cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9969212.v1
title: MOESM19 of Comparative genomics of Leishmania (Mundinia)

description: Additional file 19: Table S4. Estimates of evolutionary divergence among putative side chain arabinosyltransferase sequences. The number of amino acid differences per site from between sequences are shown. The analysis involved 20 amino acid sequences. All positions with less than 80% site coverage were eliminated. Less than 20% alignment gaps, missing data and ambiguous bases were allowed at any position. There were total of 694 positions in the final dataset. Evolutionary analyses were conducted in MEGA7.
DOI: 10.6084/m9.figshare.9969197
title: MOESM17 of Comparative genomics of Leishmania (Mundinia)

description: Additional file 17: Table S2. Estimates of evolutionary divergence among putative amastin sequences. The number of amino acid differences per site from between sequences are shown. The analysis involved 450 amino acid sequences. All ambiguous positions were removed for each sequence pair. There were a total of 1532 positions in the final dataset. Evolutionary analyses were conducted in MEGA7.
DOI: 10.6084/m9.figshare.9969203.v1
title: MOESM18 of Comparative genomics of Leishmania (Mundinia)

description: Additional file 18: Table S3. Estimates of evolutionary divergence among putative side chain galactosyltransferase sequences. The number of amino acid differences per site from between sequences are shown. The analysis involved 87 amino acid sequences. All positions with less than 80% site coverage were eliminated. Less than 20% alignment gaps, missing data and ambiguous bases were allowed at any position. There were a total of 476 positions in the final dataset. Evolutionary analyses were conducted in MEGA7. The presence of n/c in the results denotes cases in which it was not possible to estimate evolutionary distances.
DOI: 10.6084/m9.figshare.9969188
title: MOESM16 of Comparative genomics of Leishmania (Mundinia)

description: Additional file 16: Table S1. Dataset used in this study. Organisms, whose genomes and transcriptomes were sequenced in this work, are in bold.
DOI: 10.6084/m9.figshare.9969197.v1
title: MOESM17 of Comparative genomics of Leishmania (Mundinia)

description: Additional file 17: Table S2. Estimates of evolutionary divergence among putative amastin sequences. The number of amino acid differences per site from between sequences are shown. The analysis involved 450 amino acid sequences. All ambiguous positions were removed for each sequence pair. There were a total of 1532 positions in the final dataset. Evolutionary analyses were conducted in MEGA7.
DOI: 10.6084/m9.figshare.9969188.v1
title: MOESM16 of Comparative genomics of Leishmania (Mundinia)

description: Additional file 16: Table S1. Dataset used in this study. Organisms, whose genomes and transcriptomes were sequenced in this work, are in bold.
DOI: 10.6084/m9.figshare.9969104
title: MOESM2 of Using a marine microalga as a chassis for polyethylene terephthalate (PET) degradation

description: Additional file 2: Table S1. Mass spectrometry analysis results for the 40 kDa band (see Additional file 1: Figure S2). Table S3. Quantification of TPA and MHET production.
DOI: 10.6084/m9.figshare.9969104.v1
title: MOESM2 of Using a marine microalga as a chassis for polyethylene terephthalate (PET) degradation

description: Additional file 2: Table S1. Mass spectrometry analysis results for the 40 kDa band (see Additional file 1: Figure S2). Table S3. Quantification of TPA and MHET production.
DOI: 10.6084/m9.figshare.9969053
title: Additional file 3: of Transcriptomic and functional analysis of the oosome, a unique form of germ plasm in the wasp Nasonia vitripennis

description: Table S1. Posterior-enriched genes in Nasonia. The posterior-enriched genes identified in the RNA-seq experiment and validated by in-situ hybridization are sorted into 5 of the following functional categories: cellular transport/ localization (★), cytoskeletal structure/cell organization(△), transcriptional/translational regulation(◇), metabolism(☐) and unknown(•).(XLSX 43 kb)
DOI: 10.6084/m9.figshare.9969053.v1
title: Additional file 3: of Transcriptomic and functional analysis of the oosome, a unique form of germ plasm in the wasp Nasonia vitripennis

description: Table S1. Posterior-enriched genes in Nasonia. The posterior-enriched genes identified in the RNA-seq experiment and validated by in-situ hybridization are sorted into 5 of the following functional categories: cellular transport/ localization (★), cytoskeletal structure/cell organization(△), transcriptional/translational regulation(◇), metabolism(☐) and unknown(•).(XLSX 43 kb)
DOI: 10.6084/m9.figshare.12867029
title: Supplementary Figure SCA analysis using a manually curated cancer-immune-signature (SCA tutorial)

description: Dataset used to assemble Figure SCA analysis using a manually curated cancer-immune-signature in SCAtutorial vignette (https://kendomaniac.github.io/SCAtutorial/articles/SCAvignette.html)<br><strong></strong>
DOI: 10.6084/m9.figshare.9969035
title: MOESM3 of Spatially resolved transcriptomics reveals plant host responses to pathogens

description: Additional file 3. GO-term enrichments of spatial affinity propagation clustering.
DOI: 10.6084/m9.figshare.12867029.v1
title: Supplementary Figure SCA analysis using a manually curated cancer-immune-signature (SCA tutorial)

description: Dataset used to assemble Figure SCA analysis using a manually curated cancer-immune-signature in SCAtutorial vignette (https://kendomaniac.github.io/SCAtutorial/articles/SCAvignette.html)<br><strong></strong>
DOI: 10.6084/m9.figshare.9969029
title: MOESM2 of Spatially resolved transcriptomics reveals plant host responses to pathogens

description: Additional file 2. Read numbers, ENA accessions, DE genes, GO accessions, clustering information, FLARE associations of experiments.
DOI: 10.6084/m9.figshare.9969035.v1
title: MOESM3 of Spatially resolved transcriptomics reveals plant host responses to pathogens

description: Additional file 3. GO-term enrichments of spatial affinity propagation clustering.
DOI: 10.6084/m9.figshare.9969029.v1
title: MOESM2 of Spatially resolved transcriptomics reveals plant host responses to pathogens

description: Additional file 2. Read numbers, ENA accessions, DE genes, GO accessions, clustering information, FLARE associations of experiments.
DOI: 10.6084/m9.figshare.9969014
title: MOESM1 of From marginal to essential: the golden thread between nutrient sensing, medium composition and Plasmodium vivax maturation in in vitro culture

description: Additional file 1: Table S1. Comparison of the components of alternative media used in attempts to culture P. vivax in vitro. Media composition of RPMI-1640, Waymouth and McCoy5A, L15, IMDM and Williams from Sigma. Williamâ s medium is commercially available with or without glutamine, phenol red, sodium bicarbonate and Glutamax.
DOI: 10.6084/m9.figshare.9969014.v1
title: MOESM1 of From marginal to essential: the golden thread between nutrient sensing, medium composition and Plasmodium vivax maturation in in vitro culture

description: Additional file 1: Table S1. Comparison of the components of alternative media used in attempts to culture P. vivax in vitro. Media composition of RPMI-1640, Waymouth and McCoy5A, L15, IMDM and Williams from Sigma. Williamâ s medium is commercially available with or without glutamine, phenol red, sodium bicarbonate and Glutamax.
DOI: 10.6084/m9.figshare.9968999
title: MOESM4 of Heart disease in a mutant mouse model of spontaneous eosinophilic myocarditis maps to three loci

description: Additional file 4. File containing color-coded SNP genotypes for the haplotype analysis relevant to Fig. 5.
DOI: 10.6084/m9.figshare.9968999.v1
title: MOESM4 of Heart disease in a mutant mouse model of spontaneous eosinophilic myocarditis maps to three loci

description: Additional file 4. File containing color-coded SNP genotypes for the haplotype analysis relevant to Fig. 5.
DOI: 10.6084/m9.figshare.9968879
title: A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs

description: MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in the regulation of gene function by a mechanism known as RNA silencing. In a previous study, we revealed that miRNA-mediated silencing efficacy is correlated with the combinatorial thermodynamic properties of the miRNA seed–target mRNA duplex and the 5´-terminus of the miRNA duplex, which can be predicted using ‘miScore’. In this study, a robust refined-miScore was developed by integrating the thermodynamic properties of various miRNA secondary structures and the latest thermodynamic parameters of wobble base-pairing, including newly established parameters for I:C base pairing. Through repeated random sampling and machine learning, refined-miScore models calculated with either melting temperature (T<sub>m</sub>) or free energy change (ΔG) values were successfully built and validated in both wild-type and adenosine-to-inosine edited miRNAs. In addition to the previously reported contribution of the seed–target duplex and 5´-terminus region, the refined-miScore suggests that the central and 3´-terminus regions of the miRNA duplex also play a role in the thermodynamic regulation of miRNA-mediated silencing efficacy.
DOI: 10.6084/m9.figshare.9968858
title: tree topology of the simulated data

description: tree topology used to simulate sequence<br>Folder tree structuredata/trees/tips_num/ asymmetric_0.5.unroot.tree asymmetric_1.0.unroot.tree asymmetric_2.0.unroot.tree<br>where <b>asymmetric_0.5.unroot.tree</b> is used in the paper<br>Credit by Gblocks and trimAl<br>
DOI: 10.6084/m9.figshare.9968879.v1
title: A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs

description: MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in the regulation of gene function by a mechanism known as RNA silencing. In a previous study, we revealed that miRNA-mediated silencing efficacy is correlated with the combinatorial thermodynamic properties of the miRNA seed–target mRNA duplex and the 5´-terminus of the miRNA duplex, which can be predicted using ‘miScore’. In this study, a robust refined-miScore was developed by integrating the thermodynamic properties of various miRNA secondary structures and the latest thermodynamic parameters of wobble base-pairing, including newly established parameters for I:C base pairing. Through repeated random sampling and machine learning, refined-miScore models calculated with either melting temperature (T<sub>m</sub>) or free energy change (ΔG) values were successfully built and validated in both wild-type and adenosine-to-inosine edited miRNAs. In addition to the previously reported contribution of the seed–target duplex and 5´-terminus region, the refined-miScore suggests that the central and 3´-terminus regions of the miRNA duplex also play a role in the thermodynamic regulation of miRNA-mediated silencing efficacy.
DOI: 10.6084/m9.figshare.9968858.v1
title: tree topology of the simulated data

description: tree topology used to simulate sequence<br>Folder tree structuredata/trees/tips_num/ asymmetric_0.5.unroot.tree asymmetric_1.0.unroot.tree asymmetric_2.0.unroot.tree<br>where <b>asymmetric_0.5.unroot.tree</b> is used in the paper<br>Credit by Gblocks and trimAl<br>
DOI: 10.6084/m9.figshare.9968450
title: Data set for unconstrained arm movements of ADL

description: Each of these files presents data used to obtain results for each movement task presented in the figures and tables of the manuscript.
DOI: 10.6084/m9.figshare.9968450.v1
title: Data set for unconstrained arm movements of ADL

description: Each of these files presents data used to obtain results for each movement task presented in the figures and tables of the manuscript.
DOI: 10.6084/m9.figshare.9968378
title: Role of Soil Fauna in Nitrogen Cycling and Plant Succession: Soil and Plan measurements

description: Lab-based element of Patricia Gilarte's PhD project. Further details about the contents of the attached data can be found upon unzipping. Brief descriotions are included here:<br>Soil measurementsMeasurements taken in the soil.<br>moist:%: moisture in soil (loss by ignition, 104�, 24h, %water content)nematode refers to nematode inoculation: control (no nematodes); bacterial (bacterial feeding nematodes added); plant (root feeding nematodes added)Plant refers to plant mixture: acacia (acacia only); banksia (banksia alone) and both (acacia and banksia)stage refers to successional stage: early and late<br>mineral nitrogen in soil (ammonium and nitrate) was obtained through mild extracts (2N KCl) analyzed in a Discrete Multi-Chemistry Analyzer AQ2 (by Seal Analytical, Inc. Mequon, WI., analyzed at HIE, NSW, Australia).nematode refers to nematode inoculation: control (no nematodes); bacterial (bacterial feeding nematodes added); plant (root feeding nematodes added)Plant refers to plant mixture: acacia (acacia only); banksia (banksia alone) and both (acacia and banksia)stage refers to successional stage: early and late<br>nh4:NH4: ammonium content in soil (mg/L)<br>no3:NO3: nitrate content in soil (mg/L)<br>nemas:number of nematodes in soil were extracted in modified wet funnels from soil subsamples (50 g wet soil; Viglierchio and Schmitt, 1983). The total number of nematodes extracted per pot was then counted under dissecting microscope (Olympus, SZX10).nematode refers to nematode inoculation: control (no nematodes); bacterial (bacterial feeding nematodes added); plant (root feeding nematodes added)Plant refers to plant mixture: acacia (acacia only); banksia (banksia alone) and both (acacia and banksia)stage refers to successional stage: early and latenemg: number of nematodes per gram of soil
DOI: 10.6084/m9.figshare.9968414.v1
title: Research data.xlsx

description: This dataset include whole rock element concentration, iron isotopic composition, and mineral major element compositions of peridotite from the Yushigou ophiolite in the North Qilian orogen, northern Tibet.
DOI: 10.6084/m9.figshare.9968372
title: Drought, Fluorescence, & Photosynthesis Dataset

description: Data from the paper "Solar-induced chlorophyll fluorescence and short-term photosynthetic response to drought" published in Ecological Applications. <br><br>Each column heading includes a comment box which describes the data in greater detail. <br>Please email Levi Helm (lthelm@asu.edu) with any questions. <br>
DOI: 10.23641/asha.9968369
title: Hearing impairment and disrupted sleep (Clarke et al., 2019)

description: <b>Purpose: </b>Hearing impairment (HI) is the most common sensory impairment and may negatively impact sleep through reduced auditory input. Factors associated with HI such as anxiety regarding communication in daily life may also adversely impact an individual’s sleep. Here, research on the relationship between HI and sleep disruption was catalogued using scoping review methodology.<b>Method:</b> A systematic strategy was employed to search various electronic databases. This review is reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyses Scoping Review Extension.<b>Results: </b>Sixteen records met inclusion criteria. Studies have investigated sleep in HI as a primary aim in noise-exposed workers or large surveys in older participants. Experimental and quasi-experimental studies report alterations to sleep architecture of potential neuroplastic origins. Studies reporting sleep as a secondary aim generally report poorer sleep in HI participants.<b>Conclusions: </b>This scoping review has catalogued evidence that altered or negatively impacted sleep may be associated with HI. Potential confounding factors, mechanisms, and considerations for future research are discussed.<br><b>Supplemental Material S1.</b> Table of extracted data for included records.<br>Clarke, N. A., Hoare, D. J., & Kilan, E. C. (2019). Evidence for an association between hearing impairment and disrupted sleep: Scoping review. <i>American Journal of Audiology.</i> Advance online publication. https://doi.org/10.1044/2019_AJA-19-0026
DOI: 10.23641/asha.9968369.v1
title: Hearing impairment and disrupted sleep (Clarke et al., 2019)

description: <b>Purpose: </b>Hearing impairment (HI) is the most common sensory impairment and may negatively impact sleep through reduced auditory input. Factors associated with HI such as anxiety regarding communication in daily life may also adversely impact an individual’s sleep. Here, research on the relationship between HI and sleep disruption was catalogued using scoping review methodology.<b>Method:</b> A systematic strategy was employed to search various electronic databases. This review is reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyses Scoping Review Extension.<b>Results: </b>Sixteen records met inclusion criteria. Studies have investigated sleep in HI as a primary aim in noise-exposed workers or large surveys in older participants. Experimental and quasi-experimental studies report alterations to sleep architecture of potential neuroplastic origins. Studies reporting sleep as a secondary aim generally report poorer sleep in HI participants.<b>Conclusions: </b>This scoping review has catalogued evidence that altered or negatively impacted sleep may be associated with HI. Potential confounding factors, mechanisms, and considerations for future research are discussed.<br><b>Supplemental Material S1.</b> Table of extracted data for included records.<br>Clarke, N. A., Hoare, D. J., & Kilan, E. C. (2019). Evidence for an association between hearing impairment and disrupted sleep: Scoping review. <i>American Journal of Audiology.</i> Advance online publication. https://doi.org/10.1044/2019_AJA-19-0026
DOI: 10.6084/m9.figshare.9968294
title: Data from: Living myofibroblast–silicon composites for probing electrical coupling in cardiac systems

description: Deposited items: The raw data that was used to generate the following figures: Fig. 1B- Raw SEM images Fig. 1C- Z-stack of confocal imaging Fig. 1D- Raw videos of the photo-stimulations (sld files) Fig. 1E-G- Raw video of the photo-stimulation, bright filed image of the SiNWs, fluorescent image of the fluo-4, and a text file with the stimulation timings Fig. 2A-C- Raw video of the photo-stimulation Fig. 2D-F- Raw videos of the photo-stimulations (D1, D2, i, ii, iii, iv, v, and vi) Fig. 3B- Z-stack of confocal imaging of the scar Fig. 3C- Images of the scar with the scar thickness as used for statical analysis Fig. 3D- Hematoxylin and Eosin images of the scar Fig. 3E- Z-stack of confocal imaging of the scar immune-response Fig. 4B- Raw video of the photo-stimulation and the transmitted light image showing the SiNWs Fig. 4C- Raw videos of the 3 different photo-stimulations and their intensity profiles Fig. 4D- ECG recording of the optical and electrical stimulation
DOI: 10.6084/m9.figshare.9968294.v1
title: Data from: Living myofibroblast–silicon composites for probing electrical coupling in cardiac systems

description: Deposited items: The raw data that was used to generate the following figures: Fig. 1B- Raw SEM images Fig. 1C- Z-stack of confocal imaging Fig. 1D- Raw videos of the photo-stimulations (sld files) Fig. 1E-G- Raw video of the photo-stimulation, bright filed image of the SiNWs, fluorescent image of the fluo-4, and a text file with the stimulation timings Fig. 2A-C- Raw video of the photo-stimulation Fig. 2D-F- Raw videos of the photo-stimulations (D1, D2, i, ii, iii, iv, v, and vi) Fig. 3B- Z-stack of confocal imaging of the scar Fig. 3C- Images of the scar with the scar thickness as used for statical analysis Fig. 3D- Hematoxylin and Eosin images of the scar Fig. 3E- Z-stack of confocal imaging of the scar immune-response Fig. 4B- Raw video of the photo-stimulation and the transmitted light image showing the SiNWs Fig. 4C- Raw videos of the 3 different photo-stimulations and their intensity profiles Fig. 4D- ECG recording of the optical and electrical stimulation
DOI: 10.6084/m9.figshare.9968318
title: Survival estimates for the invasive American Bullfrog

description: R code and JAGs model file for fitting a robust-design Cormack-Jolly-Seber model to estimate the influence of extrinsic and intrinsic factors on apparent survival.
DOI: 10.6084/m9.figshare.9968318.v2
title: Survival estimates for the invasive American Bullfrog

description: R code and JAGs model file for fitting a robust-design Cormack-Jolly-Seber model to estimate the influence of extrinsic and intrinsic factors on apparent survival.
DOI: 10.6084/m9.figshare.9968318.v1
title: Survival estimates for the invasive American Bullfrog

description: R code and JAGs model file for fitting a robust-design Cormack-Jolly-Seber model to estimate the influence of extrinsic and intrinsic factors on apparent survival.
DOI: 10.6084/m9.figshare.9968198.v1
title: Monocytic cytokine modulation by 1,25 dihydroxyvitamin D3 and HLA-DQ risk in autoimmune polyglandular syndrome type 2

description: Supplement Table 1: Association of HLA DQ risk category on gene expression levels in HC, AD/AIT and T1D/AIT patients<br>
DOI: 10.6084/m9.figshare.9964241
title: BioCyc Tier3 Diamond index and mapping files

description: Diamond aligner (https://github.com/bbuchfink/diamond) index for Biocyc Tier3 database (V23.0) as well as files mapping aligned objects to pathways/enzymes/transporters/complexes.
DOI: 10.6084/m9.figshare.9968198.v2
title: Monocytic cytokine modulation by 1,25 dihydroxyvitamin D3 and HLA-DQ risk in autoimmune polyglandular syndrome type 2

description: Supplement Table 1: Association of HLA DQ risk category on gene expression levels in HC, AD/AIT and T1D/AIT patients<br>
DOI: 10.6084/m9.figshare.9964229
title: Manuscript_AgEE

description: Data for Maize Experiments
DOI: 10.6084/m9.figshare.9964229.v1
title: Manuscript_AgEE

description: Data for Maize Experiments
DOI: 10.6084/m9.figshare.9964181
title: grid.1013.3

description: What does Australasia Research Look like? grid.1013.3 data<br>
DOI: 10.6084/m9.figshare.9964169
title: Better all by myself: Gaining personal experience, not watching others, improves 3-year-olds’ performance in a causal trap-task (dataset)

description: Children often learn from others’ demonstrations, but in the causal domain, evidence acquired from observing others may be more ambiguous than evidence generated for oneself. Prior work involving tool-using tasks suggests that observational learning may not provide sufficient information about the causal relations involved, but it remains unclear whether these limitations can by mitigated by providing demonstrations using familiar manual actions rather than unfamiliar tools. We provided 2.5- to 3.5-year-old children (n = 67) with the opportunity to acquire experience with a causal trap-task by hand or by tool, actively or from observing others. Initially, children either generated their own experience or watched a yoked demonstration; all children then attempted the trap-task with the tool. Older children who generated their own experience outperformed those who watched demonstrations, whereas younger children performed at chance in all conditions. Though hand- or tool-use had no effect on performance with a tool, older children in the Self–Hand condition perseverated less during initial practice than their peers in Self–Tool. The implications of these findings for scaffolding self-guided learning and for demonstrations involving errors are discussed.<br>