cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/5rz4sy44zt
title: Data for: Investigating the Effects of Tree Species Diversity and Relative Density on Bird Species Richness with Acoustic Indices

description: Mixed-species forest stands may provide suitable habitats for a greater number of bird species than tree monocultures by increasing the number of niches and resources available. However, assessing the effects of forest diversity on birds over time and across multiple sites using traditional survey methods can be expensive, time-consuming and impractical. 
We used passive acoustic monitoring (PAM) and acoustic indices to investigate how tree species diversity, relative density, and other plot characteristics affect the species richness of avian communities in temperate forests. Acoustic surveys were conducted in the Hainich National Park, Germany, using plots which differed in tree species diversity and relative species density. 
Of the five acoustic indices assessed, the normalised difference soundscape index (NDSI), the acoustic complexity index (ACI) and bioacoustic index (BI) performed best in separating biophony from other soundscape elements whereas the acoustic evenness index (AEI) and temporal entropy (Ht) were biased towards geophony, anthrophony and silence. NDSI, ACI and BI displayed significant positive relationships with bird species richness but NDSI plateaued at 5 bird species. 
Plot tree species diversity had significant positive effects on ACI and BI during dawn, dusk and daytime periods. Increased basal area of sycamore (Acer pseudoplatanus) and, to a lesser degree, beech (Fagus sylvatica), had a negative effect on acoustic indices. These results could potentially be due to the earlier leaf out timings of these tree species in relation to the dates when surveys were performed. While the use of PAM and acoustic indices enabled surveys across multiple sites over longer time periods than would previously have been achievable, our results show that care should be taken when selecting the indices and interpreting acoustic index results.

Article data: This folder contains data files associated with the published article and appendices. Excel files contain ACI and BI values that were calculated for the individual audio files recorded in each plot that were used in analyses. Median values for each time period are also included. 
Audio files provided were used to assess acoustic index bias towards soundscape elements other than bird vocalizations, relationships between acoustic index values and bird species richness (Appendix B), and the effect that distance between source and receiver had on acoustic index values (Appendix C).
DOI: 10.17632/nks3nchhm4
title: COVID-19 - Student Paramedics PPE Dataset
DOI: 10.4121/13173422.v3
title: Rob2Pheno Annotated Tomato Image Dataset

description: Dataset of RGBD images of tomato plants in a production greenhouse (Enza Zaden BV) obtained using Realsense cameras, and object instance level ground truth annotations of the fruit for using object detectors such as MaskRCNN or YOLACT. These data were used to obtain the results reported in our paper Tomato Fruit Detection and Counting in Greenhouses using Deep Learning, Frontiers in Plant Science, 2020.<br>
DOI: 10.6084/m9.figshare.10009970.v1
title: Price data for Mexican agricultural products: case study Queretaro state (Mx)

description: The daily prices of several fruits and vegetables were extracted, from January 2009 to February 2019, from the National System of Market Information.<br>The products' daily prices were extracted using Python's lxml library from the SNIIM's website (http://www.economia-sniim.gob.mx/). This website provides daily information about several fruits and vegetables from many wholesale food markets in Mexico: price, packaging, origin, and quality. <br>
DOI: 10.6084/m9.figshare.20428833.v1
title: Simulated TCGA Dataset

description: Dataset made up of simulated early-stage cancer patients from TCGA mutation data.
DOI: 10.6084/m9.figshare.28449272.v1
title: SPICE simulation results for the 0/1 Knapsack Problem

description: SPICE simulation result of three examples of the 0-1 Knapsack Problem. The data includes the real-time signal received by the halt node at the end of the 1-D chain. Using the moving Fourier transform X(\nu,t) defined in our main text can obtain the spectra in the figure. The N=15 example is shown in the main text and the N=8,20 examples are in the supplementary material. The .txt files are exported from SPICE softwares, in which the English letters should be excluded to make a numerical analysis.
DOI: 10.6084/m9.figshare.28903805.v1
title: biogeo_niche_alpine_plant

description: Data and code for "Biogeochemical niche differentiation stabilizes species coexistence in alpine wetlands"All R scripts use relative paths and assume the working directory is the one where the code is located.Contents:This file contains the dataset and R code used in this study.In this dataset file, we contain 12 sheets.Sheet 1, named "Metadata" contains a detailed description of the abbreviations that appear in the dataset.Sheet 2, named "47spe_list", represents 47 wetland plant species involved in this study;Sheet 3, named "plant_BN", represents the leaf elementome data of 47 species;Sheet 4, named "plant_BN_tem ", represents the leaf elementome data of 47 species under different temperature;Sheet 5, named "spe_tem_group", represents the 10 species under different temperature;Sheet 6, named "site_spe", represents the presence/occurrence of each species in the site;Sheet 7, named "absolute_coexistence", represents the absolute coexisting frequency between the 15 species;Sheet 8, named "relative_coexistence", represents the relative coexisting frequency between the 15 species;Sheet 9, named "coex_freq", includes species coexisting frequency and elementome distance;Sheet 10, named "hypervolume_coex_corr ", includes species coexisting frequency, biogeochemical niche hypervolume distance and overlap between two species;Sheet 11, named "15spe_16ele, includes the concentrations and their differences of 16 elements among 15 species;Sheet 12, named "elementome_div", includes species richness, Shannon-Wiener index and elementome diversity at community-level.
DOI: 10.6084/m9.figshare.6265505.v1
title: Patient13

description: Male Patient with 189 slice of pulmonary embolism CT-Angiography.
DOI: 10.17632/yz5rrmvrgd
title: Calculations dataset of diatomic systems based on van der Waals density functional method

description: This dataset provides results obtained by first-principles calculations on diatomic systems and isolated systems based on SCAN+rVV10. All diatomic systems containing atomic species from H (Z=1) to Ra (Z=88) are considered. Calculations not only for diatomic systems but also for isolated systems are uploaded for evaluating binding energy, . =========================== raw_vasp_output_files [zip files (diatomic_db_raw.zip, isolated_db_raw.zip)] These zip files contain raw output files (OUTCAR and vasprun.xml) of VASP calculations. =========================== parsed_dataset [Python pickle files (diatomic_df.pickle, isolated_df.pickle) and csv files (diatomic_df.csv, isolated_df.csv)] These files contain tables of typical physical values files obtained from the VASP calculations. The python pickle files requires python environment with pandas and pymatgen. Files "*_df.pickle" and "*_df_protocol3.pickle" contains the same data, but they were saved with python pickle protocol 5 and 3, respectively. =========================== codes [diatomic_parser.zip] Simple python scripts for parsing raw VASP output files and plotting heatmaps and a scatter plot.
DOI: 10.6084/m9.figshare.16897003.v1
title: September 2021 Covid-19 Vaccines Twitter Streaming Dataset

description: The file contains Tweet IDs* for COVID-19 related tweets containing at <b>least one vaccine-related word</b> (i.e., words that start with vaccin*, vacin*, or vax*) collected in <b>September, 2021</b> from <b>Twitter's COVID-19 Streaming Endpoint </b>via a custom script developed by the <b>Social Media Lab (https://socialmedialab.ca/)</b>.<br>Visit <b>our interactive dashboard at https://stream.covid19misinfo.org</b>/ for a preview and some general stats about this COVID-19 Twitter streaming dataset.<br>For more info about <b>Twitter's COVID-19 Streaming Endpoint</b>, visit <b>https://developer.twitter.com/en/docs/labs/covid19-stream/overview</b><br><b>Note</b>: In accordance with Twitter API Terms, the dataset only includes Tweet IDs (as opposed to the actual tweets and associated metadata). To recollect tweets contained in this dataset, you can use programs such as Hydrator (https://github.com/DocNow/hydrator/) or the Python library Twarc (https://github.com/DocNow/twarc/).
DOI: 10.6084/m9.figshare.16918516.v1
title: Chlorella ITS2 sequences.masx

description: This is ITS2 sequences alignment file of <i>Chlorella</i> species
DOI: 10.6084/m9.figshare.15052155.v1
title: Speckle imaging dataset

description: Dataset from https://github.com/laboGigan/speckimg
DOI: 10.6084/m9.figshare.21923208.v1
title: Functional diversity and soil nutrients regulate the interannual variability in gross primary productivity

description: <strong>Functional diversity and soil nutrients regulate the interannual variability in gross primary productivity</strong>
DOI: 10.6084/m9.figshare.27619230.v1
title: Supplemental material

description: The folders contain raw hyperspectral images (reported in the paper) of macroalgae sampled in April and July 2024.<code><strong>cropped_HSI_images</strong></code><br>Contains cropped hyperspectral (HSI) raw images prepared for preprocessing. These images are sourced for pixel-wise analysis and further processing steps.<br><code><strong>Optical Signatures</strong></code><br>Houses spectral signatures and labels essential for model training and evaluation. It includes:<code><strong>Train</strong></code><b> Folder</b>: Contains text files of spectral signatures and labels for each preprocessed training sample. These files serve as input to the 1D Convolutional Neural Network (CNN) model, as detailed in the accompanying research paper.<code><strong>Test</strong></code><b> Folder</b>: Holds similar data for the test samples, formatted for model validation and performance evaluation.<br><code><strong>Calibration</strong></code><br>Contains text files of calibration signatures. These are applied in preprocessing for pixel-wise calibration, facilitating the conversion of intensity values to standardized global reflectance.<br><code><strong>Label_data</strong></code><br>Contains bounding box annotations for each sample, crucial for accurate preprocessing and label assignment.<br>The files are named HSI_(30), etc. and correspond to the folder files code names<br><code><strong>Meta_data_sheetmacroalgae_HSI.xlsx</strong></code><br>An Excel file listing species details, name codes, and sample types, aiding in orientation and reference for each dataset file.<br><code><strong>Reviewed_code_manus_hsi</strong></code><br>The file includes a jupyter notebook file with the code for preprocessing the raw images. Analyses of the spectral bands and training a 1D CNN model with that data as well as performing inference on the model. Please see Section 2.3 in the paper for the detailed process.The analysis can be used on your images, but to be sure the code works you are encouraged to use the data presented in the folders here. You can train the model directly without preprocessing first, by using the data in the "Optical signatures"
DOI: 10.6084/m9.figshare.27634290.v3
title: Dataset of Carbon Nanostructures for "Prediction of Carbon Nanostructure Mechanical Properties and the Role of Defects Using Machine Learning"

description: This repository contains the full 3D structure database associated with the publication "<b>Prediction of Carbon Nanostructure Mechanical Properties and the Role of Defects Using Machine Learning</b>"The dataset (SI_complete_dataset) contains 1179 3D atomic structures of CNT bundles, 958 structures of CNT junctions, and 50 structures of carbon fiber cross-sections with associated mechanical properties from complete stress-strain curves up to failure for each structure (e.g., strain at break, Young's modulus, and tensile strength). The models have a size of up to 80,000 atoms and the ground truth data were derived using the reactive INTERFACE force field, IFF-R.The database is extensible and can include larger carbon nanostructures with labels, including data using multiple computational and experimental techniques as they become available. The goal is real-time prediction of stress-strain properties of carbon nanostructures of arbitrary 3D configurations.The fileshare also contains a second folder (HS-GNN_and_small_test_model.zip) that contains the hierarchical spatial graph neural network (HS-GNN) and a runscript for XGBoost to train and apply the machine learning models for property predictions as described in the publication. The files contain the complete machine learning pipeline, and results for a small test (toy) set.Third, we share the Supporting Files from the publication, which contain sample run scripts and the force field files to reproduce molecular dynamics simulations of stress-strain curves of the carbon nanostructures up to failure using IFF-R.Fourth, we share the pre-processed graphs trained on 90% of the dataset of CNT bundles, which can be used to reproduce the predictions of mechanical properties using HS-GNN.
DOI: 10.6084/m9.figshare.3511475.v1
title: Appendix A. Tables showing values used in linear regression models to compare responses of wildlife to hiking and mountain biking.

description: Tables showing values used in linear regression models to compare responses of wildlife to hiking and mountain biking.
DOI: 10.17028/rd.lboro.16685125.v1
title: Computational Research Data for: "Sterically Demanding Macrocyclic Eu(III) Complexes for Selective Recognition of Phosphate and Adenosine Monophosphate"

description: Computational Research Data underlying the manuscript "Sterically Demanding Macrocyclic Eu(III) Complexes for Selective Recognition of Phosphate and Adenosine Monophosphate" by S. Bodman, C. Breen, E. Robertson, S. Kirkland, S. Wheeler, F. Plasser, S. J. Butler.<br>Content (names of folders and files are given in <b>bold face</b>)<br>Computations were performed on <b>EuBn</b>, <b>EupBOH2</b>, <b>EumBOH2</b>, and <b>EuoBOH2</b> as defined in the text. Each folder contains the converged geometries for- <b>Eu*_free.xyz</b> - free complex- <b>Eu*_water.xyz</b> - one bound water molecule<br>- <b>Eu*BOH3.xyz</b> - OH<sup>-</sup> bound- <b>Eu*_Pi.xyz</b> - inorganic phosphate bound- <b>Eu*AMP.xyz</b> - AMP bound- <b>EumBOH_AMP_cyclic.xyz</b> - cyclic structure (meta only)<br><br>The input files are shown in the folder <b>INPUT</b>- <b>qchem.in</b> - general input file to Q-Chem- <b>6-31G.bas</b>/<b>6-31G.pol</b> - extra basis set definition for Eu in <b>QCAUX</b><br>
DOI: 10.17632/4tr4p4h73m
title: Cardiac Interoception: a Novel Signal Detection Approach - Study 1

description: Find 3 data sets containing the data of the different tasks and one syntax file containing all descriptions.
DOI: 10.17632/v88xfw5wyx
title: An interactive database for the investigation of high-density peptide microarray guided interaction patterns and antivenom cross-reactivity

description: Snakebite envenoming is a major neglected tropical disease that affects millions of people every year. The only effective treatment against snakebite envenoming consists of unspecified cocktails of polyclonal antibodies purified from the plasma of immunized production animals. Currently, little data exists on the molecular interactions between venom toxin epitopes and antivenom antibody paratopes. To address this issue, high-density peptide microarray (hdpm) technology has recently been adapted to the field of toxinology. However, analysis of such valuable datasets requires expert understanding and, thus, complicates its broad application within the field. In the present study, we developed a user-friendly, and high-throughput web application named “Snake Toxin and Antivenom Binding Profiles” (STAB Profiles), to allow straight-forward analysis of hdpm datasets. To test our tool and evaluate its performance with a large dataset, we conducted hdpm assays using all African snake toxin protein sequences available in the UniProt database at the time of study design, together with eight commercial antivenoms in clinical use in Africa, thus representing the largest venom-antivenom dataset to date. Furthermore, we introduced a novel method for evaluating raw signals from a peptide microarray experiment and a data normalization protocol enabling intra-microarray and even inter-microarray chip comparisons. Finally, these data, alongside all the data from previous similar studies by Engmark et al., were preprocessed according to our newly developed protocol and made publicly available for download through the STAB Profiles web application (http://tropicalpharmacology.com/tools/stab-profiles/). With these data and our tool, we were able to gain key insights into toxin-antivenom interactions and were able to differentiate the ability of different antivenoms to interact with certain toxins of interest. The data, as well as the web application, we present in this article should be of significant value to the venom-antivenom research community. Knowledge gained from our current and future analyses of this dataset carry the potential to guide the improvement and optimization of current antivenoms for maximum patient benefit, as well as aid the development of next generation antivenoms.
DOI: 10.6084/m9.figshare.1448675.v1
title: Personality, Social Support and Quality of Life of Predialysis Chronic Kidney Patients

description: This data was collected from a teaching hospital in Kuala Lumpur, Malaysia. The Big 5 personality traits were measured using the Big Five Inventory, social support was measured using the Medical Outcomes Study (MOS) Social Support Questionnaire, and quality of life was measured using the Short-Form 36.
DOI: 10.6084/m9.figshare.25374901.v1
title: sourcedata

description: data
DOI: 10.6084/m9.figshare.26780050.v2
title: The quantified method for blood clot detection in the extraction socket

description: This project contains the following underlying data:<br>- Distance of blood-filled capillary tube in part I of the study.xlsx- Distance of blood-filled capillary tube and clinical observation in part II of the study.xlsx
DOI: 10.6084/m9.figshare.27048178.v1
title: <b>Impact of Rising Commodity Prices due to Russia-Ukraine War on Government and Non-Government Employees</b>

description: To accomplish our goal of the research, we selected Tangail district as our study population and draw a sample size for data collection from government and non-government employees using questionnaires and gathered primary data from 250 residents of Tangail. After a careful literature review, employees’ job status selected as dependent variable and the key economic indicators, such as inflation rates, consumer spending patterns, wage trends, seeking additional sources of income, employees' mental health, involvement in collective bargaining or labor action, and optimism about long-term prospects referred as independent variables.
DOI: 10.6084/m9.figshare.28854701.v1
title: <b>Database egg rejection latency meta analysis</b>

description: Egg rejection is the most widespread defence strategy used by hosts of avian brood parasites to mitigate the fitness costs imposed by parasitism. The time interval between the parasitic event and egg rejection is a crucial aspect of anti-parasitic host defences, yet the main factors shaping latency to egg rejection across different brood parasite-host systems and contexts remain uncertain. Through meta-analysis of egg-rejection experiments across diverse parasite-host systems, we identified key factors influencing rejection latency. We found that hosts in sympatric populations with parasites rejected eggs more quickly than those in allopatric populations. Egg characteristics significantly affected rejection timing: more mimetic eggs were rejected later; similarly-sized eggs took longest to reject, while smaller eggs were rejected fastest. Additionally, higher rejection rates were associated with faster rejection. Notably, the duration of nest monitoring by researchers was a significant factor influencing results, underscoring the importance of methodological considerations. Our findings confirm that characteristics known to trigger egg rejection often also influence rejection timing. This study advances our understanding of the key characteristics underlying host defences while emphasizing the importance of standardized methodologies, particularly in nest monitoring duration, to ensure accurate assessment of egg rejection latency.
DOI: 10.6084/m9.figshare.5127337.v1
title: Supplementary Material for: Effective Neutrophil Phagocytosis of <b><i>Aspergillus</i></b> <b><i>fumigatus</i></b> Is Mediated by Classical Pathway Complement Activation

description: <i>Aspergillus fumigatus</i> is an important airborne fungal pathogen and a major cause of invasive fungal infections. Susceptible individuals become infected via the inhalation of dormant conidia. If the immune system fails to clear these conidia, they will swell, germinate and grow into large hyphal structures. Neutrophils are essential effector cells for controlling <i>A. fumigatus</i> infection. In general, opsonization of microbial particles is crucial for efficient phagocytosis and killing by neutrophils. Although the antibodies present in human serum do bind to all fungal morphotypes, we observed no direct antibody-mediated phagocytosis of <i>A. fumigatus</i>. We show that opsonization, phagocytosis and killing by neutrophils of <i>A. fumigatus</i> is complement-dependent. Using human sera depleted of key complement components, we investigated the contribution of the different complement initiation pathways in complement activation on the fungal surface. We describe the classical complement pathway as the main initiator of complement activation on <i>A. fumigatus</i> swollen conidia and germ tubes. Antibodies play an important role in complement activation and efficient innate recognition, phagocytosis and killing of <i>A. fumigatus</i> by neutrophils.
DOI: 10.17632/b6rnphwxnv
title: Pixel 5 and Pixel 9 Pro XL raw GNSS data, 5 hours, 3 conditions

description: The dataset contains raw GNSS data from Google Pixel 5 and Pixel 9 Pro XL smartphones (folder Smartphones). It also includes internal positioning solutions in the NMEA format. The measurement was conducted under three differing conditions (open, trees' canopy, indoor), the observation period was 5 hours for each. To enable post-processing of the data, we also provide data from used Continuously Operating Reference Stations (CORS) in the "Base" folder. The configuration, used for the Static method in the RTKLib software, is in the "RTKLib config" folder. The configuration was created during our previous research - https://doi.org/10.3390/s23063136
Reference coordinates are provided in the ITRF2020 reference frame for absolute positioning methods, and in ETRF2000 frame for relative positioning with the use of provided base stations data.

The dataset is related to the paper "Tomaštík et al. (2025) Pixel 5 versus Pixel 9 Pro XL, are Android devices evolving towards better GNSS performance?", where the reader can find more details about the methodology and results.
DOI: 10.6084/m9.figshare.12751850.v1
title: COVID-19 Deaths and cases by state

description: COVID-19 confirmed cases and deaths by state as of July 28, 2020 from https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/cases-in-us.html and https://usafacts.org/visualizations/coronavirus-covid-19-spread-map The state numbers listed by the CDC are aggregated from the USAFact county data.<br>The CDC reports healthcare personnel cases and infections (120,467 and 587 as of August 1, 2020; accessed August 2, 2020) but does not disaggregate the numbers by state.<br>Healthcare worker deaths by state as of July 28, 2020 pulled from https://www.medscape.com/viewarticle/927976#vp_1