cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c57r89
title: MassIVE MSV000088105 - Fatty Acid Synthase inhibitor TVB-3166 prevents S-palmitoylation of coronavirus Spike proteins and limits infection
title: HEK293 cells expressing ACE2 and TMPRSS2 (HEK293-A2T2) and African green monkey VeroE6 cells were infected with SB3 SARS-CoV-2 for 24 hours at an MOI of 0.5. Cells were harvested and lysed. NEM was added to a final concentration of 20 mM and samples were incubated on end-to-end rotator for 1 hour at room temperature. Excess NEM was next removed via methanol chloroform precipitation, protein pellets were rinsed with methanol and air dried. Pellets were resuspended in Acyl-RAC binding buffer by sonication. Hydroxylamine (NH2OH, 400 mM final concentration; or NaCl for control samples) was added prior to incubation with 30 uL of packed acyl-RAC beads. Beads were next washed 3 times with binding buffer and 10 times with NH4HCO3. Direct digestion on beads was performed using trypsin/Lys-C. Supernatant was collected, beads were rinsed and samples were desalted and lyophilized prior to LC-MS analysis. HPLC was performed on samples reconstituted and loaded on a 20 mm pre-column and separated on a 50 mm analytical column over a 2-hour reversed-phase gradient on an EASY-nLC1200 pump in-line with a Q-Exactive HF mass spectrometer operated in positive ion mode ESI. MS scans were performed at a resolution of 60,000 (fwhm) followed by up to 20 MS/MS scans (HCD, 15,000 fwhm) of the most intense parent ions. Dynamic exclusion (within 10 ppm) was set for 5 seconds. For the sequence database search, Thermo raw files (.raw) were converted to the .mzML format using Proteowizard (v3.0.19311), then searched using XTandem (v2013.06.15.1) and Comet (2014.02 rev. 2) against Chlorocebus sabaeus RefSeq (GCF_015252025.1, v102; 61,745 entries) for the VeroE6 samples, or Human RefSeq (v104; 36,113 entries) for the HEK293-A2T2 samples. Both databases were supplemented with the SARS-CoV-2 proteome (2019-nCoC HKU-SZ-005b7). Search parameters specified a parent MS tolerance of 15 ppm and an MSMS fragment ion tolerance of 0.4 Da, with up to two missed cleavages allowed for trypsin-Lys-C. Deamidation (NQ), oxidation (M), acetylation (protein N-term), N-ethylmaleimide (C), and palmitoylation (C), were set as variable modifications. Search results were processed using the trans-proteomic pipeline (TPP v4.7), and proteins with an iProphet probability of at least 0.9 with at least 2 unique peptides matched were considered high confidence identifications.
DOI: 10.23636/wvva-3d67
title: StopsGB: Structured Timeline of Passenger Stations in Great Britain

description: Michael Quick's book _Railway Passenger Stations in Great Britain: a Chronology_ offers a uniquely rich and detailed account of Britain's changing railway infrastructure. Its listing of over 12,000 stations allows us to reconstruct the coming of rail at both micro- and macro-scales. However, being published originally as a book (and subsequently online as a PDF created from an underlying MS Word document), this resource was not well suited for systematic linking to other data. We now present a new, automatically generated dataset that provides the rich detail of this exceptional resource in a structured format. Each station described in the _Chronology_ is given certain attributes, such as operating companies and opening and closing dates, and is georeferenced and linked---whenever possible---to its corresponding entry on Wikidata. We name this structured, linked, and georeferenced dataset 'StopsGB' (Structured Timeline of Passenger Stations in Great Britain), and we make it openly available. We believe this dataset (and the method used to create it) will be of widespread interest across the historical, digital library and semantic web communities, and that it will be a key resource for ongoing research into the impact of the railway in Great Britain.
DOI: 10.5281/zenodo.5513808
title: Empirical Research on Requirements Quality: A Systematic Mapping Study - Dataset

description: We conducted a systematic mapping study on the empirical research into the quality of requirements titled "Empirical Research on Requirements Quality: A SystematicMapping Study" in the Requirements Engineering Journal. This is our replication package. Full Abstract: Research has repeatedly shown that high quality requirements are essential for the success of development projects. While the term “quality” is pervasive in the field of requirements engineering and while the body of research on requirements quality is large, there is no meta study of the field that overviews and compares the concrete quality attributes addressed by the community. To fill this knowledge gap, we conducted a systematic mapping study of the scientific literature. We retrieved 6,905 articles from six academic databases, which we filtered down to our 105 relevant primary studies: explicitly defining, improving, or evaluating quality attributes while including an empirical research component. We found that research on requirements quality focuses on improvement techniques, with very few primary studies addressing evidence-based definitions and evaluations of quality attributes. Among the 12 quality attributes identified, the most prominent in the field are ambiguity, completeness, consistency, and correctness. We identified 111 sub-types of quality attributes such as “template conformance” for consistency or “passive voice” for ambiguity. Ambiguity has the largest share of these sub-types. The artefacts being studied are mostly referred to in the broadest sense as “requirements,” while little research targets quality attributes in specific types of requirements such as use cases or user stories. We present and discuss our detailed analysis along the various quality attributes. Our findings highlightthe need to conduct more grounded research aimed at “definitions,” to use more diverse research methods, and to address a more diverse set of requirements types.
DOI: 10.5281/zenodo.5510222
title: Empirical Research on Requirements Quality: A Systematic Mapping Study - Dataset

description: We conducted a systematic mapping study on the empirical research into the quality of requirements titled "Empirical Research on Requirements Quality: A SystematicMapping Study" in the Requirements Engineering Journal. This is our replication package. Full Abstract: Research has repeatedly shown that high quality requirements are essential for the success of development projects. While the term “quality” is pervasive in the field of requirements engineering and while the body of research on requirements quality is large, there is no meta study of the field that overviews and compares the concrete quality attributes addressed by the community. To fill this knowledge gap, we conducted a systematic mapping study of the scientific literature. We retrieved 6,905 articles from six academic databases, which we filtered down to our 105 relevant primary studies: explicitly defining, improving, or evaluating quality attributes while including an empirical research component. We found that research on requirements quality focuses on improvement techniques, with very few primary studies addressing evidence-based definitions and evaluations of quality attributes. Among the 12 quality attributes identified, the most prominent in the field are ambiguity, completeness, consistency, and correctness. We identified 111 sub-types of quality attributes such as “template conformance” for consistency or “passive voice” for ambiguity. Ambiguity has the largest share of these sub-types. The artefacts being studied are mostly referred to in the broadest sense as “requirements,” while little research targets quality attributes in specific types of requirements such as use cases or user stories. We present and discuss our detailed analysis along the various quality attributes. Our findings highlightthe need to conduct more grounded research aimed at “definitions,” to use more diverse research methods, and to address a more diverse set of requirements types.
DOI: 10.5281/zenodo.5502274
title: A Daily near-surface Air Temperature Dataset for China from 1979 - 2018

description: The CDAT dataset contains near-surface air temperature data for China during the period of 1979-2018, in Celsius, daily temporal (T<sub>max</sub>, T<sub>min</sub>, T<sub>avg</sub>), and 0.1º spatial resolution. This product integrates multiple data sources such as reanalysis data (ERA5, CMFD), remote sensing data (MODIS), and in situ data, and is obtained by combining the temperature strategy to distinguish between clear sky and non-clear sky weather conditions. It is proved that this dataset has high accuracy and can be used in the further study of regional climate change.
DOI: 10.5281/zenodo.5141113
title: Groundwater and surface water quantity and quality measurement results for groundwater dependent ecosystem in Kazu leja, Latvia in 2019 and 2020

description: Groundwater and surface water quantity and quality measurement results and methodology of the investigations of the groundwater dependant ecosystem in Kazu leja, Latvia in 2019 and 2020 is presented. The data comprises: Methodology Measurement site data [2_observation_sites.csv] Field and laboratory measurement results [3_field_and_lab_results.csv] Measurement uncertainty [4_measurement_uncertainity.csv] Automated water level, temperature, and electrical conductivity measurements [5_level_temperature_electricConductivity_loggers.csv]
description: For citation please use reference to this data set and the main article: Kalvāns, A., Popovs, K., Priede, A. et al. Nitrate vulnerability of karst aquifers and associated groundwater-dependent ecosystems in the Baltic region. Environ Earth Sci 80, 628 (2021). https://doi.org/10.1007/s12665-021-09918-7
description: {"references": ["Kalv\u0101ns, A., Popovs, K., Priede, A., Koit, O., Reti\u0137e, I., Bik\u0161e, J., D\u0113li\u0146a, A., & Babre, A. Nitrate vulnerability of karst aquifers and associated groundwater-dependent ecosystems in the Baltic region. Environmental Earth Sciences."]}
DOI: 10.5281/zenodo.5141112
title: Groundwater and surface water quantity and quality measurement results for groundwater dependent ecosystem in Kazu leja, Latvia in 2019 and 2020

description: Groundwater and surface water quantity and quality measurement results and methodology of the investigations of the groundwater dependant ecosystem in Kazu leja, Latvia in 2019 and 2020 is presented. The data comprises: Methodology Measurement site data [2_observation_sites.csv] Field and laboratory measurement results [3_field_and_lab_results.csv] Measurement uncertainty [4_measurement_uncertainity.csv] Automated water level, temperature, and electrical conductivity measurements [5_level_temperature_electricConductivity_loggers.csv]
description: For citation please use reference to this data set and the main article: Kalvāns, A., Popovs, K., Priede, A. et al. Nitrate vulnerability of karst aquifers and associated groundwater-dependent ecosystems in the Baltic region. Environ Earth Sci 80, 628 (2021). https://doi.org/10.1007/s12665-021-09918-7
description: {"references": ["Kalv\u0101ns, A., Popovs, K., Priede, A., Koit, O., Reti\u0137e, I., Bik\u0161e, J., D\u0113li\u0146a, A., & Babre, A. Nitrate vulnerability of karst aquifers and associated groundwater-dependent ecosystems in the Baltic region. Environmental Earth Sciences."]}
DOI: 10.5281/zenodo.5146201
title: Predicted locations and nitrate pollution of groundwater discharge from D3pl karst aquifer in Latvia

description: <strong>Description</strong> A georeferenced raster data layer [5_predicted_D3pl_GW_discharge_zone.tif] showing predicted likelihood that groundwater polluted with nitrate (NO<sub>3</sub><sup>-</sup>) is discharging as springs or diffuse seepage from the Upper Devonian Pļaviņas (<em>D<sub>3</sub>pl</em>) dolomite karst aquifer in Latvia is presented. The cell value indicates the likelihood (0 – low, 1 - high) that groundwater with nitrate contamination is discharging from the <em>D<sub>3</sub>pl</em> aquifer at this location. Value of 0 means that no groundwater is discharging there. The BalticTM 93 (EPSG:25884) references system is used. The rationale and methodology for elaborating the map of groundwater discharge as springs or diffuse seepage from the <em>D<sub>3</sub>pl</em> dolomite karst aquifer is described in the main article (Kalvāns et al. under review). In short, a 3D regional geological model (Popovs et al. 2015), land surface elevation model and bedrock surface elevation model (Popovs et al. under review) were combined to identify locations where aquitard at the base of <em>D<sub>3</sub>pl</em> aquifer is outcropping at bedrock surface and in the nearby depressions (in a distance up to 0.25 km) the land surface was below the surface of this aquitard. The likely contamination with NO<sub>3</sub><sup>-</sup> was estimated from proportion of arable land (European Environment Agency 2018) within 4.75 km window. It is assumed that the NO<sub>3</sub><sup>-</sup> contamination in the <em>D<sub>3</sub>pl</em> karst aquifer is likely only close to its distribution margins, where groundwater table is deeper than the top of the aquifer. This work was supported by the EU Interreg Est–Lat program project GroundEco No. Est-Lat62, and base funding grant from the Latvian Ministry of Education and Science to the University of Latvia, No. ZD2016/AZ03. <strong>References</strong> European Environment Agency (2018) Corine Land Cover 2018. https://land.copernicus.eu/pan-european/corine-land-cover/clc2018?tab=download (CLC). Accessed 1 Jun 2020 Popovs K, Kalvāns A, Jemeljanova M, et al (under review) Bedrock surface topography map of Latvia. J Maps Popovs K, Saks T, Jātnieks J (2015) A comprehensive approach to the 3D geological modelling of sedimentary basins: example of Latvia, the central part of the Baltic Basin. Est J Earth Sci 64:173–188. https://doi.org/10.3176/earth.2015.25
description: For citation please use reference to this data set and the main article: Kalvāns, A., Popovs, K., Priede, A. et al. Nitrate vulnerability of karst aquifers and associated groundwater-dependent ecosystems in the Baltic region. Environ Earth Sci 80, 628 (2021). https://doi.org/10.1007/s12665-021-09918-7
description: {"references": ["Kalv\u0101ns, A., Popovs, K., Priede, A., Koit, O., Reti\u0137e, I., Bik\u0161e, J., D\u0113li\u0146a, A., & Babre, A. Nitrate vulnerability of karst aquifers and associated groundwater-dependent ecosystems in the Baltic region. Environmental Earth Sciences."]}
DOI: 10.5281/zenodo.5146200
title: Predicted locations and nitrate pollution of groundwater discharge from D3pl karst aquifer in Latvia

description: <strong>Description</strong> A georeferenced raster data layer [5_predicted_D3pl_GW_discharge_zone.tif] showing predicted likelihood that groundwater polluted with nitrate (NO<sub>3</sub><sup>-</sup>) is discharging as springs or diffuse seepage from the Upper Devonian Pļaviņas (<em>D<sub>3</sub>pl</em>) dolomite karst aquifer in Latvia is presented. The cell value indicates the likelihood (0 – low, 1 - high) that groundwater with nitrate contamination is discharging from the <em>D<sub>3</sub>pl</em> aquifer at this location. Value of 0 means that no groundwater is discharging there. The BalticTM 93 (EPSG:25884) references system is used. The rationale and methodology for elaborating the map of groundwater discharge as springs or diffuse seepage from the <em>D<sub>3</sub>pl</em> dolomite karst aquifer is described in the main article (Kalvāns et al. under review). In short, a 3D regional geological model (Popovs et al. 2015), land surface elevation model and bedrock surface elevation model (Popovs et al. under review) were combined to identify locations where aquitard at the base of <em>D<sub>3</sub>pl</em> aquifer is outcropping at bedrock surface and in the nearby depressions (in a distance up to 0.25 km) the land surface was below the surface of this aquitard. The likely contamination with NO<sub>3</sub><sup>-</sup> was estimated from proportion of arable land (European Environment Agency 2018) within 4.75 km window. It is assumed that the NO<sub>3</sub><sup>-</sup> contamination in the <em>D<sub>3</sub>pl</em> karst aquifer is likely only close to its distribution margins, where groundwater table is deeper than the top of the aquifer. This work was supported by the EU Interreg Est–Lat program project GroundEco No. Est-Lat62, and base funding grant from the Latvian Ministry of Education and Science to the University of Latvia, No. ZD2016/AZ03. <strong>References</strong> European Environment Agency (2018) Corine Land Cover 2018. https://land.copernicus.eu/pan-european/corine-land-cover/clc2018?tab=download (CLC). Accessed 1 Jun 2020 Popovs K, Kalvāns A, Jemeljanova M, et al (under review) Bedrock surface topography map of Latvia. J Maps Popovs K, Saks T, Jātnieks J (2015) A comprehensive approach to the 3D geological modelling of sedimentary basins: example of Latvia, the central part of the Baltic Basin. Est J Earth Sci 64:173–188. https://doi.org/10.3176/earth.2015.25
description: For citation please use reference to this data set and the main article: Kalvāns, A., Popovs, K., Priede, A. et al. Nitrate vulnerability of karst aquifers and associated groundwater-dependent ecosystems in the Baltic region. Environ Earth Sci 80, 628 (2021). https://doi.org/10.1007/s12665-021-09918-7
description: {"references": ["Kalv\u0101ns, A., Popovs, K., Priede, A., Koit, O., Reti\u0137e, I., Bik\u0161e, J., D\u0113li\u0146a, A., & Babre, A. Nitrate vulnerability of karst aquifers and associated groundwater-dependent ecosystems in the Baltic region. Environmental Earth Sciences."]}
DOI: 10.5255/ukda-sn-854945
title: Deep Sea Mining Study, 2016-2018

description: These data document a series of video interviews relating to the politics of deep sea mining in PNG and Australia. Recorded between 2016-2018, they focus on the various communities most proximate to the world's first proposed commercial deep sea mining site in Papua New Guinea (Solwara 1 held by Nautilus Minerals). Semi structured interviews were used and a topic guide is attached in the files along with the consent form used.
DOI: 10.5281/zenodo.5513666
title: Simulation input files: Cargo Release from Non-enveloped Viruses and Virus-like nanoparticles: Capsid Rupture or Pore Formation

description: Simulation input files, and code for modification to simulation software for article: Cargo Release from Non-enveloped Viruses and Virus-like nanoparticles: Capsid Rupture or PoreFormation Lukáš Sukeník,†,‡ Liya Mukhamedova,† Michaela Procházková,† Karel Škubník,† Pavel Plevka,† and Robert Vácha∗,†,‡,¶ †CEITEC – Central European Institute of Technology, Masaryk University, Kamenice753/5, 625 00 Brno, Czech Republic ‡Department of Condensed Matter Physics, Faculty of Science, Masaryk University,Kotl ́aˇrsk ́a 267/2, 611 37 Brno, Czech Republic ¶National Centre for Biomolecular Research, Faculty of Science, Masaryk University,Kamenice 5, 625 00 Brno, Czech Republic E-mail: robert.vacha@mail.muni.cz
DOI: 10.5281/zenodo.5513665
title: Simulation input files: Cargo Release from Non-enveloped Viruses and Virus-like nanoparticles: Capsid Rupture or Pore Formation

description: Simulation input files, and code for modification to simulation software for article: Cargo Release from Non-enveloped Viruses and Virus-like nanoparticles: Capsid Rupture or PoreFormation Lukáš Sukeník,†,‡ Liya Mukhamedova,† Michaela Procházková,† Karel Škubník,† Pavel Plevka,† and Robert Vácha∗,†,‡,¶ †CEITEC – Central European Institute of Technology, Masaryk University, Kamenice753/5, 625 00 Brno, Czech Republic ‡Department of Condensed Matter Physics, Faculty of Science, Masaryk University,Kotl ́aˇrsk ́a 267/2, 611 37 Brno, Czech Republic ¶National Centre for Biomolecular Research, Faculty of Science, Masaryk University,Kamenice 5, 625 00 Brno, Czech Republic E-mail: robert.vacha@mail.muni.cz
DOI: 10.5281/zenodo.4590731
title: Reproduction Package to "Strong Reduction of Quasiparticle Fluctuations in a Superconductor due to Decoupling of the Quasiparticle Number and Lifetime"

description: This is a reproduction package to the paper "Strong Reduction of Quasiparticle Fluctuations in a Superconductor due to Decoupling of the Quasiparticle Number and Lifetime". It contains all data and code to reproduce the figures in this paper.
description: Additional Grants: Veni Grant No. 639.041.750 and Projectruimte 680-91-127
DOI: 10.5281/zenodo.4580356
title: Reproduction Package to "Strong Reduction of Quasiparticle Fluctuations in a Superconductor due to Decoupling of the Quasiparticle Number and Lifetime"

description: This is a reproduction package to the paper "Strong Reduction of Quasiparticle Fluctuations in a Superconductor due to Decoupling of the Quasiparticle Number and Lifetime". It contains all data and code to reproduce the figures in this paper.
description: Additional Grants: Veni Grant No. 639.041.750 and Projectruimte 680-91-127
DOI: 10.5517/ccdc.csd.cc24f2f3
title: CCDC 1978774: Experimental Crystal Structure Determination

description: Related Article: Zhan-Guo Jiang, Wei-Tao Mao, Dan-Ping Huang, Yu Wang, Xiao-Juan Wang, Cai-Hong Zhan|2020|Nanoscale|12|10166|doi:10.1039/D0NR00973C
DOI: 10.5517/ccdc.csd.cc25jtbw
title: CCDC 2012158: Experimental Crystal Structure Determination

description: Related Article: Jintana Othong,  Jaursup Boonmak,  Filip Kielar,  and Sujittra Youngme|2020|ACS Applied Materials and Interfaces|12|41776|doi:10.1021/acsami.0c12014
DOI: 10.25345/c5426q
title: MassIVE MSV000088106 - PP2A/B55a substrate recruitment as defined by the retinoblastoma-related protein p107
title: Protein phosphorylation is a reversible post-translation modification essential in cell signaling. This study addresses a long-standing question as to how the most abundant serine/threonine Protein Phosphatase 2 (PP2A) holoenzyme, PP2A/B55a, specifically recognizes substrates and presents them to the enzyme active site. Here, we show how the PP2A regulatory subunit B55a recruits p107, a pRB-related tumor suppressor and B55a substrate. Using molecular and cellular approaches, we identified a conserved region 1 (R1, residues 615-626) encompassing the strongest p107 binding site. This enabled us to identify an "HxRVxxV619-625" short linear motif (SLiM) in p107 as necessary for B55a binding and dephosphorylation of the proximal pSer-615 in vitro and in cells. Numerous B55a/PP2A substrates, including TAU, contain a related SLiM C-terminal from a proximal phosphosite, "p[SSTT]-P--x(4,10)-[RK]-V-x-x-[VII]-R". Mutation of conserved SLiM residues in TAU dramatically inhibits dephosphorylation by PP2A/B55a, validating its generality. A data-guided computational model details the interaction of residues from the conserved p107 SLiM, the B55a groove, and phosphosite presentation. Altogether these data provide key insights into PP2A/B55a mechanisms of substrate recruitment and active site engagement, and also facilitate identification and validation of new substrates, a key step towards understanding PP2A/B55a role in multiple cellular processes.
DOI: 10.25345/c5083d
title: MassIVE MSV000088107 - Loss of the Wild-type KRAS Allele Promotes Pancreatic Cancer Progression through Functional Activation of YAP1
title: Loss of the Wild-type KRAS Allele Promotes Pancreatic Cancer Progression through Functional Activation of YAP1
DOI: 10.6084/m9.figshare.16635865
title: Minitab report Active Packaging - Rahmi Nurdiani

description: Minitab data for physicochemical and functional properties of edible film from fish gelatin incorporated with mangrove extracts
DOI: 10.6084/m9.figshare.16635865.v1
title: Minitab report Active Packaging - Rahmi Nurdiani

description: Minitab data for physicochemical and functional properties of edible film from fish gelatin incorporated with mangrove extracts