cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28381700.v1
title: Data and code for Shablin et al - Cuban tree frog behavior, physiology, disease

description: These files contain all data and associated R code for this experiment. Abstract for the pre-peer-reviewed manuscript is pasted below:Pathogens inflict various costs onto their hosts from sublethal changes in physiology and behavior to intense pathology and mortality. The timing of host immune responses and concomitant changes in behavior may be jointly underpinned by an increase in glucocorticoid hormones. The temporal and causal links between these interrelated responses to infection remain equivocal in many host-pathogen systems. Here, using a fungal pathogen implicated in global amphibian declines, <i>Batrachochytrium dendrobatidis </i>(<i>Bd</i>), we examined sublethal consequences of infection in the Cuban tree frog (<i>Osteopilus septentrionalis</i>). Specifically, we tracked changes in the neuroendocrine stress response by measuring urinary corticosterone (CORT) metabolites as well as immunological activation via neutrophil/lymphocyte (N/L) ratios over three consecutive rounds of <i>Bd</i> exposure. Additionally, we measured both exploratory behavior and activity level in open field arenas to evaluate whether infection-mediated changes in behavior and stress physiology coincided. Pathogen-exposed individuals began testing positive for <i>Bd</i> after two rounds of exposure. After the third exposure, <i>Bd</i>-positive frogs had higher CORT levels compared to control frogs. We found no associations between infection load and N/L ratio. Furthermore, there were no differences in exploratory behaviors or activity levels between control and <i>Bd</i>-exposed frogs. The lack of a relationship between N/L ratios and infection load may indicate a lag between neuroendocrine and immunological responses in this host-parasite system. This is further supported by the delayed increase in CORT levels only after three rounds of pathogen exposure. The varied impacts of infection on physiological biomarkers indicates a greater need for researchers to consider simultaneous changes to behavior, neuroendocrine, and immunological measures of stress in future host-pathogen studies.
DOI: 10.17632/3jk5pmnfc3
title: The knowledge ("true belief") error in 4- to 6-year-old children: When are agents aware of what they have in view? 

description: The standard view on explicit theory of mind development holds that children around the age of 4 years start to ascribe beliefs to themselves and others, typically tested with false belief (FB) tasks. The present study (N = 95, 53 female, Austrian, 41 to 80 months) systematically investigated the puzzling phenomenon that FB achievers (FB+) fail knowledge (often subsumed under “true belief”) tasks: Despite the story protagonist witnessing the displacement of an object these children predict that the protagonist will look for it in its original location. We replicate this result in Experiment 1. Interestingly, some of our children indicated uncertainty about the protagonist’s awareness of the relevant event. Thus, in Experiment 2 a new active watching condition was designed to help children understand that the protagonist attended to the critical event. This practically eradicated the knowledge error. Experiment 3 successfully replicated these results. Implications for existing explanations, perceptual access reasoning (PAR, Fabricius, et al., 2010) and pragmatic difficulties (Oktay-Gür and Rakoczy, 2017) are discussed.
DOI: 10.17632/668dzb3pdt
title: Survey Data Set on the Readiness of Hospitals for Disaster and Emergency in North Sumatra Indonesia

description: The study was a survey method. Data were collected through interviews, observations, and document reviews by referring to the form checklist of Hospital Safety Index. Data consisted of disaster potentials, structural safety, non-structural safety, and functional aspects that were then synthesized to determine the disaster preparedness level of five hospitals in North Sumatra Indonesia. The Hospital Safety Index Level for RS A, RS B, and RS E are “B" level, indicating that their ability to function during and after emergencies and disasters is potentially at risk, thus intervention measures are needed in the short term. While RS C and RS D are at level "A", indicating that both hospitals will remain operational during emergencies and disasters. The analysed data will be useful in contributing to health policies and preparedness of hospitals and other health facilities in the face of disasters, as well as for further research on the impact of hospital services during and after disasters. It will also provide insights to stakeholders and those at the managerial level of hospitals formulating appropriate intervention plans to address or mitigate problems during disasters and after disasters to patients, disaster victims, health workers, and facilities.
DOI: 10.6084/m9.figshare.25752552.v7
title: Inputs/outputs dataset supporting "Offshore Wind and Wave Energy Can Reduce Total Installed Capacity Required in Zero Emissions Grids"

description: This repository contains the SWITCH 2.0 input and output files for the study titled <i>Offshore Wind and Wave Energy Can Reduce Total Installed Capacity Required in Zero Emissions Grids</i>.
DOI: 10.6084/m9.figshare.27245481.v4
title: ab_rsmi_data

description: This repository contains the data used to generate the results in the paper "Compression theory for inhomogeneous systems".<br>Structure of the repository:<b>Data</b>The included data directories are as follows:<br><b>Graph structure details of the Ammann-Beenker tiling</b> are provided in `quasiperiodic_data/`.<br> `quasiperiodic_data/nodedata.dat` stores the node indices and their coordinates.<br> `quasiperiodic_data/edgedata.dat` stores the list of edges as tuples of node indices.<br> `quasiperiodic_data/order_of_8vtx.dat` and `quasiperiodic_data/regions/` store special symmetric nodes and regions like membranes and empires.<b>Monte Carlo configurations of dimer coverings</b> are provided in `data/`.<br> `data/configs/` stores the raw samples of dimer coverings in binary format.<br> `data/EandV/` stores extracted V and E configurations in `.npy` files.<b>Examples of RSMI-NE optimised coarse graining filters</b> are provided in `paper_data/`.<b>Software toolbox</b>This repository also includes software to prepare the data in a format that can be used by [`rsmine`](https://github.com/RSMI-NE/RSMI-NE).1-<b> Data preparation</b><br> `data_generation.ipynb` processes the raw sample datasets in `data/` to extract the V and E configurations for `rsmine` and write them into `.npy` files stored in `data/EandV/`. Each choice of coarse graining block and environment is labelled by a unique "case" number. <br> E.g. `'case_no': 51` corresponds to the four-fold deflation of the central 8-vertex using the canonical 8-star tile of the AB quasicrystal.<br> `special_vertices.ipynb` contains the details of how to construct these canonical tiles for each neighbourhood and scale transformation.`ab_rsmi_regions.ipynb` visualises V and E regions on the Ammann-Beenker tiling by taking the 'case_no', and neighbourhood index, i.e. the index of the central node for the coarse grained block V.2-<b> Analysis of RSMI-NE results</b> `clocks.ipynb` contains code that identifies coarse-grained clock variables.<br>
DOI: 10.6084/m9.figshare.27937518.v2
title: manta-mechanics-button/gear/nut/nut_cap/red_washer/round_button_cap

description: manta mechanics button/gear/nut/nut_cap/red_washer/round_button_cap
DOI: 10.6084/m9.figshare.28916795.v1
title: R project and data spreadsheet

description: The zipped R project contains the R Workspace used for this study, the R history file, the Microsoft Excel worksheet with all the data, the R project "Scanner model analysis" and the R script.The Excel spreadsheet contains all the mammary gland thickness measurements from both right and left glands of the 18 dolphins scanned with B-mode ultrasound during the 5-month project duration. Dolphins were separated by type of location and each measurement is colored according to the ultrasound scanner used. Means of all measurements are highlighted in bold. At the bottom of the measurements, there is a figure showing 3 mammary gland ultrasound images from were measurements were taken (for example purposes).
DOI: 10.17632/cyk2jg7tgt
title: Data for: Altered neural dynamics in people who report spontaneous out of body experiences.

description: These files are the raw (decimated to sampling rate of 512Hz) EEG recordings. The raw bdf files have been imported into EEG lab and saved as .set and .fdt files. No other processing has been applied. For further information about these data, please contact the first author Dr Elizabeth Milne, E.Milne@sheffield.ac.uk
DOI: 10.17632/vcg2xx4pnc
title: Individual genotyping of red fox field stools from the analysis of 14 microsatellite targets and one sex marker and the research of Echinococcus multilocularis DNA presence.

description: Individual genotyping of red fox stools sampled on the field, from the analysis of 14 microsatellite targets (AHT121, AHT137, C01.424, INU055, AHTh171, C08.618, CPH2, FH2010, C04.140, CXX0279, FH2848, REN169O18, CPH11, FH2457) and one sex marker (K9-AMELO). Em(+): Echinococcus multilocularis DNA detection in faeces, qPCRVv: qPCR for Vulpes Vulpes DNA detection on part of the CytB gene (Knapp et al., 2016) and Cq values, ND: no data. First the fox faeces were identified using a host faecal qPCR technique from total copro-DNA extracts, as previously described (Knapp et al., 2016).

The study was conducted from March 2017 to January 2020 in a grassland area of 3.18 Km² in the village of Les Alliés (006°26’46”E, 46°56’53”N, Fig. 1) in eastern France, at an average altitude of 971 m above sea level.

The QIAmp Fast DNA Stool kit (Qiagen, Hilden, Germany) was used to extract genomic DNA from faecal samples.
Fragment size analyses were performed to obtained allele size quantification for the 14 microsatellites and the sex marker, by using a SeqStudio Genetic Analyzer (Applied Biosystems, Foster City, CA). Genetic profiles were determined using the Microsatellite Analysis module available on the Thermo Fisher cloud (https://apps.thermofisher.com/editor-web/#/app/app-microsatellites-web).
Copro-DNA extracts from foxes were tested for the presence of E. multilocularis (Em(+)) using a specific E. multilocularis-qPCR, as previously described.

References
Breen, M., Jet al., 2001. Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes. Genome Res. 11, 1784–1795. 
Fredholm, M., Winterø, A.K., 1995. Variation of short tandem repeats within and between species belonging to the Canidae family. Mamm. Genome Off. J. Int. Mamm. Genome Soc. 6, 11–18. 
Holmes, N.G., et al., 1995. Eighteen canine microsatellites. Anim. Genet. 26, 132–133. 
Ichikawa, Y., et al., 2002. Identification and characterization of 40 dinucleotide microsatellites in the dog genome. Anim. Genet. 33, 400–401. 
Knapp, J., et al., 2016. Development of a Real-Time PCR for a Sensitive One-Step Coprodiagnosis Allowing both the Identification of Carnivore Feces and the Detection of Toxocara spp. and Echinococcus multilocularis. Appl. Environ. Microbiol. 82, 2950–2958.
Moore, M., et al., 2010. Thirty-one short red fox (Vulpes vulpes) microsatellite markers. Mol. Ecol. Resour. 10, 404–408. 
Ostrander, E.A., et al., 1993. Identification and characterization of dinucleotide repeat (CA)n markers for genetic mapping in dog. Genomics 16, 207–213.
DOI: 10.6084/m9.figshare.19525372.v1
title: The state of the ‘GMO’ debate - toward an increasingly favorable and less polarized media conversation on ag-biotech?

description: Although nearly three decades have passed since genetically modified crops (so-called ‘GMOs’) were widely commercialized, vociferous debate remains about the use of biotechnology in agriculture, despite a worldwide scientific consensus on their safety and utility. This study analyzes the volume and tenor of the GMO conversation as it played out on social and traditional media between 2018 and 2020, looking at 103,084 online and print articles published in English-language media around the world as well as 1,716,071 social media posts. To our knowledge, our analysis is the first comprehensive survey of the shifting traditional and online media discourse on this issue during this time period. While the volume of traditional media coverage of GMOs increased significantly during the period, this was combined with a dramatic drop in the volume of social media posts of over 80%. Traditional media tended to be somewhat more positive in their coverage than social media in 2018 and 2019, but that gap disappeared in 2020. Both traditional and social media saw trends toward increasing favorability, with the positive trend especially robust in social media. The large decline in volume of social media posts, combined with a strong trend toward greater favorability, may indicate a drop in the salience of the GMO debate among the wider population even while the volume of coverage in traditional media increased. Overall, our results suggest that both social and traditional media may be moving toward a more favorable and less polarized conversation on ag-biotech overall.
DOI: 10.6084/m9.figshare.27226464.v2
title: Dataset of simulated 3D refractive index distributions of suspended cells

description: This dataset contains an ensemble of simulated 3D refractive index (RI) distributions of suspended cells useful for testing different numerical algorithms such as denoising or tomographic reconstruction. The simulated RI distributions are obtained starting from statistics drawn from measurements made on real cells by holo-tomographic flow cytometry. This dataset is divided into three folders.<b>YeastWithSingleVacuole</b> - This dataset contains 50 realizations of 3D RI distributions of yeast cells with a single vacuole inside. The yeast cells and the vacuoles are modeled according to the statistics reported in [https://doi.org/10.1002/smtd.202300447, Supplementary Material] for the case labeled as "late G1".<b>MonocyteWithLipidDroplets</b> - This dataset contains 50 realizations of 3D RI distributions of monocytes with lipid droplets inside. The lipid droplets are modeled according to the measurements reported in [https://doi.org/10.29026/oea.2023.220048].<b>MonocyteWithVacuoles</b> - This dataset contains 50 realizations of 3D RI distributions of monocytes with cytoplasmic vacuoles. The vacuoles are modeled as regions of spatially varying RIs, inspired by the analysis in [https://doi.org/10.1002/smtd.202300447].<b>MonocyteWithLysosomesAndVacuoles</b> - This dataset contains 50 realizations of 3D RI distributions of monocytes with cytoplasmic vacuoles and lysosomes. The vacuoles are modeled as regions of spatially varying RIs, inspired by the analysis in [https://doi.org/10.1002/smtd.202300447], while the lysosomes are modelled according to the measurements reported in [https://doi.org/10.1117/1.2437765].<br>
DOI: 10.17632/vwmprpp7xr
title: Digital Elevation Model (DEM) for the State of Hawaii Statewide Coastal Highway Program Report: Kauai, Hawaii

description: In this project, we use the Light Detection and Ranging (LiDAR) data to create the Digital Elevation Model (DEM). The LiDAR data can be downloaded through the Data Access Viewer of NOAA ( https://coast.noaa.gov/dataviewer/#/lidar/search/). For Kauai, the majority of the DEM is created using the data of 2013 U.S. Army Corps of Engineers (USACE) National Coastal Mapping Program (NCMP) Topobathy LiDAR – Local Mean Sea Level (LMSL). For some areas not covered by this data set, we use the LiDAR data from 2006 FEMA LiDAR: Hawaiian Islands and 2007 JALBTCX Hawaii LiDAR: North Coasts of Hawaii (Big Island), Kauai, Maui, Molokai, Oahu, which are accessed in the Data Access Viewer of NOAA. Please read “Description of Digital Elevation Model (DEM) for Kauai, Hawaii.docx” for detailed information.
DOI: 10.6084/m9.figshare.28424213.v1
title: QR Code Dataset V2

description: This dataset consists of three folders: The first folder (<i>Unreadable Scanned QR Codes</i>) contains images obtained from the scanner that cannot be read by OpenCV's <code>QRCodeDetector</code>. The second folder (<i>Unreadable Simulated QR Codes</i>) includes QR code images that were generated to simulate real-world degradation and cannot be read by either OpenCV's <code>QRCodeDetector</code> or WeChat's QR scanner. The third folder (<i>Learning Data</i>) consists of computer-generated QR codes created by applying various distortions to mimic scanner-induced effects.
DOI: 10.6084/m9.figshare.29147681.v1
title: Replication package for "RAG-Reviewer: A Retrieval-Augmented Generation Framework for Automated Code Review Comment Generation"

description: This repository contains artifacts for the experiments described in RQ1–RQ3.<b>fine_tuned_checkpoints.zip</b><br>Checkpoints for each experimental run. Each folder follows the naming convention:<br><code>modelName_ragStrategy_finetuned_best_ckp_epoch</code>, where:<code>modelName</code> refers to the backbone model (e.g., CodeT5, CodeReviewer).<code>ragStrategy</code> denotes the prompting strategy: <code>rag_pair</code>, <code>rag_singleton</code>, or <code>vanilla</code>.<code>epoch</code> indicates the best-performing epoch based on validation performance.<b>code_embeddings.zip</b><br>Vector embeddings of source code from the Tufano et al. dataset (train/val/test splits).<br>Embeddings are stored as <code>.pkl</code> files and used for retrieval tasks.<b>rag_candidate.zip</b><br>Contains the top-K most similar training examples for each instance in the train, validation, and test sets.<br>These candidates were selected using semantic similarity for retrieval-augmented generation (RAG).The source code for reproducing these experiments is available on GitHub:<br>https://github.com/RAG-Reviewer/RAG-Reviewer
DOI: 10.6084/m9.figshare.12841418.v1
title: Comparison of gene expression of different cell types and tissues in WT pigs, 3KO.9TG pigs and PERVKO.3KO.9TG pigs

description: RNA-Seq analysis reveals constitutive expression of transgenes across multiple cell types (endothelial cells and fetal/ear fibroblasts) and tissues (heart, kidney, liver and lung), and marginal perturbation on the porcine transcriptome of 3KO·9TG pigs and PERVKO·3KO·9TG pigs. <br>
DOI: 10.6084/m9.figshare.24910674.v7
title: Supplemenary for "Earth-Moon Dynamics from Cyclostratigraphy Reveals Possible Ocean Tide Resonance in the Mesoproterozoic Era"

description: Supplementary Materials and Dataset forEarth-Moon Dynamics from Cyclostratigraphy Reveals Possible Oceanic Resonance in the Mesoproterozoic Era<br>
DOI: 10.6084/m9.figshare.25413733.v1
title: Binarized rasters describing spatial variation of myrtle rust infection risk in the Greater Wellington Region under two scenarios for an acceptably low level of risk.

description: Binarized rasters describing spatial variation of myrtle rust infection risk in the Greater Wellington Region (GWR) under two scenarios for an acceptably low level of risk. Scenarios were developed from Research Grade myrtle rust observations in the GWR recorded in iNaturalist and weekly mean predictions of infection risk generated by the Myrtle Rust Process Model. Observations and predictions covered the same <i>c.</i> four-year period (01/08/2020 - 11/01/2025). Acceptably low risk in Scenario 1 excludes all myrtle rust observations, whereas low risk in Scenario 2 excludes 75% of myrtle rust observations. In Scenario 1, risk is defined as acceptably low in areas where mean infection risk exceeds 50% in fewer than 1.7% of weeks / year. In Scenario 2, risk is defined as acceptably low in areas where mean infection risk exceeds 50% in fewer than 3.4% of weeks / year. Data are provided as geospatial .tif rasters.
DOI: 10.17632/v8h2sgd997
title: CNT concrete flexural strength and elastic modulus datasets from literatures

description: The excel file contains sets of data collected from literatures that is required to reproduce the predictive models with Artificial Intelligence (AI)-based models submitted by the author.
DOI: 10.25380/iastate.8181866.v1
title: Longitudinal Shoe Study Digital Photos of Shoe Soles

description: Photos of the soles of 160 pairs of shoes (“Nike Winflo 4” or “Adidas Seeley”; 4 sizes each), with associated measurements and data about shoe wear, surfaces, and wearers. The photos are divided up into 6 zip files.<br><br>Each pair of shoes was worn for at least 10,000 steps per week over a 6-month period, with multiple measurements of the shoe soles taken initially and during three check-in periods spaced at approximately 5 week intervals.<br><br>The images are accompanied by 3 CSV files describing the shoes, visit (information collected from surveys along with the shoes), and individual images. The codebooks contain descriptions of the variables in each of the CSV files as well as a more extensive description of the file naming scheme outlined in the README.<br><br>These files can be used to examine wear pattern development, to verify the presence of randomly acquired characteristics, and to develop algorithms which match photos of shoe soles to the corresponding prints from those soles. <br>
DOI: 10.6084/m9.figshare.26548531.v6
title: Salazar et al. 2024_EJLS

description: The Andes, with its diverse topography and climate, is a renowned cradle for adaptive radiation, particularly for vertebrate ectotherms like lizards. Yet, the role of temperature in promoting physiological specialization in the Andes remains unclear. Aseasonality in the tropics should favor physiological specialization across elevation in lizards, but empirical data are limited and equivocal. Determining how thermal tolerances are geographically and phylogenetically structured, therefore, is a priority, particularly as environments continue to rapidly change. However, there's a gap in our knowledge of thermal limits of species from the Andes, one of the planet’s most biodiverse regions. Anoles, a diverse lizard group found across thousands of meters of elevation in the Andes, can offer insights into evolutionary adaptations to temperature. This study focused on 14 anole species from two different anole clades (Dactyloa and Draconura) that independently diversified along elevational gradients in the Andes. We measured critical thermal limits (CT<sub>min</sub> and CT<sub>max</sub>) and found patterns of thermal tolerance specialization across altitude, both among and within species. Patterns of thermal specialization are similar among anole clades, indicating parallel responses to similar environmental pressures. Specifically, high-elevation anoles tolerate colder temperature and are less heat tolerant than their low elevation counterparts, rendering thermal tolerance breadths stable across elevation (thermal specialization). Evolutionary rates of physiological traits were similar, reflecting parallel specialization in heat and cold tolerance across elevation. The adaptive radiation of anole lizards reflects physiological specialization across elevation, and the endemism such specialization favors likely catalyzed their remarkable diversity in the tropical Andes.
DOI: 10.6084/m9.figshare.1544682.v2
title: 2050 Lab 1: Relationship between gender and eye colour

description: This lab analyzed the relationship between gender and eye colour. It was performed at York University in the Lumbers Building. The data was collected by observing the gender, whether male or female, of 20 participants. Next, the eye colour of each participant was recorded by asking the individual or observing.
DOI: 10.6084/m9.figshare.25562490.v1
title: The assembly statistics of <i>L. apetalum</i> genome

description: The assembly statistics of <i>L. apetalum</i> genome