cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5411215.v1
title: CCS-Sample2-with-new & former-respondents-Study2

description: Datasets 2 and 3 of the Validation studies (Study 2) of the Community Collectivism Scale.<br>Data collected via online questionnaire in <b>Dutch language.</b>
DOI: 10.17632/k54hnzxp3j
title: An advanced analytical assessment of rare earth element concentration, distribution, speciation, crystallography and solid-state chemistry in fly ash

description: Data sets from the analysis of individual monazite particles A, B and C (isolated from fly ash material) via synchrotron radiation techniques (µ-XANES, µ-XRD, µ-XRF and µ-XRF tomography), aimed at understanding the distribution and speciation of rare earth elements within the monazite particles, and also the crystallography of the monazite particles. The results obtained are essential in developing a fundamental understanding of the distribution and colocalisation of REE, U and Th within monazite particles, and therefore in the optimisation of recovery methods for such metals/minerals for both resource recovery and environmental protection.
DOI: 10.25375/uct.20444610.v1
title: Camelthorn trees Vachellia erioloba provide an important resource for breeding Southern Pied Babblers Turdoides bicolor in the southern Kalahari

description: In the southern Kalahari Desert, cooperatively breeding Southern Pied Babblers <em>Turdoides bicolor</em> frequently build their nests and forage in camelthorn trees <em>Vachellia erioloba</em>, a keystone species in the region. Using Ivlev’s electivity indices (Ei), we show that Southern Pied Babblers preferentially nest (Ei = 0.18) and forage (Ei = 0.24) in camelthorn trees. Southern Pied Babblers primarily forage on the ground, however they will make use of arboreal resource when these are available. We observed the birds spending the highest proportion of foraging time off the ground during October, when breeding is also most common, compared to all other months within the austral summer breeding season. They are most likely to be observed in camelthorn trees earlier compared to later in the breeding season.We demonstrate that Southern Pied Babblers have a strong relationship with camelthorn trees, in which they prefer to nest and forage. We highlight the importance of protecting camelthorn trees, a keystone species in the region, as part of the conservation and management of endemic Kalahari fauna such as the Southern Pied Babbler. In addition to contributing to the literature on keystone species, our observations raise interesting questions about the ways in which avian reproduction in the arid zone could be decoupled from rainfall via the phenology of deep-rooted tree species.
DOI: 10.6084/m9.figshare.19328816.v1
title: Reconstruction of Large and Complex Cranial Defects

description: This repository contains the automatically generated (with minor manual post-processing) cranial implants (in NRRD format) for the 29 craniotomy skulls in the MUG500+ dataset (https://doi.org/10.6084/m9.figshare.9616319) and the 11 defective skulls from Task 2 of the AutoImplant II challenge (https://autoimplant2021.grand-challenge.org/).<br>The video ('implant manual cleaning.mp4') shows how the resulting implant (subtraction between the reconstructed skull and the defective skull) can be post-processed manually using 3D slicer.<br>If you use any part of the dataset, please cite the following:<br>(1) Li J., et al. MUG500+: Database of 500 High-resolution Healthy Human Skulls and 29 Craniotomy Skulls and Implants. Data in Brief, Elsevier, 2021.(2) Li, J., et al. Reconstructing Large and Complex Cranial Defects Using an Image-based Statistical Shape Model<br>
DOI: 10.6084/m9.figshare.20787628.v1
title: Supplementary Tables for Constraining the timing of deep magmatic pulses from diamondiferous kimberlite and related rocks in South China and implications for mantle upwelling

description: <strong>Supplementary Tables for </strong><em><strong>Constraining the timing of deep magmatic pulses from diamondiferous kimberlite and related rocks in South China and implications for mantle upwelling</strong></em>
DOI: 10.6084/m9.figshare.24427060.v1
title: League 1 B Teams (under 23s) Bilateral Force Plate Data.xlsx

description: This spreadsheet contains anonymised force plate data for the following tests: countermovement jump, countermovement-rebound jump, and isometric mid-thigh pull.Following a dynamic warm-up, three trials of each of these tests were performed bilaterally and with maximum-effort by male B Team football players (Under 23s) from two English League One Football Clubs at the beginning of the 2023-24 football pre-season period. The tests were performed in a randomised order with around 30-60 seconds of rest between trials and at least 3-5 minutes of rest given between tests.The data were collected on Hawkin Dynamics force plates and analysed by their software. Here is the link to the Hawkin Dynamics metric database that explains how each metric included in the spreadsheet was measured: https://www.hawkindynamics.com/hawkin-metric-databaseEthics approval was granted from the author's institution and informed consent was provided by each player for their anonymised data to be uploaded to this repository for research use.
DOI: 10.6084/m9.figshare.3526157.v1
title: Appendix B. Summary assessments of productivity–plant species richness relationships not included in Mittelbach et al. (2001).

description: Summary assessments of productivity–plant species richness relationships not included in Mittelbach et al. (2001).
DOI: 10.17632/kxzkk69pr6
title: Data for: Identification of microplastics in surface water and Australian freshwater shrimp Paratya australiensis in Victoria, Australia

description: for processing water and shrimp samples from the field
DOI: 10.17632/y5662dvjgm
title: Deep learning ensembles of Long Short-Term Memory Networks to predict ammonia dynamics for aeration control in WWTPs: AdaBoost versus Bagging

description: To cite the provided dataset for building prediction models, please reference the following paper:
Shi H, Wei A, Zhu Y, Tang K, Hu H, Li N. Accurate and robust ammonia level forecasting of aeration tanks using long short-term memory ensembles: A comparative study of Adaboost and Bagging approaches. J Environ Manage. 2024;371:123173. doi: 10.1016/j.jenvman.2024.123173. 

This data article provides the data set and all the codes for the study. The dataset is the ammonia nitrogen concentration of the aerobic tank in the wastewater treatment plant, which was recorded every 2 minutes from 04 July 2022 to 2010 July 2022, with a total of 5041 samples. The codes included the Adaboost and Bagging techniques, LSTM, CNN-LSTM and the seasonal decompose function.
DOI: 10.6084/m9.figshare.20454432.v3
title: Genome assembly and gene structure annotation for S. americanum

description: Genome assemblies and annotations of S. americanum
DOI: 10.6084/m9.figshare.20533715.v2
title: Minimum temperature (PISCOt v1.2)

description: Minimum air temperature from PISCOt v1.2. (i) Monthly means (normals) are provided in one file. (ii) Daily values are divided per year from 1981 to 2020. (i) and (ii) are the results from the climate-aided interpolation at normal- and daily-scale, respectively
DOI: 10.17605/osf.io/3xwn4
title: Sound symbolism facilitates inter-species communication between humans and domestic dogs (Canis familiaris) Data
DOI: 10.6084/m9.figshare.13484715.v2
title: Subgroups of foot-ankle movement patterns can influence the responsiveness to a foot-core exercise program: a hierarchical cluster analysis

description: Demographic, anthropometric and running practice data from asymptomatic runners that participated in a randomized controlled trial testing the effects of an 8-week foot-core training program.Kinematic data include the joint angles of foot and ankle joints during the stance phase of running (normalized by stance phase time and averaged across steps) from baseline and week-8 assessment.Kinematic time-series data also included for each step (time-normalized by stance phase).
DOI: 10.6084/m9.figshare.23805456.v1
title: 2,500,000 anonymized BMP results for the manuscript "Automating the Detection of IV Fluid Contamination Using Unsupervised Machine Learning"

description: This study was approved by the Washington University Institutional Review Board (IRB #202202030). All basic metabolic panel (BMP) measurements from inpatients at a single hospital were extracted directly from the laboratory information system (Cerner, Kansas City, USA). This encompassed 25,747,291 chemistry results measured on 2,567,403 specimens drawn from 312,721 patients. Specimens drawn from patients in cardiac arrest and any other active “code blue” specimens were excluded. Results reported as above or below a threshold value were replaced with that threshold (e.g. a sodium reported as ‘&gt;180mEq/L’ was changed to 180mEq/L). Anion gap was calculated as sodium minus chloride and bicarbonate.
DOI: 10.6084/m9.figshare.28755158.v1
title: Minimal dataset for Effects of sake lees intake on fecal uremic toxins, plasma D-alanine, constipation, and gut microbiome in healthy adults: A single-arm clinical trial

description: <b>Background: </b>Sake lees consumption has the potential to reduce uremic toxins by influencing the gut microbiome. To lay the groundwork for a clinical trial targeting chronic kidney disease (CKD) patients, we conducted a pilot study to explore the relationship between sake lees intake and changes in fecal uremic toxin levels among individuals with constipation. D-alanine, a renoprotective component of sake lees, was also evaluated.<br><b>Methods:</b> This single-arm, before and after study lacked a control group. Participants met the diagnostic criteria for chronic constipation. They consumed 25 or 50 g of sake lees daily for 6 weeks. The primary endpoint was the change in fecal indole levels from baseline. Secondary endpoints included changes in plasma D-alanine, Constipation Scoring System (CSS) scores, and the composition of the fecal microbiome.<b>Results:</b> Eight participants, with a mean age of 46 years, completed the study. Percentage changes in fecal indole levels were +42%, +52%, and −6% at weeks 2, 4, and 6, respectively. Plasma D-alanine levels showed percentage changes of +39%, +24%, and +38% at the same time points. CSS scores improved from 9.2 to 6.8 by week 2 and remained stable after week 4. The proportion of the phylum Firmicutes in the gut microbiome increased slightly from 53% at baseline to 57% by week 6.<br><b>Conclusion:</b> Sake lees intake may reduce fecal uremic toxins, elevate plasma D-alanine levels, alleviate constipation, and modify the gut microbiome. However, future studies are needed to confirm these effects in patients with CKD.<b>Dataset description:</b> This dataset contains the minimal underlying data from a single-arm clinical trial investigating the effects of sake lees intake on uremic toxins, D-amino acids, and gut-related parameters in healthy adults. The study measured several biological markers before and after the intervention period, including plasma D-alanine and D-serine, as well as fecal levels of indole and p-cresol. Participant demographics such as age, sex, and BMI are also included.<br><b>Column descriptions:</b><br>group: Intervention group assignment (0 = participants who consumed 25g of sake lees per day; 1 = participants who consumed 50g of sake lees per day).week: Time point of data collection (0 = baseline, 2 = week 2, 4 = week 4, 6 = week 6).<br>age: Age of the participant (years).male: Participant sex (1 = male, 0 = female).<br>bmi: Body Mass Index (kg/m²).d_ala: Plasma D-alanine level (nmol/mL).<br>d_ser: Plasma D-serine level (nmol/mL).indole: Fecal indole level (μg/g).<br>p_cresol: Fecal p-cresol level (μg/g).
DOI: 10.17632/ccpb9jd8j6
title: ACCES Calibration and Validation of Discrete Element Method Simulations

description: Data accompanying the paper on ACCES evolutionary optimisation-based calibration of simulations, with an application on Discrete Element Method (DEM) calibration of digital models of powder-handling equipment. This dataset includes the particle size distributions (PSDs), Positron Emission Particle Tracking (PEPT) experimental trajectories of radioactively-labelled tracers, ACCES calibration scripts and logs, LIGGGHTS DEM digital models of the GranuDrum rotating drum, Pascall tumbling mixer and ResoDyn acoustic mixer (including meshes, LIGGGHTS definition and launch scripts), and post-processing scripts.
DOI: 10.17632/kmm8csh69w
title: The leakage through an inclined fracture of caprock in CO2 Sequestration
DOI: 10.6084/m9.figshare.11787096.v1
title: Additional file 1 of Metabolic engineering of the cellulolytic thermophilic fungus Myceliophthora thermophila to produce ethanol from cellobiose

description: Additional file 1. Additional tables.
DOI: 10.6084/m9.figshare.1526129.v1
title: Common names of African trees

description: This is a list of common names of African plants in many different languages. The data come from a variety of published sources which are all referenced.
DOI: 10.6084/m9.figshare.4659220.v1
title: Supplementary Material for: First Diagnosis of Atrial Fibrillation at the Time of Stroke

description: <b><i>Background:</i></b> Atrial fibrillation (AF) is a major cause of ischemic stroke. Individuals with undiagnosed AF lack the stroke protection afforded by oral anticoagulants. We obtained a contemporary estimate of the percentage of AF patients newly diagnosed at the time of stroke. <b><i>Methods:</i></b> We identified patients admitted to the Massachusetts General Hospital (MGH) from January 1, 2010 to December 31, 2013 with acute ischemic stroke and either previously or newly diagnosed AF using hospital stroke registry data and stroke and AF ICD-9 code searches of hospital databases. Reviewers categorized AF as previously known or newly diagnosed, and collected comorbidity and outcome data. To confirm AF as newly diagnosed, we searched patients' pre-event electronic medical records (EMRs) for AF terms. <b><i>Results:</i></b> AF was considered newly diagnosed in 156/856 patients (18%; 95% CI 16-21). In 136/156 cases, AF was diagnosed using 12-lead EKG, telemetry, or rhythm strips. New AF strokes had a median NIH stroke scale of 12; 60% had mRankin ≥3 at discharge, including 15% deaths. Pre-stroke CHA<sub>2</sub>DS<sub>2</sub>-VASc score was ≥2 in 89%. About half (76/156) had prior records in the MGH EMR. Evidence of pre-stroke AF, often peri-procedural, was found in 8/76, but the AF diagnosis was not carried forward. <b><i>Conclusions:</i></b> In this contemporary cohort, nearly one in 5 AF-related strokes occurred without a pre-stroke AF diagnosis. AF was readily diagnosed using standard rhythm monitoring. The vast majority of patients with newly diagnosed AF were at high enough pre-stroke risk to merit anticoagulation. In conclusion, our findings support screening for AF before stroke. Patients with past transient AF may merit more intensive screening.
DOI: 10.17632/d4rrfy3dy4
title: Expanding PyProcar for new features, maintainability, and reliability

description: This paper presents a comprehensive update to PyProcar, a versatile Python package for analyzing and visualizing density functional theory (DFT) calculations in materials science. The latest version introduces a modularized codebase, a centralized example data repository, and a robust testing framework, offering a more reliable, maintainable, and scalable platform. Expanded support for various DFT codes broadens its applicability across research environments. Enhanced documentation and an example gallery make the package more accessible to new and experienced users. Incorporating advanced features such as band unfolding, noncollinear calculations, and derivative calculations of band energies enriches its analytic capabilities, providing deeper insights into electronic and structural properties. The package also incorporates PyPoscar, a specialized toolkit for manipulating POSCAR files, broadening its utility in computational materials science. These advancements solidify PyProcar's position as a comprehensive and highly adaptable tool, effectively serving the evolving needs of the materials science community.
DOI: 10.17632/dp45bdgddn
title: Data for: Predicting the thermodynamic stability of perovskite oxides using machine learning models

description: Supplemental information for the paper: Predicting the thermodynamic stability of perovskite oxides using machine learning models. This contains the dataset of the stability data of over 1900 perovskite oxides and the source code for predicting the stability of new compositions.
DOI: 10.17632/rkfvnzydvz
title: RefWorks Literature Dataset (2003-2019)

description: The RefWorks reseach & publication dataset, which was indexed by Scopus from 2003 to 2019. The dataset contains data authors, authors ID Scopus, title, year, source title, volume, issue, article number in Scopus, DOI, link, affiliation, abstract, index keywords, references, Correspondence Address, editors, publisher, conference name, conference date, conference code, ISSN, language, document type, access type, and EID.
DOI: 10.6084/m9.figshare.2061132.v1
title: Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus

description: In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for &gt;260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome anno- tation in S. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in S. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions.
DOI: 10.6084/m9.figshare.28082420.v1
title: Microplastic Concentration by Location (Monthly Averages) (Units particlesm³).pdf

description: This study examines the concentration and effects of microplastics in Pacific coastal waters and their impact on marine organisms. Water samples from 15 different coastal locations were analyzed over 12 months. Results indicate significant microplastic contamination affecting marine life at multiple trophic levels. The findings emphasize the urgent need for improved plastic waste management and conservation measures.
DOI: 10.6084/m9.figshare.953671.v3
title: Advancing Bag-of-Visual-Words Representations for Lesion Classification in Retinal Images

description: Diabetic Retinopathy (DR) is a complication of diabetes that can lead to blindness if not timely discovered. Automated screening algorithms have the potential to improve identification of patients who need further medical attention. However, the identification of lesions must be accurate to be useful for clinical application. The bag-of-visual-words (BoVW) algorithm employs a maximum-margin classifier in a flexible framework that is able to detect the most common DR-related lesions such as microaneurysms, cotton-wool spots and hard exudates. BoVW was developed to bypass the need for pre- and post-processing of the retinographic images, as well as the need of specific <em>ad hoc </em>techniques for identification of each type of lesion. An extensive evaluation of the BoVW model, using three large retinograph datasets (DR1, DR2 and Messidor) with different resolution and collected by different healthcare personnel, was performed. The results demonstrate that the BoVW classification approach can identify different lesions within an image without having to utilize different algorithms for each lesion reducing processing time and providing a more flexible diagnostic system. Our BoVW scheme is based on sparse low-level feature detection with a Speeded-Up Robust Features (SURF) local descriptor, and mid-level features based on semi-soft coding with max pooling. The best BoVW representation for retinal image classification was an area under the receiver operating characteristic curve (AUC-ROC) of 97.8% (exudates) and 93.5% (red lesions), applying a cross-dataset validation protocol. To assess the accuracy for detecting cases that require referral within one year, the sparse extraction technique associated with semi-soft coding and max pooling obtained an AUC of 94.2±2.0%, outperforming current methods. These results indicate that, for retinal image classification tasks in clinical practice, BoVW is equal and, in some instances, surpasses results obtained using dense detection (widely believed to be the best choice in many vision problems) for the low-level descriptors.