cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5271976
title: Supplementary Material for: Effects of Self-Assembling Peptide P11-4, Fluorides, and Caries Infiltration on Artificial Enamel Caries Lesions in vitro

description: The application of a self-assembling peptide on noncavitated caries lesions is supposed to be a feasible approach to facilitate remineralization and mask their unfavorable appearance. However, demineralizing conditions are common in the oral environment, so the aim of this pH-cycling study was to compare recommended and novel treatment methods regarding their ability to hamper demineralization and as a consequence mask artificial enamel caries lesions. Artificial caries lesions were prepared in bovine enamel and randomly allocated to 11 groups (<i>n</i> = 22). Treatments before pH-cycling were as follows: the application of a self-assembling peptide (Curodont™ Repair [C]), a low-viscosity resin (Icon® [I]), 2 fluoride solutions (10,000 ppm F<sup>-</sup>: Elmex fluid [E] and 43,350 ppm F<sup>-</sup>: Tiefenfluorid® [T]), and no intervention (N). During pH-cycling (28 days, 6 × 60 min demineralization/day) half of the specimens in each group were brushed (10 s; 2 ×/day) with either fluoride-free (named e.g., C<sub>0</sub>) or NaF (1,100 ppm F<sup>-</sup>; e.g., C<sub>1</sub>) dentifrice slurry. In another subgroup specimens were pH-cycled but not brushed (N<sub>NB</sub>). Differences in integrated mineral loss (ΔΔZ), lesion depth (ΔLD), and colorimetric values (ΔΔE) were calculated between values after pre-demineralization, surface treatment, and pH-cycling. Specimens of C<sub>0</sub>, C<sub>1</sub>, N<sub>NB</sub>, N<sub>0</sub>, N<sub>1</sub>, T<sub>0</sub>, and E<sub>0</sub> showed significantly increased ΔZ and LD values after pH-cycling (<i>p</i> ≤ 0.003; paired <i>t</i> test). C<sub>0</sub>, C<sub>1</sub>, N<sub>NB</sub>, and N<sub>0</sub> showed significantly higher changes in ΔΔZ than E<sub>1</sub>, I<sub>0</sub>, I<sub>1</sub>, and T<sub>1</sub> (<i>p</i> &lt; 0.001; ANOVA). Significantly reduced colorimetric values could only be observed for I<sub>1</sub>, I<sub>0</sub>, E<sub>1</sub>, and E<sub>0</sub> after treatment and after pH-cycling (<i>p</i> ≤ 0.027; paired <i>t</i> test). In conclusion, under the conditions chosen only the application of a low-viscosity resin could mask caries lesions significantly, whereas self-assembling peptides could neither inhibit lesion progression nor mask the lesions considerably.
DOI: 10.6084/m9.figshare.5271976.v1
title: Supplementary Material for: Effects of Self-Assembling Peptide P11-4, Fluorides, and Caries Infiltration on Artificial Enamel Caries Lesions in vitro

description: The application of a self-assembling peptide on noncavitated caries lesions is supposed to be a feasible approach to facilitate remineralization and mask their unfavorable appearance. However, demineralizing conditions are common in the oral environment, so the aim of this pH-cycling study was to compare recommended and novel treatment methods regarding their ability to hamper demineralization and as a consequence mask artificial enamel caries lesions. Artificial caries lesions were prepared in bovine enamel and randomly allocated to 11 groups (<i>n</i> = 22). Treatments before pH-cycling were as follows: the application of a self-assembling peptide (Curodont™ Repair [C]), a low-viscosity resin (Icon® [I]), 2 fluoride solutions (10,000 ppm F<sup>-</sup>: Elmex fluid [E] and 43,350 ppm F<sup>-</sup>: Tiefenfluorid® [T]), and no intervention (N). During pH-cycling (28 days, 6 × 60 min demineralization/day) half of the specimens in each group were brushed (10 s; 2 ×/day) with either fluoride-free (named e.g., C<sub>0</sub>) or NaF (1,100 ppm F<sup>-</sup>; e.g., C<sub>1</sub>) dentifrice slurry. In another subgroup specimens were pH-cycled but not brushed (N<sub>NB</sub>). Differences in integrated mineral loss (ΔΔZ), lesion depth (ΔLD), and colorimetric values (ΔΔE) were calculated between values after pre-demineralization, surface treatment, and pH-cycling. Specimens of C<sub>0</sub>, C<sub>1</sub>, N<sub>NB</sub>, N<sub>0</sub>, N<sub>1</sub>, T<sub>0</sub>, and E<sub>0</sub> showed significantly increased ΔZ and LD values after pH-cycling (<i>p</i> ≤ 0.003; paired <i>t</i> test). C<sub>0</sub>, C<sub>1</sub>, N<sub>NB</sub>, and N<sub>0</sub> showed significantly higher changes in ΔΔZ than E<sub>1</sub>, I<sub>0</sub>, I<sub>1</sub>, and T<sub>1</sub> (<i>p</i> &lt; 0.001; ANOVA). Significantly reduced colorimetric values could only be observed for I<sub>1</sub>, I<sub>0</sub>, E<sub>1</sub>, and E<sub>0</sub> after treatment and after pH-cycling (<i>p</i> ≤ 0.027; paired <i>t</i> test). In conclusion, under the conditions chosen only the application of a low-viscosity resin could mask caries lesions significantly, whereas self-assembling peptides could neither inhibit lesion progression nor mask the lesions considerably.
DOI: 10.6084/m9.figshare.5271913
title: SAM simulation analysis

description: Analysis of interatomic distances for NOE NMR fitting before and after clustering into individual conformer clusters c1-c6.<br>Data for 3 different simulations: HF parameterisation, PCM parameterisation and inverted R-S isomer with PCMfitting.<br>
DOI: 10.6084/m9.figshare.5271904
title: SAM simulation, forcefield and coordinates

description: Forcefield parameter files and input coordinates for SAM simulation (for use with Amber software)
DOI: 10.6084/m9.figshare.5271913.v1
title: SAM simulation analysis

description: Analysis of interatomic distances for NOE NMR fitting before and after clustering into individual conformer clusters c1-c6.<br>Data for 3 different simulations: HF parameterisation, PCM parameterisation and inverted R-S isomer with PCMfitting.<br>
DOI: 10.6084/m9.figshare.5271904.v1
title: SAM simulation, forcefield and coordinates

description: Forcefield parameter files and input coordinates for SAM simulation (for use with Amber software)
DOI: 10.6084/m9.figshare.5271784
title: IGT_meta_dataset.cma

description: Dataset for the manuscript entitled 'Decision making measured by the Iowa Gambling Task in alcohol use disorder and gambling disorder: a systematic review and meta-analysis
DOI: 10.6084/m9.figshare.5271784.v1
title: IGT_meta_dataset.cma

description: Dataset for the manuscript entitled 'Decision making measured by the Iowa Gambling Task in alcohol use disorder and gambling disorder: a systematic review and meta-analysis
DOI: 10.6084/m9.figshare.5271766
title: Geochronology, geochemistry and isotope systematics of a mafic–intermediate dyke complex in the İstanbul Zone. New constraints on the evolution of the Black Sea in NW Turkey

description: Supplementary Table 3. Representative chemical composition (wt.%) of amphiboles from the mafic–intermediate dykes.
DOI: 10.6084/m9.figshare.5271769
title: Geochronology, geochemistry and isotope systematics of a mafic–intermediate dyke complex in the İstanbul Zone. New constraints on the evolution of the Black Sea in NW Turkey

description: Supplementary Table 1. Representative chemical composition (wt.%) of feldspars from the mafic–intermediate dykes.
DOI: 10.6084/m9.figshare.5271769.v1
title: Geochronology, geochemistry and isotope systematics of a mafic–intermediate dyke complex in the İstanbul Zone. New constraints on the evolution of the Black Sea in NW Turkey

description: Supplementary Table 1. Representative chemical composition (wt.%) of feldspars from the mafic–intermediate dykes.
DOI: 10.6084/m9.figshare.5271763
title: Geochronology, geochemistry and isotope systematics of a mafic–intermediate dyke complex in the İstanbul Zone. New constraints on the evolution of the Black Sea in NW Turkey

description: Supplementary Table 2. Representative chemical composition (wt.%) of pyroxenes from the mafic–intermediate dykes (calculated with using Winpyrox software, Yavuz 2013).
DOI: 10.6084/m9.figshare.5271766.v1
title: Geochronology, geochemistry and isotope systematics of a mafic–intermediate dyke complex in the İstanbul Zone. New constraints on the evolution of the Black Sea in NW Turkey

description: Supplementary Table 3. Representative chemical composition (wt.%) of amphiboles from the mafic–intermediate dykes.
DOI: 10.6084/m9.figshare.5271763.v1
title: Geochronology, geochemistry and isotope systematics of a mafic–intermediate dyke complex in the İstanbul Zone. New constraints on the evolution of the Black Sea in NW Turkey

description: Supplementary Table 2. Representative chemical composition (wt.%) of pyroxenes from the mafic–intermediate dykes (calculated with using Winpyrox software, Yavuz 2013).
DOI: 10.34760/5f4662361c283
title: Skeleton 2017 
title: 2
DOI: 10.6084/m9.figshare.5271712
title: Experimental demonstration that offspring fathered by old males have shorter telomeres and reduced lifespan

description: Database for the manuscript Noguera et al. PRSB
DOI: 10.6084/m9.figshare.5271715
title: Clinical implications of blood-material interaction and drug eluting stent polymers in review

description: <b>Introduction</b>: Despite advances in drug-eluting stent (DES) technology, stent thrombosis (ST) remains the most feared complication with high morbidity and mortality. <b>Areas covered</b>: Stent related factors certainly play a role in the pathophysiology of ST and more recent data suggest coating technologies have the potential to favorable modify this risk though blood material interactions. Of the polymer coatings used in DES, fluorinated polymers in particular have shown significant promise in modifying the risk of ST through their preferential interactions with albumin which is believed to prevent the adhesion and aggregation of platelets to the stent surface and thus minimize thrombus formation. Preclinical data from the porcine arteriovenous fistula model and clinical data from large network meta-analysis support a role for fluorinated polymers in reducing ST. <b>Expert commentary</b>: The search for more biocompatible anti-thrombotic polymer coatings continues and it is likely that further modification of stent based surfaces will revolutionize the field of interventional cardiology by one day obviating the need for systemic anti-platelet therapies in patients receiving intravascular devices.
DOI: 10.6084/m9.figshare.5271715.v1
title: Clinical implications of blood-material interaction and drug eluting stent polymers in review

description: <b>Introduction</b>: Despite advances in drug-eluting stent (DES) technology, stent thrombosis (ST) remains the most feared complication with high morbidity and mortality. <b>Areas covered</b>: Stent related factors certainly play a role in the pathophysiology of ST and more recent data suggest coating technologies have the potential to favorable modify this risk though blood material interactions. Of the polymer coatings used in DES, fluorinated polymers in particular have shown significant promise in modifying the risk of ST through their preferential interactions with albumin which is believed to prevent the adhesion and aggregation of platelets to the stent surface and thus minimize thrombus formation. Preclinical data from the porcine arteriovenous fistula model and clinical data from large network meta-analysis support a role for fluorinated polymers in reducing ST. <b>Expert commentary</b>: The search for more biocompatible anti-thrombotic polymer coatings continues and it is likely that further modification of stent based surfaces will revolutionize the field of interventional cardiology by one day obviating the need for systemic anti-platelet therapies in patients receiving intravascular devices.
DOI: 10.6084/m9.figshare.5271712.v1
title: Experimental demonstration that offspring fathered by old males have shorter telomeres and reduced lifespan

description: Database for the manuscript Noguera et al. PRSB
DOI: 10.6084/m9.figshare.5271646
title: Quantity table

description: Gel image analysis results
DOI: 10.6084/m9.figshare.5271643
title: RuBPS-stained CaPpZ1 KO two dimensional gel images

description: CaPpZ1 KO gel images<br>
DOI: 10.6084/m9.figshare.5271646.v1
title: Quantity table

description: Gel image analysis results
DOI: 10.6084/m9.figshare.5271637
title: Control RuBPS-stained two dimensional gel images

description: Control gel images<br>
DOI: 10.6084/m9.figshare.5271640
title: Pro-Q Diamond-stained CaPpZ1 KO two dimensional gel images

description: CaPpZ1 KO gel images
DOI: 10.6084/m9.figshare.5271625
title: Cephalopods from reef limestone of the Vasalemma Formation, northern Estonia (latest Sandbian, Upper Ordovician) and the establishment of a local warm-water fauna

description: The cephalopods of the reef limestones of the Vasalemma Formation, northern Estonia, are highly diverse and comprise 22 species belonging to 10 families and seven orders in a sample of &gt;300 specimens. Most of the specimens were collected from shell concentrations in synsedimentary cavities and are interpreted as parautochthonous, washed in from nearby habitats. Nearly all of the shells are fragmented and nearly 15% are partially encrusted by epibionts. The assemblage is dominated by small (mostly less than 30 mm wide), straight-shelled actinocerids and orthocerids; in addition, coiled tarphycerids are common. The high-level taxonomic composition of the Vasalemma cephalopod assemblage, with a dominance of actinocerids and an absence of endocerids, is in agreement with deposition in a warm-water (tropical or subtropical), shallow, subtidal regime. At the species level the assemblage is highly endemic, but the generic composition allows for a statistical comparison with other faunas. A cluster analysis of contemporary assemblages reveals a high degree of similarity with late Sandbian cephalopod faunas of epicontinental Laurentia. The palaeogeographical distribution pattern is similar to that of brachiopods, which supports earlier interpretations of these clusters as mainly controlled by water temperature and depositional depth. Several of the Vasalemma genera became conspicuous elements of epicontinental Laurentia during the Katian, which emphasizes that immigration towards Laurentia was an important factor in Late Ordovician diversity dynamics. Of the described taxa, the following are new: <i>Beloitoceras cautis</i> sp. nov., <i>Curtoceras abditus</i> sp. nov., <i>Hemibeloitoceras arduum</i> sp. nov., <i>H. molis</i> sp. nov., <i>Hoeloceras muroni</i> sp. nov., <i>Isorthoceras cavi</i> sp. nov., <i>I. maris</i> sp. nov., <i>I. padisense</i> sp. nov., <i>I. vexilli</i> sp. nov., <i>Ordogeisonoceras tartuensis</i> sp. nov., <i>Orthonybyoceras isakari</i> sp. nov., <i>O. moisense</i> sp. nov., <i>Pleurorthoceras organi</i> sp. nov., <i>Rummoceras rummuensis</i> gen. et sp. nov. and <i>Trocholites gennadii</i> sp. nov. http://zoobank.org/urn:lsid:zoobank.org:pub:E5211305-A5D0-4366-AAB1-08F96F817122
DOI: 10.6084/m9.figshare.5271631
title: Control Pro-Q Diamond stained two dimensional gel images

description: Control gel images<br>
DOI: 10.6084/m9.figshare.5271643.v1
title: RuBPS-stained CaPpZ1 KO two dimensional gel images

description: CaPpZ1 KO gel images<br>
DOI: 10.6084/m9.figshare.5271637.v1
title: Control RuBPS-stained two dimensional gel images

description: Control gel images<br>
DOI: 10.6084/m9.figshare.5271640.v1
title: Pro-Q Diamond-stained CaPpZ1 KO two dimensional gel images

description: CaPpZ1 KO gel images
DOI: 10.6084/m9.figshare.5271622
title: Dataset for: Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis

description: The three dimensional folding of mammalian genomes is cell-type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin associating factors, the mechanisms driving the co-localization of active chromosomal domains and the role of this organization in regulating the transcription program in adipocytes are not clear. Analysis of genome-wide chromosomal associations revealed cell type-specific spatial clustering of adipogenic genes in 3T3-L1 cells. Time course analysis demonstrated that the adipogenic "hub", sampled by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors tested, RXR is central to genome reorganization at the beginning of adipogenesis. Interestingly, at the end of differentiation, the adipogenic hub was shifted to an H3K27me3 repressive environment in conjunction with attenuation of gene transcription. We propose a stage-specific hierarchy for the activity of transcription factors contributing to the establishment of an adipogenic genome architecture that brings together the adipogenic genetic program. In addition, the repositioning of this network in a H3K27me3-rich environment at the end of differentiation may contribute to the stabilization of gene transcription levels and reduce the developmental plasticity of these specialized cells.
DOI: 10.6084/m9.figshare.5271625.v1
title: Cephalopods from reef limestone of the Vasalemma Formation, northern Estonia (latest Sandbian, Upper Ordovician) and the establishment of a local warm-water fauna

description: The cephalopods of the reef limestones of the Vasalemma Formation, northern Estonia, are highly diverse and comprise 22 species belonging to 10 families and seven orders in a sample of &gt;300 specimens. Most of the specimens were collected from shell concentrations in synsedimentary cavities and are interpreted as parautochthonous, washed in from nearby habitats. Nearly all of the shells are fragmented and nearly 15% are partially encrusted by epibionts. The assemblage is dominated by small (mostly less than 30 mm wide), straight-shelled actinocerids and orthocerids; in addition, coiled tarphycerids are common. The high-level taxonomic composition of the Vasalemma cephalopod assemblage, with a dominance of actinocerids and an absence of endocerids, is in agreement with deposition in a warm-water (tropical or subtropical), shallow, subtidal regime. At the species level the assemblage is highly endemic, but the generic composition allows for a statistical comparison with other faunas. A cluster analysis of contemporary assemblages reveals a high degree of similarity with late Sandbian cephalopod faunas of epicontinental Laurentia. The palaeogeographical distribution pattern is similar to that of brachiopods, which supports earlier interpretations of these clusters as mainly controlled by water temperature and depositional depth. Several of the Vasalemma genera became conspicuous elements of epicontinental Laurentia during the Katian, which emphasizes that immigration towards Laurentia was an important factor in Late Ordovician diversity dynamics. Of the described taxa, the following are new: <i>Beloitoceras cautis</i> sp. nov., <i>Curtoceras abditus</i> sp. nov., <i>Hemibeloitoceras arduum</i> sp. nov., <i>H. molis</i> sp. nov., <i>Hoeloceras muroni</i> sp. nov., <i>Isorthoceras cavi</i> sp. nov., <i>I. maris</i> sp. nov., <i>I. padisense</i> sp. nov., <i>I. vexilli</i> sp. nov., <i>Ordogeisonoceras tartuensis</i> sp. nov., <i>Orthonybyoceras isakari</i> sp. nov., <i>O. moisense</i> sp. nov., <i>Pleurorthoceras organi</i> sp. nov., <i>Rummoceras rummuensis</i> gen. et sp. nov. and <i>Trocholites gennadii</i> sp. nov. http://zoobank.org/urn:lsid:zoobank.org:pub:E5211305-A5D0-4366-AAB1-08F96F817122
DOI: 10.6084/m9.figshare.5271631.v1
title: Control Pro-Q Diamond stained two dimensional gel images

description: Control gel images<br>
DOI: 10.6084/m9.figshare.5271613
title: Dataset for: G3BP1 interacts directly with the FMDV IRES and negatively regulates translation

description: RNA-protein interactions play a pivotal role in the function of picornavirus internal ribosome entry site (IRES) elements. Here we analysed the impact of Ras GTPase SH3 domain binding protein 1 (G3BP1) in the IRES activity of foot-and-mouth disease virus (FMDV). We found that G3BP1 interacts directly with three distinct sequences of the IRES element using RNA electrophoretic mobility-shift assays. Analysis of the interaction with domain 5 indicated that the G3BP1 binding-site is placed at the single-stranded region although it allows large sequence heterogeneity and the hairpin located upstream of this region enhances retarded complex formation. In addition, G3BP1 interacts directly with the polypyrimidine tract-binding protein (PTB) and the translation initiation factor 4B (eIF4B) through the C-terminal region. Moreover, G3BP1 is cleaved during FMDV infection yielding two fragments, Ct-G3BP1 and Nt-G3BP1. Both fragments inhibit cap- and IRES-dependent translation, but the Ct-G3BP1 fragment shows a stronger effect on IRES-dependent translation. Assembly of complexes with G3BP1 results in a significantly reduced local flexibility of the IRES element, consistent with the negative effect of this protein. Our results highlight the IRES-binding capacity of G3BP1 and illustrate its function as a translation inhibitor.
DOI: 10.6084/m9.figshare.5271592
title: Mismatch_CBF_Tmax_collaterals_acute_stroke.xlsx

description: Demographic data and results pertaining to the manuscript "The mismatch between cerebral blood flow and Tmax predicts the quality of collaterals in acute ischemic stroke"
DOI: 10.6084/m9.figshare.5271619
title: Supplementary Material for: Collectin-11 Is an Important Modulator of Retinal Pigment Epithelial Cell Phagocytosis and Cytokine Production

description: In this paper, we report previously unknown roles for collectin-11 (CL-11, a soluble C-type lectin) in modulating the retinal pigment epithelial (RPE) cell functions of phagocytosis and cytokine production. We found that CL-11 and its carbohydrate ligand are expressed in both the murine and human neural retina; these resemble each other in terms of RPE and photoreceptor cells. Functional analysis of murine RPE cells showed that CL-11 facilitates the opsonophagocytosis of photoreceptor outer segments and apoptotic cells, and also upregulates IL-10 production. Mechanistic analysis revealed that calreticulin on the RPE cells is required for CL-11-mediated opsonophagocytosis whereas signal-regulatory protein α and mannosyl residues on the cells are involved in the CL-11-mediated upregulation of IL-10 production. This study is the first to demonstrate the role of CL-11 and the molecular mechanisms involved in modulating RPE cell phagocytosis and cytokine production. It provides a new insight into retinal health and disease and has implications for other phagocytic cells.