cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3468452
title: Ndt80 activates the meiotic <i>ORC1</i> transcript isoform and <i>SMA2</i> via a bi-directional middle sporulation element in <i>Saccharomyces cerevisiae</i>

description: The origin of replication complex subunit <i>ORC1</i> is important for DNA replication. The gene is known to encode a meiotic transcript isoform (<i>mORC1</i>) with an extended 5′-untranslated region (5′-UTR), which was predicted to inhibit protein translation. However, the regulatory mechanism that controls the m<i>ORC1</i> transcript isoform is unknown and no molecular biological evidence for a role of <i>mORC1</i> in negatively regulating Orc1 protein during gametogenesis is available. By interpreting RNA profiling data obtained with growing and sporulating diploid cells, mitotic haploid cells, and a starving diploid control strain, we determined that m<i>ORC1</i> is a middle meiotic transcript isoform. Regulatory motif predictions and genetic experiments reveal that the activator Ndt80 and its middle sporulation element (MSE) target motif are required for the full induction of <i>mORC1</i> and the divergently transcribed meiotic <i>SMA2</i> locus. Furthermore, we find that the MSE-binding negative regulator Sum1 represses both <i>mORC1</i> and <i>SMA2</i> during mitotic growth. Finally, we demonstrate that an MSE deletion strain, which cannot induce <i>mORC1</i>, contains abnormally high Orc1 levels during post-meiotic stages of gametogenesis. Our results reveal the regulatory mechanism that controls <i>mORC1</i>, highlighting a novel developmental stage-specific role for the MSE element in bi-directional <i>mORC1</i>/<i>SMA2</i> gene activation, and correlating <i>mORC1</i> induction with declining Orc1 protein levels. Because eukaryotic genes frequently encode multiple transcripts possessing 5′-UTRs of variable length, our results are likely relevant for gene expression during development and disease in higher eukaryotes.
DOI: 10.6084/m9.figshare.3468452.v1
title: Ndt80 activates the meiotic <i>ORC1</i> transcript isoform and <i>SMA2</i> via a bi-directional middle sporulation element in <i>Saccharomyces cerevisiae</i>

description: The origin of replication complex subunit <i>ORC1</i> is important for DNA replication. The gene is known to encode a meiotic transcript isoform (<i>mORC1</i>) with an extended 5′-untranslated region (5′-UTR), which was predicted to inhibit protein translation. However, the regulatory mechanism that controls the m<i>ORC1</i> transcript isoform is unknown and no molecular biological evidence for a role of <i>mORC1</i> in negatively regulating Orc1 protein during gametogenesis is available. By interpreting RNA profiling data obtained with growing and sporulating diploid cells, mitotic haploid cells, and a starving diploid control strain, we determined that m<i>ORC1</i> is a middle meiotic transcript isoform. Regulatory motif predictions and genetic experiments reveal that the activator Ndt80 and its middle sporulation element (MSE) target motif are required for the full induction of <i>mORC1</i> and the divergently transcribed meiotic <i>SMA2</i> locus. Furthermore, we find that the MSE-binding negative regulator Sum1 represses both <i>mORC1</i> and <i>SMA2</i> during mitotic growth. Finally, we demonstrate that an MSE deletion strain, which cannot induce <i>mORC1</i>, contains abnormally high Orc1 levels during post-meiotic stages of gametogenesis. Our results reveal the regulatory mechanism that controls <i>mORC1</i>, highlighting a novel developmental stage-specific role for the MSE element in bi-directional <i>mORC1</i>/<i>SMA2</i> gene activation, and correlating <i>mORC1</i> induction with declining Orc1 protein levels. Because eukaryotic genes frequently encode multiple transcripts possessing 5′-UTRs of variable length, our results are likely relevant for gene expression during development and disease in higher eukaryotes.
DOI: 10.6084/m9.figshare.3468434
title: Design, synthesis, and pharmacological evaluation of 5-oxo-1,2,4-oxadiazole derivatives as AT<sub>1</sub> antagonists with antihypertension activities

description: A series of new 5-oxo-1,2,4-oxadiazole derivatives with 1, 4-disubsituted or 1, 5-disubsituted indole group was designed, synthesized, and pharmacologically evaluated. These derivatives displayed high affinities to the AT<sub>1</sub> receptor at the same order of magnitude to losartan. The methyl ester with 1, 4-disubsituted indole group, 1 (5.01 ± 1.67 nM) showed high antihypertension activity on spontaneously hypertensive rats (SHRs). Its maximal response lowered 30 mmHg of mean blood pressure (MBP) at 10 mg/kg after oral administration, which was better than irbesartan, and the antihypertensive effect lasted beyond 24 h. These results made 1 deserve further investigation.
DOI: 10.6084/m9.figshare.3468434.v1
title: Design, synthesis, and pharmacological evaluation of 5-oxo-1,2,4-oxadiazole derivatives as AT<sub>1</sub> antagonists with antihypertension activities

description: A series of new 5-oxo-1,2,4-oxadiazole derivatives with 1, 4-disubsituted or 1, 5-disubsituted indole group was designed, synthesized, and pharmacologically evaluated. These derivatives displayed high affinities to the AT<sub>1</sub> receptor at the same order of magnitude to losartan. The methyl ester with 1, 4-disubsituted indole group, 1 (5.01 ± 1.67 nM) showed high antihypertension activity on spontaneously hypertensive rats (SHRs). Its maximal response lowered 30 mmHg of mean blood pressure (MBP) at 10 mg/kg after oral administration, which was better than irbesartan, and the antihypertensive effect lasted beyond 24 h. These results made 1 deserve further investigation.
DOI: 10.6084/m9.figshare.3468431
title: Characterization of protein-conjugating kinetics based on localized surface plasmon resonance of the gold nanoparticle

description: The gold nanoparticle exhibits optical property of localized surface plasmon resonance (LSPR), which dynamically alters as the surface adsorbs new ligands. We carried out a semi-quantitative analysis with the method of multivariate curve resolution, observing that the adsorption of serum albumin on gold nanoparticle was best deciphered as two-mode competitive kinetics. Interestingly, for human serum albumin, the slower mode contributed considerably to the LSPR response of protein-conjugated surfaces, while in the case of bovine serum albumin the faster mode overwhelmed the slower one at high protein concentrations. The kinetic patterns were rationalized with diversity of biomolecular orientations on the nanoparticle surface. The simple but efficient protocol supports semi-quantitative analysis combining UV-vis spectroscopy with chemometrics method for distinguishing conjugation kinetics of different types of proteins on the surface of nanoparticles at nanomolar concentration.
DOI: 10.6084/m9.figshare.3468392
title: All data and metadata related to the IDENT manuscript

description: These data files and the markdown file allow you to go through all the steps to reproduce the analyses in the manuscript entitled "Leaf bacterial diversity mediates plant diversity – ecosystem function relationships" (doi: 10.1038/nature22399).
DOI: 10.6084/m9.figshare.3468392.v1
title: All data and metadata related to the IDENT manuscript

description: These data files and the markdown file allow you to go through all the steps to reproduce the analyses in the manuscript entitled "Leaf bacterial diversity mediates plant diversity – ecosystem function relationships" (doi: 10.1038/nature22399).
DOI: 10.6084/m9.figshare.3468386
title: R Markdown Code for manuscript Leaf bacterial diversity mediates plant diversity – ecosystem function relationships

description: This markdown file goes through all the steps to reproduce the analyses in the manuscript entitled Leaf bacterial diversity mediates plant diversity – ecosystem function relationships (doi: 10.1038/nature22399).
DOI: 10.6084/m9.figshare.3468386.v1
title: R Markdown Code for manuscript Leaf bacterial diversity mediates plant diversity – ecosystem function relationships

description: This markdown file goes through all the steps to reproduce the analyses in the manuscript entitled Leaf bacterial diversity mediates plant diversity – ecosystem function relationships (doi: 10.1038/nature22399).
DOI: 10.6084/m9.figshare.3468368
title: Wiley Data Sharing Survey

description: Data set from the Wiley Data Sharing survey.<br>
DOI: 10.6084/m9.figshare.3468368.v2
title: Wiley Data Sharing Survey

description: Data set from the Wiley Data Sharing survey.<br>
DOI: 10.6084/m9.figshare.3468368.v1
title: Wiley Data Sharing Survey

description: Data set from the Wiley Data Sharing survey.<br>
DOI: 10.6084/m9.figshare.3468257
title: Supplementary Table 2: Mean survival and mortality

description: Supplementary Table 2: Mean survival and mortality (±SD) for each concentration of the mercury compounds tested.
DOI: 10.6084/m9.figshare.3468257.v1
title: Supplementary Table 2: Mean survival and mortality

description: Supplementary Table 2: Mean survival and mortality (±SD) for each concentration of the mercury compounds tested.
DOI: 10.6084/m9.figshare.3468191
title: Diffuse support for the European Union: spillover effects of the politicization of the European integration process at the domestic level

description: This article investigates the link between attitude formation at the national and the supranational level of the European Union (EU). While the existing studies have provided strong evidence that attitudes towards national institutions fundamentally condition attitudes towards the EU, the mechanisms through which these spillovers occur are not clearly spelled out. Our main contribution is to theorize the complex ways in which the national politicization of the European integration process affects support for the EU by focusing on critical moments in the EU integration process and the electoral fortunes of the political parties doing the cuing. To test our theoretical claims, we employ multilevel models using six rounds of the European Social Survey combined with party-level data from Chapel Hill Expert Survey, and various country-level data. The analyses show that spillover effects are crucially conditioned by the level of politicization of European integration at the national level.
DOI: 10.6084/m9.figshare.3468191.v1
title: Diffuse support for the European Union: spillover effects of the politicization of the European integration process at the domestic level

description: This article investigates the link between attitude formation at the national and the supranational level of the European Union (EU). While the existing studies have provided strong evidence that attitudes towards national institutions fundamentally condition attitudes towards the EU, the mechanisms through which these spillovers occur are not clearly spelled out. Our main contribution is to theorize the complex ways in which the national politicization of the European integration process affects support for the EU by focusing on critical moments in the EU integration process and the electoral fortunes of the political parties doing the cuing. To test our theoretical claims, we employ multilevel models using six rounds of the European Social Survey combined with party-level data from Chapel Hill Expert Survey, and various country-level data. The analyses show that spillover effects are crucially conditioned by the level of politicization of European integration at the national level.
DOI: 10.6084/m9.figshare.3467978
title: Supplementary Material for: Prognostic Value of ADAMTS Proteases and Their Substrates in Epithelial Ovarian Cancer

description: <br><strong><em>Background:</em></strong> ADAMTS are metalloproteases with disintegrin and thrombospondin motifs. They are secreted proteases playing a role in biological processes such as inflammation, angiogenesis, and urogenital development. ADAMTS have specific substrates, such as the proteoglycans (PG) versican, aggrecan, and brevican. Despite data indicating a role of ADAMTS in tumor invasion and metastases, effects played by these molecules in cancer progression are still controversial. In ovarian cancer, the importance of ADAMTS gene mutations was recently described and related to chemotherapy outcome. <b><i>Objective:</i></b> To analyze protein levels of ADAMTS-1, -4, and -5, and TIMP-3 in human ovarian cancer classified as benign, borderline, or malignant. We also assessed the expression of the ADAMTS substrates aggrecan, brevican, and versican in these neoplasms. Correlations between overall survival and protein expression were performed. <b><i>Methods:</i></b> Tumors were classified according to the WHO Classification of Tumors of Female Reproductive Organs. Protein and PG expression was studied by immunohistochemistry. Differences in labeling were analyzed by percent measurements of stained areas. <b><i>Results:</i></b> ADAMTS-1, ADAMTS-5, and its tissue inhibitor TIMP-3 are increased in borderline and malignant tumors compared to benign neoplasms. Aggrecan and versican levels were increased in malignant subtypes compared to benign ovarian cancer. Higher ADAMTS-1, TIMP-3, and versican expression was associated with a shorter overall survival. <b><i>Conclusions:</i></b> Comparison of protease, TIMP-3, and substrate expression showed that in malignant tumors all ADAMTS and TIMP-3 expression levels were significantly raised compared to the substrates studied.
DOI: 10.6084/m9.figshare.3467978.v1
title: Supplementary Material for: Prognostic Value of ADAMTS Proteases and Their Substrates in Epithelial Ovarian Cancer

description: <br><strong><em>Background:</em></strong> ADAMTS are metalloproteases with disintegrin and thrombospondin motifs. They are secreted proteases playing a role in biological processes such as inflammation, angiogenesis, and urogenital development. ADAMTS have specific substrates, such as the proteoglycans (PG) versican, aggrecan, and brevican. Despite data indicating a role of ADAMTS in tumor invasion and metastases, effects played by these molecules in cancer progression are still controversial. In ovarian cancer, the importance of ADAMTS gene mutations was recently described and related to chemotherapy outcome. <b><i>Objective:</i></b> To analyze protein levels of ADAMTS-1, -4, and -5, and TIMP-3 in human ovarian cancer classified as benign, borderline, or malignant. We also assessed the expression of the ADAMTS substrates aggrecan, brevican, and versican in these neoplasms. Correlations between overall survival and protein expression were performed. <b><i>Methods:</i></b> Tumors were classified according to the WHO Classification of Tumors of Female Reproductive Organs. Protein and PG expression was studied by immunohistochemistry. Differences in labeling were analyzed by percent measurements of stained areas. <b><i>Results:</i></b> ADAMTS-1, ADAMTS-5, and its tissue inhibitor TIMP-3 are increased in borderline and malignant tumors compared to benign neoplasms. Aggrecan and versican levels were increased in malignant subtypes compared to benign ovarian cancer. Higher ADAMTS-1, TIMP-3, and versican expression was associated with a shorter overall survival. <b><i>Conclusions:</i></b> Comparison of protease, TIMP-3, and substrate expression showed that in malignant tumors all ADAMTS and TIMP-3 expression levels were significantly raised compared to the substrates studied.
DOI: 10.6084/m9.figshare.3467960
title: 1.csv

description: A sample drosophila larva track.
DOI: 10.6084/m9.figshare.3467960.v1
title: 1.csv

description: A sample drosophila larva track.
DOI: 10.6084/m9.figshare.3467945
title: pedigree.txt

description: Pedigree used for data.txt
DOI: 10.6084/m9.figshare.3467942
title: data.txt

description: Declaration of effects and linear model for time event of maj infection FLOCK !A ID !P BIRTH OP !I LS !m-999 TIMEEVENT !m-999 TEST !A YEAR !I SEASON !I FYS !A MY !m-999 FAT !m-999 PRT !m-999 CAS !m-999 LCT !m-999 SCC !m-999 SCCS !m-999 CORLT !m-999 ESCCL !m-999 PASCL !m-999 PSELT !m-999 STACL !m-999 STHAU !m-999 STRCL !m-999 STPDG !m-999 STPUB !m-999 STPAG !m-999 BACIL !m-999 MAJINF !m-999 MININF !m-999 ALL !m-999 SCS !m-999<br>ped.txt !ALPHA !MAKE !REPEATfulldata_SCS.txt !NODISPLAY !MVINCLUDE !MAXIT 10000 !ASUVSTACL ALL ~ Trait.MY Trait.SCS !r Trait.FYS Trait.ide(ID) Trait.ID 1 2 3 # El último 3 indica que hay que especificar 3 matrices (FYS,ide(ID) y ID)0Trait 0 US !GFUF1 0 1 <br>Trait.FYS 2 0 US !GPUP0.170.01 1.85FYS 0 ID<br>Trait.ide(ID) 2 2 0 US !GPUP0.350.01 0.21ide(ID)<br>Trait.ID 2Trait 0 US !GPUP0.031 0.09ID
DOI: 10.6084/m9.figshare.3467942.v1
title: data.txt

description: Declaration of effects and linear model for time event of maj infection FLOCK !A ID !P BIRTH OP !I LS !m-999 TIMEEVENT !m-999 TEST !A YEAR !I SEASON !I FYS !A MY !m-999 FAT !m-999 PRT !m-999 CAS !m-999 LCT !m-999 SCC !m-999 SCCS !m-999 CORLT !m-999 ESCCL !m-999 PASCL !m-999 PSELT !m-999 STACL !m-999 STHAU !m-999 STRCL !m-999 STPDG !m-999 STPUB !m-999 STPAG !m-999 BACIL !m-999 MAJINF !m-999 MININF !m-999 ALL !m-999 SCS !m-999<br>ped.txt !ALPHA !MAKE !REPEATfulldata_SCS.txt !NODISPLAY !MVINCLUDE !MAXIT 10000 !ASUVSTACL ALL ~ Trait.MY Trait.SCS !r Trait.FYS Trait.ide(ID) Trait.ID 1 2 3 # El último 3 indica que hay que especificar 3 matrices (FYS,ide(ID) y ID)0Trait 0 US !GFUF1 0 1 <br>Trait.FYS 2 0 US !GPUP0.170.01 1.85FYS 0 ID<br>Trait.ide(ID) 2 2 0 US !GPUP0.350.01 0.21ide(ID)<br>Trait.ID 2Trait 0 US !GPUP0.031 0.09ID
DOI: 10.6084/m9.figshare.3467939
title: Supplementary Material for: Endovascular Treatment in Patients with Persistent Internal Carotid Artery Occlusion after Intravenous Tissue Plasminogen Activator: A Clinical Effectiveness Study

description: <br><strong><em>Background:</em></strong> There has been no large-scale trial comparing endovascular treatment (add-on EVT) after intravenous tissue plasminogen activator (IV tPA) and IV tPA alone in acute ischemic stroke (AIS) caused by internal carotid artery occlusion (ICAO). We aimed at investigating the effectiveness and safety of add-on EVT after IV tPA in AIS patients with ICAO. <b><i>Methods:</i></b> Between March 2010 and March 2013, 3,689 consecutive ischemic stroke patients who were hospitalized within 4.5 h of onset were identified using a prospective stroke registry at 11 centers in Korea. Among them, patients with persistent ICAO after receiving IV tPA and whose 3-month modified Rankin Scale (mRS) was available were finally enrolled. A propensity score analysis with inverse-probability of treatment weighting was used to eliminate baseline imbalances between those receiving add-on EVT and IV tPA alone. <b><i>Results:</i></b> Among 264 patients enrolled in this study (mean age 71.4; male 56.4%; median National Institute of Health Stroke Scale score 15), 117 (44.3%) received add-on EVT. The add-on EVT group had a higher frequency of favorable outcome on the mRS ≤2 (35.0 vs. 18.4%; adjusted OR (aOR) 2.79; 95% CI 1.66-4.67) and lower mortality (17.9 vs. 35.4%; aOR 0.24; 95% CI 0.13-0.42) at 3 months, when compared to the IV tPA-alone group. Add-on EVT did not significantly increase the risk of symptomatic hemorrhage (5.1 vs. 4.1%; aOR 1.01; 95% CI 0.37-2.70). The rate of successful recanalization (thrombolysis in cerebral infarction grade ≥2b) in the add-on EVT group was 69.2%. <b><i>Conclusions:</i></b> Compared to an IV tPA alone, add-on EVT can improve clinical outcomes in patients with symptomatic ICAO within 4.5 h of onset without a significant increase of symptomatic hemorrhage.
DOI: 10.6084/m9.figshare.3467936
title: Data for paper: "Inter-regional hybrids of native and invasive Centaurea solstitialis display intermediate competitive ability" Published in Ecography (2016) with DOI: 10.1111/ecog.02653

description: Root and shoot biomass of Bromus hordeaceus and Centaurea solstitialis plants from California, Spain, or inter-regional hybrids of both, grown in control pots or in competition with each other. Relative Interaction Indexes were also calculated in order to analyze competitive effects and to plot figures.<br>
DOI: 10.6084/m9.figshare.3467936.v1
title: Data from: "Inter-regional hybrids of native and invasive Centaurea solstitialis display intermediate competitive ability" published in Ecography, 2016

description: Root and shoot biomass of Bromus hordeaceus and Centaurea solstitialis plants from California, Spain, or inter-regional hybrids of both, grown in control pots or in competition with each other. Relative Interaction Indexes were also calculated in order to analyze competitive effects and to plot figures.<br>
DOI: 10.6084/m9.figshare.3467933
title: Complete chloroplast genomes of <i>Saccharum spontaneum</i>, <i>Saccharum officinarum</i> and <i>Miscanthus floridulus</i> (Panicoideae: Andropogoneae) reveal the plastid view on sugarcane origins

description: Sugarcane (<i>Saccharum</i> hybrid cultivar) ranks among the world's top 10 food crops and annually provides 60–70% of the sugar produced worldwide. Despite its economic importance there has been no large-scale systematics study of genus <i>Saccharum</i> and the existing model of sugarcane origins has remained largely unchallenged for almost 50 years. For the first time, we have assembled the complete plastid genomes of <i>Miscanthus floridulus</i> (first report for this genus), <i>Saccharum spontaneum</i> and <i>Saccharum officinarum</i> allowing us to elucidate the phylogenetic origins of <i>Saccharum s.s</i>. species. We demonstrate that <i>Saccharum s.s.</i> is divided into four species, with <i>S. spontaneum</i> diverging from the remainder of the genus about 1.5 million years ago and <i>S. robustum</i> diverging 750,000 years ago. Two separate lineages, one leading to <i>S. officinarum</i> and the other leading to modern hybrid cultivars diverged from <i>S. robustum</i> 640,000 years ago. These findings overturn all previous hypotheses on sugarcane origins, demonstrating that sugarcane's antecedents could not have arisen by human action. All modern cultivars share a common Polynesian origin, whereas Old World canes, <i>S. barberi</i> and <i>S. sinense</i>, cluster as a distinct <i>S. officinarum</i> lineage. This makes modern cultivars a distinct species of genus <i>Saccharum</i>, and we formally propose the name <i>Saccharum cultum</i> for the ancestor of all lineages currently classified as <i>Saccharum</i> hybrid cultivars.
DOI: 10.6084/m9.figshare.3467933.v1
title: Complete chloroplast genomes of <i>Saccharum spontaneum</i>, <i>Saccharum officinarum</i> and <i>Miscanthus floridulus</i> (Panicoideae: Andropogoneae) reveal the plastid view on sugarcane origins

description: Sugarcane (<i>Saccharum</i> hybrid cultivar) ranks among the world's top 10 food crops and annually provides 60–70% of the sugar produced worldwide. Despite its economic importance there has been no large-scale systematics study of genus <i>Saccharum</i> and the existing model of sugarcane origins has remained largely unchallenged for almost 50 years. For the first time, we have assembled the complete plastid genomes of <i>Miscanthus floridulus</i> (first report for this genus), <i>Saccharum spontaneum</i> and <i>Saccharum officinarum</i> allowing us to elucidate the phylogenetic origins of <i>Saccharum s.s</i>. species. We demonstrate that <i>Saccharum s.s.</i> is divided into four species, with <i>S. spontaneum</i> diverging from the remainder of the genus about 1.5 million years ago and <i>S. robustum</i> diverging 750,000 years ago. Two separate lineages, one leading to <i>S. officinarum</i> and the other leading to modern hybrid cultivars diverged from <i>S. robustum</i> 640,000 years ago. These findings overturn all previous hypotheses on sugarcane origins, demonstrating that sugarcane's antecedents could not have arisen by human action. All modern cultivars share a common Polynesian origin, whereas Old World canes, <i>S. barberi</i> and <i>S. sinense</i>, cluster as a distinct <i>S. officinarum</i> lineage. This makes modern cultivars a distinct species of genus <i>Saccharum</i>, and we formally propose the name <i>Saccharum cultum</i> for the ancestor of all lineages currently classified as <i>Saccharum</i> hybrid cultivars.