cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5267743.v1
title: Burden of rheumatoid arthritis in the Nordic region, 1990–2015: a comparative analysis using the Global Burden of Disease Study 2015

description: <b>Objective</b>: To report mortality and disability due to rheumatoid arthritis (RA) in the Nordic region (Denmark, Finland, Greenland, Iceland, Norway, and Sweden) using data from the Global Burden of Disease Study (GBD) 2015. <b>Method</b>: Using the results of GBD 2015, we present rates and trends in prevalence, mortality, years of life lost, years lived with disability (YLD), and disability-adjusted life-years (DALYs) of RA in the Nordic region during 1990–2015. <b>Results</b>: In 2015, the age-standardized prevalence of RA was higher in the Nordic region than the global level (0.44%, 95% uncertainty interval 0.40–0.48%, vs 0.35%, 0.32–0.38%). For women (men), DALYs increased by 2.4% (12.9%), from 29 263 (10 909) in 1990 to 29 966 (12 311) in 2015. The burden of RA as a proportion of total DALYs in women (men) increased from 0.90% (0.29%) in 1990 to 0.94% (0.36%) in 2015. Age-standardized DALY rates declined in all countries except Denmark and Greenland between 1990 and 2015. Of 315 conditions studied, RA was ranked as the 16th (37th) leading cause of YLD in women (men) in the region. Of 195 countries studied, Greenland, Finland, Denmark, Norway, Sweden, and Iceland had the 7th, 11th, 28th, 38th, 48th, and 78th highest age-standardized YLD rates for RA, respectively. <b>Conclusions</b>: The prevalence of RA in the Nordic region is higher than the global average. Current trends in population growth and ageing suggest a potential increase in RA burden in the coming decades in the region that should be considered in healthcare resources allocation.
DOI: 10.6084/m9.figshare.5267674
title: TAVOLE DI CONCORDANZA, di Guglielmo Bartoletti

description: Tavole di concordanza dell'Archivio della Libreria privata del Marchese Suddecano Gabriello Riccardi<br>(Appendice all'interno del volume: <b>Guglielmo Bartoletti, <i>La Libreria privata del Marchese Suddecano Gabriello Riccardi. Il fondo manoscritti</i>, Firenze, Firenze University Press, 2017</b>)<br><i><b>Legenda dell’inventario topografico</b></i><b>Collocazione</b>: si tratta di due numeri romani indicanti rispettivamente lo scaffale e il palchetto della segnatura della Libreria di Gabriello.<b>Numero: </b>è il terzo elemento della segnatura della Libreria di Gabriello, costituito da un numero arabo a correre dal 1 a 1239; seguono ad esso dei numeri convenzionali che indicano le successive tappe di incremento di tale Libreria.<b>bis</b>: si tratta dell’indicazione di una singola parte del manoscritto, nel caso in cui manoscritti di provenienza diversa fossero stati rilegati in unico volume da Gabriello.<b>Titolo</b>: è l’espressione che troviamo sul dorso originale per indicare il contenuto del volume; nel caso frequente in cui sia andato perduto, lo abbiamo sostituito, riadattandolo in parte, con l’espressione usata dall’Inventario e stima del 1810 per descrivere il medesimo manoscritto.<b>O. D. R. T</b>: si tratta della segnalazione che l’ultimo numero della segnatura di Gabriello, quello arabo, è riportato anche sul manoscritto stesso in varia forma: O = in forma originale; D = sul dorso; R = riportato da mano successiva; T = vi è rimasta solo una traccia.<b>Indici</b>: si tratta della persona che eventualmente redatto l’indice sul manoscritto stesso. Gabriello stesso o il Mehus.<b>Legatura</b>: è l’indicazione che si tratta di una legatura eseguita dal legatore di fiducia di Gabriello, Giuseppe Pagani; la sigla P indica che la legatura è attribuibile al Pagani per confronto, la sigla B significa che l’indicazione compare nella tesi di laurea di G. Bani.<b>Bullettone</b>: si indica quando il manoscritto è descritto nel catalogo alfabetico della Libreria di Gabriello, noto come “Bullettone”.<b>Mehus</b>: indica la presenza di quel manoscritto negli spogli del Mehus.<b>F/R</b>: indica che la segnatura di Gabriello è riportata, accanto alla nuova nelle illustrazioni di codici rispettivamente del Fontani e del Rigoli.<b>Provenienza</b>: sono riportate, quando individuate, le provenienze da cui Gabriello ha attinto per la costruzione della sua raccolta.<b>Ricc.</b>: è la segnatura attuale del manoscritto.<b>bis:</b> è l’indicazione della sezione cui ci si riferisce, nel caso di manoscritti compositi.<b>Osservazioni</b>: si tratta di espressioni molto concise con le quali si ritiene utile dare ulteriori informazioni o chiarimenti.
DOI: 10.6084/m9.figshare.5267623
title: QSAR, docking, ADMET, and system pharmacology studies on tormentic acid derivatives for anticancer activity

description: To explore the anticancer compounds from tormentic acid derivatives, a quantitative structure–activity relationship (QSAR) model was developed by the multiple linear regression methods. The developed QSAR model yielded a high activity–descriptors relationship accuracy of 94% referred by regression coefficient (<i>r</i><sup>2</sup> = .94) and a high activity prediction accuracy of 91%. The QSAR study indicates that chemical descriptors, chiV5, T_T_Cl_7, T_2_T_4, SsCH3count, and Epsilon3 are significantly correlated with anticancer activity. This validated model was further been used for virtual screening and thus identification of new potential breast cancer inhibitors. Lipinski’s rule of five, ADMET risk and synthetic accessibility are used to filter false positive hits. Filtered compounds were then docked to identify the possible target binding pocket, to obtain a set of aligned ligand poses and to prioritize the predicted active compounds. The scrutinized compounds, as well as their metabolites, were predicted and analyzed for different pharmacokinetics parameters such as absorption, distribution, metabolism, excretion, and toxicity. Finally, the top-ranked compound NB-12 was evaluated by system pharmacology approach. Later studied the metabolic networks, disease biomarker networks, pathway maps, drug-target networks and generate significant gene networks. The strategy applied in this research work may act as a framework for rational design of potential anticancer drugs.
DOI: 10.6084/m9.figshare.5267620
title: Molecular dynamics simulations of Hsp40 J-domain mutants identifies disruption of the critical HPD-motif as the key factor for impaired curing <i>in vivo</i> of the yeast prion [<i>URE3</i>]

description: Genetic screens using <i>Saccharomyces cerevisiae</i> have identified an array of Hsp40 (Ydj1p) J-domain mutants that are impaired in the ability to cure the yeast [<i>URE3</i>] prion through disrupting functional interactions with Hsp70. However, biochemical analysis of some of these Hsp40 J-domain mutants has so far failed to provide major insight into the specific functional changes in Hsp40-Hsp70 interactions. To explore the detailed structural and dynamic properties of the Hsp40 J-domain, 20 ns molecular dynamic simulations of 4 mutants (D9A, D36A, A30T, and F45S) and wild-type J-domain were performed, followed by Hsp70 docking simulations. Results demonstrated that although the Hsp70 interaction mechanism of the mutants may vary, the major structural change was targeted to the critical HPD motif of the J-domain. Our computational analysis fits well with previous yeast genetics studies regarding highlighting the importance of J-domain function in prion propagation. During the molecular dynamics simulations several important residues were identified and predicted to play an essential role in J-domain structure. Among these residues, Y26 and F45 were confirmed, using both <i>in silico</i> and <i>in vivo</i> methods, as being critical for Ydj1p function.
DOI: 10.6084/m9.figshare.5267623.v1
title: QSAR, docking, ADMET, and system pharmacology studies on tormentic acid derivatives for anticancer activity

description: To explore the anticancer compounds from tormentic acid derivatives, a quantitative structure–activity relationship (QSAR) model was developed by the multiple linear regression methods. The developed QSAR model yielded a high activity–descriptors relationship accuracy of 94% referred by regression coefficient (<i>r</i><sup>2</sup> = .94) and a high activity prediction accuracy of 91%. The QSAR study indicates that chemical descriptors, chiV5, T_T_Cl_7, T_2_T_4, SsCH3count, and Epsilon3 are significantly correlated with anticancer activity. This validated model was further been used for virtual screening and thus identification of new potential breast cancer inhibitors. Lipinski’s rule of five, ADMET risk and synthetic accessibility are used to filter false positive hits. Filtered compounds were then docked to identify the possible target binding pocket, to obtain a set of aligned ligand poses and to prioritize the predicted active compounds. The scrutinized compounds, as well as their metabolites, were predicted and analyzed for different pharmacokinetics parameters such as absorption, distribution, metabolism, excretion, and toxicity. Finally, the top-ranked compound NB-12 was evaluated by system pharmacology approach. Later studied the metabolic networks, disease biomarker networks, pathway maps, drug-target networks and generate significant gene networks. The strategy applied in this research work may act as a framework for rational design of potential anticancer drugs.
DOI: 10.6084/m9.figshare.5267614
title: Assessing joint destruction in the knees of patients with rheumatoid arthritis by using a semi-automated software for magnetic resonance imaging: therapeutic effect of methotrexate plus etanercept compared with methotrexate monotherapy

description: <b>Objectives:</b> To evaluate the prevention of knee joint destruction and clinical efficacy of methotrexate (MTX) plus etanercept (ETN) compared with MTX monotherapy in patients with rheumatoid arthritis (RA) by using semi-automated software for magnetic resonance imaging (MRI) scan analysis. <b>Materials and methods:</b> This study enrolled patients with active moderate-to-severe RA who displayed an inadequate response to oral MTX at screening. Patients were assigned to receive either MTX plus ETN or MTX monotherapy (≥10 mg/week). The primary endpoint was the quantitative knee cartilage volume using our software developed for MRI scan analysis. <b>Results:</b> A total of 18 female patients were enrolled in this study and allocated to the MTX + ETN group (<i>n</i> = 9) or the MTX monotherapy group (<i>n</i> = 9). At 52 weeks, the quantitative knee cartilage volume was significantly reduced compared with baseline in both groups (MTX plus ETN group: 2.3 ± 2.3 cm<sup>3</sup>; MTX monotherapy group: 2.4 ± 1.6 cm<sup>3</sup>); however, the difference was not significant. <b>Conclusion:</b> The semi-automated software for MRI scan analysis can reveal useful and potentially clinically important information about the characteristics of knee joint destruction in patients with RA.
DOI: 10.6084/m9.figshare.5267614.v1
title: Assessing joint destruction in the knees of patients with rheumatoid arthritis by using a semi-automated software for magnetic resonance imaging: therapeutic effect of methotrexate plus etanercept compared with methotrexate monotherapy

description: <b>Objectives:</b> To evaluate the prevention of knee joint destruction and clinical efficacy of methotrexate (MTX) plus etanercept (ETN) compared with MTX monotherapy in patients with rheumatoid arthritis (RA) by using semi-automated software for magnetic resonance imaging (MRI) scan analysis. <b>Materials and methods:</b> This study enrolled patients with active moderate-to-severe RA who displayed an inadequate response to oral MTX at screening. Patients were assigned to receive either MTX plus ETN or MTX monotherapy (≥10 mg/week). The primary endpoint was the quantitative knee cartilage volume using our software developed for MRI scan analysis. <b>Results:</b> A total of 18 female patients were enrolled in this study and allocated to the MTX + ETN group (<i>n</i> = 9) or the MTX monotherapy group (<i>n</i> = 9). At 52 weeks, the quantitative knee cartilage volume was significantly reduced compared with baseline in both groups (MTX plus ETN group: 2.3 ± 2.3 cm<sup>3</sup>; MTX monotherapy group: 2.4 ± 1.6 cm<sup>3</sup>); however, the difference was not significant. <b>Conclusion:</b> The semi-automated software for MRI scan analysis can reveal useful and potentially clinically important information about the characteristics of knee joint destruction in patients with RA.
DOI: 10.6084/m9.figshare.5267620.v2
title: Molecular dynamics simulations of Hsp40 J-domain mutants identifies disruption of the critical HPD-motif as the key factor for impaired curing <i>in vivo</i> of the yeast prion [<i>URE3</i>]

description: Genetic screens using <i>Saccharomyces cerevisiae</i> have identified an array of Hsp40 (Ydj1p) J-domain mutants that are impaired in the ability to cure the yeast [<i>URE3</i>] prion through disrupting functional interactions with Hsp70. However, biochemical analysis of some of these Hsp40 J-domain mutants has so far failed to provide major insight into the specific functional changes in Hsp40-Hsp70 interactions. To explore the detailed structural and dynamic properties of the Hsp40 J-domain, 20 ns molecular dynamic simulations of 4 mutants (D9A, D36A, A30T, and F45S) and wild-type J-domain were performed, followed by Hsp70 docking simulations. Results demonstrated that although the Hsp70 interaction mechanism of the mutants may vary, the major structural change was targeted to the critical HPD motif of the J-domain. Our computational analysis fits well with previous yeast genetics studies regarding highlighting the importance of J-domain function in prion propagation. During the molecular dynamics simulations several important residues were identified and predicted to play an essential role in J-domain structure. Among these residues, Y26 and F45 were confirmed, using both <i>in silico</i> and <i>in vivo</i> methods, as being critical for Ydj1p function.
DOI: 10.6084/m9.figshare.5267593
title: Stratigraphy, petrogenesis and geodynamic setting of the Late Cretaceous volcanism on the SW margin of the Black Sea, Turkey

description: The full geochemical dataset in MS Excel workbook format.
DOI: 10.6084/m9.figshare.5267599.v1
title: Density functional theory of doped superfluid liquid helium and nanodroplets

description: During the last decade, density function theory (DFT) in its static and dynamic time dependent forms, has emerged as a powerful tool to describe the structure and dynamics of doped liquid helium and droplets. In this review, we summarise the activity carried out in this field within the DFT framework since the publication of the previous review article on this subject [M. Barranco <i>et al.</i>, J. Low Temp. Phys. <b>142</b>, 1 (2006)]. Furthermore, a comprehensive presentation of the actual implementations of helium DFT is given, which have not been discussed in the individual articles or are scattered in the existing literature.
DOI: 10.6084/m9.figshare.5267620.v1
title: Molecular dynamics simulations of Hsp40 J-domain mutants identifies disruption of the critical HPD-motif as the key factor for impaired curing <i>in vivo</i> of the yeast prion [<i>URE3</i>]

description: Genetic screens using <i>Saccharomyces cerevisiae</i> have identified an array of Hsp40 (Ydj1p) J-domain mutants that are impaired in the ability to cure the yeast [<i>URE3</i>] prion through disrupting functional interactions with Hsp70. However, biochemical analysis of some of these Hsp40 J-domain mutants has so far failed to provide major insight into the specific functional changes in Hsp40-Hsp70 interactions. To explore the detailed structural and dynamic properties of the Hsp40 J-domain, 20 ns molecular dynamic simulations of 4 mutants (D9A, D36A, A30T, and F45S) and wild-type J-domain were performed, followed by Hsp70 docking simulations. Results demonstrated that although the Hsp70 interaction mechanism of the mutants may vary, the major structural change was targeted to the critical HPD motif of the J-domain. Our computational analysis fits well with previous yeast genetics studies regarding highlighting the importance of J-domain function in prion propagation. During the molecular dynamics simulations several important residues were identified and predicted to play an essential role in J-domain structure. Among these residues, Y26 and F45 were confirmed, using both <i>in silico</i> and <i>in vivo</i> methods, as being critical for Ydj1p function.
DOI: 10.6084/m9.figshare.5267572
title: <i>N</i><sup>1</sup>, <i>N</i><sup>14</sup>-diferuloylspermine as an antioxidative phytochemical contained in leaves of <i>Cardamine fauriei</i>

description: Most Brassicaceae vegetables are ideal dietary sources of antioxidants beneficial for human health. <i>Cardamine fauriei</i> (Ezo-wasabi in Japanese) is a wild, edible Brassicaceae herb native to Hokkaido, Japan. To clarify the main antioxidative phytochemical, an 80% methanol extraction from the leaves was fractionated with Diaion® HP-20, Sephadex® LH-20, and Sep-Pak® C18 cartridges, and the fraction with strong antioxidant activity depending on DPPH method was purified by HPLC. Based on the analyses using HRESIMS and MS/MS, the compound might be <i>N</i><sup>1</sup>, <i>N</i><sup>14</sup>-diferuloylspermine. This rare phenol compound was chemically synthesized, whose data on HPLC, MS and <sup>1</sup>H NMR were compared with those of naturally derived compound from <i>C. fauriei</i>. All results indicated they were the same compound. The radical-scavenging properties of diferuloylspermine were evaluated by ORAC and ESR spin trapping methods, with the diferuloylspermine showing high scavenging activities of the ROO<sup>·</sup>, O<sub>2</sub><sup>·−</sup>, and HO<sup>·</sup> radicals as was those of conventional antioxidants.
DOI: 10.6084/m9.figshare.5267593.v1
title: Stratigraphy, petrogenesis and geodynamic setting of the Late Cretaceous volcanism on the SW margin of the Black Sea, Turkey

description: The full geochemical dataset in MS Excel workbook format.
DOI: 10.6084/m9.figshare.5267572.v1
title: <i>N</i><sup>1</sup>, <i>N</i><sup>14</sup>-diferuloylspermine as an antioxidative phytochemical contained in leaves of <i>Cardamine fauriei</i>

description: Most Brassicaceae vegetables are ideal dietary sources of antioxidants beneficial for human health. <i>Cardamine fauriei</i> (Ezo-wasabi in Japanese) is a wild, edible Brassicaceae herb native to Hokkaido, Japan. To clarify the main antioxidative phytochemical, an 80% methanol extraction from the leaves was fractionated with Diaion® HP-20, Sephadex® LH-20, and Sep-Pak® C18 cartridges, and the fraction with strong antioxidant activity depending on DPPH method was purified by HPLC. Based on the analyses using HRESIMS and MS/MS, the compound might be <i>N</i><sup>1</sup>, <i>N</i><sup>14</sup>-diferuloylspermine. This rare phenol compound was chemically synthesized, whose data on HPLC, MS and <sup>1</sup>H NMR were compared with those of naturally derived compound from <i>C. fauriei</i>. All results indicated they were the same compound. The radical-scavenging properties of diferuloylspermine were evaluated by ORAC and ESR spin trapping methods, with the diferuloylspermine showing high scavenging activities of the ROO<sup>·</sup>, O<sub>2</sub><sup>·−</sup>, and HO<sup>·</sup> radicals as was those of conventional antioxidants.
DOI: 10.6084/m9.figshare.5267527
title: Refined data of forager orientation shifts under a ±45º polar filter and shifts during reorientation .xlsx

description: Data for the manuscript entitled " Polarised light use in the nocturnal bull ant <i>Myrmicea midas</i>". Published in Royal Society Open Science.
DOI: 10.6084/m9.figshare.5267527.v1
title: Refined data of forager orientation shifts under a ±45º polar filter and shifts during reorientation .xlsx

description: Data for the manuscript entitled " Polarised light use in the nocturnal bull ant <i>Myrmicea midas</i>". Published in Royal Society Open Science.
DOI: 10.6084/m9.figshare.5267473
title: forager orientation shifts and reorientation

description: Data for the manuscript entitled <b>"Polarized light use in the nocturnal bull ant, </b><i>Myrmecia midas",</i> published in Royal Society Open Science.
DOI: 10.6084/m9.figshare.5267461
title: Garlic gene

description: Full-length transcripts of garlic were obtained by single-molecule long-read sequencing.
DOI: 10.6084/m9.figshare.5267467
title: Are there autochthonous <i>Ferrissia</i> (Mollusca: Planorbidae) in the Palaearctic? Molecular evidence of a widespread North American invasion of the Old World

description: In the last few decades, findings of freshwater limpets belonging to the genus <i>Ferrissia</i> have been frequent and widely distributed throughout the Palaearctic and beyond. The widespread presence of a Nearctic alien taxon was proved, but no consensus was achieved about the possible existence of autochthonous <i>Ferrissia</i> taxa in the area, an occurrence which would be supported by the presence of gastropod fossils attributed to the genus throughout Eurasia and North Africa. In order to test the hypothesis of a possible persistence of autochthonous <i>Ferrissia</i> taxa in the Palaearctic to the present day, all the published data on the genetic diversity of <i>Ferrissia</i> populations occurring in the area were reviewed, expanding also the currently available dataset through dedicated sampling surveys in Italy, Malta and Spain. Here, based on currently published and novel large ribosomal subunit 16S rRNA (16S) and cytochrome oxidase sub-unit 1 (COI) sequences, the presence of the allochthonous <i>Ferrissia californica</i> in the whole Palaearctic was confirmed. Conversely, no evidence supporting the presence of autochthonous <i>Ferrissia</i> taxa was obtained. <i>Ferrissia californica</i> proved to be a highly invasive taxon (in spite of its extremely low genetic diversity) throughout the invaded regions, which is possibly related to the species’ ability of asexual reproduction. Finally, the need to investigate the possible impact exerted by <i>F. californica</i> on the autochthonous Palaearctic biota is briefly stressed.
DOI: 10.6084/m9.figshare.5267467.v2
title: Are there autochthonous <i>Ferrissia</i> (Mollusca: Planorbidae) in the Palaearctic? Molecular evidence of a widespread North American invasion of the Old World

description: In the last few decades, findings of freshwater limpets belonging to the genus <i>Ferrissia</i> have been frequent and widely distributed throughout the Palaearctic and beyond. The widespread presence of a Nearctic alien taxon was proved, but no consensus was achieved about the possible existence of autochthonous <i>Ferrissia</i> taxa in the area, an occurrence which would be supported by the presence of gastropod fossils attributed to the genus throughout Eurasia and North Africa. In order to test the hypothesis of a possible persistence of autochthonous <i>Ferrissia</i> taxa in the Palaearctic to the present day, all the published data on the genetic diversity of <i>Ferrissia</i> populations occurring in the area were reviewed, expanding also the currently available dataset through dedicated sampling surveys in Italy, Malta and Spain. Here, based on currently published and novel large ribosomal subunit 16S rRNA (16S) and cytochrome oxidase sub-unit 1 (COI) sequences, the presence of the allochthonous <i>Ferrissia californica</i> in the whole Palaearctic was confirmed. Conversely, no evidence supporting the presence of autochthonous <i>Ferrissia</i> taxa was obtained. <i>Ferrissia californica</i> proved to be a highly invasive taxon (in spite of its extremely low genetic diversity) throughout the invaded regions, which is possibly related to the species’ ability of asexual reproduction. Finally, the need to investigate the possible impact exerted by <i>F. californica</i> on the autochthonous Palaearctic biota is briefly stressed.