cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6154421
title: LC-MS/MS data characterising cell surface glycoproteins from chondrogenic progenitor cells and mesenchymal stem cells

description: This dataset contains LC-MS/MS data generated from chondrogenic progenitor cell (CPC) and mesenchymal stem cell (MSC) surface glycoproteins, enriched with an aminooxy-biotin-based glycocapture technique. Together these results provide proteomic data on the surfaceome of two closely related cell types relevant to cartilage biology and osteoarthritis.<br>Data were generated with a Dionex Ultimate 3000 RSLCnano liquid chromatography (LC) system coupled with a Bruker Impact II QTOF mass spectroscopy (MS) instrument with CaptiveSpray nanoBooster source. MS acquisition rate was 5 Hz, followed by 10–20 Hz MS2 acquisition rate, depending on precursor intensity. The 20 most intense ions from each MS scan were selected for fragmentation. LC-MS/MS analysis was performed in 3 biological replicates for each sample.<br>For each replicate, 4 files are provided:<br><b>.baf file</b> - A binary file in the Bruker proprietary data format, directly output from the MS instrument.<b>.xml file</b> - Peak list in an XML-based format.<b>.mgf file </b>- Peak list compiled in to the Mascot Generic Format (MGF).<b>.mzid file</b> - MZidentML search result file generated using Mascot 2.6.<br>The first 3 letters of each file name indicate the cell type from which the data was generated (CPC or MSC), each with three technical replicates.<br>
DOI: 10.6084/m9.figshare.6154421.v1
title: LC-MS/MS data characterising cell surface glycoproteins from chondrogenic progenitor cells and mesenchymal stem cells

description: This dataset contains LC-MS/MS data generated from chondrogenic progenitor cell (CPC) and mesenchymal stem cell (MSC) surface glycoproteins, enriched with an aminooxy-biotin-based glycocapture technique. Together these results provide proteomic data on the surfaceome of two closely related cell types relevant to cartilage biology and osteoarthritis.<br>Data were generated with a Dionex Ultimate 3000 RSLCnano liquid chromatography (LC) system coupled with a Bruker Impact II QTOF mass spectroscopy (MS) instrument with CaptiveSpray nanoBooster source. MS acquisition rate was 5 Hz, followed by 10–20 Hz MS2 acquisition rate, depending on precursor intensity. The 20 most intense ions from each MS scan were selected for fragmentation. LC-MS/MS analysis was performed in 3 biological replicates for each sample.<br>For each replicate, 4 files are provided:<br><b>.baf file</b> - A binary file in the Bruker proprietary data format, directly output from the MS instrument.<b>.xml file</b> - Peak list in an XML-based format.<b>.mgf file </b>- Peak list compiled in to the Mascot Generic Format (MGF).<b>.mzid file</b> - MZidentML search result file generated using Mascot 2.6.<br>The first 3 letters of each file name indicate the cell type from which the data was generated (CPC or MSC), each with three technical replicates.<br>
DOI: 10.6084/m9.figshare.6154418
title: Supporting information for paper: "A Simple Model For Scalar Relativistic Corrections To Molecular Total Atomization Energies"

description: Supporting information for paper: "A Simple Model For Scalar Relativistic Corrections To Molecular Total Atomization Energies". Computed scalar relativistic corrections to the total atomization energies of the W4-17 dataset, computed s, p, d,... populations on each atom using both NPA and MBS-projected Mulliken approaches, and predicted scalar relativistic corrections using our model.
DOI: 10.6084/m9.figshare.6154418.v1
title: Supporting information for paper: "A Simple Model For Scalar Relativistic Corrections To Molecular Total Atomization Energies"

description: Supporting information for paper: "A Simple Model For Scalar Relativistic Corrections To Molecular Total Atomization Energies". Computed scalar relativistic corrections to the total atomization energies of the W4-17 dataset, computed s, p, d,... populations on each atom using both NPA and MBS-projected Mulliken approaches, and predicted scalar relativistic corrections using our model.
DOI: 10.6084/m9.figshare.6154415
title: A new lepidosauromorph reptile from the Middle Triassic (Ladinian) of Germany and its phylogenetic relationships

description: Although lepidosaurs are by far the most diverse and widespread group of present-day nonavian reptiles, with over 10,000 formally named species, their early diversification is documented only by a handful of incomplete fossils with few diagnostic features. Recent excavations in strata of the Lower Keuper (Middle Triassic: Ladinian) of Baden-Württemberg, Germany, have yielded abundant skeletal remains of a diversity of small- to medium-sized diapsid reptiles, which include at least three taxa of lepidosauromorphs. One, here named <i>Fraxinisaura rozynekae</i>, is a small-bodied reptile characterized by (1) maxillary and dentary tooth crowns conical, with lingual striae near their apices; (2) maxilla with a dorsoventrally low facial process and long tooth-bearing portion anterior to this process; (3) jugal with a short anterior process and a very short, pointed posterior process; and (4) ilium with a tall, posterodorsally extending blade. Tooth implantation is pleurodont. Size variation in the sample sheds some light on ontogenetic changes, mainly affecting the shape of and ornamentation on cranial bones. Phylogenetic analysis recovered <i>Fraxinisaura rozynekae</i> among Lepidosauromorpha and as the sister taxon of the Middle to Late Jurassic <i>Marmoretta oxoniensis</i>. Unfortunately, currently existing character-taxon matrices do not allow confident resolution of the interrelationships of these and other early Mesozoic lepidosauromorph reptiles. http://zoobank.org/urn:lsid:zoobank.org:pub:02C69A1C-FCC8-4D0C-BA71-79BA30BC9DA7 SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Schoch, R. R., and H.-D. Sues. 2018. A new lepidosauromorph reptile from the Middle Triassic (Ladinian) of Germany and its phylogenetic relationships. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2018.1444619.
DOI: 10.6084/m9.figshare.6154400
title: Adapting air quality management for a changing climate: Survey of local districts in California

description: Air quality can be affected by weather and thus is sensitive to a changing climate. Wildfire (influenced by weather), consecutive high temperature summer days, and other extreme events are projected to become more severe and frequent with climate change. These may create challenging conditions for managing air quality despite policy targets to reduce precursor and pollutant emissions. Although extreme events are becoming more intense and interest in climate adaptation is increasing among public health practitioners, little attention in scholarly literature and policy covers climate adaptation for air quality governance. Understanding the management and managers’ perspectives at the local level provides insight about the needs for climate adaptation, including their adaptation status, perspectives, responsibilities, and roles. This study explores local manager perspectives and experiences of managing air quality within a changing climate as one puzzle piece to understand the gap in climate adaptation within the air quality sector. A broader goal is to contribute to the discussion of developing a multi-jurisdictional vision for reducing the impacts of air quality in a changing climate. In 2016 local air quality district managers in California were invited to participate in an online survey of 39 questions focused on extreme event impacts on air quality. The questionnaire focused on present air quality threats and extreme event challenges, adaptation status and strategies, adaptive capacities, perceived barriers to adaptation, and jurisdictional responsibilities and roles. Over 85 percent of the 35 local air districts in California participated in the survey, which represents 80 percent of the state’s population. High awareness and knowledge of climate change among local managers indicates they are ready to adopt and take action on policies that would support climate adaptation, but barriers reported suggests they may need policies and adequate funding to take action and make necessary changes. <i>Implications</i>: Downscaled global climate models project an increasing severity and frequency of extreme events. In the southwestern United States, these include wildfire, heat events, and dry periods, among others, all of which can place an extra burden on air quality managers and emitters to achieve air quality standards even as they reduce emissions. Despite climate change presenting increasing challenges to meet air quality standards, in the southwestern United States, policy and action to mitigate these impacts have been surprisingly absent. California presents a valuable case study on the topic because of its historic leadership in air quality management for the United States and also because of its initiatives in combating climate change. Yet still we found that adaptation has not been incorporated into air quality management thus far, but local managers seem sufficiently knowledgeable and willing.
DOI: 10.6084/m9.figshare.6154400.v2
title: Adapting air quality management for a changing climate: Survey of local districts in California

description: Air quality can be affected by weather and thus is sensitive to a changing climate. Wildfire (influenced by weather), consecutive high temperature summer days, and other extreme events are projected to become more severe and frequent with climate change. These may create challenging conditions for managing air quality despite policy targets to reduce precursor and pollutant emissions. Although extreme events are becoming more intense and interest in climate adaptation is increasing among public health practitioners, little attention in scholarly literature and policy covers climate adaptation for air quality governance. Understanding the management and managers’ perspectives at the local level provides insight about the needs for climate adaptation, including their adaptation status, perspectives, responsibilities, and roles. This study explores local manager perspectives and experiences of managing air quality within a changing climate as one puzzle piece to understand the gap in climate adaptation within the air quality sector. A broader goal is to contribute to the discussion of developing a multi-jurisdictional vision for reducing the impacts of air quality in a changing climate. In 2016 local air quality district managers in California were invited to participate in an online survey of 39 questions focused on extreme event impacts on air quality. The questionnaire focused on present air quality threats and extreme event challenges, adaptation status and strategies, adaptive capacities, perceived barriers to adaptation, and jurisdictional responsibilities and roles. Over 85 percent of the 35 local air districts in California participated in the survey, which represents 80 percent of the state’s population. High awareness and knowledge of climate change among local managers indicates they are ready to adopt and take action on policies that would support climate adaptation, but barriers reported suggests they may need policies and adequate funding to take action and make necessary changes. <i>Implications</i>: Downscaled global climate models project an increasing severity and frequency of extreme events. In the southwestern United States, these include wildfire, heat events, and dry periods, among others, all of which can place an extra burden on air quality managers and emitters to achieve air quality standards even as they reduce emissions. Despite climate change presenting increasing challenges to meet air quality standards, in the southwestern United States, policy and action to mitigate these impacts have been surprisingly absent. California presents a valuable case study on the topic because of its historic leadership in air quality management for the United States and also because of its initiatives in combating climate change. Yet still we found that adaptation has not been incorporated into air quality management thus far, but local managers seem sufficiently knowledgeable and willing.
DOI: 10.6084/m9.figshare.6154400.v1
title: Adapting air quality management for a changing climate: survey of local districts in California

description: Adapting air quality management for a changing climate: survey of local districts in California
DOI: 10.3886/e119446v24-43780
title: COVID-19 US State Policy Database

description: Database of state policies on closures, shelter-in-place orders, housing protections, changes to Medicaid and SNAP, physical distancing closures, reopening, and more created by researchers at the Boston University School of Public Health. Policies included are state-wide directives or mandates, not guidance or recommendations. In order for a policy to be included, it must apply to the entire state. We are working quickly to go through state government websites to make the policy database as complete and accurate as possible in a rapidly changing policy context. If you use data on a given policy, we encourage you to triangulate based on additional sources of policy data and to review the source documentation to consider the coding decisions that are right for your work. Of course, please email us if you note a discrepancy so we can improve the database for everyone. State policy source documentation can be found at: tinyurl.com/statepolicysources.
description: other; Contributors: Megan Cole Brahim, Noa Krawczyk, Carolyn Hoffman, Claire Corkish, Elizabeth Ferrara, Elizabeth Long, Emily Baroni, Faith Contador, Hannah Simon, Morgan Simko, Rachel Scheckman, Sarah Brewer, Sue Kulkarni, Felicia Heykoop, Manish Patel, Aishwarya Vidyasagaran, Andrew Chiao, Cara Safon, Samantha Burkhart, Harry Jung, Victor Lee, Marina MacKinnon, Aarohi Rede, Marie Vearling, Sophie Li, Christina Wang, Tim Levengood, María Jordán P. Emma Chistolini
description: State policies. Smallest Geographic Unit: State
DOI: 10.6084/m9.figshare.6154352
title: Viral titre OreR data

description: qPCR data for Kallithea virus and endogenous control (rpl32) in Kallithea-infected male and female flies with or without Wolbachia. Analyze with titre.R<br>
DOI: 10.6084/m9.figshare.6154352.v1
title: Viral titre OreR data

description: qPCR data for Kallithea virus and endogenous control (rpl32) in Kallithea-infected male and female flies with or without Wolbachia. Analyze with titre.R<br>
DOI: 10.6084/m9.figshare.6154346
title: Oogenesis phenotype data

description: Occurence of vitellogenic egg chambers and apoptosis in control and Kallithea-infected flies. Analyze with fecundity.R<br>
DOI: 10.6084/m9.figshare.6154346.v1
title: Oogenesis phenotype data

description: Occurence of vitellogenic egg chambers and apoptosis in control and Kallithea-infected flies. Analyze with fecundity.R<br>
DOI: 10.6084/m9.figshare.6154343
title: Fly mortality data

description: Mortality across in males and females, with or without Wolbachia, with or without Kallithea virus infection. Analyze with mortality.R<br>
DOI: 10.6084/m9.figshare.6154343.v1
title: Fly mortality data

description: Mortality across in males and females, with or without Wolbachia, with or without Kallithea virus infection. Analyze with mortality.R<br>
DOI: 10.6084/m9.figshare.6154340
title: Analysing methodological issues in short-term monitoring of rare European beech forests restoration

description: Monitoring restoration effectiveness implies that restoration measures should be evaluated using multiscale analysis and modelling approaches. In this way, the scale-dependent nature of ecosystem processes and dynamics can be adequately described. Here, we evaluated how grain size (i.e. the dimension of sampling units) and type of data (abundance vs. presence/absence) impact the analysis of the response to restoration management activities aiming at halting the loss of European beech forests with Abies alba in the central Apennines (Italy). The proposed analysis relies on forests sampled in three Sites of Community Importance (SCIs) located in central Italy. For each treatment (reference, control and impact), randomly located multi-scale plots were selected. Vascular plant occurrences were recorded twice in every plot during summer 2010 or 2011 (before restoration) and in 2013 or 2014 (after restoration). Analysis of species abundances, recorded at the largest grain size available (20 X 20 m plot), showed a significant change in plant species composition in restored sites just after two years from the restoration management. When presence/absence data were used previous results were less visible, for all the examined grains, in two out of the three sites, suggesting a site-dependent response.
DOI: 10.6084/m9.figshare.6154340.v1
title: Analysing methodological issues in short-term monitoring of rare European beech forests restoration

description: Monitoring restoration effectiveness implies that restoration measures should be evaluated using multiscale analysis and modelling approaches. In this way, the scale-dependent nature of ecosystem processes and dynamics can be adequately described. Here, we evaluated how grain size (i.e. the dimension of sampling units) and type of data (abundance vs. presence/absence) impact the analysis of the response to restoration management activities aiming at halting the loss of European beech forests with Abies alba in the central Apennines (Italy). The proposed analysis relies on forests sampled in three Sites of Community Importance (SCIs) located in central Italy. For each treatment (reference, control and impact), randomly located multi-scale plots were selected. Vascular plant occurrences were recorded twice in every plot during summer 2010 or 2011 (before restoration) and in 2013 or 2014 (after restoration). Analysis of species abundances, recorded at the largest grain size available (20 X 20 m plot), showed a significant change in plant species composition in restored sites just after two years from the restoration management. When presence/absence data were used previous results were less visible, for all the examined grains, in two out of the three sites, suggesting a site-dependent response.
DOI: 10.6084/m9.figshare.6154337
title: Supporting information for W4-17 core-valence benchmark paper (Mol. Phys., submitted)

description: Our best values for the inner-shell correlation contribution to the total atomization energies of the W4-17 benchmark.This set is deposited as Supporting Information for a Molecular Physics submission entitled "Probing the basis set limit for thermochemical contributions of inner-shell correlation: are core-core contributions really always negligible?" (Dieter Cremer memorial issue)
DOI: 10.6084/m9.figshare.6154337.v1
title: Supporting information for W4-17 core-valence benchmark paper (Mol. Phys., submitted)

description: Our best values for the inner-shell correlation contribution to the total atomization energies of the W4-17 benchmark.This set is deposited as Supporting Information for a Molecular Physics submission entitled "Probing the basis set limit for thermochemical contributions of inner-shell correlation: are core-core contributions really always negligible?" (Dieter Cremer memorial issue)
DOI: 10.6084/m9.figshare.6154337.v2
title: Supporting information for W4-17 core-valence benchmark paper (Mol. Phys., submitted)

description: Our best values for the inner-shell correlation contribution to the total atomization energies of the W4-17 benchmark.This set is deposited as Supporting Information for a Molecular Physics submission entitled "Probing the basis set limit for thermochemical contributions of inner-shell correlation: are core-core contributions really always negligible?" (Dieter Cremer memorial issue)
DOI: 10.6084/m9.figshare.6154331
title: Toward novel inhibitors against KdsB: a highly specific and selective broad-spectrum bacterial enzyme

description: KdsB (3-deoxy-manno-octulosonate cytidylyltransferase) is a highly specific and selective bacterial enzyme that catalyzes KDO (3-Deoxy-D-mano-oct-2-ulosonic acid) activation in KDO biosynthesis pathway. Failure in KDO biosynthesis causes accumulation of lipid A in the bacterial outer membrane that leads to cell growth arrest. This study reports a combinatorial approach comprising virtual screening of natural drugs library, molecular docking, computational pharmacokinetics, molecular dynamics simulation, and binding free energy calculations for the identification of potent lead compounds against the said enzyme. Virtual screening demonstrated 1460 druglike compounds in a total of 4800, while molecular docking illustrated Ser13, Arg14, and Asp236 as the anchor amino acids for recognizing and binding the inhibitors. Functional details of the enzyme in complex with the best characterized compound-226 were explored through two hundred nanoseconds of MD simulation. The ligand after initial adjustments jumps into the active cavity, followed by the deep cavity, and ultimately backward rotating movement toward the initial docked site of the pocket. During the entire simulation period, Asp236 remained in contact with the ligand and can be considered as a major catalytic residue of the enzyme. Radial distribution function confirmed that toward the end of the simulation, strengthening of ligand-receptor occurred with ligand and enzyme active residues in close proximity. Binding free energy calculations via MM(PB/GB)SA and Waterswap reaction coordinates, demonstrated the high affinity of the compound for enzyme active site residues. These findings can provide new avenues for designing potent compounds against notorious bacterial pathogens.
DOI: 10.6084/m9.figshare.6154331.v2
title: Toward novel inhibitors against KdsB: a highly specific and selective broad-spectrum bacterial enzyme

description: KdsB (3-deoxy-manno-octulosonate cytidylyltransferase) is a highly specific and selective bacterial enzyme that catalyzes KDO (3-Deoxy-D-mano-oct-2-ulosonic acid) activation in KDO biosynthesis pathway. Failure in KDO biosynthesis causes accumulation of lipid A in the bacterial outer membrane that leads to cell growth arrest. This study reports a combinatorial approach comprising virtual screening of natural drugs library, molecular docking, computational pharmacokinetics, molecular dynamics simulation, and binding free energy calculations for the identification of potent lead compounds against the said enzyme. Virtual screening demonstrated 1460 druglike compounds in a total of 4800, while molecular docking illustrated Ser13, Arg14, and Asp236 as the anchor amino acids for recognizing and binding the inhibitors. Functional details of the enzyme in complex with the best characterized compound-226 were explored through two hundred nanoseconds of MD simulation. The ligand after initial adjustments jumps into the active cavity, followed by the deep cavity, and ultimately backward rotating movement toward the initial docked site of the pocket. During the entire simulation period, Asp236 remained in contact with the ligand and can be considered as a major catalytic residue of the enzyme. Radial distribution function confirmed that toward the end of the simulation, strengthening of ligand-receptor occurred with ligand and enzyme active residues in close proximity. Binding free energy calculations via MM(PB/GB)SA and Waterswap reaction coordinates, demonstrated the high affinity of the compound for enzyme active site residues. These findings can provide new avenues for designing potent compounds against notorious bacterial pathogens.