cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8046920
title: Vocalization Annotation Formats Dataset

description: A dataset containing small (quick to download) examples of different file formats for recording and annotating vocalizations (currently, just birdsong). Each compressed archive represents one format, including a README that cites the original source from which the format was taken.<br>This repository is used by several libraries that need access to relatively small amounts of audio files of vocalizations, and the annotations for those files in various formats, for demonstration purposes (see links section below).<br>It is generated from the following source:https://github.com/NickleDave/vocal-annotation-formats<br><br>The original repositories are here (and linked below), please cite if you use:<br>https://figshare.com/articles/Bengalese_Finch_song_repository/4805749<br><br>https://figshare.com/articles/BirdsongRecognition/3470165<br><br><br>
DOI: 10.6084/m9.figshare.8046920.v1
title: Vocalization Annotation Formats Dataset

description: A dataset containing small (quick to download) examples of different file formats for recording and annotating vocalizations (currently, just birdsong). Each compressed archive represents one format, including a README that cites the original source from which the format was taken.<br>This repository is used by several libraries that need access to relatively small amounts of audio files of vocalizations, and the annotations for those files in various formats, for demonstration purposes (see links section below).<br>It is generated from the following source:https://github.com/NickleDave/vocal-annotation-formats<br><br>The original repositories are here (and linked below), please cite if you use:<br>https://figshare.com/articles/Bengalese_Finch_song_repository/4805749<br><br>https://figshare.com/articles/BirdsongRecognition/3470165<br><br><br>
DOI: 10.17632/4rj7k22wh6.4
title: Data for: From deforestation to afforestation: Effect of slopeland use policies on land use/cover change in Taiwan

description: slopeland land-use change in Taiwan
DOI: 10.17632/pyxd8t5js5.4
title: Data for: From deforestation to afforestation: Effect of slopeland use policies on land use/cover change in Taiwan

description: This data contains SPSS and GIS files, which regards the information of slopland in Taiwan.
DOI: 10.6084/m9.figshare.8046617
title: Uncut gel image

description: Uncut gel image (Fig. 3b)
DOI: 10.6084/m9.figshare.8046617.v1
title: Uncut gel image

description: Uncut gel image (Fig. 3b)
DOI: 10.6084/m9.figshare.8046581
title: Metabolomics data covering amino acids and acylcarnitines profile of 22 relapsing-remitting multiple sclerosis subjects and 22 healthy controls

description: Dataset contains information about amino acids (13) and acylcarnitines (30) concentrations measured in plasma of 22 RRMS patients and 22 healthy controls in two series. QC samples L1 and L2 were added to control interassay variation. Raw data were collected with API 6500QTRAP (AB Sciex) coupled with HPLC LC-20AD Prominence (Shimadzu Corporation) and 75*2.1 mm column filled with sorbent prontosil 120-3-c18 aq (Ekonova, Russia). MRM data were processed in MultiQuant<sup>TM</sup> 2.1 Software (AB Sciex). MassChrom 55000 (Chromsystems) test-system and protocol was used for sample preparation. Additional column (Calculated concentration) was added in Excel (Peak Area parameter was used for calculation).<br>
DOI: 10.6084/m9.figshare.8046581.v1
title: Metabolomics data covering amino acids and acylcarnitines profile of 22 relapsing-remitting multiple sclerosis subjects and 22 healthy controls

description: Dataset contains information about amino acids (13) and acylcarnitines (30) concentrations measured in plasma of 22 RRMS patients and 22 healthy controls in two series. QC samples L1 and L2 were added to control interassay variation. Raw data were collected with API 6500QTRAP (AB Sciex) coupled with HPLC LC-20AD Prominence (Shimadzu Corporation) and 75*2.1 mm column filled with sorbent prontosil 120-3-c18 aq (Ekonova, Russia). MRM data were processed in MultiQuant<sup>TM</sup> 2.1 Software (AB Sciex). MassChrom 55000 (Chromsystems) test-system and protocol was used for sample preparation. Additional column (Calculated concentration) was added in Excel (Peak Area parameter was used for calculation).<br>
DOI: 10.6084/m9.figshare.8046491
title: Learning by doing: enhancing hydrology lectures with individual fieldwork projects

description: Hydrology teaching deals with processes happening outside the classroom, which calls for active-learning methods to complement lectures. In a geography undergraduate course, new teaching methods and assessment were designed, in which students investigated a river of their choice by completing homework tasks and presenting their results on a poster. During a 3-year implementation process, the changes were evaluated using a combination of formal and informal student and lecturer feedback. Students mentioned that they enjoyed doing the project and that it helped their understanding of theory, their research skills, and their ability to select, organize and present information. Questionnaire results showed that, over the implementation period, students’ perceived value of homework increased strongly, while their perceived value of lectures remained high. In informal feedback, students noted that they enjoyed learning about where they live, preferred doing the projects individually and seeing each other’s projects, and spent more time on the coursework when assessed. When looking back in interviews, students commented that the projects had prepared them well for their dissertation and summer job. The advantage of using homework-based projects complementing lectures is the strong link between theory and practice, which could be further enhanced by discussing the homework in the lectures.
DOI: 10.6084/m9.figshare.8046461
title: CaseControl study for PLOS ONE

description: A database of a case control study exploring the association of copd/emphysema and lung cancer
DOI: 10.6084/m9.figshare.8046491.v1
title: Learning by doing: enhancing hydrology lectures with individual fieldwork projects

description: Hydrology teaching deals with processes happening outside the classroom, which calls for active-learning methods to complement lectures. In a geography undergraduate course, new teaching methods and assessment were designed, in which students investigated a river of their choice by completing homework tasks and presenting their results on a poster. During a 3-year implementation process, the changes were evaluated using a combination of formal and informal student and lecturer feedback. Students mentioned that they enjoyed doing the project and that it helped their understanding of theory, their research skills, and their ability to select, organize and present information. Questionnaire results showed that, over the implementation period, students’ perceived value of homework increased strongly, while their perceived value of lectures remained high. In informal feedback, students noted that they enjoyed learning about where they live, preferred doing the projects individually and seeing each other’s projects, and spent more time on the coursework when assessed. When looking back in interviews, students commented that the projects had prepared them well for their dissertation and summer job. The advantage of using homework-based projects complementing lectures is the strong link between theory and practice, which could be further enhanced by discussing the homework in the lectures.
DOI: 10.6084/m9.figshare.8046455
title: Case control study for PLOS ONE

description: A dataset of a case control study exploring the association of copd/emphysema and lung cancer
DOI: 10.6084/m9.figshare.8046461.v1
title: CaseControl study for PLOS ONE

description: A database of a case control study exploring the association of copd/emphysema and lung cancer
DOI: 10.6084/m9.figshare.8046452
title: Supplementary Material for: Ingestion of Casein Hydrolysate Induces Oral Tolerance and Suppresses Subsequent Epicutaneous Sensitization and Development of Anaphylaxis Reaction to Casein in Mice

description: <b><i>Background:</i></b> Casein is the most dominant causal allergen in cow’s milk allergy (CMA). Casein hydrolysates are frequently applied in infant formulas for children with a risk or history of CMA. However, there is limited information on the oral tolerance-inducing ability of casein hydrolysates. <b><i>Objectives:</i></b> The aim of this study was to investigate whether the ingestion of casein hydrolysate induces tolerance to casein, ultimately preventing subsequent epicutaneous sensitization and development of an anaphylaxis reaction. <b><i>Methods:</i></b> BALB/c mice were orally administered casein or a casein hydrolysate (CNH) via the drinking water and were then epicutaneously sensitized by repeated exposure of casein on tape-stripped skin. Sensitization was assessed by basophil activation tests, the serum levels of casein-specific antibodies, and cytokine production from casein-stimulated spleen and mesenteric lymph node (MLN) cells. Occurrence of an anaphylaxis reaction was evaluated by measuring rectal temperature and the plasma level of mouse mast cell protease-1 (mMCP-1) after oral casein challenges. The T cell population in the spleen and MLN was assessed by flow cytometry. Intestinal mast cells and basophils were analyzed histologically. <b><i>Results:</i></b> Sensitization and anaphylaxis reaction to casein were significantly suppressed in casein- or CNH-fed mice compared to controls. Prior ingestion of casein or CNH had no effect on the population of regulatory T cells and activated T cells in lymphoid tissues. Intestinal basophils increased by the epicutaneous sensitization of casein, which was suppressed in casein- or CNH-fed mice. Although the increase in the plasma level of mMCP-1 after oral challenge was suppressed in casein- or CNH-fed mice, there was no change in the number of intestinal mast cells. <b><i>Conclusion:</i></b> Prior ingestion of casein or CNH induced oral tolerance and suppressed subsequent epicutaneous sensitization and development of systemic anaphylaxis to casein.
DOI: 10.6084/m9.figshare.8046455.v1
title: Case control study for PLOS ONE

description: A dataset of a case control study exploring the association of copd/emphysema and lung cancer
DOI: 10.6084/m9.figshare.8046437
title: Short molecular dynamics of a peptide inside a pure DMPC membrane

description: 1 ns of molecular dynamics simulation of a 19-residue peptide inside a pure DMPC membrane, performed at the NPT ensemble - 1 atm at 310K using Berendsen (semi-isotropic) and V-rescale for pressure and temperature coupling, respectively, with 1.6 ps and 0.1ps as coupling constants. Van der Waals interactions were treated using the Verlet algorithm with a 1 nm cutoff. Electrostatics where treated with particle-mesh Ewald, with a 1 nm cutoff for the real space calculations. Both the peptide and DMPC were parameterized using the GROMOS 54A7, while SPC was used for water. LINCS restraints were used on all the bonds. <br>Peptide sequence is AAAQAAQAQWAQRQATWQA. This sequence was not taken from any real world examples, as this is a test system created for MDAnalysis datasets. The peptide was set to have be α-helical secondary structure, and was inserted manually in the membrane before minimization and equilibration. <br>More on MDAnalysis: https://www.mdanalysis.org/
DOI: 10.6084/m9.figshare.8046395.v1
title: Data and code for "Chemotaxonomy of domesticated grasses: a pathway to understanding the origins of agriculture"

description: File 'DomesticatedGrasses_spectra.txt': FTIR spectra for domesticated grass pollen, samples are in rows and wavenumbers in columns<br>File 'DomesticatedGrasses_sampleInfo.txt': metadata for each FTIR spectrum<br>The files are in the correct format to run the associated R code, which will carry out the analyses that are in the paper
DOI: 10.6084/m9.figshare.8046359
title: Genomic resources for the spotted ragged-tooth shark <i>Carcharias taurus</i>

description: Genomic data can be a useful tool in the management and conservation of biodiversity. Here, we report the development of genomic resources for the spotted ragged-tooth shark <i>Carcharias taurus</i> using genome-wide DNA data from Illumina next-generation sequencing. We explored two commonly used genetic marker types: microsatellites and mitochondrial DNA. A total of 4 394 putative microsatellites were identified, of which 10 were tested on 24 individuals and found to have ideal properties for population genetic analyses. Additionally, we reconstructed the first complete mitochondrial genome of a South African spotted ragged-tooth shark, and highlight the most informative gene regions to facilitate future primer design. The data reported here may serve as a resource for future studies and can ultimately be applied in the sustainable conservation and fisheries management of this apex predator.
DOI: 10.6084/m9.figshare.8046359.v1
title: Genomic resources for the spotted ragged-tooth shark <i>Carcharias taurus</i>

description: Genomic data can be a useful tool in the management and conservation of biodiversity. Here, we report the development of genomic resources for the spotted ragged-tooth shark <i>Carcharias taurus</i> using genome-wide DNA data from Illumina next-generation sequencing. We explored two commonly used genetic marker types: microsatellites and mitochondrial DNA. A total of 4 394 putative microsatellites were identified, of which 10 were tested on 24 individuals and found to have ideal properties for population genetic analyses. Additionally, we reconstructed the first complete mitochondrial genome of a South African spotted ragged-tooth shark, and highlight the most informative gene regions to facilitate future primer design. The data reported here may serve as a resource for future studies and can ultimately be applied in the sustainable conservation and fisheries management of this apex predator.
DOI: 10.6084/m9.figshare.8046290
title: Proteome database of Escherichia coli K-12

description: Ensemble of proteins in a bacterial species hold relevance for understanding the biochemical and metabolic activities of a cell at a global level. To this end, proteomics technologies have opened a window into the inner workings of cells, allowing rational design changes to be implemented at the cellular level for overproduction of specified metabolite through heterologous expression of particular genes or pathways. Such omics technologies generally generate large amount of information that requires bioinformatic approaches for inferring biological meaning. For example, useful information such as protein name and amino acid sequence information needs to be extracted from proteome data file automatically through bioinformatic tools. Hence, this work uses an in-house MATLAB function to construct a proteome database of <i>Escherichia coli </i>K-12. Information encapsulated in the proteome database include protein name, amino acid sequence, number of residues in protein, molecular weight of protein and nucleotide sequence of protein. In particular, protein name and amino acid sequence information are extracted from the original fasta proteome file, while number of amino acid residues, molecular weight and nucleotide sequence of each protein in the proteome are calculated using built-in functions in MATLAB. Collectively, the proteome database of <i>E. coli </i>K-12 should find use in diverse biology and biotechnology applications ranging from understanding the molecular weight of individual proteins to synthesizing a gene in molecular cloning workflow. <br>
DOI: 10.6084/m9.figshare.8046227
title: Sorotouch Leaning Data

description: Sorotouch Leaning Data
DOI: 10.6084/m9.figshare.8046227.v1
title: Sorotouch Leaning Data

description: Sorotouch Leaning Data
DOI: 10.6084/m9.figshare.8045996
title: Additional file 6: of To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae)

description: Results of the BPP A11 analysis. (ZIP 216 kb)
DOI: 10.6084/m9.figshare.8045993
title: Additional file 5: of To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae)

description: Pairwise uncorrected p-distances of the 16S gene. (CSV 6 kb)
DOI: 10.6084/m9.figshare.8045996.v1
title: Additional file 6: of To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae)

description: Results of the BPP A11 analysis. (ZIP 216 kb)
DOI: 10.6084/m9.figshare.8045990
title: Additional file 4: of To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae)

description: Molecular samples used in this study and their associated GenBank accession number. The asterisk (*) denotes newly sequenced samples for this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8045990.v1
title: Additional file 4: of To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae)

description: Molecular samples used in this study and their associated GenBank accession number. The asterisk (*) denotes newly sequenced samples for this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8045993.v1
title: Additional file 5: of To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae)

description: Pairwise uncorrected p-distances of the 16S gene. (CSV 6 kb)
DOI: 10.6084/m9.figshare.8045963
title: Additional file 3: of DNA methylation, transcriptome and genetic copy number signatures of diffuse cerebral WHO grade II/III gliomas resolve cancer heterogeneity and development

description: Table S2. List of TCGA-samples used for verification analyses. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8045963.v1
title: Additional file 3: of DNA methylation, transcriptome and genetic copy number signatures of diffuse cerebral WHO grade II/III gliomas resolve cancer heterogeneity and development

description: Table S2. List of TCGA-samples used for verification analyses. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8045954
title: Additional file 2: of DNA methylation, transcriptome and genetic copy number signatures of diffuse cerebral WHO grade II/III gliomas resolve cancer heterogeneity and development

description: Table S1. List of GGN-patients whose DNA methylation data were included into the study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8045954.v1
title: Additional file 2: of DNA methylation, transcriptome and genetic copy number signatures of diffuse cerebral WHO grade II/III gliomas resolve cancer heterogeneity and development

description: Table S1. List of GGN-patients whose DNA methylation data were included into the study. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8045915
title: Additional file 7: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Anti-dementia drugs and requirements for claiming NHIS insurance benefits. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8045915.v1
title: Additional file 7: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Anti-dementia drugs and requirements for claiming NHIS insurance benefits. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8045894
title: Additional file 5: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Disease codes and definitions associated with dental caries. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8045885
title: Additional file 4: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Treatment codes and definitions of behaviors associated with periodontal diseases. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8045894.v1
title: Additional file 5: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Disease codes and definitions associated with dental caries. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8045873
title: Additional file 3: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Disease codes and definitions associated with periodontal diseases. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8045885.v1
title: Additional file 4: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Treatment codes and definitions of behaviors associated with periodontal diseases. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8045873.v1
title: Additional file 3: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Disease codes and definitions associated with periodontal diseases. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8045855
title: Additional file 1: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Treatment codes and definition of behaviors associated with tooth extraction. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8045864
title: Additional file 2: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Disease codes and definitions associated with dementia. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8045855.v1
title: Additional file 1: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Treatment codes and definition of behaviors associated with tooth extraction. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8045864.v1
title: Additional file 2: of The effect of missing teeth on dementia in older people: a nationwide population-based cohort study in South Korea

description: Disease codes and definitions associated with dementia. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8045798
title: Additional file 1: of Fully automated quantification of biventricular volumes and function in cardiovascular magnetic resonance: applicability to clinical routine settings

description: A. Myocarditis. B. TAVR. C. HCM. D. DCM. E. Repaired ToF. F. PAH. (ZIP 23844 kb)
DOI: 10.6084/m9.figshare.8045795
title: Additional file 2: of Transcriptome analysis of normal-appearing white matter reveals cortisol- and disease-associated gene expression profiles in multiple sclerosis

description: DE genes. (XLSX 266 kb)
DOI: 10.6084/m9.figshare.8045798.v1
title: Additional file 1: of Fully automated quantification of biventricular volumes and function in cardiovascular magnetic resonance: applicability to clinical routine settings

description: A. Myocarditis. B. TAVR. C. HCM. D. DCM. E. Repaired ToF. F. PAH. (ZIP 23844 kb)
DOI: 10.6084/m9.figshare.8045786
title: Additional file 1: of Transcriptome analysis of normal-appearing white matter reveals cortisol- and disease-associated gene expression profiles in multiple sclerosis

description: GO analyses. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8045795.v1
title: Additional file 2: of Transcriptome analysis of normal-appearing white matter reveals cortisol- and disease-associated gene expression profiles in multiple sclerosis

description: DE genes. (XLSX 266 kb)
DOI: 10.6084/m9.figshare.8045786.v1
title: Additional file 1: of Transcriptome analysis of normal-appearing white matter reveals cortisol- and disease-associated gene expression profiles in multiple sclerosis

description: GO analyses. (XLSX 15 kb)