cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6118460.v1
title: Supplemental table 1 from Assessment of stem cell differentiation based on genome-wide expression profiles

description: In recent years, protocols have been established to differentiate stem and precursor cells into more mature cell types. However, progress in this field has been hampered by difficulties to assess the differentiation status of stem cell-derived cells in an unbiased manner. Here, we present an analysis pipeline based on published data and methods to quantify the degree of differentiation and to identify transcriptional control factors explaining differences to the intended target cells or tissues. The pipeline requires RNA-seq or gene array data of the stem cell starting population, derived ‘mature’ cells and primary target cells or tissue. It consists of a principle component analysis to represent global expression changes and to identify possible problems of the dataset that require special attention, such as batch effects; clustering techniques to identify gene groups with similar features; over-representation analysis to characterize biological motifs and transcriptional control factors of the identified gene clusters; and metagenes as well as gene regulatory networks for quantitative cell-type assessment and identification of influential transcription factors. Possibilities and limitations of the analysis pipeline are illustrated using the example of human embryonic stem cell and human induced pluripotent cells to generate ‘hepatocyte-like cells'. The pipeline quantifies the degree of incomplete differentiation as well as remaining stemness and identifies unwanted features, such as colon- and fibroblast-associated gene clusters that are absent in real hepatocytes but typically induced by currently available differentiation protocols. Finally, transcription factors responsible for incomplete and unwanted differentiation are identified. The proposed method is widely applicable and allows an unbiased and quantitative assessment of stem cell-derived cells.This article is part of the themed issue ‘Designer human tissue: coming to a lab near you’.
DOI: 10.6084/m9.figshare.6118454
title: Sterol and stanol % abundances from Sterols and stanols as novel tracers of waterbird population dynamics in freshwater ponds

description: Data used in figures 2 and 3
DOI: 10.6084/m9.figshare.6118454.v1
title: Sterol and stanol % abundances from Sterols and stanols as novel tracers of waterbird population dynamics in freshwater ponds

description: Data used in figures 2 and 3
DOI: 10.6084/m9.figshare.6118373
title: C-Mod-shot-1160901023-three_species_f3he_tolman.ipynb

description: Jupyter notebook. Describing how to view CQL3D distribution function. Specific case deals with <br><pre><code>Alcator C-Mod shot modeling 1160901 Sep 01 2016, 790 Three-ion (3He)-D-H ICRF heating experiments</code></pre>
DOI: 10.6084/m9.figshare.6118373.v1
title: C-Mod-shot-1160901023-three_species_f3he_tolman.ipynb

description: Jupyter notebook. Describing how to view CQL3D distribution function. Specific case deals with <br><pre><code>Alcator C-Mod shot modeling 1160901 Sep 01 2016, 790 Three-ion (3He)-D-H ICRF heating experiments</code></pre>
DOI: 10.6084/m9.figshare.6116141
title: Plasma module

description: Module to process G-EQDSK magnetic equilibrium files. To be used with attached equilibrium file.
DOI: 10.6084/m9.figshare.6116135
title: Dataset - Choosing task difficulty: effects of performance feedback, emotions and conditional reward

description: dataset of a study examining the effects of a performance feedback, related feelings and a monetary reward on decision-making
DOI: 10.6084/m9.figshare.6116135.v2
title: Dataset - Choosing task difficulty: effects of performance feedback, emotions and conditional reward

description: dataset of a study examining the effects of a performance feedback, related feelings and a monetary reward on decision-making
DOI: 10.6084/m9.figshare.6116135.v1
title: Dataset - Deciding the amount of effort to spend in a cognitive task

description: dataset of a study examining the effects of a performance feedback, related feelings and a monetary reward on decision-making
DOI: 10.6084/m9.figshare.6115994
title: Zhu et al 2018 GBC submitted Data, Tables, Figures

description: Multiple datasets reporting original measurements of fluxes from dung patches and auxilliary data.<br><br>Graphs were generated by use of Sigmaplot, data are reported in Excel<br>
DOI: 10.6084/m9.figshare.6115994.v1
title: Zhu et al 2018 GBC submitted Data, Tables, Figures

description: Multiple datasets reporting original measurements of fluxes from dung patches and auxilliary data.<br><br>Graphs were generated by use of Sigmaplot, data are reported in Excel<br>
DOI: 10.6084/m9.figshare.6115955
title: Molecular dynamics simulations showing 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) membrane mechanoporation damage under different strain paths

description: Continuum finite element material models used for traumatic brain injury lack local injury parameters necessitating nanoscale mechanical injury mechanisms be incorporated. One such mechanism is membrane mechanoporation, which can occur during physical insults and can be devastating to cells, depending on the level of disruption. The current study investigates the strain state dependence of phospholipid bilayer mechanoporation and failure. Using molecular dynamics, a simplified membrane, consisting of 72 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) phospholipids, was subjected to equibiaxial, 2:1 non-equibiaxial, 4:1 non-equibiaxial, strip biaxial, and uniaxial tensile deformations at a von Mises strain rate of 5.45 × 10<sup>8</sup> s<sup>−1</sup>, resulting in velocities in the range of 1 to 4.6 m·s<sup>−1</sup>. A water bridge forming through both phospholipid bilayer leaflets was used to determine structural failure. The stress magnitude, failure strain, headgroup clustering, and damage responses were found to be strain state-dependent. The strain state order of detrimentality in descending order was equibiaxial, 2:1 non-equibiaxial, 4:1 non-equibiaxial, strip biaxial, and uniaxial. The phospholipid bilayer failed at von Mises strains of .46, .47, .53, .77, and 1.67 during these respective strain path simulations. Additionally, a Membrane Failure Limit Diagram (MFLD) was created using the pore nucleation, growth, and failure strains to demonstrate safe and unsafe membrane deformation regions. This MFLD allowed representative equations to be derived to predict membrane failure from in-plane strains. These results provide the basis to implement a more accurate mechano-physiological internal state variable continuum model that captures lower length scale damage and will aid in developing higher fidelity injury models.
DOI: 10.6084/m9.figshare.6115955.v1
title: Molecular dynamics simulations showing 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) membrane mechanoporation damage under different strain paths

description: Continuum finite element material models used for traumatic brain injury lack local injury parameters necessitating nanoscale mechanical injury mechanisms be incorporated. One such mechanism is membrane mechanoporation, which can occur during physical insults and can be devastating to cells, depending on the level of disruption. The current study investigates the strain state dependence of phospholipid bilayer mechanoporation and failure. Using molecular dynamics, a simplified membrane, consisting of 72 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) phospholipids, was subjected to equibiaxial, 2:1 non-equibiaxial, 4:1 non-equibiaxial, strip biaxial, and uniaxial tensile deformations at a von Mises strain rate of 5.45 × 10<sup>8</sup> s<sup>−1</sup>, resulting in velocities in the range of 1 to 4.6 m·s<sup>−1</sup>. A water bridge forming through both phospholipid bilayer leaflets was used to determine structural failure. The stress magnitude, failure strain, headgroup clustering, and damage responses were found to be strain state-dependent. The strain state order of detrimentality in descending order was equibiaxial, 2:1 non-equibiaxial, 4:1 non-equibiaxial, strip biaxial, and uniaxial. The phospholipid bilayer failed at von Mises strains of .46, .47, .53, .77, and 1.67 during these respective strain path simulations. Additionally, a Membrane Failure Limit Diagram (MFLD) was created using the pore nucleation, growth, and failure strains to demonstrate safe and unsafe membrane deformation regions. This MFLD allowed representative equations to be derived to predict membrane failure from in-plane strains. These results provide the basis to implement a more accurate mechano-physiological internal state variable continuum model that captures lower length scale damage and will aid in developing higher fidelity injury models.
DOI: 10.6084/m9.figshare.6115940
title: 3D-Printed Biomolecular Structures

description: This collection contains a series of photographs of 3d-printed models of proteins and other biomolecular structures. These tangible models were created in the context of the curricular Unit "Introduction to Biological Engineering" of the Integrated Master in Biological Engineering of Instituto Superior Técnico, Lisbon, Portugal. The work flow for model printing includes: 1. downloading of relevant pdb file from the Protein Data Bank (https://www.rcsb.org/), 2. manipulation of the model with the graphic visualization software PyMOL to create a surface model of the structure, 3. export of the corresponding wrl file, 4. transformation of the wrl file into an stl file with meshconv (http://www.patrickmin.com/meshconv/) and 5. 3D printing. 5. 3D printing of the model. The examples shown include:<br>-calcium channel-CBM64: carbohydrate binding module 64-FMV pentamer: foot and mouth disease virus pentamer-GFP: green fluorescent protein-hemoglobin-immunoglobulin G<br>-liver vault-pneumolysin<br>-Taq polymerase-TYMV: turnip yellow-mosaic virus -Zika virus<br>
DOI: 10.6084/m9.figshare.6115925
title: Sequencing of 231 forensic genetic markers using the MiSeq FGx™ forensic genomics system – an evaluation of the assay and software

description: The MiSeq FGx™ Forensic Genomics System types 231 genetic markers in one multiplex polymerase chain reaction (PCR) assay. The markers include core forensic short tandem repeats (STRs) as well as identity, ancestry and phenotype informative short nucleotide polymorphisms (SNPs). In this work, the MiSeq FGx™ Forensic Genomics System was evaluated by analysing reproducibility, sensitivity, mixture identification and forensic phenotyping capabilities of the assay. Furthermore, the genotype calling of the ForenSeq™ Universal Analysis Software was verified by analysing fastq.gz files from the MiSeq FGx™ platform using the softwares STRinNGS and GATK. Overall, the performance of the MiSeq FGx™ Forensic Genomics System was high. However, locus and allele drop-outs were relatively frequent at six loci (two STRs and four human identification SNPs) due to low read depth or skewed heterozygote balances, and the stutter ratios were larger than those observed with conventional STR genotyping methods. The risk of locus and allele drop-outs increased dramatically when the amount of DNA in the first PCR was lower than 250 pg. Two-person 50:1 mixtures were identified as mixtures, whereas 100:1 and 1 000:1 mixtures were not. Y-chromosomal short tandem repeats (Y-STRs) alleles were detected in the 100:1 and 1 000:1 female/male mixtures. The ForenSeq™ Universal Analysis Software provided the data analyst with useful alerts that simplified the analysis of the large number of markers. Many of the alerts were due to user-defined, locus-specific criteria. The results shown here indicated that the default settings should be altered for some loci. Also, recommended changes to the assay and software are discussed.
DOI: 10.6084/m9.figshare.6115925.v1
title: Sequencing of 231 forensic genetic markers using the MiSeq FGx™ forensic genomics system – an evaluation of the assay and software

description: The MiSeq FGx™ Forensic Genomics System types 231 genetic markers in one multiplex polymerase chain reaction (PCR) assay. The markers include core forensic short tandem repeats (STRs) as well as identity, ancestry and phenotype informative short nucleotide polymorphisms (SNPs). In this work, the MiSeq FGx™ Forensic Genomics System was evaluated by analysing reproducibility, sensitivity, mixture identification and forensic phenotyping capabilities of the assay. Furthermore, the genotype calling of the ForenSeq™ Universal Analysis Software was verified by analysing fastq.gz files from the MiSeq FGx™ platform using the softwares STRinNGS and GATK. Overall, the performance of the MiSeq FGx™ Forensic Genomics System was high. However, locus and allele drop-outs were relatively frequent at six loci (two STRs and four human identification SNPs) due to low read depth or skewed heterozygote balances, and the stutter ratios were larger than those observed with conventional STR genotyping methods. The risk of locus and allele drop-outs increased dramatically when the amount of DNA in the first PCR was lower than 250 pg. Two-person 50:1 mixtures were identified as mixtures, whereas 100:1 and 1 000:1 mixtures were not. Y-chromosomal short tandem repeats (Y-STRs) alleles were detected in the 100:1 and 1 000:1 female/male mixtures. The ForenSeq™ Universal Analysis Software provided the data analyst with useful alerts that simplified the analysis of the large number of markers. Many of the alerts were due to user-defined, locus-specific criteria. The results shown here indicated that the default settings should be altered for some loci. Also, recommended changes to the assay and software are discussed.
DOI: 10.6084/m9.figshare.6115871
title: Origin of Earth and Circadian Clocks

description: Four billion years ago, shortly after the origin of the Earth-Moon System, it is predicted that the length of day was close to four hours. Life on Earth originated not long after that. Since then the length of day changed continuously to the 24 hour day as we know it today. One group of prokaryotes that lived through all these changes are cyanobacteria, which are among the oldest organisms on Earth. Cyanobacteria are a unique group of bacteria as they are the only known prokaryotes to perform oxygenic photosynthesis as well as the only known prokaryotes to have a circadian clock.
DOI: 10.6084/m9.figshare.6115847
title: The diversity and paleoenvironmental significance of <i>Calophyllum</i> (Clusiaceae) from the Miocene of southeastern China

description: Three species within the genus <i>Calophyllum</i> collected from middle Miocene Fotan Group sediments in Zhangpu County, Fujian, southeastern China are described in this paper. These fossils include <i>Calophyllum zhangpuensis</i> sp. nov., <i>Calophyllum striatum</i>, and <i>Calophyllum suraikholaensis</i>. The new fossil species <i>C. zhangpuensis</i> sp. nov. is oval, possesses entire leaves with closely spaced parallel secondary veins and has a round, or slightly retuse, apex. These specimens represent the first known fossil records of this relative wide leaf-type form of <i>Calophyllum</i> from China and have a length:width (L:W) ratio less than 3:1. In combination with the known modern geographic distribution and habitats of this wide leaf-type <i>Calophyllum</i> and other plants, data suggest that the middle Miocene Fotan flora is indicative of a warm climate. Thus, based on available fossil data, we speculate that this genus probably originated in India during the Paleocene before spreading from India to Bangladesh and into China, Sumatra, Malaysia, Indonesia, and Java during the Neogene, leading to its modern distribution. At least, the 3 fossil species in this region can explain floristic exchange between India, Fujian, and South China, which is consistent with previous studies; the occurrence of these 3 species indicates that <i>Calophyllum</i> began to diversity in China no later than the Miocene.
DOI: 10.6084/m9.figshare.6115847.v1
title: The diversity and paleoenvironmental significance of <i>Calophyllum</i> (Clusiaceae) from the Miocene of southeastern China

description: Three species within the genus <i>Calophyllum</i> collected from middle Miocene Fotan Group sediments in Zhangpu County, Fujian, southeastern China are described in this paper. These fossils include <i>Calophyllum zhangpuensis</i> sp. nov., <i>Calophyllum striatum</i>, and <i>Calophyllum suraikholaensis</i>. The new fossil species <i>C. zhangpuensis</i> sp. nov. is oval, possesses entire leaves with closely spaced parallel secondary veins and has a round, or slightly retuse, apex. These specimens represent the first known fossil records of this relative wide leaf-type form of <i>Calophyllum</i> from China and have a length:width (L:W) ratio less than 3:1. In combination with the known modern geographic distribution and habitats of this wide leaf-type <i>Calophyllum</i> and other plants, data suggest that the middle Miocene Fotan flora is indicative of a warm climate. Thus, based on available fossil data, we speculate that this genus probably originated in India during the Paleocene before spreading from India to Bangladesh and into China, Sumatra, Malaysia, Indonesia, and Java during the Neogene, leading to its modern distribution. At least, the 3 fossil species in this region can explain floristic exchange between India, Fujian, and South China, which is consistent with previous studies; the occurrence of these 3 species indicates that <i>Calophyllum</i> began to diversity in China no later than the Miocene.
DOI: 10.6084/m9.figshare.6115844
title: An experimental study of a museum-based, science PD programme’s impact on teachers and their students

description: We present results of an experimental study of an urban, museum-based science teacher PD programme. A total of 125 teachers and 1676 of their students in grades 4–8 were tested at the beginning and end of the school year in which the PD programme took place. Teachers and students were assessed on subject content knowledge and attitudes towards science, along with teacher classroom behaviour. Subject content questions were mostly taken from standardised state tests and literature, with an ‘Explain:’ prompt added to some items. Teachers in the treatment group showed a 7% gain in subject content knowledge over the control group. Students of teachers in the treatment group showed a 4% gain in subject content knowledge over the control group on multiple-choice items and an 11% gain on the constructed response items. There was no overall change in science attitudes of teachers or students over the control groups but we did find differences in teachers’ reported self-efficacy and teaching anxiety levels, plus PD teachers reported doing more student-centered science teaching activities than the control group. All teachers came into the PD with high initial excitement, perhaps reflecting its context within an informal learning environment.
DOI: 10.6084/m9.figshare.6115844.v1
title: An experimental study of a museum-based, science PD programme’s impact on teachers and their students

description: We present results of an experimental study of an urban, museum-based science teacher PD programme. A total of 125 teachers and 1676 of their students in grades 4–8 were tested at the beginning and end of the school year in which the PD programme took place. Teachers and students were assessed on subject content knowledge and attitudes towards science, along with teacher classroom behaviour. Subject content questions were mostly taken from standardised state tests and literature, with an ‘Explain:’ prompt added to some items. Teachers in the treatment group showed a 7% gain in subject content knowledge over the control group. Students of teachers in the treatment group showed a 4% gain in subject content knowledge over the control group on multiple-choice items and an 11% gain on the constructed response items. There was no overall change in science attitudes of teachers or students over the control groups but we did find differences in teachers’ reported self-efficacy and teaching anxiety levels, plus PD teachers reported doing more student-centered science teaching activities than the control group. All teachers came into the PD with high initial excitement, perhaps reflecting its context within an informal learning environment.
DOI: 10.6084/m9.figshare.6115823

description: 1000 tree downloaded from Bird.tree
DOI: 10.6084/m9.figshare.6115667
title: dou345.xml

description: law br
DOI: 10.6084/m9.figshare.6115667.v1
title: dou345.xml

description: law br
DOI: 10.6084/m9.figshare.6115655
title: mmgenome2 example data

description: Raw example dataset for the R-package mmgenome2<br>
DOI: 10.6084/m9.figshare.6115655.v2
title: mmgenome2 example data

description: Raw example dataset for the R-package mmgenome2<br>
DOI: 10.6084/m9.figshare.6115655.v1
title: mmgenome2 example data

description: Raw example dataset for the R-package mmgenome2<br>
DOI: 10.6084/m9.figshare.6115634
title: Language use in Hungary (counties Baranya, Tolna)

description: Digitized dataset: data on language use in Southern Hungary (counties Baranya, Tolna) from the Hungarian/Austro-Hungarian census<br><br> Original data (accessed 22-10-2018): <br> 1880 https://library.hungaricana.hu/en/view/NEDA_1881_02/?pg=10&layout=s <br>1890 https://library.hungaricana.hu/en/view/NEDA_1892_helysegnevtar/?pg=15&layout=s <br>1900 https://library.hungaricana.hu/en/view/NEDA_1900_01/?pg=59&layout=s <br> 1910 https://library.hungaricana.hu/en/view/NEDA_1910_01/?pg=69&layout=s <br>1920 https://library.hungaricana.hu/en/view/NEDA_1920_01/?pg=47&layout=s <br>1930 https://library.hungaricana.hu/en/view/NEDA_1930_01/?pg=127&layout=s <br>1941 https://library.hungaricana.hu/hu/view/NEDA_1941_02/?pg=170&layout=s <br> Geographical coordinates retrieved from geonames.org <br><br>
DOI: 10.6084/m9.figshare.6115634.v2
title: Language use in Hungary (counties Baranya, Tolna)

description: Digitized dataset: data on language use in Southern Hungary (counties Baranya, Tolna) from the Hungarian/Austro-Hungarian census<br><br> Original data (accessed 22-10-2018): <br> 1880 https://library.hungaricana.hu/en/view/NEDA_1881_02/?pg=10&layout=s <br>1890 https://library.hungaricana.hu/en/view/NEDA_1892_helysegnevtar/?pg=15&layout=s <br>1900 https://library.hungaricana.hu/en/view/NEDA_1900_01/?pg=59&layout=s <br> 1910 https://library.hungaricana.hu/en/view/NEDA_1910_01/?pg=69&layout=s <br>1920 https://library.hungaricana.hu/en/view/NEDA_1920_01/?pg=47&layout=s <br>1930 https://library.hungaricana.hu/en/view/NEDA_1930_01/?pg=127&layout=s <br>1941 https://library.hungaricana.hu/hu/view/NEDA_1941_02/?pg=170&layout=s <br> Geographical coordinates retrieved from geonames.org <br><br>
DOI: 10.6084/m9.figshare.6115634.v1
title: Language use in Hungary (counties Baranya, Tolna)

description: Digitized dataset: data on language use in Southern Hungary (counties Baranya, Tolna) from the Hungarian/Austro-Hungarian census<br><br> Original data (accessed 2018-04-09): <br>1881 https://library.hungaricana.hu/en/view/NEDA_1881_02/?pg=10&layout=s <br>1900 https://library.hungaricana.hu/en/view/NEDA_1900_01/?pg=59&layout=s <br>1910 https://library.hungaricana.hu/en/view/NEDA_1910_01/?pg=69&layout=s <br>1920 https://library.hungaricana.hu/en/view/NEDA_1920_01/?pg=47&layout=s <br>1930 https://library.hungaricana.hu/en/view/NEDA_1930_01/?pg=127&layout=s <br> <br> For 1891, no language data for individual settlements is available. <br> <br> Geographical coordinates retrieved from geonames.org <br><br>
DOI: 10.6084/m9.figshare.6115538
title: Carotenoids - Berry seed oils.xlsx

description: Chemical composition of berry seed oils.