cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7012202
title: Update 2018 - The future cost of electrical energy storage based on experience rates

description: This dataset compiles cumulative capacity and product price data for electrical energy storage technologies, including the respective regression parameters to construct experience curves. <br><br>The update includes new data from up to 2017. <br><br>Update to paper: O. Schmidt, A. Hawkes, A. Gambhir & I. Staffell. The future cost of electrical energy storage based on experience rates. Nat. Energy 2, 17110 (2017).<br>Link to the original paper with original dataset: http://dx.doi.org/10.1038/nenergy.2017.110<br>
DOI: 10.6084/m9.figshare.7012163
title: Supplementary Material for: Long-Term Neurodevelopmental Outcome of Monochorionic Twins after Laser Therapy or Umbilical Cord Occlusion for Twin-Twin Transfusion Syndrome

description: <b><i>Introduction:</i></b> We sought to assess the incidence of severe neurodevelopmental impairment (NDI) in monochorionic twins treated for twin-twin transfusion syndrome (TTTS) and compare it to the incidence in uncomplicated monochorionic twins. <b><i>Material and Methods:</i></b> We included TTTS pregnancies treated by fetoscopic selective laser coagulation (FSLC) or umbilical cord occlusion (UCO) in 2004–2015. Primary outcome was severe NDI defined as cerebral palsy, bilateral blindness or bilateral deafness (ICD-10 diagnoses), and severe cognitive and/or motor delay (assessed by the Ages and Stages Questionnaires [ASQ]). <b><i>Results:</i></b> A total of 124 children after TTTS and 98 controls were followed up at 25 months of age (SD 11.4). Severe NDI was found in 8.9% of the TTTS children (10.5% [9/86] after FSLC; 5.3% [2/38] after UCO) compared to 3.1% in the control group (<i>p</i> = 0.10). The odds ratio for severe NDI was 1.8 in cases versus controls (<i>p</i> = 0.37). The total ASQ score was significantly lower in the TTTS group than in controls (<i>p</i> = 0.03) after FSLC (<i>p</i> = 0.03) and after UCO (<i>p</i> = 0.14). <b><i>Discussion:</i></b> Children after TTTS appear to have a higher risk of severe NDI and score significantly lower on the ASQ compared to monochorionic twins from uncomplicated pregnancies.
DOI: 10.6084/m9.figshare.7012160
title: Optimizing DNA transduction by selection of mutations that evade bacterial defense systems

description: We recently developed a platform where phage-transducing particles optimize DNA delivery to a wide range of hosts. Here, we use this platform to optimize DNA transduction into hosts that naturally restrict specific DNA sequences. We first show that a specific plasmid is restricted for transduction into a particular <i>Salmonella</i> strain. Using the platform, we select for a mutated plasmid that overcomes the restriction barrier. Insertion of the non-mutated sequence into a permissive plasmid restricts transduction. We further show that epigenetic modification enables the DNA to evade restriction by the putative defense system. Our results validate this straightforward genetic approach for optimization of DNA transduction into new hosts.
DOI: 10.6084/m9.figshare.7012160.v1
title: Optimizing DNA transduction by selection of mutations that evade bacterial defense systems

description: We recently developed a platform where phage-transducing particles optimize DNA delivery to a wide range of hosts. Here, we use this platform to optimize DNA transduction into hosts that naturally restrict specific DNA sequences. We first show that a specific plasmid is restricted for transduction into a particular <i>Salmonella</i> strain. Using the platform, we select for a mutated plasmid that overcomes the restriction barrier. Insertion of the non-mutated sequence into a permissive plasmid restricts transduction. We further show that epigenetic modification enables the DNA to evade restriction by the putative defense system. Our results validate this straightforward genetic approach for optimization of DNA transduction into new hosts.
DOI: 10.6084/m9.figshare.7012154
title: Assessing the partners of the RBP9-mRNP complex in <i>Trypanosoma cruzi</i> using shotgun proteomics and RNA-seq

description: Gene expression regulation in trypanosomes differs from other eukaryotes due to absence of transcriptional regulation for most of their genes. RNA-binding proteins (RBPs) associate with mRNAs and other regulatory proteins to form ribonucleoprotein complexes (mRNPs), which play a major role in post-transcriptional regulation. Here, we show that RBP9 is a cytoplasmic RBP in <i>Trypanosoma cruzi</i> with one RNA-recognition motif (RRM). The RBP9 sedimentation profile in a sucrose gradient indicated its presence in cytoplasmic translational complexes, suggesting its involvement in translation regulation. Taking this result as a motivation, we used shotgun proteomics and RNA-seq approaches to assess the core of the RBP9-mRNP complex. In epimastigotes in exponential growth, the complex was composed mostly by RBPs involved in RNA metabolism, such as ZC3H39, UBP1/2, NRBD1, and ALBA3/4. When parasites were subjected to nutritional stress, our analysis identified regulatory RBPs and the translation initiation factors eIF4E5, eIF4G5, eIF4G1, and eIF4G4. The RNA-seq results showed that RBP9-mRNP complex regulates transcripts encoding some RBPs – e.g. RBP5, RBP6, and RBP10 -, and proteins involved in metabolic processes. Therefore, we argue that RBP9 is part of cytoplasmic mRNPs complexes associated with mRNA metabolism and translation regulation in <i>T. cruzi</i>.
DOI: 10.6084/m9.figshare.7012154.v2
title: Assessing the partners of the RBP9-mRNP complex in <i>Trypanosoma cruzi</i> using shotgun proteomics and RNA-seq

description: Gene expression regulation in trypanosomes differs from other eukaryotes due to absence of transcriptional regulation for most of their genes. RNA-binding proteins (RBPs) associate with mRNAs and other regulatory proteins to form ribonucleoprotein complexes (mRNPs), which play a major role in post-transcriptional regulation. Here, we show that RBP9 is a cytoplasmic RBP in <i>Trypanosoma cruzi</i> with one RNA-recognition motif (RRM). The RBP9 sedimentation profile in a sucrose gradient indicated its presence in cytoplasmic translational complexes, suggesting its involvement in translation regulation. Taking this result as a motivation, we used shotgun proteomics and RNA-seq approaches to assess the core of the RBP9-mRNP complex. In epimastigotes in exponential growth, the complex was composed mostly by RBPs involved in RNA metabolism, such as ZC3H39, UBP1/2, NRBD1, and ALBA3/4. When parasites were subjected to nutritional stress, our analysis identified regulatory RBPs and the translation initiation factors eIF4E5, eIF4G5, eIF4G1, and eIF4G4. The RNA-seq results showed that RBP9-mRNP complex regulates transcripts encoding some RBPs – e.g. RBP5, RBP6, and RBP10 -, and proteins involved in metabolic processes. Therefore, we argue that RBP9 is part of cytoplasmic mRNPs complexes associated with mRNA metabolism and translation regulation in <i>T. cruzi</i>.
DOI: 10.6084/m9.figshare.7012154.v1
title: Assessing the partners of RBP9-mRNP complex in <i>Trypanosoma cruzi</i> using shotgun proteomics and RNA-seq

description: Gene expression regulation in trypanosomes differs from other eukaryotes due to absence of transcriptional regulation for most of their genes. RNA-binding proteins (RBPs) associate with mRNAs and other regulatory proteins to form ribonucleoprotein complexes (mRNPs), which play a major role in post-transcriptional regulation. Here, we show that RBP9 is a cytoplasmic RBP in <i>Trypanosoma cruzi</i> with one RNA-recognition motif (RRM). The RBP9 sedimentation profile in a sucrose gradient indicated its presence in cytoplasmic translational complexes, suggesting its involvement in translation regulation. Taking this result as a motivation, we used shotgun proteomics and RNA-seq approaches to assess the core of the RBP9-mRNP complex. In epimastigotes in exponential growth, the complex was composed mostly by RBPs involved in RNA metabolism, such as ZC3H39, UBP1/2, NRBD1, and ALBA3/4. When parasites were subjected to nutritional stress, our analysis identified regulatory RBPs and the translation initiation factors eIF4E5, eIF4G5, eIF4G1, and eIF4G4. The RNA-seq results showed that RBP9-mRNP complex regulates transcripts encoding some RBPs – e.g. RBP5, RBP6, and RBP10 -, and proteins involved in metabolic processes. Therefore, we argue that RBP9 is part of cytoplasmic mRNPs complexes associated with mRNA metabolism and translation regulation in <i>T. cruzi</i>.
DOI: 10.6084/m9.figshare.7012031
title: Blue Jet Results

description: Blue Jet Results
DOI: 10.6084/m9.figshare.7012028
title: Supplementary Material for: The Utility of Virtual Bronchoscopy Using a Computed Tomography Workstation for Conducting Conventional Bronchoscopy: A Retrospective Analysis of Clinical Practice

description: <b><i>Background:</i></b> Recent clinical trials demonstrated the benefits of several guided-bronchoscopy technologies for the diagnosis of peripheral pulmonary lesions (PPLs). However, introduction of these technologies is expensive. Therefore, in clinical practice, these are unavailable in many hospitals. In contrast, virtual bronchoscopy (VB) using the computed tomography (CT) workstation can be made available immediately without additional cost as many hospitals already have the CT scan facility. However, the effectiveness of VB alone remains to be shown. <b><i>Objectives:</i></b> The aim of this study was to investigate the effect of VB using the CT workstation in hospitals performing conventional bronchoscopy. <b><i>Methods:</i></b> Results from consecutive patients who underwent bronchoscopy for small PPLs (major diameter ≤30 mm) were retrospectively reviewed. Sixty-nine patients who underwent bronchoscopy without VB from April 2014 to March 2015 and 56 patients who underwent bronchoscopy with VB from April 2015 to December 2015 were assigned to non-VB and VB groups, respectively. We compared the two groups and analyzed the factors affecting the diagnostic yield. <b><i>Results:</i></b> The VB group had a significantly higher diagnostic yield than the non-VB group (57.1 vs. 33.3%; <i>p</i> = 0.008). In the multivariate analysis, VB was identified as a significant factor affecting the diagnostic yield (odds ratio: 3.30, <i>p</i> = 0.011). <b><i>Conclusions:</i></b> In the conventional bronchoscopy settings, VB using the CT workstation is efficient for the diagnosis of PPLs when other guided-bronchoscopy techniques are unavailable.
DOI: 10.6084/m9.figshare.7012028.v1
title: Supplementary Material for: The Utility of Virtual Bronchoscopy Using a Computed Tomography Workstation for Conducting Conventional Bronchoscopy: A Retrospective Analysis of Clinical Practice

description: <b><i>Background:</i></b> Recent clinical trials demonstrated the benefits of several guided-bronchoscopy technologies for the diagnosis of peripheral pulmonary lesions (PPLs). However, introduction of these technologies is expensive. Therefore, in clinical practice, these are unavailable in many hospitals. In contrast, virtual bronchoscopy (VB) using the computed tomography (CT) workstation can be made available immediately without additional cost as many hospitals already have the CT scan facility. However, the effectiveness of VB alone remains to be shown. <b><i>Objectives:</i></b> The aim of this study was to investigate the effect of VB using the CT workstation in hospitals performing conventional bronchoscopy. <b><i>Methods:</i></b> Results from consecutive patients who underwent bronchoscopy for small PPLs (major diameter ≤30 mm) were retrospectively reviewed. Sixty-nine patients who underwent bronchoscopy without VB from April 2014 to March 2015 and 56 patients who underwent bronchoscopy with VB from April 2015 to December 2015 were assigned to non-VB and VB groups, respectively. We compared the two groups and analyzed the factors affecting the diagnostic yield. <b><i>Results:</i></b> The VB group had a significantly higher diagnostic yield than the non-VB group (57.1 vs. 33.3%; <i>p</i> = 0.008). In the multivariate analysis, VB was identified as a significant factor affecting the diagnostic yield (odds ratio: 3.30, <i>p</i> = 0.011). <b><i>Conclusions:</i></b> In the conventional bronchoscopy settings, VB using the CT workstation is efficient for the diagnosis of PPLs when other guided-bronchoscopy techniques are unavailable.
DOI: 10.6084/m9.figshare.7012031.v1
title: Blue Jet Results

description: Blue Jet Results
DOI: 10.6084/m9.figshare.7012031.v3
title: Blue Jet Results

description: Blue Jet Results
DOI: 10.6084/m9.figshare.7012031.v2
title: Blue Jet Results

description: Blue Jet Results
DOI: 10.6084/m9.figshare.7012004
title: a-Synuclein MD simulations:homo-(A53T+S87N)

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-(A53T+S87N)
DOI: 10.5066/p9hrs2c3
title: Mercury Data from the Bad River Watershed, Wisconsin, 2004 - 2018

description: This release includes eight data files that provide concentrations of mercury (Hg) chemical species and ancillary chemical and physical data that quantify and document aspects of the Hg cycle in stream and rivers located on tribal lands of the Bad River Band of Lake Superior Chippewa. These files were transferred to the U.S. Geological Survey by Lacey Hill Kastern, Natural Resources Department, Bad River Band of Lake Superior Chippewa in May, 2018. Files listed as Child Items in this release include data on Hg concentrations in: bald eagle feathers (Mercury Concentrations in Bald Eagle Feathers, Bad River Watershed, Wisconsin, 2014 - 2016.csv), bed sediment (Mercury Concentrations in Bed Sediment, Bad River Watershed, 2006-2015.csv), fish tissue (Mercury Concentrations in Fish Tissue, Bad River Watershed, Wisconsin, 2004-2013.csv), green frog tissue (Mercury Concentrations in Green Frog Tissue, Bad River Watershed, Wisconsin, 2012-2013.csv), litterfall (Mercury Concentrations in Litterfall, Bad River Watershed, Wisconsin, 2012-2018.csv), river otter hair (Mercury Concentrations in River Otter Hair, Bad River Watershed, Wisconsin.csv), surface waters (Mercury Concentrations in Surface Waters, Bad River Watershed, Wisconsin, 2006-2016.csv), and wild rice (Mercury Concentrations in Wild Rice, Bad River Watershed, Wisconsin, 2006.csv). Attributes describing the contents of each of these data files are provided in the .xml file that accompanies each Child Item. Note that documentation of some data sets was incomplete as received from the Natural Resources Department. Any data items in the .csv files that were not available are marked with "NA" indicating not available. This data release includes as much documentation as was provided to the U.S. Geological Survey. Neither sample collection nor Hg analyses were performed by the U.S. Geological Survey, New York Water Science Center.
DOI: 10.6084/m9.figshare.7012004.v1
title: a-Synuclein MD simulations:homo-(A53T+S87N)

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-(A53T+S87N)
DOI: 10.6084/m9.figshare.7012001
title: a-Synuclein MD simulations:homo-(G68E+V95G)

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-(G68E+V95G)
DOI: 10.6084/m9.figshare.7012004.v2
title: a-Synuclein MD simulations:homo-(A53T+S87N)

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-(A53T+S87N)
DOI: 10.6084/m9.figshare.7012001.v1
title: a-Synuclein MD simulations:homo-(G68E+V95G)

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-(G68E+V95G)
DOI: 10.6084/m9.figshare.7012004.v3
title: a-Synuclein MD simulations:homo-(A53T+S87N)

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-(A53T+S87N)
DOI: 10.6084/m9.figshare.7012001.v2
title: a-Synuclein MD simulations:homo-(G68E+V95G)

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-(G68E+V95G)
DOI: 10.6084/m9.figshare.7012004.v4
title: a-Synuclein MD simulations:homo-(A53T+S87N)

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-(A53T+S87N)
DOI: 10.6084/m9.figshare.7012001.v3
title: a-Synuclein MD simulations:homo-(G68E+V95G)

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-(G68E+V95G)
DOI: 10.6084/m9.figshare.7011998
title: a-Synuclein MD simulations:homo-S87N

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-S87N
DOI: 10.6084/m9.figshare.7012004.v5
title: a-Synuclein MD simulations:homo-(A53T+S87N)

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-(A53T+S87N)
DOI: 10.6084/m9.figshare.7011995
title: a-Synuclein MD simulations:homo-H50Q

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-H50Q
DOI: 10.6084/m9.figshare.7012004.v6
title: a-Synuclein MD simulations:homo-(A53T+S87N)

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-(A53T+S87N)
DOI: 10.6084/m9.figshare.7011998.v1
title: a-Synuclein MD simulations:homo-S87N

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-S87N
DOI: 10.6084/m9.figshare.7011995.v1
title: a-Synuclein MD simulations:homo-H50Q

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-H50Q
DOI: 10.6084/m9.figshare.7011998.v2
title: a-Synuclein MD simulations:homo-S87N

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-S87N
DOI: 10.6084/m9.figshare.7011995.v2
title: a-Synuclein MD simulations:homo-H50Q

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-H50Q
DOI: 10.6084/m9.figshare.7011998.v3
title: a-Synuclein MD simulations:homo-S87N

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-S87N
DOI: 10.6084/m9.figshare.7011995.v3
title: a-Synuclein MD simulations:homo-H50Q

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-H50Q
DOI: 10.6084/m9.figshare.7011998.v4
title: a-Synuclein MD simulations:homo-S87N

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-S87N
DOI: 10.6084/m9.figshare.7011983
title: Plotting Codes

description: Plotting codes<br>
DOI: 10.6084/m9.figshare.7011989
title: a-Synuclein MD simulations:homo-G51D

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-G51D
DOI: 10.6084/m9.figshare.7011983.v1
title: Plotting Codes

description: Plotting codes<br>
DOI: 10.6084/m9.figshare.7011989.v3
title: a-Synuclein MD simulations:homo-G51D

description: Molecular dynamics simulations of a-Synuclein amyloids, homo-G51D
DOI: 10.6084/m9.figshare.7011980
title: Mud acts as a noise dampener in Australian passerine nests

description: Research into the effects of anthropogenic noise on birds has revealed that individuals are susceptible to negative impacts of noise at all life stages. Scientists are particularly concerned about the effects of noise on embryos and nestlings, because of potential survival and fitness consequences. However, almost nothing is known about how background anthropogenic noise is experienced within nests. Many natural materials and shapes are effective noise dampeners, thus we would expect that nest inhabitants may be subject to differing levels of environmental noise than those detected by researchers outside of a nest. Similarly, noise levels may vary between nests of different shapes and materials. A test was conducted on 250 museum nest specimens to discover whether these properties might contribute to the detectable levels of noise inside the nest. Most nests were generally ineffective at dampening environmental noise. Strikingly, however, mud nests showed major differences in detectable noise levels compared with all other nest types, with levels being up to 6 dB lower than control conditions. This insight will hopefully inform future studies into the effects of noise on birds and provide valuable information regarding how this extended behavioural phenotype might contribute to a species’ resilience against harmful environmental conditions.
DOI: 10.6084/m9.figshare.7011980.v1
title: Mud acts as a noise dampener in Australian passerine nests

description: Research into the effects of anthropogenic noise on birds has revealed that individuals are susceptible to negative impacts of noise at all life stages. Scientists are particularly concerned about the effects of noise on embryos and nestlings, because of potential survival and fitness consequences. However, almost nothing is known about how background anthropogenic noise is experienced within nests. Many natural materials and shapes are effective noise dampeners, thus we would expect that nest inhabitants may be subject to differing levels of environmental noise than those detected by researchers outside of a nest. Similarly, noise levels may vary between nests of different shapes and materials. A test was conducted on 250 museum nest specimens to discover whether these properties might contribute to the detectable levels of noise inside the nest. Most nests were generally ineffective at dampening environmental noise. Strikingly, however, mud nests showed major differences in detectable noise levels compared with all other nest types, with levels being up to 6 dB lower than control conditions. This insight will hopefully inform future studies into the effects of noise on birds and provide valuable information regarding how this extended behavioural phenotype might contribute to a species’ resilience against harmful environmental conditions.
DOI: 10.6084/m9.figshare.7011890
title: Geological landscape and stone heritage of the Genoa Walls Urban Park and surrounding area (Italy)

description: In the last 20 years the conservation and enhancement of cultural and landscape heritage sites have been increasingly promoted by specific national and international laws. Thematic maps from scientific studies facilitate the public promotion and understanding of landscape and cultural heritage. This work introduces a novel geological landscape and stone heritage map of the Genoa Walls Urban Park (1:10.000 scale). The park is located in the immediate surroundings of Genoa city centre and it includes a complex system of historical fortifications. Today the park is frequented by hikers, mountain bikers and tourists. The map shows three different elements of the park: lithological and geomorphological elements, cultural and landscape heritage sites and the trail network. This map offers new insights into the way in which the park authority can promote the sustainable fruition of a highly valuable area, characterised by landscape and historical interest next to one of the largest historical centres of Europe, part of which is inscribed in the list of Unesco World Heritage Sites.
DOI: 10.6084/m9.figshare.7011983.v2
title: Plotting Codes

description: Plotting codes<br>
DOI: 10.6084/m9.figshare.7011890.v1
title: Geological landscape and stone heritage of the Genoa Walls Urban Park and surrounding area (Italy)

description: In the last 20 years the conservation and enhancement of cultural and landscape heritage sites have been increasingly promoted by specific national and international laws. Thematic maps from scientific studies facilitate the public promotion and understanding of landscape and cultural heritage. This work introduces a novel geological landscape and stone heritage map of the Genoa Walls Urban Park (1:10.000 scale). The park is located in the immediate surroundings of Genoa city centre and it includes a complex system of historical fortifications. Today the park is frequented by hikers, mountain bikers and tourists. The map shows three different elements of the park: lithological and geomorphological elements, cultural and landscape heritage sites and the trail network. This map offers new insights into the way in which the park authority can promote the sustainable fruition of a highly valuable area, characterised by landscape and historical interest next to one of the largest historical centres of Europe, part of which is inscribed in the list of Unesco World Heritage Sites.