cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5436892
title: Taxon-binned contigs

description: MEGAN6 taxonomically binned CLC de novo contigs based on blastn (xxxx.<b>nucl</b>.taxon.fasta) and blastx (xxxx.<b>prot</b>.taxon.fasta) annotations.<br><br>The bash script ("merger.sh", see repository SCRIPTS) was written to merge nucl and prot files into xxxx.<b>both</b>.taxon.fasta.<br><br>The file double_contigs.txt includes a summary of the contigs that were binned in more than one taxon and manually binned or left out.<br>
DOI: 10.6084/m9.figshare.5436895
title: The relative isotopic abundance (<i>δ</i><sup>13</sup>C, <i>δ</i><sup>15</sup>N) during composting of agricultural wastes in relation to compost quality and feedstock

description: Variations in the relative isotopic abundance of C and N (<i>δ</i><sup>13</sup>C and <i>δ</i><sup>15</sup>N) were measured during the composting of different agricultural wastes using bench-scale bioreactors. Different mixtures of agricultural wastes (horse bedding manure + legume residues; dairy manure + jatropha mill cake; dairy manure + sugarcane residues; dairy manure alone) were used for aerobic–thermophilic composting. No significant differences were found between the <i>δ</i><sup>13</sup>C values of the feedstock and the final compost, except for dairy manure + sugarcane residues (from initial ratio of −13.6 ± 0.2 ‰ to final ratio of −14.4 ± 0.2 ‰). <i>δ</i><sup>15</sup>N values increased significantly in composts of horse bedding manure + legumes residues (from initial ratio of +5.9 ± 0.1 ‰ to final ratio of +8.2 ± 0.5 ‰) and dairy manure + jatropha mill cake (from initial ratio of +9.5 ± 0.2 ‰ to final ratio of +12.8 ± 0.7 ‰) and was related to the total N loss (mass balance). <i>δ</i><sup>13</sup>C can be used to differentiate composts from different feedstock (e.g. C<sub>3</sub> or C<sub>4</sub> sources). The quantitative relationship between N loss and <i>δ</i><sup>15</sup>N variation should be determined.
DOI: 10.6084/m9.figshare.5436892.v1
title: Taxon-binned contigs

description: MEGAN6 taxonomically binned CLC de novo contigs based on blastn (xxxx.<b>nucl</b>.taxon.fasta) and blastx (xxxx.<b>prot</b>.taxon.fasta) annotations.<br><br>The bash script ("merger.sh", see repository SCRIPTS) was written to merge nucl and prot files into xxxx.<b>both</b>.taxon.fasta.<br><br>The file double_contigs.txt includes a summary of the contigs that were binned in more than one taxon and manually binned or left out.<br>
DOI: 10.6084/m9.figshare.5436895.v1
title: The relative isotopic abundance (<i>δ</i><sup>13</sup>C, <i>δ</i><sup>15</sup>N) during composting of agricultural wastes in relation to compost quality and feedstock

description: Variations in the relative isotopic abundance of C and N (<i>δ</i><sup>13</sup>C and <i>δ</i><sup>15</sup>N) were measured during the composting of different agricultural wastes using bench-scale bioreactors. Different mixtures of agricultural wastes (horse bedding manure + legume residues; dairy manure + jatropha mill cake; dairy manure + sugarcane residues; dairy manure alone) were used for aerobic–thermophilic composting. No significant differences were found between the <i>δ</i><sup>13</sup>C values of the feedstock and the final compost, except for dairy manure + sugarcane residues (from initial ratio of −13.6 ± 0.2 ‰ to final ratio of −14.4 ± 0.2 ‰). <i>δ</i><sup>15</sup>N values increased significantly in composts of horse bedding manure + legumes residues (from initial ratio of +5.9 ± 0.1 ‰ to final ratio of +8.2 ± 0.5 ‰) and dairy manure + jatropha mill cake (from initial ratio of +9.5 ± 0.2 ‰ to final ratio of +12.8 ± 0.7 ‰) and was related to the total N loss (mass balance). <i>δ</i><sup>13</sup>C can be used to differentiate composts from different feedstock (e.g. C<sub>3</sub> or C<sub>4</sub> sources). The quantitative relationship between N loss and <i>δ</i><sup>15</sup>N variation should be determined.
DOI: 10.6084/m9.figshare.5436868
title: CLC de novo contigs

description: This repository contains multifasta files of contiguous sequences that were in silico assembled by the CLC de novo assembler algorithm. The high-quality RNA-Seq reads that were used as input originate from raw NGS read files deposited under the BioProject PRJNA411946.
DOI: 10.6084/m9.figshare.5436868.v1
title: CLC de novo contigs

description: This repository contains multifasta files of contiguous sequences that were in silico assembled by the CLC de novo assembler algorithm. The high-quality RNA-Seq reads that were used as input originate from raw NGS read files deposited under the BioProject PRJNA411946.
DOI: 10.6084/m9.figshare.5436805
title: Brake Pad Coefficient of Restitution Measurements

description: A steel ball bearing was released from a height of 200 mm above a composite brake pad and captured using a high speed video camera at a rate of 430 frames per second. A circle detection algorithm was used to detect the centre of the ball and plot the ball kinetics. The kinetics were used to calculate the velocity of the ball before and after impact to calculate the coefficient of restitution of the collision
DOI: 10.6084/m9.figshare.5436787.v1
title: Supplementary Tables

description: Data citation 2: Supplementary Tables 1-9.
DOI: 10.6084/m9.figshare.5436763
title: S5 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: 32-instruction set.
DOI: 10.6084/m9.figshare.5436745
title: S4 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Conguration of the adaptive scenario.
DOI: 10.6084/m9.figshare.5436748
title: S1 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: 33-instruction set.
DOI: 10.6084/m9.figshare.5436757
title: S10 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Hosts.
DOI: 10.6084/m9.figshare.5436745.v1
title: S4 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Conguration of the adaptive scenario.
DOI: 10.6084/m9.figshare.5436748.v1
title: S1 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: 33-instruction set.
DOI: 10.6084/m9.figshare.5436757.v1
title: S10 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Hosts.
DOI: 10.6084/m9.figshare.5436736
title: S6 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Merely-viable organisms.
DOI: 10.6084/m9.figshare.5436742
title: S2 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Host-parasite pairs used as ancestors.
DOI: 10.6084/m9.figshare.5436754
title: S7 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Viable organisms capable of computing the NOT logic function.
DOI: 10.6084/m9.figshare.5436733
title: S3 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Conguration of the non-adaptive and adaptive scenario.
DOI: 10.6084/m9.figshare.5436742.v1
title: S2 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Host-parasite pairs used as ancestors.
DOI: 10.6084/m9.figshare.5436727
title: S9 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Parasites.
DOI: 10.6084/m9.figshare.5436718
title: Simulations association net noise from The conceptual foundations of network-based diffusion analysis: choosing networks and interpreting results

description: Code for running simulations to test NBDA using an association network with random noise
DOI: 10.6084/m9.figshare.5436724
title: Simulations dynamic obs net error from The conceptual foundations of network-based diffusion analysis: choosing networks and interpreting results

description: Code for running simulations to test NBDA using a dynamic observation network with error
DOI: 10.6084/m9.figshare.5436727.v1
title: S9 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Parasites.
DOI: 10.6084/m9.figshare.5436718.v1
title: Simulations association net noise from The conceptual foundations of network-based diffusion analysis: choosing networks and interpreting results

description: Code for running simulations to test NBDA using an association network with random noise
DOI: 10.6084/m9.figshare.5436712
title: Simulations association net variation in Bj from The conceptual foundations of network-based diffusion analysis: choosing networks and interpreting results

description: Code for running simulations to test NBDA (weighted and unweighted versions) using an association network with variation in performance rates
DOI: 10.6084/m9.figshare.5436715
title: S8 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Viable and mutationally-robust organisms capable of computing the NOT logic function.
DOI: 10.6084/m9.figshare.5436724.v1
title: Simulations dynamic obs net error from The conceptual foundations of network-based diffusion analysis: choosing networks and interpreting results

description: Code for running simulations to test NBDA using a dynamic observation network with error
DOI: 10.6084/m9.figshare.5436712.v1
title: Simulations association net variation in Bj from The conceptual foundations of network-based diffusion analysis: choosing networks and interpreting results

description: Code for running simulations to test NBDA (weighted and unweighted versions) using an association network with variation in performance rates
DOI: 10.6084/m9.figshare.5436715.v1
title: S8 File from Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms<sup>†</sup>

description: Viable and mutationally-robust organisms capable of computing the NOT logic function.
DOI: 10.6084/m9.figshare.5436697
title: Simulations association net bias from The conceptual foundations of network-based diffusion analysis: choosing networks and interpreting results

description: Code for running simulations to test NBDA using an association network with bias
DOI: 10.6084/m9.figshare.5436697.v1
title: Simulations association net bias from The conceptual foundations of network-based diffusion analysis: choosing networks and interpreting results

description: Code for running simulations to test NBDA using an association network with bias
DOI: 10.6084/m9.figshare.5436604
title: Raw data used for analysis of 2010s roadkill patterns from Why did the pheasant cross the road? Long-term road mortality patterns in relation to management changes

description: Raw data used for analysis of 2010s roadkill patterns
DOI: 10.6084/m9.figshare.5436604.v1
title: Raw data used for analysis of 2010s roadkill patterns from Why did the pheasant cross the road? Long-term road mortality patterns in relation to management changes

description: Raw data used for analysis of 2010s roadkill patterns
DOI: 10.6084/m9.figshare.5436520
title: Raw data from Enemy recognition is linked to soldier size in a polymorphic stingless bee

description: This file contains the raw data used for the analysis
DOI: 10.6084/m9.figshare.5436520.v1
title: Raw data from Enemy recognition is linked to soldier size in a polymorphic stingless bee

description: This file contains the raw data used for the analysis
DOI: 10.6084/m9.figshare.5436493
title: Seismotectonic map of September 2017 intraplate earthquakes in Mexico

description: Rapid seismotectonic map of September 2017 earthquakes in Mexico. The three events are extensional (normal faulting mechanisms). Two (Mw8.2, Mw7.1) broke in the downgoing slab of the Cocos plate: first one (Mw8.2) close to the trench where the plate first bends, second one (Mw7.1) near the deeper sharp bend where slab dip changes from flat to steep. Last one (Mw6.1) is more shallow and broke as a normal fault rupture in the upper continental plate.<i> </i>Epicenters, and past megathrust ruptures are from Servicio Seismológico Nacional Mexico. Earthquake source mechanisms from IPGP-Geoscope.<br><br><i>Carte sismotectonique des séismes de Septembre 2017 au Mexique. Les 3 séismes majeurs sont extensifs (ruptures en faille normale). Deux (Mw8.2, Mw7.1) ont rompu dans la plaque inférieure (plaque Cocos) en subduction. Le premier (Mw8.2) est proche de la fosse, là où la plaque plie et fléchit une première fois, le second (Mw7.1) s’est produit au coude entre la subduction plate sous le Mexique central et sa partie profonde plongeant fortement. Le dernier (Mw6.1), plus superficiel, a rompu dans la plaque supérieure continentale. Les épicentres et les zones de ruptures des séismes passés sont d’après le Servicio Seismológico Nacional Mexico, les mécanismes des séismes d’après Geoscope-IPGP.</i><br>
DOI: 10.6084/m9.figshare.5436481
title: Development of sensitive indirect enzyme-linked immunosorbent assays for specific detection of antibodies against fowl adenovirus serotypes 1 and 4 in chickens

description: Conventional serological methods for detection and differentiation of antibodies against fowl aviadenoviruses (FAdVs) are laborious and time-consuming, therefore ELISAs based upon recombinant proteins were developed in the present study to overcome this limitation for clinically relevant serotypes FAdV-1 and FAdV-4. In order to develop serotype-specific ELISAs, the two distinct fibers, fiber-1 (fib-1) and fiber-2 (fib-2), characteristically present only in FAdV-1 and FAdV-4, were applied separately as coating antigens. Sera raised against each recombinant fib-1 and fib-2 of FAdV-1 and FAdV-4 did not react with any of the heterologous fiber ELISAs, as anticipated by the low degree of amino acid identity between those FAdV fibers (23.1–41.2%), indicating that heterologous fibers do not share common epitopes. Testing of 172 monospecific sera, raised against all FAdV serotypes (1–8a and 8b–11), retrieved specificities between 99.3% and 100.0% for the ELISAs, further substantiating the serotype-specificity of fibers. Investigating sera from chickens experimentally inoculated with different FAdV-1 or FAdV-4 strains revealed that ELISAs were equally or more sensitive than the virus-neutralization (VN) test. Furthermore, strong correlations were demonstrated between fiber antibody titres and neutralization activity. Particularly, sera directed against live virus showed a pronounced fiber antibody response, which might be explained by an excessive production of fibers during infection. Application of the newly developed fiber ELISAs on field sera with heterogeneous serological status demonstrated high sensitivity and serotype-specificity of this test system, providing for the first time a diagnostic tool for mass screening of chicken flocks against FAdV serotypes, namely FAdV-1 and FAdV-4.
DOI: 10.6084/m9.figshare.5436481.v1
title: Development of sensitive indirect enzyme-linked immunosorbent assays for specific detection of antibodies against fowl adenovirus serotypes 1 and 4 in chickens

description: Conventional serological methods for detection and differentiation of antibodies against fowl aviadenoviruses (FAdVs) are laborious and time-consuming, therefore ELISAs based upon recombinant proteins were developed in the present study to overcome this limitation for clinically relevant serotypes FAdV-1 and FAdV-4. In order to develop serotype-specific ELISAs, the two distinct fibers, fiber-1 (fib-1) and fiber-2 (fib-2), characteristically present only in FAdV-1 and FAdV-4, were applied separately as coating antigens. Sera raised against each recombinant fib-1 and fib-2 of FAdV-1 and FAdV-4 did not react with any of the heterologous fiber ELISAs, as anticipated by the low degree of amino acid identity between those FAdV fibers (23.1–41.2%), indicating that heterologous fibers do not share common epitopes. Testing of 172 monospecific sera, raised against all FAdV serotypes (1–8a and 8b–11), retrieved specificities between 99.3% and 100.0% for the ELISAs, further substantiating the serotype-specificity of fibers. Investigating sera from chickens experimentally inoculated with different FAdV-1 or FAdV-4 strains revealed that ELISAs were equally or more sensitive than the virus-neutralization (VN) test. Furthermore, strong correlations were demonstrated between fiber antibody titres and neutralization activity. Particularly, sera directed against live virus showed a pronounced fiber antibody response, which might be explained by an excessive production of fibers during infection. Application of the newly developed fiber ELISAs on field sera with heterogeneous serological status demonstrated high sensitivity and serotype-specificity of this test system, providing for the first time a diagnostic tool for mass screening of chicken flocks against FAdV serotypes, namely FAdV-1 and FAdV-4.
DOI: 10.6084/m9.figshare.5436460
title: nuclei-hl60.zip

description: Synthetic images of fluorescently stained nuclei of the HL60 Cell Line (fixed cells) created with Cytopacq. From the dataset at <br>http://cbia.fi.muni.cz/projects/cytopacq-a-simulation-toolbox_6.html<br>the middle image of each 3D stack of images has been selected. There are two times 4 datasets. One time with high noise images and one time with low noise images. The four datasets in each case have different probabilities for clustering of nuclei (0, 0.25, 0.5 and 0.75).<br>For each input image an indexed mask as the correct segmentation result is included.<br><br>. The dataset was generated using the virtual microscope imitating the microscope Zeiss S100 (objective Zeiss 63x/1.40 Oil DIC) attached to confocal unit Atto CARV and CCD camera Micromax 1300-YHS.<br><br>If you use this data cite:<br><br>Svoboda D., Homola O., Stejskal S. Generation of 3D Digital Phantoms of Colon Tissue, In International Conference on Image Analysis and Recognition - ICIAR 2011, Part II, LNCS 6754, Berlin, Heidelberg: Springer-Verlag, pp 31-39, June 2011, ISBN 978-3-642-21595-7 <br><br><br>
DOI: 10.6084/m9.figshare.5436457
title: A basal ornithopod dinosaur from the Cenomanian of the Czech Republic

description: During their long evolutionary history, neornithischian dinosaurs diverged into several clades with distinctive adaptations. However, the early evolution within Neornithischia and the resolution of the phylogenetic relationships of taxa situated near the base of the clade remain problematic. This is especially true for those taxa traditionally placed at the base of Ornithopoda, either as ‘hypsilophodontids’ or at the base of the diverse clade Iguanodontia. Recent studies are improving our understanding of the anatomy and relationships of these taxa, with discoveries of several new non-ankylopollexian ornithopods from South America and Europe providing key insights into early ornithopod evolution and palaeobiogeography. Here, we describe a new basal ornithopod, <i>Burianosaurus augustai</i> gen. et sp. nov., based on a well-preserved femur from the upper Cenomanian strata (Korycany Beds of the Peruc-Korycany Formation) of the Czech Republic. The new taxon is diagnosed by a unique suite of characters and represents the only occurrence of a Cenomanian non-avian dinosaur in Central Europe north of the Alpine Tethyan areas. Histological examination of the type specimen reveals the presence of a loosely packed Haversian system which suggests relatively mature bone from a possible young adult. Phylogenetic analyses of two different data sets, selected to test the placement of <i>B. augustai</i> in various parts of the neornithischian tree, reconstruct <i>B. augustai</i> as a basal ornithopod, firmly nested outside Ankylopollexia. These results also support a diverse Elasmaria as a basal clade within Ornithopoda and reconstruct <i>Hypsilophodon</i> outside Ornithopoda as the sister taxon to Cerapoda. However, the relationships of ‘hypsilophodontids’ within Neornithischia remain contentious. http://zoobank.org/urn:lsid:zoobank.org:pub:D28A9FB8-A253-4032-8710-4F51668A1E4F
DOI: 10.6084/m9.figshare.5436409
title: Task-dependent function of striatal cholinergic interneurons in behavioural flexibility

description: This is a data set for "Task-dependent function of striatal cholinergic interneurons in behavioural flexibility", which was used in the study of Okada et al (2017).
DOI: 10.6084/m9.figshare.5436409.v1
title: Task-dependent function of striatal cholinergic interneurons in behavioural flexibility

description: This is a data set for "Task-dependent function of striatal cholinergic interneurons in behavioural flexibility", which was used in the study of Okada et al (2017).
DOI: 10.6084/m9.figshare.5436301
title: figshare for Institutions - Japanese

description: Japanese Edition:<br>figshare for Institutions - managing and disseminating research data to make it more citable, shareable and discoverable.<br>info@figshare.com
DOI: 10.6084/m9.figshare.5436277
title: Dataset for: Tadalafil, a long acting phosphodiesterase inhibitor, promotes bone marrow stem cell survival and their homing into ischemic myocardium for cardiac repair

description: The aim was to evaluate the tadalafil-mediated effects at molecular level on bone marrow-derived mesenchymal stem cells (MSCs) survival and their homing into the infarcted hearts to promote cardiac repair and improve function. MSCs were pretreated in vitro with tadalafil (+/-H2O2, oxidative stress) and with PKG, MAPK, FasL, nitric oxide synthase (NOS) (L-NAME), CXCR4 (AMD3100), or miR-21 inhibitors (+/-luciferase construction +/-Fas) for 2h before tadalafil. Rats were subjected to acute myocardial infarction (AMI), and then followed by injection of saline or 1.5x106 MSCs-treated +/- tadalafil into infarcted area. In another group, AMI was performed in 1-month post-myelo-ablated rats, were injected intraperitoneally (IP) with tadalafil +/- AMD3100 or L-NAME for 5 days. Also, in another group, AMI mice were treated with IP +/- tadalafil before intravenous injection with 111In-oxine-MSCs followed by CT/SPECT imaging to locate mobilized MSCs. Cardiac function was assessed by echocardiography. MSCs and heart extracts were analyzed by molecular bioassays. Tadalafil-treated MSCs had higher expression of cGMP, NOS, SDF-1α, p-VASP, p-Erk1/2, p-STAT3, p-Akt, PKG1 and Bcl-xl; expression of these molecules was reduced with PKG1, MAPK, NOS or FasL inhibitors. Tadalafil inhibited apoptosis through increased miR-21 expression and improved cell survival by inhibiting Fas (restored by PKG1, MAPK or miR-21 inhibitors). In vivo, heart function, grafted cell survival, MSCs mobilization and homing were improved in tadalafil-treated AMI animals versus controls. Conclusions: Tadalafil prolonged MSCs survival via up-regulation of miR-21 dependent suppression of Fas, and increased MSCs mobilization and their homing into infarcted myocardium resulting in improved cardiac repair and function.
DOI: 10.6084/m9.figshare.5436268
title: Ramie gene

description: The coding sequences of 42,463 genes predicted from the ramie genome