cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8138147.v1
title: Does butein affect adipogenesis?

description: Butein is a plant flavonoid chalcone, with presumed anti-adipogenic properties. It was reported to impair preadipocyte differentiation, limit adipose tissue (AT) development and enhance white AT browning in rodents. In this study, we investigated the hypothesis that these effects of butein may occur via reduction of ADAMTS5 (A Disintegrin And Metalloproteinase with ThromboSpondin motifs 5) expression. Murine 3T3-L1 or 3T3-F442A preadipocytes were differentiated into mature adipocytes in the presence of butein or vehicle. At regular time intervals RNA was collected for gene expression studies. Male hemizygous mice for Tg(Ucp1-luc2,-tdTomato)1Kajim (ThermoMouse) were exposed to butein or vehicle, after which ATs were analyzed for <i>Adamts5</i> and uncoupling protein-1 (<i>Ucp-1</i>) mRNA level changes. During preadipocyte differentiation, butein (25 – 50 mM) did not affect <i>Adamts5</i> or <i>Ucp-1</i> expression. Oil Red O analysis and monitoring of differentiation markers failed to demonstrate effects of butein on the differentiation extent. Furthermore, butein administration to the ThermoMouse (10 or 20 mg/kg, 4 days) or to the C57BL6/Rj mice (20 mg/kg, 4 weeks) did not enhance <i>Adamts5</i> or <i>Ucp-1</i> expression. Thus, we could not demonstrate marked effects of butein on the preadipocyte differentiation extent or AT development and browning, nor on <i>Adamts5</i> or <i>Ucp-1</i> gene expression during these processes.
DOI: 10.6084/m9.figshare.8138129
title: Inselbergs persist as islands of diversity in a heavily grazed rangeland mosaic at the nexus of three arid biomes

description: Inselbergs are regarded as ‘islands of diversity’ due to the high number of plant species present and level of endemism. They also act as natural sources of fodder for livestock and thus risk becoming homogenised in a heavily grazed rangeland. The aim of this study was to compare plant diversity on inselbergs and matrices in heavily grazed sections of three arid biomes of South Africa’s west. The inselbergs are scattered in a matrix of rangeland vegetation in the Desert, Nama-Karoo and Succulent Karoo biomes where pastoral herding is the main land use. Plant composition, cover and growth forms were quantified in plots and along transects in 21 inselberg and matrix sites. Inselbergs had more diverse plant and growth forms and greater cover than adjacent matrices. Defoliated plants on inselbergs are able to recover due to more mesic conditions and because inselbergs are largely grazed during drier periods, species are able to flower and set seed during winter. Inselbergs are also less accessible to livestock due to their unique geomorphology. Therefore, inselbergs are able to persist as islands of diversity and warrant inclusion into conservation and rangeland farming management plans since climate change will result in biome boundary shifts.
DOI: 10.6084/m9.figshare.8138129.v2
title: Inselbergs persist as islands of diversity in a heavily grazed rangeland mosaic at the nexus of three arid biomes

description: Inselbergs are regarded as ‘islands of diversity’ due to the high number of plant species present and level of endemism. They also act as natural sources of fodder for livestock and thus risk becoming homogenised in a heavily grazed rangeland. The aim of this study was to compare plant diversity on inselbergs and matrices in heavily grazed sections of three arid biomes of South Africa’s west. The inselbergs are scattered in a matrix of rangeland vegetation in the Desert, Nama-Karoo and Succulent Karoo biomes where pastoral herding is the main land use. Plant composition, cover and growth forms were quantified in plots and along transects in 21 inselberg and matrix sites. Inselbergs had more diverse plant and growth forms and greater cover than adjacent matrices. Defoliated plants on inselbergs are able to recover due to more mesic conditions and because inselbergs are largely grazed during drier periods, species are able to flower and set seed during winter. Inselbergs are also less accessible to livestock due to their unique geomorphology. Therefore, inselbergs are able to persist as islands of diversity and warrant inclusion into conservation and rangeland farming management plans since climate change will result in biome boundary shifts.
DOI: 10.6084/m9.figshare.8138129.v1
title: Inselbergs persist as islands of diversity in a heavily grazed rangeland mosaic at the nexus of three arid biomes

description: Inselbergs are regarded as ‘islands of diversity’ due to the high number of plant species present and level of endemism. They also act as natural sources of fodder for livestock and thus risk becoming homogenised in a heavily grazed rangeland. The aim of this study was to compare plant diversity on inselbergs and matrices in heavily grazed sections of three arid biomes of South Africa’s west. The inselbergs are scattered in a matrix of rangeland vegetation in the Desert, Nama-Karoo and Succulent Karoo biomes where pastoral herding is the main land use. Plant composition, cover and growth forms were quantified in plots and along transects in 21 inselberg and matrix sites. Inselbergs had more diverse plant and growth forms and greater cover than adjacent matrices. Defoliated plants on inselbergs are able to recover due to more mesic conditions and because inselbergs are largely grazed during drier periods, species are able to flower and set seed during winter. Inselbergs are also less accessible to livestock due to their unique geomorphology. Therefore, inselbergs are able to persist as islands of diversity and warrant inclusion into conservation and rangeland farming management plans since climate change will result in biome boundary shifts.
DOI: 10.6084/m9.figshare.8138114
title: Age of respondents.xlsx

description: Medic et al. Declining seroprevalence of hepatitis A in Vojvodina, Serbia. Age of respondents<br>
DOI: 10.6084/m9.figshare.8138114.v1
title: Age of respondents.xlsx

description: Medic et al. Declining seroprevalence of hepatitis A in Vojvodina, Serbia. Age of respondents<br>
DOI: 10.6084/m9.figshare.8138105
title: The DECOCI project

description: the DECOCI raw dataset<br>
DOI: 10.6084/m9.figshare.8138105.v1
title: The DECOCI project

description: the DECOCI raw dataset<br>
DOI: 10.6084/m9.figshare.8138045
title: Dataset containing aggregate data from studies investigating treatments for pain in osteoarthritis

description: Two versions of a dataset of aggregate study-level results collected during a systematic review by Martin Boucher. Data have been cleaned and prepared by Hugo Pedder.<br>OsteoarthritisData.csv contains data from 23 RCTs that have conducted their analysis using Last Observation Carried Forward (LOCF) to deal with dropouts, comparing 29 treatments for pain relief in osteoarthritis. SDs are available at baseline for most studies but have been imputed for 269 out of 345 observations.<br>AugmentedInconsistencyData.csv contains the same data but with additional studies, as it does not restrict study analyses to only LOCF (30 RCTs in total comparing 29 treatments).
DOI: 10.6084/m9.figshare.8138033
title: Bivalency in <i>Drosophila</i> embryos is associated with strong inducibility of Polycomb target genes

description: Polycomb group (PcG) and Trithorax group (TrxG) proteins orchestrate development of a multicellular organism by faithfully maintaining cell fate decisions made early in embryogenesis. An important chromatin mark connected to PcG/TrxG regulation is bivalent domains, the simultaneous presence of H3K27me3 and H3K4me3 on a given locus, originally identified in mammalian embryonic stem cells but considered to be absent in invertebrates. Here, we provide evidence for the existence of bivalency in fly embryos. Using a recently described PcG reporter fly line, we observed a strong reporter inducibility in the embryo and its sharp decrease in larval and adult stages. Analysis of the chromatin landscape of the reporter revealed a strong signal for the repressive PcG mark, H3K27me3, in all three developmental stages and, surprisingly, a strong signal for a transcriptionally activating H3K4me3 mark in the embryo. Using re-chromatin immunoprecipitation experiments, bivalent domains were also uncovered at endogenous PcG targets like the Hox genes.
DOI: 10.6084/m9.figshare.8138033.v3
title: Bivalency in <i>Drosophila</i> embryos is associated with strong inducibility of Polycomb target genes

description: Polycomb group (PcG) and Trithorax group (TrxG) proteins orchestrate development of a multicellular organism by faithfully maintaining cell fate decisions made early in embryogenesis. An important chromatin mark connected to PcG/TrxG regulation is bivalent domains, the simultaneous presence of H3K27me3 and H3K4me3 on a given locus, originally identified in mammalian embryonic stem cells but considered to be absent in invertebrates. Here, we provide evidence for the existence of bivalency in fly embryos. Using a recently described PcG reporter fly line, we observed a strong reporter inducibility in the embryo and its sharp decrease in larval and adult stages. Analysis of the chromatin landscape of the reporter revealed a strong signal for the repressive PcG mark, H3K27me3, in all three developmental stages and, surprisingly, a strong signal for a transcriptionally activating H3K4me3 mark in the embryo. Using re-chromatin immunoprecipitation experiments, bivalent domains were also uncovered at endogenous PcG targets like the Hox genes.
DOI: 10.6084/m9.figshare.8138018
title: qPCRrawdata.zip

description: The data set includes files related to qPCR runs (one for each file), whose results are presented in the manuscript "DNA extraction and amplicon production strategies deeply influence the outcome of gut mycobiome studies” (<i>Scientific Reports</i><b> volume 9</b>, Article number: 9328 (2019)). Details of the methods can be found in the manuscript itself. In the folder there are 14 files, all related to figure 1 of the manuscript. The name of the files indicates the species or sample type used as template in that run. If the calibration curve was run on a separate experiment, the relative file is also present.<br><br>Figure 1A and C:<br>AfumigatusCalCurve+PSP.txt<br>AfumigatusQSK.txt<br>CalbicansCalCurve.txt <br>CalbicansPSP.txtCalbicansQSK.txtMfurfurCalCurve+PSP.txt<br>Pcrysogenum_CalCurve+PSP.txt<br>CneoformansCalCurvePSP.txt<br>Scerevisiae_CalCurive+PSP.txt<br>CtropicalisCalCurve+PSP.txt<br><br>Figure 1D:<br>SpikedStoolCalCurve+data.txt<br><br>Figure 1E:<br>Donors1.txt<br>Donors2.txt<br>DonorsCalCurve.txt<br><br>
DOI: 10.6084/m9.figshare.8138018.v2
title: qPCRrawdata.zip

description: The data set includes files related to qPCR runs (one for each file), whose results are presented in the manuscript "DNA extraction and amplicon production strategies deeply influence the outcome of gut mycobiome studies” (<i>Scientific Reports</i><b> volume 9</b>, Article number: 9328 (2019)). Details of the methods can be found in the manuscript itself. In the folder there are 14 files, all related to figure 1 of the manuscript. The name of the files indicates the species or sample type used as template in that run. If the calibration curve was run on a separate experiment, the relative file is also present.<br><br>Figure 1A and C:<br>AfumigatusCalCurve+PSP.txt<br>AfumigatusQSK.txt<br>CalbicansCalCurve.txt <br>CalbicansPSP.txtCalbicansQSK.txtMfurfurCalCurve+PSP.txt<br>Pcrysogenum_CalCurve+PSP.txt<br>CneoformansCalCurvePSP.txt<br>Scerevisiae_CalCurive+PSP.txt<br>CtropicalisCalCurve+PSP.txt<br><br>Figure 1D:<br>SpikedStoolCalCurve+data.txt<br><br>Figure 1E:<br>Donors1.txt<br>Donors2.txt<br>DonorsCalCurve.txt<br><br>
DOI: 10.6084/m9.figshare.8138018.v1
title: qPCRrawdata.zip

description: The data set includes files related to qPCR runs (one for each file), whose results are presented in the manuscript "DNA extraction and amplicon production strategies deeply influence the outcome of gut mycobiome studies”. Details of the methods can be found in the manuscript itself. In the folder there are 14 files, all related to figure 1 of the manuscript. The name of the files indicates the species or sample type used as template in that run. If the calibration curve was run on a separate experiment, the relative file is also present.<br><br>Figure 1A and C:<br>AfumigatusCalCurve+PSP.txt<br>AfumigatusQSK.txt<br>CalbicansCalCurve.txt <br>CalbicansPSP.txtCalbicansQSK.txtMfurfurCalCurve+PSP.txt<br>Pcrysogenum_CalCurve+PSP.txt<br>CneoformansCalCurvePSP.txt<br>Scerevisiae_CalCurive+PSP.txt<br>CtropicalisCalCurve+PSP.txt<br><br>Figure 1D:<br>SpikedStoolCalCurve+data.txt<br><br>Figure 1E:<br>Donors1.txt<br>Donors2.txt<br>DonorsCalCurve.txt<br><br>
DOI: 10.6084/m9.figshare.12493685.v1
title: An economic evaluation of eribulin for advanced breast cancer treatment based on the Southeast Netherlands advanced breast cancer registry

description: <b>Background:</b> In 2013, eribulin was reimbursed under a coverage with evidence development (CED) as third or later chemotherapy line for advanced breast cancer (ABC) patients in the Netherlands because of uncertain cost effectiveness. In 2016, the final decision of reimbursing eribulin was taken without considering the evidence collected during CED research. We analysed the cost effectiveness of eribulin versus non-eribulin chemotherapy, using real-world data. <b>Methods:</b> A three health states (progression-free, progressed disease, dead) partitioned survival model was developed. The SOuth East Netherlands Advanced BREast Cancer (SONABRE) registry informed the effectiveness and costs inputs. Health state utility values were obtained from the literature. Incremental cost-effectiveness ratio (ICER) between the eribulin and matched non-eribulin chemotherapy was estimated. Deterministic and probabilistic sensitivity analyses and scenario analyses were performed. The financial risk (i.e., the expected value of perfect information (EVPI) plus the expected monetary loss (eML) associated with reimbursing eribulin) and budget impact associated with reimbursing eribulin were calculated. <b>Results:</b> Eribulin led to higher health benefits (0.07 quality-adjusted life year (QALY)) and costs (€15,321) compared with non-eribulin chemotherapy. This resulted in an ICER of €220,608. At a €80,000 per QALY threshold, the risk of reimbursing eribulin was €9,791 per patient (EVPI €13, eML €9,778). Scaled up to the Dutch population, the estimated annual budget impact was €1.9 million and the annual risk of reimbursing eribulin was €2.7 million. <b>Conclusion:</b> From a Dutch societal perspective, eribulin is not cost effective when considering its list price as third and later chemotherapy line for ABC patients.
DOI: 10.6084/m9.figshare.8137949
title: Gene prediction

description: Genome annotation information
DOI: 10.6084/m9.figshare.8137949.v1
title: Gene prediction

description: Genome annotation information
DOI: 10.6084/m9.figshare.8137940
title: Repeat regions

description: Genome repeat annotation
DOI: 10.6084/m9.figshare.8137940.v1
title: Repeat regions

description: Genome repeat annotation
DOI: 10.6084/m9.figshare.8137934
title: Genome Assembly

description: Genome Assembly Sequence
DOI: 10.6084/m9.figshare.8137883
title: S5: Sample location. Detrital zircon U–Pb insights into the timing and provenance of the South Pyrenean Jaca Basin

description: Supplementary material 5: Sample location for the analyzed samples.
DOI: 10.6084/m9.figshare.8137883.v1
title: S5: Sample location. Detrital zircon U–Pb insights into the timing and provenance of the South Pyrenean Jaca Basin

description: Supplementary material 5: Sample location for the analyzed samples.
DOI: 10.6084/m9.figshare.8137880
title: S4: zHe data. Detrital zircon U–Pb insights into the timing and provenance of the South Pyrenean Jaca Basin

description: Supplementary material 4: Reduced detrital zircon double dating (U–Th)/ (He–Pb) data for Cenozoic aged zircons.
DOI: 10.6084/m9.figshare.8137880.v1
title: S4: zHe data. Detrital zircon U–Pb insights into the timing and provenance of the South Pyrenean Jaca Basin

description: Supplementary material 4: Reduced detrital zircon double dating (U–Th)/ (He–Pb) data for Cenozoic aged zircons.
DOI: 10.6084/m9.figshare.8137877
title: S2: U–Pb data. Detrital zircon U–Pb insights into the timing and provenance of the South Pyrenean Jaca Basin

description: Supplementary material 2: Reduced detrital zircon U–Pb dataset for all analysis.
DOI: 10.6084/m9.figshare.8137877.v1
title: S2: U–Pb data. Detrital zircon U–Pb insights into the timing and provenance of the South Pyrenean Jaca Basin

description: Supplementary material 2: Reduced detrital zircon U–Pb dataset for all analysis.
DOI: 10.6084/m9.figshare.8137871
title: Instances of the Shortest Common Supersequence Problem

description: Shortest Common Supersequence Problem: https://en.wikipedia.org/wiki/Shortest_common_supersequence_problem<br>Each problem instance comprises <i>n</i> strings (each of them of a possibly different length) taken from an alphabet with <i>m</i> symbols. <br><br>The collection includes both randomly generated instances and instances obtained from biological sequences.<br>
DOI: 10.6084/m9.figshare.8137865
title: BridgeDb SNP collections Ensembl version 96

description: Gene-to-variant BridgeDb mapping database for Ensembl version 96Status: incomplete (PTV_Missense and Missense missing)<br>
DOI: 10.6084/m9.figshare.8137865.v1
title: BridgeDb SNP collections Ensembl version 96

description: Gene-to-variant BridgeDb mapping database for Ensembl version 96
DOI: 10.6084/m9.figshare.8137865.v3
title: BridgeDb SNP collections Ensembl version 96

description: Gene-to-variant BridgeDb mapping database for Ensembl version 96Status: incomplete (PTV_Missense and Missense missing)<br>
DOI: 10.6084/m9.figshare.8137865.v2
title: BridgeDb SNP collections Ensembl version 96

description: Gene-to-variant BridgeDb mapping database for Ensembl version 96
DOI: 10.6084/m9.figshare.8137844
title: Supplementary Material for: Understanding and Classification of Ocular Lymphomas

description: <b><i>Background:</i></b> Lymphomas that involve the tissues of the ocular adnexae and the eye itself can be confusing for both the new and seasoned learner alike. In this review, I present a simple way of classifying these disorders that will help to facilitate understanding of these myriad entities. <b><i>Summary:</i></b> Classifications of lymphomas have changed significantly over the last 40 years, but in recent decades, the basic structure of the WHO classification has remained the same, facilitating understanding. <b><i>Key Messages:</i></b> The ocular lymphomas can be divided into those that are external to the eye (ocular adnexae) and those that are internal (vitreoretinal and uveal). At each of these sites specific subtypes of lymphoma are common. Focusing on these common subtypes can aid the learner to create a scaffold that enables current understanding and upon which they can build for the future.
DOI: 10.6084/m9.figshare.8137844.v1
title: Supplementary Material for: Understanding and Classification of Ocular Lymphomas

description: <b><i>Background:</i></b> Lymphomas that involve the tissues of the ocular adnexae and the eye itself can be confusing for both the new and seasoned learner alike. In this review, I present a simple way of classifying these disorders that will help to facilitate understanding of these myriad entities. <b><i>Summary:</i></b> Classifications of lymphomas have changed significantly over the last 40 years, but in recent decades, the basic structure of the WHO classification has remained the same, facilitating understanding. <b><i>Key Messages:</i></b> The ocular lymphomas can be divided into those that are external to the eye (ocular adnexae) and those that are internal (vitreoretinal and uveal). At each of these sites specific subtypes of lymphoma are common. Focusing on these common subtypes can aid the learner to create a scaffold that enables current understanding and upon which they can build for the future.
DOI: 10.6084/m9.figshare.8137805
title: Variation in juvenile stages and success of male acquisition in Danish and French populations of the parasitic barnacle <i>Sacculina carcini</i> (Cirripedia: Rhizocephala) parasitizing the shore crab <i>Carcinus maenas</i>

description: Population and developmental characteristics of the rhizocephalan parasite <i>Sacculina carcini</i> were studied in the Limfjord, Denmark and at Roscoff, France. The frequency of juvenile externae in the Limfjord was higher during summer (69.8% of all externae) than during winter (43%). At Roscoff, 62.6% of externae were juvenile in May-June, but only 8.4% in September. The percentage of juveniles with settled males in the Limfjord was higher in summer (20.7% of all juveniles) compared to winter (6.7%). Juveniles at Roscoff in summer had less success in male acquisition (18.0%). The mean number of settled male cyprids per juvenile externa was 0.56 in summer and 0.12 during winter in the Limfjord, but only 0.27 in the summer at Roscoff. Laboratory kept virgin externae invaded by male cyprids ceased to attract additional males within 5–6 days after the first male settlement and then grew into adults within 3 weeks. Externae without males, kept in isolation, did not grow or show any other signs of maturation. Our results confirm and extend previous data on the role of males and their effect on externa development in <i>S. carcini</i>, and show that the success of male acquisition is susceptible to both seasonal and regional variation.
DOI: 10.6084/m9.figshare.8137805.v1
title: Variation in juvenile stages and success of male acquisition in Danish and French populations of the parasitic barnacle <i>Sacculina carcini</i> (Cirripedia: Rhizocephala) parasitizing the shore crab <i>Carcinus maenas</i>

description: Population and developmental characteristics of the rhizocephalan parasite <i>Sacculina carcini</i> were studied in the Limfjord, Denmark and at Roscoff, France. The frequency of juvenile externae in the Limfjord was higher during summer (69.8% of all externae) than during winter (43%). At Roscoff, 62.6% of externae were juvenile in May-June, but only 8.4% in September. The percentage of juveniles with settled males in the Limfjord was higher in summer (20.7% of all juveniles) compared to winter (6.7%). Juveniles at Roscoff in summer had less success in male acquisition (18.0%). The mean number of settled male cyprids per juvenile externa was 0.56 in summer and 0.12 during winter in the Limfjord, but only 0.27 in the summer at Roscoff. Laboratory kept virgin externae invaded by male cyprids ceased to attract additional males within 5–6 days after the first male settlement and then grew into adults within 3 weeks. Externae without males, kept in isolation, did not grow or show any other signs of maturation. Our results confirm and extend previous data on the role of males and their effect on externa development in <i>S. carcini</i>, and show that the success of male acquisition is susceptible to both seasonal and regional variation.
DOI: 10.6084/m9.figshare.8137802
title: I haven’t a clue! Attention and memory-based expectations facilitate perceptual experience of ambiguous images

description: Data, Stimuli and Experiment Code
DOI: 10.6084/m9.figshare.8137802.v2
title: I haven’t a clue! Semantic information facilitates detection of objects in ambiguous images

description: Data, Stimuli and Experiment Code
DOI: 10.6084/m9.figshare.8137748.v1
title: readme_figshare_gmst.txt

description: Description of the content of this collection<br>
DOI: 10.6084/m9.figshare.8137748.v2
title: readme_figshare_gmst.txt

description: Description of the content of this collection<br>
DOI: 10.6084/m9.figshare.8137748.v3
title: readme_figshare_gmst.txt

description: Description of the content of this collection<br>
DOI: 10.6084/m9.figshare.8137739
title: Data

description: Manual and automated fiber counts from from wildtype and SDC3KO tissue sections.<br>
DOI: 10.6084/m9.figshare.8137739.v1
title: Data

description: Manual and automated fiber counts from from wildtype and SDC3KO tissue sections.<br>