cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3492941.v1
title: Exploring phylogenetic relationships of Pteraspidiformes heterostracans (stem-gnathostomes) using continuous and discrete characters

description: Ostracoderms are a paraphyletic group of extinct jawless fishes comprising the gnathostome stem and are fundamental to our understanding of early vertebrate evolution. However, only a handful of these clades have robust phylogenies in place, hindering our interpretation of early vertebrate histories. A new phylogeny is proposed for the Pteraspidiformes – the largest and most-studied clade of heterostracan ostracoderms. Difficulties such as large amounts of missing data and the limited morphological variability within the group have led us to explore different coding strategies such as the inclusion of quantitative data and implied weighting. We present a new comprehensive data set including all described genera of Pteraspidiformes (47 taxa) analysed using discrete characters only, a combination of discrete and continuous characters, and gap-coding strategies (transforming the continuous into discrete characters), along with a Bayesian analysis. Two representatives of the Psammosteidae (<i>Drepanaspis</i> and <i>Psammosteus</i>) are also incorporated within the analysis to elucidate their inclusiveness within the Pteraspidiformes. Well-resolved trees are only achieved under re-weighted (implied weighting) analyses. Here, we show that many ‘classic’ Pteraspidiformes clades hold true under our different coding methods, with the implied weighting of discrete characters and inclusion of continuous characters giving very similar topologies. In all instances, the Psammosteidae are found to belong within the Pteraspidiformes, nested with the Spitsbergen genera <i>Doryaspis</i>, <i>Xylaspis</i> and <i>Woodfjordaspis</i>. Gap coding, however, results in a different tree topology to other analyses, perhaps due to the high sensitivity to missing data. Our results indicate that careful consideration and justifications should be applied to quantitative characters when reconstructing relationships of homoplastic ostracoderms. Superfamily Doryaspidae superfam. nov. is introduced. http://zoobank.org/urn:lsid:zoobank.org:pub:BF5255A1-1417-432B-AC64-BF132A0BCC65
DOI: 10.6084/m9.figshare.3492878.v1
title: Supplement - Bog Turtle Demographics within the Southern Population

description: Supplemental tables associated with the Copeia publication "Bog Turtle Demographics within the Southern Population."
DOI: 10.6084/m9.figshare.3492878.v2
title: Supplement - Bog Turtle Demographics within the Southern Population

description: Supplemental tables associated with the Copeia publication "Bog Turtle Demographics within the Southern Population."
DOI: 10.6084/m9.figshare.3492779
title: PiantadosiAslin2016.zip

description: Data from Piantadosi & Aslin (2016) in which children were taught two individual functions and tested on their composition. <br>
DOI: 10.6084/m9.figshare.3492779.v1
title: PiantadosiAslin2016.zip

description: Data from Piantadosi & Aslin (2016) in which children were taught two individual functions and tested on their composition. <br>
DOI: 10.6084/m9.figshare.3492776
title: Structure prediction and functional analyses of a thermostable lipase obtained from <i>Shewanella putrefaciens</i>

description: Previous experimental studies on thermostable lipase from <i>Shewanella putrefaciens</i> suggested the maximum activity at higher temperatures, but with little information on its conformational profile. In this study, the three-dimensional structure of lipase was predicted and a 60 ns molecular dynamics (MD) simulation was carried out at temperatures ranging from 300 to 400 K to better understand its thermostable nature at the molecular level. MD simulations were performed in order to predict the optimal activity of thermostable lipase. The results suggested strong conformational temperature dependence. The thermostable lipase maintained its bio-active conformation at 350 K during the 60 ns MD simulations.
DOI: 10.6084/m9.figshare.3492776.v1
title: Structure prediction and functional analyses of a thermostable lipase obtained from <i>Shewanella putrefaciens</i>

description: Previous experimental studies on thermostable lipase from <i>Shewanella putrefaciens</i> suggested the maximum activity at higher temperatures, but with little information on its conformational profile. In this study, the three-dimensional structure of lipase was predicted and a 60 ns molecular dynamics (MD) simulation was carried out at temperatures ranging from 300 to 400 K to better understand its thermostable nature at the molecular level. MD simulations were performed in order to predict the optimal activity of thermostable lipase. The results suggested strong conformational temperature dependence. The thermostable lipase maintained its bio-active conformation at 350 K during the 60 ns MD simulations.
DOI: 10.6084/m9.figshare.3492773
title: Retinal thickness raw data.xlsx

description: Raw thickness data for intra-retinal layer segmentation by both the Iowa Reference Algorithms, and on-board commercial software. Both fixed-axial eye length and axial eye length-dependent scaling are used.
DOI: 10.6084/m9.figshare.3492758
title: A Window to the Subsurface: Microbial Diversity in Hot Springs of a Sulfidic Cave (Kaklik, Turkey)

description: Caves are windows to the extreme habitats of deep subsurface, and provide answers of unknowns about the underground life. Furthermore, sulfidic caves are important analogues for the early Earth environments, since some environmental conditions are common, such as high sulfur concentration, high temperature and oxygen-poor conditions. Kaklik Cave (Denizli, Turkey) with its travertine formation, carbonate- and sulfur-rich thermal springs, exhibits a unique ecosystem as a sulfidic cave. This study represents the first molecular survey of the microbial community in the Kaklik Cave, Turkey using high-throughput 16S rRNA gene amplicon sequencing analysis. An average of 859–2,416 operational taxonomic units per sample were observed including 25 bacterial phyla and 3 archaeal phyla. The bacterial diversity profiles were generally dominated by <i>Epsilonproteobacteria</i> and <i>Gammaproteobacteria</i>. At the carbonate-rich hot spring, that formed travertine structure, 9.7% of sequence reads affiliated with <i>Thiofaba</i> spp. In contrast, 38.74% of the total sequence reads at the sulfidic hot spring samples associated with the genus <i>Sulfurimonas</i> and <i>Sulfurovum</i>. In the archaeal community composition, <i>Thermoplasmata</i> was the most abundant group in all sampling areas. The 454-pyrotag results provide leads about ammonia-, nitrite- and sulfur-oxidation as well as sulfur-reduction, carbon dioxide fixation, and nitrogen fixation.
DOI: 10.6084/m9.figshare.3492758.v2
title: A Window to the Subsurface: Microbial Diversity in Hot Springs of a Sulfidic Cave (Kaklik, Turkey)

description: Caves are windows to the extreme habitats of deep subsurface, and provide answers of unknowns about the underground life. Furthermore, sulfidic caves are important analogues for the early Earth environments, since some environmental conditions are common, such as high sulfur concentration, high temperature and oxygen-poor conditions. Kaklik Cave (Denizli, Turkey) with its travertine formation, carbonate- and sulfur-rich thermal springs, exhibits a unique ecosystem as a sulfidic cave. This study represents the first molecular survey of the microbial community in the Kaklik Cave, Turkey using high-throughput 16S rRNA gene amplicon sequencing analysis. An average of 859–2,416 operational taxonomic units per sample were observed including 25 bacterial phyla and 3 archaeal phyla. The bacterial diversity profiles were generally dominated by <i>Epsilonproteobacteria</i> and <i>Gammaproteobacteria</i>. At the carbonate-rich hot spring, that formed travertine structure, 9.7% of sequence reads affiliated with <i>Thiofaba</i> spp. In contrast, 38.74% of the total sequence reads at the sulfidic hot spring samples associated with the genus <i>Sulfurimonas</i> and <i>Sulfurovum</i>. In the archaeal community composition, <i>Thermoplasmata</i> was the most abundant group in all sampling areas. The 454-pyrotag results provide leads about ammonia-, nitrite- and sulfur-oxidation as well as sulfur-reduction, carbon dioxide fixation, and nitrogen fixation.
DOI: 10.6084/m9.figshare.3492758.v1
title: A window to the subsurface: Microbial diversity in hot springs of a sulfidic cave (Kaklik, Turkey)

description: Caves are windows to the extreme habitats of deep subsurface, and provide answers of unknowns about the underground life. Furthermore, sulfidic caves are important analogues for the early Earth environments, since some environmental conditions are common, such as high sulfur concentration, high temperature and oxygen-poor conditions. Kaklik Cave (Denizli, Turkey) with its travertine formation, carbonate and sulfur rich thermal springs, exhibits a unique ecosystem as a sulfidic cave. This study represents the first molecular survey of the microbial community in the Kaklik Cave, Turkey using high-throughput 16S rRNA gene amplicon sequencing analysis. An average of 859- 2,416 operational taxonomic units per sample were observed including 25 bacterial phyla and 3 archaeal phyla. The bacterial diversity profiles were generally dominated by <i>Epsilonproteobacteria</i> and <i>Gammaproteobacteria</i>. At the carbonate rich hot spring, that formed travertine structure, 9.7% of sequence reads affiliated with <i>Thiofaba</i> spp. In contrast, 38.74% of the total sequence reads at the sulfidic hot spring samples associated with the genus <i>Sulfurimonas</i> and <i>Sulfurovum</i>. In the archaeal community composition, <i>Thermoplasmata</i> was the most abundant group in all sampling areas. The 454-pyrotag results provide leads about ammonia-, nitrite- and sulfur-oxidation as well as sulfur-reduction, carbon dioxide fixation, nitrogen fixation.
DOI: 10.6084/m9.figshare.3492722
title: Cirrus HD-OCT repeatability dataset.tif

description: Repeatability dataset comprising OCT (20°x20°; 512x128) images obtained on 25 participants, at two separate imaging sessions, using a Zeiss Cirrus HD-OCT.
DOI: 10.6084/m9.figshare.3492719
title: Long-wavelength OCT repeatability dataset.tif

description: Repeatability dataset comprising OCT (20°x20°; 512x128) images obtained on 25 participants, at two separate imaging sessions, using a long-wavelength Spectral Domain OCT.
DOI: 10.6084/m9.figshare.3492707
title: Topcon 3D-OCT 1000 repeatability dataset.tif

description: Repeatability dataset comprising OCT (20°x20°; 512x128) images obtained on 25 participants, at two separate imaging sessions, using a Topcon 3-D OCT 1000.
DOI: 10.6084/m9.figshare.3492620
title: Supplementary Material for: Estimating the Quantitative Demand of NOAC Antidote Doses on Stroke Units

description: <i>Background:</i> The first specific antidote for non-vitamin K antagonist oral anticoagulants (NOAC) has recently been approved. NOAC antidotes will allow specific treatment for 2 hitherto problematic patient groups: patients with oral anticoagulant therapy (OAT)-associated intracerebral hemorrhage (ICH) and maybe also thrombolysis candidates presenting on oral anticoagulation (OAT). We aimed to estimate the frequency of these events and hence the quantitative demand of antidote doses on a stroke unit. <i>Methods:</i> We extracted data of patients with acute ischemic stroke and ICH (&lt;24 h after symptom onset) in the years 2012-2015 from a state-wide prospective stroke inpatient registry. We selected 8 stroke units and determined the mode of OAT upon admission in 2012-2013. In 2015, the mode of OAT became a mandatory item of the inpatient registry. From the number of anticoagulated patients and the NOAC share, we estimated the current and future demand for NOAC antidote doses on stroke units. <i>Results:</i> Eighteen percent of ICH patients within 6 h of symptom onset or an unknown symptom onset were on OAT. Given a NOAC share at admission of 40%, about 7% of all ICH patients may qualify for NOAC reversal therapy. Thirteen percent of ischemic stroke patients admitted within 4 h presented on anticoagulation. Given the availability of an appropriate antidote, a NOAC share of 50% could lead to a 6.1% increase in thrombolysis rate. <i>Conclusions:</i>Stroke units serving populations with a comparable demographic structure should prepare to treat up to 1% of all acute ischemic stroke patients and 7% of all acute ICH patients with NOAC antidotes. These numbers may increase with the mounting prevalence of atrial fibrillation and an increasing use of NOAC.
DOI: 10.6084/m9.figshare.3492620.v1
title: Supplementary Material for: Estimating the Quantitative Demand of NOAC Antidote Doses on Stroke Units

description: <i>Background:</i> The first specific antidote for non-vitamin K antagonist oral anticoagulants (NOAC) has recently been approved. NOAC antidotes will allow specific treatment for 2 hitherto problematic patient groups: patients with oral anticoagulant therapy (OAT)-associated intracerebral hemorrhage (ICH) and maybe also thrombolysis candidates presenting on oral anticoagulation (OAT). We aimed to estimate the frequency of these events and hence the quantitative demand of antidote doses on a stroke unit. <i>Methods:</i> We extracted data of patients with acute ischemic stroke and ICH (&lt;24 h after symptom onset) in the years 2012-2015 from a state-wide prospective stroke inpatient registry. We selected 8 stroke units and determined the mode of OAT upon admission in 2012-2013. In 2015, the mode of OAT became a mandatory item of the inpatient registry. From the number of anticoagulated patients and the NOAC share, we estimated the current and future demand for NOAC antidote doses on stroke units. <i>Results:</i> Eighteen percent of ICH patients within 6 h of symptom onset or an unknown symptom onset were on OAT. Given a NOAC share at admission of 40%, about 7% of all ICH patients may qualify for NOAC reversal therapy. Thirteen percent of ischemic stroke patients admitted within 4 h presented on anticoagulation. Given the availability of an appropriate antidote, a NOAC share of 50% could lead to a 6.1% increase in thrombolysis rate. <i>Conclusions:</i>Stroke units serving populations with a comparable demographic structure should prepare to treat up to 1% of all acute ischemic stroke patients and 7% of all acute ICH patients with NOAC antidotes. These numbers may increase with the mounting prevalence of atrial fibrillation and an increasing use of NOAC.
DOI: 10.6084/m9.figshare.3492545
title: Experiment #2

description: Culture #2
DOI: 10.6084/m9.figshare.3492545.v1
title: New draft item

description: Culture #2
DOI: 10.6084/m9.figshare.3492539
title: LGR5 and CD133 as prognostic and predictive markers for fluoropyrimidine-based adjuvant chemotherapy in colorectal cancer

description: <b>Background:</b> Expression of leucine-rich-repeat-containing G-protein-coupled receptor 5 (LGR5) gene is associated with a metastatic phenotype and poor prognosis in colorectal cancer (CRC). CD133 expression is a putative cancer stem cell marker and a proposed prognostic marker in CRC, whereas the predictive value of CD133 expression for effect of adjuvant chemotherapy in CRC is unclear. <b>Material and methods:</b> For the study of LGR5 mRNA and CD133 expression, tissue microarrays from 409 primary CRC stage II and III tumors, where patients had been randomized to adjuvant chemotherapy or surgery only, were available. LGR5 mRNA and CD133 expression were assessed by in situ hybridization (ISH) and immunohistochemistry (IHC), respectively. LGR5 mRNA and CD133 expression as prognostic and predictive markers were evaluated by univariate and multivariate analyses. <b>Results:</b> For all CRC patients, positive LGR5 mRNA and CD133 expression were associated with classic adenocarcinoma histology type (p = 0.001 and p = 0.014, respectively). Positive LGR5 mRNA expression was also associated with smaller tumor diameter for CRC stage II (p = 0.005), but not for CRC stage III (p = 0.054). For CRC stage II, lack of LGR5 mRNA expression was associated with longer time to recurrence (TTR) in Kaplan-Meier (p = 0.045) and in multivariate Cox analysis (HR 0.27, 95% CI 0.08–0.95, p = 0.041). For colon cancer stage III patients, lack of CD133 expression was associated with better effect of adjuvant chemotherapy (p = 0.016) in Kaplan-Meier univariate analysis, but the interaction between CD133 and adjuvant chemotherapy was not statistically significant in multivariate analysis (HR 0.59, 95% CI 0.18–1.89, p = 0.374). <b>Conclusion:</b> LGR5 mRNA expression is a prognostic factor for CRC stage II patients, whereas the value of CD133 expression as prognostic and predictive biomarker is inconclusive.
DOI: 10.6084/m9.figshare.3492539.v1
title: LGR5 and CD133 as prognostic and predictive markers for fluoropyrimidine-based adjuvant chemotherapy in colorectal cancer

description: <b>Background:</b> Expression of leucine-rich-repeat-containing G-protein-coupled receptor 5 (LGR5) gene is associated with a metastatic phenotype and poor prognosis in colorectal cancer (CRC). CD133 expression is a putative cancer stem cell marker and a proposed prognostic marker in CRC, whereas the predictive value of CD133 expression for effect of adjuvant chemotherapy in CRC is unclear. <b>Material and methods:</b> For the study of LGR5 mRNA and CD133 expression, tissue microarrays from 409 primary CRC stage II and III tumors, where patients had been randomized to adjuvant chemotherapy or surgery only, were available. LGR5 mRNA and CD133 expression were assessed by in situ hybridization (ISH) and immunohistochemistry (IHC), respectively. LGR5 mRNA and CD133 expression as prognostic and predictive markers were evaluated by univariate and multivariate analyses. <b>Results:</b> For all CRC patients, positive LGR5 mRNA and CD133 expression were associated with classic adenocarcinoma histology type (p = 0.001 and p = 0.014, respectively). Positive LGR5 mRNA expression was also associated with smaller tumor diameter for CRC stage II (p = 0.005), but not for CRC stage III (p = 0.054). For CRC stage II, lack of LGR5 mRNA expression was associated with longer time to recurrence (TTR) in Kaplan-Meier (p = 0.045) and in multivariate Cox analysis (HR 0.27, 95% CI 0.08–0.95, p = 0.041). For colon cancer stage III patients, lack of CD133 expression was associated with better effect of adjuvant chemotherapy (p = 0.016) in Kaplan-Meier univariate analysis, but the interaction between CD133 and adjuvant chemotherapy was not statistically significant in multivariate analysis (HR 0.59, 95% CI 0.18–1.89, p = 0.374). <b>Conclusion:</b> LGR5 mRNA expression is a prognostic factor for CRC stage II patients, whereas the value of CD133 expression as prognostic and predictive biomarker is inconclusive.
DOI: 10.6084/m9.figshare.3492527.v1
title: CERN@school: A simple source - potassium chloride

description: We present some instructions for making a safe source of beta radiation using potassium chloride (KCl). This can then be used for testing the operation of your CERN@school Timepix detector and doing some basic analysis with the Pixelman particle counting software. Instructions are provided within.<br><br>To find out more about taking part in authentic research with the CERN@school programme, please visit:<br><br>http://researchinschools.org/CERN<br>
DOI: 10.6084/m9.figshare.3492527.v2
title: CERN@school: A simple source - potassium chloride

description: We present some instructions for making a safe source of beta radiation using potassium chloride (KCl). This can then be used for testing the operation of your CERN@school Timepix detector and doing some basic analysis with the Pixelman particle counting software. Instructions are provided within.<br><br>To find out more about taking part in authentic research with the CERN@school programme, please visit:<br><br>http://researchinschools.org/CERN<br>
DOI: 10.6084/m9.figshare.3492518
title: Supplement raw data.zip

description: Supplement data of the MS "Characterization of the fishing lines in Titiwai (=Arachnocampa luminosa Skuse, 1890) from New Zealand and Australia"
DOI: 10.6084/m9.figshare.3492518.v1
title: Supplement raw data.zip

description: Supplement data of the MS "Characterization of the fishing lines in Titiwai (=Arachnocampa luminosa Skuse, 1890) from New Zealand and Australia"
DOI: 10.6084/m9.figshare.3492515
title: Diversity and convergences in the evolution of feeding adaptations in ankylosaurs (Dinosauria: Ornithischia)<sup>*</sup>

description: Ankylosaurian dinosaurs were low-browsing quadrupeds that were traditionally thought of as simple orthal pulpers exhibiting minimal tooth occlusion during feeding, as in many extant lizards. Recent studies, however, have demonstrated that effective chewing with tooth occlusion and palinal jaw movement was present in some members of this group. Qualitative and quantitative analysis of feeding characters (i.e. craniodental features, tooth wear patterns, origin and insertion of jaw adductors) reveal at least three different jaw mechanisms during the evolution of Ankylosauria. Whereas, in basal members, food processing was restricted to simple orthal pulping, in late Early and Late Cretaceous North American and European forms a precise tooth occlusion evolved convergently in many lineages (including nodosaurids and ankylosaurids) complemented by palinal power stroke. In contrast, Asian forms retained the primitive mode of feeding without any biphasal chewing, a phenomenon that might relate to the different types of vegetation consumed by these low-level feeders in different habitats on different landmasses. Further, a progressive widening of the muzzle is demonstrated both in Late Cretaceous North American and Asian ankylosaurs, and the width and general shape of the muzzle probably correlates with foraging time and food type, as in herbivorous mammals.
DOI: 10.6084/m9.figshare.3492515.v1
title: Diversity and convergences in the evolution of feeding adaptations in ankylosaurs (Dinosauria: Ornithischia)<sup>*</sup>

description: Ankylosaurian dinosaurs were low-browsing quadrupeds that were traditionally thought of as simple orthal pulpers exhibiting minimal tooth occlusion during feeding, as in many extant lizards. Recent studies, however, have demonstrated that effective chewing with tooth occlusion and palinal jaw movement was present in some members of this group. Qualitative and quantitative analysis of feeding characters (i.e. craniodental features, tooth wear patterns, origin and insertion of jaw adductors) reveal at least three different jaw mechanisms during the evolution of Ankylosauria. Whereas, in basal members, food processing was restricted to simple orthal pulping, in late Early and Late Cretaceous North American and European forms a precise tooth occlusion evolved convergently in many lineages (including nodosaurids and ankylosaurids) complemented by palinal power stroke. In contrast, Asian forms retained the primitive mode of feeding without any biphasal chewing, a phenomenon that might relate to the different types of vegetation consumed by these low-level feeders in different habitats on different landmasses. Further, a progressive widening of the muzzle is demonstrated both in Late Cretaceous North American and Asian ankylosaurs, and the width and general shape of the muzzle probably correlates with foraging time and food type, as in herbivorous mammals.