cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7140032
title: The genetic structure and diversity of <i>Gentiana lutea</i> subsp. <i>lutea</i> (Gentianaceae) in Sardinia: further insights for its conservation planning

description: Knowledge of the levels of genetic diversity and of the spatial genetic structure of plant species is important to ensure their effective management and conservation, especially in the case of endangered species. <i>Gentiana lutea</i> L. subsp. <i>lutea</i> is a long-lived plant which occurs in central and southern European mountains. It has a long-standing history of human exploitation, mainly in the liqueur and in the pharmaceutical industries and it is currently listed in the EU Habitats Directive 92/43/EEC Annex V. Mainly due to a prolonged root harvesting, its current distribution range in Sardinia consists of only a few groups of individuals limited to small areas of the Gennargentu massif (Central-Eastern area of the island). In this study, we investigated the levels of genetic diversity and the genetic structure of the species in Sardinia. We used AFLP (amplified fragment length polymorphism) markers to investigate the genetic variability of 182 samples from 13 subpopulations. A total of 433 fragments were detected, of which 75.5% were polymorphic. The levels of genetic diversity were generally high, but they tended to decrease in smaller subpopulations. Of the genetic variability 88% was found within subpopulations, while the genetic structure among them was fairly weak. In order to ensure the survival of these subpopulations, especially the smaller ones, <i>ex situ</i> and <i>in situ</i> management actions should be planned, such as the long term conservation of its seeds in germplasm repositories and their population reinforcements and monitoring.
DOI: 10.6084/m9.figshare.7140035.v1
title: mutations_pos.bed

description: List of the mutated sites of the hg19 reference genome used in de Filippo et al. "Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences".
DOI: 10.6084/m9.figshare.7140032.v1
title: The genetic structure and diversity of <i>Gentiana lutea</i> subsp. <i>lutea</i> (Gentianaceae) in Sardinia: further insights for its conservation planning

description: Knowledge of the levels of genetic diversity and of the spatial genetic structure of plant species is important to ensure their effective management and conservation, especially in the case of endangered species. <i>Gentiana lutea</i> L. subsp. <i>lutea</i> is a long-lived plant which occurs in central and southern European mountains. It has a long-standing history of human exploitation, mainly in the liqueur and in the pharmaceutical industries and it is currently listed in the EU Habitats Directive 92/43/EEC Annex V. Mainly due to a prolonged root harvesting, its current distribution range in Sardinia consists of only a few groups of individuals limited to small areas of the Gennargentu massif (Central-Eastern area of the island). In this study, we investigated the levels of genetic diversity and the genetic structure of the species in Sardinia. We used AFLP (amplified fragment length polymorphism) markers to investigate the genetic variability of 182 samples from 13 subpopulations. A total of 433 fragments were detected, of which 75.5% were polymorphic. The levels of genetic diversity were generally high, but they tended to decrease in smaller subpopulations. Of the genetic variability 88% was found within subpopulations, while the genetic structure among them was fairly weak. In order to ensure the survival of these subpopulations, especially the smaller ones, <i>ex situ</i> and <i>in situ</i> management actions should be planned, such as the long term conservation of its seeds in germplasm repositories and their population reinforcements and monitoring.
DOI: 10.7284/122801
title: GNSS (Global Navigation Satellite System) data collected during research cruise WS15264 using a Raytheon 320 WAAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7139999
title: Dinosaur trackway

description: “txt” file columns: X Y Z R G B;"pcd": file format defined in Point Cloud Library.
DOI: 10.7284/122802
title: Gyrocompass data collected during research cruise WS15264 using a SGB Meridian instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122812
title: Hygrometer data collected during research cruise WS15264 using a RM Young 41372VC instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7139780
title: Modified hg19 reference genome

description: Modified hg19 reference genome as described in de Filippo et al. 2018.
DOI: 10.6084/m9.figshare.7139774
title: methods used by data contributors to estimate geographic locations from Global Location Sensor

description: CSV file listing the methods used by data contributors to estimate geographic locations from Global Location Sensor (GLS) tag raw data (487 individuals). The field ‘gls_method’ can be one of: ‘GEOLight’ 27(Lisovski & Hahn 2012), ‘SGAT’ 29(Wotherspoon 2017), ‘Twilight-free’ 28(Bindoff 2017), ‘BasTrak’ 25(Phillips et al. 2004) or ‘tripEstimation’ 26(Sumner et al. 2009). The field ‘gls_sst’ indicates whether sea surface temperature data were used for location estimation and can be one of: ‘N’ (no), ‘Y’ (yes) or ‘T’ (unknown; depending on the specific tag used). Records for each individual can be linked to the metadata and data files using the field ‘individual_id’.
DOI: 10.6084/m9.figshare.7139780.v1
title: Modified hg19 reference genome

description: Modified hg19 reference genome as described in de Filippo et al. 2018.
DOI: 10.6084/m9.figshare.7139771
title: Data Authors and Citations

description: CSV file listing contact persons and citations for datasets contributed to the RAATD dataset.
DOI: 10.6084/m9.figshare.7139774.v1
title: methods used by data contributors to estimate geographic locations from Global Location Sensor

description: CSV file listing the methods used by data contributors to estimate geographic locations from Global Location Sensor (GLS) tag raw data (487 individuals). The field ‘gls_method’ can be one of: ‘GEOLight’ 27(Lisovski & Hahn 2012), ‘SGAT’ 29(Wotherspoon 2017), ‘Twilight-free’ 28(Bindoff 2017), ‘BasTrak’ 25(Phillips et al. 2004) or ‘tripEstimation’ 26(Sumner et al. 2009). The field ‘gls_sst’ indicates whether sea surface temperature data were used for location estimation and can be one of: ‘N’ (no), ‘Y’ (yes) or ‘T’ (unknown; depending on the specific tag used). Records for each individual can be linked to the metadata and data files using the field ‘individual_id’.
DOI: 10.7284/122810
title: INS (Inertial Navigation System) data collected during research cruise WS15264 using a Applanix POS/MV-320 V2 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7139762
title: Supplementary Material for: Interference with NTSR1 Expression Exerts an Anti-Invasion Effect via the Jun/miR-494/SOCS6 Axis of Glioblastoma Cells

description: <b><i>Background/Aims:</i></b> Glioblastoma is the most common and aggressive brain tumor and carries a poor prognosis. Previously, we found that neurotensin receptor 1 (NTSR1) contributes to glioma progression, but the underlying mechanisms of NTSR1 in glioblastoma invasion remain to be clarified. The aim of this study was to investigate the molecular mechanisms of NTSR1 in glioblastoma invasion. <b><i>Methods:</i></b> Cell migration and invasion were evaluated using wound-healing and transwell assays. Cell proliferation was detected using CCK-8. The expression of NTSR1, Jun, and suppressor of cytokine signaling 6 (SOCS6) was detected using western blotting. The expression of miR-494 was detected by Quantitative real-time PCR. Chromatin immunoprecipitation assay was performed to examine the interaction between Jun and miR-494 promoter. Dual-luciferase reporter assay and western blotting were performed to identify the direct regulation of SOCS6 by miR-494. An orthotopic xenograft mouse model was conducted to assess tumor growth and invasion. <b><i>Results:</i></b> NTSR1 knockdown attenuated the invasion of glioblastoma cells. Jun was positively regulated by NTSR1, which promoted miR-494 expression through binding to miR-494 promoter. SOCS6 was confirmed as a direct target of miR-494, thus, NTSR1-induced miR-494 upregulation resulted in SOCS6 downregulation. Both miR-494 and SOCS6 were involved in the NTSR1-induced invasion of glioblastoma cells. <i>In vivo</i>, tumor invasion and growth were inhibited by NTSR1 knockdown, but were restored with miR-494 overexpression. <b><i>Conclusion:</i></b> NTSR1 knockdown inhibited glioblastoma invasion via the Jun/miR-494/SOCS6 axis.
DOI: 10.6084/m9.figshare.7139771.v1
title: Data Authors and Citations

description: CSV file listing contact persons and citations for datasets contributed to the RAATD dataset.
DOI: 10.7284/122803
title: Radiometer data collected during research cruise WS15264 using a Eppley PSP instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7139762.v1
title: Supplementary Material for: Interference with NTSR1 Expression Exerts an Anti-Invasion Effect via the Jun/miR-494/SOCS6 Axis of Glioblastoma Cells

description: <b><i>Background/Aims:</i></b> Glioblastoma is the most common and aggressive brain tumor and carries a poor prognosis. Previously, we found that neurotensin receptor 1 (NTSR1) contributes to glioma progression, but the underlying mechanisms of NTSR1 in glioblastoma invasion remain to be clarified. The aim of this study was to investigate the molecular mechanisms of NTSR1 in glioblastoma invasion. <b><i>Methods:</i></b> Cell migration and invasion were evaluated using wound-healing and transwell assays. Cell proliferation was detected using CCK-8. The expression of NTSR1, Jun, and suppressor of cytokine signaling 6 (SOCS6) was detected using western blotting. The expression of miR-494 was detected by Quantitative real-time PCR. Chromatin immunoprecipitation assay was performed to examine the interaction between Jun and miR-494 promoter. Dual-luciferase reporter assay and western blotting were performed to identify the direct regulation of SOCS6 by miR-494. An orthotopic xenograft mouse model was conducted to assess tumor growth and invasion. <b><i>Results:</i></b> NTSR1 knockdown attenuated the invasion of glioblastoma cells. Jun was positively regulated by NTSR1, which promoted miR-494 expression through binding to miR-494 promoter. SOCS6 was confirmed as a direct target of miR-494, thus, NTSR1-induced miR-494 upregulation resulted in SOCS6 downregulation. Both miR-494 and SOCS6 were involved in the NTSR1-induced invasion of glioblastoma cells. <i>In vivo</i>, tumor invasion and growth were inhibited by NTSR1 knockdown, but were restored with miR-494 overexpression. <b><i>Conclusion:</i></b> NTSR1 knockdown inhibited glioblastoma invasion via the Jun/miR-494/SOCS6 axis.
DOI: 10.6084/m9.figshare.7139702
title: voxelwise resting state HRF shape (WM and GM)

description: We used our rsHRF tool https://www.nitrc.org/projects/rshrf to retrieve a proxy of the hemodynamic response function from BOLD signal recorded at each voxel, both in grey and in white matter.These figures report the average relevant parameters (Height, Full Width at Half Maximum, Time to Peak) from Human Connectome Project data.We report results using two sets of basis functions: Canonical Shape with two derivatives (Canon2dd), and Finite Impulse Response (FIR).<br>The 3D nifti images can be found here https://neurovault.org/collections/3584/
DOI: 10.7284/122804
title: Radiometer data collected during research cruise WS15264 using a Eppley TUV instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7139699
title: Supplementary Material for: Incidence and Outcomes of Pituitary Microadenomas in Children with Short Stature/Growth Hormone Deficiency

description: <b><i>Background/Aims:</i></b> Patients with short stature (SS)/growth hormone deficiency (GHD) and precocious puberty (PP) undergo brain MRI to evaluate for structural brain abnormalities or pituitary lesions, and pituitary microadenomas are a common finding. Theoretically, a mass effect from these lesions could cause GHD and growth hormone treatment could cause them to enlarge, but they should not cause PP, at least in females. <b><i>Methods:</i></b> We investigated if pituitary microadenomas cause GHD by comparing their incidence in patients with SS/GHD to that in females with PP. We performed a retrospective chart review of patients with these disorders who had a brain MRI between 2000 and 2013. <b><i>Results:</i></b> The incidence of microadenoma was high in both groups, 18.5% for SS (<i>n</i> = 346) and 21.1% for PP females (<i>n</i> = 194), but did not differ between groups (<i>p</i> = 0.46). In patients with microadenomas, repeat imaging showed resolution in 58% (SS, <i>n</i> = 33) and 67% (PP females, <i>n</i> = 21). Importantly, none of the lesions grew, even in patients treated with growth hormone. <b><i>Conclusions:</i></b> Pituitary microadenomas are common in children with GHD/SS and PP, but it does not appear that they are a cause of GHD. They appear to be of limited clinical significance and should not be considered a contraindication to growth hormone therapy.
DOI: 10.7284/122808
title: Radiometer data collected during research cruise WS15264 using a Eppley PIR instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7139702.v1
title: voxelwise resting state HRF shape (WM and GM)

description: We used our rsHRF tool https://www.nitrc.org/projects/rshrf to retrieve a proxy of the hemodynamic response function from BOLD signal recorded at each voxel, both in grey and in white matter.These figures report the average relevant parameters (Height, Full Width at Half Maximum, Time to Peak) from Human Connectome Project data.We report results using two sets of basis functions: Canonical Shape with two derivatives (Canon2dd), and Finite Impulse Response (FIR).<br>The 3D nifti images can be found here https://neurovault.org/collections/3584/
DOI: 10.7284/122807
title: Rain Gauge data collected during research cruise WS15264 using a OSI ORG-815 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7139669
title: Data sheet

description: Dataset contains all data included in manuscript
DOI: 10.6084/m9.figshare.7139669.v1
title: Data sheet

description: Dataset contains all data included in manuscript
DOI: 10.7284/122815
title: Singlebeam Echosounder data collected during research cruise WS15264 using a Knudsen 3260 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122805
title: Water Temperature data collected during research cruise WS15264 using a Sea-Bird SBE-38 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122806
title: TSG (Thermosalinograph) data collected during research cruise WS15264 using a Sea-Bird SBE-45 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/122830
title: Multiplexed data collected during research cruise WS15271 using a Miami VIDS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7139579
title: Identification of loci for single/double flower trait by combing genome-wide association analysis

description: The SNP for association analysis with double flower in peach
DOI: 10.7284/122832
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise WS15271 using a Hawaii UHDAS instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7139567
title: <i>Laosuchus naga</i> gen. et sp. nov., a new chroniosuchian from South-East Asia (Laos) with internal structures revealed by micro-CT scan and discussion of its palaeobiology

description: Chroniosuchians were a clade of non-amniotic tetrapods known from the Guadalupian (middle Permian) to Late Triassic, mainly from Russia and China. The rarity of complete or articulated remains means that relatively little is known about this group in terms of its anatomy, palaeobiology or evolutionary history. Based on a nearly complete skull with a left hemimandible, we describe the first chroniosuchian from Laos from rocks preserving the Permian–Triassic boundary in the Luang Prabang Basin, which is located on the tectonic Indochina Block. This specimen is referred to a new genus and species, <i>Laosuchus naga</i>, based on numerous diagnostic features, including an extremely reduced pineal foramen; absence of palatal dentition; well-developed transverse flange of the pterygoid that contacts the maxilla; internal crest on and above the dorsal side the palate; otic notch closed by the tabular horn and the posterior part of the squamosal, forming a continuous wall; thin and high ventromedial ridge on parasphenoid. A phylogenetic analysis of 51 characters and 25 taxa reveals a basal position for <i>Laosuchus naga</i> among Chroniosuchia. In addition, CT scan data reveal internal structures and provide new insights about the anatomy and palaeobiology of chroniosuchians. <i>Laosuchus naga</i> was likely amphibious and spent most of its time in water, rather than in terrestrial environments. As chroniosuchians are non-marine tetrapods previously known on the North China Block, South China Block and Laurussia, the occurrence of <i>Laosuchus naga</i> on the Indochina Block supports the hypothesis of physical connections between all these tectonic plates by the time of the Permo–Triassic boundary. http://zoobank.org/urn:lsid:zoobank.org:pub:11D07FA3-0F4C-4EF9-A416-E8E6BE76C970
DOI: 10.7284/122829
title: Anemometer data collected during research cruise WS15271 using a RM Young 05106 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7139510
title: Artificial dataset for clustering algorithms(Complete)

description: This file contains a number of randomly generated datasets. The properties of each dataset are indicated in the name of each respective file: 'C' indicates the number of classes, 'F' indicates the number of features, 'Ne' indicates the number of objects contained in each class, 'A' is related to the average separation between classes and 'R' is an index used to differentiate distinct random trials. So, for instance, the file C2F10N2Ne5A1.2R0 is a dataset containing 2 classes, 10 features, 5 objects for each class and having a typical separation between classes of 1.2. The methodology used for generating the datasets is described in the accompanying reference.<br>
DOI: 10.6084/m9.figshare.7139567.v1
title: <i>Laosuchus naga</i> gen. et sp. nov., a new chroniosuchian from South-East Asia (Laos) with internal structures revealed by micro-CT scan and discussion of its palaeobiology

description: Chroniosuchians were a clade of non-amniotic tetrapods known from the Guadalupian (middle Permian) to Late Triassic, mainly from Russia and China. The rarity of complete or articulated remains means that relatively little is known about this group in terms of its anatomy, palaeobiology or evolutionary history. Based on a nearly complete skull with a left hemimandible, we describe the first chroniosuchian from Laos from rocks preserving the Permian–Triassic boundary in the Luang Prabang Basin, which is located on the tectonic Indochina Block. This specimen is referred to a new genus and species, <i>Laosuchus naga</i>, based on numerous diagnostic features, including an extremely reduced pineal foramen; absence of palatal dentition; well-developed transverse flange of the pterygoid that contacts the maxilla; internal crest on and above the dorsal side the palate; otic notch closed by the tabular horn and the posterior part of the squamosal, forming a continuous wall; thin and high ventromedial ridge on parasphenoid. A phylogenetic analysis of 51 characters and 25 taxa reveals a basal position for <i>Laosuchus naga</i> among Chroniosuchia. In addition, CT scan data reveal internal structures and provide new insights about the anatomy and palaeobiology of chroniosuchians. <i>Laosuchus naga</i> was likely amphibious and spent most of its time in water, rather than in terrestrial environments. As chroniosuchians are non-marine tetrapods previously known on the North China Block, South China Block and Laurussia, the occurrence of <i>Laosuchus naga</i> on the Indochina Block supports the hypothesis of physical connections between all these tectonic plates by the time of the Permo–Triassic boundary. http://zoobank.org/urn:lsid:zoobank.org:pub:11D07FA3-0F4C-4EF9-A416-E8E6BE76C970
DOI: 10.6084/m9.figshare.7139567.v2
title: <i>Laosuchus naga</i> gen. et sp. nov., a new chroniosuchian from South-East Asia (Laos) with internal structures revealed by micro-CT scan and discussion of its palaeobiology

description: Chroniosuchians were a clade of non-amniotic tetrapods known from the Guadalupian (middle Permian) to Late Triassic, mainly from Russia and China. The rarity of complete or articulated remains means that relatively little is known about this group in terms of its anatomy, palaeobiology or evolutionary history. Based on a nearly complete skull with a left hemimandible, we describe the first chroniosuchian from Laos from rocks preserving the Permian–Triassic boundary in the Luang Prabang Basin, which is located on the tectonic Indochina Block. This specimen is referred to a new genus and species, <i>Laosuchus naga</i>, based on numerous diagnostic features, including an extremely reduced pineal foramen; absence of palatal dentition; well-developed transverse flange of the pterygoid that contacts the maxilla; internal crest on and above the dorsal side the palate; otic notch closed by the tabular horn and the posterior part of the squamosal, forming a continuous wall; thin and high ventromedial ridge on parasphenoid. A phylogenetic analysis of 51 characters and 25 taxa reveals a basal position for <i>Laosuchus naga</i> among Chroniosuchia. In addition, CT scan data reveal internal structures and provide new insights about the anatomy and palaeobiology of chroniosuchians. <i>Laosuchus naga</i> was likely amphibious and spent most of its time in water, rather than in terrestrial environments. As chroniosuchians are non-marine tetrapods previously known on the North China Block, South China Block and Laurussia, the occurrence of <i>Laosuchus naga</i> on the Indochina Block supports the hypothesis of physical connections between all these tectonic plates by the time of the Permo–Triassic boundary. http://zoobank.org/urn:lsid:zoobank.org:pub:11D07FA3-0F4C-4EF9-A416-E8E6BE76C970
DOI: 10.7284/122827
title: Fluorometer data collected during research cruise WS15271 using a Turner Cyclops-7 instrument system onboard the platform RV F.G. Walton Smith

description: Original (unprocessed) data collected during a Field_expedition