cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/4wkt6thgp6
title: Data for: Accurate Machine Learning-Based Germination Detection, Prediction and Quality Assessment of Various Seed Cultivars

description: Assessment of seed germination is an essential task for seed researchers to measure the quality and performance of seeds. Usually, seed assessments are done mainly manual, which is a cumbersome, time consuming and error-prone process. Classical image analyses methods are not well suited for large-scale germination experiments, because they often rely on manual adjustments of color-based thresholds. We here propose a machine learning approach using modern artificial neural networks for accurate seed germination detection for high-throughput seed germination experiments.

This dataset contains captures of Germination Experiments of 824 Zea mays seeds, 811 Secale cereale seeds and 814 Pennisetum glaucum seeds. Approximately 10 seeds were placed in one petri dish and captured by a low-cost Raspberry Pi Camera Module (v2.1) in intervals of 30 minutes for ~ 2 days. All Images were annotated by Bounding Boxes containing their germination state (germinated/non-germinated). The code for running the models that are built with this data can be found on GitHub (https://github.com/grimmlab/GerminationPrediction). 
Please cite our original publication if you have used the data in your project or in any follow-up analysis (https://doi.org/10.1186/s13007-020-00699-x):

@article{genze_accurate_2020,
	title = {Accurate machine learning-based germination detection, prediction and quality assessment of three grain crops},
	volume = {16},
	issn = {1746-4811},
	url = {https://doi.org/10.1186/s13007-020-00699-x},
	doi = {10.1186/s13007-020-00699-x},
	abstract = {Assessment of seed germination is an essential task for seed researchers to measure the quality and performance of seeds. Usually, seed assessments are done manually, which is a cumbersome, time consuming and error-prone process. Classical image analyses methods are not well suited for large-scale germination experiments, because they often rely on manual adjustments of color-based thresholds. We here propose a machine learning approach using modern artificial neural networks with region proposals for accurate seed germination detection and high-throughput seed germination experiments.},
	number = {1},
	journal = {Plant Methods},
	author = {Genze, Nikita and Bharti, Richa and Grieb, Michael and Schultheiss, Sebastian J. and Grimm, Dominik G.},
	month = dec,
	year = {2020},
	pages = {157},
}
DOI: 10.17632/zj7ytsrsgj
title: Polarization data for 28 mL MFC reactors

description: Microbial Fuel Cell polarization data collected for 202 days. Data includes: voltage, current, current density, power and power density for 6 reactors.
DOI: 10.6084/m9.figshare.19323527.v1
title: Food Stores Data in Austin

description: These two datasets contain healthy food outlets and unhealthy food outlets in Austin Texas in 2017.
DOI: 10.17632/gmn27hzh3f
title: Supplementary files for JAAD research letter

description: Supplementary files for the paper entitled "The impact of psoriasis on idiopathic pulmonary fibrosis: A two-sample Mendelian randomization study"
DOI: 10.6084/m9.figshare.1383260.v2
title: No-Signaling in Time Raw Data

description: Raw data of the study "A Macroscopic Behavioral Violation of No Signaling In Time Inequalities"
DOI: 10.6084/m9.figshare.23515770.v1
title: KO-to-COGmapping

description: Worksheet includes the mapping of both tRNA modification-relevant and -irrelevant K numbers to their respective overlapping COGs. Representative sequences of Object 4-S2 informed overlap at the sequence-level, maintaining the theme of data being generated and curated corresponding to support provided by published data. Additional tabs include the same data with expanded names as well as other KEGG K number and representative sequence entry-sourced data (e.g., EC numbers).
DOI: 10.6084/m9.figshare.25658037.v1
title: The raw data of the paper named "Ventral subiculum promotes wakefulness through several pathways in male mice".

description: The raw data of the paper named "Ventral subiculum promotes wakefulness through several pathways in male mice".
DOI: 10.6084/m9.figshare.29155688.v1
title: <b>Land use overrides climatic controls on soil organic nitrogen transformations</b>

description: 1. Soil organic nitrogen (SON) transformation is critical for global nutrient cycling and ecosystem productivity, yet how its sensitivity to climate change differs across diverse land use types remains poorly resolved.2. Here, we investigated gross protein depolymerization (GPD), microbial growth, gross N mineralization (GNM), and microbial N use efficiency (NUE) in paired forest and cropland soils along a significant climatic gradient in subtropical China. We aimed to determine the differential climate sensitivity of these SON transformations and elucidate the distinct biogeochemical controls.3. Forest soils exhibited 82% higher GPD and 132% higher microbial N growth rates, alongside 26% higher NUE than cropland soils, despite comparable GMN rates. Critically, SON transformations in forests were highly sensitive to climate with elevated mean annual temperature and precipitation generally enhancing GPD, microbial growth, and GMN, but reducing NUE. In contrast, cropland SON transformations showed markedly dampened responses, with only minor increases in microbial growth and NUE observed with higher temperature. Mechanistic analyses elucidated distinct regulation pathways. In forests, climate indirectly influenced SON transformations via mineral-enzyme interactions (e.g., iron/aluminum oxides modulating protease activity) and resource stoichiometry (e.g., dissolved organic carbon: available phosphorus ratios). GPD was tightly coupled to microbial growth and GMN, acting as a rate-limiting step. In croplands, temperature effects were indirect, mediated through a cascade involving base cation to iron/aluminum oxides ratios, resource availability (free amino acid, carbon to N ratios), and microbial functional gene abundances, with SON transformation processes largely decoupled.
DOI: 10.17632/3tmwgj3g3p
title: Orientation to happiness in university students from Mexico

description: Orientation to happiness is a construct composed of 3 types of happiness: pleasure, meaning, and engagement. This dataset presents the answers from 628 university students in two cities from Sonora, a northeastern state in Mexico. With this data, comparisons by gender, semester, and age can be performed.
DOI: 10.17632/tkwnhzxfh6
title: NOD1 regulates leukocyte dynamics and inflammation in obesity-associated acute lung injury

description: Obesity is a chronic metabolic condition that alters innate immune responses, thereby modulating outcomes in inflammatory diseases such as acute lung injury (ALI). Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) is a cytosolic pattern recognition receptor involved in bacterial sensing and inflammatory signaling. While NOD1 has been implicated in metabolic inflammation, its role in obesity-associated ALI remains unknown. Here, we investigated the impact of NOD1 deficiency on pulmonary inflammation in a model of LPS-induced ALI during obesity. Wild type (WT) and Nod1-/- female mice were fed a control or high-fat diet (HFD) for 10 weeks, followed by intranasal LPS administration and evaluation after 24 hours. In obese Nod1-/- mice, we observed reduced leukocyte and neutrophil recruitment to the bronchoalveolar lavage (BAL), accompanied by increased levels of pro-inflammatory cytokines (TNF-α, IL-1β, IL-6, IL-17A, IL-22), suggesting impaired neutrophil clearance. In the lung parenchyma, NOD1 deficiency during obesity led to elevated neutrophil accumulation, enhanced myeloperoxidase activity and expression, increased cellular senescence (SA-β-Gal), and reduced CD163⁺ macrophages, alongside a shift toward a pro-inflammatory, M1-like phenotype. Furthermore, Nod1-/- obese mice displayed enhanced NF-κB and ERK1/2 activation and reduced p38 phosphorylation. Gene expression analysis confirmed upregulation of chemokines, adhesion molecules, and inflammasome components, along with downregulation of M2 polarization markers. Our findings identify NOD1 as a modulator of leukocyte dynamics and inflammation during obesity-associated ALI. These results suggest NOD1’s protective role in regulating pulmonary immune responses under metabolic stress.
DOI: 10.17632/vy629dngm8
title: Seasonal Corn Leaf Disease Dataset: A Multi-Year Collection for Robust Analysis

description: 1. The horticulture industry places a high value on corn plants because of their economic importance and widespread consumption. Nevertheless, several diseases might substantially negatively influence their well-being and output, making cultivation difficult. For a therapy to be effective, leaf diseases must be accurately and quickly identified. High-resolution images of corn plant leaves were taken from various fields site in Gurudaspur, Natore, Rajshahi, Bangladesh, and are included in this dataset. The images are divided into five distinct classes: Healthy (1038 images), Bacterial Leaf Streak (190 images), Common_rust (129 images), Gray_leaf_spot(1497 images) and Maize Chlorotic Mottle Virus (89images). These classes represent both damaged and healthy leaves. The dataset has 2943 images in total. Comprehensive comments describing the condition's nature and severity are included with every photograph. This data is essential for accurate and trustworthy model training and validation. The information also contains metadata that records the location and surrounding circumstances at the time the photograph was taken. Understanding the environmental factors influencing the prevalence of disease and enhancing the accuracy of predictive models require this contextual information.
2. At the moment, there are a lot of potential deep learning and computer vision techniques to handle these kinds of categorization and detection problems.
3. To create deep learning techniques, an extensive corn leaf disease dataset is provided. The subject matter expert from an agricultural institute collaborated with us to construct the classifications for this dataset.
4. From several different corn farms at the Gurudaspur site in Natore, Bangladesh, a total of 2943 images depicting Healthy (1038 images), Bacterial Leaf Streak (190 images), Common_rust (129 images), Gray_leaf_spot(1497 images) and Maize Chlorotic Mottle Virus (89images) were collected. Then, using methods like flipping, width shifting, height shifting, brightening, rotating, shearing, and zooming, 7500 augmented images are made from these original photos to increase the quantity of data sets.
DOI: 10.6084/m9.figshare.1422174.v1
title: Characterization of Salivary Microbiome in Patients with Pancreatic Cancer

description: TorresEtAl_seqs_FigshareVer_052115.fna is the processed and quality checked data from QIIME, after having run the split_libraries command. It is the seqs.fna file. TorresEtAl_MappingFile_FigshareVer_052115.txt is the mapping file for the sequences that has the metadata and runs in QIIME.
DOI: 10.6084/m9.figshare.16553010.v1
title: Supplementary Material for: Transaminase concentrations cannot separate NAFL and NASH in morbidly obese patients irrespective of histological algorithm

description: Medicine
DOI: 10.6084/m9.figshare.28840769.v1
title: Metagenome-Assembled Genomes from agricultural soils under Managed Aquifer Recharge

description: This dataset contains 160 Metagenome-Assembled Genomes (MAGs) reconstructed from agricultural soils under Managed Aquifer Recharge (MAR) in a vineyard in California, USA. MAGs were assembled from shotgun metagenomic sequences obtained from soil samples collected at different depths, before and after a MAR event. The dataset includes genome files (.fasta) and a table (Quality Metrics) summarizing genome statistics, including completeness, contamination, genome size, N50, L50, GC content, sequencing coverage, and the estimated number of rRNA and tRNA genes. Additionally, corresponding BioSample and GenBank accession numbers are provided for cross-referencing with public repositories.
DOI: 10.6084/m9.figshare.1472857.v2
title: MINI-SPIN sav data

description: MINI-SPIN sav data
DOI: 10.6084/m9.figshare.19145432.v2
title: Online learning experiences of social work students in India.sav

description: This is a dataset on the online learning experience of 202 social work students from India, collected in 2022. The full article associated with this dataset can be found at- https://www.researchgate.net/publication/374820796_Online_learning_experiences_of_social_work_students_in_India
DOI: 10.6084/m9.figshare.22359883.v2
title: <strong>EHPGS: A Statistical Package for Evaluation of Hybrid Performance in Plant Breeding via Genomic Selection </strong>

description: The dataset was used in the article "<strong>EHPGS: A Statistical Package for Evaluation of Hybrid Performance in Plant Breeding via Genomic Selection</strong>". In the dataset, the file name containing TP is the training population file, and the file name containing BP is the breeding population file. The pumpkin dataset is originally from Wu et al. (2019) [1] ,and maize dataset and wheat dataset are originally from Guo et al. (2019) [2]. <br> 1. Wu, PY, Tung, CW, Lee, CY, and Liao, CT (2019) Genomic prediction of pumpkin hybrid performance. Plant Genome 12: 180082. 2. Guo, T, Yu, X, Li, X, Zhang, H, Zhu, C, Flint-Garcia, S. Michael, D, McMullen, JB, Holland, SJ, Szalma, RJ, and Yu, WJ (2019) Optimal Designs for Genomic Selection in Hybrid Crops. Mol Plant 12: 390-401.
DOI: 10.6084/m9.figshare.28381523.v1
title: Concept Inventories Database 2025

description: This dataset includes 49 published biology concept inventories developed between 1987 and 2021. We summarized the content areas, development procedures, and evaluation procedures undertaken for each of these inventories.
DOI: 10.6084/m9.figshare.28045556.v2
title: Genome annotation of <i>Osmia excavata</i>

description: Genome annotation (repeats and protein-coding genes)
DOI: 10.6084/m9.figshare.3522683.v1
title: Appendix A. The forward filtering backward smoothing algorithm.

description: The forward filtering backward smoothing algorithm.
DOI: 10.6084/m9.figshare.8797184.v1
title: Transcriptome assembly of Richtersius coronifer with annotated BLAST result against Ramazzottius varieornatus.

description: For transcriptome sequencing and assembly, total RNA was extracted from a single specimen of tardigrade using Direct-zol RNA kit (Zymo Research) and was amplified using SMARTer Ultra Low Input RNA Kit for Sequencing v.3 (Clonetech). Illumina libraries were prepared using KAPA HyperPlus Kit (KAPA BIosystems), and the library was sequenced using a NextSeq 500 High Output Mode 75 cycles kit (Illumina) as single-end 75bp layout. Protocols are detailed in Arakawa et al. (2016)andYoshida et al. (2018). Sequences were filtered for adapters and demultiplexed using the bcl2fastq v.2 software (Illumina), and were assembled <i>de novo</i>using Bridger software with default parameters (Chang et al. 2015). Completeness of the assembly was assessed using BUSCO v.2/3 transcriptome mode with Eukaryote reference through gVolante server (Nishimura et al. 2017). Gene content was compared with <i>Ramazzottius varieornatus</i>and <i>Hypsibius exemplaris </i>genomes (Yoshida et al. 2017), as well as <i>Drosophila melanogaster</i>and <i>Caenorhabditis elegans</i>reference proteomes obtained from Flybase and Wormbase, respectively. Annotated BLAST result to <i>R. varieornatus </i>reference proteome with BLASTX (-e 1e-5) is also provided with the transcriptome assembly.
DOI: 10.17632/3xdpk76v8b
title: Supplementary Material - Regression trees to identify combinations of farming practices that afford the best overall intrinsic quality of milk

description: Supplementary file S1 Adaptations made on the assessments from Rey-Cadilhac et al. (2021)
Supplementary file S2 Correlation between dimension scores and both overall quality and indicator scores of the UHT milk assessment.
Table S1 Milking machine routine score calculation
Table S2 Teat cleaning routine score calculation
Table S3: Definition of the modalities of the variable Complexity of the milking equipment pipeline
Table S4 Description of modalities of the variable Diet_forage
Table S5 Description of the indicators at the base of the sensory, technological, health and nutrional dimensions of the cheese assessment 
Table S6 Correlation coefficients between quantitative farming practices variables
Table S7 Correlation ratios between quantitative and qualitative farming practices variables
Table S8 Cramer's V coefficients between qualitative farming practices variables
Figure S1 Variable importance plots obtained from random forest analysis for construction of overall cheese quality (A), and cheese sensory (B), technological (C), health (D) and nutritional (E) dimensions regression trees
Figure S2 Variable importance plots obtained from random forest analysis for construction of overall UHT milk quality (A), and UHT milk sensory (B), technological (C), health (D) and nutritional (E) dimension regression trees
Figure S3 Regression trees explaining UHT milk sensory, technological, health and nutritional dimensions from farming practices.
DOI: 10.6084/m9.figshare.24131754.v1
title: IDENT tree trait database

description: Soon...
DOI: 10.17632/22symh9gs4
title: TGA-Data

description: Thermogravimetry Data
DOI: 10.17632/2p7mbbhn47
title: Design and Validation of an Open-Sourced Automation System for Vertical Farming

description: The Modular Automated Crop Array Online System (MACARONS) is a scalable, customiseable and open-sourced platform designed for plant care, monitoring, and transportation. It offers specific dosing for individual plants, automated data logging of temperature, humidity, and images, and custom behaviours programmable in Python. Monitoring and control of the system is achieved through a web-interface. The system was validated by autonomously caring for five lettuce plants over a five-week period. The system is estimated to perform the tasks required 30% faster than a human operator and can handle payloads of up to 5kg with a maximum footprint of 750mm x 500mm. The designs are released and meets the requirements of CERN-OSH-W, which includes step-by-step graphical build instructions and can be built at a cost of GBP 2241.72.
DOI: 10.17632/6nhpgnxf3y
title: Post-Gastrulation Synthetic Embryos Generated Ex Utero Solely from Naïve ESCs

description: Four Supplementary figures  (M1-M6) that were peer reviewed, but due to space limitations are deposited on Mendeley and are directly linked to the parental published manuscript.
DOI: 10.17632/knns8w4wwy
title: Dataset: Teachers, Scientific Practices in the School and Artificial Intelligence

description: Search codes and databases for a systematic review on school scientific practices involving artificial intelligence. This summary details the databases used, the specific date range covered, the exact search codes applied, the total number of studies identified, and the final selection process for eligible studies within the review's scope. Additionally, it includes a list of the selected empirical studies and the appendices with the data coding.
DOI: 10.6084/m9.figshare.13728271.v1
title: MODIS_satellite_data

description: Remote sensing component of data in Newman & Furbank (2021) Sci. Data.<br>
DOI: 10.6084/m9.figshare.14813154.v1
title: PLUMEX current data

description: Current data measured by a shipboard Teledyne RDI Ocean Surveyor and a Mariner Workhorse Acoustic Doppler Current Profiler sensors (ADCP) aboard R/V Sally Ride during the discharge and tracking of the CCFZ sediment plume.<br>
DOI: 10.6084/m9.figshare.9938138.v1
title: Supplementary Material for: Clinical and Spectrophotometric Evaluation of Skin Photoadaptation in Vitiligo Patients after a Short Cycle of NB-UVB Phototherapy

description: <b><i>Background:</i></b> The phenomenon of photoadaptation to narrow-band ultraviolet B (NB-UVB) radiation has been previously described in vitiligo and has usually been clinically measured by the assessment of the minimal erythema dose (MED) after phototesting. <b><i>Objectives:</i></b> To assess the photoadaptive response in vitiligo and healthy skin after NB-UVB phototherapy not only clinically, but also by spectrophotometry. <b><i>Materials and Methods:</i></b> Fourteen patients affected by generalized vitiligo underwent NB-UVB phototherapy twice weekly for 12 weeks. Before and after phototherapy, a phototesting procedure was administered on vitiligo patches and adjacent healthy skin with a solar simulated radiation (SSR). Visual assessment of the MED took place after 24 h. A spectrophotometer was used to assess the a* value and the melanin index (MI*), as signs of skin erythema and pigmentation. The photoadaptation factor (MED-PF) and the a* photoadaptation factor (a*-PF) were calculated. <b><i>Results:</i></b> After NB-UVB phototherapy, both vitiligo and healthy skin showed an increase in MED and MI* values and a reduction of skin erythema compared to baseline (<i>p</i> &lt; 0.05). MED-PF data showed a photoadaptation in 10 (71.4%) vitiligo lesions and in 12 (85.7%) healthy skin areas. The assessment of the a*-PF showed a negative mean percentage value in all affected and unaffected skin areas. <b><i>Conclusions:</i></b> A short cycle of NB-UVB phototherapy can induce photoadaptation in vitiligo by increasing the MED and reducing skin erythema after stimulation with SSR. This is most likely due to the physical filter function induced by ultraviolet radiation.
DOI: 10.17632/9nv3m2y2jg
title: Effects of two types of environmental enrichment on the behavior of shelter dogs

description: Data used to evaluate the effects of different enrichment items on the behavior of shelter dogs in Ouro Preto, Brazil
DOI: 10.15468/dl.54fu2q
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Paspalidium paludivagum (Hitchc. & Chase) Parodi",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 39 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013046-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/64d66xntjx
title: Study on high and low quality and frozen semen protein omics of Sewa sheep

description: Different groups of semen differential protein data and differential protein GO and KRGG analysis data.
DOI: 10.17632/mtvfdwm3dt
title: DATA SET OF LEARNING STYLE PREFERENCE

description: The data presents the learning styles of elementary school students in the province of DIY. The total number of participants was 992 elementary school students in grades 4-5 in five districts in DIY. Participants were sampled from two types of school systems being non-religious schools and religious school. The data collection method uses an open questionnaire to see three aspects of learning styles, namely visual, auditory, and kinesthetic. Analysis of the data can provide insight into the types of learning styles so that it is beneficial for teachers to choose the right learning strategy. This data can also be used as a reference in developing student learning style interventions according to the type of learning.