cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29517702.v1
title: Fusion transcripts landscape in hepatocellular carcinoma and potential impact on the expression of fusion partners

description: Fusion transcripts (FTs) are RNA molecules, also known as chimeric transcripts, formed through chromosomal rearrangements or transcriptional processes, contributing to tumorigenesis. This study systematically examined tumour-specific FTs in hepatocellular carcinoma (HCC) using high-throughput RNA sequencing data from independent datasets and The Cancer Genome Atlas (TCGA). Our <i>meta cohort</i> analysis included 328 HCC samples. Using STAR-Fusion, we identified 15 novel tumour-specific FTs, with SERPINA1-H19 as the most recurrent fusion event. Comparative expression analysis of fusion partner genes revealed significant downregulation in HCC tumours relative to normal adjacent liver tissues (NAT). We validated the expression levels of the key partner genes with 436 TCGA samples serving as an <i>in silico validation cohort</i> and in <i>wet lab validation cohorts</i> with 42 samples. ALB, APOA2, IGF2, MT2A, SERPINA1, and H19, which are key liver-associated genes, were frequently involved in tumour-specific fusion events suggesting either a loss of tumour suppressor property or gaining a novel function playing a role in hepatocarcinogenesis. Detailed characterization of SERPINA1-H19 identified 16 transcript variants with distinct structural modifications that may impact its functional output. Furthermore, low expression of SERPINA1 and H19 was associated with more aggressive HCC phenotypes. Overall, this study established a comprehensive repository of FTs for the first time, offering valuable insights into their role in HCC and their potential to serve as diagnostic and prognostic biomarkers for HCC.
DOI: 10.1594/pangaea.962915
title: Shipboard ADCP current measurements (38 kHz) during RV METEOR cruise M189

description: Current velocities of the upper water column along the cruise track of R/V Meteor III cruise MET189 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 (-44.7816° +/- 0.5790°) and scale factor (1.0033 +/- 0.0097) 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.962916
title: Shipboard ADCP current measurements (75 kHz) during RV METEOR cruise M189

description: Current velocities of the upper water column along the cruise track of R/V Meteor III cruise MET189 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. 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. To reduce acoustic interference with other acoustic devices the transducer orientation with respect to the ship's centerline was adjusted during the cruise from 45° to 0°. Data post-processing included water track calibration of the misalignment angle (Setting 1: -44.7838° +/- 0.6174°, Setting 2: -0.2047° +/- 0.4679°) and scale factor (Setting 1: 1.0092 +/- 0.0114, Setting 2: 1.0035 +/- 0.0076) 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: 10.6084/m9.figshare.29957759
title: Opposing mechanisms by which miRNAs mediate distinct Nrf1 and Nrf2 regulation of epithelial–mesenchymal transition in hepatocellular carcinoma

description: Accumulation of various genetics and epigenetics alterations are accepted to result in the initiation and progression of hepatocellular carcinoma (HCC), and its high metastasis is viewed as a critical bottleneck leading to its treatment failure. Amongst them, the microRNAs arising from the lack of the antioxidant transcription factor Nrf2 lead to cancer metastasis. However, much less is known about the regulation of microRNAs by Nrf1, even though it acts as an essential determinon of cell homoeostasis by governing the transcriptional expression of those driver genes contributing to the EMT involved in its metastasis. In this study, distinct EMT phenotypes resulted from specific knockouts of Nrf1 and Nrf2 in HepG2 cells, as accompanied by their differential migratory and invasive capabilities. The <i>Nrf1α</i><sup><i>–/–</i></sup>-leading EMT results from a significant decrease in the epithelial CDH1 expression, plus another increased expression of the mesenchymal CDH2. Such distinct phenotypes of <i>Nrf1α</i><sup>–<i>/</i>–</sup> from <i>Nrf2</i><sup>–<i>/</i>–</sup> cell lines were also attributable to differential regulation of two key microRNAs, i.e. <i>miR-3187-3p</i> and <i>miR-1247-5p</i>. Further experiments also unravelled that Nrf1 activates the <i>miR-3187-3p</i> expression, directly targeting for the inhibition of <i>SNAI1</i>, leading to CDH1 activation but with CDH2 inhibition insomuch as to prevent the process of EMT. By contrast, Nrf2 inhibits the <i>miR-1247-5p</i> expression, relieving its inhibitory effect on MMP15 and MMP17 to promote the EMT. Collectively, these results demonstrate that the EMT of HCC is likely prevented by Nrf1 <i>via</i> the miR-3187-3p signalling to SNAI1-CDH1/2 axis, but conversely promoted by Nrf2 through the miR-1247-5p-MMP15/17 signalling axis.
DOI: 10.6084/m9.figshare.29957759.v1
title: Opposing mechanisms by which miRNAs mediate distinct Nrf1 and Nrf2 regulation of epithelial–mesenchymal transition in hepatocellular carcinoma

description: Accumulation of various genetics and epigenetics alterations are accepted to result in the initiation and progression of hepatocellular carcinoma (HCC), and its high metastasis is viewed as a critical bottleneck leading to its treatment failure. Amongst them, the microRNAs arising from the lack of the antioxidant transcription factor Nrf2 lead to cancer metastasis. However, much less is known about the regulation of microRNAs by Nrf1, even though it acts as an essential determinon of cell homoeostasis by governing the transcriptional expression of those driver genes contributing to the EMT involved in its metastasis. In this study, distinct EMT phenotypes resulted from specific knockouts of Nrf1 and Nrf2 in HepG2 cells, as accompanied by their differential migratory and invasive capabilities. The <i>Nrf1α</i><sup><i>–/–</i></sup>-leading EMT results from a significant decrease in the epithelial CDH1 expression, plus another increased expression of the mesenchymal CDH2. Such distinct phenotypes of <i>Nrf1α</i><sup>–<i>/</i>–</sup> from <i>Nrf2</i><sup>–<i>/</i>–</sup> cell lines were also attributable to differential regulation of two key microRNAs, i.e. <i>miR-3187-3p</i> and <i>miR-1247-5p</i>. Further experiments also unravelled that Nrf1 activates the <i>miR-3187-3p</i> expression, directly targeting for the inhibition of <i>SNAI1</i>, leading to CDH1 activation but with CDH2 inhibition insomuch as to prevent the process of EMT. By contrast, Nrf2 inhibits the <i>miR-1247-5p</i> expression, relieving its inhibitory effect on MMP15 and MMP17 to promote the EMT. Collectively, these results demonstrate that the EMT of HCC is likely prevented by Nrf1 <i>via</i> the miR-3187-3p signalling to SNAI1-CDH1/2 axis, but conversely promoted by Nrf2 through the miR-1247-5p-MMP15/17 signalling axis.
DOI: 10.1594/pangaea.962917
title: Shipboard ADCP current measurements (38 kHz) during RV METEOR cruise M189/2

description: Current velocities of the upper water column along the cruise track of R/V Meteor III cruise MET189_2 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. 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 (-44.9032° +/- 0.5594°) and scale factor (1.0036 +/- 0.0116) 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.964215
title: Master tracks in different resolutions of METEOR cruise M192/2, Piraeus - Limassol, 2023-08-20 - 2023-09-05

description: Raw data acquired by position sensors on board RV METEOR during expedition M192/2 were processed to receive a validated master track which can be used as reference of further expedition data. During M192/2 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: 10.6084/m9.figshare.28112945
title: Translational regulation of PKD1 by evolutionarily conserved upstream open reading frames

description: Mutations in <i>PKD1</i> coding sequence and abnormal PKD1 expression levels contribute to the development of autosomal-dominant polycystic kidney disease, the most common genetic disorder. Regulation of PKD1 expression by factors located in the promoter and 3´ UTR have been extensively studied. Less is known about its regulation by 5´ UTR elements. In this study, we investigated the effects of uORFs and uORF-affecting variants by combining bioinformatic analyses, luciferase reporter assays, RT-qPCR and immunoblotting experiments. Our analyses demonstrate that <i>PKD1</i> mRNA contains two evolutionarily conserved translation-inhibitory uORFs. uORF1 is translatable, and uORF2 is likely not translatable. The 5´ UTR and uORFs do not modulate downstream protein output under endoplasmic reticulum stress and oxidative stress conditions. Some of uORF-perturbing variants in the SNP database are predicted to affect gene translation. Luciferase reporter assays and RT-qPCR results reveal that rs2092942382 and rs1596636969 increase, while rs2092942900 decreases main gene translation without affecting transcription. Antisense oligos targeting the uORFs reduce luciferase protein levels without altering luciferase mRNA levels. Our results establish <i>PKD1</i> as a novel target of uORF-mediated translational regulation and mutations that perturb uORFs may dysregulate PKD1 protein level.
DOI: 10.6084/m9.figshare.28112945.v2
title: Translational regulation of PKD1 by evolutionarily conserved upstream open reading frames

description: Mutations in <i>PKD1</i> coding sequence and abnormal PKD1 expression levels contribute to the development of autosomal-dominant polycystic kidney disease, the most common genetic disorder. Regulation of PKD1 expression by factors located in the promoter and 3´ UTR have been extensively studied. Less is known about its regulation by 5´ UTR elements. In this study, we investigated the effects of uORFs and uORF-affecting variants by combining bioinformatic analyses, luciferase reporter assays, RT-qPCR and immunoblotting experiments. Our analyses demonstrate that <i>PKD1</i> mRNA contains two evolutionarily conserved translation-inhibitory uORFs. uORF1 is translatable, and uORF2 is likely not translatable. The 5´ UTR and uORFs do not modulate downstream protein output under endoplasmic reticulum stress and oxidative stress conditions. Some of uORF-perturbing variants in the SNP database are predicted to affect gene translation. Luciferase reporter assays and RT-qPCR results reveal that rs2092942382 and rs1596636969 increase, while rs2092942900 decreases main gene translation without affecting transcription. Antisense oligos targeting the uORFs reduce luciferase protein levels without altering luciferase mRNA levels. Our results establish <i>PKD1</i> as a novel target of uORF-mediated translational regulation and mutations that perturb uORFs may dysregulate PKD1 protein level.
DOI: 10.6084/m9.figshare.28196172
title: Identification of differentially expressed non-coding RNAs in the plasma of women with preterm birth

description: This study aimed to identify differentially expressed non-coding RNAs (ncRNAs) associated with preterm birth (PTB) and determine biological pathways being influenced in the context of PTB. We processed cell-free RNA sequencing data and identified seventeen differentially expressed (DE) ncRNAs that could be involved in the onset of PTB. Per the validation via customized RT-qPCR, the recorded variations in expressions of eleven ncRNAs were concordant with the <i>in-silico</i> analyses. The results of this study provide insights into the role of DE ncRNAs and their impact on pregnancy-related biological pathways that could lead to PTB. Further studies are required to elucidate the precise mechanisms by which these DE ncRNAs contribute to adverse pregnancy outcomes (APOs) and their potential as diagnostic biomarkers.
DOI: 10.6084/m9.figshare.28196172.v1
title: Identification of differentially expressed non-coding RNAs in the plasma of women with preterm birth

description: This study aimed to identify differentially expressed non-coding RNAs (ncRNAs) associated with preterm birth (PTB) and determine biological pathways being influenced in the context of PTB. We processed cell-free RNA sequencing data and identified seventeen differentially expressed (DE) ncRNAs that could be involved in the onset of PTB. Per the validation via customized RT-qPCR, the recorded variations in expressions of eleven ncRNAs were concordant with the <i>in-silico</i> analyses. The results of this study provide insights into the role of DE ncRNAs and their impact on pregnancy-related biological pathways that could lead to PTB. Further studies are required to elucidate the precise mechanisms by which these DE ncRNAs contribute to adverse pregnancy outcomes (APOs) and their potential as diagnostic biomarkers.
DOI: 10.6084/m9.figshare.28112945.v1
title: Translational regulation of PKD1 by evolutionarily conserved upstream open reading frames

description: Mutations in <i>PKD1</i> coding sequence and abnormal PKD1 expression levels contribute to the development of autosomal-dominant polycystic kidney disease, the most common genetic disorder. Regulation of PKD1 expression by factors located in the promoter and 3´ UTR have been extensively studied. Less is known about its regulation by 5´ UTR elements. In this study, we investigated the effects of uORFs and uORF-affecting variants by combining bioinformatic analyses, luciferase reporter assays, RT-qPCR and immunoblotting experiments. Our analyses demonstrate that <i>PKD1</i> mRNA contains two evolutionarily conserved translation-inhibitory uORFs. uORF1 is translatable, and uORF2 is likely not translatable. The 5´ UTR and uORFs do not modulate downstream protein output under endoplasmic reticulum stress and oxidative stress conditions. Some of uORF-perturbing variants in the SNP database are predicted to affect gene translation. Luciferase reporter assays and RT-qPCR results reveal that rs2092942382 and rs1596636969 increase, while rs2092942900 decreases main gene translation without affecting transcription. Antisense oligos targeting the uORFs reduce luciferase protein levels without altering luciferase mRNA levels. Our results establish <i>PKD1</i> as a novel target of uORF-mediated translational regulation and mutations that perturb uORFs may dysregulate PKD1 protein level.
DOI: 10.1594/pangaea.924286
title: Multibeam bathymetry raw data (Kongsberg EM710 entire dataset) of RV METEOR during cruise M158

description: Multibeam bathymetry raw data was recorded in the Atlantic during cruise M158 that took place between 2019-09-19 and 2019-10-26. The data was collected using the ship's own Kongsberg EM 710. This data is part of the DAM (German Marine Research Alliance) underway research data project.
description: These data should not be used for navigational purposes.
DOI: 10.1594/pangaea.924176
title: Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV METEOR during cruise M159

description: Multibeam bathymetry raw data was recorded in the Atlantic during cruise M159 that took place between 2019-10-29 and 2019-11-20. The data was collected using the ship's own Kongsberg EM 122. This data is part of the DAM (German Marine Research Alliance) underway research data project.
description: These data should not be used for navigational purposes.
DOI: 10.15468/dl.5mffzt
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Thailand",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Tapirus indicus",
 "Year 2025-2025"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048462-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.923421
title: Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV MARIA S. MERIAN during cruise MSM55

description: Multibeam bathymetry raw data using the ship's own Kongsberg EM 122 multibeam echosounder was not continuously recorded during RV MARIA S. MERIAN cruise MSM55. Data were recorded on 8 days between 13.06.2016 and 29.06.2016 at different locations. The data were primarily 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. During data acquisition, sound velocity measurements using sound velocity profiles (SVP) was applied on the data for data calibration. SVP raw data are not part of this dataset publication.
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.923694
title: Multibeam bathymetry raw data (EM 1002 echosounder entire dataset) of RV MARIA S. MERIAN during cruise MSM55

description: Multibeam bathymetry raw data using the ship's own Kongsberg (Simrad) EM 1002 multibeam echosounder was almost continuously recorded during RV MARIA S. MERIAN cruise MSM55. Data were recorded on 13 days between 15.06.2016 and 28.06.2016. The data were primarily 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. During data acquisition, sound velocity measurements using sound velocity profiles (SVP) was applied on the data for data calibration. SVP raw data are not part of this dataset publication
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.923071
title: Multibeam bathymetry raw data (Kongsberg EM 122 entire dataset) of RV MARIA S. MERIAN during cruise MSM25

description: Multibeam bathymetry raw data was recorded in the Atlantic during cruise MSM25 that took place between 2013-01-24 and 2013-03-05. The data was collected using the ship's own Kongsberg EM 122. This data is part of the DAM (German Marine Research Alliance) underway research data project. Underway data is collected continuously on German research vessels and can include data from transits or from the entire cruise. Underway data is shared in line with the FAIR principles.
description: These data should not be used for navigational purposes.