cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5592631
title: AI vs Dermatologist Test PDF Docoment

description: We created a test .pdf file by combining 25 images of each malignancy and 20 images of each benign conditions.<br>Original resolution of images were extracted from the Asan test dataset and the Edinburgh Dermofit library, and doPDF (http://www.dopdf.com) was used with high resolution mode to create the test pdf. <br>The filenames of the selected images from the Edinburgh dataset was listed in list_edin.txt. (The Edinburgh dataset is a commercial library)<br>https://licensing.edinburgh-innovations.ed.ac.uk/item.php?item=dermofit-image-library<br>
DOI: 10.6084/m9.figshare.5592412
title: Data and description of analysis of the paper "Defensive behavior and caudal autotomy rate in Coleodactylus meridionalis (Squamata: Sphaerodactylidae)"

description: Lizards can display several antipredatory behaviors. Here, we describe antipredatory behaviors of Coleodactylus meridionalis in an Atlantic Forest fragment in Pernambuco, Northeastern Brazil using Ad libtum method for behavioral observation. We also tested if body size and sex predict the incidence of caudal autotomy. We recorded six antipredatory behaviors in 253 specimens. Hiding was the most common behavior (55.34%), followed by immobility (18.18%), run away (17.79%), caudal autotomy (4.35%), cloacal discharge (2.37%), and escape by jumps (1.97%). Of the 223 specimens collected for analysis of caudal autotomy, 48.9% had autotomized tails and 51.1% had intact tails. About 55% of individuals with autotomized tail were found with a regenerating tail and 45% did not. The tail had at least two points of autotomy: a distal one and a basal one. The frequency of tail loss was 46.7%. The probability of autotomy decreased with increasing body size independently of sex. Our results can help understand the causes of tail autotomy and guide future studies on behavioral ecology of this lizard species.
DOI: 10.6084/m9.figshare.5592412.v1
title: Data and description of analysis of the paper "Defensive behavior and caudal autotomy rate in Coleodactylus meridionalis (Squamata: Sphaerodactylidae)"

description: Lizards can display several antipredatory behaviors. Here, we describe antipredatory behaviors of Coleodactylus meridionalis in an Atlantic Forest fragment in Pernambuco, Northeastern Brazil using Ad libtum method for behavioral observation. We also tested if body size and sex predict the incidence of caudal autotomy. We recorded six antipredatory behaviors in 253 specimens. Hiding was the most common behavior (55.34%), followed by immobility (18.18%), run away (17.79%), caudal autotomy (4.35%), cloacal discharge (2.37%), and escape by jumps (1.97%). Of the 223 specimens collected for analysis of caudal autotomy, 48.9% had autotomized tails and 51.1% had intact tails. About 55% of individuals with autotomized tail were found with a regenerating tail and 45% did not. The tail had at least two points of autotomy: a distal one and a basal one. The frequency of tail loss was 46.7%. The probability of autotomy decreased with increasing body size independently of sex. Our results can help understand the causes of tail autotomy and guide future studies on behavioral ecology of this lizard species.
DOI: 10.6084/m9.figshare.5591227
title: Data repository: Adaptations of an RNA virus to increasing thermal stress (revised)

description: Raw data and R analysis scripts for revised version of paper "Adaptations of an RNA Virus to Increasing Thermal Stress." <br><br>Includes lineage survival during the evolution experiment, measured thermostability of single and double mutants, and measured competitive fitness of single and double mutants.<br>
DOI: 10.6084/m9.figshare.5591227.v1
title: Data repository: Adaptations of an RNA virus to increasing thermal stress (revised)

description: Raw data and R analysis scripts for revised version of paper "Adaptations of an RNA Virus to Increasing Thermal Stress." <br><br>Includes lineage survival during the evolution experiment, measured thermostability of single and double mutants, and measured competitive fitness of single and double mutants.<br>
DOI: 10.6084/m9.figshare.5591107
title: Intraflagellar transport proteins are involved in thrombocyte filopodia formation and secretion

description: Intraflagellar transport (IFT) proteins are vital for the genesis and maintenance of cilia. Our identification of <i>ift122</i> transcripts in zebrafish thrombocytes that lack primary cilia was unexpected. IFT proteins serve transport in cilia, whose narrow dimensions may have necessitated the evolution of IFT from vesicular transport in ancestral eukaryotes. We hypothesized that IFTs might also facilitate transport within the filopodia that form when thrombocytes are activated. To test this possibility, we knocked down <i>ift122</i> expression by injecting antisense Morpholino oligonucleotides (MOs) into zebrafish embryos. Laser-induced arterial thrombosis showed prolonged time to occlusion (TTO) of the vessel, as would be expected with defective thrombocyte function. Acute effects in adult zebrafish were evaluated by Vivo-Morpholino (Vivo-MO) knockdown of <i>ift122</i>. Vivo-MO morphants showed a prolonged time to thrombocyte aggregation (TTA) in the plate tilt assay after thrombocyte activation by the following agonists: ADP, collagen, PAR1 peptide, and epinephrine. A luminescence assay for ATP revealed that ATP secretion by thrombocytes was reduced in collagen-activated blood of Vivo-MO <i>ift122</i> morphants. Moreover, DiI-C18 labeled morphant thrombocytes exposed to collagen showed reductions in filopodia number and length. Analysis of <i>ift</i> mutants, in which cilia defects have been noted, also showed prolongation of TTO in our arterial laser thrombosis assay. Additionally, collagen activation of wild-type thrombocytes led to a concentration of IFT122 both within and at the base of filopodia. Taken together these results, suggest that IFT proteins are involved in both the extension of filopodia and secretion of ATP, which are critical in thrombocyte function.
DOI: 10.6084/m9.figshare.5591107.v1
title: Intraflagellar transport proteins are involved in thrombocyte filopodia formation and secretion

description: Intraflagellar transport (IFT) proteins are vital for the genesis and maintenance of cilia. Our identification of <i>ift122</i> transcripts in zebrafish thrombocytes that lack primary cilia was unexpected. IFT proteins serve transport in cilia, whose narrow dimensions may have necessitated the evolution of IFT from vesicular transport in ancestral eukaryotes. We hypothesized that IFTs might also facilitate transport within the filopodia that form when thrombocytes are activated. To test this possibility, we knocked down <i>ift122</i> expression by injecting antisense Morpholino oligonucleotides (MOs) into zebrafish embryos. Laser-induced arterial thrombosis showed prolonged time to occlusion (TTO) of the vessel, as would be expected with defective thrombocyte function. Acute effects in adult zebrafish were evaluated by Vivo-Morpholino (Vivo-MO) knockdown of <i>ift122</i>. Vivo-MO morphants showed a prolonged time to thrombocyte aggregation (TTA) in the plate tilt assay after thrombocyte activation by the following agonists: ADP, collagen, PAR1 peptide, and epinephrine. A luminescence assay for ATP revealed that ATP secretion by thrombocytes was reduced in collagen-activated blood of Vivo-MO <i>ift122</i> morphants. Moreover, DiI-C18 labeled morphant thrombocytes exposed to collagen showed reductions in filopodia number and length. Analysis of <i>ift</i> mutants, in which cilia defects have been noted, also showed prolongation of TTO in our arterial laser thrombosis assay. Additionally, collagen activation of wild-type thrombocytes led to a concentration of IFT122 both within and at the base of filopodia. Taken together these results, suggest that IFT proteins are involved in both the extension of filopodia and secretion of ATP, which are critical in thrombocyte function.
DOI: 10.6084/m9.figshare.5591062.v1
title: Spice Compact model for bipolar RRAMs based on truncated-cone conductive filaments

description: Spice Compact model for bipolar RRAMs based on truncated-cone conductive filaments.<br><br>Code test in LTspice <br><br>Reference: G. Gonzalez-Cordero, J. B. Roldan, F. Jimenez-Molinos, J. Suñé, S. Long and M. Liu, “A new compact model for bipolar RRAMs based on truncated cone conductive filaments, a Verilog-A approach,” Semicond. Sci. Technol., vol. 31, no. 11, pp. 1–13, 2016. DOI: 10.1088/0268-1242/31/11/115013 , URL: http://iopscience.iop.org/article/10.1088/0268-1242/31/11/115013<br>
DOI: 10.6084/m9.figshare.5590900
title: Heatmap results of the Asan test dataset

description: 1) We created heatmap figures by using a python Grad-CAM. ( https://github.com/gcucurull/CAM-Python )<br>2)<b>/heatmap_fig2</b>The heatmap result of the case of malignant melanoma and basal cell carcinoma. (Fig 2)<b><br></b><b>/heatmap_top1_correct</b>model's Top 1 prediction == correct diagnosis<br><br><b>/heatmap_all</b>all heatmap results for the Asan test dataset (260 images * 12 diagnosis = 3120 images)<br><br>
DOI: 10.6084/m9.figshare.5590396
title: Fossil Bird Track, Mammoth Site of Hot Springs

description: 3D model of small bird track from the Hot Springs mammoth site, originally described by Falkingham et al 2010.<br>Dataset includes 6 photos and photogrammetric model.<br>Photos were not taken with photogrammetry in mind, so scale bar moves between images, and there aren't many.
DOI: 10.6084/m9.figshare.5590024
title: Table S1 BLAST2GO functional annotation against nr database.xlsx

description: BLAST2GO functional annotation of <i>Eisenia fetida</i> nerve cord transcripts against nr database
DOI: 10.6084/m9.figshare.5590900.v2
title: Heatmap results of the Asan test dataset

description: 1) We created heatmap figures by using a python Grad-CAM. ( https://github.com/gcucurull/CAM-Python )<br>2)<b>/heatmap_fig2</b>The heatmap result of the case of malignant melanoma and basal cell carcinoma. (Fig 2)<b><br></b><b>/heatmap_top1_correct</b>model's Top 1 prediction == correct diagnosis<br><br><b>/heatmap_all</b>all heatmap results for the Asan test dataset (260 images * 12 diagnosis = 3120 images)<br><br>
DOI: 10.6084/m9.figshare.5590015
title: Simulation results

description: This is the dataset to accompany the paper.
DOI: 10.6084/m9.figshare.5590003
title: Symphodus_melops.fasta

description: Corkwing wrasse genome assebmled using PacBio SMRT sequencing (x28.8) followed by error correction with paired-end Illumina data (x132.9). The genome assembly consists of 5040 contigs (N50=461,652 bp) and a total size of 614 Mbp
DOI: 10.6084/m9.figshare.5590021
title: Dataset for: DISTRIBUTION AND SOURCE OF REES IN PM2.5 IN XIAMEN, CHINA

description: PM2.5 (particulate matter with diameter ≤ 2.5 μm) is a serious atmospheric pollutant. Composition and source analyses are essential for controlling PM2.5. Rare earth elements (REEs) have received little attention as a component of PM2.5. In the present study, PM2.5 samples were collected in urban and suburban areas in Xiamen, and analyzed for REEs. The concentration range of total REEs (∑REE) is 12.07 to 98.45 mg/kg with the mean of 38.53 mg/kg in urban PM2.5, and 16.44 to 160.62 mg/kg with the mean of 42.94 mg/kg in suburban PM2.5. Light rare earth element (LREE) concentrations are higher in suburban PM2.5, whereas heavy rare earth element (HREE) concentrations are higher in urban PM2.5, implying distinct sources of REEs in urban and suburban PM2.5. δEu-∑REE and La–Ce–Sm 3D-scatter plots suggest that REEs in urban PM2.5 originate from gasoline and diesel vehicle exhaust, whereas those in suburban PM2.5 are mainly influenced by gasoline vehicle exhaust.
DOI: 10.6084/m9.figshare.5590021.v1
title: Dataset for: DISTRIBUTION AND SOURCE OF REES IN PM2.5 IN XIAMEN, CHINA

description: PM2.5 (particulate matter with diameter ≤ 2.5 μm) is a serious atmospheric pollutant. Composition and source analyses are essential for controlling PM2.5. Rare earth elements (REEs) have received little attention as a component of PM2.5. In the present study, PM2.5 samples were collected in urban and suburban areas in Xiamen, and analyzed for REEs. The concentration range of total REEs (∑REE) is 12.07 to 98.45 mg/kg with the mean of 38.53 mg/kg in urban PM2.5, and 16.44 to 160.62 mg/kg with the mean of 42.94 mg/kg in suburban PM2.5. Light rare earth element (LREE) concentrations are higher in suburban PM2.5, whereas heavy rare earth element (HREE) concentrations are higher in urban PM2.5, implying distinct sources of REEs in urban and suburban PM2.5. δEu-∑REE and La–Ce–Sm 3D-scatter plots suggest that REEs in urban PM2.5 originate from gasoline and diesel vehicle exhaust, whereas those in suburban PM2.5 are mainly influenced by gasoline vehicle exhaust.
DOI: 10.6084/m9.figshare.5589997
title: maker.aed-1.0.pfam.eggnog.gff

description: MAKER gene predictions with ortolog predictions.
DOI: 10.6084/m9.figshare.5590015.v2
title: Simulation results

description: This is the dataset to accompany the paper.
DOI: 10.6084/m9.figshare.5590015.v1
title: Simulation results

description: This is the dataset to accompany the paper.
DOI: 10.6084/m9.figshare.5589949
title: Reservoir-Condition Pore-Scale Imaging of Dolomite Reaction with Supercritical CO2 Acidified Brine: Effect of Pore-Structure on Reaction Rate using Velocity Distribution Analysis

description: For further information please contact corresponding author: q.lin11@imperial.ac.uk
DOI: 10.6084/m9.figshare.5589949.v1
title: Reaction Rates in Chemically Heterogeneous Rock: Coupled Impact of Structure and Flow Properties Studied by X‑ray Microtomography

description: For further information please contact corresponding author: q.lin11@imperial.ac.uk
DOI: 10.6084/m9.figshare.5589931
title: Revision of Late Permian tetrapod tracks from the Dolomites (Trentino-Alto Adige, Italy)

description: The Val Gardena Formation of the Dolomites region in northern Italy preserves the most significant assemblage of Late Permian tetrapod footprints in the world. More than 120 years of collecting resulted in about 900 publicly accessible specimens from the study area. This huge amount of data is comprehensively revised in the light of recent advances in the study of Late Palaeozoic – Early Mesozoic tetrapod ichnofossils. According to our analyses, the Val Gardena Sandstone Formation includes tracks that can be assigned to cf. <i>Batrachichnus</i> isp. (temnospondyl amphibian), <i>Capitosauroides</i> isp. (amphibian), <i>Dicynodontipus</i> isp. (cynodont therapsid), <i>Dolomitipes accordii</i> n. igen. n. comb. (dicynodont therapsid), cf. <i>Dromopus</i> isp. (neodiapsid), <i>Pachypes dolomiticus</i> (pareiasaurian parareptile), <i>Paradoxichnium problematicum</i> (archosauromorph neodiapsid), <i>Procolophonichnium tirolensis</i> n. comb. (procolophonoid parareptile), cf. <i>Protochirotherium</i> isp. (archosauriform neodiapsid) and <i>Rhynchosauroides pallinii</i> (neodiapsid). The ichnoassociation is dominated by tracks of neodiapsid and parareptilian tetrapods, whereas synapsid and anamniote tracks are rather minor components. It includes 10 out of 12 tetrapod ichnogenera known from Lopingian deposits and thus it constitutes a reference for the <i>Paradoxichnium</i> biochron. It shows striking similarities with other low-latitude non-aeolian contemporaneous ichnoassociations of Europe and North Africa, differences may be linked to the palaeoenvironment. Moreover, it shows a clear Triassic affinity. The new ichnogenus <i>Dolomitipes</i> was registered in Zoobank.org. urn:lsid:zoobank.org:act:5B4D871C-D16A-4E93-8211-CEE08019BA60
DOI: 10.6084/m9.figshare.5589931.v1
title: Revision of Late Permian tetrapod tracks from the Dolomites (Trentino-Alto Adige, Italy)

description: The Val Gardena Formation of the Dolomites region in northern Italy preserves the most significant assemblage of Late Permian tetrapod footprints in the world. More than 120 years of collecting resulted in about 900 publicly accessible specimens from the study area. This huge amount of data is comprehensively revised in the light of recent advances in the study of Late Palaeozoic – Early Mesozoic tetrapod ichnofossils. According to our analyses, the Val Gardena Sandstone Formation includes tracks that can be assigned to cf. <i>Batrachichnus</i> isp. (temnospondyl amphibian), <i>Capitosauroides</i> isp. (amphibian), <i>Dicynodontipus</i> isp. (cynodont therapsid), <i>Dolomitipes accordii</i> n. igen. n. comb. (dicynodont therapsid), cf. <i>Dromopus</i> isp. (neodiapsid), <i>Pachypes dolomiticus</i> (pareiasaurian parareptile), <i>Paradoxichnium problematicum</i> (archosauromorph neodiapsid), <i>Procolophonichnium tirolensis</i> n. comb. (procolophonoid parareptile), cf. <i>Protochirotherium</i> isp. (archosauriform neodiapsid) and <i>Rhynchosauroides pallinii</i> (neodiapsid). The ichnoassociation is dominated by tracks of neodiapsid and parareptilian tetrapods, whereas synapsid and anamniote tracks are rather minor components. It includes 10 out of 12 tetrapod ichnogenera known from Lopingian deposits and thus it constitutes a reference for the <i>Paradoxichnium</i> biochron. It shows striking similarities with other low-latitude non-aeolian contemporaneous ichnoassociations of Europe and North Africa, differences may be linked to the palaeoenvironment. Moreover, it shows a clear Triassic affinity. The new ichnogenus <i>Dolomitipes</i> was registered in Zoobank.org. urn:lsid:zoobank.org:act:5B4D871C-D16A-4E93-8211-CEE08019BA60
DOI: 10.6084/m9.figshare.5589925
title: Characterization of a novel VIIl sub-genotype of Newcastle disease virus circulating in Iran

description: Newcastle disease is an economically important and highly contagious disease affecting wild and domestic avian species. Despite extensive vaccination efforts within the poultry industry, Newcastle disease virus (NDV) outbreaks causing significant economic losses still occur. Rural chickens may act as a potential reservoir of NDVs for commercial poultry due to poor biosecurity and inadequate vaccination. The aim of this study was to investigate the phylogenetic relationship and molecular characterization of eight NDVs isolated from backyard poultry in Iran during 2011–2013. The complete coding sequence of fusion (F) and haemagglutinin-neuraminidase (HN) genes of eight NDVs were determined and compared with other published NDVs. Based on inter-population distances and phylogenetic topology between available NDV categories, Iranian isolates formed a novel VIIl sub-genotype distinct from previous groups designated in genotype VII. Furthermore, both F and HN genes of the Iranian isolates shared high nucleotide sequence similarity with viruses isolated in China. All viruses analysed contained a polybasic cleavage site motif (<sup>111</sup>G/RRRQKR↓F<sup>117</sup>), indicating that all isolates could be categorized as a virulent pathotype. No mutation was observed in the neutralizing epitopes of the F protein. Analysis of amino acids associated with neutralizing antigenic sites within the HN protein revealed that all isolates exhibited a unique amino acid (Q) at position 347. These results emphasize the need for strengthening the biosecurity measures implemented on village flocks and practicing a mandatory vaccination programme for local poultry. Moreover, continuous monitoring of NDVs in different species of birds can help to gain more knowledge about the evolution of this virus and prevent future panzootics.
DOI: 10.6084/m9.figshare.5589925.v1
title: Characterization of a novel VIIl sub-genotype of Newcastle disease virus circulating in Iran

description: Newcastle disease is an economically important and highly contagious disease affecting wild and domestic avian species. Despite extensive vaccination efforts within the poultry industry, Newcastle disease virus (NDV) outbreaks causing significant economic losses still occur. Rural chickens may act as a potential reservoir of NDVs for commercial poultry due to poor biosecurity and inadequate vaccination. The aim of this study was to investigate the phylogenetic relationship and molecular characterization of eight NDVs isolated from backyard poultry in Iran during 2011–2013. The complete coding sequence of fusion (F) and haemagglutinin-neuraminidase (HN) genes of eight NDVs were determined and compared with other published NDVs. Based on inter-population distances and phylogenetic topology between available NDV categories, Iranian isolates formed a novel VIIl sub-genotype distinct from previous groups designated in genotype VII. Furthermore, both F and HN genes of the Iranian isolates shared high nucleotide sequence similarity with viruses isolated in China. All viruses analysed contained a polybasic cleavage site motif (<sup>111</sup>G/RRRQKR↓F<sup>117</sup>), indicating that all isolates could be categorized as a virulent pathotype. No mutation was observed in the neutralizing epitopes of the F protein. Analysis of amino acids associated with neutralizing antigenic sites within the HN protein revealed that all isolates exhibited a unique amino acid (Q) at position 347. These results emphasize the need for strengthening the biosecurity measures implemented on village flocks and practicing a mandatory vaccination programme for local poultry. Moreover, continuous monitoring of NDVs in different species of birds can help to gain more knowledge about the evolution of this virus and prevent future panzootics.
DOI: 10.6084/m9.figshare.5589916
title: Does more favourable handling of the cerebrospinal fluid increase the diagnostic sensitivity of <i>Borrelia burgdorferi</i> sensu lato-specific PCR in Lyme neuroborreliosis?

description: <b>Background:</b> Tests for direct detection of <i>Borrelia burgdorferi</i> sensu lato <i>(Bb)</i> in Lyme neuroborreliosis (LNB) are needed. Detection of <i>Bb</i> DNA using PCR is promising, but clinical utility is hampered by low diagnostic sensitivity. We aimed to examine whether diagnostic sensitivity can be improved by the use of larger cerebrospinal fluid (CSF) volumes and faster handling of samples. <b>Methods:</b> Patients who underwent CSF examination for LNB were included. We collected two millilitres of CSF for PCR analysis, extracted DNA from the pellets within 24 h and analysed the eluate by two real-time PCR protocols (16S rRNA and OspA). Patients who fulfilled diagnostic criteria for LNB were classified as LNB cases and the rest as controls. <b>Results:</b><i>Bb</i> DNA in CSF was detected by PCR in seven of 28 adults with LNB. Two were <i>Bb</i> antibody negative. No <i>Bb</i> DNA was detected in CSF from 137 controls. Diagnostic sensitivity was 25% and specificity 100%. There was a non-significant trend towards larger CSF sample volume, faster handling of the sample, shorter duration of symptoms, and higher CSF cell count in the PCR-positive cases. <b>Conclusion:</b> We did not find that optimized handling of CSF increased diagnostic sensitivity of PCR in adults with LNB. However, our case series is small and we hypothesize that the importance of these factors will be clarified in further studies with larger case series and altered study design. PCR for diagnosis of LNB may be useful in cases without <i>Bb</i> antibodies due to short duration of symptoms.