cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3806235
title: Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods

description: RNA-binding protein with multiple splicing (RBPMS) is critical for axon guidance, smooth muscle plasticity, and regulation of cancer cell proliferation and migration. Recently, different states of the RNA-recognition motif (RRM) of RBPMS, one in its free form and another in complex with CAC-containing RNA, were determined by X-ray crystallography. In this article, the free RRM domain, its wild type complex and 2 mutant complex systems are studied by molecular dynamics (MD) simulations. Through comparison of free RRM domain and complex systems, it's found that the RNA binding facilitates stabilizing the RNA-binding interface of RRM domain, especially the C-terminal loop. Although both R38Q and T103A/K104A mutations reduce the binding affinity of RRM domain and RNA, the underlining mechanisms are different. Principal component analysis (PCA) and Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) methods were used to explore the dynamical and recognition mechanisms of RRM domain and RNA. R38Q mutation is positioned on the homodimerization interface and mainly induces the large fluctuations of RRM domains. This mutation does not directly act on the RNA-binding interface, but some interfacial hydrogen bonds are weakened. In contrast, T103A/K104A mutations are located on the RNA-binding interface of RRM domain. These mutations obviously break most of high occupancy hydrogen bonds in the RNA-binding interface. Meanwhile, the key interfacial residues lose their favorable energy contributions upon RNA binding. The ranking of calculated binding energies in 3 complex systems is well consistent with that of experimental binding affinities. These results will be helpful in understanding the RNA recognition mechanisms of RRM domain.
DOI: 10.6084/m9.figshare.3806235.v1
title: Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods

description: RNA-binding protein with multiple splicing (RBPMS) is critical for axon guidance, smooth muscle plasticity, and regulation of cancer cell proliferation and migration. Recently, different states of the RNA-recognition motif (RRM) of RBPMS, one in its free form and another in complex with CAC-containing RNA, were determined by X-ray crystallography. In this article, the free RRM domain, its wild type complex and 2 mutant complex systems are studied by molecular dynamics (MD) simulations. Through comparison of free RRM domain and complex systems, it's found that the RNA binding facilitates stabilizing the RNA-binding interface of RRM domain, especially the C-terminal loop. Although both R38Q and T103A/K104A mutations reduce the binding affinity of RRM domain and RNA, the underlining mechanisms are different. Principal component analysis (PCA) and Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) methods were used to explore the dynamical and recognition mechanisms of RRM domain and RNA. R38Q mutation is positioned on the homodimerization interface and mainly induces the large fluctuations of RRM domains. This mutation does not directly act on the RNA-binding interface, but some interfacial hydrogen bonds are weakened. In contrast, T103A/K104A mutations are located on the RNA-binding interface of RRM domain. These mutations obviously break most of high occupancy hydrogen bonds in the RNA-binding interface. Meanwhile, the key interfacial residues lose their favorable energy contributions upon RNA binding. The ranking of calculated binding energies in 3 complex systems is well consistent with that of experimental binding affinities. These results will be helpful in understanding the RNA recognition mechanisms of RRM domain.
DOI: 10.6084/m9.figshare.3804363
title: Cadherin-6 is a putative tumor suppressor and target of epigenetically dysregulated miR-429 in cholangiocarcinoma

description: Cholangiocarcinoma (CC) is a rare malignancy of the extrahepatic or intrahepatic biliary tract with an outstanding poor prognosis. Non-surgical therapeutic regimens result in minimally improved survival of CC patients. Global genomic analyses identified a few recurrently mutated genes, some of them in genes involved in epigenetic patterning. In a previous study, we demonstrated global DNA methylation changes in CC, indicating major contribution of epigenetic alterations to cholangiocarcinogenesis. Here, we aimed at the identification and characterization of CC-related, differentially methylated regions (DMRs) in potential microRNA promoters and of genes targeted by identified microRNAs. Twenty-seven hypermethylated and 13 hypomethylated potential promoter regions of microRNAs, known to be associated with cancer-related pathways like Wnt, ErbB, and PI3K-Akt signaling, were identified. Selected DMRs were confirmed in 2 independent patient cohorts. Inverse correlation between promoter methylation and expression suggested miR-129-2 and members of the miR-200 family (miR-200a, miR-200b, and miR-429) as novel tumor suppressors and oncomiRs, respectively, in CC. Tumor suppressor genes <i>deleted in liver cancer 1</i> (<i>DLC1</i>), <i>F-box/WD-repeat-containing protein 7</i> (<i>FBXW7</i>), and <i>cadherin-6</i> (<i>CDH6</i>) were identified as presumed targets in CC. Tissue microarrays of a representative and well-characterized cohort of biliary tract cancers (n=212) displayed stepwise downregulation of CDH6 and association with poor patient outcome. Ectopic expression of <i>CDH6</i> on the other hand, delayed growth in the CC cell lines EGI-1 and TFK-1, together suggesting a tumor suppressive function of <i>CDH6</i>. Our work represents a valuable repository for the study of epigenetically altered miRNAs in cholangiocarcinogenesis and novel putative, CC-related tumor suppressive miRNAs and oncomiRs.
DOI: 10.6084/m9.figshare.3804363.v1
title: Cadherin-6 is a putative tumor suppressor and target of epigenetically dysregulated miR-429 in cholangiocarcinoma

description: Cholangiocarcinoma (CC) is a rare malignancy of the extrahepatic or intrahepatic biliary tract with an outstanding poor prognosis. Non-surgical therapeutic regimens result in minimally improved survival of CC patients. Global genomic analyses identified a few recurrently mutated genes, some of them in genes involved in epigenetic patterning. In a previous study, we demonstrated global DNA methylation changes in CC, indicating major contribution of epigenetic alterations to cholangiocarcinogenesis. Here, we aimed at the identification and characterization of CC-related, differentially methylated regions (DMRs) in potential microRNA promoters and of genes targeted by identified microRNAs. Twenty-seven hypermethylated and 13 hypomethylated potential promoter regions of microRNAs, known to be associated with cancer-related pathways like Wnt, ErbB, and PI3K-Akt signaling, were identified. Selected DMRs were confirmed in 2 independent patient cohorts. Inverse correlation between promoter methylation and expression suggested miR-129-2 and members of the miR-200 family (miR-200a, miR-200b, and miR-429) as novel tumor suppressors and oncomiRs, respectively, in CC. Tumor suppressor genes <i>deleted in liver cancer 1</i> (<i>DLC1</i>), <i>F-box/WD-repeat-containing protein 7</i> (<i>FBXW7</i>), and <i>cadherin-6</i> (<i>CDH6</i>) were identified as presumed targets in CC. Tissue microarrays of a representative and well-characterized cohort of biliary tract cancers (n=212) displayed stepwise downregulation of CDH6 and association with poor patient outcome. Ectopic expression of <i>CDH6</i> on the other hand, delayed growth in the CC cell lines EGI-1 and TFK-1, together suggesting a tumor suppressive function of <i>CDH6</i>. Our work represents a valuable repository for the study of epigenetically altered miRNAs in cholangiocarcinogenesis and novel putative, CC-related tumor suppressive miRNAs and oncomiRs.
DOI: 10.6084/m9.figshare.3804360
title: Non-pollinator fig wasp impact on the reproductive success of an invasive fig tree: why so little?

description: Classical biological control agents fail to achieve an impact on their hosts for a variety of reasons and an understanding of why they fail can help shape decisions on subsequent releases. Ornamental <i>Ficus microcarpa</i> is a widely planted avenue fig tree that is invasive in countries where its pollinator (<i>Eupristina verticillata</i>) is also introduced. This tree also supports more than 20 species of non-pollinating fig wasps (NPFW) that feed in the figs and have the potential to reduce the plant’s reproduction. <i>Odontofroggatia galili</i>, one of the most widely introduced NPFW, has larvae that develop in galled ovules that might otherwise develop into seeds or support pollinator larvae. We examined the distribution and relative abundance of the pollinator and <i>O. galili</i> on <i>F. microcarpa</i> in China, towards the northern limit of the tree’s natural range, and in Italy where the two species have been introduced. Where they co-existed, we also recorded the impact of varying densities of <i>O. galili</i> on <i>F. microcarpa</i> seed and pollinator production. <i>O. galili</i> and <i>E. verticillata</i> displayed contrasting habitat preferences in China, with <i>O. galili</i> almost absent from warmer sites. <i>O. galili</i> abundance and sex ratios varied between the natural and introduced ranges. Figs with more <i>O. galili</i> contained fewer seeds and pollinator offspring, but reproduction was rarely inhibited totally. Additional species with a greater impact in the figs they occupy are needed if biocontrol of <i>F. microcarpa</i> is to be effective.
DOI: 10.6084/m9.figshare.3804360.v1
title: Non-pollinator fig wasp impact on the reproductive success of an invasive fig tree: why so little?

description: Classical biological control agents fail to achieve an impact on their hosts for a variety of reasons and an understanding of why they fail can help shape decisions on subsequent releases. Ornamental <i>Ficus microcarpa</i> is a widely planted avenue fig tree that is invasive in countries where its pollinator (<i>Eupristina verticillata</i>) is also introduced. This tree also supports more than 20 species of non-pollinating fig wasps (NPFW) that feed in the figs and have the potential to reduce the plant’s reproduction. <i>Odontofroggatia galili</i>, one of the most widely introduced NPFW, has larvae that develop in galled ovules that might otherwise develop into seeds or support pollinator larvae. We examined the distribution and relative abundance of the pollinator and <i>O. galili</i> on <i>F. microcarpa</i> in China, towards the northern limit of the tree’s natural range, and in Italy where the two species have been introduced. Where they co-existed, we also recorded the impact of varying densities of <i>O. galili</i> on <i>F. microcarpa</i> seed and pollinator production. <i>O. galili</i> and <i>E. verticillata</i> displayed contrasting habitat preferences in China, with <i>O. galili</i> almost absent from warmer sites. <i>O. galili</i> abundance and sex ratios varied between the natural and introduced ranges. Figs with more <i>O. galili</i> contained fewer seeds and pollinator offspring, but reproduction was rarely inhibited totally. Additional species with a greater impact in the figs they occupy are needed if biocontrol of <i>F. microcarpa</i> is to be effective.
DOI: 10.6084/m9.figshare.3804357
title: Data imputation: an application on wind speed data for Entebbe International Airport

description: The windspeed data are daily aggregated values for wind speed data for Entebbe International Airport, located at Entebbe, Uganda. This data has undergone multivariate imputations given that the initial dataset for the period 1995 through 2008 had over 10% missing completely at random (MCAR).
DOI: 10.6084/m9.figshare.3804357.v1
title: Decadal wind speed data for Entebbe International Airport

description: The windspeed data are daily aggregated values for wind speed data for Entebbe International Airport, located at Entebbe, Uganda. This data has undergone multivariate imputations given that the initial dataset for the period 1995 through 2008 had over 10% missing completely at random (MCAR).
DOI: 10.6084/m9.figshare.3804357.v2
title: Data imputation: an application on wind speed data for Entebbe International Airport

description: The windspeed data are daily aggregated values for wind speed data for Entebbe International Airport, located at Entebbe, Uganda. This data has undergone multivariate imputations given that the initial dataset for the period 1995 through 2008 had over 10% missing completely at random (MCAR).
DOI: 10.6084/m9.figshare.3804336
title: Comparison of efficacy and local tolerability of estradiol metered-dose transdermal spray to estradiol patch in a network meta-analysis

description: <b>Objectives:</b> Transdermal hormone replacement therapy is preferred for menopausal vasomotor symptoms. Our purpose was to compare the efficacy and local tolerability of a patch and a metered-dose transdermal spray that have never been directly compared. <b>Method:</b> The relative change in the number of hot flushes between baseline and week 12 was selected as an efficacy indicator and the frequency of local skin reactions as a tolerability indicator. A network meta-analysis was performed to compare efficacy. Application site tolerability was compared descriptively. <b>Results:</b> Overall 46 studies were identified. In the efficacy analysis, eight active treatment arms and a placebo arm were determined based on the estradiol daily dose (from 14 μg to 50 μg). All but one had a significantly higher effect on relative change in the number of hot flushes than did the placebo. We found no evidence for different efficacy of the patch and the metered-dose transdermal spray. The latter performed better in terms of local skin reactions. <b>Conclusion:</b> The patch and the metered-dose transdermal spray seem to have the same efficacy on vasomotor symptoms in estradiol hormone replacement. The local tolerability of the metered-dose transdermal spray is favorable.
DOI: 10.6084/m9.figshare.3804318.v1
title: “Rotating Snakes Illusion – Quantitative analysis reveals region in luminance space with opposite illusory rotation” – data set and R scripts

description: Strength of the “Rotating Snakes Illusion” was measured by a nulling procedure (veridical motion compensating illusory motion). Independent variables were the luminance levels of the asymmetric grey steps embracing the black and white anchor steps in the luminance sequence.
DOI: 10.6084/m9.figshare.3804318.v2
title: “Rotating Snakes Illusion – Quantitative analysis reveals region in luminance space with opposite illusory rotation” – data set and R scripts

description: Strength of the “Rotating Snakes Illusion” was measured by a nulling procedure (veridical motion compensating illusory motion). Independent variables were the luminance levels of the asymmetric grey steps embracing the black and white anchor steps in the luminance sequence.
DOI: 10.6084/m9.figshare.3804318.v3
title: “Rotating Snakes Illusion – Quantitative analysis reveals region in luminance space with opposite illusory rotation” – data set and R scripts

description: Strength of the “Rotating Snakes Illusion” was measured by a nulling procedure (veridical motion compensating illusory motion). Independent variables were the luminance levels of the asymmetric grey steps embracing the black and white anchor steps in the luminance sequence.
DOI: 10.6084/m9.figshare.3804318.v4
title: “Rotating Snakes Illusion – Quantitative analysis reveals region in luminance space with opposite illusory rotation” – data set and R scripts

description: Strength of the “Rotating Snakes Illusion” was measured by a nulling procedure (veridical motion compensating illusory motion). Independent variables were the luminance levels of the asymmetric grey steps embracing the black and white anchor steps in the luminance sequence.
DOI: 10.6084/m9.figshare.3804318.v5
title: “Rotating Snakes Illusion – Quantitative analysis reveals region in luminance space with opposite illusory rotation” – data set and R scripts

description: Strength of the “Rotating Snakes Illusion” was measured by a nulling procedure (veridical motion compensating illusory motion). Independent variables were the luminance levels of the asymmetric grey steps embracing the black and white anchor steps in the luminance sequence.<br>Revision 2012--11-17: different colours in plot<br><br>
DOI: 10.6084/m9.figshare.3804318.v6
title: “Rotating Snakes Illusion – Quantitative analysis reveals region in luminance space with opposite illusory rotation” – data set and R scripts

description: Strength of the “Rotating Snakes Illusion” was measured by a nulling procedure (veridical motion compensating illusory motion). Independent variables were the luminance levels of the asymmetric grey steps embracing the black and white anchor steps in the luminance sequence.<br>Revision 2012--11-17: different colours in plot<br><br>
DOI: 10.6084/m9.figshare.3804210
title: SED Template Fits to the zCOSMOS Bright 10k Survey

description: The results of fitting the spectral energy distribution templates from Assef et al. 2010 to the catalog of galaxies from Lilly et al. 2009 (zCOSMOS 10k bright catalog, version 2) using COSMOS photometry from Capak et al. 2007, SCOSMOS photometry from Sanders et al. 2007, photometry from SDSS-dr10 (Ahn et al. 2014), and the AllWISE data release of the WISE survey. Full description is available in Lake and Wright 2016 at https://arxiv.org/abs/1603.07299 or https://dx.doi.org/10.21105/astro.1603.07299 .<br>
DOI: 10.6084/m9.figshare.3804210.v1
title: zCOSMOS_Template_Fractions.tbl.gz

description: The results of fitting the spectral energy distribution templates from Assef et al. 2010 to the catalog of galaxies from Lilly et al. 2009 (zCOSMOS 10k bright catalog, version 2) using COSMOS photometry from Capak et al. 2007, SCOSMOS photometry from Sanders et al. 2007, photometry from SDSS-dr10 (Ahn et al. 2014), and the AllWISE data release of the WISE survey. Full description is available in Lake and Wright 2016 at https://arxiv.org/abs/1603.07299 .<br>
DOI: 10.6084/m9.figshare.3804078
title: Alkaline-rich quartz syenite intrusions of the Western Karelia subprovince

description: Tables detailing geochemical analyses, analytical data for the five age samples and oxygen-isotope analyses from this study
DOI: 10.6084/m9.figshare.3804078.v1
title: Alkaline-rich quartz syenite intrusions of the Western Karelia subprovince

description: Tables detailing geochemical analyses, analytical data for the five age samples and oxygen-isotope analyses from this study
DOI: 10.6084/m9.figshare.3804075
title: Alkaline-rich quartz syenite intrusions of the Western Karelia subprovince

description: Tables detailing geochemical analyses, analytical data for the five age samples and oxygen-isotope analyses from this study
DOI: 10.6084/m9.figshare.3804075.v1
title: Alkaline-rich quartz syenite intrusions of the Western Karelia subprovince

description: Tables detailing geochemical analyses, analytical data for the five age samples and oxygen-isotope analyses from this study
DOI: 10.6084/m9.figshare.3804072
title: Alkaline-rich quartz syenite intrusions of the Western Karelia subprovince

description: Tables detailing geochemical analyses, analytical data for the five age samples and oxygen-isotope analyses from this study
DOI: 10.6084/m9.figshare.3804072.v1
title: Alkaline-rich quartz syenite intrusions of the Western Karelia subprovince

description: Tables detailing geochemical analyses, analytical data for the five age samples and oxygen-isotope analyses from this study
DOI: 10.5519/qd.sqqqln3i
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (65 records)
DOI: 10.6084/m9.figshare.3803955.v1
title: Plant community palatability and orthopteran communities along an elevation gradient

description: DataOrtho.txt: This dataset contains the richness and abundance of 175 orthopteran (Ensifera and Caelifera) communities sampled along an elevation gradient in the Swiss Alps. <br>DataTrait_Species: This dataset contains the leaf traits (SLA, LDMC, C:N, leaf palatability) collected for 287 species along an elevation gradient in the Swiss Alps.<br>DataTrait_CWM: This dataset contains the community weighted mean of the traits (SLA, LDMC, C:N, leaf palatability) calculated for 307 plant communities along an elevation gradient in the Swiss Alps. <br>
DOI: 10.6084/m9.figshare.3803955.v2
title: Plant palatability and orthopteran communities along an elevation gradient

description: DataOrtho.txt: This dataset contains the richness and abundance of 175 orthopteran (Ensifera and Caelifera) communities sampled along an elevation gradient in the Swiss Alps. <br>DataTrait_Species.txt: This dataset contains the leaf traits (SLA, LDMC, C:N, leaf palatability) collected for 287 species along an elevation gradient in the Swiss Alps.<br>DataTrait_CWM.txt: This dataset contains the community weighted mean of the traits (SLA, LDMC, C:N, leaf palatability) calculated for 307 plant communities along an elevation gradient in the Swiss Alps. <br>
DOI: 10.6084/m9.figshare.3803955
title: Data from: Community-level plant palatability increases with elevation as insect herbivore abundance declines

description: <b>When using these datasets, please cite the following reference: </b><br>Descombes, P., Marchon, J., Pradervand, J.-N., Bilat, J., Guisan, A., Rasmann, S., & Pellissier, L. (2017). Community-level plant palatability increases with elevation as insect herbivore abundance declines. <i>Journal of Ecology</i>, 105, 142–151. https://doi.org/10.1111/1365-2745.12664<br>Details on the data sampling are fully described in the aforementioned reference.<br>DataOrtho.txt: This dataset contains the richness and abundance of 175 orthopteran (Ensifera and Caelifera) communities sampled along an elevation gradient in the Swiss Alps (only above 1000m). <br>DataOrtho_Total.txt: This dataset contains the richness and abundance of 190 orthopteran (Ensifera and Caelifera) communities sampled along an elevation gradient in the Swiss Alps. <br>DataTrait_Species.txt: This dataset contains the leaf traits (SLA, LDMC, C:N, leaf palatability) collected for 287 species along an elevation gradient in the Swiss Alps.<br>DataTrait_CWM.txt: This dataset contains the community weighted mean of the traits (SLA, LDMC, C:N, leaf palatability) calculated for 307 plant communities along an elevation gradient in the Swiss Alps. <br>
DOI: 10.6084/m9.figshare.3803955.v5
title: Data from: Community-level plant palatability increases with elevation as insect herbivore abundance declines

description: <b>When using these datasets, please cite the following reference: </b><br>Descombes, P., Marchon, J., Pradervand, J.-N., Bilat, J., Guisan, A., Rasmann, S., & Pellissier, L. (2017). Community-level plant palatability increases with elevation as insect herbivore abundance declines. <i>Journal of Ecology</i>, 105, 142–151. https://doi.org/10.1111/1365-2745.12664<br>Details on the data sampling are fully described in the aforementioned reference.<br>DataOrtho.txt: This dataset contains the richness and abundance of 175 orthopteran (Ensifera and Caelifera) communities sampled along an elevation gradient in the Swiss Alps (only above 1000m). <br>DataOrtho_Total.txt: This dataset contains the richness and abundance of 190 orthopteran (Ensifera and Caelifera) communities sampled along an elevation gradient in the Swiss Alps. <br>DataTrait_Species.txt: This dataset contains the leaf traits (SLA, LDMC, C:N, leaf palatability) collected for 287 species along an elevation gradient in the Swiss Alps.<br>DataTrait_CWM.txt: This dataset contains the community weighted mean of the traits (SLA, LDMC, C:N, leaf palatability) calculated for 307 plant communities along an elevation gradient in the Swiss Alps. <br>
DOI: 10.5519/qd.qiey1ty0
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (15 records)