cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6237197.v1
title: Rediscovering a forgotten rodent of Patagonia and its phylogenetic implications

description: Cephalomyidae is an enigmatic caviomorph ‘family’ recorded in the Deseadan–Colhuehuapian SALMAs (South American Land Mammal Age) of Bolivia and Argentina. The validity and phylogenetic relationships of this group remain unconfirmed. <i>Litodontomys chubutensis</i> is one of the most poorly known cephalomyids, recorded only by a partial mandible with the complete dental series. Here we present a new specimen of <i>Litodontomys</i> from the same Deseadan locality as the holotype (Cabeza Blanca, Chubut, Argentina). It is a more complete and better preserved specimen from a larger and older individual. A phylogenetic analysis, performed to test the position of the genus and the validity and relationships of the family Cephalomyidae, recovered <i>Litodontomys</i> as the sister taxon of <i>Cephalomys</i> and confirmed the monophyly of the clade for the first time in an updated matrix and broader phylogenetic context.
DOI: 10.6084/m9.figshare.6237140
title: Supplemental Table 2

description: List of individuals and taxa collected and analyzed with the respective unique barcode voucher number. Each r18S sequence, entity revealed with GMYC, and OTU is associated to an ID code. Identical ID codes indicate identical r18S sequences, EEs, or OTUs. The same ID codes are shown in the phylogenetic trees. <br>
DOI: 10.6084/m9.figshare.6237140.v1
title: TableS2.csv

description: List of individuals and taxa collected and analyzed with the respective unique barcode voucher number. Each r18S sequence, entity revealed with GMYC, and OTU is associated to an ID code. Identical ID codes indicate identical r18S sequences, EEs, or OTUs. The same ID codes are shown in the phylogenetic trees. <br>
DOI: 10.6084/m9.figshare.6237140.v2
title: TableS2.csv

description: List of individuals and taxa collected and analyzed with the respective unique barcode voucher number. Each r18S sequence, entity revealed with GMYC, and OTU is associated to an ID code. Identical ID codes indicate identical r18S sequences, EEs, or OTUs. The same ID codes are shown in the phylogenetic trees. <br>
DOI: 10.6084/m9.figshare.6237140.v4
title: Supplemental Table 2

description: List of individuals and taxa collected and analyzed with the respective unique barcode voucher number. Each r18S sequence, entity revealed with GMYC, and OTU is associated to an ID code. Identical ID codes indicate identical r18S sequences, EEs, or OTUs. The same ID codes are shown in the phylogenetic trees. <br>
DOI: 10.6084/m9.figshare.6237140.v3
title: Supplemental Table 2

description: List of individuals and taxa collected and analyzed with the respective unique barcode voucher number. Each r18S sequence, entity revealed with GMYC, and OTU is associated to an ID code. Identical ID codes indicate identical r18S sequences, EEs, or OTUs. The same ID codes are shown in the phylogenetic trees. <br>
DOI: 10.6084/m9.figshare.6237014
title: Isoquercitrin, ingredients in <i>Tetrastigma hemsleyanum</i> Diels et Gilg, inhibits hepatocyte growth factor/scatter factor-induced tumor cell migration and invasion

description: Aberrant activation of hepatocyte growth factor/scatter factor (HGF/SF) and its receptor, Met, is involved in the development and progression of many human cancers. In the screening assay of extracts from the root tuber of <i>Tetrastigma hemsleyanum</i> Diels et Gilg, isoquercitrin inhibited HGF/SF-Met signaling as indicated by its inhibitory activity on HGF/SF-induced cell scattering. Further analysis revealed that isoquercitrin specifically inhibited HGF/SF-induced tyrosine phosphorylation of Met. We also found that isoquercitrin decreased HGF-induced migration and invasion by parental or HGF/SF-transfected bladder carcinoma cell line NBT-II cells. Furthermore, isoquercitrin inhibited HGF/SF-induced epithelial mesenchymal transition <i>in vitro</i> and the invasion/metastasis of HGF/SF-transfected NBT-II cells <i>in vivo</i>. Our data suggest the possible use of isoquercitrin in human cancers associated with dysregulated HGF/SF-Met signaling.
DOI: 10.6084/m9.figshare.6237014.v1
title: <b>Isoquercitrin, ingredients in <i>Tetrastigma</i> <i>hemsleyanum</i> Diels et Gilg, inhibits hepatocyte growth factor/scatter factor-induced tumor cell migration and invasion</b>

description: Aberrant activation of hepatocyte growth factor/scatter factor (HGF/SF) and its receptor, Met, is involved in the development and progression of many human cancers. In the screening assay of extracts from the root tuber of <i>Tetrastigma hemsleyanum</i> Diels et Gilg, isoquercitrin inhibited HGF/SF-Met signaling as indicated by its inhibitory activity on HGF/SF-induced cell scattering. Further analysis revealed that isoquercitrin specifically inhibited HGF/SF-induced tyrosine phosphorylation of Met. We also found that isoquercitrin decreased HGF-induced migration and invasion by parental or HGF/SF-transfected bladder carcinoma cell line NBT-II cells. Furthermore, isoquercitrin inhibited HGF/SF-induced epithelial mesenchymal transition <i>in vitro</i> and the invasion/metastasis of HGF/SF-transfected NBT-II cells <i>in vivo</i>. Our data suggest the possible use of isoquercitrin in human cancers associated with dysregulated HGF/SF-Met signaling.
DOI: 10.6084/m9.figshare.6237014.v2
title: Isoquercitrin, ingredients in <i>Tetrastigma hemsleyanum</i> Diels et Gilg, inhibits hepatocyte growth factor/scatter factor-induced tumor cell migration and invasion

description: Aberrant activation of hepatocyte growth factor/scatter factor (HGF/SF) and its receptor, Met, is involved in the development and progression of many human cancers. In the screening assay of extracts from the root tuber of <i>Tetrastigma hemsleyanum</i> Diels et Gilg, isoquercitrin inhibited HGF/SF-Met signaling as indicated by its inhibitory activity on HGF/SF-induced cell scattering. Further analysis revealed that isoquercitrin specifically inhibited HGF/SF-induced tyrosine phosphorylation of Met. We also found that isoquercitrin decreased HGF-induced migration and invasion by parental or HGF/SF-transfected bladder carcinoma cell line NBT-II cells. Furthermore, isoquercitrin inhibited HGF/SF-induced epithelial mesenchymal transition <i>in vitro</i> and the invasion/metastasis of HGF/SF-transfected NBT-II cells <i>in vivo</i>. Our data suggest the possible use of isoquercitrin in human cancers associated with dysregulated HGF/SF-Met signaling.
DOI: 10.6084/m9.figshare.6237011
title: Investigation of rumen metagenome in Italian Simmental and Italian Holstein cows using a whole-genome shotgun sequencing technique

description: The study aimed at investigating the rumen microbiome composition and functional activity in mid lactating cows of Italian Holstein (IH) and Italian Simmental (IS) breeds. Eight IH and eight IS pluriparous cows with days in milking (DIM) ranging from 90 to 180 were selected and rumen contents were sampled with oesophageal tube. Rumen metagenome was analysed using a whole shotgun sequencing. Data were analysed for taxonomic classification and microbial genes. The relative abundance of Archaea, the Archaea to Bacteria ratio and the Archaea to Eukarya ratio were higher (<i>p</i> Bactroidaceae, <i>Bacteroides</i>, <i>Prevotellaceae</i> and <i>Prevotella</i> lower (<i>p</i> Euryarchaeota (<i>p</i> Methanosphera (<i>p</i> Methanothermobacter (<i>p</i>
DOI: 10.6084/m9.figshare.6237011.v1
title: Investigation of rumen metagenome in Italian Simmental and Italian Holstein cows using a whole-genome shotgun sequencing technique

description: The study aimed at investigating the rumen microbiome composition and functional activity in mid lactating cows of Italian Holstein (IH) and Italian Simmental (IS) breeds. Eight IH and eight IS pluriparous cows with days in milking (DIM) ranging from 90 to 180 were selected and rumen contents were sampled with oesophageal tube. Rumen metagenome was analysed using a whole shotgun sequencing. Data were analysed for taxonomic classification and microbial genes. The relative abundance of Archaea, the Archaea to Bacteria ratio and the Archaea to Eukarya ratio were higher (<i>p</i> Bactroidaceae, <i>Bacteroides</i>, <i>Prevotellaceae</i> and <i>Prevotella</i> lower (<i>p</i> Euryarchaeota (<i>p</i> Methanosphera (<i>p</i> Methanothermobacter (<i>p</i>
DOI: 10.6084/m9.figshare.6236972
title: Source codes and data files from Application of low-order potential solutions to higher-order vertical traction boundary problems in an elastic half-space

description: New solutions of potential functions for the bilinear vertical traction boundary condition are derived and presented. The discretization and interpolation of higher-order tractions and the superposition of the bilinear solutions provide a method of forming approximate and continuous solutions for the equilibrium state of a homogeneous and isotropic elastic half-space subjected to arbitrary normal surface tractions. Past experimental measurements of contact pressure distributions in granular media are reviewed in conjunction with the application of the proposed solution method to analysis of elastic settlement in shallow foundations. A numerical example is presented for an empirical ‘saddle-shaped’ traction distribution at the contact interface between a rigid square footing and a supporting soil medium. Non-dimensional soil resistance is computed as the reciprocal of normalized surface displacements under this empirical traction boundary condition, and the resulting internal stresses are compared to classical solutions to uniform traction boundary conditions.
DOI: 10.6084/m9.figshare.6236972.v1
title: Source codes and data files from Application of low-order potential solutions to higher-order vertical traction boundary problems in an elastic half-space

description: New solutions of potential functions for the bilinear vertical traction boundary condition are derived and presented. The discretization and interpolation of higher-order tractions and the superposition of the bilinear solutions provide a method of forming approximate and continuous solutions for the equilibrium state of a homogeneous and isotropic elastic half-space subjected to arbitrary normal surface tractions. Past experimental measurements of contact pressure distributions in granular media are reviewed in conjunction with the application of the proposed solution method to analysis of elastic settlement in shallow foundations. A numerical example is presented for an empirical ‘saddle-shaped’ traction distribution at the contact interface between a rigid square footing and a supporting soil medium. Non-dimensional soil resistance is computed as the reciprocal of normalized surface displacements under this empirical traction boundary condition, and the resulting internal stresses are compared to classical solutions to uniform traction boundary conditions.
DOI: 10.6084/m9.figshare.6236921
title: DataSets - Identification and characterization of Facebook user profiles considering interaction aspects

description: Dataset used in Article "Identification and characterization of Facebook user profiles considering interaction aspects"
DOI: 10.6084/m9.figshare.6236903.v1
title: RAVEN 2.0: a versatile platform for metabolic network reconstruction and a case study on Streptomyces coelicolor

description: Supplementary Information to the paper "RAVEN 2.0: a versatile platform for metabolic network reconstruction and a case study on <i>Streptomyces coelicolor</i>", as posted on bioRxiv.<br>RAVEN 2.0 is available from GitHub.<br>Sco4 is available from GitHub.<br><b>S1 Data. Model structure after merging three <i>de novo</i> draft reconstructions.</b><b><br></b> <b>S1 Table. Mapping of reactions to <i>de novo </i>reconstructions.</b> To facilitate comparison of the existing iMK1208 model and the <i>de novo </i>reconstructions, iMK1208 reactions are mapped to their respective KEGG and MetaCyc counterparts.<br> <b>S2 Table. Association of metabolites to KEGG and MetaCyc identifiers. </b>To facilitate comparison of the existing iMK1208 model and the <i>de novo </i>reconstructions, iMK1208 metabolites are matched to their respective KEGG and MetaCyc identifiers.<br> <b>S3 Table. Reactions from the <i>de novo </i>draft models used in <i>Sco4</i> generation. </b>A set of reactions was selected from the <i>de novo</i> draft model for manual curation of the existing model towards <i>Sco4</i>.<br> <b>S4 Table. Missing gene-associations in that were filled by <i>de novo</i> reconstruction. </b>These reactions had no gene associated in iMK1208, but <i>de novo</i> reconstruction with RAVEN 2.0 identified the responsible genes.<br> <b>S5 Table. Spontaneous reactions included in <i>Sco4</i> model, as identified from MetaCyc.</b><b><br></b> <b>S6 Table. Transport reactions added to <i>Sco4</i> model based on MetaCyc-based reconstruction and manual curation.</b><b><br></b> <b>S7 Table: Complete list of invalid KEGG identifiers and their replacements.</b><b><br></b> <b>S8 Table. Comparison of growth media validation results between iMK1208 and Sco4. </b>The growth media validation on iMK1208 and Sco4 models. The culture and simulating conditions were described previously [28]. Predictions on iMK1208 and Sco4 showed identical results.<br> <b>S9 Table: Identification of putative essential genes from mutagenesis study and predictions from the iMK1208 and <i>Sco4</i> models. </b>Logical indicating whether a gene has been identified in any of the three analyses.<br> <b>S10 Table. Combined FSEOF results on the secondary metabolites included in <i>Sco4</i> model. </b>Target reactions identified for each of the secondary metabolites are indicated, together their gene association. Direction indicates whether a reaction is reversible and running in the forward direction (1), running in the reverse direction (-1), or is irreversible (0).<br> <b>S11 Table. Definition of RAVEN model structure fields. </b>Where applicable, corresponding COBRA model structure fields are indicated.<br> <b>S12 Table. Reaction identifier correspondence between KEGG and MetaCyc. </b>The mapping information was provided by MetaCyc and expanded using function linkMetaCycKEGGRxns. <b></b><br> <b>S13 Table. Metabolite identifier correspondence between KEGG and MetaCyc. </b>The mapping information was provided by MetaCyc.
DOI: 10.6084/m9.figshare.6236759
title: Plant and insect data

description: Raw dataset including flowering plants (pl.csv), insects (ins.csv) and geographic coordinates (xy.csv). <br>
DOI: 10.6084/m9.figshare.6236645
title: Dickerson, Ainge, Seed.xlsx

description: The complete dataset from Experiments 1-3 from the paper Dickerson, Ainge & Seed: 'The role of association in preschoolers solutions to 'Spoon tests' of future planning'
DOI: 10.6084/m9.figshare.6236549
title: When SUMO met splicing

description: Spliceosomal proteins have been revealed as SUMO conjugation targets. Moreover, we have reported that many of these are in a SUMO-conjugated form when bound to a pre-mRNA substrate during a splicing reaction. We demonstrated that SUMOylation of Prp3 (PRPF3), a component of the U4/U6 di-snRNP, is required for U4/U6•U5 tri-snRNP formation and/or recruitment to active spliceosomes. Expanding upon our previous results, we have shown that the splicing factor SRSF1 stimulates SUMO conjugation to several spliceosomal proteins. Given the relevance of the splicing process, as well as the complex and dynamic nature of its governing machinery, the spliceosome, the molecular mechanisms that modulate its function represent an attractive topic of research. We posit that SUMO conjugation could represent a way of modulating spliceosome assembly and thus, splicing efficiency. How cycles of SUMOylation/de-SUMOylation of spliceosomal proteins become integrated throughout the highly choreographed spliceosomal cycle awaits further investigation.
DOI: 10.6084/m9.figshare.6236549.v1
title: When SUMO met splicing

description: Spliceosomal proteins have been revealed as SUMO conjugation targets. Moreover, we have reported that many of these are in a SUMO-conjugated form when bound to a pre-mRNA substrate during a splicing reaction. We demonstrated that SUMOylation of Prp3 (PRPF3), a component of the U4/U6 di-snRNP, is required for U4/U6•U5 tri-snRNP formation and/or recruitment to active spliceosomes. Expanding upon our previous results, we have shown that the splicing factor SRSF1 stimulates SUMO conjugation to several spliceosomal proteins. Given the relevance of the splicing process, as well as the complex and dynamic nature of its governing machinery, the spliceosome, the molecular mechanisms that modulate its function represent an attractive topic of research. We posit that SUMO conjugation could represent a way of modulating spliceosome assembly and thus, splicing efficiency. How cycles of SUMOylation/de-SUMOylation of spliceosomal proteins become integrated throughout the highly choreographed spliceosomal cycle awaits further investigation.
DOI: 10.6084/m9.figshare.6236540
title: Vaginal Health: Insights, Views & Attitudes (VIVA-LATAM): results from a survey in Latin America

description: <b>Objective:</b> To investigate awareness in Latin America, knowledge of postmenopausal vaginal atrophy was evaluated in a sample of women from this region. <b>Methods:</b> A total of 2509 postmenopausal women aged 55–65 years, resident in Argentina, Brazil, Chile, Colombia and Mexico, completed a structured online questionnaire. <b>Results:</b> Over half the surveyed population (57%) reported experiencing symptoms of vaginal atrophy. Only 6% of the overall cohort attributed symptoms of vaginal atrophy directly to the condition, and 71% did not consider the condition to be chronic, resulting in many women not accessing effective therapy. Half the women (49%) affected by vaginal atrophy had used lubricating gels and creams; 36% had used some form of local hormone treatment. To understand symptoms and/or treatment options for vaginal discomfort, the majority of survey participants (92%) were willing to seek advice from health-care professionals; most (61%) felt/would feel comfortable talking to their doctor about this. <b>Conclusion:</b> Many women in Latin America lack knowledge of postmenopausal vaginal atrophy, not appreciating the chronic nature of the condition, and may benefit from dialog initiated by health-care professionals to facilitate greater understanding and increased awareness of the availability of effective treatment.
DOI: 10.6084/m9.figshare.6236540.v1
title: Vaginal Health: Insights, Views & Attitudes (VIVA-LATAM): results from a survey in Latin America

description: <b>Objective:</b> To investigate awareness in Latin America, knowledge of postmenopausal vaginal atrophy was evaluated in a sample of women from this region. <b>Methods:</b> A total of 2509 postmenopausal women aged 55–65 years, resident in Argentina, Brazil, Chile, Colombia and Mexico, completed a structured online questionnaire. <b>Results:</b> Over half the surveyed population (57%) reported experiencing symptoms of vaginal atrophy. Only 6% of the overall cohort attributed symptoms of vaginal atrophy directly to the condition, and 71% did not consider the condition to be chronic, resulting in many women not accessing effective therapy. Half the women (49%) affected by vaginal atrophy had used lubricating gels and creams; 36% had used some form of local hormone treatment. To understand symptoms and/or treatment options for vaginal discomfort, the majority of survey participants (92%) were willing to seek advice from health-care professionals; most (61%) felt/would feel comfortable talking to their doctor about this. <b>Conclusion:</b> Many women in Latin America lack knowledge of postmenopausal vaginal atrophy, not appreciating the chronic nature of the condition, and may benefit from dialog initiated by health-care professionals to facilitate greater understanding and increased awareness of the availability of effective treatment.
DOI: 10.6084/m9.figshare.6236477
title: Supplementary Material for: Transcriptome Profile Analysis of Mechanisms of Black and White Plumage Determination in Black-Bone Chicken

description: <b><i>Background/Aims:</i></b> Melanin is a major and ubiquitous component of plumage colouration, and patterns of melanin pigmentation in birds are extremely varied. However, the molecular mechanism of pigmentation in avian plumage is still largely unknown. <b><i>Methods:</i></b> To elucidate the molecular mechanisms involved in the formation of black and white plumage, this study takes advantage of high-throughput sequencing technology to compare differences in the transcriptome between black and white chicken feather bulbs. In total, we constructed six cDNA libraries from black (Group B) and white (Group W) feather bulbs in the dorsal plumage of Muchuan black-boned chickens. <b><i>Results:</i></b> A comparison between Groups B and W revealed 61 differentially expressed genes, with 47 displaying higher, and 14 displaying lower, levels of expression in white feather bulbs. Our results revealed a set of candidate genes and two potential metabolic pathways involved in black-bone chicken plumage melanogenesis. These include four homeobox genes (HOXB9, HOXC8, HOXA9, and HOXC 9), two glutathione (GSH) metabolism-related genes (CHAC1 and GPX3), and the transforming growth factor beta (TGF-β) signalling pathway. Two known genes, TYR and MITF, were also shown to play a role in melanin formation. <b><i>Conclusion:</i></b> our data provide a valuable resource for discovering genes important in plumage melanin formation and will help further elucidate the molecular mechanisms for black and white plumage.
DOI: 10.6084/m9.figshare.6236456.v1
title: iTreg paper highlights

description: Highlights from the publication:<br>Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3<br>Angelika Schmidt*, Francesco Marabita*, Narsis A. Kiani, Catharina C. Gross, Henrik J. Johansson, Szabolcs Éliás, Sini Rautio, Matilda Eriksson, Sunjay Jude Fernandes, Gilad Silberberg, Ubaid Ullah, Urvashi Bhatia, Harri Lähdesmäki, Janne Lehtiö, David Gomez-Cabrero, Heinz Wiendl, Riitta Lahesmaa and Jesper Tegnér<br>*equal contribution
DOI: 10.6084/m9.figshare.6236444
title: Supplementary Material for: Differences in Reporting the Ragweed Pollen Season Using Google Trends across 15 Countries

description: <b><i>Background:</i></b> Google Trends (GT) searches trends of specific queries in Google, which potentially reflect the real-life epidemiology of allergic rhinitis. We compared GT terms related to ragweed pollen allergy in American and European Union countries with a known ragweed pollen season. Our aim was to assess seasonality and the terms needed to perform the GT searches and to compare these during the spring and summer pollen seasons. <b><i>Methods:</i></b> We examined GT queries from January 1, 2011, to January 4, 2017. We included 15 countries with a known ragweed pollen season and used the standard 5-year GT graphs. We used the GT translation for all countries and the untranslated native terms for each country. <b><i>Results:</i></b> The results of “pollen,” “ragweed,” and “allergy” searches differed between countries, but “ragweed” was clearly identified in 12 of the 15 countries. There was considerable heterogeneity of findings when the GT translation was used. For Croatia, Hungary, Romania, Serbia, and Slovenia, the GT translation was inappropriate. The country patterns of “pollen,” “hay fever,” and “allergy” differed in 8 of the 11 countries with identified “ragweed” queries during the spring and the summer, indicating that the perception of tree and grass pollen allergy differs from that of ragweed pollen. <b><i>Conclusions:</i></b> To investigate ragweed pollen allergy using GT, the term “ragweed” as a plant is required and the translation of “ragweed” in the native language needed.