cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5285/61cd9961ecef43edadae89f842598f47
title: Arctic Cloud Summer Expedition (ACSE): composite temperature, humidity and wind profiles and derived variables from the NCAS AMF radiosondes launched from Icebreaker Oden

description: This dataset contains composite temperature, humidity and wind profiles, plus derived products, from the National Centre for Atmospheric Science's Atmospheric Measurement Facility (NCAS AMF) radiosondes launched from the Swedish Icebreaker Oden durning Arctic Cloud Summer Expedition (ACSE). ACSE took place in the Arctic during summer 2014. These measurements were used to complement a suite of other observations taken during the cruise. Those of the UK contribution, as well as selected other data, are available within the associated data collection in the Centre for Environmental Data Analysis (CEDA) archives. Other cruise data may be available in the NOAA ACSE and The Bolin Centre for Climate Research SWERUS (SWEdish-Russian-US) holdings - see online resources linked to this record.

These data consist of individual radiosonde profiles as 2D time/height fields, with all profiles interpolated onto a fixed vertical grid for ease of analysis/plotting across the outward (leg 1) and return (leg 2) parts of the expedition.

The vertical grid used is: 1m step to 5km, 10m step between 5 and 12 km, 50m step between 12 and 20 km. The data also includes derived variables (potential temperature etc).

Barbara Brooks (NCAS AMF) was responsible for the radiosonde ascents during the voyage and for the original data, whilst Ian Brookes prepared these data for archiving.


The Arctic Cloud Summer Expedition (ACSE) was a collaboration between the University of Leeds, the University of Stockholm, and NOAA-CIRES. ACSE aimed to study the response of Arctic boundary layer cloud to changes in surface conditions in the Arctic Ocean as a working package of the larger Swedish-Russian-US Investigation of Climate, Cryosphere and Carbon interaction (SWERUS-C3) Expedition in Summer 2014. This expedition was a core component to the overall SWERUS-C3 programme and was supported by the Swedish Polar Research Secretariat.

ACSE took place during a 3-month cruise of the Swedish Icebreaker Oden from Tromso, Norway to Barrow, Alaska and back over the summer of 2014. During this cruise ACSE scientists measured surface turbulent exchange, boundary layer structure, and cloud properties. Many of the measurements used remote sensing approaches - radar, lidar, and microwave radiometers - to retrieve vertical profiles of the dynamic and microphysical properties of the lower atmosphere and cloud.

The UK participation of ACSE was funded by the Natural Environment Research Council (NERC, grant: NE/K011820/1) and involved instrumentation from the Atmospheric Measurement Facility of the UK's National Centre for Atmospheric Science (NCAS AMF). This dataset collection contains data mainy from the UK contribution with some additional data from other institutes also archived to complement the suite of meteorological measurements.
DOI: 10.5285/bfa8b9457e1a4cb6aa506316295564b2
title: Arctic Cloud Summer Expedition (ACSE): turbulence wind and sonic temperature measurements from the University of Leeds Metek USA-100 sonic anemometer on board Icebreaker Oden

description: This dataset contains turbulent winds and sonic temperature measurements by the University of Leeds' Metek USA-100 sonic anemometer during the Arctic Cloud Summer Expedition (ACSE). The ACSE cruise took place in the Arctic during summer 2014. These data were obtained to complement a suite of other observations taken during the cruise. Those of the UK contribution, as well as selected other data, are available within the associated data collection in the Centre for Environmental Data Analysis (CEDA) archives. Other cruise data may be available in the NOAA ACSE and The Bolin Centre for Climate Research SWERUS (SWEdish-Russian-US) holdings - see online resources linked to this record.

Measurements were made at 20Hz from which 20-minute average fluxes were then derived.

The sonic anemometer was located on the foremast of the Icebreaker Oden ship at 20.58 m above the waterline. Data here includes the raw measurements and fully corrected turbulent winds (motion correction, flow distortion correction, etc), along with sonic temperature. For details of motion and flow distortion see the linked documentation. 

Note that while the Metek anemometer uses a left-handed reference frame, all measurements have been transformed to a right-handed frame here. The anemometer x-axis was rotated 30 deg anticlockwise from ship bow.

The Arctic Cloud Summer Expedition (ACSE) was a collaboration between the University of Leeds, the University of Stockholm, and NOAA-CIRES. ACSE aimed to study the response of Arctic boundary layer cloud to changes in surface conditions in the Arctic Ocean as a working package of the larger Swedish-Russian-US Investigation of Climate, Cryosphere and Carbon interaction (SWERUS-C3) Expedition in Summer 2014. This expedition was a core component to the overall SWERUS-C3 programme and was supported by the Swedish Polar Research Secretariat.

ACSE took place during a 3-month cruise of the Swedish Icebreaker Oden from Tromso, Norway to Barrow, Alaska and back over the summer of 2014. During this cruise ACSE scientists measured surface turbulent exchange, boundary layer structure, and cloud properties. Many of the measurements used remote sensing approaches - radar, lidar, and microwave radiometers - to retrieve vertical profiles of the dynamic and microphysical properties of the lower atmosphere and cloud.

The UK participation of ACSE was funded by the Natural Environment Research Council (NERC, grant: NE/K011820/1) and involved instrumentation from the Atmospheric Measurement Facility of the UK's National Centre for Atmospheric Science (NCAS AMF). This dataset collection contains data mainy from the UK contribution with some additional data from other institutes also archived to complement the suite of meteorological measurements.
DOI: 10.5285/ce693b9c237d4e8cb7968ef76dfc9584
title: Arctic Cloud Summer Expedition (ACSE): composite lidar wind profile data from the NCAS AMF Halo Doppler lidar on board Icebreaker Oden

description: This dataset contains composite lidar wind profile data from the NCAS AMF Halo Doppler lidar mounted on a motion stabilised platform on board the Swedish Icebreaker Oden durning Arctic Cloud Summer Expedition (ACSE). ACSE took place in the Arctic during summer 2014. These measurements were used to complement a suite of other observations taken during the cruise. Those of the UK contribution, as well as selected other data, are available within the associated data collection in the Centre for Environmental Data Analysis (CEDA) archives. Other cruise data may be available in the NOAA ACSE and The Bolin Centre for Climate Research SWERUS (SWEdish-Russian-US) holdings - see online resources linked to this record.

The Arctic Cloud Summer Expedition (ACSE) was a collaboration between the University of Leeds, the University of Stockholm, and NOAA-CIRES. ACSE aimed to study the response of Arctic boundary layer cloud to changes in surface conditions in the Arctic Ocean as a working package of the larger Swedish-Russian-US Investigation of Climate, Cryosphere and Carbon interaction (SWERUS-C3) Expedition in Summer 2014. This expedition was a core component to the overall SWERUS-C3 programme and was supported by the Swedish Polar Research Secretariat.

ACSE took place during a 3-month cruise of the Swedish Icebreaker Oden from Tromso, Norway to Barrow, Alaska and back over the summer of 2014. During this cruise ACSE scientists measured surface turbulent exchange, boundary layer structure, and cloud properties. Many of the measurements used remote sensing approaches - radar, lidar, and microwave radiometers - to retrieve vertical profiles of the dynamic and microphysical properties of the lower atmosphere and cloud.

The UK participation of ACSE was funded by the Natural Environment Research Council (NERC, grant: NE/K011820/1) and involved instrumentation from the Atmospheric Measurement Facility of the UK's National Centre for Atmospheric Science (NCAS AMF). This dataset collection contains data mainy from the UK contribution with some additional data from other institutes also archived to complement the suite of meteorological measurements.
DOI: 10.5285/e4b9bd20c2b144e9a34fb2d0ed2d0333
title: Arctic Cloud Summer Expedition (ACSE): air temperature and relative humidity measurements from the Stockholm University's Rotronic T/RH sensor on board Icebreaker Oden

description: This dataset contains surface air temperature (T) and relative humidity (RH) measurements from the Meteorologiska Institutionen Stockholms Universitet (MISU) Rotronic T/RH sensor mounted on board the Swedish Icebreaker Oden durning Arctic Cloud Summer Expedition (ACSE). ACSE took place in the Arctic during summer 2014. These measurements were used to complement a suite of other observations taken during the cruise. Those of the UK contribution, as well as selected other data, are available within the associated data collection in the Centre for Environmental Data Analysis (CEDA) archives. Other cruise data may be available in the NOAA ACSE and The Bolin Centre for Climate Research SWERUS (SWEdish-Russian-US) holdings - see online resources linked to this record.

Measurements were made at 1 Hz frequency and this dataset was prepared for archiving by Ian Brooks, University of Leeds.

The Arctic Cloud Summer Expedition (ACSE) was a collaboration between the University of Leeds, the University of Stockholm, and NOAA-CIRES. ACSE aimed to study the response of Arctic boundary layer cloud to changes in surface conditions in the Arctic Ocean as a working package of the larger Swedish-Russian-US Investigation of Climate, Cryosphere and Carbon interaction (SWERUS-C3) Expedition in Summer 2014. This expedition was a core component to the overall SWERUS-C3 programme and was supported by the Swedish Polar Research Secretariat.

ACSE took place during a 3-month cruise of the Swedish Icebreaker Oden from Tromso, Norway to Barrow, Alaska and back over the summer of 2014. During this cruise ACSE scientists measured surface turbulent exchange, boundary layer structure, and cloud properties. Many of the measurements used remote sensing approaches - radar, lidar, and microwave radiometers - to retrieve vertical profiles of the dynamic and microphysical properties of the lower atmosphere and cloud.

The UK participation of ACSE was funded by the Natural Environment Research Council (NERC, grant: NE/K011820/1) and involved instrumentation from the Atmospheric Measurement Facility of the UK's National Centre for Atmospheric Science (NCAS AMF). This dataset collection contains data mainy from the UK contribution with some additional data from other institutes also archived to complement the suite of meteorological measurements.
DOI: 10.25345/c51x6d
title: MassIVE Reanalysis RMSV000000287.3 - CCMS Conversion MSV000084857 MaxQuant msms.txt -&gt; mzTab
title: Conversion of original msms.txt from MaxQuant to mzTab
DOI: 10.25345/c5330g
title: MassIVE MSV000083223 - GNPS-1465-A1
title: Fungi of the genus Preussia are known as
endophytes of tropical higher plants, which are common in their
distribution, and many are saprobes, while others are either pathogenic
or endophytic to living plants.
DOI: 10.25345/c55q9q
title: MassIVE Reanalysis RMSV000000287.1 - DDA for interactors of B2AR, DOR, ENDO, PM + MSstats
title: To identify proteins that scored as interactors for the different time points. Digested peptide mixtures were analyzed by LC-MS/MS on a Thermo Scientific LTQ Orbitrap Elite mass spectrometry system equipped with a Proxeon Easy nLC 1000 ultra high-pressure liquid chromatography and autosampler system. Samples were injected onto a C18 column (25 cm x 75 mm I.D. packed with ReproSil Pur C18 AQ 1.9 mm particles) in 0.1% formic acid and then separated with a 90 min gradient from 5% to 30% ACN in 0.1% formic acid at a flow rate of 300 nl/min. The mass spectrometer collected data in a data-dependent fashion, collecting one full scan in the Orbitrap at 120,000 resolution followed by 10 collision-induced dissociation MS/MS scans in the dual linear ion trap for the 10 most intense peaks from the full scan. Dynamic exclusion was enabled for 30 s with a repeat count of 1. Charge state screening was employed to reject analysis of singly charged species or species for which a charge could not be assigned. The resulting data were analyzed using MaxQuant for identification and quantification. Data were searched against a database containing SwissProt Human (downloaded 12/2014), and the APEX2 sequence, concatenated to a decoy database where each sequence was randomized in order to estimate the false discovery rate (FDR). Variable modifications were allowed for methionine oxidation and protein N terminus acetylation. A fixed modi- fication was indicated for cysteine carbamidomethylation. Full trypsin specificity was required. The first search was performed with a mass accuracy of + or - 20 parts per million and the main search was performed with a mass accuracy of + or -4.5 parts per million. A maximum of 5 modifications and 2 missed cleavages were allowed per peptide. The maximum charge was set to 7+. Individual peptide mass tolerances were allowed. For MS/MS matching, the mass tolerance was set to 0.8 Da and the top 8 peaks per 100 Da were analyzed. MS/MS matching was allowed for higher charge states, water and ammonia loss events. The data were filtered to obtain a peptide, protein, and site-level false discovery rate of 0.01. The minimum peptide length was 7 amino acids. Results were matched between runs with a time window of 2 min for biological replicates. MSstats was used for statistical analysis.
DOI: 10.25345/c56w3g
title: MassIVE MSV000083222 - GNPS-A1
title: Fungi of the genus Pestalotiopsis (Amphisphaeriaceae) are known as
endophytes of tropical higher plants, which are common in their
distribution, and many are saprobes, while others are either pathogenic
or endophytic to living plants
DOI: 10.25345/c58f1v
title: MassIVE Reanalysis RMSV000000290.1 - EGDe-Qvalue : Quantification and differential abundance analysis by MSstats
title: Proteomics experiment on Listeria monocytogenes strains EGD-e was performed in biological triplicates (control, high osmolarity, low pH, bile), except for EGD-e bile, where we could only quantify duplicates. All Listeria data sets data were analyzed using Spectronaut v12 (Biognosys) using standard settings (dynamic peak detection, automatic precision nonlinear iRT calibration, interference correction, and cross run normalization). Results were filtered for a qvalue of 0.01 on the peptide level. Peptides for protein group quantitation were selected using Qvalue (only individual values passing the qvalue threshold of 0.01 were considered, NAs in data matrix) without imputation. MSstats v3.12 was used for differential abundance analysis.
DOI: 10.25345/c59f0s
title: MassIVE Reanalysis RMSV000000286.4 - MaxQuant reanalysis with id+quant mzTab
title: Reanalysis attachment with id+quant mzTab files. Please note that in order to view the analyte abundances in the mzTab file you will need to download the file by (1) clicking the "FTP Download" button on the right, (2) opening the "result" folder and (3) saving the mzTab file. Alternatively you can also download the same mzTab file by (a) clicking on the "Browse Results" button on the right, (b) clicking "Download" tab at the top of the table and (c) clicking the "Download" button in the popup panel (the mzTab file will be in the "result" folder inside the zip file).
DOI: 10.25345/c5fc70
title: MassIVE MSV000083228 - Mortalin ANT
title: MS analysis of 1D gel bands from Mortalin-interactome immunoprecipitation experiments.
DOI: 10.25345/c5hx6r
title: MassIVE Reanalysis RMSV000000288.4 - MaxQuant reanalysis with id+quant mzTab
title: Reanalysis attachment with id+quant mzTab files. Please note that in order to view the analyte abundances in the mzTab file you will need to download the file by (1) clicking the "FTP Download" button on the right, (2) opening the "result" folder and (3) saving the mzTab file. Alternatively you can also download the same mzTab file by (a) clicking on the "Browse Results" button on the right, (b) clicking "Download" tab at the top of the table and (c) clicking the "Download" button in the popup panel (the mzTab file will be in the "result" folder inside the zip file).
DOI: 10.25345/c5k316
title: MassIVE MSV000083227 - Tobramycin reduces key virulence determinants in the proteome of Pseudomonas aeruginosa outer membrane vesicles
title: Tobramycin is commonly used to treat Pseudomonas aeruginosa lung infections in patients with Cystic Fibrosis (CF). Tobramycin treatment leads to increased lung function and fewer clinical exacerbations in CF patients, and modestly reduces the density of P. aeruginosa in the lungs. P. aeruginosa resides primarily in the mucus overlying lung epithelial cells and secretes outer membrane vesicles (OMVs) that diffuse through the mucus and fuse with airway epithelial cells, thus delivering virulence factors into the cytoplasm that modify the innate immune response. The goal of this study was to test the hypothesis that Tobramycin reduces the abundance of virulence factors in OMVs secreted by P. aeruginosa. Characterization of the proteome of OMVs isolated from control or Tobramycin-exposed P. aeruginosa strain PAO1 revealed that Tobramycin reduced several OMV-associated virulence determinants, including AprA, an alkaline protease that enhances P. aeruginosa survival in the lung, and is predicted to contribute to the inhibitory effect of P. aeruginosa on Phe508del-CFTR Cl- secretion by primary human bronchial epithelial cells. Deletion of the gene encoding AprA reduced the inhibitory effect of P. aeruginosa on Phe508del-CFTR Cl- secretion. Moreover, as predicted by our proteomic analysis, OMVs isolated from Tobramycin treated P. aeruginosa had a diminished inhibitory effect on Phe508del-CFTR Cl- secretion compared to OMVs isolated from control P. aeruginosa. Taken together, our proteomic analysis of OMVs and biological validation suggest that Tobramycin may improve lung function in CF patients infected with P. aeruginosa by reducing several key virulence factors in OMVs that reduce CFTR Cl- secretion, which is essential for bacterial clearance from the lungs.
DOI: 10.25345/c5nq92
title: MassIVE Reanalysis RMSV000000288.3 - CCMS Conversion MSV000084857 MaxQuant msms.txt -&gt; mzTab
title: Conversion of original msms.txt from MaxQuant to mzTab
DOI: 10.25345/c5pw3t
title: MassIVE MSV000083226 - Etude COBRA 181130_Negatif
title: Analyses sur colonne BEH shield - Mode survey - Standards et deux extraits de plantes
DOI: 10.25345/c5sf04
title: MassIVE Reanalysis RMSV000000288.1 - DDA for interactors of DOR location + MSstats
title: To identify localization markers for DOR. Digested peptide mixtures were analyzed by LC-MS/MS on a Thermo Scientific LTQ Orbitrap Elite mass spectrometry system equipped with a Proxeon Easy nLC 1000 ultra high-pressure liquid chromatography and autosampler system. Samples were injected onto a C18 column (25 cm x 75 mm I.D. packed with ReproSil Pur C18 AQ 1.9 mm particles) in 0.1% formic acid and then separated with a 90 min gradient from 5% to 30% ACN in 0.1% formic acid at a flow rate of 300 nl/min. The mass spectrometer collected data in a data-dependent fashion, collecting one full scan in the Orbitrap at 120,000 resolution followed by 10 collision-induced dissociation MS/MS scans in the dual linear ion trap for the 10 most intense peaks from the full scan. Dynamic exclusion was enabled for 30 s with a repeat count of 1. Charge state screening was employed to reject analysis of singly charged species or species for which a charge could not be assigned. The resulting data were analyzed using MaxQuant for identification and quantification. Data were searched against a database containing SwissProt Human (downloaded 12/2014), and the APEX2 sequence, concatenated to a decoy database where each sequence was randomized in order to estimate the false discovery rate (FDR). Variable modifications were allowed for methionine oxidation and protein N terminus acetylation. A fixed modification was indicated for cysteine carbamidomethylation. Full trypsin specificity was required. The first search was performed with a mass accuracy of + or - 20 parts per million and the main search was performed with a mass accuracy of + or - 4.5 parts per million. A maximum of 5 modifications and 2 missed cleavages were allowed per peptide. The maximum charge was set to 7+. Individual peptide mass tolerances were allowed. For MS/MS matching, the mass tolerance was set to 0.8 Da and the top 8 peaks per 100 Da were analyzed. MS/MS matching was allowed for higher charge states, water and ammonia loss events. The data were filtered to obtain a peptide, protein, and site-level false discovery rate of 0.01. The minimum peptide length was 7 amino acids. Results were matched between runs with a time window of 2 min for biological replicates. MSstats was used for statistical analysis
DOI: 10.25345/c5tk5q
title: MassIVE MSV000083225 - GNPS-1465SPE2
title: Fungi of the genus preussia are known as
endophytes of tropical higher plants, which are common in their
distribution, and many are saprobes, while others are either pathogenic
or endophytic to living plants.
DOI: 10.25345/c5x73f
title: MassIVE Reanalysis RMSV000000287.4 - MaxQuant reanalysis with id+quant mzTab
title: Reanalysis attachment with id+quant mzTab files. Please note that in order to view the analyte abundances in the mzTab file you will need to download the file by (1) clicking the "FTP Download" button on the right, (2) opening the "result" folder and (3) saving the mzTab file. Alternatively you can also download the same mzTab file by (a) clicking on the "Browse Results" button on the right, (b) clicking "Download" tab at the top of the table and (c) clicking the "Download" button in the popup panel (the mzTab file will be in the "result" folder inside the zip file).
DOI: 10.25345/c5zc81
title: MassIVE MSV000083224 - GNPS-1465A1
title: Fungi of the genus preussia are known as
endophytes of tropical higher plants, which are common in their
distribution, and many are saprobes, while others are either pathogenic
or endophytic to living plants.
DOI: 10.25345/c50x63
title: MassIVE Reanalysis RMSV000000291.1 - ScottA-Qvalue : Quantification and differential abundance analysis by MSstats
title: Proteomics experiment on Listeria monocytogenes strains ScottA was performed in biological triplicates (control, high osmolarity, low pH, bile), except for EGD-e bile, where we could only quantify duplicates. All Listeria data sets data were analyzed using Spectronaut v12 (Biognosys) using standard settings (dynamic peak detection, automatic precision nonlinear iRT calibration, interference correction, and cross run normalization). Results were filtered for a qvalue of 0.01 on the peptide level. Peptides for protein group quantitation were selected using Qvalue (only individual values passing the qvalue threshold of 0.01 were considered, NAs in data matrix) without imputation. MSstats v3.12 was used for differential abundance analysis.
DOI: 10.25345/c5231j
title: MassIVE MSV000083231 - Browne et al. J Am Chem Soc, doi:10.1021/jacs.8b07911 (2018) Proteomics Datasets
title: Sample information for CITe-Id and phosphoproteomics experiments from: 

Browne, C. M. et al. A Chemoproteomic Strategy for Direct and Proteome-wide Covalent Inhibitor Target-site Identification. J Am Chem Soc, doi:10.1021/jacs.8b07911 (2018).

See readme.docx for detailed parameters for these files.