cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28744844.v1
title: Protocols

description: Concentrating and diluting - spreadsheet that automatically calculates concentration and dilutions based on quantification values (ng/uL), used during 2024 MEPA Field+Genomics WorkshopConcentration protocol - in-house DNA concentration protocol used during 2024 MEPA Field+Genomics WorkshopExtraction protocol - MagAttract HMW DNA extraction kit from Qiagen used during 2024 MEPA Field+Genomics WorkshopFlow cell wash kit (EXP-WSH004) used during the 2024 MEPA Field+Genomics WorkshopLibrary preparation protocol (SQK-NBD114.24) used during the 2024 MEPA Field+Genomics Workshop
DOI: 10.6084/m9.figshare.13562582.v1
title: Data from: Sequential colonization of oceanic archipelagos led to a species-level radiation in the common chaffinch complex (Aves: Fringilla coelebs)

description: We include the vcf files used for the different analysis and a file with individuals information:<br><b><br></b><b>PIN_CCHAZEFI_MAC_biall_dp460_q30_maf0018_hwe00001_miss075_count166</b><br><b><br></b>Complete dataset of 159,534 SNPs after initial filtering.<br><b>PIN_CCHAZEFI_MAC_biall_dp460_q30_maf0018_hwe00001_miss075_count166_neutral01_LE05</b><br><b><br></b>Dataset of 100,166.166 neutral SNPs from 82 individuals in vcf format. Includes an individual of <i>F.teydea </i>as outgroup (TEN4).Used in RAxML analysis.<br><b><br></b><b>PIN_CCHAZEFI_MAC_biall_dp460_q30_maf0018_hwe00001_miss075_count166_neutral01_LE05_noTEN4</b><br><br>Dataset of 100.166 neutral SNPs from 81 individuals (excluding the outgroup) in vcf format.<b><br></b><b>PIN_CCHAZEFI_MAC_biall_dp460_q30_maf0018_hwe00001_miss095_count166_neutral01_LE05_2indv_outg_SNAPP.</b><br><br>Dataset of 15,836 neutral SNPs, including 19 individuals (2 per population + outgroup) used for SNAPP analysis.<b><br></b><b>PIN_CCHAZEFI_MAC_biall_dp460_q30_maf0018_hwe00001_miss095_count166_neutral01_LE05_STRUCTURE</b><br><br>Dataset of 16,416 independent neutral SNPs from 81 samples (no outgroup) in vcf format for STRUCTURE analysis.<br><br><b>MAC_indvs_vcfs</b><b><br></b>Information about the individuals included in the vcfs.<br><br>
DOI: 10.6084/m9.figshare.24619197.v2
title: Developing Deep Learning-based Large-scale Organic Reaction Classification Model via Sigma-profiles

description: The "<b>Train_AE.zip</b>" contains the scripts for training an auto-encoder.The "<b>Train_DL_Models.zip</b>" contains the scripts for training deep learning-based models.The "<b>sigma_profiles_dict.npy</b>" contains the sigma-profiles of millions of different molecules. The SMILES of a molecule is used as key to query the corresponding sigma-profiles.The "<b>sorted_agent_dict.npy</b>" contains the statistical results of USPTO_TPL dataset concerning the frequency of occurrence of agents. The agents are shown in an descending manner.The "<b>sorted_agent_combination_dict.npy</b>" contains the statistical results of USPTO_TPL dataset concerning the frequency of occurrence of agent combinations. The combinations are shown in an descending manner.<br>The "<b>USPTO_TPL_own_version.xlsx</b>" contains the reactions that used for training/validation/testing.<br>
DOI: 10.17632/ncn3k3tzm5
title: A Reconsideration of the Failure of Uncovered Interest Parity for the U.S. Dollar

description: This is the replication file for A Reconsideration of the Failure of Uncovered Interest Parity for the U.S. Dollar.
DOI: 10.17632/vd7fms9rwp
title: Data for: Ionic Additive in an Ionogel for a Large Area Long Lived High Contrast Electrochromic Device

description: The raw data for all the graphical figures (Figures1-4 and Figure S1) is provided.
DOI: 10.6084/m9.figshare.12555329.v1
title: Codes and data - Ting, et al. CABN 2020

description: This folder contains all codes and data necessary to reproduce the behavioral analyses and results reported in Ting, et al. (2020) CABN. <br><br>[Ting CC, Palminteri S, Engelmann JB** & Lebreton M** (2020) Robust valence-induced biases on motor response and confidence in human reinforcement learning. Cogn. Aff. Behav. Neuro, 20(6), 1184-1199]<br>Please note that the codes needs Matlab R2014b or a more resent version, with the Statistics and Machine Learning toolbox.
DOI: 10.6084/m9.figshare.15073797.v1
title: Supplementary Metadata

description: Supplementary metadata utilised for the ordination approach applied to the microbiota data in this study.<b><b><br></b>Table S1</b> - Dietary information obtained from study participants.<b>Table S2</b> - Magnetic resonance imaging (MRI) metrics utilised for the direct ordination approach.<b>Table S3</b> Summary statistics: Mean % Kcal Protein.<br><b>Table S4</b> Summary statistics: Mean % Kcal CHO.<br><b>Table S5</b> Summary statistics: Mean % Kcal Fat.<br><b>Table S6</b> Summary statistics: Mean % Fibre (g).<br>
DOI: 10.6084/m9.figshare.17134688.v1
title: Supplementary Material for: Immunoadsorption Improves Remission Rates of Patients with Antineutrophil Cytoplasmic Antibody-Associated Vasculitis and Severe Kidney Involvement

description: <b><i>Introduction:</i></b> The role of plasma exchange in treatment of antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) with severe kidney involvement is controversial. It is urgent to find effective treatments to improve prognosis of AAV patients. In this retrospective study, the outcomes of immunoadsorption (IA) onto protein A in AAV patients with severe kidney involvement were evaluated. <b><i>Methods:</i></b> Clinical data of 60 patients with AAV and severe kidney involvement were analyzed. Patients received cyclophosphamide or rituximab for remission induction, among which 16 were additionally treated with IA. Remission, end-stage kidney disease (ESKD), death, and relapse were compared. <b><i>Results:</i></b> Of 60 patients, 56 patients (93.3%) were positive for myeloperoxidase (MPO)-ANCA. At diagnosis, the estimated glomerular filtration rate and Birmingham Vasculitis Activity Score (BVAS) was 13.0 (7.7, 18.7) mL/min/1.73 m<sup>2</sup> and 11.1 ± 3.4, respectively. After 3–17 days (mean 10.4 days) of induction treatment, the disease activity decreased more obviously in the IA group (<i>p</i> = 0.022) than the control group. IA showed superior over standard regimen in clearance of MPO-ANCA within 3–31 days (median 11 days) after treatment (78.4% vs. 9.3%, <i>p</i> = 0.005). After a median follow-up of 20.2 months, remission was achieved more quickly (<i>p</i> = 0.035) and higher (hazard ratio (HR) = 2.3, 95% confidence interval (CI): 1.1∼7.2<i>, p</i> = 0.033) in the IA group than the control group. IA therapy showed an advantage in reducing death (HR = 0.2, 95% CI: 0.1∼0.9<i>, p</i> = 0.032). There was no difference in developing into ESKD in both groups (HR = 0.7, 95% CI: 0.3∼2.0<i>, p</i> = 0.504). Multivariate Cox regression analysis indicated that early-stage remission was an independent predictor for ESKD (HR = 0.03, 95% CI: 0.003∼0.25, <i>p</i> = 0.001) and death (HR = 0.07, 95% CI: 0.01∼0.51, <i>p</i> = 0.009). <b><i>Conclusion:</i></b> IA treatment induces quicker and higher remission and lower mortality in AAV patients with severe kidney involvement. The early remission independently predicts the outcomes for these patients.
DOI: 10.6084/m9.figshare.26503279.v1
title: Supplementary Material for: Clinical and Immunological Features of Bronchial Asthma Comorbid Chronic Urticaria: A Retrospective Study

description: Introduction: Asthma and chronic urticaria (CU) are two high prevalent diseases and often coexist. The underlying relationship and potential immunological mechanism between the two diseases are still unclear. To investigate the clinical and immunological feature of asthma comorbid with CU. 
Methods: A retrospective study was conducted. 50 patients with asthma comorbid CU,50 patients of with asthma, 50 patients of with CU alone. Age and sex of the patients enrolled were matched. Data of demographic characteristics, clinical manifestations including disease severity (frequency of symptoms, age of onset, disease duration, symptom score, complication with allergic rhinitis) as well as serum immunological index including total IgE(tIgE), allergen specific IgE (sIgE) and food specific IgG4 (FS-IgG4), were collected and analyzed. 
Results: No significant differences in the frequency of symptoms, age of onset and disease duration were found among the three groups. The score of asthma control test (ACT) in patients with asthma comorbid CU was significantly lower than that of asthma (p=0.005), however, compared with patients with CU, the 7-day urticaria activity score(UAS7) of patients with asthma comorbid CU didn’t show obvious differences. Immunological index showed that the positive rate of tIgE, house dust mite (HDM)-sIgE, and FS-IgG4 were different among the three groups (p&lt;0.05). Patients with asthma comorbid CU had the highest rate of positive tIgE, moderate and severe positive sIgE to HDM. Egg specific IgG4 (egg-sIgG4) had the highest positive rate in all groups.Patients of asthma comorbid CU obtained the highest rate of severe positive of egg-sIgG4.
Conclusion: Our results demonstrated that patients with asthma comorbid CU has lower control level of asthma symptoms, higher tIgE and HDM-sIgE level, and highest rate of severe positive egg-sIgG4. These results indicate that comorbidity of CU in asthma obviously increases the severity of allergens.
DOI: 10.6084/m9.figshare.3559896.v1
title: Appendix A. Pine matrix sampling and patch-matrix comparisons.

description: Pine matrix sampling and patch-matrix comparisons.
DOI: 10.17632/jxmhtsghry
title: Enhancing Freeze-Thaw Resistance in Clayey Soil: Incorporating Jute Fiber and Brick Powder for Sustainable Soil Stabilization

description: Abstract 
The study is centered on enhancing geotechnical properties of clayey soil by incorporating jute fiber and brick powder, aiming to optimize its suitability for sub-grade applications. Soil stabilization endeavours to reinforce mechanical attributes, including load-bearing capacity and stability, while simultaneously mitigating risks associated with erosion and degradation. Examining the consequence of freeze-thaw cycles on clayey soil, the study focuses on two key factors: stress-strain characteristics and unconfined compressive strength (UCS).Laboratory experiments involved varying proportions of stabilizers, including jute fiber at 0.2%, 0.3%, 0.5%, 0.75%, and 1%, and combinations of jute fiber and brick powder at ratios of 0.75% + 10%, 0.75% + 20%, and 0.75% + 30%. The overarching aim of stabilization efforts is to minimize settlement, ensuring structural integrity, while simultaneously enhancing resistance to moisture and temperature fluctuations, thereby ensuring sustained stability over time. Significant improvements in UCS were observed across freeze-thaw cycles, particularly noteworthy with the incorporation of 0.75% jute fiber and 30% brick powder. These findings underscore the potential efficacy of employing jute fiber and brick powder in enhancing freeze-thaw resistance within soil stabilization practices. Such promising results offer avenues for the development of more durable and sustainable engineering structures and infrastructure. The integration of jute fiber and brick powder presents a viable strategy for augmenting freeze-thaw resistance of stabilized soil, thereby contributing to advancement of soil stabilization techniques in engineering applications
DOI: 10.6084/m9.figshare.19963991.v1
title: Tree location of trees in a permanent sample plot

description: File: treelocation.dat Author: Christian Salas-Eljatib Email: cseljatib AT gmail DOT com web: www.eljatib.com <br> Tree location in a permanent sample plot in south-central Chile. <br> The columns are as follows: 1. tree.code: tree id code 2. spp.name: species common name 3. dbh : diameter at breast-height age, in cm.
DOI: 10.6084/m9.figshare.28104986.v1
title: DiffCDD_uncond_cond

description: Files in DiffCDD_uncond_cond/Models folder
DOI: 10.17632/bdw29yxwxp
title: Kobler et al., 2020

description: Data relating to Kobler, J.M.; Rodriguez Jimenez, F. J.; Petcu, I.; Grunwald Kadow, I. C.: Immune Receptor Signaling and the Mushroom Body Mediate Post-ingestion Pathogen Avoidance. Current Biology, 2020
DOI: 10.6084/m9.figshare.21988229.v1
title: Data File.xlsx

description: The data file consists of demographic details of respondents and also responses pertaining to specific questions
DOI: 10.6084/m9.figshare.5532214.v1
title: Microsecond-long molecular dynamics trajectory of an aggregate of elastin-like peptides in water

description: This binary file is provided as supplementary material for a research article on the structure and self-assembly of elastin-like peptides (1). It was generated by the molecular dynamics program GROMACS, version 4.6 (2). It contains the last microsecond of a 5-microsecond molecular dynamics trajectory of 27 (GVPGV)<sub>7</sub> peptides in water. See ref. 1 for details.(1) S. Rauscher and R. Pomès. The liquid structure of elastin. eLife, in press (2017). DOI: 10.7554/eLife.26526(2) Hess, B., Kutzner, C., van der Spoel, D. & Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. <i>J. Chem. Theory Comput.</i> <b>4,</b> 435–447 (2008). DOI: 10.1021/ct700301q
DOI: 10.60893/figshare.apl.27680142.v1
title: Supplementary material

description: detailed supplementary material
DOI: 10.6084/m9.figshare.13467033.v1
title: Additional file 2 of annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

description: Additional file 2: Table S1. Sources for annotation of fusions and gene partners. Listed are annotations utilized by annoFuse for prioritization of oncogenic gene fusions, along with reference files and their sources.
DOI: 10.6084/m9.figshare.20060927.v2
title: Soil-atmosphere Fluxes of CO2, CH4, and N2O Across an Experimentally-grown, Successional Gradient of Biocrust Community Types

description: Biological soil crusts (biocrusts) are critical components of dryland and other ecosystems worldwide, and are increasingly recognized as novel model ecosystems from which more general principles of ecology can be elucidated. Biocrusts are often diverse communities, comprised of both eukaryotic and prokaryotic organisms with a range of metabolic lifestyles that enable the fixation of atmospheric carbon and nitrogen. However, how the function of these biocrust communities varies with succession is incompletely characterized, especially in comparison to more familiar terrestrial ecosystem types such as forests. We conducted a greenhouse experiment to investigate how community composition and soil-atmosphere trace gas fluxes of CO2, CH4, and N2O varied from early successional light cyanobacterial biocrusts to mid-successional dark cyanobacteria biocrusts and late-successional moss-lichen biocrusts and as biocrusts of each successional stage matured. Cover type richness increased as biocrusts developed, and richness was generally highest in the late-successional moss-lichen biocrusts. Microbial community composition varied in relation to successional stage, but microbial diversity did not differ significantly among stages. Net photosynthetic uptake of CO2 by each biocrust type also increased as biocrusts developed but tended to be moderately greater (by up to 20%) for the mid-successional dark cyanobacteria biocrusts than the early-successional light cyanobacterial biocrusts or the moss-lichen biocrusts. Rates of soil C accumulation were highest for the dark cyanobacteria biocrusts and early successional light cyanobacteria biocrusts, and lowest for the moss-lichen biocrusts and bare soil controls. Biocrust CH4 and N2O fluxes were not consistently distinguishable from the same fluxes measured from bare soil controls; the measured rates were also substantially lower than have been reported in previous biocrust studies. Our experiment, which uniquely used greenhouse-grown biocrusts to manipulate community composition and accelerate biocrust development, shows how biocrust function varies along a dynamic gradient of biocrust successional stages. <br> This data set includes community composition surveys, microbial sequence data, fluxes of CO2, CH4 and N2O, and measurements of organic matter content.
DOI: 10.6084/m9.figshare.3561882.v1
title: Supplement 1. R script files and data from both the field introduction and the mesocosm experiment to execute the models described in the manuscript and in Appendix E.

description: File List Gamma_Negbin_Fecund.R (MD5: 7cd8437e8cd555f777499ef6e3bc279e) -- # R code for fecundity predictions NegBinFecund.R (MD5: fd282a2e324e20d7529bf51d2d2e14ef) -- # R code for seed model Gamma_Biomass.R (MD5: 5926e4126625a807b86ebf3b48aa1b93) -- # R code for biomass model generalBAYESIANcode.R (MD5: bce9894d372872da18a3ee5305f571f5) -- # R code for functions used in above code garden.csv (MD5: 19d443db46af62e515e38ad07d8ee499) -- # Field introduction data light_exp_seed.csv (MD5: ac8be1d03af3befc0e1f32e8c5311af8) -- # Mesocosm data Description These files are provided to assist in reproduction of our modeling results using the statistical package R. The first supplement (Gamma_Negbin_Fecund) contains R code that jointly samples from the two data sets (garden.csv and light_exp_seed.csv) in order to create predictions of plant fecundity in the field. The hierarchical biomass model (Gamma_Biomass.R) and the seed production model (NegBinFecund.R) are also included separately.
DOI: 10.6084/m9.figshare.8986340.v1
title: pat 2 CT

description: Admire, Pinnacle, and Velocity denote structure sets after a deformable or rigid registration was applied to the MRI holding the CT as primary.<br>
DOI: 10.6084/m9.figshare.c.3677749_d3.v1
title: Additional file 12: Table S11. of High-dimensional assessment of B-cell responses to quadrivalent meningococcal conjugate and plain polysaccharide vaccine

description: Gene set enrichment analysis of gene expression data 7Â days after a second dose of MenACWY-CRM in those primed with MenACWY-CRM compared to those who previously received a dose of MenACWY-PS. (XLS 100 kb)
DOI: 10.6084/m9.figshare.14444351.v1
title: Collaboration Quality Dataset

description: This dateset is collected from a collaborative learning settings conducted in a classroom. Audio and logs data were collected from the session. Three different types of data were extracted from the data - Basic features, Acoustic features, Linguistic features. The dataset also contains the annotated labels for collaboration quality for 306 episodes (each of 30 seconds time window)
DOI: 10.6084/m9.figshare.21311088.v1
title: Supplementary Material for: Obesity Exacerbates Lupus Activity in Fc Gamma Receptor IIb Deficient Lupus Mice Partly through Saturated Fatty Acid-Induced Gut Barrier Defect and Systemic Inflammation

description: The prevalence of obesity is increasing, and the coexistence of obesity and systemic lupus erythematosus (lupus) is possible. A high-fat diet (HFD) was orally administered for 6 months in female 8-week-old Fc gamma receptor IIb deficient (FcgRIIb−/−) lupus or age and gender-matched wild-type (WT) mice. Lupus nephritis (anti-dsDNA, proteinuria, and increased creatinine), gut barrier defect (fluorescein isothiocyanate dextran), serum lipopolysaccharide (LPS), serum interleukin (IL)-6, liver injury (alanine transaminase), organ fibrosis (liver and kidney pathology), spleen apoptosis (activated caspase 3), and aorta thickness (but not weight gain and lipid profiles) were more prominent in HFD-administered FcgRIIb−/− mice than the obese WT, without injury in regular diet-administered mice (both FcgRIIb−/− and WT). In parallel, combined palmitic acid (PA; a saturated fatty acid) with LPS (PA + LPS) induced higher tumor necrotic factor-α, IL-6, and IL-10 in the supernatant, inflammatory genes (inducible nitric oxide synthase and IL-1β), reactive oxygen species (dihydroethidium), and glycolysis with reduced mitochondrial activity (extracellular flux analysis) when compared with the activation by each molecule alone in both FcgRIIb−/− and WT macrophages. However, the alterations of these parameters were more prominent in PA + LPS-administered FcgRIIb−/− than in the WT cells. In conclusion, obesity accelerated inflammation in FcgRIIb−/− mice, partly due to the more potent responses from the loss of inhibitory FcgRIIb against PA + LPS with obesity-induced gut barrier defect.
DOI: 10.21233/1dtw-jz58
title: Aoki ostracode surface sample dataset

description: Raw data for the Aoki ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.6084/m9.figshare.12932762.v1
title: Supplementary Material for: Uncovering the Potential Differentially Expressed miRNAs and mRNAs in Ischemic Stroke Based on Integrated Analysis in the Gene Expression Omnibus Database

description: <b><i>Introduction:</i></b> Ischemic stroke is the third leading cause of death. There is no known treatment or cure for the disease. Moreover, the pathological mechanism of ischemic stroke remains unclear. <b><i>Objective:</i></b> We aimed to identify potential microRNAs (miRNAs) and mRNAs, contributing to understanding the pathology of ischemic stroke. <b><i>Methods:</i></b> First, the data of miRNA and mRNA were downloaded for differential expression analysis. Then, the regulatory network between miRNA and mRNAs was constructed. Third, top 100 differentially expressed mRNAs were used to construct a protein-protein interaction network followed by the function annotation of mRNAs. In addition, in vitro experiment was used to validate the expression of mRNAs. Last, receiver operating characteristic diagnostic analysis of differentially methylated genes was performed. <b><i>Results:</i></b> Totally, up to 26 differentially expressed miRNAs and 1,345 differentially expressed mRNAs were identified. Several regulatory interaction pairs between miRNA and mRNAs were identified, such as hsa-miR-206-HMGCR/PICALM, hsa-miR-4491-TMEM97, hsa-miR-3622b-5p/hsa-miR-548k-KLF12, and hsa-miR-302a-3p/hsa-miR-3145-3p-CTSS. MAPK signaling pathway (involved DUSP1) and the Notch signaling pathway (involved NUMB and CREBBP) were identified. The expression validation of KLF12, ARG1, ITGAM, SIRT4, SERPINH1, and DUSP1 was consistent with the bioinformatics analysis. Interestingly, hsa-miR-206, hsa-miR-4491, hsa-miR-3622b-5p, hsa-miR-548k, hsa-miR-302a-3p, hsa-miR-3145-3p, KLF12, and ID3 had the potential diagnostic value of ischemic stroke. <b><i>Conclusions:</i></b> The identified differentially expressed miRNAs and mRNAs may be associated with the development of ischemic stroke.