cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3141802.v2
title: Behavioral data from Experiment 1 in the manuscript "The Importance of Search Strategy for Finding Targets in Open Terrain".

description: Behavioral data from Experiment 1 in the manuscript "The Importance of Search Strategy for Finding Targets in Open Terrain".<br>Abstract:<br>Some real world search tasks (i.e., IED detection) require searchers to search exhaustively across open ground. In the present study we simulated this problem by asking individuals (Experiment 1) and dyads (Experiment 2) to search for coin targets pseudo-randomly located in a bounded area of open grassland terrain. In Experiment 1, accuracy, search time and the route for searching were measured. Participants tended to use an ‘S’ shaped pattern with a common width of search lane. Increased accuracy was associated with slower, but also variable search speed. In Experiment 2, accuracy, search time, and the search strategy used by dyads was measured. While dyads were more accurate than individuals, dyads that opted to conduct two independent searches were more accurate than those who opted to split the search space. The implications of these results for individuals and pairs when searching for targets in open space are discussed.
DOI: 10.6084/m9.figshare.3141751
title: Index of crown vigour in centenarian oaks

description: This file contain data on ICV of centenarian oaks inside and outside Vera
DOI: 10.6084/m9.figshare.3141766.v1
title: ICV of non-centenarian oaks

description: This file contains data concerning ICV of non-centenarian oaks
DOI: 10.6084/m9.figshare.3141751.v1
title: Index of crown vigour in centenarian oaks

description: This file contain data on ICV of centenarian oaks inside and outside Vera
DOI: 10.6084/m9.figshare.3141718
title: CDC-25.2, a <i>C. elegans</i> ortholog of <i>cdc25</i>, is essential for the progression of intestinal divisions

description: Intestinal divisions in <i>Caenorhabditis elegans</i> take place in 3 stages: (1) cell divisions during embryogenesis, (2) binucleations at the L1 stage, and (3) endoreduplications at the end of each larval stage. Here, we report that CDC-25.2, a <i>C. elegans</i> ortholog of Cdc25, is required for these specialized division cycles between the 16E cell stage and the onset of endoreduplication. Results of our genetic analyses suggest that CDC-25.2 regulates intestinal cell divisions and binucleations by counteracting WEE-1.3 and by activating the CDK-1/CYB-1 complex. CDC-25.2 activity is then repressed by LIN-23 E3 ubiquitin ligase before the onset of intestinal endoreduplication, and this repression is maintained by LIN-35, the <i>C. elegans</i> ortholog of Retinoblastoma (Rb). These findings indicate that timely regulation of CDC-25.2 activity is essential for the progression of specialized division cycles and development of the <i>C. elegans</i> intestine.
DOI: 10.6084/m9.figshare.3141718.v1
title: CDC-25.2, a <i>C. elegans</i> ortholog of <i>cdc25</i>, is essential for the progression of intestinal divisions

description: Intestinal divisions in <i>Caenorhabditis elegans</i> take place in 3 stages: (1) cell divisions during embryogenesis, (2) binucleations at the L1 stage, and (3) endoreduplications at the end of each larval stage. Here, we report that CDC-25.2, a <i>C. elegans</i> ortholog of Cdc25, is required for these specialized division cycles between the 16E cell stage and the onset of endoreduplication. Results of our genetic analyses suggest that CDC-25.2 regulates intestinal cell divisions and binucleations by counteracting WEE-1.3 and by activating the CDK-1/CYB-1 complex. CDC-25.2 activity is then repressed by LIN-23 E3 ubiquitin ligase before the onset of intestinal endoreduplication, and this repression is maintained by LIN-35, the <i>C. elegans</i> ortholog of Retinoblastoma (Rb). These findings indicate that timely regulation of CDC-25.2 activity is essential for the progression of specialized division cycles and development of the <i>C. elegans</i> intestine.
DOI: 10.6084/m9.figshare.3141724
title: Arv1 promotes cell division by recruiting IQGAP1 and myosin to the cleavage furrow

description: Cell division is strictly regulated by a diversity of proteins and lipids to ensure proper duplication and segregation of genetic material and organelles. Here we report a novel role of the putative lipid transporter <i>ACAT-related protein required for viability 1</i> (Arv1) during telophase. We observed that the subcellular localization of Arv1 changes according to cell cycle progression and that Arv1 is recruited to the cleavage furrow in early telophase by epithelial protein lost in neoplasm (EPLIN). At the cleavage furrow Arv1 recruits myosin heavy chain 9 (MYH9) and myosin light chain 9 (MYL9) by interacting with IQ-motif-containing GTPase-activating protein (IQGAP1). Consequently the lack of Arv1 delayed telophase-progression, and a strongly increased incidence of furrow regression and formation of multinuclear cells was observed both in human cells in culture and in follicle epithelial cells of egg chambers of <i>Drosophila melanogaster in vivo</i>. Interestingly, the cholesterol-status at the cleavage furrow did not affect the recruitment of either IQGAP1, MYH9 or MYL. These results identify a novel function for Arv1 in regulation of cell division through promotion of the contractile actomyosin ring, which is independent of its lipid transporter activity.
DOI: 10.6084/m9.figshare.3141712
title: Isoproterenol directs hair follicle-associated pluripotent (HAP) stem cells to differentiate <i>in vitro</i> to cardiac muscle cells which can be induced to form beating heart-muscle tissue sheets

description: Nestin-expressing hair-follicle-associated pluripotent (HAP) stem cells are located in the bulge area of the follicle. Previous studies have shown that HAP stem cells can differentiate to neurons, glia, keratinocytes, smooth muscle cells, and melanocytes in vitro. HAP stem cells effected nerve and spinal cord regeneration in mouse models. Recently, we demonstrated that HAP stem cells differentiated to beating cardiac muscle cells. The differentiation potential to cardiac muscle cells was greatest in the upper part of the follicle. The beat rate of the cardiac muscle cells was stimulated by isoproterenol. In the present study, we observed that isoproterenol directs HAP stem cells to differentiate to cardiac muscle cells in large numbers in culture compared to HAP stem cells not supplemented with isoproterenol. The addition of activin A, bone morphogenetic protein 4, and basic fibroblast growth factor, along with isoproternal, induced the cardiac muscle cells to form tissue sheets of beating heart muscle cells. These results demonstrate that HAP stem cells have great potential to form beating cardiac muscle cells in tissue sheets.
DOI: 10.6084/m9.figshare.3141724.v1
title: Arv1 promotes cell division by recruiting IQGAP1 and myosin to the cleavage furrow

description: Cell division is strictly regulated by a diversity of proteins and lipids to ensure proper duplication and segregation of genetic material and organelles. Here we report a novel role of the putative lipid transporter <i>ACAT-related protein required for viability 1</i> (Arv1) during telophase. We observed that the subcellular localization of Arv1 changes according to cell cycle progression and that Arv1 is recruited to the cleavage furrow in early telophase by epithelial protein lost in neoplasm (EPLIN). At the cleavage furrow Arv1 recruits myosin heavy chain 9 (MYH9) and myosin light chain 9 (MYL9) by interacting with IQ-motif-containing GTPase-activating protein (IQGAP1). Consequently the lack of Arv1 delayed telophase-progression, and a strongly increased incidence of furrow regression and formation of multinuclear cells was observed both in human cells in culture and in follicle epithelial cells of egg chambers of <i>Drosophila melanogaster in vivo</i>. Interestingly, the cholesterol-status at the cleavage furrow did not affect the recruitment of either IQGAP1, MYH9 or MYL. These results identify a novel function for Arv1 in regulation of cell division through promotion of the contractile actomyosin ring, which is independent of its lipid transporter activity.
DOI: 10.6084/m9.figshare.3141709
title: MiRImpact, a new bioinformatic method using complete microRNA expression profiles to assess their overall influence on the activity of intracellular molecular pathways

description: MicroRNAs (miRs) are short noncoding RNA molecules that regulate expression of target mRNAs. Many published sources provide information about miRs and their targets. However, bioinformatic tools elucidating higher level impact of the established total miR profiles, are still largely missing. Recently, we developed a method termed OncoFinder enabling quantification of the activities of intracellular molecular pathways basing on gene expression data. Here we propose a new technique, MiRImpact, which enables to link miR expression data with its estimated outcome on the regulation of molecular pathways, like signaling, metabolic, cytoskeleton rearrangement, and DNA repair pathways. MiRImpact uses OncoFinder rationale for pathway activity calculations, with the major distinctions that (i) it deals with the concentrations of miRs - known regulators of gene products participating in molecular pathways, and (ii) miRs are considered as negative regulators of target molecules, if other is not specified. MiRImpact operates with 2 types of databases: for molecular targets of miRs and for gene products participating in molecular pathways. We applied MiRImpact to compare regulation of human bladder cancer-specific signaling pathways at the levels of mRNA and miR expression. We took 2 most complete alternative databases of experimentally validated miR targets – miRTarBase and DianaTarBase, and an OncoFinder database featuring 2725 gene products and 271 signaling pathways. We showed that the impact of miRs is orthogonal to pathway regulation at the mRNA level, which stresses the importance of studying posttranscriptional regulation of gene expression. We also report characteristic set of miR and mRNA regulation features linked with bladder cancer.
DOI: 10.6084/m9.figshare.3141706
title: The WEE1 regulators CPEB1 and miR-15b switch from inhibitor to activators at G2/M

description: MicroRNAs (miRNAs) in the AGO-containing RISC complex control messenger RNA (mRNA) translation by binding to mRNA 3′ untranslated region (3′UTR). The relationship between miRNAs and other regulatory factors that also bind to mRNA 3′UTR, such as CPEB1 (cytoplasmic polyadenylation element-binding protein), remains elusive. We found that both CPEB1 and miR-15b control the expression of WEE1, a key mammalian cell cycle regulator. Together, they repress WEE1 protein expression during G1 and S-phase. Interestingly, the 2 factors lose their inhibitory activity at the G2/M transition, at the time of the cell cycle when WEE1 expression is maximal, and, moreover, rather activate <i>WEE1</i> translation in a synergistic manner. Our data show that translational regulation by RISC and CPEB1 is essential in cell cycle control and, most importantly, is coordinated, and can be switched from inhibition to activation during the cell cycle.
DOI: 10.6084/m9.figshare.3141706.v1
title: The WEE1 regulators CPEB1 and miR-15b switch from inhibitor to activators at G2/M

description: MicroRNAs (miRNAs) in the AGO-containing RISC complex control messenger RNA (mRNA) translation by binding to mRNA 3′ untranslated region (3′UTR). The relationship between miRNAs and other regulatory factors that also bind to mRNA 3′UTR, such as CPEB1 (cytoplasmic polyadenylation element-binding protein), remains elusive. We found that both CPEB1 and miR-15b control the expression of WEE1, a key mammalian cell cycle regulator. Together, they repress WEE1 protein expression during G1 and S-phase. Interestingly, the 2 factors lose their inhibitory activity at the G2/M transition, at the time of the cell cycle when WEE1 expression is maximal, and, moreover, rather activate <i>WEE1</i> translation in a synergistic manner. Our data show that translational regulation by RISC and CPEB1 is essential in cell cycle control and, most importantly, is coordinated, and can be switched from inhibition to activation during the cell cycle.
DOI: 10.6084/m9.figshare.3141709.v1
title: MiRImpact, a new bioinformatic method using complete microRNA expression profiles to assess their overall influence on the activity of intracellular molecular pathways

description: MicroRNAs (miRs) are short noncoding RNA molecules that regulate expression of target mRNAs. Many published sources provide information about miRs and their targets. However, bioinformatic tools elucidating higher level impact of the established total miR profiles, are still largely missing. Recently, we developed a method termed OncoFinder enabling quantification of the activities of intracellular molecular pathways basing on gene expression data. Here we propose a new technique, MiRImpact, which enables to link miR expression data with its estimated outcome on the regulation of molecular pathways, like signaling, metabolic, cytoskeleton rearrangement, and DNA repair pathways. MiRImpact uses OncoFinder rationale for pathway activity calculations, with the major distinctions that (i) it deals with the concentrations of miRs - known regulators of gene products participating in molecular pathways, and (ii) miRs are considered as negative regulators of target molecules, if other is not specified. MiRImpact operates with 2 types of databases: for molecular targets of miRs and for gene products participating in molecular pathways. We applied MiRImpact to compare regulation of human bladder cancer-specific signaling pathways at the levels of mRNA and miR expression. We took 2 most complete alternative databases of experimentally validated miR targets – miRTarBase and DianaTarBase, and an OncoFinder database featuring 2725 gene products and 271 signaling pathways. We showed that the impact of miRs is orthogonal to pathway regulation at the mRNA level, which stresses the importance of studying posttranscriptional regulation of gene expression. We also report characteristic set of miR and mRNA regulation features linked with bladder cancer.
DOI: 10.6084/m9.figshare.3141712.v1
title: Isoproterenol directs hair follicle-associated pluripotent (HAP) stem cells to differentiate <i>in vitro</i> to cardiac muscle cells which can be induced to form beating heart-muscle tissue sheets

description: Nestin-expressing hair-follicle-associated pluripotent (HAP) stem cells are located in the bulge area of the follicle. Previous studies have shown that HAP stem cells can differentiate to neurons, glia, keratinocytes, smooth muscle cells, and melanocytes in vitro. HAP stem cells effected nerve and spinal cord regeneration in mouse models. Recently, we demonstrated that HAP stem cells differentiated to beating cardiac muscle cells. The differentiation potential to cardiac muscle cells was greatest in the upper part of the follicle. The beat rate of the cardiac muscle cells was stimulated by isoproterenol. In the present study, we observed that isoproterenol directs HAP stem cells to differentiate to cardiac muscle cells in large numbers in culture compared to HAP stem cells not supplemented with isoproterenol. The addition of activin A, bone morphogenetic protein 4, and basic fibroblast growth factor, along with isoproternal, induced the cardiac muscle cells to form tissue sheets of beating heart muscle cells. These results demonstrate that HAP stem cells have great potential to form beating cardiac muscle cells in tissue sheets.
DOI: 10.6084/m9.figshare.3141670.v1
title: SVJ632_External_MDAnderson_Hu_SILAC_Summary.xlsx

description: SILAC proteomic analysis of QKI-null (QPP9) and QKI-wt (PP8) pre-malignant neural stem cells.
DOI: 10.21227/62fj-8b04
title: Additional material of "SNSR: Robot-Sensor Network Security Architecture"

description: This dataset includes the additional material attached to paper entitled ”SNSR: Robot-Sensor Network Security Architecture”, submitted for publication in IEEE Internet of Things Journal.We attach detailed material from the performed experiments such as NTDB versions, numerical values obtained (and shown figures of the paper), examples of the certificates used, among others. We also include the definition of NTDB and management application messages using Protocol Buffers formats. The attached material refers to the implemented SNSR. In the attached material it can be seen how the implementation-dependant fields defined in the SNSR architecture have been defined for our implementation.
DOI: 10.21227/1aeg-1p60
title: Additional material of "SNSR: Robot-Sensor Network Security Architecture"

description: This dataset includes the additional material attached to paper entitled ”SNSR: Robot-Sensor Network Security Architecture”, submitted for publication in IEEE Internet of Things Journal.We attach detailed material from the performed experiments such as NTDB versions, numerical values obtained (and shown figures of the paper), examples of the certificates used, among others. We also include the definition of NTDB and management application messages using Protocol Buffers formats. The attached material refers to the implemented SNSR. In the attached material it can be seen how the implementation-dependant fields defined in the SNSR architecture have been defined for our implementation.
DOI: 10.6084/m9.figshare.3141532
title: A shared numerical representation for action and perception. Raw data

description: The folder contains raw and tabulated data files for all the different experimental conditions.
DOI: 10.6084/m9.figshare.3141358
title: Effects of rooting media on root growth and morphology of <i>Brassica rapa</i> seedlings

description: Rooting media used in current root phenotyping studies can have substantial effect. In this study, the effects of three different nutrient conducting papers (Black construction paper, Anchor blue germination paper and Kimpak paper) and soil-filled boxes on root growth and root system architecture (RSA) of <i>Brassica rapa</i> (cultivars ‘R500’ and ‘IMB211’) were investigated. Seedlings of the two <i>B. rapa</i> genotypes were supplied with nutrients on the nutrient conducting papers and in the soil-filled boxes. The papers and soil-filled boxes were fixed to flatbed scanners and two-dimensional images of roots were periodically taken and analysed. Root media effects on shoot and root biomass and on topological indices (TI) were observed. For example, root branching was more pronounced on the construction paper. Mean TI of 0.82 and 0.93, recorded for R500 and IMB211, respectively, on the construction paper indicated that substrates affect the herringbone pattern of brassica roots. Whilst it was indicated that different results could be obtained for the same RSA when different germination papers are used, the results showed that Anchor blue germination paper is an ideal proxy for soil in phenotyping seedlings for RSA traits and root growth.
DOI: 10.6084/m9.figshare.3141550
title: A Comparison of Inverse-Wishart Prior Specifications for Covariance Matrices in Multilevel Autoregressive Models

description: Multilevel autoregressive models are especially suited for modeling between-person differences in within-person processes. Fitting these models with Bayesian techniques requires the specification of prior distributions for all parameters. Often it is desirable to specify prior distributions that have negligible effects on the resulting parameter estimates. However, the conjugate prior distribution for covariance matrices—the Inverse-Wishart distribution—tends to be informative when variances are close to zero. This is problematic for multilevel autoregressive models, because autoregressive parameters are usually small for each individual, so that the variance of these parameters will be small. We performed a simulation study to compare the performance of three Inverse-Wishart prior specifications suggested in the literature, when one or more variances for the random effects in the multilevel autoregressive model are small. Our results show that the prior specification that uses plug-in ML estimates of the variances performs best. We advise to always include a sensitivity analysis for the prior specification for covariance matrices of random parameters, especially in autoregressive models, and to include a data-based prior specification in this analysis. We illustrate such an analysis by means of an empirical application on repeated measures data on worrying and positive affect.
DOI: 10.6084/m9.figshare.3141337
title: Cork oak growth

description: <br>This file contains data concerning centenarian cork oak growth inside and outside Vera.
DOI: 10.6084/m9.figshare.3141550.v1
title: A Comparison of Inverse-Wishart Prior Specifications for Covariance Matrices in Multilevel Autoregressive Models

description: Multilevel autoregressive models are especially suited for modeling between-person differences in within-person processes. Fitting these models with Bayesian techniques requires the specification of prior distributions for all parameters. Often it is desirable to specify prior distributions that have negligible effects on the resulting parameter estimates. However, the conjugate prior distribution for covariance matrices—the Inverse-Wishart distribution—tends to be informative when variances are close to zero. This is problematic for multilevel autoregressive models, because autoregressive parameters are usually small for each individual, so that the variance of these parameters will be small. We performed a simulation study to compare the performance of three Inverse-Wishart prior specifications suggested in the literature, when one or more variances for the random effects in the multilevel autoregressive model are small. Our results show that the prior specification that uses plug-in ML estimates of the variances performs best. We advise to always include a sensitivity analysis for the prior specification for covariance matrices of random parameters, especially in autoregressive models, and to include a data-based prior specification in this analysis. We illustrate such an analysis by means of an empirical application on repeated measures data on worrying and positive affect.
DOI: 10.6084/m9.figshare.3141358.v2
title: Effects of rooting media on root growth and morphology of <i>Brassica rapa</i> seedlings

description: Rooting media used in current root phenotyping studies can have substantial effect. In this study, the effects of three different nutrient conducting papers (Black construction paper, Anchor blue germination paper and Kimpak paper) and soil-filled boxes on root growth and root system architecture (RSA) of <i>Brassica rapa</i> (cultivars ‘R500’ and ‘IMB211’) were investigated. Seedlings of the two <i>B. rapa</i> genotypes were supplied with nutrients on the nutrient conducting papers and in the soil-filled boxes. The papers and soil-filled boxes were fixed to flatbed scanners and two-dimensional images of roots were periodically taken and analysed. Root media effects on shoot and root biomass and on topological indices (TI) were observed. For example, root branching was more pronounced on the construction paper. Mean TI of 0.82 and 0.93, recorded for R500 and IMB211, respectively, on the construction paper indicated that substrates affect the herringbone pattern of brassica roots. Whilst it was indicated that different results could be obtained for the same RSA when different germination papers are used, the results showed that Anchor blue germination paper is an ideal proxy for soil in phenotyping seedlings for RSA traits and root growth.