cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10312457
title: Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi

description: <b>Background:</b> Symbiotic relationships between microbes and their hosts are widespread and diverse, often providing protection or nutrients, and may be either obligate or facultative. However, the genetic mechanisms allowing organisms to maintain host-symbiont associations at the molecular level are still mostly unknown, and in the case of bacterial-animal associations, most genetic studies have focused on adaptations and mechanisms of the bacterial partner. The gutless tubeworms (Siboglinidae, Annelida) are obligate hosts of chemoautotrophic endosymbionts (except for <i>Osedax </i>which houses heterotrophic Oceanospirillales), which rely on the sulfide-oxidizing symbionts for nutrition and growth. Whereas several siboglinid endosymbiont genomes have been characterized, genomes of hosts and their adaptations to this symbiosis remain unexplored.<b>Results:</b> Here, we present and characterize adaptations of the cold-seep dwelling tubeworm <i>Lamellibrachia</i><i>luymesi</i>, one of the longest-lived invertebrates. We sequenced the worm’s ~688 Mb haploid genome with an overall completeness of ~95% and discovered that <i>L. luymesi</i> lacks many genes essential in amino acid biosynthesis, obligating them to products provided by symbionts. Interestingly, the host is known to carry hydrogen sulfide to thiotrophic endosymbionts using hemoglobin. We also found an expansion of hemoglobin B1 genes, many of which possess a free cysteine residue which is hypothesized to function in sulfide-binding. Contrary to previous analyses, the sulfide-binding mediated by zinc ions is not conserved across tubeworms. Thus, the sulfide-binding mechanisms in sibgolinids need to be further explored and B1 globins might play a more important role than previously thought. Our comparative analyses also suggest the Toll-like receptor pathway may be essential for tolerance/sensitivity to symbionts and pathogens. Several genes related to the worm’s unique life history that are known to play important roles in apoptosis, cell proliferation, and aging were also identified. Last, molecular clock analyses based on phylogenomic data suggest modern siboglinid diversity originated in 267MYA (± 70 MY), support previous hypotheses indicating a Late Mesozoic or Cenozoic origins of approximately 50-126 MYA for vestimentiferans. <b>Conclusions:</b> Here, we elucidate several specific adaptations along various molecular pathways that link phenome to genome to improve understanding of holobiont evolution. Our findings of adaptation in genomic mechanisms to reducing environments likely extends to other chemosynthetic symbiotic systems.
DOI: 10.6084/m9.figshare.10314245.v2
title: TCM_and_streakline dataset

description: Tilt current meter data and streakline flow direction data.
DOI: 10.6084/m9.figshare.10312457.v1
title: Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi

description: <b>Background:</b> Symbiotic relationships between microbes and their hosts are widespread and diverse, often providing protection or nutrients, and may be either obligate or facultative. However, the genetic mechanisms allowing organisms to maintain host-symbiont associations at the molecular level are still mostly unknown, and in the case of bacterial-animal associations, most genetic studies have focused on adaptations and mechanisms of the bacterial partner. The gutless tubeworms (Siboglinidae, Annelida) are obligate hosts of chemoautotrophic endosymbionts (except for <i>Osedax </i>which houses heterotrophic Oceanospirillales), which rely on the sulfide-oxidizing symbionts for nutrition and growth. Whereas several siboglinid endosymbiont genomes have been characterized, genomes of hosts and their adaptations to this symbiosis remain unexplored.<b>Results:</b> Here, we present and characterize adaptations of the cold-seep dwelling tubeworm <i>Lamellibrachia</i><i>luymesi</i>, one of the longest-lived invertebrates. We sequenced the worm’s ~688 Mb haploid genome with an overall completeness of ~95% and discovered that <i>L. luymesi</i> lacks many genes essential in amino acid biosynthesis, obligating them to products provided by symbionts. Interestingly, the host is known to carry hydrogen sulfide to thiotrophic endosymbionts using hemoglobin. We also found an expansion of hemoglobin B1 genes, many of which possess a free cysteine residue which is hypothesized to function in sulfide-binding. Contrary to previous analyses, the sulfide-binding mediated by zinc ions is not conserved across tubeworms. Thus, the sulfide-binding mechanisms in sibgolinids need to be further explored and B1 globins might play a more important role than previously thought. Our comparative analyses also suggest the Toll-like receptor pathway may be essential for tolerance/sensitivity to symbionts and pathogens. Several genes related to the worm’s unique life history that are known to play important roles in apoptosis, cell proliferation, and aging were also identified. Last, molecular clock analyses based on phylogenomic data suggest modern siboglinid diversity originated in 267MYA (± 70 MY), support previous hypotheses indicating a Late Mesozoic or Cenozoic origins of approximately 50-126 MYA for vestimentiferans. <b>Conclusions:</b> Here, we elucidate several specific adaptations along various molecular pathways that link phenome to genome to improve understanding of holobiont evolution. Our findings of adaptation in genomic mechanisms to reducing environments likely extends to other chemosynthetic symbiotic systems.
DOI: 10.6084/m9.figshare.10312406
title: 03.png

description: jasljdfknfdsj
DOI: 10.6084/m9.figshare.10312406.v1
title: 03.png

description: jasljdfknfdsj
DOI: 10.6084/m9.figshare.10312439
title: <i>Plenasium</i> (<i>Aurealcaulis</i>) <i>elegans</i> sp. nov. from the Eocene of Vietnam – a connecting link in the evolution of modern Royal Ferns (Osmundeae, Osmundaceae)

description: Osmundales is the most ancient of all extant groups of leptosporangiate ferns, with an extensive fossil record from Permian to Cenozoic deposits worldwide. The group was particularly diverse during the late Palaeozoic and early Mesozoic, whereas nearly all records of fossil Osmundales from the mid-Cretaceous onwards can be assigned to the sole surviving subfamily Osmundoideae. The single exception has long remained the enigmatic <i>Aurealcaulis</i> – a genus of large, presumably arborescent Osmundaceae stems from the Cretaceous and Palaeogene of North America. Due to similarities especially in the unusual mode of leaf-trace formation, <i>Aurealcaulis</i> has recently been suggested to represent a close relative of modern <i>Plenasium</i>, but definite evidence for this hypothesis has thus far been lacking. Here, we describe <i>Plenasium</i> (<i>Aurealcaulis</i>) <i>elegans</i> sp. nov. based on a calcified trunk from the Na Duong Formation (upper middle to upper Eocene) of northern Vietnam, forming the first record of <i>Aurealcaulis</i> outside North America. The new species differs from all previously described members of <i>Aurealcaulis</i> in its uniquely thick xylem siphon and in the characteristic distribution of sclerenchyma in the stipular wings, with a single thick mass surrounded by numerous smaller strands. In its combination of anatomical features, <i>Plenasium elegans</i> appears intermediate between the remaining species of <i>Aurealcaulis</i> and fossil and extant members of <i>Plenasium sensu stricto</i>. Together with its comparatively young geological age and unusual geographical occurrence within the biogeographical range of extant <i>Plenasium</i> species, <i>Plenasium elegans</i> forms a threefold connecting link in the phylogeny of modern Royal Ferns.
DOI: 10.6084/m9.figshare.10312439.v1
title: <i>Plenasium</i> (<i>Aurealcaulis</i>) <i>elegans</i> sp. nov. from the Eocene of Vietnam – a connecting link in the evolution of modern Royal Ferns (Osmundeae, Osmundaceae)

description: Osmundales is the most ancient of all extant groups of leptosporangiate ferns, with an extensive fossil record from Permian to Cenozoic deposits worldwide. The group was particularly diverse during the late Palaeozoic and early Mesozoic, whereas nearly all records of fossil Osmundales from the mid-Cretaceous onwards can be assigned to the sole surviving subfamily Osmundoideae. The single exception has long remained the enigmatic <i>Aurealcaulis</i> – a genus of large, presumably arborescent Osmundaceae stems from the Cretaceous and Palaeogene of North America. Due to similarities especially in the unusual mode of leaf-trace formation, <i>Aurealcaulis</i> has recently been suggested to represent a close relative of modern <i>Plenasium</i>, but definite evidence for this hypothesis has thus far been lacking. Here, we describe <i>Plenasium</i> (<i>Aurealcaulis</i>) <i>elegans</i> sp. nov. based on a calcified trunk from the Na Duong Formation (upper middle to upper Eocene) of northern Vietnam, forming the first record of <i>Aurealcaulis</i> outside North America. The new species differs from all previously described members of <i>Aurealcaulis</i> in its uniquely thick xylem siphon and in the characteristic distribution of sclerenchyma in the stipular wings, with a single thick mass surrounded by numerous smaller strands. In its combination of anatomical features, <i>Plenasium elegans</i> appears intermediate between the remaining species of <i>Aurealcaulis</i> and fossil and extant members of <i>Plenasium sensu stricto</i>. Together with its comparatively young geological age and unusual geographical occurrence within the biogeographical range of extant <i>Plenasium</i> species, <i>Plenasium elegans</i> forms a threefold connecting link in the phylogeny of modern Royal Ferns.
DOI: 10.6084/m9.figshare.10312199
title: Data from: Regional-scale variation on Dromiciops gliroides occurrence, abundance, and activity patterns along a habitat disturbance gradient

description: Original data from: Rodríguez-Gómez, G.B. & F.E. Fontúrbel. Regional-scale variation on Dromiciops gliroides occurrence, abundance, and activity patterns along a habitat disturbance gradient. Journal of Mammalogy.<br>Please see readme.txt file for details.
DOI: 10.6084/m9.figshare.10312130
title: Data Supplement for "Upregulated Phospholipase D Activity Towards Glycosylphosphatidylinositol-Anchored Proteins in Micelle-Like Serum Complexes in Metabolically Deranged Rats and Humans"

description: Data Supplement for Publication<br> Glycosylphosphatidylinositol-anchored proteins (GPI-AP) with the complete glycolipid anchor attached have previously been shown to be released from the outer plasma membrane leaflet of rat adipocytes in positive correlation to cell size and blood glucose/insulin levels of the donor rats. Furthermore, they are present in rat and human serum, however, at amounts which are lower in insulin-resistant/obese rats compared to normal ones. These findings prompted further evaluation of the potential of full-length GPI-AP for the prediction and stratification of metabolically deranged states. A comparison of the signatures of horizontal surface acoustic waves which were generated by full-length GPI-AP in course of their specific capture by and subsequent dissociation from a chip-based sensor between those from rat serum and those reconstituted into lipidic structures strongly argues for expression of full-length GPI-AP in serum in micelle-like complexes in concert with phospholipids, lysophospholipids and cholesterol. Both the reconstituted and the rat serum complexes were highly sensitive towards mechanical forces, such as vibration. Furthermore, full-length GPI-AP reconstituted into micelle-like complexes represented efficient substrates for cleavage by serum glycosylphosphatidylinositol-specific phospholipase D (GPI-PLD). These findings raised the possibility that the upregulated release of full-length GPI-AP into micelle-like serum complexes from metabolically deranged cells is compensated by elevated GPI-PLD activity. In fact, serum GPI-PLD activity towards full-length GPI-AP in micelle-like complexes, but not in detergent micelles, was positively correlated to early states of insulin resistance and obesity in genetic and diet-induced rat models as well as to the body weight in humans. Moreover, the differences in the degradation of GPI-AP in micelle-like complexes were found to rely in part on the interaction of serum GPI-PLD with an activating serum factor. These data suggest, that serum GPI-PLD activity measured with GPI-AP in micelle-like complexes is indicative of enhanced release of full-length GPI-AP from relevant tissues into the circulation as a consequence of early metabolic derangement in rats and humans. <br>
DOI: 10.6084/m9.figshare.10312097
title: Simplified shape file for mapping

description: In this directory, there are 6 geojson files which were used for mapping.1. Lake_Arc_simplify: Boundary of Lakes in and around Ontario2. Ontario_arc: Boundary lines of Ontario3. Municipal_Arc_simplify: Boundary lines of municipalities4. Municipal_Polygon: Polygons of the municipalities5. Stations151: Locations of 151 weather stations (municipalites)6.polygon9864: Rectangle areas centered at the 9864 grid points<br>source:https://github.com/LAMPSYORKU/OntarioClimateDataPortal/tree/master/shapefiles
DOI: 10.6084/m9.figshare.10311875
title: Studies_Systematic Map_RIS

description: This is a RIS file with all studies entailed in out systematic map
DOI: 10.6084/m9.figshare.10311920
title: Reviews_Systematic Map_RIS

description: This is an RIS library of the reviews we retrieved as part of our systematic map.<br>
DOI: 10.6084/m9.figshare.10312130.v1
title: Data Supplement for "Upregulated Phospholipase D Activity Towards Glycosylphosphatidylinositol-Anchored Proteins in Micelle-Like Serum Complexes in Metabolically Deranged Rats and Humans"

description: Data Supplement for Publication<br> Glycosylphosphatidylinositol-anchored proteins (GPI-AP) with the complete glycolipid anchor attached have previously been shown to be released from the outer plasma membrane leaflet of rat adipocytes in positive correlation to cell size and blood glucose/insulin levels of the donor rats. Furthermore, they are present in rat and human serum, however, at amounts which are lower in insulin-resistant/obese rats compared to normal ones. These findings prompted further evaluation of the potential of full-length GPI-AP for the prediction and stratification of metabolically deranged states. A comparison of the signatures of horizontal surface acoustic waves which were generated by full-length GPI-AP in course of their specific capture by and subsequent dissociation from a chip-based sensor between those from rat serum and those reconstituted into lipidic structures strongly argues for expression of full-length GPI-AP in serum in micelle-like complexes in concert with phospholipids, lysophospholipids and cholesterol. Both the reconstituted and the rat serum complexes were highly sensitive towards mechanical forces, such as vibration. Furthermore, full-length GPI-AP reconstituted into micelle-like complexes represented efficient substrates for cleavage by serum glycosylphosphatidylinositol-specific phospholipase D (GPI-PLD). These findings raised the possibility that the upregulated release of full-length GPI-AP into micelle-like serum complexes from metabolically deranged cells is compensated by elevated GPI-PLD activity. In fact, serum GPI-PLD activity towards full-length GPI-AP in micelle-like complexes, but not in detergent micelles, was positively correlated to early states of insulin resistance and obesity in genetic and diet-induced rat models as well as to the body weight in humans. Moreover, the differences in the degradation of GPI-AP in micelle-like complexes were found to rely in part on the interaction of serum GPI-PLD with an activating serum factor. These data suggest, that serum GPI-PLD activity measured with GPI-AP in micelle-like complexes is indicative of enhanced release of full-length GPI-AP from relevant tissues into the circulation as a consequence of early metabolic derangement in rats and humans. <br>
DOI: 10.6084/m9.figshare.10311875.v2
title: Studies_Systematic Map_RIS

description: This is a RIS file with all studies entailed in out systematic map
DOI: 10.6084/m9.figshare.10311920.v2
title: Reviews_Systematic Map_RIS

description: This is an RIS library of the reviews we retrieved as part of our systematic map.<br>
DOI: 10.6084/m9.figshare.10311638
title: Rawdata.zip

description: Knockdown of CDCA8 inhibits the proliferation and enhances the apoptosis of bladder cancer cells.
DOI: 10.6084/m9.figshare.10311875.v1
title: Studies_Systematic Map_RIS

description: This is a RIS file with all studies entailed in out systematic map
DOI: 10.6084/m9.figshare.10311920.v1
title: Reviews_Systematic Map_RIS

description: This is an RIS library of the reviews we retrieved as part of our systematic map.<br>
DOI: 10.6084/m9.figshare.10311605
title: Toward a Surgically-Precise Technical Debt Estimation - Replication package

description: The replication package for paper "Toward a Surgically-Precise Technical Debt Estimation".<br>The package contains data and scripts that were used to calculate the results presented in the paper. The package also contains more detailed results than presented in the paper. Both study 1 and 2 contain all scripts and instructions about how to extract data and to run the analysis.<br><br>The data used in the analysis is from the "Technical Debt Dataset" that is online and available to everyone. The dataset links to a paper explaining where the data in the dataset has been extracted from. A link to the dataset is in the Figshare's references. <br><br>
DOI: 10.6084/m9.figshare.10311638.v1
title: Rawdata.zip

description: Knockdown of CDCA8 inhibits the proliferation and enhances the apoptosis of bladder cancer cells.
DOI: 10.6084/m9.figshare.10311548
title: Supplementary Tables from Mechanisms and drivers of belemnite body-size dynamics across the Pliensbachian–Toarcian crisis

description: Body-size reduction is considered an important response to current climate warming and has been observed during past biotic crises, including the Pliensbachian–Toarcian crisis, a second-order mass extinction. However, in fossil cephalopod studies, the mechanisms and their potential link with climate are rarely investigated and palaeobiological scales of organization are not usually differentiated. Here, we hypothesize that belemnites reduce their adult size across the Pliensbachian–Toarcian boundary warming event. Belemnite body-size dynamics across the Pliensbachian–Toarcian boundary in the Peniche section (Lusitanian Basin, Portugal) were analysed based on the newly collected field data. We disentangle the mechanisms and the environmental drivers of the size fluctuations observed from the individual to the assemblage scale. Despite the lack of a major taxonomic turnover, a 40% decrease in rostrum volume is observed across the Pliensbachian–Toarcian boundary, before the Toarcian Oceanic Anoxic Event where belemnites go locally extinct. The pattern is mainly driven by a reduction in adult size of the two dominant species, <i>Pseudohastites longiformis</i> and <i>Passaloteuthis bisulcata.</i> Belemnite-size distribution is best correlated with fluctuations in a palaeotemperature proxy (stable oxygen isotopes); however, potential indirect effects of volcanism and carbon cycle perturbations may also play a role. This highlights the complex interplay between environmental stressors (warming, deoxygenation, nutrient input) and biotic variables (productivity, competition, migration) associated with these hyperthermal events in driving belemnite body size.
DOI: 10.6084/m9.figshare.10311548.v1
title: Supplementary Tables from Mechanisms and drivers of belemnite body-size dynamics across the Pliensbachian–Toarcian crisis

description: Body-size reduction is considered an important response to current climate warming and has been observed during past biotic crises, including the Pliensbachian–Toarcian crisis, a second-order mass extinction. However, in fossil cephalopod studies, the mechanisms and their potential link with climate are rarely investigated and palaeobiological scales of organization are not usually differentiated. Here, we hypothesize that belemnites reduce their adult size across the Pliensbachian–Toarcian boundary warming event. Belemnite body-size dynamics across the Pliensbachian–Toarcian boundary in the Peniche section (Lusitanian Basin, Portugal) were analysed based on the newly collected field data. We disentangle the mechanisms and the environmental drivers of the size fluctuations observed from the individual to the assemblage scale. Despite the lack of a major taxonomic turnover, a 40% decrease in rostrum volume is observed across the Pliensbachian–Toarcian boundary, before the Toarcian Oceanic Anoxic Event where belemnites go locally extinct. The pattern is mainly driven by a reduction in adult size of the two dominant species, <i>Pseudohastites longiformis</i> and <i>Passaloteuthis bisulcata.</i> Belemnite-size distribution is best correlated with fluctuations in a palaeotemperature proxy (stable oxygen isotopes); however, potential indirect effects of volcanism and carbon cycle perturbations may also play a role. This highlights the complex interplay between environmental stressors (warming, deoxygenation, nutrient input) and biotic variables (productivity, competition, migration) associated with these hyperthermal events in driving belemnite body size.
DOI: 10.6084/m9.figshare.10311605.v1
title: Toward a Surgically-Precise Technical Debt Estimation

description: The replication package for paper "Toward a Surgically-Precise Technical Debt Estimation".<br>The package contains data and scripts that were used to calculate the results presented in the paper. The package also contains more detailed results than presented in the paper.<br>
DOI: 10.6084/m9.figshare.10311605.v2
title: Toward a Surgically-Precise Technical Debt Estimation

description: The replication package for paper "Toward a Surgically-Precise Technical Debt Estimation".<br>The package contains data and scripts that were used to calculate the results presented in the paper. The package also contains more detailed results than presented in the paper.<br>
DOI: 10.6084/m9.figshare.10311605.v4
title: Toward a Surgically-Precise Technical Debt Estimation - Replication package

description: The replication package for paper "Toward a Surgically-Precise Technical Debt Estimation".<br>The package contains data and scripts that were used to calculate the results presented in the paper. The package also contains more detailed results than presented in the paper. Both study 1 and 2 contain all scripts and instructions about how to extract data and to run the analysis.<br><br>The data used in the analysis is from the "Technical Debt Dataset" that is online and available to everyone. The dataset links to a paper explaining where the data in the dataset has been extracted from. A link to the dataset is in the Figshare's references. <br><br>
DOI: 10.6084/m9.figshare.10311605.v3
title: Toward a Surgically-Precise Technical Debt Estimation - Replication package

description: The replication package for paper "Toward a Surgically-Precise Technical Debt Estimation".<br>The package contains data and scripts that were used to calculate the results presented in the paper. The package also contains more detailed results than presented in the paper.<br>