cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28220186.v1
title: ALK in complex with lorlatinib with in-silico mutated residues

description: PyMol session file (.pse) files of the structure of ALK in complex with lorlatinib (original PDB accession 4CLJ) with <i>in-silico</i> mutated residues as reported in figure 4. Computational mutagenesis was applied to residues known to confer resistance to TKIs in order to highlight their potential impact on drug binding and efficacy. The mutated residues are represented simultaneously for illustrative purposes.
DOI: 10.6084/m9.figshare.21867636.v1
title: Article_Supplementary_Table_1_Final (002).docx

description: This study examines the impact of reduced skeletal muscle DHA content on whole body glucose and insulin tolerance.
DOI: 10.6084/m9.figshare.24125037.v1
title: Abundance table (input)

description: The table data used as the input described in the journal paper: "<b>Data mining techniques for endometriosis detection in a data-scarce medical dataset</b>".FormatCSV (comma-separated) with headers.To use it with the algorithms of the journal paper, it needs to be converted into a tab-separated file.
DOI: 10.6084/m9.figshare.28937054.v1
title: Analizler.docx

description: The main purpose of this study is to design a culture acquisition self-efficacy scale for learners of Turkish as a foreign language. For this purpose, a conceptual framework was drawn by analyzing the literature and the Common European Framework of Reference for Languages (CEFR, 2018). The study group the research was 411 B2 level students who learn Turkish in different Turkish language teaching centers. Firstly, exploratory factor analysis was applied for construct validity and a structure consisting of 21 items under four factors (daily life, social relations, values, and behaviors) was obtained. The scale is a five-point Likert scale. In the five-point scale, (1 point) Strongly Disagree, (2 points) Disagree, (3 points) Partially Agree, (4 points) Agree, (5 points) Strongly Agree values were used. Confirmatory factor analysis was then applied and determined that the obtained structure showed a good fit. Cronbach's alpha reliability coefficient calculated for the reliability studies of the scale was found to be .886. The overall reliability of the Culture Acquisition Self-Efficacy Scale is good. As a result of the analyses, the scale was found to be valid and reliable. As a result of the research, various suggestions were made.
DOI: 10.15468/dl.9usy5t
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Holtbyrnia innesi (Fowler, 1934)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((26.1447 -34.2546,26.6413 -34.1504,17.9648 -34.1504,17.9648 -34.5378,18.3444 -34.8391,18.8711 -34.8843,19.4851 -35.2658,19.9376 -35.3352,20.7057 -34.9616,21.9281 -34.8692,22.6401 -34.5158,23.3842 -34.6063,23.712 -34.499,24.8223 -34.7143,25.2443 -34.5061,25.7729 -34.5304,26.1447 -34.2546))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013399-250525065834625/datasets/export for details.
DOI: 10.6084/m9.figshare.11692038.v1
title: Ammonia emission from agricultural synthetic nitrogen fertilizer use in the contiguous U.S. during 1900-2015: a set of gridded time-series data

description: The increasing demands of food and biofuel promote century-long cropland expansion and nitrogen (N) fertilizer management development in the United States. However, the role of such long-term reshaping agricultural system in influencing the spatiotemporal and seasonal pattern of Ammonia (NH<sub>3</sub>) emission remains poorly understood. By using an empirical model driven by time-series data sets of environmental forcing, such as climate variability, soil properties, land use and cover changes, and agricultural N fertilizer management practices, we have estimated monthly ammonia emissions from synthetic nitrogen fertilizer uses in the contiguous U.S. during 1900 to 2015. For ease of access, we have resampled the original 1km × 1 km data set to a resolution of 5 km × 5 km. This data set can serve to facilitate national and regional air quality modeling and nitrogen budget assessment.
DOI: 10.6084/m9.figshare.11962068.v1
title: L2 Section, Sample 03. 84 Year Old Female

description: A 3 mm thick para-sagittal slice of L2 vertebra from an 84 year old female embedded in PMMA then micro-milled block surfaces carbon coated for quantitative 20kV BSE SEM.<br><br>Later polished to remove coating and then imaged with high-contrast X-Ray Micro-tomography at 90 kV with 30 micron voxel size.<br><br>There is also a 3D VR model of this sample available : https://skfb.ly/6QSrZ<br>
DOI: 10.6084/m9.figshare.5100304.v3
title: Abies cephalonica chorology

description: Distribution map of Greek fir (<i>Abies cephalonica</i>)<br><br>These maps were produced by combining numerous and heterogeneous data collected from atlas monographs providing complete species distribution maps, from national to regional atlases, occurrence geo-databases, scientific and grey literature.<br>The maps were created using ESRI shapefiles (*.shp, *.shx, *.dbf, *.prj files) archived in the ZIP file. Species range is mapped with polygon features (name suffix "plg"), which define continuous areas of occupancy of the species, and with point features (name suffix "pnt"), which identify more fragmented and isolated populations. If synanthropic occurrences are reported outside the species natural range, additional point and/or polygon shapefiles are also present (suffix "syn"). <br>Polygon borders delimiting species ranges are generalized across the mainland and sea boundaries. This offers the possibility to mask sea areas or to clip and extract the terrestrial range parts using GIS data layers of the users' choice. An additional version of polygon ranges are clipped with a coastline (name suffix "clip"), which have been derived from Natural Earth dataset "Admin 0 - Countries" 1:50M version 4.1.0 (https://www.naturalearthdata.com). <br><br>Please cite as:<br>Caudullo, G., Welk, E., San-Miguel-Ayanz, J., 2017. Chorological maps for the main European woody species. Data in Brief 12, 662-666. DOI: doi.org/10.1016/j.dib.2017.05.007 <br><br>Additional information and used references are on 'supplementary materials' document:<br>https://doi.org/10.6084/m9.figshare.5091901<br><br>Chorological maps are part of the "European Atlas of Forest Tree Species" project:<br>https://w3id.org/mtv/FISE-Comm/v01
DOI: 10.6084/m9.figshare.7550744.v1
title: SuppData-2: P.waltl genes BLASTP result

description: Supplementary Data 2: BLASTP search of P. waltl gene models (PLEWA04_ORF) against NCBI nr database. Top hit of each model is summarized in the table.
DOI: 10.17632/j65f2wd784
title: Rasmussen's Encephalitis Retrospective Dataset

description: This file contains retrospective data collected from a single centre. Patients with a diagnosis of Rasmussen's encephalitis were included if they fulfilled the European consensus criteria (2005, Bien et al). Clinical data included age at onset, presentation, seizure characteristics, treatment details and Engel Score outcome. MRI data was generated by visual assessment of MRI characteristics. The research questions were: 1) Does macroscopic extent of radiological pathology and expedited Radiological Stage progression associate with a younger age at onset? 2) Are specific patterns of preferential sparing or involvement present within the hemisphere? 3) If present, Is there a pathophysiological link between anatomical patterns and the age peculiarities ?
DOI: 10.26188/27217086.v1
title: Crombie et al. 2025 - RT-SIRM, ZFC-FC and hysteresis data

description: This data is part of a study looking at a novel approach to the analysis and characterisation of archaeological ochres, working towards the application of magnetic analytical methods to the provenance of ochre pigments. The use of measurements such as room temperature – saturation isothermal remnant magnetisation (RT-SIRM), magnetic hysteresis loops and zero-field-cooled/field-cooled (ZFC-FC) allow for the identification of a magnetic mineral profile in the ochre samples, which can, in turn, be used to fingerprint sources.
DOI: 10.6084/m9.figshare.28582994.v1
title: Supplementary Material for: Sex differences in progression of neurodegeneration: the AGES-Reykjavik Study

description: Introduction: Advancing age is associated with global brain atrophy. Cross-sectional studies have found sex differences in neuroanatomy; however, longitudinal studies assessing sex differences in neurodegeneration are currently scarce. The effects of age and sex on brain atrophy may not be uniform across the whole brain and may partially explain the sex differences observed in dementia. The current study aimed to examine sex differences in longitudinal atrophy patterns in gray and white matter regions in older adults. 
Methods: The study sample included 1480 individuals from the AGES-Reykjavik Study, a population-based cohort study, that underwent two MRI scans within an average of 5 years between assessments. Individuals were also followed-up for incident dementia diagnosis. Linear regression models were used to assess sex differences between mean differences in gray and white matter regions, correcting for age, education, baseline intracranial volume, baseline regional volumes, hypertension, body mass index, and APOE e4 allele status. 
Results: Men showed increased longitudinal atrophy in the total gray matter, as well as in the parietal cortex, cingulate cortex, caudate nucleus, brainstem, left cerebellum, precentral gyrus, putamen, globus pallidus, and orbitofrontal cortex. Whereas women exhibited greater atrophy over time in total white matter, but not in specific regions. No moderation was found between sex differences on incident dementia regarding atrophy patterns. 
Conclusions: While men show larger gray matter volumes cross-sectionally, their rates of atrophy over time are steeper compared to women. Sex differences in brain atrophy seem to be specifically detrimental in men in regions related to executive functioning, motor control, and emotion processing.
DOI: 10.6084/m9.figshare.8250842.v1
title: Isolation by Distance and Proximity to Urban Areas Affect Genetic Differentiation Among Collections of English Sole (Parophrys vetulus, family Pleuronectidae) in the Pacific Northwest and Salish Sea

description: This is a GENEPOP file that contains genotypes for English Sole Parophrys vetulus (family Pleuronectidae) at 15 microsatellite loci using a diploid, 1 column format <br>where a 129131 is a 129/131 heterozygote individual, etc. Each line contains the 15 genotypes for a fish. The fish are grouped by collections called POP and the first data line for a POP has an abbreviation for the location as described in Winans et al in prep to be submitted to Northwest Science by the same title. Collections range from 52.7257 N, <br>130.68387 W to 44.4348 N, 124.07113 W. Loci and PCR conditions are described in Winans et al. 2014, Conservation Genetics Resources 6:417-419.<br>
DOI: 10.6084/m9.figshare.1549717.v1
title: Monocot PATHd8 tree with support

description: Monocot phylogeny. Generated using RAxML and made ultrametric using PATHd8 and 20 fossil calibrations.
DOI: 10.6084/m9.figshare.5129944.v1
title: Supplementary Material for: Serum Bicarbonate and Structural and Functional Cardiac Abnormalities in Chronic Kidney Disease - A Report from the Chronic Renal Insufficiency Cohort Study

description: <b><i>Background:</i></b> Heart failure (HF) is a frequent occurrence in chronic kidney disease (CKD) patients and predicts poor survival. Serum bicarbonate is associated with increased rates of HF in CKD; however, the mechanisms leading to this association are incompletely understood. This study aims to assess whether serum bicarbonate is independently associated with structural and functional cardiac abnormalities in CKD. <b><i>Methods:</i></b> The association between serum bicarbonate and left ventricular (LV) hypertrophy (LVH), LV mass indexed to height<sup>2.7</sup>, LV geometry, ejection fraction (EF) and diastolic dysfunction was assessed in 3,483 participants without NYHA class III/IV HF, enrolled in the Chronic Renal Insufficiency Cohort study. <b><i>Results:</i></b> The mean estimated glomerular filtration rate was 42.5 ± 17 ml/min/1.73 m<sup>2</sup>. The overall prevalence of LVH was 51.2%, with 57.8, 50.9 and 47.7% for bicarbonate categories &lt;22, 22-26 and &gt;26 mmol/l, respectively. Participants with low bicarbonate were more likely to have LVH and abnormal LV geometry (OR 1.32; 95% CI 1.07-1.64, and OR 1.57; 95% CI 1.14-2.16, respectively). However, the association was not statistically significant after adjustment for demographics, traditional cardiovascular risk factors, medications and kidney function (OR 1.07; 95% CI 0.66-1.72, and OR 1.27; 95% CI 0.64-2.51, respectively). No association was found between bicarbonate and systolic or diastolic dysfunction. During follow-up, no significant changes in LV mass or EF were observed in any bicarbonate strata. <b><i>Conclusions:</i></b> In a large CKD study, serum bicarbonate was associated with LV mass and concentric LVH; however, this association was attenuated after adjustment for clinical factors suggesting that the observed cardiac effects are mediated through yet unknown mechanisms.
DOI: 10.6084/m9.figshare.16641313.v1
title: Main and extended data figures source data

description: Source data for the figures
DOI: 10.6084/m9.figshare.22188280.v1
title: Transposable element characterization in molluscs

description: <strong>DDE.D_Bivalves_V2.nr.fa</strong>: Library of curated Class II DDE/D-related families mined from bivalve genomes. These families correspond to full length elements. All sequences have been classified following a RepeatMasker formatting style. <strong>LINEs_Bivalves_V2.nr.fa</strong>: Library of curated LINE families mined from bivalve genomes. All sequences have been classified following a RepeatMasker formatting style. <strong>SINEs_Bivalves_V2.nr.fa</strong>: Library of curated SINE families mined from bivalve genomes. All sequences have been classified following a RepeatMasker formatting style. <strong>LINE_Trees.txt</strong>: Phylogenetic trees of mollusc LINE elements based on RVT domain. <strong>LINEs_RVT.aln</strong>: LINE-derived RVT protein sequences identified in mollusc genomes and used for phylogenetic inference. <br> For more informations over the methodology and the assembly used please visit: https://github.com/CompBio-BO/Bivalvia_TEs
DOI: 10.6084/m9.figshare.29149031.v2
title: <b>Reimagining AI Integration in Higher Education through a Motivational-Cognitive Model for AI-Augmented Learning.</b>

description: This study introduces a new motivational-cognitive framework that examines how perceived intelligence and cognitive trust mediate the relationship between AI tool usage and AI-augmented learning. Drawing from expectancy-value theory and cognitive trust literature, we surveyed 356 university students across three developing countries (North Cyprus, the Democratic Republic of Congo and Nigeria).
DOI: 10.6084/m9.figshare.4109769.v1
title: sample_news.zip

description: A sample of news stream used in our paper: News Stream Summarization using Burst Information Networks (EMNLP2016: http://aclweb.org/anthology/D/D16/D16-1075.pdf)<br>Each day, we sample 2500 news articles. The full dataset will be uploaded later. Each line in a file is a news article. Paragraphs are split by '\t' in a line (article).
DOI: 10.6084/m9.figshare.12744977.v1
title: Overhead Imagery of Wind Turbines

description: This is a set of overhead images of wind turbines taken from https://figshare.com/articles/Power_Plant_Satellite_Imagery_Dataset/5307364. These images were then hand labeled and converted into formatted .txt files that contain the class, x and y coordinates and the height and width of the bounding boxes. These images and the labels are contained in original_images_and_labels.<br><br>This data was then preprocessed into smaller images with dimensions of 608x608 and their corresponding labels with the same YOLOv3 format of class, x, y, height, width. These images are contained in wind_turbine_images and the labels are contained in wind_turbine_labels.<br>
DOI: 10.6084/m9.figshare.5124319.v1
title: Supplementary Material for: Talar Maturity Determined by Epiphyseal Closure of the Calcaneus

description: The talus is used in many kinds of studies on primates including fossil species, and most of the individuals studied are adults. One of the most important indicators of adult individuals is epiphyseal closure; however, because the talus has no epiphysis, it is difficult to determine the maturity of the talus. The calcaneus has one epiphysis, and it has been used along with the talus in some analyses. The objective of this study was to quantify the maturation trajectory of the talus using epiphyseal closure of the calcaneus as a benchmark. We used 71 skeletons of free-ranging <i>Macaca fuscata fuscata</i> males of known day-age. We did not identify any size increase with age in talar dimensions among specimens with complete calcaneal epiphyseal closure. Thus, in male <i>M. fuscata</i><i>fuscata</i>, the maturation trajectory of the talus can be quantified using epiphyseal closure of the calcaneus as a benchmark.
DOI: 10.6084/m9.figshare.14134196.v1
title: Supplementary Material for: Estimating the Odds of Ulcerative Colitis-Associated Pyoderma Gangrenosum: A Population-Based Case-Control Study

description: <b><i>Background:</i></b> Ulcerative colitis (UC) is a well-known underlying comorbidity of pyoderma gangrenosum (PG). However, the risk conferred by UC for the subsequent development of PG is yet to be elucidated. We aimed to estimate the magnitude of the association between UC and the subsequent occurrence of PG, which would enable us to assess the odds of PG developing in individuals with a history of UC. <b><i>Methods:</i></b> A population-based case-control study was conducted to compare PG patients (<i>n</i> = 302) and age-, sex- and ethnicity-matched control subjects (<i>n</i> = 1,497) regarding the presence of UC. Logistic regression models were utilized for univariate and multivariate analyses. <b><i>Results:</i></b> The prevalence of preexisting UC was greater in patients with PG than in controls (7.3 vs. 0.5%; <i>p</i> &lt; 0.001). A 15-fold increase in the odds of PG in individuals with preexisting UC was observed (OR 14.62, 95% CI 6.45–33.18). The greatest risk of developing PG occurred in the first years following the diagnosis of UC (OR 35.50, 95% CI 4.35–289.60), and decreased thereafter to 10.03 (95% CI 1.83–55.03), 6.69 (95% CI 1.49–30.02), and 10.03 (95% CI 1.83–55.03) at 1–5, 5–10, and 10–15 years after the diagnosis of UC, respectively. This association retained its statistical significance following the adjustment for confounding factors (adjusted OR 10.78, 95% CI 4.55–25.52). Patients with both PG and UC were younger and had a lower prevalence of smoking than the remaining patients with PG. <b><i>Conclusions:</i></b> UC increases the odds of developing PG by 15-fold, with the highest probability of developing PG occurring within the first year after the diagnosis of UC. Patients with UC may be advised to avoid additional precipitating factors for the development of PG.
DOI: 10.6084/m9.figshare.19100603.v1
title: Additional file 1.sav

description: This is a dataset of a cross-sectional study that assessed psychosocial hazards among traffic police officers in Kathmandu Metropolitan City, Nepal.
DOI: 10.6084/m9.figshare.20342655.v4
title: CLN025 folding represented via dihedrals or heavy atom distances

description: 41580 frames from a replica-exchange molecular dynamics simulation (400 ns, 340 K replica, dt = 2 fs) of the 10-residue peptide CLN025, which folds into a beta hairpin.<br><br>In "cln025traj_dihedrals.npy" the frames are represented using the 32 dihedral angles of the peptide, given in the following order<br>phi1 phi2 phi3 phi4 phi5 phi6 phi7 phi8 phi9psi1 psi2 psi3 psi4 psi5 psi6 psi7 psi8 psi9chi1_1 chi1_2 chi1_3 chi1_5 chi1_6 chi1_8 chi1_9 chi1_10chi2_1 chi2_2 chi2_3 chi2_5 chi2_9 chi2_10.<br><br>In "cln025traj_distances.npy" the frames are represented using the set of all the 4278 distances between heavy atoms of the molecule.<br><br>The additional files ending with "_decimated_equilibrated" are smaller trajectories generated from the original ones by:- first, taking 1 element every 10 via numpy command array[::10].- then, removing the first 400 elements via array[400:].<br>If you find this dataset useful for your research, please cite the following publication@article{carli2021statistically,title={Statistically unbiased free energy estimates from biased simulations},author={Carli, Matteo and Laio, Alessandro},journal={Molecular Physics},volume={119},number={19-20},pages={e1899323},year={2021},publisher={Taylor \& Francis}}<br><br>
DOI: 10.6084/m9.figshare.28197497.v2
title: Data from: <b>NeoFrugivory: A comprehensive database for frugivory interactions and functional traits in the Neotropics</b>

description: Frugivory plays a crucial role in shaping Neotropical ecosystems, influencing plant dispersal, community dynamics, and ecosystem function. Despite its ecological significance, a systematic understanding of frugivore-fruit interactions spanning the entire Neotropical realm has been lacking. Therefore, we compiled the NeoFrugivory database, which addresses this gap by synthesizing data from a wide range of sources, including peer-reviewed literature, field studies, and existing databases. NeoFrugivory represents a comprehensive compilation of 10,175 unique frugivory interactions across the Neotropical region, the most diverse in terms of vertebrate frugivores, and consolidates information from 419 studies spanning from 1967 to 2023. It includes 2,375 plant species and 758 terrestrial vertebrate species. In addition to documenting frugivory interactions, NeoFrugivory includes information on functional traits for both plants and vertebrates, such as body weight, diet, fruit morphology, and seed characteristics. The database encompasses diverse terrestrial vertebrate taxa including species belonging to taxonomic groups such as Primates, Chiroptera, Birds, Artiodactyla/Perissodactyla, Reptilia, Carnivora, Marsupialia, and Rodentia. By providing a centralized repository of frugivory interactions, NeoFrugivory facilitates comprehensive analyses of ecological networks, evolutionary patterns, and ecosystem dynamics across the Neotropics, and NeoFrugivory provides a unique resource for researchers interested in exploring the intricate dynamics of plant-animal frugivory interactions in the Neotropics. This database enables researchers to explore the ecological roles of different frugivore taxa, identify keystone species, assess the resilience of mutualistic networks, and evaluate the impacts of environmental change on fruit-frugivore interactions. Furthermore, NeoFrugivory serves as a valuable resource for conservation practitioners, supporting the design and implementation of targeted conservation strategies aimed at preserving biodiversity and ecosystem function in the Neotropical region. Overall, NeoFrugivory represents a significant advancement in our understanding of frugivory dynamics in the Neotropics and provides a foundation for future research and conservation efforts in this ecologically diverse and critically important region.