cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6729305
title: Dataset for: FFA4 activation induces LPA1 desensitization independent of LPA1 internalization and of FFA4-LPA1 heterodimerization

description: HEK 293 cells co-expressing fluorescent protein-tagged FFA4 and LPA1 receptors were used to explore LPA1 desensitization. FFA4 activation induced functional desensitization of LPA1 receptors (calcium signaling and ERK 1/2 phosphorylation) and phosphorylation of both FFA4 and LPA1. LPA1 activation induced phosphorylation of LPA1, but not of FFA4 and induced internalization of both receptors into heterogeneous types of vesicles. Interestingly, DHA induced internalization of FFA4 but not of LPA1. Evidence for fatty acid-induced FFA4-LPA1 interaction was obtained by both Förster resonance energy transfer and co-immunoprecipitation studies. Such interaction took place after desensitization was already established. Data indicate that FFA4 activation induces LPA1 desensitization in an internalization-independent process and that complex cellular processes participate in the crosstalk of these receptors.
DOI: 10.6084/m9.figshare.6729305.v1
title: Dataset for: FFA4 activation induces LPA1 desensitization independent of LPA1 internalization and of FFA4-LPA1 heterodimerization

description: HEK 293 cells co-expressing fluorescent protein-tagged FFA4 and LPA1 receptors were used to explore LPA1 desensitization. FFA4 activation induced functional desensitization of LPA1 receptors (calcium signaling and ERK 1/2 phosphorylation) and phosphorylation of both FFA4 and LPA1. LPA1 activation induced phosphorylation of LPA1, but not of FFA4 and induced internalization of both receptors into heterogeneous types of vesicles. Interestingly, DHA induced internalization of FFA4 but not of LPA1. Evidence for fatty acid-induced FFA4-LPA1 interaction was obtained by both Förster resonance energy transfer and co-immunoprecipitation studies. Such interaction took place after desensitization was already established. Data indicate that FFA4 activation induces LPA1 desensitization in an internalization-independent process and that complex cellular processes participate in the crosstalk of these receptors.
DOI: 10.6084/m9.figshare.6729290
title: Building a Collaboration Network

description: The Dimensions API’s flexible query syntax and native json results format integrate well with data science workbenches such as Jupyter notebooks. (Jupyter notebook and HTML rendering files attached).
DOI: 10.6084/m9.figshare.6729290.v1
title: Jupyter Notebook

description: The Dimensions API’s flexible query syntax and native json results format integrate well with data science workbenches such as Jupyter notebooks.
DOI: 10.6084/m9.figshare.6729287
title: DFT output files for 'Control of Uniaxial Negative Thermal Expansion in Layered Perovskites by Tuning Layer Thickness'

description: Output files with .castep extension for all DFT calculations related to the manuscript 'Control of Uniaxial Negative Thermal Expansion in Layered Perovskites by Tuning Layer Thickness' performed using CASTEP v7.0.3.<br>
DOI: 10.6084/m9.figshare.6729290.v2
title: Building a Collaboration Network

description: The Dimensions API’s flexible query syntax and native json results format integrate well with data science workbenches such as Jupyter notebooks. (Jupyter notebook and HTML rendering files attached).
DOI: 10.6084/m9.figshare.6729290.v3
title: Building a Collaboration Network

description: The Dimensions API’s flexible query syntax and native json results format integrate well with data science workbenches such as Jupyter notebooks. (Jupyter notebook and HTML rendering files attached).
DOI: 10.6084/m9.figshare.6729290.v4
title: Building a Collaboration Network

description: The Dimensions API’s flexible query syntax and native json results format integrate well with data science workbenches such as Jupyter notebooks. (Jupyter notebook and HTML rendering files attached).
DOI: 10.6084/m9.figshare.12889616.v1
title: R0189_20170928a_videos

description: Rat 0189, skilled reaching data collected on 9/28/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.6729143
title: Partition file of 13 CDS and 2 rRNAs by IQ-TREE

description: Partition file of 13 CDS and 2 rRNAs by IQ-TREE
DOI: 10.6084/m9.figshare.6729143.v1
title: Partition file of 13 CDS and 2 rRNAs by IQ-TREE

description: Partition file of 13 CDS and 2 rRNAs by IQ-TREE
DOI: 10.6084/m9.figshare.6729143.v2
title: Partition file of 13 CDS and 2 rRNAs by IQ-TREE

description: Partition file of 13 CDS and 2 rRNAs by IQ-TREE
DOI: 10.6084/m9.figshare.6729143.v3
title: Partition file of 13 CDS and 2 rRNAs by IQ-TREE

description: Partition file of 13 CDS and 2 rRNAs by IQ-TREE
DOI: 10.6084/m9.figshare.6729122.v1
title: Cellular senescence induces replication stress without affecting DNA replication timing

description: Organismal aging entails a gradual decline of normal physiological functions and a major contributor to this decline is withdrawal of the cell cycle, known as senescence. Senescence can result from telomere diminution leading to a finite number of population doublings, known as replicative senescence, or from oncogene overexpression, as a protective mechanism against cancer. Senescence is associated with large-scale chromatin re-organization and changes in gene expression. Replication stress is a complex phenomenon, defined as the slowing or stalling of replication fork progression and/or DNA synthesis, which has serious implications for genome stability, and consequently in human diseases. Aberrant replication fork structures activate the replication stress response leading to the activation of dormant origins, which is thought to be a safeguard mechanism to complete DNA replication on place and time. However, the relationship between replicative stress and the changes in the spatiotemporal program of DNA replication in senescence progression remains unclear. To investigate the relationship between replication stress and senescence, we studied the DNA replication program during senescence progression, in proliferative and pre-senescent cells from donors of various ages, by single DNA fiber combing of replicated DNA, origin mapping by sequencing short nascent strands and genome-wide profiling of replication timing. We demonstrate that, progression into replicative senescence leads to reduced replication fork rates and activation of dormant origins, which are the hallmarks of replication stress. However, with the exception of a delay in replication timing of the <i>CREB5</i> gene in all pre-senescent cells, replication timing was unaffected by replication stress during entry into either oncogene-induced or replicative senescence. Consequently, we conclude that replication timing alterations associated with physiological and accelerated aging, do not result from senescence progression. Our results clarify the interplay between senescence, aging and replication programs and demonstrate that replication timing is largely resistant to replication stress.
DOI: 10.6084/m9.figshare.6729107
title: Natura 2000 habitat of Mt. Argentario promontory (southern Tuscany, Italy)

description: The Mt. Argentario promontory (southern Tuscany, Italy) is a protected area hosting habitats and species of European importance. The Mt. Argentario Natura 2000 habitat map (1:10,000) was compiled from photo-interpretation and field surveys, integrated with data from past cartographic and phytosociological studies. Conventional geographical information system procedures were used to select and manage spatial information, and delimit the map polygons. The following attributes were assigned to each map polygon: (i) habitat type name, with Natura 2000 code and (ii) percentage cover of the habitat type. Where multiple habitat types were associated in a mosaic attributed to the same polygon, the percentage cover of each habitat type was estimated. The survey allowed to identify and map a total of 13 Natura 2000 habitat types covering more than 40% of the study area. Presence and conservation importance of the detected habitat types are discussed, together with the usefulness of this kind of maps for monitoring and managing purposes.
DOI: 10.6084/m9.figshare.6729107.v1
title: Natura 2000 habitat of Mt. Argentario promontory (southern Tuscany, Italy)

description: The Mt. Argentario promontory (southern Tuscany, Italy) is a protected area hosting habitats and species of European importance. The Mt. Argentario Natura 2000 habitat map (1:10,000) was compiled from photo-interpretation and field surveys, integrated with data from past cartographic and phytosociological studies. Conventional geographical information system procedures were used to select and manage spatial information, and delimit the map polygons. The following attributes were assigned to each map polygon: (i) habitat type name, with Natura 2000 code and (ii) percentage cover of the habitat type. Where multiple habitat types were associated in a mosaic attributed to the same polygon, the percentage cover of each habitat type was estimated. The survey allowed to identify and map a total of 13 Natura 2000 habitat types covering more than 40% of the study area. Presence and conservation importance of the detected habitat types are discussed, together with the usefulness of this kind of maps for monitoring and managing purposes.
DOI: 10.6084/m9.figshare.6729095
title: Elderly virome contigs

description: Characterization of the gut DNA virome of elderly individuals (&gt;65 years of age) residing in Ireland.
DOI: 10.6084/m9.figshare.6729095.v1
title: Elderly virome contigs

description: Characterization of the gut DNA virome of elderly individuals (&gt;65 years of age) residing in Ireland.
DOI: 10.6084/m9.figshare.6729074
title: Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca)

description: Crustaceans of the order Notostraca (Branchiopoda) are worldwide-distributed and known for their remarkable morphological stasis between extant and Permian fossil species. Moreover, they show relevant ecological traits and a wide panel of reproductive strategies. However, genomic studies on notostracans are fairly limited. We here present the genome sequences of two notostracan taxa, Lepidurus arcticus and L. apus lubbocki. Taking advantage of the small genome size (~0.11 pg), we set the sequencing on Illumina HiSeq X platform for a single run on a single individual per species. We finally assembled 73.2 Mbp - L. arcticus - and 90.3 Mbp - L. apus lubbocki long genomes. Assembly cover up to 80% of estimated genome size, with a gene completeness &gt;97% for both genomes. 10-15% of assembled genomes consist of repeats and, although L. apus lubbocki experienced a marked increase of LTR and DNA transposons, there is no significant difference in copy number. The analysis of 2,376 ortholog genes indicates a ~7% of divergence between the two Lepidurus species, with a nucleotide substitution rate significantly lower than the Daphnia one. Ka/Ks analyses suggests purifying selection in both branchiopod lineages, raising the question whether the lower substitution rate is correlated with the Lepidurus morphological conservation or it is attributable to specific biological traits. Our analysis demonstrates that in these organisms it is possible to obtain draft genomes with high completeness from single individuals with a relatively small sequencing effort. This makes Lepidurus, and Notostraca, an interesting model for studies in population, ecological and evolutionary genomics.<br><br>
DOI: 10.6084/m9.figshare.6729056
title: Polarity and morphogenesis of the eye epithelium requires the adhesion junction associated adaptor protein Traf4

description: During development, neuroepithelial progenitors acquire apico-basal polarity and adhere to one another via apically located tight and adherens junction complexes. This polarized neuroepithelium must continue to integrate cells arising through cell divisions and intercalation, and allow for cell movements, at the same time as undergoing morphogenesis. Cell proliferation, migration and intercalation all occur in the morphing embryonic eye. To understand how eye development might depend on dynamic epithelial adhesion, we investigated the function of a known regulator of junctional plasticity, Tumour necrosis factor receptor-associated factor 4 (Traf4). <i>traf4a</i> mRNA is expressed in the developing eye vesicle over the period of optic cup morphogenesis, and Traf4a loss leads to disrupted evagination and elongation of the eye vesicles, and aberrant organization and apico-basal polarity of the eye epithelium. We propose a model whereby Traf4a regulates apical junction plasticity in nascent eye epithelium, allowing for its polarization and morphogenesis. <b>Symbols and Abbreviations</b>: AB: apico-basal; aPKC: atypical protein kinase-C; CRISPR: clustered regularly-interspaced short palindromic repeats; GFP: green fluorescent protein; hpf: hours post-fertilization; MO: antisense morpholino oligonucleotide; pHH3: phospho histone H3; ss: somite stage; Traf4: Tumour necrosis factor receptor-associated factor 4; ZO-1: zona occludens-1
DOI: 10.6084/m9.figshare.6729056.v1
title: Polarity and morphogenesis of the eye epithelium requires the adhesion junction associated adaptor protein Traf4

description: During development, neuroepithelial progenitors acquire apico-basal polarity and adhere to one another via apically located tight and adherens junction complexes. This polarized neuroepithelium must continue to integrate cells arising through cell divisions and intercalation, and allow for cell movements, at the same time as undergoing morphogenesis. Cell proliferation, migration and intercalation all occur in the morphing embryonic eye. To understand how eye development might depend on dynamic epithelial adhesion, we investigated the function of a known regulator of junctional plasticity, Tumour necrosis factor receptor-associated factor 4 (Traf4). <i>traf4a</i> mRNA is expressed in the developing eye vesicle over the period of optic cup morphogenesis, and Traf4a loss leads to disrupted evagination and elongation of the eye vesicles, and aberrant organization and apico-basal polarity of the eye epithelium. We propose a model whereby Traf4a regulates apical junction plasticity in nascent eye epithelium, allowing for its polarization and morphogenesis. <b>Symbols and Abbreviations</b>: AB: apico-basal; aPKC: atypical protein kinase-C; CRISPR: clustered regularly-interspaced short palindromic repeats; GFP: green fluorescent protein; hpf: hours post-fertilization; MO: antisense morpholino oligonucleotide; pHH3: phospho histone H3; ss: somite stage; Traf4: Tumour necrosis factor receptor-associated factor 4; ZO-1: zona occludens-1
DOI: 10.6084/m9.figshare.6728999
title: Assessing the role of dens in the spread, establishment and persistence of sarcoptic mange in an endangered canid

description: Data of 16 scenarios (8 during the epidemic period and 8 during the endemic period) in which the San Joaquin kit fox population in Bakersfield, California, was simulated and the mite sarcoptes scabiei was introduced (epidemic period) or was already present (endemic period). If the files do not contain the word "endemic" then, it belong to the epidemic period, except for "No disease". <br>The raw outputs files are contain in the zip files. These files start with "No_" or "Fox_"<br>The codes to load these files are also present here. Just modify the paths.<br>Finally, the outputs after their processing are also ready in the "Output" zip files
DOI: 10.6084/m9.figshare.6728999.v1
title: Assessing the role of dens in the spread, establishment and persistence of sarcoptic mange in an endangered canid

description: Data of 16 scenarios (8 during the epidemic period and 8 during the endemic period) in which the San Joaquin kit fox population in Bakersfield, California, was simulated and the mite sarcoptes scabiei was introduced (epidemic period) or was already present (endemic period). If the files do not contain the word "endemic" then, it belong to the epidemic period, except for "No disease". <br>The raw outputs files are contain in the zip files. These files start with "No_" or "Fox_"<br>The codes to load these files are also present here. Just modify the paths.<br>Finally, the outputs after their processing are also ready in the "Output" zip files
DOI: 10.6084/m9.figshare.6728477
title: 100V_pre.bam

description: 100_pre.bam for IGV
DOI: 10.6084/m9.figshare.6728462
title: Beberapa Contoh Fenomena Lanskap Linguistik Kota Surakarta

description: Foto-foto berikut ini merupakan contoh papan nama dan petunjuk jalan yang ada di sekitar kota Surakarta.
DOI: 10.6084/m9.figshare.6728423
title: Crop pollination service supply demand table

description: The data table have the information of pollination supply and demand at county level. Column names PS13 and PD13 in the data table show the supply (wild bee abundance index) and the demand (pollination-dependency weighted crop area, 1000 ha). This table was used to generate Figure 1D in Koh et al. 2016 PNAS.
DOI: 10.6084/m9.figshare.6728423.v1
title: Crop pollination service supply demand table

description: The data table have the information of pollination supply and demand at county level. Column names PS13 and PD13 in the data table show the supply (wild bee abundance index) and the demand (pollination-dependency weighted crop area, 1000 ha). This table was used to generate Figure 1D in Koh et al. 2016 PNAS.
DOI: 10.6084/m9.figshare.6728396
title: Effect of Microencapsulated Essential Oil form Chamaecyparis obtusa on Monocyte-derived Dendritic Cell Activation and CD4+ T Cell Polarization

description: the immunologic characteristics of <i>Chamaecyparis obtusa </i>essential oil and the influence on Th cell polarization
DOI: 10.6084/m9.figshare.6728384
title: Evidence that emergent <i>Nothofagus dombeyi</i> do not depress carbon sequestration rates of canopy species in an old-growth Chilean temperate forest

description: The influence of functional diversity on ecosystem productivity has practical implications for the carbon sequestration potential of forest ecosystems. Vertical stratification may be one key aspect of functional diversity that influences stand productivity through differential resource use. Although additive basal area of canopy and emergent species has been reported in some forests, it is unclear whether this represents significant additive productivity, or mainly a reflection of the great longevity of the emergent trees. We asked if the presence of emergent <i>Nothofagus dombeyi</i> influences carbon sequestration in wood of the associated canopy species in an old-growth temperate forest in south-central Chile, the canopy species all being more shade-tolerant than <i>N. dombeyi</i>. We estimated wood volume increment of all trees on four pairs of plots in old-growth stands in Parque Nacional Puyehue, each pair consisting of one 25×25 m plot with emergent trees and another lacking emergents. Heights and diameters of all trees were measured, and increment cores were extracted to permit back-estimation of the same variables 2 years earlier. Published data on density and carbon content of wood were then used to convert wood volume production to carbon sequestration rates. Rates of carbon sequestration in wood of the canopy species were very similar on plots with and without <i>N. dombeyi</i>, showing that productivity of the emergent trees was additive to that of the canopy species. As a result, the average total carbon sequestration rate of plots with emergents was nearly twice that of plots lacking emergents (2.8 versus 1.5 T C ha<sup>−1</sup> yr<sup>−1</sup>). The occurrence of additive productivity highlights the importance of functional diversity and vertical stratification for forest management and carbon sequestration. Conservation of vertical stratification is desirable when complementary light-use characteristics of the dominant species optimise carbon sequestration.
DOI: 10.6084/m9.figshare.6728384.v1
title: Evidence that emergent <i>Nothofagus dombeyi</i> do not depress carbon sequestration rates of canopy species in an old-growth Chilean temperate forest

description: The influence of functional diversity on ecosystem productivity has practical implications for the carbon sequestration potential of forest ecosystems. Vertical stratification may be one key aspect of functional diversity that influences stand productivity through differential resource use. Although additive basal area of canopy and emergent species has been reported in some forests, it is unclear whether this represents significant additive productivity, or mainly a reflection of the great longevity of the emergent trees. We asked if the presence of emergent <i>Nothofagus dombeyi</i> influences carbon sequestration in wood of the associated canopy species in an old-growth temperate forest in south-central Chile, the canopy species all being more shade-tolerant than <i>N. dombeyi</i>. We estimated wood volume increment of all trees on four pairs of plots in old-growth stands in Parque Nacional Puyehue, each pair consisting of one 25×25 m plot with emergent trees and another lacking emergents. Heights and diameters of all trees were measured, and increment cores were extracted to permit back-estimation of the same variables 2 years earlier. Published data on density and carbon content of wood were then used to convert wood volume production to carbon sequestration rates. Rates of carbon sequestration in wood of the canopy species were very similar on plots with and without <i>N. dombeyi</i>, showing that productivity of the emergent trees was additive to that of the canopy species. As a result, the average total carbon sequestration rate of plots with emergents was nearly twice that of plots lacking emergents (2.8 versus 1.5 T C ha<sup>−1</sup> yr<sup>−1</sup>). The occurrence of additive productivity highlights the importance of functional diversity and vertical stratification for forest management and carbon sequestration. Conservation of vertical stratification is desirable when complementary light-use characteristics of the dominant species optimise carbon sequestration.
DOI: 10.6084/m9.figshare.6728396.v1
title: Effect of Microencapsulated Essential Oil form Chamaecyparis obtusa on Monocyte-derived Dendritic Cell Activation and CD4+ T Cell Polarization

description: the immunologic characteristics of <i>Chamaecyparis obtusa </i>essential oil and the influence on Th cell polarization
DOI: 10.6084/m9.figshare.6728396.v3
title: Effect of Microencapsulated Essential Oil form Chamaecyparis obtusa on Monocyte-derived Dendritic Cell Activation and CD4+ T Cell Polarization

description: the immunologic characteristics of <i>Chamaecyparis obtusa </i>essential oil and the influence on Th cell polarization
DOI: 10.6084/m9.figshare.6728396.v2
title: Effect of Microencapsulated Essential Oil form Chamaecyparis obtusa on Monocyte-derived Dendritic Cell Activation and CD4+ T Cell Polarization

description: the immunologic characteristics of <i>Chamaecyparis obtusa </i>essential oil and the influence on Th cell polarization
DOI: 10.6084/m9.figshare.6728342
title: 2016-12 Data paper kwaliteitszorg - Liesbeth Lamsens.xlsx

description: Control and experimental group
DOI: 10.6084/m9.figshare.6728348
title: DeepGMAP-data

description: A supplementary data set to reproduce https://doi.org/10.1101/355974
DOI: 10.6084/m9.figshare.6728342.v1
title: 2016-12 Data paper kwaliteitszorg - Liesbeth Lamsens.xlsx

description: Control and experimental group
DOI: 10.6084/m9.figshare.6728348.v1
title: DeepGMAP-data

description: A supplementary data set to reproduce https://doi.org/10.1101/355974