cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20250126.v1
title: Shahan_chamber_data.xlsx

description: Daytime soil CO<sub>2</sub> and CH<sub>4</sub> chamber flux data collected from June 2020 to June 2021 in a restored tidal saltmarsh at the Eden Landing Ecological Reserve. The soil surface within a given collar was 79 cm<sup>2</sup> and the average volume was 1,860 cm<sup>3</sup>. The collars were inserted 19 cm into the soil with 0.5 cm holes drilled to allow for water flow. The chamber top was opaque to simulate dark conditions, equipped with a fan to promote mixing, and connected via tubing to a CO<sub>2</sub> and CH<sub>4</sub> gas analyzer (LI‑7810, LI-COR, Lincoln, NE, USA). CO<sub>2</sub> and CH<sub>4</sub> concentrations were measured and recorded with 1 Hz frequency, allowing soil chamber closure time to be short around 3 min. Therefore, all collar locations were measured within a 2 hr window, minimizing the difference in ambient conditions between collar measurements. The trace gas analyzer was calibrated every three to six months in the laboratory.
DOI: 10.6084/m9.figshare.24746607.v1
title: Antimicrobial peptides

description: The data set collected 5,000 antimicrobial peptide chains for research combining deep learning and clinical medicine
DOI: 10.6084/m9.figshare.29005283.v1
title: <b>Human Urine Sediment Induces Apoptosis in Esophageal Squamous Cell Carcinoma through the Nonanedioic Acid–BAK1 Axis: Network Pharmacology, Molecular Docking, and In Vitro Validation </b>

description: Esophageal squamous cell carcinoma (ESCC) remains refractory to chemoradiotherapy and relapses frequently. Human urine sediment, a traditional medicine known as Ren Zhong Bai, has historical indications for throat ulceration, yet its anticancer mechanism is undefined. Integrated mass spectrometry, network pharmacology and molecular docking were applied to link HUS constituents with differentially expressed genes from The Cancer Genome Atlas. Immune infiltration and drug sensitivity were explored bioinformatically. In vitro efficacy was assessed in KYSE‑30 and KYSE‑150 cells by Cell Counting Kit‑8 proliferation assay and Annexin V flow cytometry. Four hundred forty‑six HUS target genes overlapped with tumor gene dysregulation and were enriched for apoptotic and PI3K–Akt pathways. Serum metabolomics identified 15 absorbed compounds, and Nonanedioic acid uniquely docked with high affinity to lysine-87 of the pro‑apoptotic protein BAK1. Tumors showed higher BAK1 expression than normal tissue and worse differentiation with elevated expression. High BAK1 correlated with resting natural killer cell infiltration, while low BAK1 predicted greater sensitivity to multiple cytotoxic and targeted agents. HUS serum significantly reduced proliferation and increased apoptosis in both ESCC lines, whereas blank serum had no effect.<b> </b>These findings pave the way for further research to validate that HUS exerts antiproliferative activity in ESCC through a Nonanedioic‑acid–BAK1 axis that activates mitochondrial apoptosis and reshapes the immune microenvironment. BAK1 emerges as a dual biomarker for HUS responsiveness and drug stratification, providing a molecular rationale to repurpose a traditional remedy as an adjunct to current therapy.
DOI: 10.17632/328bk4nynr
title: The Cross-border Effects of Bank Capital Regulation: Replication Files

description: This dataset provides replication files for "The Cross-border Effects of Bank Capital Regulation." by Saleem Bahaj and Fred Malherbe published in the Journal of Financial Economics. The code is to replication Figure 3.
DOI: 10.17632/bsbj9fbgyy
title: A database of 98 climate-relevant social protection programs in emerging and developing economies

description: The database maps the integration of climate considerations in social protection programs in emerging and developing economies. Using a mixed-methods approach, we identified 98 climate-relevant social protection programs and collected data on over 70 variables related to their scope and climate relevance at policy, design, and implementation level. 
The database might periodically be revised to improve the data points for each program (including referencing, coding, etc.). We do not intend to add new programs to it. 
Please ensure to download and cite the latest version of the database available in this page for the most up-to-date and precise data. 
We encourage researchers and practitioners to use the database in building a more comprehensive understanding of climate-relevant social protection programs worldwide.
DOI: 10.6084/m9.figshare.22643245.v1
title: Read-count data of 11 angiosperm species under different time points of cold treatments

description: Read count datasets of 11 representative angiosperm species under different time points of cold stress treatments. At: <em>Arabidopsis thatliana</em> Bp: <em>Betula pendula</em> Pt: <em>Populus trichocarpa</em> Ci: <em>Carya illinoinensis</em> Gm: <em>Glycine max</em> Cs: <em>Cucumis sativus</em> Os: <em>Oryza sativa</em> Si: <em>Setaria italica</em> Hv: <em>Hordeum vulgare</em> Zm: <em>Zea mays</em> Pe: <em>Phyllostachys edulis</em>
DOI: 10.6084/m9.figshare.28871030.v1
title: Data associated with "Piercing the veil: A novel amoebozoan (<i>Janelia veilia</i> n. gen. n. sp.) reveals deep clades within Discosea through phylogenomics". This includes RNAseq assemblies from new taxa sequenced, phylogenetic datasets (alignments - Trimmed and Untrimmed) for the SSU rRNA gene tree, Phylogenomic datasets (alignments - Trimmed and Untrimmed) from the PhyloFisher dataset, all phylogenetic and phylogenomic trees, and supplemental videos of taxa.

description: This is the data associated with the manuscript "Piercing the veil: A novel amoebozoan (<i>Janelia veilia</i> n. gen. n. sp.) reveals deep clades within Discosea through phylogenomics" by Jones et al.<b>ABSTRACT</b>Three major groups of primarily amoeboid taxa are present across Amoebozoa: Discosea, Evosea, and Tubulinea. While each of these groups were thought to have morphologically unique traits and members, the morphologic boundaries between each group have recently blurred. For example, it is demonstrated that several taxa in each group display monopodial limax amoebae, a characteristic most often associated with Tubulinea. Here we describe a novel discosean amoeba isolated from a freshwater pond, <i>Janelia veilia</i> n. gen. n. sp. Its cells have variable morphologies, but often display monopodial limax amoebae, with a unique trailing structure that appears to be derived from cellular material. In some cases, cells have conical pseudopodia or pointed pseudopodia. Using phylogenomics, we find that this taxon branches as sister to the recently described discosean <i>Mycamoeba</i> <i>gemmipara</i> and the sporocarpic protosteloid amoeba <i>Microglomus</i> <i>paxillus</i>, forming an order-level group we term Mycamoebida. Mycamoebida is fully supported as sister to Dermamoebida, together forming a subclass we term Dermelia. SSU rRNA phylogenies show that <i>Janelia veilia</i> n. gen. n. sp. is molecularly unique from any known organism, but branches with high support in a clade containing <i>Mycamoeba</i> <i>gemmipara</i> and several environmental sequences suggesting a larger diverse clade within Discosea.<br>
DOI: 10.6084/m9.figshare.29045501.v1
title: Data supporting the findings

description: Data supporting the findings of the study: EVALUATING THE ACCURACY OF GENERATIVE AI MODELS IN DENTAL AGE ESTIMATION BASED ON THE DEMIRJIAN METHOD
DOI: 10.6084/m9.figshare.29100578.v1
title: Exceptionally low genomic diversity in the underutilised legume Kersting’s groundnut (Macrotyloma geocarpum)

description: Identifying crops with novel and climate resilience traits is imperative to ensure food security. Many of these underutilised crops suffer from a lack of international recognition and without some basic understanding of their genomes and genomic diversity they will remain to be underutilised, or could even become lost, without breeding programmes being able to utilise their diversity. Kersting’s groundnut (<i>Macrotyloma geocarpum</i> (Harms) Maréchal & Baudet) is one such crop, regarded as a useful, drought tolerant and sometimes valuable legume which grows its beans underground akin to peanut. In this work we used whole genome resequencing to analyse the amount and partitioning of genomic variation.
DOI: 10.17632/9zxrt6pf2k
title: Operational Data for Fault Prognosis in Particle Accelerators with Machine Learning

description: This repository showcases real-world operational data gathered from the power systems of the Spallation Neutron Source facility, renowned for delivering the world's most intense neutron beam. This dataset serves as a valuable resource for crafting techniques and algorithms aimed at preemptively identifying system faults, enabling timely operator intervention, and effective maintenance oversight. The authors utilized a radio-frequency test facility (RFTF) to conduct controlled laboratory experiments simulating system failures, all without triggering a catastrophic system breakdown. The dataset comprises waveform signals obtained during both regular system operations and deliberate fault induction efforts, offering a substantial amount of data for training statistical or machine learning models. Afterward, the authors carried out 21 test experiments wherein they gradually introduced faults into the RFTF system to evaluate the models' effectiveness in detecting and preempting impending faults. These experiments involved combinations of magnetic flux compensation and adjustments to start pulse width, leading to a gradual deterioration in various waveform aspects such as system output voltage and current. These alterations effectively mimicked real fault scenarios. All experiments took place at the Oak Ridge National Laboratory's Spallation Neutron Source facility in Oak Ridge, Tennessee, United States, during July 2022. The users of this dataset may include researchers in control, predictive maintenance, machine learning, and signal processing.
DOI: 10.6084/m9.figshare.1314550.v1
title: Helioprop Table

description: Output from Helioprop code for charge dependent modulation
DOI: 10.6084/m9.figshare.14813121.v3
title: Parameters and load data

description: " <strong>Parameters and load data1.xlsx</strong>": The parameters and load data of the modified Barry Island HE-IES and an industrial park HE-IES. The original data is refered from "X. Qin, X. Shen, Y. Guo, Z. Pan, and Q. Guo, “Combined electric and heat system testbeds for power flow analysis and economic dispatch,” CSEE J. Power Energy Syst., vol. 7, no. 1, pp. 34–44, Jan. 2021.". " <strong>Case-data of large-scale EH-IES.xlsx</strong>": The parameters and load data of a large-scale EH-IES modified from "X. Qin, X. Shen, Y. Guo, Z. Pan, and Q. Guo, “S. Yao, W. Gu, S. Lu, S. Zhou, Z. Wu, G. Pan, and Di He, “Dynamic optimal energy flow in the heat and electricity integrated energy system,”IEEE Trans. Sustain. Energy, vol. 12, no. 1, pp. 179–190, Aug. 2021.".
DOI: 10.6084/m9.figshare.19586503.v1
title: Phylogeny, taxonomy, and character evolution in Entoloma subgenus Nolanea — Alignments

description: Alignments to the corresponding phylogenetic trees in the respective paper on Entoloma subg. Nolanea. <br> Multi_locus_full = used for the multi-locus tree <br> ITS_full = used for the large ITS-tree (Suppl. 1) and several pieces with collapsed clades in several figures <br> ACR_algn = used for the ancestral character state analyses <br> starting with "Ktreedist..." = used to test the performance of the different loci
DOI: 10.6084/m9.figshare.23598684.v1
title: <strong>Plant traits modulate grassland stability during drought and post-drought periods</strong>

description: 1. Grasslands are subject to climate change, such as severe drought, and an important aspect of their functioning is temporal stability in response to the extreme climatic events. Previous research has explored the impacts of extreme drought and post-drought periods on grassland stability, yet the mechanistic pathways behind these changes have rarely been studied. 2. Here, we implemented an experiment with four years of drought and three years of recovery to assess the effects of drought and post-drought on the temporal stability of aboveground net primary productivity (ANPP) and its underlying mechanisms. To do so, we measured community-weighted mean of six plant growth and nine seed traits, functional diversity, population stability, and species asynchrony across two cold-semiarid grasslands in northern China. We also performed piecewise structural equation models (SEMs) to assess the relationships between ANPP stability and its underlying mechanisms, and how drought and post-drought periods alter the relative contribution of these mechanisms to ANPP stability. 3. We found that temporal stability of ANPP was not reduced during drought due to grasses maintaining productivity, which compensated for increased variation of forb productivity. Moreover, ANPP recovered rapidly after drought, and both grasses and forbs contributed to community stability during the post-drought period. Overall, ANPP stability decreased during the combined drought and post-drought periods because of rapid changes in ANPP from drought to post-drought. SEMs revealed that the temporal stability of ANPP during drought and post-drought periods was modulated by functional diversity and community-weighted mean (CWM) traits directly and indirectly by altering species asynchrony and population stability. Specifically, the temporal stability of ANPP was positively correlated with functional divergence of plant communities. CWMs of seed traits (e.g., seed width and thickness), rather than plant growth traits (e.g., specific leaf area and leaf nutrient content), stabilized grassland ANPP. Productivity of plant communities with large and thick seeds was less sensitive to precipitation changes over time. 4. These results emphasize the importance of considering both the functional trait distribution among species and seed traits of dominant species since their combined effects can stabilize ecosystem functions under global climate change scenarios.
DOI: 10.6084/m9.figshare.23613939.v1
title: Neisseria mucosa

description: This dataset contains GWAS summary file generated from sputum metagenomic data for COPD patients.
DOI: 10.6084/m9.figshare.3511412.v1
title: Appendix A. A list of boreal bird species used in the analysis, organized by habitat affinity.

description: A list of boreal bird species used in the analysis, organized by habitat affinity.
DOI: 10.6084/m9.figshare.16897048.v1
title: UAV

description: NDVI observations from a UAV platform for a winter wheat field near Sun River, Montana as described in https://eartharxiv.org/repository/view/2670/
DOI: 10.6084/m9.figshare.22491997.v5
title: CROPGRIDS

description: CROPGRIDS is a comprehensive global, geo-referenced dataset providing area information for 173 crops circa the year 2020, at a resolution of 0.05˚ (~5.6 km at the equator). It represents a major update of the Monfreda et al. (2008) dataset (hereafter MRF), the most widely used geospatial dataset previously available, covering 175 crops with reference year 2000 at 10 km spatial resolution. CROPGRIDS builds on information originally provided in MRF and expands it using 25 selected published gridded datasets, providing more recent crop information at regional, national, and global levels, largely covering the period 2015 – 2020. By combining the gridded information and the 2020 national-level statistics from FAOSTAT, CROPGRIDS reports the updated harvested and crop (physical) area for 173 crops. The new CROPGRIDS data represent a useful input into modelling studies and sustainability analyses including in support of the 2030 Sustainable Development Agenda.<br>For more information, please refer to:Tang F. H. M., Nguyen T. H., Conchedda G., Casse L., Tubiello F., and Maggi F. (2023). CROPGRIDS, a global geo-referenced dataset of 173 crops, submitted to Scientific Data.
DOI: 10.6084/m9.figshare.28651805.v1
title: HirelData1.mat

description: Data
DOI: 10.6084/m9.figshare.7610987.v1
title: Archaeological grape seeds genotype data

description: Genotype data for the archaeological grape seeds sequenced for Ramos-Madrigal J <i>et al.</i> Nat Plants 2018 10.1038/s41477-019-0437-5<br>
DOI: 10.17632/6rhg32kf7g
title: Interbrain Synchrony Mitigates the Polarizing Effect of Echo Chambers

description: The folder includes raw neural and behavioral data and R scripts used to run data analyses.
DOI: 10.17632/9y86jkf9dz
title: Data for: Machine-Learning Based Error Prediction Approach for Coarse-Grid Computational Fluid Dynamics (CG-CFD)

description: Lid-driven cavity flow variables distribution in a cubic domain. Reynolds numbers range from 6000 :12000. Various grids and aspect ratios. These data are the inputs and the outputs for a regression model that predicts the local grid-induced error given the coarse-grid local fluid flow features.
DOI: 10.17632/w56x9jrhxr
title: Brain Tumor MRI Classification Dataset (Tumor vs. No Tumor)

description: Authors: Ahta Shamul Hoque Emran, Hafija Akter, Farhan Masud Nayem
Supervisor: Abdullah Al Shiam

Description:
This dataset has been developed as part of an academic thesis focused on brain tumor detection and classification using deep learning methods. It contains MRI (Magnetic Resonance Imaging) brain scans categorized into two classes: Tumor and No Tumor.
The initial dataset was imbalanced, with a significantly higher number of "No Tumor" images compared to the "Tumor" class. To address this imbalance and improve model performance, we applied data augmentation techniques to the Tumor class.

After augmentation, the dataset contains a nearly balanced number of images across both classes:
-Tumor (Original): 3,671 images
-No Tumor: 13,273 images
-Tumor (After Augmentation): 13,252 images

The total dataset used for training and analysis includes:
Tumor: 13,252 images
No Tumor: 13,273 images
All images are stored in JPG format. The size of the images in this dataset is different.

Augmentation Details:

We used TensorFlow's ImageDataGenerator for on-disk augmentation. The following parameters were applied:
- rotation_range=90: Randomly rotates images up to 90 degrees.
- rescale=1./255: Normalizes pixel values to [0, 1].
- fill_mode='nearest': Fills in missing pixels after transformation.
- Other transformations like shift, shear, zoom, and flipping were not used to retain medical image structure.

This dataset can be used for:
- Training and testing machine learning and deep learning models
- Research on medical image classification
- Developing automated systems for early detection of brain tumors
DOI: 10.25452/figshare.plus.27241997.v1
title: RNA-seq analysis dataset for <i>Pseudomonas aeruginosa </i>PAO1 37°C vs. 43°C

description: The data in this item includes raw RNA-sequencing data from post-43°C exposure and during the recovery period to assess transcript-level effect.<b>Sample preparation: </b>Overall, 18 samples included 3 replicates of <i>Pseudomonas aeruginosa</i> after exposure to 37<i> </i>°C (control) or 43<i> </i>°C (heat shock), at 3 time points (T=0hr, T=18hr, and T=54hr). Samples from the T=0 groups are simply labeled “37” or “43”.<b> </b>For RNA sequencing, 2 ug of total RNA was used for the RiboMinus™ Bacteria Transcriptome Isolation Kit (Invitrogen). The library was constructed with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions using 30 ng of depleted RNA. The final quality was evaluated by TapeStation High Sensitivity D1000 Assay (Agilent Technologies, CA, USA). Sequencing was performed based on Qubit values and loaded onto an Illumina MiSeq using the MiSeq V2 (50- cycles) Kit (Illumina, CA, USA). Paired-end RNA-seq protocol was used, yielding about 3.4-6.5 million paired-end reads per sample. FastQC (v0.11.2) was used to assess the quality of raw reads.<b>Analysis</b>: Reads were aligned to <i>Pseudomonas aeruginosa </i>PAO1 strain (assembly GCF_000006765.1 ) using the bowtie2 aligner software (v2.3.2) with default parameters. GTF annotation file for the PAO1 strain was downloaded from NCBIPseudomonas Genome DB ( www.pseudomonas.com). Raw read counts for gene-level features were determined using HTSeq-count with the intersection-strict mode. Differentially expressed genes were determined with the R Bioconductor package DESeq2 (Release 3.14). The p-values were corrected with the Benjamini-Hochberg FDR procedure. Genes with adjusted p-values; 0.05.<br>
DOI: 10.6084/m9.figshare.12804824.v1
title: JVASP-14204 to JVASP-14902

description: JARVIS-DFT
DOI: 10.6084/m9.figshare.25999717.v1
title: Supplementary Table 2

description: <b>Supplementary Table 2 – Preprocessing parameters used to filter and quality control cells in each data set, sorted by batch and donor (orig.ident).</b>
DOI: 10.6084/m9.figshare.26790289.v1
title: Supplementary tree and alignment files for the paper entitle "Disentangling the basidiomycete family <i>Agaricaceae</i>"

description: Supplementary tree and alignment files for the paper entitled "Disentangling the basidiomycete family <i>Agaricaceae</i>":1_agaricaceae_seqs.nexus: contains the alignment for the DNA dataset2_agaricaceae_picsord.nexus: contains the alignment for the recoded ambiguous regionsagaricaceae_all.nexus.con.tre: The Bayesian tree analysis generated with MrBayesIQTREE_partitions.nex.contree.nexus.tre<b>: </b>The Maximum Likelihood analysis generated with IQ-TREEsupport_20220503_FSB.raxml.support.nexus.tre: The Maximum Likelihood analysis generated with RAxML-NG using the Felsenstein Bootstrap valuessupport_20220503_TBE.raxml.support.nexus.tre: The Maximum Likelihood analysis generated with RAxML-NG using the Transfer Bootstrap ExpectationRAxML_treeterrace.tre: The treefile containing the different tree topology hypotheses found on the tree terrace as predicted with RAxML-NG
DOI: 10.6084/m9.figshare.27861948.v1
title: Supplementary Material for: The One Anastomosis Gastric Bypass is a suitable alternative to Roux-en-Y Gastric Bypass in patients with BMI &gt; 50 kg/m2 : a propensity-score matched analysis

description: Introduction: Body Mass Index (BMI) ≥ 50 kg/m2 is more challenging for the bariatric surgeon, because of a thicker abdominal wall, more visceral fat, and hepatomegaly by liver steatosis. This study aims to give an overview of 5-year outcomes after OAGB and RYGB in these patients in terms of weight loss, remission of comorbidities, and complications.
Methods: This retrospective single-center cohort study focused on patients with BMI ≥ 50 kg/m2 undergoing OAGB or RYGB between 2015 and 2017 at a non-academic teaching hospital in the Netherlands. A 1:1 propensity-score matched (PSM) comparison was conducted. 
Results: In total, 158 patients underwent OAGB and 32 patients RYGB. After performing a 1:1 PSM, we obtained two nearly identical cohorts of 28 patients. Follow-up data after five years was available in 79% of the patients after OAGB and 82% of the patients after RYGB. Both procedures resulted in equal weight loss, remission of comorbidities, and short-term complications. More minor mid-term complications were seen after OAGB (50% versus 18%; p=0.011) due to reflux complaints (50% versus 7%; p&lt;0.001). The number of patients with major mid-term complications did not differ (7% after OAGB versus 14% after RYGB; p=0.388). The only major complication after OAGB was conversion to RYGB due to reflux in 7.1% of the patients. In contrast, major complications following RYGB were more diverse.
Conclusion: Both procedures resulted in similar weight loss, remission of comorbidities, short-term complications, and major mid-term complications; making OAGB a suitable alternative to RYGB for patients with a BMI &gt; 50 kg/m2.