cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14792100
title: MLSA phylogeny of 40 Agrobacterium spp.

description: For this MLSA of 40 Agrobacterium spp. strains, we extracted the CDS alignments of parE, gyrB, recA, and rpoB from the Pantagruel pangenome database and concatenated into a multi-locus alignment, totaling 9,968 positions. ML Phylogenies were then inferred based on these alignments with RAxML-NG 1.0.0 with the options ‘--model GTR+G4 --all’, implying the use of the model GTR+FO+G4m, and that 20 independent inferences were run, starting with 10 random trees and 10 parsimony-optimized tree, and retaining the the best ML tree from these 20 inferences. Branch supports were estimated with 200 Felsentein bootstrap trees.Separate and concatenated alignments of the 4 marker gene families are provided. The correspondance between genome code (prefix of locus tags) and organism name is provided in 'organism_code.tab'. Sequence similarity matrices for each locus are also provided.
DOI: 10.6084/m9.figshare.14792100.v5
title: MLSA phylogeny of 40 Agrobacterium spp.

description: For this MLSA of 40 Agrobacterium spp. strains, we extracted the CDS alignments of parE, gyrB, recA, and rpoB from the Pantagruel pangenome database and concatenated into a multi-locus alignment, totaling 9,968 positions. ML Phylogenies were then inferred based on these alignments with RAxML-NG 1.0.0 with the options ‘--model GTR+G4 --all’, implying the use of the model GTR+FO+G4m, and that 20 independent inferences were run, starting with 10 random trees and 10 parsimony-optimized tree, and retaining the the best ML tree from these 20 inferences. Branch supports were estimated with 200 Felsentein bootstrap trees.Separate and concatenated alignments of the 4 marker gene families are provided. The correspondance between genome code (prefix of locus tags) and organism name is provided in 'organism_code.tab'. Sequence similarity matrices for each locus are also provided.
DOI: 10.6084/m9.figshare.16586055
title: Review of jellyfish trophic interactions in the Baltic Sea

description: Despite the diversity and oftentimes large biomass of jellyfish in marine systems, their ecological role remains poorly understood. We here provide the first systematic review of studies on jellyfish trophic ecology in the Baltic Sea (a regional marine system under strong multiple global and regional anthropogenic pressures). In total, we identified 57 peer-reviewed publications, with notable taxonomic bias towards two species (<i>Aurelia aurita</i>; non-indigenous <i>Mnemiopsis leidyi</i>) and spatial bias towards five areas (Bornholm Basin, Kiel Bight, Kertinge Nor, Lim- and Gullmarsfjord). The studies provide evidence for diverse trophic roles of jellyfish as predators and as competitors of other jellyfish, zooplankton and fish species. In combination, the studies also highlight potentially large impacts via top-down (grazing) and bottom-up (nutrient excretion) effects, but also, strong spatio-temporal variability in the magnitude of these effects, depending on the occurrence of jellyfish blooms. Studies on the role of jellyfish as prey for fish, seabirds or marine mammals, and for benthic systems via food-falls, were limited or lacking for the Baltic Sea, despite increasing focus on these topics globally. Improved understanding of the temporal (seasonal, inter-annual, long-term) and spatial variability of blooms and corresponding trophic effects, would provide more systematic understanding of the ecological role of jellyfish in the spatio-temporally variable Baltic Sea. A broader spatial coverage, inclusion of more jellyfish taxa and under-studied early life history stages, as well as the implementation and continuation of long-term data series would represent important steps towards this goal.
DOI: 10.6084/m9.figshare.16586055.v1
title: Review of jellyfish trophic interactions in the Baltic Sea

description: Despite the diversity and oftentimes large biomass of jellyfish in marine systems, their ecological role remains poorly understood. We here provide the first systematic review of studies on jellyfish trophic ecology in the Baltic Sea (a regional marine system under strong multiple global and regional anthropogenic pressures). In total, we identified 57 peer-reviewed publications, with notable taxonomic bias towards two species (<i>Aurelia aurita</i>; non-indigenous <i>Mnemiopsis leidyi</i>) and spatial bias towards five areas (Bornholm Basin, Kiel Bight, Kertinge Nor, Lim- and Gullmarsfjord). The studies provide evidence for diverse trophic roles of jellyfish as predators and as competitors of other jellyfish, zooplankton and fish species. In combination, the studies also highlight potentially large impacts via top-down (grazing) and bottom-up (nutrient excretion) effects, but also, strong spatio-temporal variability in the magnitude of these effects, depending on the occurrence of jellyfish blooms. Studies on the role of jellyfish as prey for fish, seabirds or marine mammals, and for benthic systems via food-falls, were limited or lacking for the Baltic Sea, despite increasing focus on these topics globally. Improved understanding of the temporal (seasonal, inter-annual, long-term) and spatial variability of blooms and corresponding trophic effects, would provide more systematic understanding of the ecological role of jellyfish in the spatio-temporally variable Baltic Sea. A broader spatial coverage, inclusion of more jellyfish taxa and under-studied early life history stages, as well as the implementation and continuation of long-term data series would represent important steps towards this goal.
DOI: 10.6084/m9.figshare.14792100.v4
title: MLSA phylogeny of 40 Agrobacterium spp.

description: For this MLSA of 40 Agrobacterium spp. strains, we extracted the CDS alignments of parE, gyrB, recA, and rpoB from the Pantagruel pangenome database and concatenated into a multi-locus alignment, totaling 9,968 positions. ML Phylogenies were then inferred based on these alignments with RAxML-NG 1.0.0 with the options ‘--model GTR+G4 --all’, implying the use of the model GTR+FO+G4m, and that 20 independent inferences were run, starting with 10 random trees and 10 parsimony-optimized tree, and retaining the the best ML tree from these 20 inferences. Branch supports were estimated with 200 Felsentein bootstrap trees.<br>
DOI: 10.6084/m9.figshare.14605154
title: The use of reTURB in T1 bladder cancer: a Norwegian population-based study

description: To evaluate the use of repeat transurethral resection of the bladder (reTURB) in stage T1 bladder cancer and its impact on treatment and survival in a Norwegian population-based cohort. 1130 patients registered at the Cancer Registry of Norway between 2008 and 2012 with primary urothelial T1 cancer were included. Information on surgical and medical procedures was provided by the Norwegian Patient Registry. Descriptive statistics were used to evaluate characteristics of patients receiving reTURB or not within 12 weeks from primary TURB (primTURB). Survival models identified risk factors and estimated cause-specific survival rates (CSS) adjusted for sex, age, WHO grade, concomitant cis and detrusor muscle at primTURB and treatment. The 648 (57%) T1 patients with reTURB were significantly younger and had more WHO high grade tumors compared to those without reTURB. Of 275 patients without detrusor muscle at primTURB 114 (41%) had no reTURB. Of reTURB patients, 45 (7%) had muscle invasive tumor, 110 (17%) T1 and 378 (58%) Ta, cis or T0. Two-thirds of 81 patients receiving early cystectomy after reTURB had T1 or muscle invasive bladder cancer at reTURB. ReTURB did not impact adjusted CSS, but patients with T1 at reTURB had significantly lower CSS than those with Almost half of the T1 patients did not undergo reTURB as recommended in guidelines. We show that reTURB makes the histology result more reliable with impact on both treatment and survival. Our results support the use of reTURB as recommended by EAU guidelines.
DOI: 10.6084/m9.figshare.16699105
title: Supplementary Material for: Serum biomarker status with a distinctive pattern in prognosis of gastroenteropancreatic neuroendocrine carcinoma

description: Medicine
DOI: 10.6084/m9.figshare.16699105.v1
title: Supplementary Material for: Serum biomarker status with a distinctive pattern in prognosis of gastroenteropancreatic neuroendocrine carcinoma

description: Medicine
DOI: 10.6084/m9.figshare.7361429
title: Inventory of geo-hydrological phenomena in Genova municipality (NW Italy)

description: In Italy geo-hydrological phenomena are the most common hazards: every year landslides and floods cause damage and fatalities; Genova city is one of the most affected areas. Since 2000 scientific studies have demonstrated an increase in events, due to the rainfall regime variation and to the urbanization. Thematic maps are an essential tool for evaluating the interaction between geomorphological processes and the elements at risk. In the present work, we have prepared an original geo-hydrological phenomena inventory map of Genova at 1:45,000 scale (the ‘A1’ size). The map shows the floodable areas, landslides and deep-seated gravitational slope deformation, the urban fabric and the cultural heritage sites. The map gives an overview of the geo-hydrological phenomena through the integration of the different hazard sources, of the exposed elements and of their spatial distribution, allowing for a first analysis of the risk: in a 240 km<sup>2</sup> area, more than 3600 residential buildings are located on the 4 km<sup>2</sup> high hazard floodable areas and more than 360 on the about 500 active landslides.
DOI: 10.6084/m9.figshare.7361429.v1
title: Inventory of geo-hydrological phenomena in Genova municipality (NW Italy)

description: In Italy geo-hydrological phenomena are the most common hazards: every year landslides and floods cause damage and fatalities; Genova city is one of the most affected areas. Since 2000 scientific studies have demonstrated an increase in events, due to the rainfall regime variation and to the urbanization. Thematic maps are an essential tool for evaluating the interaction between geomorphological processes and the elements at risk. In the present work, we have prepared an original geo-hydrological phenomena inventory map of Genova at 1:45,000 scale (the ‘A1’ size). The map shows the floodable areas, landslides and deep-seated gravitational slope deformation, the urban fabric and the cultural heritage sites. The map gives an overview of the geo-hydrological phenomena through the integration of the different hazard sources, of the exposed elements and of their spatial distribution, allowing for a first analysis of the risk: in a 240 km<sup>2</sup> area, more than 3600 residential buildings are located on the 4 km<sup>2</sup> high hazard floodable areas and more than 360 on the about 500 active landslides.
DOI: 10.6084/m9.figshare.9879728
title: Interpretation of the tectonic evolution of the western part of the Sava Depression: structural analysis of seismic attributes and subsurface structural modeling

description: This paper presents the results of an extensive structural investigation of the western part of the Sava Depression (SW part of the Pannonian Basin System) and provides insights in the tectonic evolution of the investigated area. Structural analyses were based on the 3D seismic volume of the study area, analysis of seismic attributes, and construction of 3D structural model and structural maps. Our results pinpoint to three tectonic phases in the structural development of the Sava Depression. The first tectonic phase is characterized by extensional tectonic features developed from the Early to Middle Miocene. The second tectonic phase follows thermal subsidence and general deepening of the study area and inherited tectonic features during the Late Miocene, while the final tectonic phase is characterized by structural reactivation and tectonic inversion of inherited and newly formed tectonic features from the Pliocene to the Quaternary.
DOI: 10.6084/m9.figshare.9879728.v1
title: Interpretation of the tectonic evolution of the western part of the Sava Depression: structural analysis of seismic attributes and subsurface structural modeling

description: This paper presents the results of an extensive structural investigation of the western part of the Sava Depression (SW part of the Pannonian Basin System) and provides insights in the tectonic evolution of the investigated area. Structural analyses were based on the 3D seismic volume of the study area, analysis of seismic attributes, and construction of 3D structural model and structural maps. Our results pinpoint to three tectonic phases in the structural development of the Sava Depression. The first tectonic phase is characterized by extensional tectonic features developed from the Early to Middle Miocene. The second tectonic phase follows thermal subsidence and general deepening of the study area and inherited tectonic features during the Late Miocene, while the final tectonic phase is characterized by structural reactivation and tectonic inversion of inherited and newly formed tectonic features from the Pliocene to the Quaternary.
DOI: 10.6084/m9.figshare.8859584
title: Phytoavailable phosphorus (P<sub>2</sub>O<sub>5</sub>) and potassium (K<sub>2</sub>O) in topsoil for apple orchards and vineyards, South Tyrol, Italy

description: Accurate fertilization management is a present-day challenge and can conciliate profitability and sustainability in agriculture production. This study presents topsoil concentrations of P<sub>2</sub>O<sub>5</sub> and K<sub>2</sub>O in apple orchards and vineyards in South Tyrol, Italy. Sixteen thousand georeferenced soil samples were collected and spatialized using ordinary local kriging. Measured average and maximum concentrations of P<sub>2</sub>O<sub>5</sub> were 260 and 1500 mg/kg, respectively, in apple orchards, and 280 and 880 mg/kg, respectively, in vineyards. Similarly, measured average and maximum concentrations of K<sub>2</sub>O were 210 and 1040 mg/kg, respectively, in apple orchards, and 250 and 820 mg/kg, respectively, in vineyards. Overall, K<sub>2</sub>O concentration was mostly within the recommended thresholds, while P<sub>2</sub>O<sub>5</sub> concentration was frequently higher than the target level for optimal production. The resulting maps (1:25,000 scale) of P<sub>2</sub>O<sub>5</sub> and K<sub>2</sub>O showed modest accuracy with RMSE of 115.7 and 78.3 mg/kg, respectively. These maps can support evidence-based decision making by multiple stakeholders.
DOI: 10.6084/m9.figshare.8859584.v1
title: Phytoavailable phosphorus (P<sub>2</sub>O<sub>5</sub>) and potassium (K<sub>2</sub>O) in topsoil for apple orchards and vineyards, South Tyrol, Italy

description: Accurate fertilization management is a present-day challenge and can conciliate profitability and sustainability in agriculture production. This study presents topsoil concentrations of P<sub>2</sub>O<sub>5</sub> and K<sub>2</sub>O in apple orchards and vineyards in South Tyrol, Italy. Sixteen thousand georeferenced soil samples were collected and spatialized using ordinary local kriging. Measured average and maximum concentrations of P<sub>2</sub>O<sub>5</sub> were 260 and 1500 mg/kg, respectively, in apple orchards, and 280 and 880 mg/kg, respectively, in vineyards. Similarly, measured average and maximum concentrations of K<sub>2</sub>O were 210 and 1040 mg/kg, respectively, in apple orchards, and 250 and 820 mg/kg, respectively, in vineyards. Overall, K<sub>2</sub>O concentration was mostly within the recommended thresholds, while P<sub>2</sub>O<sub>5</sub> concentration was frequently higher than the target level for optimal production. The resulting maps (1:25,000 scale) of P<sub>2</sub>O<sub>5</sub> and K<sub>2</sub>O showed modest accuracy with RMSE of 115.7 and 78.3 mg/kg, respectively. These maps can support evidence-based decision making by multiple stakeholders.
DOI: 10.6084/m9.figshare.7931051
title: Monthly RUSLE soil erosion risk of Swiss grasslands

description: This study presents the first mapping of soil erosion risk modelling based on the Revised Universal Soil Loss Equation (RUSLE) at a sub-annual (monthly) temporal resolution and national scale (100 m spatial resolution). The monthly maps show highest water erosion rates on Swiss grasslands in August (1.25 t ha<sup>–1</sup> month<sup>–1</sup>). In summer, the mean monthly soil loss by water erosion is 48 times higher than the mean soil loss in winter. Considering the annual average fraction of green vegetation cover of 54%, the predicted soil erosion rate for the Swiss national grassland area would add up to a total eroded soil mass of 5.26 Mt yr<sup>–1</sup>. The RUSLE application with an intact 100% vegetation cover would largely reduce the soil loss to an average annual rate of 0.14 t ha<sup>–1</sup> year<sup>–1</sup>. These findings clearly highlight the importance to consider and maintain the current status of the vegetation cover for soil erosion prediction and soil conservation, respectively.
DOI: 10.6084/m9.figshare.9860687
title: Plants and animals in the oikonyms of Lithuania

description: Two toponymical maps presented in this paper show 2332 inhabited places of Lithuania that have names (oikonyms) associated with vegetation and animals. The maps and the dataset are the outcomes of a project that is aimed at combining the outcomes of professional onomastic research with an environment that fosters exploration. The oikonyms were extracted from the reference base dataset of Lithuania by means of an automated algorithm. Original cartographic symbols have been designed for depicting categories and species. The multiscale map application, with its exploratory tools, makes it easy to see spatial distribution of geographic names related with particular groups of plants and animals. Analysis of map data enables the assertion that local toponymy reflects a distribution of species that were characteristic to the territory over past centuries. The maps are supplemented by comparative density maps and statistical charts. The reference scale of the main maps is 1: 500,000.
DOI: 10.6084/m9.figshare.9860687.v1
title: Plants and animals in the oikonyms of Lithuania

description: Two toponymical maps presented in this paper show 2332 inhabited places of Lithuania that have names (oikonyms) associated with vegetation and animals. The maps and the dataset are the outcomes of a project that is aimed at combining the outcomes of professional onomastic research with an environment that fosters exploration. The oikonyms were extracted from the reference base dataset of Lithuania by means of an automated algorithm. Original cartographic symbols have been designed for depicting categories and species. The multiscale map application, with its exploratory tools, makes it easy to see spatial distribution of geographic names related with particular groups of plants and animals. Analysis of map data enables the assertion that local toponymy reflects a distribution of species that were characteristic to the territory over past centuries. The maps are supplemented by comparative density maps and statistical charts. The reference scale of the main maps is 1: 500,000.
DOI: 10.6084/m9.figshare.7931051.v3
title: Monthly RUSLE soil erosion risk of Swiss grasslands

description: This study presents the first mapping of soil erosion risk modelling based on the Revised Universal Soil Loss Equation (RUSLE) at a sub-annual (monthly) temporal resolution and national scale (100 m spatial resolution). The monthly maps show highest water erosion rates on Swiss grasslands in August (1.25 t ha<sup>–1</sup> month<sup>–1</sup>). In summer, the mean monthly soil loss by water erosion is 48 times higher than the mean soil loss in winter. Considering the annual average fraction of green vegetation cover of 54%, the predicted soil erosion rate for the Swiss national grassland area would add up to a total eroded soil mass of 5.26 Mt yr<sup>–1</sup>. The RUSLE application with an intact 100% vegetation cover would largely reduce the soil loss to an average annual rate of 0.14 t ha<sup>–1</sup> year<sup>–1</sup>. These findings clearly highlight the importance to consider and maintain the current status of the vegetation cover for soil erosion prediction and soil conservation, respectively.
DOI: 10.6084/m9.figshare.7609964.v1
title: Little Ice Age glacial systems and related natural instability processes in the Orco Valley (North-Western Italy)

description: Glaciated and recently (post-Little Ice Age) deglaciated areas are very dynamic environments, undergoing continuous changes, in particular as a consequence of climatic fluctuations and cryosphere changes. The intense geomorphic activity that takes place here conditions natural hazard, sediment transport and tourist fruition. A geo-morphological mapping with applicative purposes has to take into account the peculiarities and the dynamism of these specific areas. We here propose a methodological approach based on the interpretation of a multitemporal set of aerial photos (from 1983 to 2012), in a GIS environment, with application to the sectors modeled by Little Ice Age glaciers in the upper Orco Valley (NW Italy). The result is a geo-morphological map focused on the elements that are most relevant for application purposes, complemented by a map of the spatio-temporal distribution of the natural instability processes identified in the study area for the reference period, aimed to highlight the recent dynamism of the geomorphological elements in the map.
DOI: 10.6084/m9.figshare.7609964
title: Little Ice Age glacial systems and related natural instability processes in the Orco Valley (North-Western Italy)

description: Glaciated and recently (post-Little Ice Age) deglaciated areas are very dynamic environments, undergoing continuous changes, in particular as a consequence of climatic fluctuations and cryosphere changes. The intense geomorphic activity that takes place here conditions natural hazard, sediment transport and tourist fruition. A geo-morphological mapping with applicative purposes has to take into account the peculiarities and the dynamism of these specific areas. We here propose a methodological approach based on the interpretation of a multitemporal set of aerial photos (from 1983 to 2012), in a GIS environment, with application to the sectors modeled by Little Ice Age glaciers in the upper Orco Valley (NW Italy). The result is a geo-morphological map focused on the elements that are most relevant for application purposes, complemented by a map of the spatio-temporal distribution of the natural instability processes identified in the study area for the reference period, aimed to highlight the recent dynamism of the geomorphological elements in the map.
DOI: 10.6084/m9.figshare.7720304.v1
title: Geology of the central part of the Amatrice Basin (Central Apennines, Italy)

description: A 1:5,000 scale geological map and 31 geological cross-sections are presented for the surroundings of Amatrice village (central Apennines, Italy), epicentral area of the first damaging earthquake of the 2016–2017 seismic sequence. This detailed geological dataset focuses on: (i) the extent, the thickness, and the internal stratigraphic architecture of the Quaternary continental deposits; (ii) the bedding and the thickness of the Miocene substratum; and (iii) the spatial distribution of the main fault systems. The provided dataset would update the available regional geological maps in deciphering the syn-to-post-orogenic history of the Amatrice Basin. Eventually, the accuracy of the geological mapping would represent a basic tool for interpreting and integrating the multidisciplinary dataset deriving from post-seismic activities.