cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5620396.v1
title: THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy

description: Macroautophagy/autophagy is a highly conserved process for degrading cytoplasmic contents, determines cell survival or death, and regulates the cellular homeostasis. Besides ATG proteins, numerous regulators together with various post-translational modifications (PTMs) are also involved in autophagy. In this work, we collected 4,237 experimentally identified proteins regulated in autophagy and cell death pathways from the literature. Then we computationally identified potential orthologs of known proteins, and developed a comprehensive database of The Autophagy, Necrosis, ApopTosis OrchestratorS (THANATOS, http://thanatos.biocuckoo.org), containing 191,543 proteins potentially associated with autophagy and cell death pathways in 164 eukaryotes. We performed an evolutionary analysis of <i>ATG</i> genes, and observed that ATGs required for the autophagosome formation are highly conserved across eukaryotes. Further analyses revealed that known cancer genes and drug targets were overrepresented in human autophagy proteins, which were significantly associated in a number of signaling pathways and human diseases. By reconstructing a human kinase-substrate phosphorylation network for ATG proteins, our results confirmed that phosphorylation play a critical role in regulating autophagy. In total, we mapped 65,015 known sites of 11 types of PTMs to collected proteins, and revealed that all types of PTM substrates were enriched in human autophagy. In addition, we observed multiple types of PTM regulators such as protein kinases and ubiquitin E3 ligases or adaptors were significantly associated with human autophagy, and again the results emphasized the importance of PTM regulations in autophagy. We anticipated THANATOS can be a useful resource for further studies.
DOI: 10.5281/zenodo.48225
title: Cookie-cutter shark bites on four species of large whale

description: This dataset contains information on cookie-cutter shark bitemarks on four large whale species: sei whales (Balaenoptera borealis), fin whales (Balaenoptera physalus), offshore Bryde’s whales (Balaenoptera brydeii sp) and sperm whales (Physeter macrocephalus). These data were collected from whales harvested at Donkergat whaling station, South Africa, during 1963. The data were personally collected by Peter Barrington Best, who was a research officer with the Fisheries Development Corporation of South Africa at that time. Hence, no permits were required for the collection of data. Permission to examine carcasses, while they were on the platform prior to flensing, was granted by the commercial use company (Saldanha Whaling Co. Ltd).
description: If you would like to use this dataset and require any additional information, please contact Theoni Photopoulou at the following address: theoni.photopoulou@gmail.com
DOI: 10.5281/zenodo.631470
title: Cookie-cutter shark bites on four species of large whale

description: This dataset contains information on cookie-cutter shark bitemarks on four large whale species: sei whales (Balaenoptera borealis), fin whales (Balaenoptera physalus), offshore Bryde’s whales (Balaenoptera brydeii sp) and sperm whales (Physeter macrocephalus). These data were collected from whales harvested at Donkergat whaling station, South Africa, during 1963. The data were personally collected by Peter Barrington Best, who was a research officer with the Fisheries Development Corporation of South Africa at that time. Hence, no permits were required for the collection of data. Permission to examine carcasses, while they were on the platform prior to flensing, was granted by the commercial use company (Saldanha Whaling Co. Ltd).
description: If you would like to use this dataset and require any additional information, please contact Theoni Photopoulou at the following address: theoni.photopoulou@gmail.com
DOI: 10.6084/m9.figshare.5619766
title: Script and raw data;supplementary informations from Bioclimatic niches are conserved and unrelated to pollination syndromes in Antillean Gesneriaceae

description: R script and data used for the analyses presented in the paper;supplementary tables and figures
DOI: 10.6084/m9.figshare.5619766.v1
title: Script and raw data;supplementary informations from Bioclimatic niches are conserved and unrelated to pollination syndromes in Antillean Gesneriaceae

description: R script and data used for the analyses presented in the paper;supplementary tables and figures
DOI: 10.6084/m9.figshare.5619742
title: Topographic control on shallow fault structure and strain partitioning near Whataroa, New Zealand demonstrates weak Alpine Fault

description: It is notoriously difficult to characterise the strength and stress states of major plate boundaries. By taking advantage of the well-constrained stress contribution of topography adjacent to a segmented section of the Alpine Fault, New Zealand, we have identified a mechanical mix that produces the distinct fault segmentation pattern seen in field observations. Slope-generated shear and normal stresses rotate the principal stresses relative to the regional tectonically derived stress state and under certain strength states influence the displacement pattern. Three-dimensional models show that the scale and form of the near-surface partitioning depend on both topographic relief and local fault strength relative to the bedrock. The models suggest the Alpine Fault is weak to moderately weak relative to the bedrock and is a single structure to within c. 500 m of the surface, above which segmentation occurs. Adjacent to the Alpine Fault, the stress state is highly variable. The intermediate principal stress, <i>σ</i><sub>2</sub>, is rotated from tectonically dominated, near-vertical beneath ridges to near-horizontal beneath large valleys. Individual segments along the Alpine Fault dominated by strike-slip faulting, oblique thrusting or thrusting, can be identified by extracting the topographic contribution to the stress state from numerical models.
DOI: 10.6084/m9.figshare.5619748
title: Generating vague neighbourhoods through data mining of passive web data

description: Neighbourhoods have been described as <i>‘the building blocks of public services society’</i>. Their subjective nature, however, and the resulting difficulties in collecting data, means that in many countries there are no officially defined neighbourhoods either in terms of names or boundaries. This has implications not only for policy but also business and social decisions as a whole. With the absence of neighbourhood boundaries many studies resort to using standard administrative units as proxies. Such administrative geographies, however, often have a poor fit with those perceived by residents. Our approach detects these important social boundaries by <i>automatically</i> mining the Web en masse for passively declared neighbourhood data within postal addresses. Focusing on the United Kingdom (UK), this research demonstrates the feasibility of automated extraction of urban neighbourhood names and their subsequent mapping as vague entities. Importantly, and unlike previous work, our process does not require any neighbourhood names to be established a priori.
DOI: 10.6084/m9.figshare.5619742.v1
title: Topographic control on shallow fault structure and strain partitioning near Whataroa, New Zealand demonstrates weak Alpine Fault

description: It is notoriously difficult to characterise the strength and stress states of major plate boundaries. By taking advantage of the well-constrained stress contribution of topography adjacent to a segmented section of the Alpine Fault, New Zealand, we have identified a mechanical mix that produces the distinct fault segmentation pattern seen in field observations. Slope-generated shear and normal stresses rotate the principal stresses relative to the regional tectonically derived stress state and under certain strength states influence the displacement pattern. Three-dimensional models show that the scale and form of the near-surface partitioning depend on both topographic relief and local fault strength relative to the bedrock. The models suggest the Alpine Fault is weak to moderately weak relative to the bedrock and is a single structure to within c. 500 m of the surface, above which segmentation occurs. Adjacent to the Alpine Fault, the stress state is highly variable. The intermediate principal stress, <i>σ</i><sub>2</sub>, is rotated from tectonically dominated, near-vertical beneath ridges to near-horizontal beneath large valleys. Individual segments along the Alpine Fault dominated by strike-slip faulting, oblique thrusting or thrusting, can be identified by extracting the topographic contribution to the stress state from numerical models.
DOI: 10.6084/m9.figshare.5619748.v2
title: Generating vague neighbourhoods through data mining of passive web data

description: Neighbourhoods have been described as <i>‘the building blocks of public services society’</i>. Their subjective nature, however, and the resulting difficulties in collecting data, means that in many countries there are no officially defined neighbourhoods either in terms of names or boundaries. This has implications not only for policy but also business and social decisions as a whole. With the absence of neighbourhood boundaries many studies resort to using standard administrative units as proxies. Such administrative geographies, however, often have a poor fit with those perceived by residents. Our approach detects these important social boundaries by <i>automatically</i> mining the Web en masse for passively declared neighbourhood data within postal addresses. Focusing on the United Kingdom (UK), this research demonstrates the feasibility of automated extraction of urban neighbourhood names and their subsequent mapping as vague entities. Importantly, and unlike previous work, our process does not require any neighbourhood names to be established a priori.
DOI: 10.6084/m9.figshare.5619748.v1
title: Generating vague neighbourhoods through data mining of passive web data

description: Neighbourhoods have been described as <i>‘the building blocks of public services society’</i>. Their subjective nature, however, and the resulting difficulties in collecting data, means that in many countries there are no officially defined neighbourhoods either in terms of names or boundaries. This has implications not only for policy but also business and social decisions as a whole. With the absence of neighbourhood boundaries many studies resort to using standard administrative units as proxies. Such administrative geographies, however, often have a poor fit with those perceived by residents. Our approach detects these important social boundaries by <i>automatically</i> mining the Web en masse for passively declared neighbourhood data within postal addresses. Focusing on the United Kingdom (UK), this research demonstrates the feasibility of automated extraction of urban neighbourhood names and their subsequent mapping as vague entities. Importantly, and unlike previous work, our process does not require any neighbourhood names to be established a priori.
DOI: 10.6084/m9.figshare.5619733
title: Breeding phenology and nest survival of Cinereous (<i>Circus cinereus</i>) and Long-winged (<i>C. buffoni</i>) Harriers in the agricultural landscapes of north-east Patagonia, Argentina

description: We present novel data on breeding ecology and nest survival of the Cinereous (<i>Circus cinereus</i>) and Long-winged (<i>C. buffoni</i>) Harriers in modified grasslands of southern Argentina and we evaluate variations in daily nest survival rates (DSR) in relation to temporal and habitat variables. We studied three mixed nesting colonies embedded in agricultural landscapes along a road. We found that DSR decreased linearly with time of breeding and increased with vegetation height above the nest and the distance to the road. This is the first and most complete reproductive study concerning two species of conservation concern, namely the Cinereous and Long-winged Harriers in Patagonia. Our study provides valuable and novel insights into the population dynamics of these little-known species.
DOI: 10.6084/m9.figshare.5619730
title: Bird species richness, composition and abundance in pastures are affected by vegetation structure and distance from natural habitats: a single tree in pastures matters

description: Throughout the world, natural habitats have been replaced by pastures. Thus, bird conservation requires making pastures more accessible for birds. The use of pastures by birds inhabiting the surrounding natural habitats may be affected by the structure of pastures and their distance from natural habitats. In this study we tested whether bird species richness, composition and abundance in pastures of the Brazilian Cerrado are linked to habitat and dietary requirements and affected by vegetation structure and the distance to natural habitats. We found that pastures with more trees and shrubs had greater richness of forest birds, forest insectivorous birds and semi-forest insectivorous-frugivorous birds. Pastures with taller trees had greater richness of semi-forest insectivorous birds, and pastures closer to natural habitats had greater richness of forest frugivorous birds. Bird composition in pastures changed according to vegetation structure and distance from natural habitats, and the abundance of some bird species was positively correlated to vegetation structure and negatively correlated to distance from natural habitats. These findings highlight the importance of trees and shrubs in pastures and maintaining patches of natural habitats near pastures. Management measures can make pastures more accessible for birds from surrounding natural environments and could help in bird conservation.
DOI: 10.6084/m9.figshare.5619733.v1
title: Breeding phenology and nest survival of Cinereous (<i>Circus cinereus</i>) and Long-winged (<i>C. buffoni</i>) Harriers in the agricultural landscapes of north-east Patagonia, Argentina

description: We present novel data on breeding ecology and nest survival of the Cinereous (<i>Circus cinereus</i>) and Long-winged (<i>C. buffoni</i>) Harriers in modified grasslands of southern Argentina and we evaluate variations in daily nest survival rates (DSR) in relation to temporal and habitat variables. We studied three mixed nesting colonies embedded in agricultural landscapes along a road. We found that DSR decreased linearly with time of breeding and increased with vegetation height above the nest and the distance to the road. This is the first and most complete reproductive study concerning two species of conservation concern, namely the Cinereous and Long-winged Harriers in Patagonia. Our study provides valuable and novel insights into the population dynamics of these little-known species.
DOI: 10.6084/m9.figshare.5619739.v1
title: Regulation of BECN1-Mediated Autophagy by HSPB6: Insights from A Human HSPB6<sup>S10F</sup> Mutant

description: HSPB6/Hsp20 (heat shock protein family B [small] member 6) has emerged as a novel cardioprotector against stress-induced injury. We identified a human mutant of HSPB6 (HSPB6<sup>S10F</sup>) exclusively present in dilated cardiomyopathy (DCM) patients. Cardiac expression of this mutant in mouse hearts resulted in remodeling and dysfunction, which progressed to heart failure and early death. These detrimental effects were associated with reduced interaction of mutant HSPB6<sup>S10F</sup> with BECN1/Beclin 1, leading to BECN1 ubiquitination and its proteosomal degradation. As a result, autophagy flux was substantially inhibited and apoptosis was increased in HSPB6<sup>S10F</sup>-mutant hearts. In contrast, overexpression of wild-type HSPB6 (HSPB6 WT) not only increased BECN1 levels, but also competitively suppressed binding of BECN1 to BCL2, resulting in stimulated autophagy. Indeed, preinhibition of autophagy attenuated the cardioprotective effects of HSPB6 WT. Taken together, these findings reveal a new regulatory mechanism of HSPB6 in cell survival through its interaction with BECN1. Furthermore, Ser10 appears to be crucial for the protective effects of HSPB6 and transversion of this amino acid to Phe contributes to cardiomyopathy.
DOI: 10.6084/m9.figshare.5619730.v1
title: Bird species richness, composition and abundance in pastures are affected by vegetation structure and distance from natural habitats: a single tree in pastures matters

description: Throughout the world, natural habitats have been replaced by pastures. Thus, bird conservation requires making pastures more accessible for birds. The use of pastures by birds inhabiting the surrounding natural habitats may be affected by the structure of pastures and their distance from natural habitats. In this study we tested whether bird species richness, composition and abundance in pastures of the Brazilian Cerrado are linked to habitat and dietary requirements and affected by vegetation structure and the distance to natural habitats. We found that pastures with more trees and shrubs had greater richness of forest birds, forest insectivorous birds and semi-forest insectivorous-frugivorous birds. Pastures with taller trees had greater richness of semi-forest insectivorous birds, and pastures closer to natural habitats had greater richness of forest frugivorous birds. Bird composition in pastures changed according to vegetation structure and distance from natural habitats, and the abundance of some bird species was positively correlated to vegetation structure and negatively correlated to distance from natural habitats. These findings highlight the importance of trees and shrubs in pastures and maintaining patches of natural habitats near pastures. Management measures can make pastures more accessible for birds from surrounding natural environments and could help in bird conservation.
DOI: 10.6084/m9.figshare.5619658
title: Inventory and review of the Mio–Pleistocene São Jorge flora (Madeira Island, Portugal): palaeoecological and biogeographical implications

description: The occurrence of plant fossils on Madeira Island has been known since the mid-nineteenth century. Charles Lyell and George Hartung discovered a leaf bed rich in Lauraceae and fern fossils at São Jorge in 1854. The determinations were controversial but a full review was never performed. Here we propose possible geological settings for the fossiliferous outcrop, and present an inventory and a systematic review of the surviving specimens of the São Jorge macroflora. The São Jorge leaf bed no longer outcrops due to a landslide in 1865. It was possible to establish the two alternative volcano-stratigraphical settings in the sedimentary intercalations from the Middle Volcanic Complex, ranging in age from 7 to 1.8 Ma. The descriptions of Heer (1857), Bunbury (1859) and Hartung & Mayer (1864) are reviewed based on 82 surviving specimens. From the initial 37 taxa, we recognize only 20: <i>Osmunda</i> sp., <i>Pteridium aquilinum</i>, <i>Asplenium</i> cf. <i>onopteris</i>, aff. <i>Asplenium</i>, cf. <i>Polystichum</i>, cf. <i>Davallia</i>, <i>Woodwardia radicans</i>, Filicopsida gen. et sp. indet. 1 and 2, <i>Ocotea foetens</i>, <i>Salix</i> sp., <i>Erica arborea</i>, cf. <i>Vaccinium</i>, <i>Rubus</i> sp, cf. <i>Myrtus</i>, Magnoliopsida gen. et sp. indet. 1 to 3, Liliopsida gen. et sp. indet. 1. Magnoliopsida gen. et sp. indet. 4 is based on one previously undescribed flower or fruit. The floristic composition of the São Jorge fossils resembles the current floristic association of temperate stink laurel (<i>Ocotea foetens</i>) forest, suggesting a warm and humid palaeoclimate and indicating that laurel forests were present in Macaronesia at least since the Gelasian, a time when the palaeotropical geofloral elements were almost extinct in Europe.
DOI: 10.6084/m9.figshare.5619658.v1
title: Inventory and review of the Mio–Pleistocene São Jorge flora (Madeira Island, Portugal): palaeoecological and biogeographical implications

description: The occurrence of plant fossils on Madeira Island has been known since the mid-nineteenth century. Charles Lyell and George Hartung discovered a leaf bed rich in Lauraceae and fern fossils at São Jorge in 1854. The determinations were controversial but a full review was never performed. Here we propose possible geological settings for the fossiliferous outcrop, and present an inventory and a systematic review of the surviving specimens of the São Jorge macroflora. The São Jorge leaf bed no longer outcrops due to a landslide in 1865. It was possible to establish the two alternative volcano-stratigraphical settings in the sedimentary intercalations from the Middle Volcanic Complex, ranging in age from 7 to 1.8 Ma. The descriptions of Heer (1857), Bunbury (1859) and Hartung & Mayer (1864) are reviewed based on 82 surviving specimens. From the initial 37 taxa, we recognize only 20: <i>Osmunda</i> sp., <i>Pteridium aquilinum</i>, <i>Asplenium</i> cf. <i>onopteris</i>, aff. <i>Asplenium</i>, cf. <i>Polystichum</i>, cf. <i>Davallia</i>, <i>Woodwardia radicans</i>, Filicopsida gen. et sp. indet. 1 and 2, <i>Ocotea foetens</i>, <i>Salix</i> sp., <i>Erica arborea</i>, cf. <i>Vaccinium</i>, <i>Rubus</i> sp, cf. <i>Myrtus</i>, Magnoliopsida gen. et sp. indet. 1 to 3, Liliopsida gen. et sp. indet. 1. Magnoliopsida gen. et sp. indet. 4 is based on one previously undescribed flower or fruit. The floristic composition of the São Jorge fossils resembles the current floristic association of temperate stink laurel (<i>Ocotea foetens</i>) forest, suggesting a warm and humid palaeoclimate and indicating that laurel forests were present in Macaronesia at least since the Gelasian, a time when the palaeotropical geofloral elements were almost extinct in Europe.
DOI: 10.6084/m9.figshare.5619637
title: The intron landscape of the mtDNA <i>cytb</i> gene among the Ascomycota: introns and intron-encoded open reading frames

description: Fungal mitochondrial genes are frequently noted for the presence of introns. These introns are self-splicing and can be assigned to either group I or II introns and they can encode open reading frames (ORFs). This study examines the introns present within the cytochrome b (<i>cytb</i>) gene of ascomycetes fungi. Cytochrome b gene sequences were sampled from GenBank and supplemented with our own data for species of <i>Leptographium</i> and <i>Ophiostoma</i>. Group I introns were encountered most frequently, many encoding either LAGLIDADG or GIY-YIG homing endonucleases (HEs). Numerous examples of different intron/ORF arrangements were observed including nested ORFs, multiple ORFs within a single intron and intron ORFs at various stages of erosion due to the accumulation of mutations. In addition, we noted one example of a nested intron and one complex group II intron that could potentially allow for alternative splicing. Documenting the distribution of introns within the same gene across a range of species allows for a better understanding of the evolution of introns and intronic ORFs. Intron landscapes also are a resource that can help in annotating genes and in bioprospecting for potentially active HEs, which are rare-cutting DNA endonucleases with applications in biotechnology.