cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1598001.v1
title: Lipopolysaccharides may aggravate apoptosis through accumulation of autophagosomes in alveolar macrophages of human silicosis

description: Silica dust mainly attacks alveolar macrophages (AMs) and increases the apoptosis of AMs in silicosis patients. However, it is still unclear whether autophagy is affected. Autophagy mainly has defensive functions in response to stress, contributing to cell survival in adverse conditions, and conversely it has also been implicated in cell death. Lipopolysaccharide (LPS) is able to induce autophagy and apoptosis in macrophages. The role of LPS in autophagy and apoptosis in AMs of silicosis patients is unknown. In this study, we collected AMs from 53 male workers exposed to silica and divided them into an observer (control) group, and stage I, II and III patient groups. We found increased levels of LC3B, SQSTM1/p62 and BECN1, whereas the phosphorylation of MTOR, and levels of LAMP2, TLR4, MYD88, TICAM1, as well as the number of lysosomes decreased with the development of silicosis. LPS stimulation triggered autophagy and increased levels of SQSTM1 in AMs. The autophagy inhibitor, 3-methyladenine (3MA), inhibited LPS-induced apoptosis in the AMs of silicosis patients. Moreover, 3 MA reversed the LPS-induced decrease in BCL2 and the increase in BAX and CASP3 levels in AMs. These results suggest that autophagosomes accumulate in AMs during silicosis progression. LPS can induce the formation of autophagosomes through a TLR4-dependent pathway, and LPS may exacerbate the apoptosis in AMs. Blockade of the formation of autophagosomes may inhibit LPS-induced apoptosis via the intrinsic apoptotic pathway in AMs. These findings describe novel mechanisms that may lead to new preventive and therapeutic strategies for pulmonary fibrosis.
DOI: 10.6084/m9.figshare.1597994
title: Infectivity-associated PrP<sup>Sc</sup> and disease duration-associated PrP<sup>Sc</sup> of mouse BSE prions

description: Disease-related prion protein (PrP<sup>Sc</sup>), which is a structural isoform of the host-encoded cellular prion protein, is thought to be a causative agent of transmissible spongiform encephalopathies. However, the specific role of PrP<sup>Sc</sup> in prion pathogenesis and its relationship to infectivity remain controversial. A time-course study of prion-affected mice was conducted, which showed that the prion infectivity was not simply proportional to the amount of PrP<sup>Sc</sup> in the brain. Centrifugation (20,000 ×<i>g</i>) of the brain homogenate showed that most of the PrP<sup>Sc</sup> was precipitated into the pellet, and the supernatant contained only a slight amount of PrP<sup>Sc</sup>. Interestingly, mice inoculated with the obtained supernatant showed incubation periods that were approximately 15 d longer than those of mice inoculated with the crude homogenate even though both inocula contained almost the same infectivity. Our results suggest that a small population of fine PrP<sup>Sc</sup> may be responsible for prion infectivity and that large, aggregated PrP<sup>Sc</sup> may contribute to determining prion disease duration.
DOI: 10.6084/m9.figshare.1597995.v2
title: Pegasus Basin, eastern New Zealand: A stratigraphic record of subsidence and subduction, ancient and modern

description: The stratigraphic architecture of a thick (c. 9000 m) Albian–Recent sedimentary succession within the Pegasus Basin is presented here, based primarily on interpretation of the New Zealand Government's ‘PEG09’ 2D reconnaissance seismic survey. The basin lies immediately east and outboard of the Hikurangi subduction zone, and formed mainly because of Neogene downwarping of the underlying Pacific Plate near the transition from subduction to oblique-slip faulting. The basin fill is little deformed by the Neogene–Recent convergent margin tectonics that pervasively deform the adjacent East Coast Basin. Four large-scale tectonostratigraphic units are differentiated: (1) metasedimentary ‘basement’ rocks, deposited and accreted within the Gondwana Mesozoic accretionary wedge; (2) Early Cretaceous Large Igneous Province crust of the Hikurangi Plateau; (3) non-accreted ‘cover’ strata, incorporating rocks age-equivalent to the youngest parts of the Gondwana accretionary wedge, plus the overlying Late Cretaceous and Paleogene rocks deposited during thermal subsidence; and (4) Neogene–Recent strata deposited since the renewal of subduction beneath eastern North Island. The pre-Neogene geology illustrated by the seismic data describes the Mesozoic subduction along the Gondwana margin, ‘frozen’ at the time when active subduction accretion ceased at c. 110–105 Ma. The geology of Pegasus Basin also provides an insight into the much-debated relationship between ‘basement’ and ‘cover’ rocks in the East Coast Basin. This study is also relevant to the assessment of the petroleum potential of the basin, which is currently held under licence.
DOI: 10.6084/m9.figshare.1597994.v2
title: Infectivity-associated PrP<sup>Sc</sup> and disease duration-associated PrP<sup>Sc</sup> of mouse BSE prions

description: Disease-related prion protein (PrP<sup>Sc</sup>), which is a structural isoform of the host-encoded cellular prion protein, is thought to be a causative agent of transmissible spongiform encephalopathies. However, the specific role of PrP<sup>Sc</sup> in prion pathogenesis and its relationship to infectivity remain controversial. A time-course study of prion-affected mice was conducted, which showed that the prion infectivity was not simply proportional to the amount of PrP<sup>Sc</sup> in the brain. Centrifugation (20,000 ×<i>g</i>) of the brain homogenate showed that most of the PrP<sup>Sc</sup> was precipitated into the pellet, and the supernatant contained only a slight amount of PrP<sup>Sc</sup>. Interestingly, mice inoculated with the obtained supernatant showed incubation periods that were approximately 15 d longer than those of mice inoculated with the crude homogenate even though both inocula contained almost the same infectivity. Our results suggest that a small population of fine PrP<sup>Sc</sup> may be responsible for prion infectivity and that large, aggregated PrP<sup>Sc</sup> may contribute to determining prion disease duration.
DOI: 10.6084/m9.figshare.1597995.v1
title: Pegasus Basin, eastern New Zealand: A stratigraphic record of subsidence and subduction, ancient and modern

description: The stratigraphic architecture of a thick (c. 9000 m) Albian–Recent sedimentary succession within the Pegasus Basin is presented here, based primarily on interpretation of the New Zealand Government's ‘PEG09’ 2D reconnaissance seismic survey. The basin lies immediately east and outboard of the Hikurangi subduction zone, and formed mainly because of Neogene downwarping of the underlying Pacific Plate near the transition from subduction to oblique-slip faulting. The basin fill is little deformed by the Neogene–Recent convergent margin tectonics that pervasively deform the adjacent East Coast Basin. Four large-scale tectonostratigraphic units are differentiated: (1) metasedimentary ‘basement’ rocks, deposited and accreted within the Gondwana Mesozoic accretionary wedge; (2) Early Cretaceous Large Igneous Province crust of the Hikurangi Plateau; (3) non-accreted ‘cover’ strata, incorporating rocks age-equivalent to the youngest parts of the Gondwana accretionary wedge, plus the overlying Late Cretaceous and Paleogene rocks deposited during thermal subsidence; and (4) Neogene–Recent strata deposited since the renewal of subduction beneath eastern North Island. The pre-Neogene geology illustrated by the seismic data describes the Mesozoic subduction along the Gondwana margin, ‘frozen’ at the time when active subduction accretion ceased at c. 110–105 Ma. The geology of Pegasus Basin also provides an insight into the much-debated relationship between ‘basement’ and ‘cover’ rocks in the East Coast Basin. This study is also relevant to the assessment of the petroleum potential of the basin, which is currently held under licence.
DOI: 10.6084/m9.figshare.1597994.v1
title: Infectivity-associated PrP<sup>Sc</sup> and disease duration-associated PrP<sup>Sc</sup> of mouse BSE prions

description: SummaryDisease-related prion protein (PrP<sup>Sc</sup>), which is a structural isoform of the host-encoded cellular prion protein, is thought to be a causative agent of transmissible spongiform encephalopathies. However, the specific role of PrP<sup>Sc</sup> in prion pathogenesis and its relationship to infectivity remain controversial. A time-course study of prion-affected mice was conducted, which showed that the prion infectivity was not simply proportional to the amount of PrP<sup>Sc</sup> in the brain. Centrifugation (20,000 ×<i>g</i>) of the brain homogenate showed that most of the PrP<sup>Sc</sup> was precipitated into the pellet, and the supernatant contained only a slight amount of PrP<sup>Sc</sup>. Interestingly, mice inoculated with the obtained supernatant showed incubation periods that were approximately 15 days longer than those of mice inoculated with the crude homogenate even though both inocula contained almost the same infectivity. Our results suggest that a small population of fine PrP<sup>Sc</sup> may be responsible for prion infectivity and that large, aggregated PrP<sup>Sc</sup> may contribute to determining prion disease duration.
DOI: 10.6084/m9.figshare.1597730
title: <i>Ophrys pseudomigoutiana</i> (Orchidaceae), a new species from Tunisia

description: The studied taxon has been attached since its discovery in Tunisia to <i>Ophrys migoutiana</i> H. Gay, a plant described in Algeria, which remains little known to botanists. This was already a net progress, ending the historical confusion that mixed many taxa under the name “<i>O. fusca</i>”. However, the recent observation of the true <i>O. migoutiana</i> near Medea in Algeria allowed us to distinguish the Algerian and the Tunisian taxa, the latter being <i>a priori</i> not yet formally described. The Tunisian taxon shares some similarities with oriental taxa of the <i>Ophrys cinereophila</i> / <i>Ophrys creberrima</i> group, and is named here as a new species <i>Ophrys pseudomigoutiana</i>. Its phenotypic variability is illustrated by several photographs and colour plates with fresh dissected flowers. Its chorology in Tunisia is detailed and suggests that it could also be present in eastern Algeria.
DOI: 10.6084/m9.figshare.1597730.v1
title: <i>Ophrys pseudomigoutiana</i> (Orchidaceae), a new species from Tunisia

description: The studied taxon has been attached since its discovery in Tunisia to <i>Ophrys migoutiana</i> H. Gay, a plant described in Algeria, which remains little known to botanists. This was already a net progress, ending the historical confusion that mixed many taxa under the name “<i>O. fusca</i>”. However, the recent observation of the true <i>O. migoutiana</i> near Medea in Algeria allowed us to distinguish the Algerian and the Tunisian taxa, the latter being <i>a priori</i> not yet formally described. The Tunisian taxon shares some similarities with oriental taxa of the <i>Ophrys cinereophila</i> / <i>Ophrys creberrima</i> group, and is named here as a new species <i>Ophrys pseudomigoutiana</i>. Its phenotypic variability is illustrated by several photographs and colour plates with fresh dissected flowers. Its chorology in Tunisia is detailed and suggests that it could also be present in eastern Algeria.
DOI: 10.6084/m9.figshare.1597726
title: ￼Cybersecurity for Science: Risk Management-based Approach from the Center for Trustworthy Scientific Cyberinfrastructure

description: Notes from lecture to Indiana University Information Security Law, B587 class. November 9th, 2015.
DOI: 10.6084/m9.figshare.1597730.v3
title: <i>Ophrys pseudomigoutiana</i> (Orchidaceae), a new species from Tunisia

description: The studied taxon has been attached since its discovery in Tunisia to <i>Ophrys migoutiana</i> H. Gay, a plant described in Algeria, which remains little known to botanists. This was already a net progress, ending the historical confusion that mixed many taxa under the name “<i>O. fusca</i>”. However, the recent observation of the true <i>O. migoutiana</i> near Medea in Algeria allowed us to distinguish the Algerian and the Tunisian taxa, the latter being <i>a priori</i> not yet formally described. The Tunisian taxon shares some similarities with oriental taxa of the <i>Ophrys cinereophila</i> / <i>Ophrys creberrima</i> group, and is named here as a new species <i>Ophrys pseudomigoutiana</i>. Its phenotypic variability is illustrated by several photographs and colour plates with fresh dissected flowers. Its chorology in Tunisia is detailed and suggests that it could also be present in eastern Algeria.
DOI: 10.6084/m9.figshare.1597726.v1
title: ￼Cybersecurity for Science: Risk Management-based Approach from the Center for Trustworthy Scientific Cyberinfrastructure

description: Notes from lecture to Indiana University Information Security Law, B587 class. November 9th, 2015.
DOI: 10.6084/m9.figshare.1597730.v2
title: <i>Ophrys pseudomigoutiana</i> (Orchidaceae), a new species from Tunisia

description: The studied taxon has been attached since its discovery in Tunisia to <i>Ophrys migoutiana</i> H. Gay, a plant described in Algeria, which remains little known to botanists. This was already a net progress, ending the historical confusion that mixed many taxa under the name “<i>O. fusca</i>”. However, the recent observation of the true <i>O. migoutiana</i> near Medea in Algeria allowed us to distinguish the Algerian and the Tunisian taxa, the latter being <i>a priori</i> not yet formally described. The Tunisian taxon shares some similarities with oriental taxa of the <i>Ophrys cinereophila</i> / <i>Ophrys creberrima</i> group, and is named here as a new species <i>Ophrys pseudomigoutiana</i>. Its phenotypic variability is illustrated by several photographs and colour plates with fresh dissected flowers. Its chorology in Tunisia is detailed and suggests that it could also be present in eastern Algeria.
DOI: 10.6084/m9.figshare.1597719
title: Improving the Network Scale-Up Estimator: Incorporating Means of Sums, Recursive Back Estimation, and Sampling Weights Data File

description: In the spring of 2014 the Nebraska Community Survey was sent to a random sample of 2,000 households in Nebraska. The sample was obtained from the United States Postal Service delivery sequence file (DSF) through the Bureau of Sociological Research at the University of Nebraska-Lincoln. Seasonal and vacant households were removed from the sample by the provider. The DSF covers approximately 97 percent of U.S. Households and provides a reasonable frame for the Nebraska population. The Institutional Review Board at the University of Nebraska-Lincoln approved the research protocol and granted the project an exempt status (IRB# 20140314288 EX). Each household in the sample was sent a packet which included a letter introducing the survey, a one dollar incentive, a copy of the survey questionnaire, and a pre-paid return envelope. The person in the household to take the survey was selected using the next-birthday method, a quasi-probability selection design. Eligible respondents had to be at least 19 years old, the age of majority in Nebraska, and be the next person in the household to have a birthday after April 14, 2014. A week after the initial mailing a reminder postcard was sent to any households that had not responded to the initial mailing. Three weeks later, a second survey packet was sent to non-responding households. If at any time a respondent asked to be removed from the address list all further mailings were stopped. After the third mailing data was collected for approximately another six weeks, allowing respondents ample time to complete and return their survey. More information can be found in the complete publication.
DOI: 10.6084/m9.figshare.1597720
title: Codebook - Improving the Network Scale-Up Estimator: Incorporating Means of Sums, Recursive Back Estimation, and Sampling Weights

description: Codebook for the MoS datafile and PLOS ONE paper Improving the Network Scale-Up Estimator: Incorporating Means of Sums, Recursive Back Estimation, and Sampling Weights.
DOI: 10.6084/m9.figshare.1597718
title: Invasive-Plant Management and Nitrogen Removal

description: This project contains field data from three locations on the Hudson River (NY, USA). We monitored small-scale removals of Phragmites australis to determine effects on sediment nitrogen concentrations and microbial denitrification rates. We also characterized the plant communities that recolonized treated locations, relative to reference (untreated) communities dominated by either <i>Phragmites </i>or <i>Typha angustifolia</i>.<br>Results from analyses of these data are reported in Alldred et al. 2016, "Effects of invasive-plant management on nitrogen-removal ecosystem services in freshwater tidal marshes." When using these data, please use the following citation:<br>Alldred M, Baines SB, Findlay S (2016) Effects of Invasive-Plant Management on Nitrogen-Removal Services in Freshwater Tidal Marshes. PLoS ONE 11(2): e0149813. https://doi.org/10.1371/journal.pone.0149813<br>
DOI: 10.6084/m9.figshare.1597712
title: Figures for Scrapie strain-Tau Manuscript

description: These figures display the data for comparing total and phosphorylated tau data from 139A, ME7 and 22L infected mice and contrast that with CJD.
DOI: 10.6084/m9.figshare.1597718.v1
title: Invasive-Plant Management and Nitrogen Removal

description: This project contains field data from three locations on the Hudson River (NY, USA). We monitored small-scale removals of Phragmites australis to determine effects on sediment nitrogen concentrations and microbial denitrification rates. We also characterized the plant communities that recolonized treated locations, relative to reference (untreated) communities dominated by either <i>Phragmites </i>or <i>Typha angustifolia</i>.<br>Results from analyses of these data are reported in Alldred et al. 2016, "Effects of invasive-plant management on nitrogen-removal ecosystem services in freshwater tidal marshes." When using these data, please use the following citation:<br>Alldred M, Baines SB, Findlay S (2016) Effects of Invasive-Plant Management on Nitrogen-Removal Services in Freshwater Tidal Marshes. PLoS ONE 11(2): e0149813. https://doi.org/10.1371/journal.pone.0149813<br>
DOI: 10.6084/m9.figshare.1597712.v1
title: Figures for Scrapie strain-Tau Manuscript

description: These figures display the data for comparing total and phosphorylated tau data from 139A, ME7 and 22L infected mice and contrast that with CJD.
DOI: 10.6084/m9.figshare.1597710
title: A genome-scale investigation of how sequence-, function-, and tree-based gene properties influence phylogenetic inference

description: Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, GC content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal and could be useful in guiding the choice of phylogenetic markers.
DOI: 10.6084/m9.figshare.1597701
title: Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus

description: In <i>Staphylococcus aureus</i>, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in <i>S. aureus</i>, we generated updated GenBank files for three commonly used <i>S. aureus </i>strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for &gt;260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in <i>S. aureus</i>, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome anno- tation in <i>S. aureus</i>, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in <i>S. aureus </i>and demonstrate that the newly identified <i>tsr25 </i>is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the <i>S. aureus </i>research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions. <br>