cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5510035
title: Data for "Unfolding the Structural Stability of Nanoalloys via a Combination of Symmetry-Constrained Genetic Algorithm and Neural Network Potential"

description: PtNi_alloy_eam.db is the dataset (ase.db object) consisting of 55982 intially sampled Pt-Ni alloy structures with EAM energies and forces. PtNi_alloy_dft.db is the dataset (ase.db object) consisting of the final 6828 resampled Pt-Ni alloy structures with DFT energies and forces calculated by VASP. This is the training set for the NNP, and could be very useful for fitting other machine learning models. PtNi_nanoalloy_vertices_nnp.db is the dataset (ase.db object) consisting of all the vertices (stable structures) on the convex hulls obtained from NNP-based SCGA runs on 36 Pt-Ni nanoalloy systems. The energies are given by the NNP. Additional information such as mixing energy, motif and symmetry axis are also saved in the dataset and can be queried by the 'data' keyword. Input_and_scripts.zip provides all the input files and scripts for hybrid MC-MD simulations, QBC resampling, DFT calculations, NNP training, NNP-based SCGA runs and convex hull analysis.
DOI: 10.6084/m9.figshare.16622302
title: Annotation of Acrocephalus scirpaceus genome

description: The softmasked genome assembly of the reed warbler (Acrocephalus scirpaceus) and the softmasked genome assemblies of 9 bird species downloaded from NCBI were used with Mash v. 2.3 to estimate a distance matrix, which was converted into a full matrix and used as input to RapidNJ v. 2.3.2 to create a guide tree based on the neighbour-joining method. Cactus v. 1.3.0 was run with the guide tree and the softmasked genome assemblies as input. We also used Comparative Annotation Toolkit (CAT) v. 2.2.1-36-gfc1623d together with the hierarchical alignment format file from Cactus, with chicken (Gallus gallus) as reference genome, reed warbler as the target genome and the AUGUSTUS species parameter set to ‘chicken’. InterProScan v. 5.34-73 was run on the predicted proteins to find functional annotations, and DIAMOND v. 2.0.7 was used to compare the predicted proteins against UniProtKB/Swiss-Prot release 2021_03. AGAT v. 0.5.3 was used to generate statistics from the GFF3 file with annotations and to add functional annotations from InterProScan and gene names from UniProtKB/Swiss-Prot. We predicted 14,645 protein coding genes.
DOI: 10.5281/zenodo.5510038
title: Can emerging technologies be effective in improving alexithymia due to brain lesion?

description: About 66% of stroke survivors present with cognitive or physical consequences, which are often complicated by emotional instability. Alexithymia is defined as “a difficulty in identifying and describing feelings”, although there is no consensus on the exact diagnosis and treatment. A 36-year-old right-handed man, affected by ischemic stroke (which occurred about 3 months before admission) involving the right hemisphere (ie, the fronto-parieto-temporal region) with left hemiparesis and behavioral abnormalities, came to our observation for intensive rehabilitation. He was treated unsuccessfully with a traditional and behavioral training. Alexithymia due to ischemic stroke. Then, a specific combined protocol using computerized emotional and virtual emotional training was applied in a semi-immersive virtual reality environment using the BTS-Nirvana device. At the end of this novel rehabilitation approach, the patient showed a significant improvement in emotional skills, cognitive performances, and coping strategies. Virtual reality, in addition to standard therapy, may be a valuable tool in improving emotional abnormalities due to brain lesions, such as alexithymia.
DOI: 10.5281/zenodo.5510037
title: Can emerging technologies be effective in improving alexithymia due to brain lesion?

description: About 66% of stroke survivors present with cognitive or physical consequences, which are often complicated by emotional instability. Alexithymia is defined as “a difficulty in identifying and describing feelings”, although there is no consensus on the exact diagnosis and treatment. A 36-year-old right-handed man, affected by ischemic stroke (which occurred about 3 months before admission) involving the right hemisphere (ie, the fronto-parieto-temporal region) with left hemiparesis and behavioral abnormalities, came to our observation for intensive rehabilitation. He was treated unsuccessfully with a traditional and behavioral training. Alexithymia due to ischemic stroke. Then, a specific combined protocol using computerized emotional and virtual emotional training was applied in a semi-immersive virtual reality environment using the BTS-Nirvana device. At the end of this novel rehabilitation approach, the patient showed a significant improvement in emotional skills, cognitive performances, and coping strategies. Virtual reality, in addition to standard therapy, may be a valuable tool in improving emotional abnormalities due to brain lesions, such as alexithymia.
DOI: 10.6084/m9.figshare.16589744
title: Biome effect on phenotypic and genomic differences in the South America marsh rats

description: Scripts and input files used in the paper submitted to the Biological Journal of the Linnean Society:<br>Prado et al. 2021. Biome effect on phenotypic and genomic differences in the South America marsh rats.<br>(1) Niche Similarity<br>Environmental variables can be download from WorldClim (Hijmans et al., 2005) and ENVIREM (Title & Bemmels, 2018).<br>1-Select&Edit_env_variables.R: Select and edit environmental variables for reduction of environmental self-correlation<br>2-Rarefy_points.R: Filter occurrence points for reduction of spatial self-correlation<br>3-ModelComplexity.R: Select the best parameter combination to achieve a balance between goodness‐of‐fit and model complexity<br>4-Cut_model_by_threshold.R: Construct binary maps based on maxent's threshold<br>5-Niche_Similarity.R: Characterize the ecological niche similarity applying two different approaches: (1) the multivariate environmental niche overlap quantified with the ‘PCA-env’ (Broennimann et al., 2012), and (2) the estimation of n-dimensional environmental hypervolume (Hutchinson, 1957; Blonder et al., 2014).<br>(2) Genomic Structure and Bioinformatics<br>6-Create_whitelist_stacks2e.R: Create a whitelist to remove SNP’s positioned at the end of all loci due to an artificially increased number of SNPs observed at these last positions. Also, it removes loci with high theta values (above the 95 percentiles), given these are suggestive of sequencing and assembly errors.<br>7-sumstat.R: Check the genetic diversity summary statistics for significant differences, and plots their means values and standard errors.<br>8-Pop_structure.R: Perform Principal Component Analysis (PCA), Tracy-Widom test, and Mantel test<br>9-moving&best_lhood.R: Move files among folders to facilitate Fastsimcoal analysis<br>(3) Morphometric Structure<br>10-Morphometrics.R: Perform Normality tests, Principal Component Analysis (PCA), Discriminant Analysis, MANOVA, Student's t-test, Mann-Whitney t-test, Boxplots showing means values and standard errors of variables(4) Association between Environment, Genome, and Morphometry<br>11-dbRDA.R: Perfom Distance-based redundancy analyzes (dbRDA; Legendre & Anderson, 1999) to test for an association between environmental variables and genomic and morphometric distance with and without the effect of the geographic distance
DOI: 10.5281/zenodo.5510042
title: Dataset gathered in HLU6 – UC02 (TC03) - CROSSBOW PROJECT

description: Monitored voltages (kV), active power (MW) and reactive power(MVAr).
DOI: 10.5281/zenodo.5510041
title: Dataset gathered in HLU6 – UC02 (TC03) - CROSSBOW PROJECT

description: Monitored voltages (kV), active power (MW) and reactive power(MVAr).
DOI: 10.5281/zenodo.5233380
title: Detecting Hogweed on the Ground-Level View Photographs: Dataset

description: Semantic segmentation highlighting Sosnowsky's hogweed on ground-level view images. Photographic images are hosted on Zenodo. COCO-formatted (*.json) polygons are to be published on Github: https://github.com/alexeyev/hogweed-ground-level-view
DOI: 10.5281/zenodo.5233379
title: Detecting Hogweed on the Ground-Level View Photographs: Dataset

description: Semantic segmentation highlighting Sosnowsky's hogweed on ground-level view images. Photographic images are hosted on Zenodo. COCO-formatted (*.json) polygons are to be published on Github: https://github.com/alexeyev/hogweed-ground-level-view
DOI: 10.5281/zenodo.5510045
title: Data and code for analysis in "Fighting over defence chemicals disrupts mating behaviour"

description: Data and annotated code for analysis in "Fighting over defence chemicals disrupts mating behaviour". The point at which each data sheet is used in the analysis is specified in the code and code for each respective figure in paper is also given. A renv lockfile is also included for version control, but all package versions are also included in paper's methods section.
description: Notes on new version: Minor edits were made to code between the second and third versions, to increase resolution of figures and to improve the future accessibility of code.
DOI: 10.5281/zenodo.4537746
title: Data and code for analysis in "Fighting over defence chemicals disrupts mating behaviour"

description: Data and annotated code for analysis in "Fighting over defence chemicals disrupts mating behaviour". The point at which each data sheet is used in the analysis is specified in the code and code for each respective figure in paper is also given. A renv lockfile is also included for version control, but all package versions are also included in paper's methods section.
description: Notes on new version: Minor edits were made to code between the second and third versions, to increase resolution of figures and to improve the future accessibility of code.
DOI: 10.5281/zenodo.5508747
title: Dataset related to the publication "Thermal properties of nanocrystalline silicon nanobeams", DOI: 10.1002/adfm.202105767

description: This folder contains the raw data from which the graphs in paper "Thermal properties of nanocrystalline silicon nanobeams", DOI: 10.1002/adfm.202105767, have been obtained.
DOI: 10.5281/zenodo.5508746
title: Dataset related to the publication "Thermal properties of nanocrystalline silicon nanobeams", DOI: 10.1002/adfm.202105767

description: This folder contains the raw data from which the graphs in paper "Thermal properties of nanocrystalline silicon nanobeams", DOI: 10.1002/adfm.202105767, have been obtained.
DOI: 10.5281/zenodo.3958784
title: Differences in carbon acquisition could explain adaptive responses in a Baltic Sea pico-phytoplankton

description: The data uploaded are the basis of study on the carbon update in a Baltic Sea Pico-plankton species. Our study addresses a challenging question concerning the adaptive responses to warming and carbon uptake related strategies in a pico-phytoplankton species, which are, unlike bloom-forming, larger phytoplankton, contributing to the carbon cycle and the base of food-webs all year round. In addition, we address this question also in non-exponential growth conditions. This is important considering that most phytoplankton species are likely not at exponential phase all the time. We show that space for time substitution experiments provide a valid method for investigating questions about the adaptive potential in pico-phytoplankton that the measurements of potential growth on organic carbon sources can potentially highlight differences in carbon acquisition strategies.
DOI: 10.5281/zenodo.3958783
title: Differences in carbon acquisition could explain adaptive responses in a Baltic Sea pico-phytoplankton

description: The data uploaded are the basis of study on the carbon update in a Baltic Sea Pico-plankton species. Our study addresses a challenging question concerning the adaptive responses to warming and carbon uptake related strategies in a pico-phytoplankton species, which are, unlike bloom-forming, larger phytoplankton, contributing to the carbon cycle and the base of food-webs all year round. In addition, we address this question also in non-exponential growth conditions. This is important considering that most phytoplankton species are likely not at exponential phase all the time. We show that space for time substitution experiments provide a valid method for investigating questions about the adaptive potential in pico-phytoplankton that the measurements of potential growth on organic carbon sources can potentially highlight differences in carbon acquisition strategies.
DOI: 10.5281/zenodo.5510104
title: Dataset gathered in HLU6 – UC05 (TC04) - CROSSBOW PROJECT

description: Monitored voltages (kV), active power (MW) and reactive power(MVAr).
DOI: 10.5281/zenodo.5510103
title: Dataset gathered in HLU6 – UC05 (TC04) - CROSSBOW PROJECT

description: Monitored voltages (kV), active power (MW) and reactive power(MVAr).
DOI: 10.5281/zenodo.5510098
title: The Arizona Ring Experiments Dataset

description: This dataset comes from experiments done with 20 vehicles at Arizona State in a test similar to the famous Sugiyama experiment on vehicle waves smoothing.
DOI: 10.5281/zenodo.5510097
title: The Arizona Ring Experiments Dataset

description: This dataset comes from experiments done with 20 vehicles at Arizona State in a test similar to the famous Sugiyama experiment on vehicle waves smoothing.
DOI: 10.5281/zenodo.5510102
title: Agregación familiar para Asma bronquial y factores de riesgo

description: Base de datos
DOI: 10.15131/shef.data.15082455
title: Low Excess Noise of Al0.85Ga0.15As0.56Sb0.44 Avalanche Photodiode from Pure Electron Injection

description: The files correspond to experimental results in paper: <b>Low Excess Noise of Al0.85Ga0.15As0.56Sb0.44 Avalanche Photodiode from Pure Electron Injection</b><br>There are two types of files:- .png which correspond to the figures- .csv, which are raw data in figures and tables<br>This work presents gain and excess noise data for Al0.85Ga0.15As0.56Sb0.44 p-i-n with an i-region of 600 nm for pure electron and two mixed injection profiles. <br><br><br><br>J. Taylor-Mew, V. Shulyak, B. White, C. H. Tan and J. S. Ng, "Low Excess Noise of Al<sub>0.85</sub>Ga<sub>0.15</sub>As<sub>0.56</sub>Sb<sub>0.44</sub> Avalanche Photodiode From Pure Electron Injection," in <em>IEEE Photonics Technology Letters</em>, vol. 33, no. 20, pp. 1155-1158, Oct.15, 15 2021, doi: 10.1109/LPT.2021.3110123.<br>
DOI: 10.15131/shef.data.15082455.v1
title: Low Excess Noise of Al0.85Ga0.15As0.56Sb0.44 Avalanche Photodiode from Pure Electron Injection

description: The files correspond to experimental results in paper: <b>Low Excess Noise of Al0.85Ga0.15As0.56Sb0.44 Avalanche Photodiode from Pure Electron Injection</b><br>There are two types of files:- .png which correspond to the figures- .csv, which are raw data in figures and tables<br>This work presents gain and excess noise data for Al0.85Ga0.15As0.56Sb0.44 p-i-n with an i-region of 600 nm for pure electron and two mixed injection profiles. <br><br><br><br>J. Taylor-Mew, V. Shulyak, B. White, C. H. Tan and J. S. Ng, "Low Excess Noise of Al<sub>0.85</sub>Ga<sub>0.15</sub>As<sub>0.56</sub>Sb<sub>0.44</sub> Avalanche Photodiode From Pure Electron Injection," in <em>IEEE Photonics Technology Letters</em>, vol. 33, no. 20, pp. 1155-1158, Oct.15, 15 2021, doi: 10.1109/LPT.2021.3110123.<br>
DOI: 10.5281/zenodo.5510121
title: Advances in the rehabilitation of intensive care unit acquired weakness

description: Traditional physiotherapy is currently the best approach to manage patients with intensive care unit acquired weakness (ICUAW). We report on a patient with ICUAW, who was provided with an intensive, in-patient regimen, that is, conventional plus robot-assisted physiotherapy. Aim of this case study was to assess the efficacy of a combined approach (conventional plus robot-assisted physiotherapy), on muscle strength, overall mobility, and disability burden in a patient with ICUAW in post-ICU intensive rehabilitation setting. Patient concerns: A 56-years-old male who was unable to stand and walk independently after hospitalization in an Intensive Care Unit. He initially was provided with daily sessions of conventional physiotherapy for 2 months, with mild results. The patient was affected by ICUAW. Given that the patient showed a relatively limited improvement after conventional physiotherapy, he was provided with daily sessions of robot-aided training for upper and lower limbs and virtual reality-aided rehabilitation for other 4 months, beyond conventional physiotherapy. At the discharge (6 months after the admission), the patient reached the standing station and was able to ambulate with double support. Our case suggests that patients with ICUAW should be intensively treated in in-patient regimen with robot-aided physiotherapy. Even though our approach deserves confirmation, the combined rehabilitation strategy may offer some advantage in maximizing functional recovery and containing disability.
DOI: 10.5281/zenodo.5510120
title: Advances in the rehabilitation of intensive care unit acquired weakness

description: Traditional physiotherapy is currently the best approach to manage patients with intensive care unit acquired weakness (ICUAW). We report on a patient with ICUAW, who was provided with an intensive, in-patient regimen, that is, conventional plus robot-assisted physiotherapy. Aim of this case study was to assess the efficacy of a combined approach (conventional plus robot-assisted physiotherapy), on muscle strength, overall mobility, and disability burden in a patient with ICUAW in post-ICU intensive rehabilitation setting. Patient concerns: A 56-years-old male who was unable to stand and walk independently after hospitalization in an Intensive Care Unit. He initially was provided with daily sessions of conventional physiotherapy for 2 months, with mild results. The patient was affected by ICUAW. Given that the patient showed a relatively limited improvement after conventional physiotherapy, he was provided with daily sessions of robot-aided training for upper and lower limbs and virtual reality-aided rehabilitation for other 4 months, beyond conventional physiotherapy. At the discharge (6 months after the admission), the patient reached the standing station and was able to ambulate with double support. Our case suggests that patients with ICUAW should be intensively treated in in-patient regimen with robot-aided physiotherapy. Even though our approach deserves confirmation, the combined rehabilitation strategy may offer some advantage in maximizing functional recovery and containing disability.
DOI: 10.5066/p9ra15i0
title: Barrier island vegetation and elevation survey, Dauphin Island, AL, 2018-19

description: Vegetation and elevation survey data were collected in 4-square-meter quadrats via Real-Time Kinematic GPS from September 9, 2018 to April 17, 2019 on Dauphin Island, AL. Vegetation data included total percent herbaceous cover, percent cover by plant species, and mean height of vegetation within the quadrat. The percent cover by species was used to determine the dominant species for the plot.
DOI: 10.25375/uct.14464716
title: Gross Replacement Ratio Financial Model

description: This metadata record relates to a dataset that contains a financial model to calculate the gross replacement ratio for a sample of individuals with varying ages, marital status, salaries and salary increases. <br><br>The financial model utilises verifiable external input assumptions to forecast what the gross replacement ratio of an individual will be in retirement. <br><br>The financial model is available on request from the researchers as detailed per the below email addresses:<br>1. Author’s email address – mitbir13@gmail.com or brdmit001@myuct.ac.za<br>2. Supervisor’s email address – gizelle.willows@uct.ac.za<br><br>A private, secure ZivaHub download link for the data will be provided to the requestor.
DOI: 10.25375/uct.14464716.v1
title: Gross Replacement Ratio Financial Model

description: This metadata record relates to a dataset that contains a financial model to calculate the gross replacement ratio for a sample of individuals with varying ages, marital status, salaries and salary increases. <br><br>The financial model utilises verifiable external input assumptions to forecast what the gross replacement ratio of an individual will be in retirement. <br><br>The financial model is available on request from the researchers as detailed per the below email addresses:<br>1. Author’s email address – mitbir13@gmail.com or brdmit001@myuct.ac.za<br>2. Supervisor’s email address – gizelle.willows@uct.ac.za<br><br>A private, secure ZivaHub download link for the data will be provided to the requestor.
DOI: 10.6084/m9.figshare.14637450
title: Supplementary Files

description: Supplementary Microsoft Excel files containing extended data that is referenced in the text.<br>These include:<b>File 1</b>: Select proteins’ 30MY ERC lists, contains multiple-test corrected p-values. <b>File 2</b>: Pairwise ρ and unadjusted p-value 30MY ERC matrices for all proteins. <b>File 3</b>: Enrichment results for select top ERC protein sets. <b>File 4</b>: Zip file containing the mammalian time-scaled phylogeny and maximum likelihood protein trees in newick format. <b>File 5</b>: Table depicting the total number of taxa present for each protein’s sequence data, along with the number of taxa for which there are paralogy in the uncorrected and 30MY corrected data. <b>File 6</b>: Branch time to terminal branch rate correlation results for the protein set. <b>File 7</b>: Chi-squared test results for all proteins testing for whether there is an overrepresentation of rates below the regression line for short branches (&lt;30MY). <b>File 8</b>: Branch time vs terminal branch rate residuals to branch time correlation results for the protein set. <b>File 9</b>: Wilcoxon matched signed-rank test significance values testing for branch adjustments following 20MY and 30MY adjustments. <b>File 10</b>: Coefficients for the select proteins used for the linear models containing ACE2 rate rank, Btime rate rank, and taxonomic orders as independent variables. <b>File 11</b>: 30MY-adjusted ERC comparisons within and between CORUM complex members.
DOI: 10.6084/m9.figshare.14637450.v3
title: Supplementary Files

description: Supplementary Microsoft Excel files containing extended data that is referenced in the text.<br>These include:<b>File 1</b>: Select proteins’ 30MY ERC lists, contains multiple-test corrected p-values. <b>File 2</b>: Pairwise ρ and unadjusted p-value 30MY ERC matrices for all proteins. <b>File 3</b>: Enrichment results for select top ERC protein sets. <b>File 4</b>: Zip file containing the mammalian time-scaled phylogeny and maximum likelihood protein trees in newick format. <b>File 5</b>: Table depicting the total number of taxa present for each protein’s sequence data, along with the number of taxa for which there are paralogy in the uncorrected and 30MY corrected data. <b>File 6</b>: Branch time to terminal branch rate correlation results for the protein set. <b>File 7</b>: Chi-squared test results for all proteins testing for whether there is an overrepresentation of rates below the regression line for short branches (&lt;30MY). <b>File 8</b>: Branch time vs terminal branch rate residuals to branch time correlation results for the protein set. <b>File 9</b>: Wilcoxon matched signed-rank test significance values testing for branch adjustments following 20MY and 30MY adjustments. <b>File 10</b>: Coefficients for the select proteins used for the linear models containing ACE2 rate rank, Btime rate rank, and taxonomic orders as independent variables. <b>File 11</b>: 30MY-adjusted ERC comparisons within and between CORUM complex members.