cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.963981
title: Master tracks in different resolutions of METEOR cruise M192/1, Piraeus - Piraeus, 2023-08-08 - 2023-08-18

description: Raw data acquired by position sensors on board RV METEOR during expedition M192/1 were processed to receive a validated master track which can be used as reference of further expedition data. During M192/1 the motion reference unit Kongsberg SeaTex AS MRU-5 combined with Kongsberg SeaTex AS Seapath 320 and two C and C Technologies GPS receivers C-NAV3050 were used as navigation sensors. Data were downloaded from DAVIS SHIP data base (https://dship.bsh.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report. Processed data are provided as a master track with 1 sec resolution derived from the position sensors' data selected by priority and a generalized track with a reduced set of the most significant positions of the master track.
description: This dataset contains the master track in 10 min resolution, for other resolutions please see "Other version" references.
DOI: 10.1594/pangaea.952267
title: Water column raw data (Kongsberg EM 122 entire dataset) of RV SONNE during cruise SO268/3

description: Water column raw data using the ship's own Kongsberg EM 122 multibeam echosounder was almost continuously recorded during RV SONNE cruise SO268/3. Data were recorded 30 days between 2019-05-31 and 2019-06-28 in the North Pacific Ocean.The data are archived at the Federal Maritime and Hydrographic Agency of Germany (Bundesamt für Seeschifffahrt und Hydrographie, BSH) and provided to PANGAEA database for data curation and publication. Ancillary sound velocity profiles (SVP) files from the cruise are archived at the BSH and added to the corresponding multibeam raw dataset doi:10.1594/PANGAEA.952266This publication is conducted within the efforts of the German Marine Research Alliance in the core area 'Data management and Digitalization' (Deutsche Allianz Meeresforschung, DAM).
description: These data should not be used for navigational purposes.
DOI: 10.1594/pangaea.963745
title: Shipboard ADCP current measurements (38 kHz) during RV METEOR cruise M190

description: Current velocities of the upper water column along the cruise track of R/V Meteor cruise M190 were collected by a vessel-mounted 38 kHz RDI Ocean Surveyor ADCP. The ADCP transducer was located at 5.0 m below the water line. The instrument was operated in narrowband mode (WM10) with a bin size of 16.00 m, a blanking distance of 8.00 m, and a total of 80 bins, covering the depth range between 29.0 m and 1293.0 m. Heading, pitch and roll data from the ship's motion reference unit and the navigation data from the Global Positioning systems were used by the data acquisition software VmDAS internally to convert ADCP velocities into earth coordinates. Measured velocities and bin-depth mapping were corrected due to occasional incorrect temperature measurements at the transducer that affected the sound velocity calculation. Corrected sound velocity values were derived using temperature measured by the ship's thermosalinograph.Single-ping data / ping ensembles were screened for bottom signals and, where appropriate, a bottom mask was manually processed. The ship's velocity was calculated from position fixes obtained by the Global Positioning System (GPS). Accuracy of the ADCP velocities mainly depends on the quality of the position fixes and the ship's heading data. Further errors stem from a misalignment of the transducer with the ship's centerline. Data post-processing included water track calibration of the misalignment angle (-44.8257° +/- 0.5032°) and scale factor (1.0023 +/- 0.0091) of the Ocean Surveyor signal. The velocity data were averaged in time using an average interval of 60 s. Velocity quality flagging is based on following threshold criteria: abs(UC) or abs(VC) &gt; 1.5 m/s, rms(UC_z) or rms(VC_z) &gt; 0.3.
DOI: 10.1594/pangaea.963747
title: Shipboard ADCP current measurements (75 kHz) during RV SONNE cruise SO298

description: Current velocities of the upper water column along the cruise track of R/V Sonne cruise SO298 were collected by a vessel-mounted 75 kHz RDI Ocean Surveyor ADCP. The ADCP transducer was located at 6.0 m below the water line. The instrument was operated in narrowband mode (WM10) with a bin size of 8.00 m, a blanking distance of 4.00 m, and a total of 100 bins, covering the depth range between 18.0 m and 810.0 m. Heading, pitch and roll data from the ship's motion reference unit and the navigation data from the Global Positioning systems were used by the data acquisition software VmDAS internally to convert ADCP velocities into earth coordinates. Single-ping data / ping ensembles were screened for bottom signals and, where appropriate, a bottom mask was manually processed. The ship's velocity was calculated from position fixes obtained by the Global Positioning System (GPS). Accuracy of the ADCP velocities mainly depends on the quality of the position fixes and the ship's heading data. Further errors stem from a misalignment of the transducer with the ship's centerline. Data post-processing included water track calibration of the misalignment angle (-0.1294° +/- 0.3975°) and scale factor (0.9979 +/- 0.0094) of the Ocean Surveyor signal. The velocity data were averaged in time using an average interval of 60 s. Velocity quality flagging is based on following threshold criteria: abs(UC) or abs(VC) &gt; 3.0 m/s, rms(UC_z) or rms(VC_z) &gt; 0.2.
DOI: 10.1594/pangaea.948203
title: Master tracks in different resolutions of SONNE cruise SO292, Noumea - Noumea, 2022-05-14 - 2022-06-20

description: Raw data acquired by position sensors on board RV SONNE during expedition SO292 were processed to receive a validated master track which can be used as reference of further expedition data. During SO292 the motion reference unit Kongsberg SeaTex AS MRU-5 combined with Kongsberg SeaTex AS Seapath 320 and two GPS receivers SAAB MGL-4 were used as navigation sensors. Data were downloaded from DAVIS SHIP data base (https://dship.bsh.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report. Processed data are provided as a master track with 1 sec resolution derived from the position sensors' data selected by priority and a generalized track with a reduced set of the most significant positions of the master track.
description: This dataset contains the master track in 10 min resolution, for other resolutions please see "Further details" and "Other version" references.
DOI: 10.1594/pangaea.963746
title: Shipboard ADCP current measurements (75 kHz) during RV METEOR cruise M190

description: Current velocities of the upper water column along the cruise track of R/V Meteor cruise M190 were collected by a vessel-mounted 75 kHz RDI Ocean Surveyor ADCP. The ADCP transducer was located at 5.0 m below the water line. The instrument was operated in narrowband mode (WM10) with a bin size of 8.00 m, a blanking distance of 4.00 m, and a total of 100 bins, covering the depth range between 17.0 m and 809.0 m. Beam velocities as recorded by the data acquistion software VmDAS were transformed to ship coordinates and after merging with the navigation data from the ship's Motion Reference Unit and Global Positioning systems into earth coordinates. Single-ping data / ping ensembles were screened for bottom signals and, where appropriate, a bottom mask was manually processed. The ship's velocity was calculated from position fixes obtained by the Global Positioning System (GPS). Accuracy of the ADCP velocities mainly depends on the quality of the position fixes and the ship's heading data. Further errors stem from a misalignment of the transducer with the ship's centerline. Data post-processing included water track calibration of the misalignment angle (0.1185° +/- 0.4417°) and scale factor (1.0030 +/- 0.0084) of the Ocean Surveyor signal. The velocity data were averaged in time using an average interval of 60 s. Velocity quality flagging is based on following threshold criteria: abs(UC) or abs(VC) &gt; 1.5 m/s, rms(UC_z) or rms(VC_z) &gt; 0.3.
DOI: 10.1594/pangaea.947839
title: Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV MARIA S. MERIAN during cruise MSM79/2

description: Multibeam bathymetry raw data using the ship's own Kongsberg EM 122 multibeam echosounder was almost continuously recorded during RV MARIA S. MERIAN cruise MSM79/2. Data was recorded on 11 days between 2018-12-06 and 2018-12-18. This dataset contains an elongated transit survey at the North Atlantic Ocean passing the Rocket Seamount. Also data at the Caribbean Sea was acquired. The approximate average depth of the entire dataset is around 3500m.The data are archived at the Federal Maritime and Hydrographic Agency of Germany (Bundesamt für Seeschifffahrt und Hydrographie, BSH) and provided to PANGAEA database for data curation and publication. Ancillary sound velocity profiles (SVP) files from the cruise are archived at the BSH, thus SVP files are added to this dataset. However, data analysis of the multibeam raw data revealed that SVP has not been changed during the survey.This publication is conducted within the efforts of the German Marine Research Alliance in the core area 'Data management and Digitalization' (Deutsche Allianz Meeresforschung, DAM).Data are unprocessed and therefore contains incorrect depth measurements (artifacts) without further processing. Note that refraction errors can be expected due to the lack of proper SVP. Overall, it appears that the data quality is rather good since the gridded hillshade data showed relatively few obstacles.Data can be processed e.g. with the open source software package MB-System (Caress, D. W., and D. N. Chayes, MB-System: Mapping the Seafloor, http://www.mbari.org/products/research-software/mb-system/, 2022).
description: These data should not be used for navigational purposes.Data publishing was realized by Daniel Damaske, MARUM - Center for Marine Environmental Sciences (University Bremen).
DOI: 10.1594/pangaea.952266
title: Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV SONNE during cruise SO268/3

description: Multibeam bathymetry raw data using the ship's own Kongsberg EM 122 multibeam echosounder was almost continuously recorded during RV SONNE cruise SO268/3. Data was recorded on 29 days between 2019-05-31 and 2019-06-28. This dataset contains a transit survey in the North Pacific Ocean. The approximate average depth of the entire dataset is around 5300m.The data are archived at the Federal Maritime and Hydrographic Agency of Germany (Bundesamt für Seeschifffahrt und Hydrographie, BSH) and provided to PANGAEA database for data curation and publication. Ancillary sound velocity profiles (SVP) files from the cruise are archived at the BSH, thus SVP files are added to this dataset. Also data analysis of the multibeam raw data revealed that SVP has been changed several times during the survey.This publication is conducted within the efforts of the German Marine Research Alliance in the core area 'Data management and Digitalization' (Deutsche Allianz Meeresforschung, DAM).Data are unprocessed and therefore contains incorrect depth measurements (artifacts) without further processing. Note that refraction errors can be expected due to the lack of proper SVP. Overall, it appears that the data quality is rather good since the gridded hillshade data showed relatively few obstacles.Data can be processed e.g. with the open source software package MB-System (Caress, D. W., and D. N. Chayes, MB-System: Mapping the Seafloor, http://www.mbari.org/products/research-software/mb-system/, 2022).
description: These data should not be used for navigational purposes.
DOI: 10.1594/pangaea.963748
title: Shipboard ADCP current measurements (38 kHz) during RV SONNE cruise SO298

description: Current velocities of the upper water column along the cruise track of R/V Sonne cruise SO298 were collected by a vessel-mounted 38 kHz RDI Ocean Surveyor ADCP. The ADCP transducer was located at 6.0 m below the water line. The instrument was operated in narrowband mode (WM10) with a bin size of 32.00 m, a blanking distance of 16.00 m, and a total of 55 bins, covering the depth range between 54.0 m and 1782.0 m. Heading, pitch and roll data from the ship's motion reference unit and the navigation data from the Global Positioning systems were used by the data acquisition software VmDAS internally to convert ADCP velocities into earth coordinates. Single-ping data / ping ensembles were screened for bottom signals and, where appropriate, a bottom mask was manually processed. The ship's velocity was calculated from position fixes obtained by the Global Positioning System (GPS). Accuracy of the ADCP velocities mainly depends on the quality of the position fixes and the ship's heading data. Further errors stem from a misalignment of the transducer with the ship's centerline. Data post-processing included water track calibration of the misalignment angle (-0.2504° +/- 0.4404°) and scale factor (1.0012 +/- 0.0095) of the Ocean Surveyor signal. The velocity data were averaged in time using an average interval of 60 s. Velocity quality flagging is based on following threshold criteria: abs(UC) or abs(VC) &gt; 2.2 m/s, rms(UC_z) or rms(VC_z) &gt; 0.2.
DOI: 10.6084/m9.figshare.28937250
title: Cleavage sequence specificity of Nsp15

description: Nsp15 is an EndoU nuclease that is partially responsible for SARS-CoV-2’s ability to evade the immune system response. Despite its importance, the sequence specificity of Nsp15 remains difficult to fully determine. In this work, we use a systematic approach to measure Nsp15’s sequence specificity by testing all 16 dinucleotides for cleavage activity. The results show a preference for uridine in the first dinucleotide position, but with varying specificity in the second position. Using Alphafold3 predictions to examine the structural basis of this specificity suggests important contacts 3’ of the dinucleotide sequence as well as contacts to the dinucleotides that agree with the cleavage specificity.
DOI: 10.6084/m9.figshare.28937250.v2
title: Cleavage sequence specificity of Nsp15

description: Nsp15 is an EndoU nuclease that is partially responsible for SARS-CoV-2’s ability to evade the immune system response. Despite its importance, the sequence specificity of Nsp15 remains difficult to fully determine. In this work, we use a systematic approach to measure Nsp15’s sequence specificity by testing all 16 dinucleotides for cleavage activity. The results show a preference for uridine in the first dinucleotide position, but with varying specificity in the second position. Using Alphafold3 predictions to examine the structural basis of this specificity suggests important contacts 3’ of the dinucleotide sequence as well as contacts to the dinucleotides that agree with the cleavage specificity.
DOI: 10.1594/pangaea.964014
title: Master tracks in different resolutions of MARIA S. MERIAN cruise MSM118, Ponta Delgada - St. John's, 2023-06-18 - 2023-07-04

description: Raw data acquired by position sensors on board RV MERIAN during expedition MSM118 were processed to receive a validated master track which can be used as reference of further expedition data. During MSM118 the motion reference unit Kongsberg SeaTex AS MRU-5 combined with Kongsberg SeaTex AS Seapath 320 and the GPS receivers Trimble SPS855 and SAAB R4 were used as navigation sensors. Data were downloaded from DAVIS SHIP data base (https://dship.bsh.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report. Processed data are provided as a master track with 1 sec resolution derived from the position sensors' data selected by priority and a generalized track with a reduced set of the most significant positions of the master track.
description: This dataset contains the master track in 10 min resolution, for other resolutions please see "Other version" references.
DOI: 10.1594/pangaea.964018
title: Master tracks in different resolutions of MARIA S. MERIAN cruise MSM119, St. John's - St. John's, 2023-07-08 - 2023-08-12

description: Raw data acquired by position sensors on board RV MERIAN during expedition MSM119 were processed to receive a validated master track which can be used as reference of further expedition data. During MSM119 the motion reference unit Kongsberg SeaTex AS MRU-5 combined with Kongsberg SeaTex AS Seapath 320 and the GPS receivers Trimble SPS855 and SAAB R4 were used as navigation sensors. Data were downloaded from DAVIS SHIP data base (https://dship.bsh.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report. Processed data are provided as a master track with 1 sec resolution derived from the position sensors' data selected by priority and a generalized track with a reduced set of the most significant positions of the master track.
description: This dataset contains the master track in 10 min resolution, for other resolutions please see "Other version" references.
DOI: 10.6084/m9.figshare.28714593
title: Prp16 enables efficient splicing of introns with diverse exonic consensus elements in the short-intron rich <i>Cryptococcus neoformans</i> transcriptome

description: DEAH box splicing helicase Prp16 in budding yeast governs spliceosomal remodelling from the branching conformation (C complex) to the exon ligation conformation (C* complex). In this study, we examined the genome-wide functions of Prp16 in the short intron-rich genome of the basidiomycete yeast <i>Cryptococcus neoformans</i>. The presence of multiple introns per transcript with intronic features that are more similar to those of higher eukaryotes makes it a promising model for studying spliceosomal splicing. Using a promoter-shutdown conditional Prp16 knockdown strain, we uncovered genome-wide but substrate-specific roles in <i>C. neoformans</i> splicing. The splicing functions of Prp16 are dependent on helicase motifs I and II, which are conserved motifs for helicase activity. A small subset of introns spliced independent of Prp16 activity was investigated to discover that exonic sequences at the 5’ splice site (5’SS) and 3’ splice site (3’SS) with stronger affinity for U5 loop 1 are a common feature in these introns. Furthermore, short (60–100nts) and ultrashort introns (&lt;60nts) prevalent in the <i>C. neoformans</i> transcriptome were more sensitive to Prp16 knockdown than longer introns, indicating that Prp16 is required for the efficient splicing of short and ultrashort introns. We propose that stronger U5 snRNA-pre-mRNA interactions enable efficient transition of the spliceosome from the first to the second catalytic confirmation in Prp16 knockdown, particularly for short introns and introns with suboptimal features. This study provides insights into fine-tuning spliceosomal helicase function with variations in <i>cis-</i>element features.
DOI: 10.6084/m9.figshare.28714593.v1
title: Prp16 enables efficient splicing of introns with diverse exonic consensus elements in the short-intron rich <i>Cryptococcus neoformans</i> transcriptome

description: DEAH box splicing helicase Prp16 in budding yeast governs spliceosomal remodelling from the branching conformation (C complex) to the exon ligation conformation (C* complex). In this study, we examined the genome-wide functions of Prp16 in the short intron-rich genome of the basidiomycete yeast <i>Cryptococcus neoformans</i>. The presence of multiple introns per transcript with intronic features that are more similar to those of higher eukaryotes makes it a promising model for studying spliceosomal splicing. Using a promoter-shutdown conditional Prp16 knockdown strain, we uncovered genome-wide but substrate-specific roles in <i>C. neoformans</i> splicing. The splicing functions of Prp16 are dependent on helicase motifs I and II, which are conserved motifs for helicase activity. A small subset of introns spliced independent of Prp16 activity was investigated to discover that exonic sequences at the 5’ splice site (5’SS) and 3’ splice site (3’SS) with stronger affinity for U5 loop 1 are a common feature in these introns. Furthermore, short (60–100nts) and ultrashort introns (&lt;60nts) prevalent in the <i>C. neoformans</i> transcriptome were more sensitive to Prp16 knockdown than longer introns, indicating that Prp16 is required for the efficient splicing of short and ultrashort introns. We propose that stronger U5 snRNA-pre-mRNA interactions enable efficient transition of the spliceosome from the first to the second catalytic confirmation in Prp16 knockdown, particularly for short introns and introns with suboptimal features. This study provides insights into fine-tuning spliceosomal helicase function with variations in <i>cis-</i>element features.
DOI: 10.6084/m9.figshare.28937250.v1
title: Cleavage sequence specificity of Nsp15

description: Nsp15 is an EndoU nuclease that is partially responsible for SARS-CoV-2’s ability to evade the immune system response. Despite its importance, the sequence specificity of Nsp15 remains difficult to fully determine. In this work, we use a systematic approach to measure Nsp15’s sequence specificity by testing all 16 dinucleotides for cleavage activity. The results show a preference for uridine in the first dinucleotide position, but with varying specificity in the second position. Using Alphafold3 predictions to examine the structural basis of this specificity suggests important contacts 3’ of the dinucleotide sequence as well as contacts to the dinucleotides that agree with the cleavage specificity.
DOI: 10.1594/pangaea.950201
title: Multibeam bathymetry processed data (Kongsberg EM 122 entire dataset) of RV MARIA S. MERIAN during cruise MSM94

description: Multibeam bathymetry raw data were recorded in the Atlantic during cruise MSM94 that took place between 2020-08-02 and 2020-09-06. The data were collected using the ship's own Kongsberg EM 122. Sound velocity profiles (SVP) were applied on the data for calibration. Please see environmental data (zip file) and the cruise report for details. The data were processed using QPS Qimera software v2.4.5 with manual editing in the UTM28N coordinate system (EPSG:32628). Data products include an XYZ ASCII file with accepted soundings with a minimum depth value of -237,1 m and a maximum depth value of -4846,4 m and a GeoTIFF with a resolution of 200 m for overview purposes only and not for scientific analysis or navigation. The resolution was chosen according to the median depth of the cleaned soundings (-2896 m) and the depth-variable resolution goal of the Nippon Foundation GEBCO Seabed 2030 Project (Mayer et al. 2018; doi:10.3390/geosciences8020063).
description: These data should not be used for navigational purposes.
DOI: 10.1594/pangaea.964020
title: Master tracks in different resolutions of MARIA S. MERIAN cruise MSM120, St. John's - Nuuk (Greenland), 2023-08-15 - 2023-09-20

description: Raw data acquired by position sensors on board RV MERIAN during expedition MSM120 were processed to receive a validated master track which can be used as reference of further expedition data. During MSM120 the motion reference unit Kongsberg SeaTex AS MRU-5 combined with Kongsberg SeaTex AS Seapath 320 and the GPS receivers Trimble SPS855 and SAAB R4 were used as navigation sensors. Data were downloaded from DAVIS SHIP data base (https://dship.bsh.de) with a resolution of 1 sec. Processing and evaluation of the data is outlined in the data processing report. Processed data are provided as a master track with 1 sec resolution derived from the position sensors' data selected by priority and a generalized track with a reduced set of the most significant positions of the master track.
description: This dataset contains the master track in 10 min resolution, for other resolutions please see "Other version" references.