cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22728371.v1
title: humann_pathabundance_cpm_unstratified.tsv

description: Metagenomic sequence analysis. Unstratified pathway abundance analysis in counts per millions (CPM).
DOI: 10.6084/m9.figshare.23292485.v1
title: tunes.csv

description: Dataset of Traditional Irish Tunes in ABC format
DOI: 10.6084/m9.figshare.23501715.v1
title: data.tar.gz

description: Datasets used in the study named <em>Tackling Data Scarcity with Transfer Learning: A Case Study of Thickness Characterization from Optical Spectra of Perovskite Thin Films.</em>
DOI: 10.6084/m9.figshare.5121553.v1
title: Supplementary Material for: Steroid and Ursodesoxycholic Acid Combination Therapy in Severe Drug-Induced Liver Injury

description: <i>Background:</i> Drug-induced liver injury (DILI) is the leading cause of acute severe liver disease in Western countries. Treatment strategies for DILI are still not well defined. <i>Aim:</i> We studied the safety and outcomes of steroid/ursodesoxycholic acid (UDCA) combination therapy in DILI patients. <i>Patients, Materials and Methods:</i> 15 consecutive patients with severe DILI were analyzed for clinical, biochemical and histological data. Nine patients were treated with a steroid step-down therapy with reduction of the daily dose over several weeks; 6 patients received a steroid pulse therapy for 3 days. UDCA was administered for several weeks in both groups. <i>Results:</i> Patients without histological signs of preexistent liver damage (n = 10) showed the most favorable clinical course. Bilirubin and serum transaminases dropped to &lt;50% of peak values within 2 weeks, and normalized within 4–8 weeks. In contrast, patients with positive autoimmune antibodies (anti-nuclear antibodies and/or soluble liver antigen) and/or histological features of chronic hepatitis (n = 3) exhibited a slower reduction in bilirubin and serum transaminase levels. These patients were given immunosuppressants (steroids, azathioprine) for a further 6 months. <i>Conclusion:</i> Treatment of severe DILI with corticosteroids (both pulse and step-down therapy) and UDCA appears to be safe, and leads to a more rapid reduction in bilirubin and transaminases after DILI.
DOI: 10.6084/m9.figshare.5721427.v1
title: Additional file 3: Table S3. of Tsetse fly (Glossina pallidipes) midgut responses to Trypanosoma brucei challenge

description: Canonical gene set enrichment analysis (GSEA) of significantly differentially expressed transcripts in the female G. pallidipes 24 or 48Â h post-challenge with T. B. brucei. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.14225945.v6
title: Gender Sensitization scale data

description: This dataset consist of four materials: One is the total variance explained table enlisted as Appendix_S1 where Principal Axis Factoring method was used with oblique rotation. <br> Second one is the table consisting communality value of the items after the PAF enlisted as Table_S1. <br> The third (Table_S2) consists of the Factor loadings from Principal Axis Factor Analysis (PAF) with Promax Rotation . <br> The fourth (Table_S3) consists of the Factor Correlation Matrix of the extracted qualified factors.
DOI: 10.6084/m9.figshare.21334266.v1
title: Supplementary Material for: Getting in a Spin Over the Therapeutic Process: QBism and a Gyroscopic Model of the Vital Force

description: Background: In the previous paper, a relatively new interpretation of quantum theory called QBism, was introduced as an alternative quantum metaphor for the therapeutic process (TP). This is because previous metaphors have been based on conventional quantum theory and its notion that quantum states belong to a strongly objective shared reality. QBism suggests otherwise, quantum states being merely subjective degrees of belief made by the individual agents assigning those states. It suggests QBism’s explicit subjectivity is more in line with practitioners’ (Pr) and patient’s (Px) implicitly subjective experience of the TP. Objective: To investigate the impact on this suggestion of a previously developed gyroscopic model of the Vital Force, Vf. Method: Based on an original starting wavefunction for the Vf, a sequence of equations and transformations between them are generated and then interpreted as the Vf interacting with and moving into and out of dis-ease (Dx) states, in essence, a physics of health. Results/Discussion & Conclusion: These equations and their transformations manage to predict (a) homeopathic aggravation from the curative remedy (Rx), and (b) the logic behind Hahnemann’s development of the LM potencies. Further, displaying these equations and their interactions pictorially and geometrically (as a stellated octahedron) suggests that the recently developed gyroscopic model for the Vf supports a metaphor for the therapeutic process (based on the subjectivity explicit in QBism), that is indeed viable and potentially superior to previous metaphors based on the strong objectivity of conventional quantum theory (CQT).
DOI: 10.6084/m9.figshare.17167316.v1
title: Supporting data: Surface Flooding as a Key Driver of Groundwater Arsenic Contamination in Southeast Asia (ES&T, 10.1021/acs.est.1c05955)

description: Supporting data for "Surface Flooding as a Key Driver of Groundwater Arsenic Contamination in Southeast Asia" (ES&T, 10.1021/acs.est.1c05955)<br>User Information:Read me file (read_me.txt)RMarkdown html file (r_markdown.html)RMarkdown Rmd file (r_markdown.Rmd)<br>Datasets:Data to generate results and analysis (input_dataset.csv)Model output data table (output_dataset.csv)<br>30 m-resolution groundwater arsenic prediction maps:Concentrations (output_data_concentration_30m.tif)Probability &gt; 10 ug/L (output_data_probability_10_30m.tif)Probability &gt; 50 ug/L (output_data_probability_50_30m.tif)Probability &gt; 100 ug/L (output_data_probability_100_30m.tif)<br>1 km-resolution groundwater arsenic prediction maps:Concentrations (output_data_concentration_1km.tif)Probability &gt; 10 ug/L (output_data_probability_10_1km.tif)Probability &gt; 50 ug/L (output_data_probability_50_1km.tif)Probability &gt; 100 ug/L (output_data_probability_100_1km.tif)
DOI: 10.6084/m9.figshare.13325666.v1
title: Supplementary Material for: The Role of Nrf2 in D-Galactose-Induced Cardiac Aging in Mice: Involvement of Oxidative Stress

description: <b><i>Introduction:</i></b> Cardiac aging is the major risk factor for advanced heart disease, which is the leading cause of death in developed countries, accounting for &gt;30% of deaths worldwide. <b><i>Objective:</i></b> To discover the detailed mechanism of cardiac aging and develop an effective therapeutic candidate drug to treat or delay cardiac aging. <b><i>Methods:</i></b> We used D-galactose to induce cardiac aging in Nrf2<sup>+/+</sup> and Nrf2<sup>–/–</sup> mice, and then treated these mice with vehicle or the Nrf2 activator, CDDO-imidazolide (CDDO-Im). <b><i>Results and Conclusions:</i></b> D-galactose injection significantly induced cardiac aging, cell apoptosis, and oxidative stress in Nrf2<sup>+/+</sup> mice, all of which were further exacerbated in Nrf2<sup>–/–</sup> mice. CDDO-Im treatment can effectively weaken oxidative stress and enhance the activities of antioxidant enzymes, but CDDO-Im lost its antioxidative effect in the Nrf2<sup>–/–</sup> mice. Nrf2 activator CDDO-Im could therefore effectively protect against D-galactose-induced cardiac aging by inhibiting oxidative stress, suggesting that CDDO-Im might be a potential and promising therapeutic candidate drug to treat cardiac aging.
DOI: 10.6084/m9.figshare.14955450.v1
title: Authentication of bisphenol F (BPF)

description: Authentication of bisphenol F (BPF) by GC-MS. The title compound was obtained from a commercial source. The purity (&gt;99%) of the compound was determined based on relative peak area by GC-MS.
DOI: 10.6084/m9.figshare.16625603.v1
title: Additional file 6 of Finding functional associations between prokaryotic virus orthologous groups: a proof of concept

description: Additional file 6. Main table containing all processed pVOG pairs, their predicted label (0 for negative, 1 for positive), prediction probability, available annotations (raw and processed) and features values. Accessible via https://zenodo.org/record/4576466
DOI: 10.6084/m9.figshare.22102379.v3
title: ECOPICS_MX_Gravimetric soil moisture and tension at Pico de Orizaba Protected Park

description: <strong>ECOPICS Project : Gravimetric moisture and tension data</strong> Field campaign February 2017 to March 2018 Monitoring time: April 2017 to March 2018 Last modification : September 2022 by <strong>Beatriz E. Marín Castro</strong> Soil moisture monitoring was done according to the manuals of the Watermark sensors (<strong>W</strong>), for tension moisture. For gravimetric moisture, Decagon sensors (<strong>D</strong>) were used. Each soil moisture monitoring station (SMS) is related to the altitudinal gradient analysis and the soil data pit level. The pits, one per altitudinal level, samples were taken from different soil horizons.
DOI: 10.6084/m9.figshare.13125563.v1
title: Personal spending Halloween

description: Data scraped from National Retail Federation webpage
DOI: 10.6084/m9.figshare.19706773.v2
title: PAMpal Workshop - PAMGuard Data

description: This contains folders of processed PAMGuard data for use in the PAMpal tutorial. The "Databases" and "Binary" folders in the main directory are used for creating the "Training" dataset, and the same folders within the "Prediction" folder are for the "Prediction" dataset. This dataset contains acoustic detections of odontocete species from NOAA's CalCurCEAS 2014 cruise.
DOI: 10.6084/m9.figshare.24844875.v1
title: Orthovenn and others

description: Orthovenn3 results including STRING interactions and functional enrichments.Virulence and antibiotic resistance genes identified using ABRICATE<br>
DOI: 10.6084/m9.figshare.28300673.v1
title: raw data for ARGIC study

description: raw data for ARGIC study, includes mass loss, hardness, flexural strength, ion release
DOI: 10.6084/m9.figshare.24465793.v1
title: Waymo labels and predictions

description: The file provided the predictions for the dataset <i>Waymo</i> generated by M-detector introduced in the paper titled "Moving Event Detection from LiDAR Point Streams".
DOI: 10.6084/m9.figshare.25304545.v1
title: Virulence genes (in-house database)

description: Results of antibiotic resistance genes –assemblies’ screening- using Abricate v0.8 and in-house database of Klebsiella pneumoniae virulence genes.
DOI: 10.6084/m9.figshare.28554446.v2
title: Transcriptomic and metabolomic profiling of a poplar variety infested by <i>Anoplophora glabripennis</i> adults

description: These data are transcriptomic and metabolomic expression profiles of the insect-resistant poplar <i>Populus deltoides </i>‘Shalinyang’ (PdS) in response to feeding by adult <i>Anoplophora glabripennis</i>, including genes and metabolites, respectively.
DOI: 10.6084/m9.figshare.28801472.v1
title: 针刺干预对实验性自身免疫性甲状腺炎大鼠血清代谢组的影响

description: 为了探讨针灸对大鼠实验性自身免疫性甲状腺炎的治疗效果，以及硒酵母治疗是否存在共同的代谢物靶点，我们检查了大鼠的血清代谢组。
DOI: 10.25387/g3.28541393.v1
title: Supplemental Material for Franco Ortega et al., 2025

description: Hibrid genome= ONT + Illumina
<br>
Chloroplast and mitochondrial genomes were assembled using CANU (version 2.1.1) and polished using RACON version 1.4.20 and MEDAKA version 1.0.3. (Files=Mitochondria_F.excelsior_2451S.fasta, Chloroplast_F.excelsior_2451S.fasta)
Both chloroplast and mitochondria genomes were annotated using MPI-MP Chlorobox GeSeq tool  (Files=Mitochondria_F.excelsior_2451S.annotation.CDS, Mitochondria_F.excelsior_2451S.annotation.gff3, Mitochondria_F.excelsior_2451S.annotation.gtf,Mitochondria_F.excelsior_2451S.annotation.proteins.fasta;Chloroplast_F.excelsior_2451S.annotation.CDS,Chloroplast_F.excelsior_2451S.annotation.gff3, Chloroplast_F.excelsior_2451S.annotation.gtf,Chloroplast_F.excelsior_2451S.annotation.proteins.fasta  )
<br>
Genome with the reads that did not map against the chloroplast or mitochondria were assembled using CANU. PURGE HAPLOTIGS was used to phase the genome and then it was polished using Illumina reads (ERR1399574; Sollars et al., 2016) with PILON version 1.24 (Walker et al., 2014) (File=F.excelsior_ONT.genome.fasta)
<br>
Annotation was done with REPEATMODELER (version 2.1) and REPEATMASKER(version 2.1) to masked the genome and then de-novo gene models were retrieved with BRAKER (version 1.9) using the 5 mRNA-Seq samples previously published and belonging to roots (ERR1399494), cambium (ERR1399492), leaves (mother tree and 2461s, ERR1399495, ERR1399573) and flowers (ERR1399493). TSEBRA with default configuration was used to combine the results of both proteins (viridiplantae) and mRNA-Seq predictions. 
GFACS (Version 1.1.2) + ENTAP (Hart et al., 2020) + EGGNOGG (Huerta-Cepas et al., 2019) were used for functional characterization of the gene models. (Files= F.excelsior.annotation.cds, F.excelsior.annotation.pep, F.excelsior_ONT_annotation.gff3, F.excelsior_ONT_annotation.gtf, F.excelsior_ONT_funtional.annotations)
Transposable elements (TE) and tandem repeats were identified using the Extensive de-novo TE Annotator (EDTA) (F.excelsior_ONT.fasta.mod.EDTA.TEanno.gff3)
Methylation was called with nanopolish (version 0.13.2) (File=GSE214553_all_methylation_data_genome_Ash_complete_NEW.tsv.gz, GSE214553_all_methylation_data_genome_Ash_frequency_complete_new.tsv.gz)
Pseudochromosomes against F. pennsylvanica genome (Huff et al., 2022), were created using NTJOIN (version 4.2.1) + NUCMER version 3.1 (Files= contig_to_ntJoin.txt, F.excelsior_ONT_contig_pseudochromosomes.agp, F.excelsior_ONT_contigs_assigned_pseudochromosomes.fa ---&gt; contigs assigned into pseudochromosomes; Files =F.excelsior_ONT_contigs_not_assigned.fa & contigs assigned into pseudochromosomes.agp---&gt; contigs NOT assigned into pseudochromosomes
<br>
We remapped the transcriptomic data of a Danish ash population of 182 trees from Harper et al. 2016, aginst this genome. Salmon was also used to obtain TPMs using this genome as reference. We used these outputs to perform associative transcriptomic and idenitiy gene associated markers to ash dieback tolerance.
DOI: 10.6084/m9.figshare.16722961.v1
title: Table S 1: Details of previously sequenced samples used for in silico down sampling analysis.

description: Details of genomes used in the down sampling analysis.
DOI: 10.6084/m9.figshare.25879741.v1
title: Data files for the phylogeny in Figure 1 of "Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts"

description: Files for a concatenated marker gene phylogeny of the gammaproteobacterial orders Berkiellales, JABCZS01 and UBA6186. The genomes/mags included were obtained from the Genome Taxonomy Database (GTDB) and the genomic catalog of earth's microbiomes (GEM).<br><br>references:<br>GTDB: <br>https://academic.oup.com/nar/article/50/D1/D785/6370255 & https://gtdb.ecogenomic.org/<br>GEM: <br>https://www.nature.com/articles/s41587-020-0718-6 & https://genome.jgi.doe.gov/portal/GEMs/GEMs.home.html
DOI: 10.6084/m9.figshare.28661462.v1
title: Data and extra graphics for "Variation in vessel element diameters and densities across habitats at the community and species levels in Southeast Florida"

description: These data are vessel element densities and vessel element diameters sampled at the community level and at the individual species level (Chrysobalanus icaco, Ximenia americana, Morella cerifera, Myrsine cubana) across habitats in South Florida in 2024. The habitats involved are cypress swamp, pinewoods and similar habitats, hammock, and scrub.
DOI: 10.6084/m9.figshare.1541106.v1
title: Denitrification measurements in various plant communities

description: Data table of denitrification measurements included in the meta-analysis, "Effects of wetland plants on denitrification rates." All denitrification measurements were converted to the same units (g N m-2 h-1). Measurements are categorized by the dominant species in the plant community; the genus, family, and growth form of the dominant species and whether it is a monocot or dicot; the type of wetland system in which the study was conducted; and the method used to measure denitrification rates. The effect size of vegetation on denitrification rates and variance in effect size are reported in columns “lnR” and “Var(lnR),” respectively.
DOI: 10.6084/m9.figshare.27641478.v1
title: Supplementary Material for: One-step leaping evolution from an autosomal pair to the heteromorphic sex chromosomes

description: Background: Sex chromosomes evolve from an autosomal pair after the acquisition of a sex-determining gene. The primary sex chromosomes are homomorphic in both sexes and often undergo heteromorphism in either sex (XY in males or ZW in females) in association with chromosome rearrangements such as inversion, which creates a non-recombining region, called a stratum. Then, multiple strata may form by sequential inversions and extend the non-recombining region, where gene divergence accelerates, and degeneration of the Y or W chromosome progressively occurs. Summary: Contrast to the conventional theory, we propose a shortcut in heteromorphic sex chromosome evolution, where an autosomal pair directly evolves into a heteromorphic sex chromosome pair. We illustrate this with two frog cases where Y chromosome or autosome, which is morphologically inverted, was introgressed from another species through interspecific hybridization, instantly forming a new heteromorphic sex chromosome pair. This event resulted in a distinct non-recombining region immediately after hybridization. Key messages: The introduction of an inverted chromosome from a different species may be associated with benefits in morphology, breeding behavior, hybrid viability, sex determination, and recovery of the sex ratio of the hybrids. We discuss the molecular mechanisms driving preferential mutations in the introduced, inverted chromosome through interspecific hybridization.
DOI: 10.6084/m9.figshare.22269499.v1
title: fores_all.tif

description: forestry residues map
DOI: 10.6084/m9.figshare.26196461.v1
title: Dataset supporting High glass transition catalyst-free polybenzoxazine vitrimer through one-pot solventless method

description: The dataset consists of the results of NMR and FTIR spectroscopy, DSC cure and Tg measurement, single frequency temperature ramp DMA and DMA stress relaxation, TGA studies, swelling tests and self-heling tests by profilometry carried out on a benzoxazine vitrimer named DHPDS-a (monomer) or polyDHPDS-a (polymer). The data are organised in 8 Excel files, one for each experimental technique used. The first row of each column contains the quantity and the unit of measurement.The files are as follows:- NMR file (NMR_spectroscopy.xlsx) comprises <sup>1</sup>H and <sup>13</sup>C NMR spectra of the monomer. <sup>1</sup>H NMR and <sup>13</sup>C NMR spectra are presented in separate spreadsheets.- FTIR file (FTIR_spectroscopy.xlsx) comprises FTIR spectra of the monomer and the polymer. The experimental results for monomer and polymer are presented in separate spreadsheets.- DSC file (DSC_cure_Tg.xlsx) contains temperature and normalised heat flow for dynamic DSC ramp at 10°C/min carried out using uncured monomer (from -50°C to 245°C) and cured polymer (from 0°C to 243°C), each in a separate spreadsheet.- Rheology file (Rheology.xlsx) comprises dynamic flow rheology performed at 2°C/min heating rate from 70°C to 153°C.- DMA file (DMA_Tg_stress_relaxation.xlsx) contains the dynamic and relaxation DMA data. The dynamic DMA data (in ‘Dynamic DMA’ spreadsheet) reports results (storage modulus, loss modulus, tan delta and complex modulus) of a single frequency scan at 3°C/min from 35°C to 217°C. The transient stress relaxation data are organised in spreadsheets per experimental temperature (5 tests carried out at 175°C, 180°C, 185°C, 190°C and 195°C), reporting relaxation time, strain, relaxation modulus and normalised relaxation modulus.- TGA file (TGA.xlsx) consists of weight percent versus temperature for 10°C/min scan carried out on the polyDHPDS-a under nitrogen purge from 50°C to 905°C.- Swelling file (Swelling.xlsx) is organised in 6 spreadsheets, each corresponding to one of the solvents used. In each spreadsheet, the weight of four specimens at different times up to 31 days is reported. The final weight after drying is also reported.- Profilometry file (Profilometry-dataset.xlsx) contains profilometric surface profile measurements of a scratched specimen of polyDHPDS-a before and after self-healing experiment.
DOI: 10.48420/28359653.v1
title: The impact of anti-gravity treadmill training on quality of life in patients with motor neurone disease: A pilot study

description: This document contains the anonymous data collected during our pilot study on the use of anti-gravity treadmill training for people living with motor neurone disease. <b>Objective:</b> Exercise programmes should be considered for people living with motor neuron disease (MND) to maintain joint movement, reduce stiffness, and maintain function. Traditional treadmill training is inappropriate for this patient cohort due to the fall risk. However, anti-gravity treadmill technology could provide a safe environment to train gait for symptom management. This study aimed to investigate the impact of anti-gravity treadmill training on the quality of life of people living with MND.<br><b>Participants:</b> Five people with a clinical diagnosis of MND.<br><b>Intervention:</b> Three 30-minute training sessions on an anti-gravity treadmill over a 5-week period.<br><b>Main measures:</b> At the first and last visit, self-reported quality of life was recorded via the Amyotrophic Lateral Sclerosis Assessment Questionnaire (ALSAQ-40) and Short Form-12 (SF-12) questionnaire. Sit-to-stand assessments were also performed at these visits.
DOI: 10.6084/m9.figshare.17303921.v1
title: New Zealand Coelopid size variation and mating success

description: These data include body size measurements of two New Zealand Coelopid fly species used for allometry analyses and records of mating behaviour for one of these species (Chaetocoelopa littoralis) from lab-based mating trials. Both files contain read me tabs with detailed descriptions of the data.<br>Mating trials involved 10 randomly selected and individually marked individuals of each sex being placed in a mesh cage and observed over a period of one hour. <br><br>
DOI: 10.6084/m9.figshare.28428659.v1
title: Dietary omega-3 long chain polyunsaturated fatty acids can enhance ecologically relevant cognitive traits in juvenile brown trout.csv

description: This dataset contains behavioural and cognitive measurements of brown trout coming from 5 populations both from lake and river. Together with this, measures of fork length, body mass and stomach content parameters for evaluation of resource acquisition are included. The aim of this research is to examine the effect of omega-3 long chain polyunsaturated fatty acids (n-3 LC PUFA) dietary treatment in the development of brown trout's cognition and resource acquisition, by combining laboratory behavioural tests with experiments in a semi-natural stream mesocosm. Behavioural tests focused on evaluation of boldness (latency time to leave the shelter, and probability of emergence across trials); activity (distance the fish swam inside the experimental arena) and aggressiveness (time spent by the fish in front of their own mirror image). Cognition was evaluated through the inhibitory control detour test (time before the fish passed the transparent barrier). In the seminatural stream mesocosm we inspected fish stomach content to evaluate their resource acquisition. Measured we focused on were: stomach content biomass, prey size and proportion of benthic prey versus drifting prey. Data were analysed in R using linear mixed (LMM) and generalized linear mixed (GLMM) models. The research complied with Federal Act on the Protection of Animals, Austria (http://www.ris.bka.gv.at) and EU Directive 2010/63. The host institute possessed ethical permission to carry out all the tasks necessary for this project (BMBWF - v/3b (Tierversuchwesen und Gentechnik), license number: 2023-0.053.856).<br><br>