cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4924355
title: Neutron tomography of <i>Austrosequoia novae-zeelandia</i>e comb. nov. (Late Cretaceous, Chatham Islands, New Zealand): implications for Sequoioideae phylogeny and biogeography

description: The Tupuangi Flora of the Chatham Islands, New Zealand, reveals a south polar forest ecosystem, and important biogeographical links between eastern and western Gondwana. We employed neutron tomography (NT) to image fossil Cupressaceae seed cones from the Upper Cretaceous (Cenomanian) strata of the Tupuangi Formation. This technique facilitated the non-destructive ‘virtual extraction’ of three-dimensional, coalified specimens, whilst they were still embedded within a large volume of supporting silicate sedimentary rock. This study is the first reported application of NT in palaeobotanical taxonomy, and the combination of virtual and manual extraction techniques enabled a more complete treatment than would otherwise be possible if taxonomic data were limited to only one of these approaches. The seed cones were identified as <i>Austrosequoia novae-zeelandiae</i> (Ettingshausen) Mays & Cantrill comb. nov. In this case, NT data supplemented the compression fossil data by providing details such as the three-dimensional measurements of the gross morphology, and accurate estimations of bract-scale complex number. Furthermore, this technique appears to show promise in differentiating between organic compounds within an individual specimen. However, anatomical details and fine-scale morphology were indiscernible due to present limitations in spatial resolution. <i>Austrosequoia novae-zeelandiae</i> is interpreted as a stem group of Sequoioideae; it shares synapomorphic seed cone characters with extant sequoioids (e.g. <i>Sequoia</i> and <i>Sequoiadendron</i>), and plesiomorphic stomatal structures and leaf morphology. Abundant epiphyllous fungi (<i>Plochmopeltinites</i> sp.; Microthyriaceae) were also identified on the leaf cuticles of <i>A. novae-zeelandiae</i>. The high abundance of <i>Austrosequoia</i> in the Tupuangi Flora supports a cupressaceous floral province at south polar latitudes during the early Late Cretaceous. Furthermore, this stem group of Sequoioideae in eastern Gondwana during the early Late Cretaceous suggests an alternative, south-to-north dispersal route of sequoioids before the final continental separation of eastern and western Gondwana.
DOI: 10.6084/m9.figshare.4924439.v1
title: II.8 - Agrogenom synthesis of genome evolution scenarios

description: Integration of recons of ancestral states and events in each gene (sub)family into a genome-wide synthesis.<br>This synthesis is generated by ancestral_content.py script ; note it could be done within the same run as as ancestral content reconstruction (previous step #II.7). The output notably includes:- <i>synthesis/</i> folder: - <i>genome_synthesis.*</i> files: species tree annotated with the sum of events (duplication, transfer, origination, loss, replacement) and of gene counts over all families, in extended Newick format (with bracketed comments at nodes) and as a serialized Python object (pickle) - <i>genome_*_synthesis.nhx</i> files: idem but separating annotation of gene count (states) and event count - <i>phylogenetic_profiles/</i> folder: tables of state count per gene family or orthologous subfamily, and by species tree node (any or extant nodes = "leaf" only)<br> - <i>annottables/</i> folder: tables of orthologous gene subfamilies specifically gained/lost at a species tree node, or specifically present/absent in a clade, with the list of corresponding genes in extant genomes, their coordinates and their functional annotation.<br>- <i>ortho_subfam_*.tab</i> files: tables of orthologous subfamilies assignation of gene sequence identifiers or of unique event identifiers, respectively.<br> - <i>specific_gene_dump.tab</i> file: relational database table dump listing the specific gene sets (see <i>annottables/</i> folder)<br> - <i>phylogenetic_profile_dump.tab</i> file: relational database table dump listing presence/absence states of (sub)families at each species tree node (see - <i>phylogenetic_profiles/</i> folder<i>)<br></i>- <i>reconciliation_collection/</i> folder: updated and final set of reconciled gene trees in phyloXML and serialized Python object (pickle) formats.<br><br>
DOI: 10.6084/m9.figshare.4924394.v1
title: †Peltosynidae, a new beetle family from the Middle–Late Triassic of Kyrgyzstan: its affinities with Polyphaga (Insecta, Coleoptera) and the groundplan of this megadiverse suborder

description: Middle–Late Triassic fossil beetles previously assigned to Polyphaga <i>incertae sedis</i> and new material from this period are described and illustrated. †Peltosynidae fam. nov. is introduced to contain the type genus <i>Peltosyne</i>, and species <i>P. triassica</i> Ponomarenko, 1977, together with the new species <i>P. varyvrosa</i> sp. nov. Two new monospecific genera, <i>Gnathopeltos</i> gen. nov. and <i>Ofthalmopeltos</i> gen. nov., with type species <i>G. dixis</i> sp. nov. and <i>O. synkritos</i> sp. nov., are also included in †Peltosynidae. Morphological characters evaluated with respect to their phylogenetic significance confirm that the family belongs to the suborder Polyphaga, mainly supported by the apomorphic internalized propleura. †Peltosynidae is characterized by a large transverse head, long and prominent, strongly developed mandibles, a short prosternum with a narrow, relatively short prosternal process, an interlocking mechanism between this process and a groove of the anteromedian process of the mesoventrite, striated elytra, a short metakatepisternum, transverse coxae, and a short abdomen with five ventrites. The large and transverse head is a potential autapomorphy. †Peltosynidae do not fit into any of the seven extant major polyphagan infraorders (series). The presence of a mesothoracic transverse katepisternal ridge in †<i>Peltosyne</i> is a plesiomorphic feature distinguishing the new family from all other groups of the suborder and suggesting its placement in the stem-group of Polyphaga. The strongly prominent mandibles and the coarse body sculpture resemble features found in extant Archostemata. It is likely that the beetles were xylophagous and adapted to subcortical habitats, arguably maintaining plesiomorphies. The polyphagan groundplan is reconstructed based on recent phylogenies and features found in †Peltosynidae and other extinct and extant groups. A scenario for the evolution of non-archostematan beetles in the late Permian and early Mesozoic is presented. http://zoobank.org/urn:lsid:zoobank.org:pub:58428459-33EF-4C1C-AD69-A066D3D33ADF
DOI: 10.6084/m9.figshare.4924349
title: A new stem bythinine in Cretaceous Burmese amber and early evolution of specialized predatory behaviour in pselaphine rove beetles (Coleoptera: Staphylinidae)

description: Comprising more than 10,000 valid species, the staphylinid subfamily Pselaphinae is a major element of epigean habitats, and among the most diverse groups of rove beetles. Pselaphinae is split basally into two principal clades: the small supertribe Faronitae, and its sister group, the hyper-diverse ‘higher Pselaphinae’ containing the remaining five supertribes. Deducing the origins and divergence times of major higher Pselaphinae clades requires direct fossil evidence. Here we describe a new pselaphine rove beetle, <i>Cretobythus excavatus</i> Yin, Parker & Cai gen. et sp. nov., based on a well-preserved individual embedded in mid-Cretaceous amber from Myanmar (Cenomanian, <i>c</i>. 99 Ma). <i>Cretobythus</i> does not obviously belong to any Recent tribe, but Bayesian phylogenetic placement using morphological characters supports a position within the stem-group of the tribe Bythinini, sister to <i>Boreotethys</i> Parker, a genus also recently described from Burmese amber. Together, <i>Cretobythus</i> + <i>Boreotethys</i> comprise the sister group of modern Bythinini. Despite some external similarities to Recent Bythinini, <i>Cretobythus</i> exhibits several plesiomorphic traits, including a generally flattened body plan, and metacoxae that are positioned close to the ventral midline. The resemblance in form of the enlarged maxillary palpi of <i>Cretobythus</i> to extant bythinines implies a similar function in prey capture, indicating that the unusual employment of the maxillary palps to trap moving prey in Bythinini had probably evolved by the mid-Cretaceous, at the latest. http://zoobank.org/urn:lsid:zoobank.org:pub:9FEB523F-76A7-4502-AF02-FCC0FAAB262A
DOI: 10.6084/m9.figshare.4924295
title: Bioengineered gold nanoparticles targeted to mesenchymal cells from patients with bronchiolitis obliterans syndrome does not rise the inflammatory response and can be safely inhaled by rodents

description: The use of gold nanoparticles (GNPs) as drug delivery system represents a promising issue for diseases without effective pharmacological treatment due to insufficient local drug accumulation and excessive systemic toxicity. Bronchiolitis obliterans syndrome (BOS) represents about 70% of cases of chronic lung allograft dysfunction, the main challenge to long-term lung transplantation. It is believed that due to repeated insults to epithelial bronchiolar cells local inflammatory response creates a milieu that favors epithelial–mesenchymal transition and activation of local mesenchymal cells (MCs) leading to airway fibro-obliteration. In a previous work, we engineered GNPs loaded with the mammalian target of rapamycin inhibitor everolimus, specifically decorated with an antibody against CD44, a surface receptor expressed by primary MCs isolated from bronchoalveolar lavage of BOS patients. We proved <i>in vitro</i> that these GNPs (GNP-HCe) were able to specifically inhibit primary MCs without affecting the bronchial epithelial cell. In the present work, we investigated the effect of these bioengineered nanoconstructs on inflammatory cells, given that a stimulating effect on macrophages, neutrophils or lymphocytes is strongly unwanted in graft airways since it would foster fibrogenesis. In addition, we administered GNP-HCe by the inhalatory route to normal mice for a preliminary assessment of their pulmonary and peripheral (liver, spleen and kidney) uptake. By these experiments, an evaluation of tissue toxicity was also performed. The present study proves that our bioengineered nanotools do not rise an inflammatory response and, under the tested inhalatory conditions that were used, are non-toxic.
DOI: 10.6084/m9.figshare.4924349.v1
title: A new stem bythinine in Cretaceous Burmese amber and early evolution of specialized predatory behaviour in pselaphine rove beetles (Coleoptera: Staphylinidae)

description: Comprising more than 10,000 valid species, the staphylinid subfamily Pselaphinae is a major element of epigean habitats, and among the most diverse groups of rove beetles. Pselaphinae is split basally into two principal clades: the small supertribe Faronitae, and its sister group, the hyper-diverse ‘higher Pselaphinae’ containing the remaining five supertribes. Deducing the origins and divergence times of major higher Pselaphinae clades requires direct fossil evidence. Here we describe a new pselaphine rove beetle, <i>Cretobythus excavatus</i> Yin, Parker & Cai gen. et sp. nov., based on a well-preserved individual embedded in mid-Cretaceous amber from Myanmar (Cenomanian, <i>c</i>. 99 Ma). <i>Cretobythus</i> does not obviously belong to any Recent tribe, but Bayesian phylogenetic placement using morphological characters supports a position within the stem-group of the tribe Bythinini, sister to <i>Boreotethys</i> Parker, a genus also recently described from Burmese amber. Together, <i>Cretobythus</i> + <i>Boreotethys</i> comprise the sister group of modern Bythinini. Despite some external similarities to Recent Bythinini, <i>Cretobythus</i> exhibits several plesiomorphic traits, including a generally flattened body plan, and metacoxae that are positioned close to the ventral midline. The resemblance in form of the enlarged maxillary palpi of <i>Cretobythus</i> to extant bythinines implies a similar function in prey capture, indicating that the unusual employment of the maxillary palps to trap moving prey in Bythinini had probably evolved by the mid-Cretaceous, at the latest. http://zoobank.org/urn:lsid:zoobank.org:pub:9FEB523F-76A7-4502-AF02-FCC0FAAB262A
DOI: 10.6084/m9.figshare.4924295.v1
title: Bioengineered gold nanoparticles targeted to mesenchymal cells from patients with bronchiolitis obliterans syndrome does not rise the inflammatory response and can be safely inhaled by rodents

description: The use of gold nanoparticles (GNPs) as drug delivery system represents a promising issue for diseases without effective pharmacological treatment due to insufficient local drug accumulation and excessive systemic toxicity. Bronchiolitis obliterans syndrome (BOS) represents about 70% of cases of chronic lung allograft dysfunction, the main challenge to long-term lung transplantation. It is believed that due to repeated insults to epithelial bronchiolar cells local inflammatory response creates a milieu that favors epithelial–mesenchymal transition and activation of local mesenchymal cells (MCs) leading to airway fibro-obliteration. In a previous work, we engineered GNPs loaded with the mammalian target of rapamycin inhibitor everolimus, specifically decorated with an antibody against CD44, a surface receptor expressed by primary MCs isolated from bronchoalveolar lavage of BOS patients. We proved <i>in vitro</i> that these GNPs (GNP-HCe) were able to specifically inhibit primary MCs without affecting the bronchial epithelial cell. In the present work, we investigated the effect of these bioengineered nanoconstructs on inflammatory cells, given that a stimulating effect on macrophages, neutrophils or lymphocytes is strongly unwanted in graft airways since it would foster fibrogenesis. In addition, we administered GNP-HCe by the inhalatory route to normal mice for a preliminary assessment of their pulmonary and peripheral (liver, spleen and kidney) uptake. By these experiments, an evaluation of tissue toxicity was also performed. The present study proves that our bioengineered nanotools do not rise an inflammatory response and, under the tested inhalatory conditions that were used, are non-toxic.
DOI: 10.6084/m9.figshare.4924355.v2
title: Neutron tomography of <i>Austrosequoia novae-zeelandia</i>e comb. nov. (Late Cretaceous, Chatham Islands, New Zealand): implications for Sequoioideae phylogeny and biogeography

description: The Tupuangi Flora of the Chatham Islands, New Zealand, reveals a south polar forest ecosystem, and important biogeographical links between eastern and western Gondwana. We employed neutron tomography (NT) to image fossil Cupressaceae seed cones from the Upper Cretaceous (Cenomanian) strata of the Tupuangi Formation. This technique facilitated the non-destructive ‘virtual extraction’ of three-dimensional, coalified specimens, whilst they were still embedded within a large volume of supporting silicate sedimentary rock. This study is the first reported application of NT in palaeobotanical taxonomy, and the combination of virtual and manual extraction techniques enabled a more complete treatment than would otherwise be possible if taxonomic data were limited to only one of these approaches. The seed cones were identified as <i>Austrosequoia novae-zeelandiae</i> (Ettingshausen) Mays & Cantrill comb. nov. In this case, NT data supplemented the compression fossil data by providing details such as the three-dimensional measurements of the gross morphology, and accurate estimations of bract-scale complex number. Furthermore, this technique appears to show promise in differentiating between organic compounds within an individual specimen. However, anatomical details and fine-scale morphology were indiscernible due to present limitations in spatial resolution. <i>Austrosequoia novae-zeelandiae</i> is interpreted as a stem group of Sequoioideae; it shares synapomorphic seed cone characters with extant sequoioids (e.g. <i>Sequoia</i> and <i>Sequoiadendron</i>), and plesiomorphic stomatal structures and leaf morphology. Abundant epiphyllous fungi (<i>Plochmopeltinites</i> sp.; Microthyriaceae) were also identified on the leaf cuticles of <i>A. novae-zeelandiae</i>. The high abundance of <i>Austrosequoia</i> in the Tupuangi Flora supports a cupressaceous floral province at south polar latitudes during the early Late Cretaceous. Furthermore, this stem group of Sequoioideae in eastern Gondwana during the early Late Cretaceous suggests an alternative, south-to-north dispersal route of sequoioids before the final continental separation of eastern and western Gondwana.
DOI: 10.6084/m9.figshare.4924355.v1
title: Neutron tomography of <i>Austrosequoia novae-zeelandia</i>e comb. nov. (Late Cretaceous, Chatham Islands, New Zealand): implications for Sequoioideae phylogeny and biogeography

description: The Tupuangi Flora of the Chatham Islands, New Zealand, reveals a south polar forest ecosystem, and important biogeographical links between eastern and western Gondwana. We employed neutron tomography (NT) to image fossil Cupressaceae seed cones from the Upper Cretaceous (Cenomanian) strata of the Tupuangi Formation. This technique facilitated the non-destructive ‘virtual extraction’ of three-dimensional, coalified specimens, whilst they were still embedded within a large volume of supporting silicate sedimentary rock. This study is the first reported application of NT in palaeobotanical taxonomy, and the combination of virtual and manual extraction techniques enabled a more complete treatment than would otherwise be possible if taxonomic data were limited to only one of these approaches. The seed cones were identified as <i>Austrosequoia novae-zeelandiae</i> (Ettingshausen) Mays & Cantrill comb. nov. In this case, NT data supplemented the compression fossil data by providing details such as the three-dimensional measurements of the gross morphology, and accurate estimations of bract-scale complex number. Furthermore, this technique appears to show promise in differentiating between organic compounds within an individual specimen. However, anatomical details and fine-scale morphology were indiscernible due to present limitations in spatial resolution. <i>Austrosequoia novae-zeelandiae</i> is interpreted as a stem group of Sequoioideae; it shares synapomorphic seed cone characters with extant sequoioids (e.g. <i>Sequoia</i> and <i>Sequoiadendron</i>), and plesiomorphic stomatal structures and leaf morphology. Abundant epiphyllous fungi (<i>Plochmopeltinites</i> sp.; Microthyriaceae) were also identified on the leaf cuticles of <i>A. novae-zeelandiae</i>. The high abundance of <i>Austrosequoia</i> in the Tupuangi Flora supports a cupressaceous floral province at south polar latitudes during the early Late Cretaceous. Furthermore, this stem group of Sequoioideae in eastern Gondwana during the early Late Cretaceous suggests an alternative, south-to-north dispersal route of sequoioids before the final continental separation of eastern and western Gondwana.
DOI: 10.6084/m9.figshare.4924283
title: Pain, sensory disturbances and psychological distress are common sequelae after treatment of ductal carcinoma <i>in situ</i>: a cross-sectional study

description: Sequelae such as pain, sensory disturbances and psychological distress are well known after treatment for invasive breast cancer (IBC). Patients treated for ductal carcinoma <i>in situ</i> (DCIS) receive a similar treatment as low-risk IBC. The aim of this cross-sectional study was to describe prevalence of postoperative pain, sensory disturbances, psychological distress and rehabilitation needs among Danish women with DCIS. <b>Methods:</b> A total of 574 women treated for DCIS in Denmark in 2013 and 2014 were enrolled and 473 (82%) completed a detailed questionnaire on demographic factors, pain, sensory disturbances, psychological aspects and rehabilitation needs 1–3 years after surgery. <b>Results:</b> Median age was 60 years. A total of 33% of patients reported any pain and 12% reported moderate to severe pain in the area of surgery. Younger age (&lt;50 years OR 4.7 (95% CI: 1.6–14.0, <i>p</i> = 0.006)), aged 50 to 65 years OR 2.8 (95% CI: 1.1–7.0, <i>p</i> = 0.02) and anxiety and depression (measured by HADS<sub>total</sub> &gt;15 OR of 3.1 (95% CI: 1.5–6.3, <i>p</i> = 0.003)) were significantly associated with moderate to severe pain. Approximately one-third of the patients reported sensory disturbances such as pins and needles (32%), numbness (37%) and painful itch (30%) and 94 women (20%) reported anxiety ≥8, 26 (6%) depression and 51 (11%) reported distress. <b>Conclusions:</b> This cross-sectional study showed that women treated for DCIS suffered from pain, sensory disturbances and psychological impairment and had unmet rehabilitation needs. Further research is warranted, specifically addressing rehabilitation after diagnosis and treatment of DCIS.
DOI: 10.6084/m9.figshare.4924283.v1
title: Pain, sensory disturbances and psychological distress are common sequelae after treatment of ductal carcinoma <i>in situ</i>: a cross-sectional study

description: Sequelae such as pain, sensory disturbances and psychological distress are well known after treatment for invasive breast cancer (IBC). Patients treated for ductal carcinoma <i>in situ</i> (DCIS) receive a similar treatment as low-risk IBC. The aim of this cross-sectional study was to describe prevalence of postoperative pain, sensory disturbances, psychological distress and rehabilitation needs among Danish women with DCIS. <b>Methods:</b> A total of 574 women treated for DCIS in Denmark in 2013 and 2014 were enrolled and 473 (82%) completed a detailed questionnaire on demographic factors, pain, sensory disturbances, psychological aspects and rehabilitation needs 1–3 years after surgery. <b>Results:</b> Median age was 60 years. A total of 33% of patients reported any pain and 12% reported moderate to severe pain in the area of surgery. Younger age (&lt;50 years OR 4.7 (95% CI: 1.6–14.0, <i>p</i> = 0.006)), aged 50 to 65 years OR 2.8 (95% CI: 1.1–7.0, <i>p</i> = 0.02) and anxiety and depression (measured by HADS<sub>total</sub> &gt;15 OR of 3.1 (95% CI: 1.5–6.3, <i>p</i> = 0.003)) were significantly associated with moderate to severe pain. Approximately one-third of the patients reported sensory disturbances such as pins and needles (32%), numbness (37%) and painful itch (30%) and 94 women (20%) reported anxiety ≥8, 26 (6%) depression and 51 (11%) reported distress. <b>Conclusions:</b> This cross-sectional study showed that women treated for DCIS suffered from pain, sensory disturbances and psychological impairment and had unmet rehabilitation needs. Further research is warranted, specifically addressing rehabilitation after diagnosis and treatment of DCIS.
DOI: 10.6084/m9.figshare.4924226
title: Physicians_questionaire_2013.sav

description: The survey was conducted from 29 October to 31 December 2013 with 379 Polish physicians.
DOI: 10.6084/m9.figshare.4924226.v1
title: Physicians_questionaire_2013.sav

description: The survey was conducted from 29 October to 31 December 2013 with 379 Polish physicians.
DOI: 10.17028/rd.lboro.4924181
title: Algorithms for the paper "Finite orbits of the pure braid group on the monodromy of the 2-variable Garnier system"

description: These are the algorithms needed in the paper "Finite orbits of the pure braid group on the monodromy of the 2-variable Garnier system" by P. Calligaris and M. Mazzocco.<br>More information on using these algorithms can be found in the file "README.pdf"<br>An updated version of the algorithms was uploaded on 8th September 2017.
DOI: 10.17028/rd.lboro.4924181.v2
title: Algorithms for the paper "Finite orbits of the pure braid group on the monodromy of the 2-variable Garnier system"

description: These are the algorithms needed in the paper "Finite orbits of the pure braid group on the monodromy of the 2-variable Garnier system" by P. Calligaris and M. Mazzocco.<br>More information on using these algorithms can be found in the file "README.pdf"<br>An updated version of the algorithms was uploaded on 8th September 2017.