220
title: Data files associated with the article entitled: "High-throughput behavioral phenotyping of tiny arthropods: chemosensory traits in a mesostigmatic hematophagous mite" (submitted)

description: Here are provided three groups of datasets, corresponding respectively to the data obtained from MiteMap bioassays (1) with the monomolecular reference substances (geraniol and NH<sub>3</sub>), (2) with the patented blend MIX1.0, (3) with the odors emitted by the mites' bodies. These datasets were analyzed using the script provided in RMarkdown format in the Zenodo repository DOI 10.5281/zenodo.6109388. A folder is also provided with the heatmaps associated with these data grouped in subfolders by farm x modality.