cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4286432
title: <i>O</i>-GlcNAc glycosylation stoichiometry of the FET protein family: only EWS is glycosylated with a high stoichiometry

description: Of the FET (fused in sarcoma [FUS]/Ewing sarcoma protein [EWS]/TATA binding protein-associated factor 15 [TAF15]) family of heterogeneous nuclear ribonucleoprotein particle proteins, FUS and TAF15 are consistently and EWS variably found in inclusion bodies in neurodegenerative diseases such as frontotemporal lobar degeneration associated with FUS. It is speculated that dysregulation of FET proteins at the post-translational level is involved in their cytoplasmic deposition. Here, the <i>O</i>-linked β-<i>N</i>-acetylglucosamine (<i>O</i>-GlcNAc) glycosylation stoichiometry of the FET proteins was chemoenzymatically analyzed, and it was found that only EWS is dynamically glycosylated with a high stoichiometry in the neural cell lines tested and in mouse brain. It was also confirmed that EWS, but not FUS and TAF15, is glycosylated with a high stoichiometry not only in the neural cells but also in the non-neural cell lines tested. These results indicate that <i>O</i>-GlcNAc glycosylation imparts a physicochemical property on EWS that is distinct from that of the other FET proteins in most of cell lineages or tissues.
DOI: 10.6084/m9.figshare.4286432.v1
title: <i>O</i>-GlcNAc glycosylation stoichiometry of the FET protein family: only EWS is glycosylated with a high stoichiometry

description: Of the FET (fused in sarcoma [FUS]/Ewing sarcoma protein [EWS]/TATA binding protein-associated factor 15 [TAF15]) family of heterogeneous nuclear ribonucleoprotein particle proteins, FUS and TAF15 are consistently and EWS variably found in inclusion bodies in neurodegenerative diseases such as frontotemporal lobar degeneration associated with FUS. It is speculated that dysregulation of FET proteins at the post-translational level is involved in their cytoplasmic deposition. Here, the <i>O</i>-linked β-<i>N</i>-acetylglucosamine (<i>O</i>-GlcNAc) glycosylation stoichiometry of the FET proteins was chemoenzymatically analyzed, and it was found that only EWS is dynamically glycosylated with a high stoichiometry in the neural cell lines tested and in mouse brain. It was also confirmed that EWS, but not FUS and TAF15, is glycosylated with a high stoichiometry not only in the neural cells but also in the non-neural cell lines tested. These results indicate that <i>O</i>-GlcNAc glycosylation imparts a physicochemical property on EWS that is distinct from that of the other FET proteins in most of cell lineages or tissues.
DOI: 10.6084/m9.figshare.4286426
title: Taxonomic description of <i>in situ</i> bee pollen from the middle Eocene of Germany

description: The middle Eocene Messel and Eckfeld localities are renowned for their excellently preserved faunas and diverse floras. Here we describe for the first time pollen from insect-pollinated plants found <i>in situ</i> on well-preserved ancient bees using light and scanning electron microscopy. There have been 140 pollen types reported from Messel and 162 pollen types from Eckfeld. Here we document 23 pollen types, six from Messel and 18 from Eckfeld (one is shared). The taxa reported here are all pollinated by insects and mostly not recovered in the previously studied dispersed fossil pollen records. Typically, a single or two pollen types are found on each fossil bee specimen, the maximum number of distinct pollen types on a single individual is five. Only five of the 23 pollen types obtained are angiosperms of unknown affinity, the remainder cover a broad taxonomic range of angiosperm trees and include members of several major clades: monocots (1 pollen type), fabids (7), malvids (4), asterids (5) and other core eudicots (1). Seven types each can be assigned to individual genera or infrafamilial clades. Since bees visit only flowers in the relative vicinity of their habitat, the recovered pollen provides a unique insight into the autochthonous palaeo-flora. The coexistence of taxa such as <i>Decodon, Elaeocarpus, Mortoniodendron</i> and other Tilioideae, Mastixoideae, <i>Olax, Pouteria</i> and <i>Nyssa</i> confirms current views that diverse, thermophilic forests thrived at the Messel and Eckfeld localities, probably under a warm subtropical, fully humid climate. Our study calls for increased attention to pollen found <i>in situ</i> on pollen-harvesting insects such as bees, which can provide new insights on insect-pollinated plants and complement even detailed palaeo-palynological knowledge obtained mostly from pollen of wind-pollinated plants in the dispersed pollen record of sediments. In the case of <i>Elaeocarpus, Mortoniodendron, Olax</i> and <i>Pouteria</i> the pollen collected by the middle Eocene bees represent the earliest unambiguous records of their respective genera.
DOI: 10.6084/m9.figshare.4286426.v1
title: Taxonomic description of <i>in situ</i> bee pollen from the middle Eocene of Germany

description: The middle Eocene Messel and Eckfeld localities are renowned for their excellently preserved faunas and diverse floras. Here we describe for the first time pollen from insect-pollinated plants found <i>in situ</i> on well-preserved ancient bees using light and scanning electron microscopy. There have been 140 pollen types reported from Messel and 162 pollen types from Eckfeld. Here we document 23 pollen types, six from Messel and 18 from Eckfeld (one is shared). The taxa reported here are all pollinated by insects and mostly not recovered in the previously studied dispersed fossil pollen records. Typically, a single or two pollen types are found on each fossil bee specimen, the maximum number of distinct pollen types on a single individual is five. Only five of the 23 pollen types obtained are angiosperms of unknown affinity, the remainder cover a broad taxonomic range of angiosperm trees and include members of several major clades: monocots (1 pollen type), fabids (7), malvids (4), asterids (5) and other core eudicots (1). Seven types each can be assigned to individual genera or infrafamilial clades. Since bees visit only flowers in the relative vicinity of their habitat, the recovered pollen provides a unique insight into the autochthonous palaeo-flora. The coexistence of taxa such as <i>Decodon, Elaeocarpus, Mortoniodendron</i> and other Tilioideae, Mastixoideae, <i>Olax, Pouteria</i> and <i>Nyssa</i> confirms current views that diverse, thermophilic forests thrived at the Messel and Eckfeld localities, probably under a warm subtropical, fully humid climate. Our study calls for increased attention to pollen found <i>in situ</i> on pollen-harvesting insects such as bees, which can provide new insights on insect-pollinated plants and complement even detailed palaeo-palynological knowledge obtained mostly from pollen of wind-pollinated plants in the dispersed pollen record of sediments. In the case of <i>Elaeocarpus, Mortoniodendron, Olax</i> and <i>Pouteria</i> the pollen collected by the middle Eocene bees represent the earliest unambiguous records of their respective genera.
DOI: 10.6084/m9.figshare.4286423.v1
title: Birth of the cool: a two-centuries decline in emotional expression in Anglophone fiction

description: The presence of emotional words and content in stories has been shown to enhance a story’s memorability, and its cultural success. Yet, recent cultural trends run in the opposite direction. Using the Google Books corpus, coupled with two metadata-rich corpora of Anglophone fiction books, we show a decrease in emotionality in English-speaking literature starting plausibly in the nineteenth century. We show that this decrease cannot be explained by changes unrelated to emotionality (such as demographic dynamics concerning age or gender balance, changes in vocabulary richness, or changes in the prevalence of literary genres), and that, in our three corpora, the decrease is driven almost entirely by a decline in the proportion of <i>positive</i> emotion-related words, while the frequency of <i>negative</i> emotion-related words shows little if any decline. Consistently with previous studies, we also find a link between ageing and negative emotionality at the individual level.
DOI: 10.6084/m9.figshare.4286411
title: A divergent McMurry coupling of the bis-salisaldehyde with methylene linker: The characterization of a key by-product with the possible pathway formation

description: The McMurry coupling of a bis-salisaldehyde <b>3a</b> with methyl linker as the smallest member of its alkyl series is known to give the remarkably lower yield of the corresponding stilbenophanes. The half part of this molecule, unlike bigger analogues, is a good leaving group which affords<i>threo</i> isomer of 4H, 4′H–4,4′-bibenzo[d][1,3]dioxine <b>4</b> in high diastereoisomeric ratio (99&gt;). A further study showed that the formation of this key by-product is the reason for formation of other by-products, namely, 5a,10b-dihydrobenzofuro[2,3-b]benzofuran <b>9</b> and 2-(2,3-dihydrobenzofuran-2-yl)phenol <b>10</b>. Two reaction pathways for the formation of by-products have been proposed which are responsible for the unusual activity of dialdehyde <b>3a</b>.
DOI: 10.6084/m9.figshare.4286411.v2
title: A divergent McMurry coupling of the bis-salisaldehyde with methylene linker: The characterization of a key by-product with the possible pathway formation

description: The McMurry coupling of a bis-salisaldehyde <b>3a</b> with methyl linker as the smallest member of its alkyl series is known to give the remarkably lower yield of the corresponding stilbenophanes. The half part of this molecule, unlike bigger analogues, is a good leaving group which affords<i>threo</i> isomer of 4H, 4′H–4,4′-bibenzo[d][1,3]dioxine <b>4</b> in high diastereoisomeric ratio (99&gt;). A further study showed that the formation of this key by-product is the reason for formation of other by-products, namely, 5a,10b-dihydrobenzofuro[2,3-b]benzofuran <b>9</b> and 2-(2,3-dihydrobenzofuran-2-yl)phenol <b>10</b>. Two reaction pathways for the formation of by-products have been proposed which are responsible for the unusual activity of dialdehyde <b>3a</b>.
DOI: 10.6084/m9.figshare.4286411.v1
title: A Divergent Mcmurry Coupling of the Bis-Salisaldehyde with Methylene Linker: The Characterization of a Key by-Product with the Possible Pathway Formation

description: The McMurry coupling of a bis-salisaldehyde <b>3a</b> with methyl linker as the smallest members of its alkyl series is known to give the remarkably lower yield of the corresponding stilbenophanes. The half part of this molecule, unlike bigger analogues, is a good leaving group which afford<i>threo</i> isomer of 4H,4'H-4,4′-bibenzo[d][1,3]dioxine <b>4</b> in high diastereoisomeric ratio (99 &gt; ). A further study showed that the formation of this key by-product is the reason of the formation other by-products, namely 5a,10b-dihydrobenzofuro[2,3-b]benzofuran <b>9</b> and 2-(2,3-dihydrobenzofuran-2-yl)phenol <b>10</b>. Two reaction pathways for the formation of by-products have been proposed which are responsible for the unusual activity of dialdehyde <b>3a.</b>
DOI: 10.6084/m9.figshare.4286399
title: One-pot synthesis of bis (phenylimino dihydro thiazolyl-2<i>H</i>-chromene) derivatives

description: A novel series of bis (phenylimino dihydro thiazolyl-2<i>H</i>-chromene) derivatives have been synthesized through an efficient one-pot multicomponent approach involving different substituted of 3-(2-bromoacetyl)-2<i>H</i>-chromen-2-ones, phenyl isothiocyanates and <i>para</i>-phenylenediamine in presence of dimethylformamide solvent. The target compounds were obtained in a shorter reaction time through simple reaction work up with good yields. All the synthesized products were characterized by their spectral and analytical data like IR, <sup>1</sup>H NMR, <sup>13</sup>C NMR, Roesy, and mass spectral data.
DOI: 10.6084/m9.figshare.4286399.v2
title: One-pot synthesis of bis (phenylimino dihydro thiazolyl-2<i>H</i>-chromene) derivatives

description: A novel series of bis (phenylimino dihydro thiazolyl-2<i>H</i>-chromene) derivatives have been synthesized through an efficient one-pot multicomponent approach involving different substituted of 3-(2-bromoacetyl)-2<i>H</i>-chromen-2-ones, phenyl isothiocyanates and <i>para</i>-phenylenediamine in presence of dimethylformamide solvent. The target compounds were obtained in a shorter reaction time through simple reaction work up with good yields. All the synthesized products were characterized by their spectral and analytical data like IR, <sup>1</sup>H NMR, <sup>13</sup>C NMR, Roesy, and mass spectral data.
DOI: 10.6084/m9.figshare.4286399.v1
title: One pot synthesis of bis (phenylimino dihydro thiazolyl-2<i>H</i>-chromene) derivatives

description: A novel series of bis (phenylimino dihydro thiazolyl-2-<i>H</i>-chromene) derivatives have been synthesized via an efficient one pot multicomponent approach involving different substituted of 3-(2-bromoacetyl)-2<i>H</i>-chromen-2-ones, phenylisothiocyanates and para phenylenediamine in presence of DMF solvent. The target compounds were obtained in a shorter reaction time through simple reaction work up with good yields. All the synthesized products were characterized by thier spectral and analytical data like IR, <sup>1</sup>H NMR, <sup>13</sup>C NMR, Roesy and Mass spectral data.
DOI: 10.6084/m9.figshare.4286375
title: Recommendations for a nomenclature system for reporting methylation aberrations in imprinted domains

description: The analysis of DNA methylation has become routine in the pipeline for diagnosis of imprinting disorders, with many publications reporting aberrant methylation associated with imprinted differentially methylated regions (DMRs). However, comparisons between these studies are routinely hampered by the lack of consistency in reporting sites of methylation evaluated. To avoid confusion surrounding nomenclature, special care is needed to communicate results accurately, especially between scientists and other health care professionals. Within the European Network for Human Congenital Imprinting Disorders we have discussed these issues and designed a nomenclature for naming imprinted DMRs as well as for reporting methylation values. We apply these recommendations for imprinted DMRs that are commonly assayed in clinical laboratories and show how they support standardized database submission. The recommendations are in line with existing recommendations, most importantly the Human Genome Variation Society nomenclature, and should facilitate accurate reporting and data exchange among laboratories and thereby help to avoid future confusion.
DOI: 10.6084/m9.figshare.4286375.v1
title: Recommendations for a nomenclature system for reporting methylation aberrations in imprinted domains

description: The analysis of DNA methylation has become routine in the pipeline for diagnosis of imprinting disorders, with many publications reporting aberrant methylation associated with imprinted differentially methylated regions (DMRs). However, comparisons between these studies are routinely hampered by the lack of consistency in reporting sites of methylation evaluated. To avoid confusion surrounding nomenclature, special care is needed to communicate results accurately, especially between scientists and other health care professionals. Within the European Network for Human Congenital Imprinting Disorders we have discussed these issues and designed a nomenclature for naming imprinted DMRs as well as for reporting methylation values. We apply these recommendations for imprinted DMRs that are commonly assayed in clinical laboratories and show how they support standardized database submission. The recommendations are in line with existing recommendations, most importantly the Human Genome Variation Society nomenclature, and should facilitate accurate reporting and data exchange among laboratories and thereby help to avoid future confusion.
DOI: 10.6084/m9.figshare.4286372
title: The histone methyltransferases Set5 and Set1 have overlapping functions in gene silencing and telomere maintenance

description: Genes adjacent to telomeres are subject to transcriptional repression mediated by an integrated set of chromatin modifying and remodeling factors. The telomeres of <i>Saccharomyces cerevisiae</i> have served as a model for dissecting the function of diverse chromatin proteins in gene silencing, and their study has revealed overlapping roles for many chromatin proteins in either promoting or antagonizing gene repression. The H3K4 methyltransferase Set1, which is commonly linked to transcriptional activation, has been implicated in telomere silencing. Set5 is an H4 K5, K8, and K12 methyltransferase that functions with Set1 to promote repression at telomeres. Here, we analyzed the combined role for Set1 and Set5 in gene expression control at native yeast telomeres. Our data reveal that Set1 and Set5 promote a Sir protein-independent mechanism of repression that may primarily rely on regulation of H4K5ac and H4K8ac at telomeric regions. Furthermore, cells lacking both Set1 and Set5 have highly correlated transcriptomes to mutants in telomere maintenance pathways and display defects in telomere stability, linking their roles in silencing to protection of telomeres. Our data therefore provide insight into and clarify potential mechanisms by which Set1 contributes to telomere silencing and shed light on the function of Set5 at telomeres.
DOI: 10.6084/m9.figshare.4286372.v2
title: The histone methyltransferases Set5 and Set1 have overlapping functions in gene silencing and telomere maintenance

description: Genes adjacent to telomeres are subject to transcriptional repression mediated by an integrated set of chromatin modifying and remodeling factors. The telomeres of <i>Saccharomyces cerevisiae</i> have served as a model for dissecting the function of diverse chromatin proteins in gene silencing, and their study has revealed overlapping roles for many chromatin proteins in either promoting or antagonizing gene repression. The H3K4 methyltransferase Set1, which is commonly linked to transcriptional activation, has been implicated in telomere silencing. Set5 is an H4 K5, K8, and K12 methyltransferase that functions with Set1 to promote repression at telomeres. Here, we analyzed the combined role for Set1 and Set5 in gene expression control at native yeast telomeres. Our data reveal that Set1 and Set5 promote a Sir protein-independent mechanism of repression that may primarily rely on regulation of H4K5ac and H4K8ac at telomeric regions. Furthermore, cells lacking both Set1 and Set5 have highly correlated transcriptomes to mutants in telomere maintenance pathways and display defects in telomere stability, linking their roles in silencing to protection of telomeres. Our data therefore provide insight into and clarify potential mechanisms by which Set1 contributes to telomere silencing and shed light on the function of Set5 at telomeres.
DOI: 10.6084/m9.figshare.4286372.v1
title: The histone methyltransferases Set5 and Set1 have overlapping functions in gene silencing and telomere maintenance

description: Genes adjacent to telomeres are subject to transcriptional repression mediated by an integrated set of chromatin modifying and remodeling factors. The telomeres of <i>Saccharomyces cerevisiae</i> have served as a model for dissecting the function of diverse chromatin proteins in gene silencing, and their study has revealed overlapping roles for many chromatin proteins in either promoting or antagonizing gene repression. The H3K4 methyltransferase Set1, which is commonly linked to transcriptional activation, has been implicated in telomere silencing. Set5 is an H4 K5, K8, and K12 methyltransferase that functions with Set1 to promote repression at telomeres. Here, we analyzed the combined role for Set1 and Set5 in gene expression control at native yeast telomeres. Our data reveal that Set1 and Set5 promote a Sir protein-independent mechanism of repression that may primarily rely on regulation of H4K5ac and H4K8ac at telomeric regions. Furthermore, cells lacking both Set1 and Set5 have highly correlated transcriptomes to mutants in telomere maintenance pathways and display defects in telomere stability, linking their roles in silencing to protection of telomeres. Our data therefore provide insight into and clarify potential mechanisms by which Set1 contributes to telomere silencing and shed light on the function of Set5 at telomeres.
DOI: 10.6084/m9.figshare.4286348
title: Exploiting heterogeneous publicly available data sources for drug safety surveillance: computational framework and case studies

description: <b>Objective</b>: Driven by the need of pharmacovigilance centres and companies to routinely collect and review all available data about adverse drug reactions (ADRs) and adverse events of interest, we introduce and validate a computational framework exploiting dominant as well as emerging publicly available data sources for drug safety surveillance. <b>Methods</b>: Our approach relies on appropriate query formulation for data acquisition and subsequent filtering, transformation and joint visualization of the obtained data. We acquired data from the FDA Adverse Event Reporting System (FAERS), PubMed and Twitter. In order to assess the validity and the robustness of the approach, we elaborated on two important case studies, namely, clozapine-induced cardiomyopathy/myocarditis versus haloperidol-induced cardiomyopathy/myocarditis, and apixaban-induced cerebral hemorrhage. <b>Results</b>: The analysis of the obtained data provided interesting insights (identification of potential patient and health-care professional experiences regarding ADRs in Twitter, information/arguments against an ADR existence across all sources), while illustrating the benefits (complementing data from multiple sources to strengthen/confirm evidence) and the underlying challenges (selecting search terms, data presentation) of exploiting heterogeneous information sources, thereby advocating the need for the proposed framework. <b>Conclusions</b>: This work contributes in establishing a continuous learning system for drug safety surveillance by exploiting heterogeneous publicly available data sources via appropriate support tools.
DOI: 10.6084/m9.figshare.4286348.v2
title: Exploiting heterogeneous publicly available data sources for drug safety surveillance: computational framework and case studies

description: <b>Objective</b>: Driven by the need of pharmacovigilance centres and companies to routinely collect and review all available data about adverse drug reactions (ADRs) and adverse events of interest, we introduce and validate a computational framework exploiting dominant as well as emerging publicly available data sources for drug safety surveillance. <b>Methods</b>: Our approach relies on appropriate query formulation for data acquisition and subsequent filtering, transformation and joint visualization of the obtained data. We acquired data from the FDA Adverse Event Reporting System (FAERS), PubMed and Twitter. In order to assess the validity and the robustness of the approach, we elaborated on two important case studies, namely, clozapine-induced cardiomyopathy/myocarditis versus haloperidol-induced cardiomyopathy/myocarditis, and apixaban-induced cerebral hemorrhage. <b>Results</b>: The analysis of the obtained data provided interesting insights (identification of potential patient and health-care professional experiences regarding ADRs in Twitter, information/arguments against an ADR existence across all sources), while illustrating the benefits (complementing data from multiple sources to strengthen/confirm evidence) and the underlying challenges (selecting search terms, data presentation) of exploiting heterogeneous information sources, thereby advocating the need for the proposed framework. <b>Conclusions</b>: This work contributes in establishing a continuous learning system for drug safety surveillance by exploiting heterogeneous publicly available data sources via appropriate support tools.