cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5926555
title: Generation of Minimum Tree-like Witnesses for Existential CTL

description: This artifact consists of the executable of the model checker <b>SMART</b>, the benchmark suite, and the original data presented in the TACAS 2018 conference paper, <i>Generation of Minimum Tree-like Witnesses for Existential CTL</i>. We compared the performance of our minimum witness generation approach and the traditional breadth-first approach. The results are reproducible.<br><br>The artifact is a single .zip archive holding script files, data and benchmarks in different subdirectories.<br><br>See the file HOW-TO for detailed guidance on running SMART for experiments of: <br> 1. EV+MDD (edge-valued multiway decision diagram)-based approach to generate minimum tree-like witnesses (<b>MinWit</b>), and<br> 2. traditional MDD (multiway decision diagram)-based BFS approach to generate (not necessarily minimum) tree-like witnesses (<b>Wit</b>).<br><br>The benchmarking suite consists of nine Petri net models from the 2017 Model Checking Contest (https://mcc.lip6.fr/2017/). <b>.sm</b> files are SMART files automatically converted from source PNML files. All models have one or more scaling parameters affecting the number of states and state-to-state transitions, thus the model size and complexity. See the subdirectory /data for datasets presented in the paper (the specific formulas are listed in Table 1 of the linked TACAS paper).<br><br><b>Background</b><br><br>An advantage of model checking is its ability to generate witnesses or counterexamples. Approaches exist to generate small or minimum witnesses for simple unnested formulas, but no existing method guarantees minimality for general nested ones. The related paper linked from this data record provides a definition of witness size, uses edge-valued decision diagrams to recursively compute the minimum witness size for each subformula, and describes a general approach to build minimum tree-like witnesses for existential CTL.<br>
DOI: 10.6084/m9.figshare.5926555.v1
title: Generation of Minimum Tree-like Witnesses for Existential CTL

description: This artifact consists of the executable of the model checker <b>SMART</b>, the benchmark suite, and the original data presented in the TACAS 2018 conference paper, <i>Generation of Minimum Tree-like Witnesses for Existential CTL</i>. We compared the performance of our minimum witness generation approach and the traditional breadth-first approach. The results are reproducible.<br><br>The artifact is a single .zip archive holding script files, data and benchmarks in different subdirectories.<br><br>See the file HOW-TO for detailed guidance on running SMART for experiments of: <br> 1. EV+MDD (edge-valued multiway decision diagram)-based approach to generate minimum tree-like witnesses (<b>MinWit</b>), and<br> 2. traditional MDD (multiway decision diagram)-based BFS approach to generate (not necessarily minimum) tree-like witnesses (<b>Wit</b>).<br><br>The benchmarking suite consists of nine Petri net models from the 2017 Model Checking Contest (https://mcc.lip6.fr/2017/). <b>.sm</b> files are SMART files automatically converted from source PNML files. All models have one or more scaling parameters affecting the number of states and state-to-state transitions, thus the model size and complexity. See the subdirectory /data for datasets presented in the paper (the specific formulas are listed in Table 1 of the linked TACAS paper).<br><br><b>Background</b><br><br>An advantage of model checking is its ability to generate witnesses or counterexamples. Approaches exist to generate small or minimum witnesses for simple unnested formulas, but no existing method guarantees minimality for general nested ones. The related paper linked from this data record provides a definition of witness size, uses edge-valued decision diagrams to recursively compute the minimum witness size for each subformula, and describes a general approach to build minimum tree-like witnesses for existential CTL.<br>
DOI: 10.6084/m9.figshare.5926513
title: De novo whole genome shotgun assembly of Brachypodium distachyon accession Luc1

description: Resequencing data was obtained from the Joint Genome Institute Genome Portal (http://genome.jgi.doe.gov/) from project 1000598 (Luc1). These sequence data were produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/) in collaboration with the user community. De novo assemblies were created from the raw reads using default settings and parameters of the CLC Assembly Cell (version 4.2.0). <br><br>
DOI: 10.6084/m9.figshare.5926513.v1
title: De novo whole genome shotgun assembly of Brachypodium distachyon accession Luc1

description: Resequencing data was obtained from the Joint Genome Institute Genome Portal (http://genome.jgi.doe.gov/) from project 1000598 (Luc1). These sequence data were produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/) in collaboration with the user community. De novo assemblies were created from the raw reads using default settings and parameters of the CLC Assembly Cell (version 4.2.0). <br><br>
DOI: 10.6084/m9.figshare.5926510
title: De novo whole genome shotgun assembly of Brachypodium distachyon accession Jer1

description: Resequencing data was obtained from the Joint Genome Institute Genome Portal (http://genome.jgi.doe.gov/) from project 404166 (Jer1). These sequence data were produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/) in collaboration with the user community. De novo assemblies were created from the raw reads using default settings and parameters of the CLC Assembly Cell (version 4.2.0). <br><br>
DOI: 10.6084/m9.figshare.5926510.v1
title: De novo whole genome shotgun assembly of Brachypodium distachyon accession Jer1

description: Resequencing data was obtained from the Joint Genome Institute Genome Portal (http://genome.jgi.doe.gov/) from project 404166 (Jer1). These sequence data were produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/) in collaboration with the user community. De novo assemblies were created from the raw reads using default settings and parameters of the CLC Assembly Cell (version 4.2.0). <br><br>
DOI: 10.6084/m9.figshare.5926504
title: De novo whole genome shotgun assembly of Brachypodium distachyon accession Foz1

description: Resequencing data was obtained from the Joint Genome Institute Genome Portal (http://genome.jgi.doe.gov/) from project 404167 (Foz1). These sequence data were produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/) in collaboration with the user community. De novo assemblies were created from the raw reads using default settings and parameters of the CLC Assembly Cell (version 4.2.0). <br><br>
DOI: 10.6084/m9.figshare.5926504.v1
title: De novo whole genome shotgun assembly of Brachypodium distachyon accession Foz1

description: Resequencing data was obtained from the Joint Genome Institute Genome Portal (http://genome.jgi.doe.gov/) from project 404167 (Foz1). These sequence data were produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/) in collaboration with the user community. De novo assemblies were created from the raw reads using default settings and parameters of the CLC Assembly Cell (version 4.2.0). <br><br>
DOI: 10.6084/m9.figshare.5926498
title: Mobile AR Frameworks

description: List of Augmented Reality frameworks with mobile development support.
DOI: 10.6084/m9.figshare.5926477
title: tuberculosis drug resistant db.xls

description: Database includiing genotiping information from drug and multidrug resistant isolates from tuberculosis circulating in the state of Veracruz, Mexico.<br>
DOI: 10.6084/m9.figshare.5926498.v1
title: Mobile AR Frameworks

description: List of Augmented Reality frameworks with mobile development support.
DOI: 10.6084/m9.figshare.5926465
title: Lamprolaima rhami sequences (mitochondrial and nuclear DNA)

description: Data files from mitochondrial and nuclear DNA of <i>Lamprolaima rhami</i> (Aves: Trochilidae). These sequences are from the manuscript titled: ¨Genetic and phenotypic divergence in the Garnet-Throated Hummingbird <i>Lamprolaima rhami </i>(Aves: Trochilidae)" . Databases belong to four nuclear and four mitochondrial genes:- Control region, CR.- Subunits 6 and 8 from ATPase, ATPase6&8.- NADH dehydrogenase subunit 2, ND2.- NADH dehydrogenase subunit 4, ND4.- Intron 7 of the beta fibrinogen gene, BFIB.- Exons 4 and 5 of the Muscle Skeletal Receptor Tyrosine Kinase, MUSK.- End of exon 6 - beginning of exon 8 of Ornithine Decarboxylase, ODC.- Intron 5 of Adenylate kinase, AK1.<br>
DOI: 10.6084/m9.figshare.5926465.v1
title: Lamprolaima rhami sequences (mitochondrial and nuclear DNA)

description: Data files from mitochondrial and nuclear DNA of <i>Lamprolaima rhami</i> (Aves: Trochilidae). These sequences are from the manuscript titled: ¨Genetic and phenotypic divergence in the Garnet-Throated Hummingbird <i>Lamprolaima rhami </i>(Aves: Trochilidae)" under revision. Databases belong to four nuclear and four mitochondrial genes:- Control region, CR.- Subunits 6 and 8 from ATPase, ATPase6&8.- NADH dehydrogenase subunit 2, ND2.- NADH dehydrogenase subunit 4, ND4.- Intron 7 of the beta fibrinogen gene, BFIB.- Exons 4 and 5 of the Muscle Skeletal Receptor Tyrosine Kinase, MUSK.- End of exon 6 - beginning of exon 8 of Ornithine Decarboxylase, ODC.- Intron 5 of Adenylate kinase, AK1.<br>
DOI: 10.6084/m9.figshare.5926453
title: Immune Co-Culture Images JPEGs

description: J774.A1 macrophages were either left unprimed or primed with either IFNγ, LPS, or both and subsequently co-cultured with JC CRL 2116 tumor cells. J774.A1 cells were labeled with PE-conjugated anti-CD11b antibodies (red surface stain) while JC CRL 2116 cells were labeled with Vybrant (green cytoplasmic stain). Both cells were also stained with DAPI. Experiment was conducted in triplicates (three wells/images correspond to one condition).
DOI: 10.6084/m9.figshare.5926453.v1
title: Immune Co-Culture Images JPEGs

description: J774.A1 macrophages were either left unprimed or primed with either IFNγ, LPS, or both and subsequently co-cultured with JC CRL 2116 tumor cells. J774.A1 cells were labeled with PE-conjugated anti-CD11b antibodies (red surface stain) while JC CRL 2116 cells were labeled with Vybrant (green cytoplasmic stain). Both cells were also stained with DAPI. Experiment was conducted in triplicates (three wells/images correspond to one condition).
DOI: 10.6084/m9.figshare.5926441
title: J774 DAPI-Antibody-Vybrant Run JPEGs

description: A linear dilution series of J774.A1 cells going from 10,000 cells/well down to 1,000 cells/well was plated on a 48-well plate. Cells were stained with Vybrant CFDA SE (cytoplasmic stain), phycoerythrin (PE)-conjugated anti-CD11b antibodies (surface stain), and DAPI (nuclear stain). Experiment was conducted in triplicates (three wells/images correspond to one condition).
DOI: 10.6084/m9.figshare.5926441.v1
title: J774 DAPI-Antibody-Vybrant Run JPEGs

description: A linear dilution series of J774.A1 cells going from 10,000 cells/well down to 1,000 cells/well was plated on a 48-well plate. Cells were stained with Vybrant CFDA SE (cytoplasmic stain), phycoerythrin (PE)-conjugated anti-CD11b antibodies (surface stain), and DAPI (nuclear stain). Experiment was conducted in triplicates (three wells/images correspond to one condition).
DOI: 10.6084/m9.figshare.5926417
title: The Economic Impact of Subthreshold and Clinical Childhoo Mental Disorders: Supplemental Material

description: Supplemental online material for the Journal of Mental Health article "The Economic Impact of Subthreshold and Clinical Childhood Mental Disorders". <br> Background: Mental disorders are common health problems associated with serious impairment and economic impact. Aims: To estimate the costs of clinical and subthreshold mental disorders in a sample of Brazilian children. Method: The High Risk Cohort Study is a community study conducted in two major Brazilian cities. Subjects were 6-14 years old children being registered at school. From an initial pool of 9,937 children, two subgroups were further investigated using a random-selection (n=958) and high-risk group selection procedure (n=1,554), resulting in a sample of 2,512 subjects. Mental disorder assessment was made using the Development and Well-Being Assessment. Costs for each child were estimated from the following components: mental health and social services use, school problems and parental loss of productivity. Results: Child subthreshold and clinical mental disorders showed lifetime mean total cost of $1,750.9 and $3,141.2, respectively. National lifetime cost estimate was $10.8 billion for subthreshold mental disorders and $12.8 billion for clinical mental disorders (values in US$ purchasing power parity). Conclusions: This study provides evidence that child mental disorders have a great economic impact on society. There is an urgent need to plan an effective system of care with cost-effective programs of treatment and prevention to reduce economic burden.
DOI: 10.6084/m9.figshare.5926417.v1
title: The Economic Impact of Subthreshold and Clinical Childhoo Mental Disorders: Supplemental Material

description: Supplemental online material for the Journal of Mental Health article "The Economic Impact of Subthreshold and Clinical Childhood Mental Disorders". <br> Background: Mental disorders are common health problems associated with serious impairment and economic impact. Aims: To estimate the costs of clinical and subthreshold mental disorders in a sample of Brazilian children. Method: The High Risk Cohort Study is a community study conducted in two major Brazilian cities. Subjects were 6-14 years old children being registered at school. From an initial pool of 9,937 children, two subgroups were further investigated using a random-selection (n=958) and high-risk group selection procedure (n=1,554), resulting in a sample of 2,512 subjects. Mental disorder assessment was made using the Development and Well-Being Assessment. Costs for each child were estimated from the following components: mental health and social services use, school problems and parental loss of productivity. Results: Child subthreshold and clinical mental disorders showed lifetime mean total cost of $1,750.9 and $3,141.2, respectively. National lifetime cost estimate was $10.8 billion for subthreshold mental disorders and $12.8 billion for clinical mental disorders (values in US$ purchasing power parity). Conclusions: This study provides evidence that child mental disorders have a great economic impact on society. There is an urgent need to plan an effective system of care with cost-effective programs of treatment and prevention to reduce economic burden.
DOI: 10.6084/m9.figshare.5926411
title: Lower Range Test JPEGs

description: Various concentrations of JC CRL 2116 cells going from 100 cells/well down to 1 cell/well were plated on a 48-well plate. CellProfiler-derived counts of DAPI stained nuclei were compared with cell counts obtained by human assessment of associated brightfield images for each well.
DOI: 10.6084/m9.figshare.5926411.v1
title: Lower Range Test JPEGs

description: Various concentrations of JC CRL 2116 cells going from 100 cells/well down to 1 cell/well were plated on a 48-well plate. CellProfiler-derived counts of DAPI stained nuclei were compared with cell counts obtained by human assessment of associated brightfield images for each well.
DOI: 10.6084/m9.figshare.5926408
title: Orders of Magnitude JPEGs

description: Half-log dilutions of JC CRL 2116 cells going from 100,000 cells/well down to 100 cells/well were plated on a 12-well plate (an experiment spanning three orders of magnitude). Cell nuclei stained with DAPI were then quantified and used to generate a linear curve. Experiment was conducted in triplicates (three wells/images correspond to one condition).
DOI: 10.6084/m9.figshare.5926408.v1
title: Orders of Magnitude JPEGs

description: Half-log dilutions of JC CRL 2116 cells going from 100,000 cells/well down to 100 cells/well were plated on a 12-well plate (an experiment spanning three orders of magnitude). Cell nuclei stained with DAPI were then quantified and used to generate a linear curve. Experiment was conducted in triplicates (three wells/images correspond to one condition).
DOI: 10.6084/m9.figshare.5926405
title: Linear Test DAPI JPEGs

description: A linear dilution series of JC CRL 2116 cells going from 10,000 cells/well down to 1,000 cells/well was plated on a 48-well plate. Whole-well images of cell nuclei stained with DAPI were then captured and processed to determine cell count and generate a linear curve. Experiment was conducted in triplicates (three wells/images correspond to one condition).
DOI: 10.6084/m9.figshare.5926378
title: Data from: Effects of short- and long-term variation in resource conditions on soil fungal communities and plant responses to soil biota

description: Data files include fungal sequence data (SSU and ITS2) from the field sampling and greenhouse experiment, percent colonization by AMF on plant roots, and plant trait data measured in the greenhouse experiment.<br>
DOI: 10.6084/m9.figshare.5926240
title: Sequencing Primers Co1.xlsx

description: Sequencing primers for the Co1 amplicon. These are referenced in the paper: Madden et al. 2016. The diversity of arthropods in homes across the United States as determined by environmental DNA analyses. Molecular Ecology.
DOI: 10.6084/m9.figshare.5926240.v1
title: Sequencing Primers Co1.xlsx

description: Sequencing primers for the Co1 amplicon. These are referenced in the paper: Madden et al. 2016. The diversity of arthropods in homes across the United States as determined by environmental DNA analyses. Molecular Ecology.
DOI: 10.6084/m9.figshare.5925274
title: R code triangle plot simulations from Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

description: We possess limited understanding of how speciation unfolds in the most species rich region of the planet—the Amazon basin. Hybrid zones provide valuable information on the evolution of reproductive isolation, but few studies of Amazonian vertebrate hybrid zones have rigorously examined the genome-wide underpinnings of reproductive isolation. We used genome-wide genetic datasets to show that two deeply diverged, but morphologically cryptic sister species of forest understory birds show little evidence for prezygotic reproductive isolation, but substantial postzygotic isolation. Patterns of heterozygosity and hybrid index revealed that hybrid classes with heavily recombined genomes are rare and closely match simulations with high levels of selection against hybrids. Genomic and geographical clines exhibit a remarkable similarity across loci in cline centres, and have exceptionally narrow cline widths, suggesting that postzygotic isolation is driven by genetic incompatibilities at many loci, rather than a few loci of strong effect. We propose Amazonian understory forest birds speciate slowly via gradual accumulation of postzygotic genetic incompatibilities, with prezygotic barriers playing a less important role. Our results suggest many cryptic Amazonian taxa classified as subspecies could have substantial postzygotic isolation deserving species recognition and that species richness is likely to be substantially underestimated in Amazonia.
DOI: 10.6084/m9.figshare.5925274.v1
title: R code triangle plot simulations from Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

description: We possess limited understanding of how speciation unfolds in the most species rich region of the planet—the Amazon basin. Hybrid zones provide valuable information on the evolution of reproductive isolation, but few studies of Amazonian vertebrate hybrid zones have rigorously examined the genome-wide underpinnings of reproductive isolation. We used genome-wide genetic datasets to show that two deeply diverged, but morphologically cryptic sister species of forest understory birds show little evidence for prezygotic reproductive isolation, but substantial postzygotic isolation. Patterns of heterozygosity and hybrid index revealed that hybrid classes with heavily recombined genomes are rare and closely match simulations with high levels of selection against hybrids. Genomic and geographical clines exhibit a remarkable similarity across loci in cline centres, and have exceptionally narrow cline widths, suggesting that postzygotic isolation is driven by genetic incompatibilities at many loci, rather than a few loci of strong effect. We propose Amazonian understory forest birds speciate slowly via gradual accumulation of postzygotic genetic incompatibilities, with prezygotic barriers playing a less important role. Our results suggest many cryptic Amazonian taxa classified as subspecies could have substantial postzygotic isolation deserving species recognition and that species richness is likely to be substantially underestimated in Amazonia.
DOI: 10.6084/m9.figshare.5925268
title: Supplementary table 1 from Genome-wide analyses of the bHLH superfamily in crustaceans: reappraisal of higher-order groupings and evidence for lineage-specific duplications

description: List of accession numbers for species used in this study.
DOI: 10.6084/m9.figshare.5925268.v1
title: Supplementary table 1 from Genome-wide analyses of the bHLH superfamily in crustaceans: reappraisal of higher-order groupings and evidence for lineage-specific duplications

description: List of accession numbers for species used in this study.
DOI: 10.6084/m9.figshare.5925262
title: Database S2 from Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

description: Xiphorhynchus sample details
DOI: 10.6084/m9.figshare.5925262.v1
title: Database S2 from Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

description: Xiphorhynchus sample details
DOI: 10.6084/m9.figshare.5925259
title: Supplementary table 2 from Genome-wide analyses of the bHLH superfamily in crustaceans: reappraisal of higher-order groupings and evidence for lineage-specific duplications

description: List of Pfam annotated bHLH genes and associated e-values in crustaceans and other arthropods.
DOI: 10.6084/m9.figshare.5925259.v1
title: Supplementary table 2 from Genome-wide analyses of the bHLH superfamily in crustaceans: reappraisal of higher-order groupings and evidence for lineage-specific duplications

description: List of Pfam annotated bHLH genes and associated e-values in crustaceans and other arthropods.
DOI: 10.6084/m9.figshare.5925250
title: Database S1 from Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

description: Willisornis sample details
DOI: 10.6084/m9.figshare.5925250.v1
title: Database S1 from Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

description: Willisornis sample details
DOI: 10.15468/dl.r33aw2
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-105.33555801968915 20.600197145225113,-105.1978606522931 20.600197145225113,-105.1978606522931 20.737894512621157,-105.33555801968915 20.737894512621157,-105.33555801968915 20.600197145225113))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Pegantha clara R.P.Bigelow, 1909"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021319-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.35078/ye7zne/ddnrg9
title: Riachinho I A.jpg

description: :unav
DOI: 10.35078/znr8wk/ktbs6f
title: São Bento A.jpg

description: :unav
DOI: 10.35078/ye7zne/xaeq3s
title: Morro C.jpg

description: :unav
DOI: 10.35078/ye7zne/b5kf4b
title: Sossego II A.jpg

description: :unav