cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7058900
title: Modelling the brain response to arbitrary visual stimulation patterns for a flexible high-speed Brain-Computer Interface

description: <b>1. General description</b>Data was recorded using BCI2000 with g.USBamp (g.tec, Austria) EEG amplifier. 32 electrodes were used. Sampling rate was set to 600 Hz and data was bandpass filtered by the amplifier between 0.1 Hz and 60 Hz using a Chebyshev filter of order 8 and notch-filtered at 50 Hz. Data was stored as MATLAB mat-File, whereas each file is the data of one participant. <br><b>2. Experimental description</b>The experiment was split in three parts: spatial filter runs, training runs, testing runs. The stimulation patterns were presented with 60 bits per second and each run consits of 32 trials. During the testing runs, the runs were alternated between using random stimulation patterns and optimized stimulation patterns. As all trials were concatenated, this has to be taken into account. Furthermore, the participants had to perform the trials of each run in lexicographic order.<b><br></b><b>3. Variable description</b>Each file VP*.mat contains the following variables:- spfilter_data_x contains the raw EEG data of the spatial filter runs split by each m-sequence cyle. As there were 3 runs with 32 trials and 3 m-sequence cycles each, there are 3*32*3=192 m-sequence cycles in total. Since the m-sequence was shifted by 2 bits for each succesive target, the trials were lag-fixed previously. As the m-sequence consists of 63 bits, the data consists of 63/60*600=630 samples. Therefore the matrix has the following dimension: #m-sequences X #channels X #samples- spfilter_data_y contains the stimulation pattern for each m-sequenze cycle upsampled to be synchronized with the EEG data. The matrix has the following dimension: #m-sequences X #samples- train_data_x_*s contains the raw EEG data of the training runs split by trials. As different trial durations were used during training, * denotes the duration in seconds. The matrix has the following dimension: #trials X #channels X #samples- train_data_y_*s contains the stimulation pattern for each target during the training runs, upsampled to be synchronized with the EEG data. As the layout consits of 32 targets, the matrix has the following dimension: #trials X #targets X #samples- test_data_x contains the raw EEG data of the training runs split by trials. The trial duration was 2 seconds, therefore, there are 1200 samples per trial. The matrix has the following dimension: #trials X #channels X #samples- test_data_y contains the stimulation pattern for each target during the testing runs, upsampled to be synchronized with the EEG data. As the layout consits of 32 targets, the matrix has the following dimension: #trials X #targets X #samples There is an additional file "targetdelys.mat" containing a variable with the number of samples for each target (in lexicographic order) used to correct the raster latency.
DOI: 10.6084/m9.figshare.7058618
title: Contrast-enhanced CTscans with manual organ segmentation

description: Contrast-enhanced CT scans with manual organ segmentation
DOI: 10.6084/m9.figshare.7058600
title: Raw data files of anatomical parameters in four porcine biomembranes

description: 4 porcine biomembranes were investigatedPL = plica venae cavaeCT = centrum tendineumPE = pericardSIS = small intestinal submucosa<br>in terms of:1. Membrane thickness (native state of the membrane)2. D-periodicity, a collagen-specific feature (using scanning electron microscopy on fixed membranes)3. Fibril diameter of collagen fibers (using Scanning electron microscopy) 4. Volumetric Index (using multiphoton microscopy on native membranes) indicating volumes (v) of the collagen and elastin: V<sub>Elastin</sub>-V<sub>Collagen</sub>/V<sub>Elastin</sub>+V<sub>Collagen</sub>This calculation yielded indexes from +1 (100% elastin) to -1 (100% collagen).<br>
DOI: 10.6084/m9.figshare.7058615
title: Native CTscans with manual organ segmentation

description: Native CT scans with manual organ segmentation
DOI: 10.6084/m9.figshare.7058600.v1
title: Raw data files of anatomical parameters in four porcine biomembranes

description: 4 porcine biomembranes were investigatedPL = plica venae cavaeCT = centrum tendineumPE = pericardSIS = small intestinal submucosa<br>in terms of:1. Membrane thickness (native state of the membrane)2. D-periodicity, a collagen-specific feature (using scanning electron microscopy on fixed membranes)3. Fibril diameter of collagen fibers (using Scanning electron microscopy) 4. Volumetric Index (using multiphoton microscopy on native membranes) indicating volumes (v) of the collagen and elastin: V<sub>Elastin</sub>-V<sub>Collagen</sub>/V<sub>Elastin</sub>+V<sub>Collagen</sub>This calculation yielded indexes from +1 (100% elastin) to -1 (100% collagen).<br>
DOI: 10.6084/m9.figshare.7058543
title: A pathogen in plain sight: disease-causing genotypes of the commensal skin bacterium Staphylococcus epidermidis

description: Assembled microbial genomes associated with the paper published in Nature Communications (doi:xxx). <br><br>
DOI: 10.6084/m9.figshare.7058144
title: mainly patients characteristic

description: Patient charcteristics for resarch
DOI: 10.6084/m9.figshare.7058144.v1
title: mainly patients characteristic

description: Patient charcteristics for resarch
DOI: 10.6084/m9.figshare.7058138
title: EZR data

description: Fourteen scored features along with the histopathological diagnosis, UIP versus NSIP, were compared between IIP and CTD-IP.
DOI: 10.6084/m9.figshare.7058114
title: scoring data

description: we reviewed 205 video-assisted thoracoscopy (VATS) biopsies diagnosed by MDD at a single institution between 2008 and 2013 .We selected 105 consecutive cases of IIP (79 usual interstitial pneumonia and 26 nonspecific interstitial pneumonia) .Histological parameters were evaluated independently by two pathologists for derivation group and graded into 0 to 3.<br><br>
DOI: 10.6084/m9.figshare.7058138.v1
title: EZR data

description: Fourteen scored features along with the histopathological diagnosis, UIP versus NSIP, were compared between IIP and CTD-IP.
DOI: 10.6084/m9.figshare.7058102
title: Argon isotopes of quartz samples by crushing. from Ar–Ar dating for hydrothermal quartz from the 2.4 Ga Ongeluk Formation, South Africa: implications for seafloor hydrothermal circulation

description: Raw data sets of argon isotopes.
DOI: 10.6084/m9.figshare.7058102.v1
title: Argon isotopes of quartz samples by crushing. from Ar–Ar dating for hydrothermal quartz from the 2.4 Ga Ongeluk Formation, South Africa: implications for seafloor hydrothermal circulation

description: Raw data sets of argon isotopes.
DOI: 10.6084/m9.figshare.7058084
title: Supplementary Material for: Minimal Reporting Standards for Active Middle Ear Hearing Implants

description: There is currently no standardized method for reporting audiological, surgical and subjective outcome measures in clinical trials with active middle ear implants (AMEIs). It is often difficult to compare studies due to data incompatibility and to perform meta-analyses across different centres is almost impossible. A committee of ENT and audiological experts from Germany, Austria and Switzerland decided to address this issue by developing new minimal standards for reporting the outcomes of AMEI clinical trials. The consensus presented here aims to provide a recommendation to enable better inter-study comparability.
DOI: 10.6084/m9.figshare.7058096
title: Supplementary Material for: Discovery and Characterization of a High-Affinity Small Peptide Ligand, H1, Targeting FGFR2IIIc for Skin Wound Healing

description: <b><i>Background/Aims:</i></b> How to aid recovery from severe skin injuries, such as burns, chronic or radiation ulcers, and trauma, is a critical clinical problem. Current treatment methods remain limited, and the discovery of ideal wound-healing therapeutics has been a focus of research. Functional recombinant proteins such as basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) have been developed for skin repair, however, some disadvantages in their use remain. This study reports the discovery of a novel small peptide targeting fibroblast growth factor receptor 2 IIIc (FGFR2IIIc) as a potential candidate for skin wound healing. <b><i>Methods:</i></b> A phage-displayed peptide library was used for biopanning FGFR2IIIc-targeting small peptides. The selected small peptides binding to FGFR2IIIc were qualitatively evaluated by an enzyme-linked immunosorbent assay. Their biological function was detected by a cell proliferation assay. Among them, an optimized small peptide named H1 was selected for further study. The affinity of the H1 peptide and FGFR2IIIc was determined by an isothermal titration calorimetry device. The ability of theH1 peptide to promote skin wound repair was investigated using an endothelial cell tube formation assay and wound healing scratch assay <i>in vitro</i>. Subsequently, the H1 peptide was assessed using a rat skin full-thickness wound model and chorioallantoic membrane (CAM) assays <i>in vivo</i>. To explore its molecular mechanisms, RNA-Seq, quantitative real-time PCR, and western blot assays were performed. Computer molecular simulations were also conducted to analyze the binding model. <b><i>Results:</i></b> We identified a novel FGFR2IIIc-targeting small peptide, called H1, with 7 amino acid residues using phage display. H1 had high binding affinity with FGFR2IIIc. The H1 peptide promoted the proliferation and motility of fibroblasts and vascular endothelial cells <i>in vitro</i>. In addition, the H1 peptide enhanced angiogenesis in the chick chorioallantoic membrane and accelerated wound healing in a rat full-thickness wound model <i>in vivo</i>. The H1 peptide activated both the PI3K-AKT and MAPK-ERK1/2 pathways and simultaneously increased the secretion of vascular endothelial growth factor. Computer analysis demonstrated that the model of H1 peptide binding to FGFR2IIIc was similar to that of FGF2 and FGFR2IIIc. <b><i>Conclusion:</i></b> The H1 peptide has a high affinity for FGFR2IIIc and shows potential as a wound healing agent. As a substitute for bFGF, it could be developed into a novel therapeutic candidate for skin wound repair in the future.
DOI: 10.6084/m9.figshare.7058084.v1
title: Supplementary Material for: Minimal Reporting Standards for Active Middle Ear Hearing Implants

description: There is currently no standardized method for reporting audiological, surgical and subjective outcome measures in clinical trials with active middle ear implants (AMEIs). It is often difficult to compare studies due to data incompatibility and to perform meta-analyses across different centres is almost impossible. A committee of ENT and audiological experts from Germany, Austria and Switzerland decided to address this issue by developing new minimal standards for reporting the outcomes of AMEI clinical trials. The consensus presented here aims to provide a recommendation to enable better inter-study comparability.
DOI: 10.6084/m9.figshare.7058096.v1
title: Supplementary Material for: Discovery and Characterization of a High-Affinity Small Peptide Ligand, H1, Targeting FGFR2IIIc for Skin Wound Healing

description: <b><i>Background/Aims:</i></b> How to aid recovery from severe skin injuries, such as burns, chronic or radiation ulcers, and trauma, is a critical clinical problem. Current treatment methods remain limited, and the discovery of ideal wound-healing therapeutics has been a focus of research. Functional recombinant proteins such as basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) have been developed for skin repair, however, some disadvantages in their use remain. This study reports the discovery of a novel small peptide targeting fibroblast growth factor receptor 2 IIIc (FGFR2IIIc) as a potential candidate for skin wound healing. <b><i>Methods:</i></b> A phage-displayed peptide library was used for biopanning FGFR2IIIc-targeting small peptides. The selected small peptides binding to FGFR2IIIc were qualitatively evaluated by an enzyme-linked immunosorbent assay. Their biological function was detected by a cell proliferation assay. Among them, an optimized small peptide named H1 was selected for further study. The affinity of the H1 peptide and FGFR2IIIc was determined by an isothermal titration calorimetry device. The ability of theH1 peptide to promote skin wound repair was investigated using an endothelial cell tube formation assay and wound healing scratch assay <i>in vitro</i>. Subsequently, the H1 peptide was assessed using a rat skin full-thickness wound model and chorioallantoic membrane (CAM) assays <i>in vivo</i>. To explore its molecular mechanisms, RNA-Seq, quantitative real-time PCR, and western blot assays were performed. Computer molecular simulations were also conducted to analyze the binding model. <b><i>Results:</i></b> We identified a novel FGFR2IIIc-targeting small peptide, called H1, with 7 amino acid residues using phage display. H1 had high binding affinity with FGFR2IIIc. The H1 peptide promoted the proliferation and motility of fibroblasts and vascular endothelial cells <i>in vitro</i>. In addition, the H1 peptide enhanced angiogenesis in the chick chorioallantoic membrane and accelerated wound healing in a rat full-thickness wound model <i>in vivo</i>. The H1 peptide activated both the PI3K-AKT and MAPK-ERK1/2 pathways and simultaneously increased the secretion of vascular endothelial growth factor. Computer analysis demonstrated that the model of H1 peptide binding to FGFR2IIIc was similar to that of FGF2 and FGFR2IIIc. <b><i>Conclusion:</i></b> The H1 peptide has a high affinity for FGFR2IIIc and shows potential as a wound healing agent. As a substitute for bFGF, it could be developed into a novel therapeutic candidate for skin wound repair in the future.
DOI: 10.6084/m9.figshare.7058048
title: Temporal changes in prey composition and biomass delivery to African Crowned Eagle nestlings in urban areas of KwaZulu-Natal, South Africa

description: Globally urban areas are expanding rapidly and this usually has negative effects on biodiversity. Despite this, some species manage to persist in urban areas, as is the case with African Crowned Eagles <i>Stephanoaetus coronatus</i> in KwaZulu-Natal, South Africa. As relatively little is known about African Crowned Eagle nestling diet, especially about how it changes with nestling age, we investigated this with nest camera-traps. We analysed temporal changes in prey composition and biomass delivery during the nestling stage. We also recorded which adults provisioned and attended the nest. The main prey fed to nestlings were Rock Hyrax <i>Procavia capensis</i> and Hadeda Ibis <i>Bostrychia hagedash</i>. Adult males did most of the food provisioning, especially at the start of the nestling period. We found a decrease in total prey number and biomass with nestling age. This may be caused by changing requirements of nestlings. Furthermore, delivering fewer prey at later nestling stages may be a facilitating mechanism to enhance fledging of the nestling. Although the total number of prey brought to the nest decreased, we found an increase in numbers of Vervet Monkey <i>Chlorocebus pygerythrus</i> in the diet with nestling age. This indicated an increase in larger prey being delivered to the nests as the nestling aged. We suggest that this could be caused by increased participation in hunting by the larger female as her nest attendance time decreased as the nestling aged. We conclude with emphasising the importance of protecting the Durban Metropolitan Open Space System (D’MOSS) zones for the persistence of this Near Threatened raptor species, and populations of its prey in urban areas for its breeding success.
DOI: 10.6084/m9.figshare.7058045
title: Urban bird trends in a rapidly growing tropical city

description: Long-term studies of urban birds are relatively scarce, especially in Africa. We analysed trends in species richness and bird species occurrence over a 32-year period in Kampala, Uganda, in order to assess changes in the bird community in a period that has shown rapid expansion of the city's human population. Given that species may respond to urbanisation according to their diet, we also analysed bird community trends of species groups defined according to predominant diet. There was an overall decline in species richness that was largely driven by declines in insectivores and granivores. General declines were evident also when the trends in the most common individual species in these two groups were considered. The occurrence of the commonest predator and scavenger species tended to increase over the period considered. Insectivorous species are likely to be especially affected by increasing urbanisation due to air pollution. Predators and scavengers are likely to have benefitted from the inability of municipal waste management to keep pace with growth in the human population, hence providing more potential food resources. Both insectivores and predators/scavengers are therefore good candidates for the development of urban indicators.
DOI: 10.6084/m9.figshare.7058048.v1
title: Temporal changes in prey composition and biomass delivery to African Crowned Eagle nestlings in urban areas of KwaZulu-Natal, South Africa

description: Globally urban areas are expanding rapidly and this usually has negative effects on biodiversity. Despite this, some species manage to persist in urban areas, as is the case with African Crowned Eagles <i>Stephanoaetus coronatus</i> in KwaZulu-Natal, South Africa. As relatively little is known about African Crowned Eagle nestling diet, especially about how it changes with nestling age, we investigated this with nest camera-traps. We analysed temporal changes in prey composition and biomass delivery during the nestling stage. We also recorded which adults provisioned and attended the nest. The main prey fed to nestlings were Rock Hyrax <i>Procavia capensis</i> and Hadeda Ibis <i>Bostrychia hagedash</i>. Adult males did most of the food provisioning, especially at the start of the nestling period. We found a decrease in total prey number and biomass with nestling age. This may be caused by changing requirements of nestlings. Furthermore, delivering fewer prey at later nestling stages may be a facilitating mechanism to enhance fledging of the nestling. Although the total number of prey brought to the nest decreased, we found an increase in numbers of Vervet Monkey <i>Chlorocebus pygerythrus</i> in the diet with nestling age. This indicated an increase in larger prey being delivered to the nests as the nestling aged. We suggest that this could be caused by increased participation in hunting by the larger female as her nest attendance time decreased as the nestling aged. We conclude with emphasising the importance of protecting the Durban Metropolitan Open Space System (D’MOSS) zones for the persistence of this Near Threatened raptor species, and populations of its prey in urban areas for its breeding success.
DOI: 10.6084/m9.figshare.7058045.v1
title: Urban bird trends in a rapidly growing tropical city

description: Long-term studies of urban birds are relatively scarce, especially in Africa. We analysed trends in species richness and bird species occurrence over a 32-year period in Kampala, Uganda, in order to assess changes in the bird community in a period that has shown rapid expansion of the city's human population. Given that species may respond to urbanisation according to their diet, we also analysed bird community trends of species groups defined according to predominant diet. There was an overall decline in species richness that was largely driven by declines in insectivores and granivores. General declines were evident also when the trends in the most common individual species in these two groups were considered. The occurrence of the commonest predator and scavenger species tended to increase over the period considered. Insectivorous species are likely to be especially affected by increasing urbanisation due to air pollution. Predators and scavengers are likely to have benefitted from the inability of municipal waste management to keep pace with growth in the human population, hence providing more potential food resources. Both insectivores and predators/scavengers are therefore good candidates for the development of urban indicators.
DOI: 10.6084/m9.figshare.7058030
title: Molecular dynamics trajectory of I-FABP for testing and benchmarking solvent dynamics analysis

description: The trajectory is a short MD run of I-FABP (intestinal fatty acid binding protein) in water.<br><br>It was simulated in CHARMM for 500 ps with a 2 fs timestep. Frames were saved every 1 ps and the trajectory was RMSD-fitted to the protein.<br><br>There are 500 frames in the trajectory.<br>It is used as a test case for the hop package https://github.com/Becksteinlab/hop.<br>
DOI: 10.17028/rd.lboro.7057994
title: An investigation of the effect of acute pain on logical reasoning: Data and analysis scripts

description: Data and analysis scripts for the three experiments reported in the paper "An investigation of the effect of experimental pain on logical reasoning".
DOI: 10.17028/rd.lboro.7057994.v1
title: An investigation of the effect of acute pain on logical reasoning: Data and analysis scripts

description: Data and analysis scripts for the three experiments reported in the paper "An investigation of the effect of experimental pain on logical reasoning".
DOI: 10.6084/m9.figshare.7057985
title: Gd@C74(CF3)-2 from Isolation and structure determination of missing fullerenes Gd@C74(CF3)<i>n</i> through <i>in situ</i> trifluoromethylation

description: xyz structure file of DFT optimised Gd@C74(CF3) molecule, first regioisomer / second regioisomer
DOI: 10.6084/m9.figshare.7057985.v1
title: Gd@C74(CF3)-2 from Isolation and structure determination of missing fullerenes Gd@C74(CF3)<i>n</i> through <i>in situ</i> trifluoromethylation

description: xyz structure file of DFT optimised Gd@C74(CF3) molecule, first regioisomer / second regioisomer
DOI: 10.6084/m9.figshare.7057982
title: Gd@C74(CF3)-1 from Isolation and structure determination of missing fullerenes Gd@C74(CF3)<i>n</i> through <i>in situ</i> trifluoromethylation

description: xyz structure file of DFT optimised Gd@C74(CF3) molecule, first regioisomer / second regioisomer
DOI: 10.6084/m9.figshare.7057982.v1
title: Gd@C74(CF3)-1 from Isolation and structure determination of missing fullerenes Gd@C74(CF3)<i>n</i> through <i>in situ</i> trifluoromethylation

description: xyz structure file of DFT optimised Gd@C74(CF3) molecule, first regioisomer / second regioisomer
DOI: 10.6084/m9.figshare.7057976
title: C74

description: xyz structure file of DFT optimised C74 molecule
DOI: 10.6084/m9.figshare.7057973
title: Gd@C74

description: xyz structure file of DFT optimised Gd@C74 molecule
DOI: 10.6084/m9.figshare.7057976.v1
title: C74

description: xyz structure file of DFT optimised C74 molecule
DOI: 10.6084/m9.figshare.7057970
title: Gd@C74(CF3)3 from Isolation and structure determination of missing fullerenes Gd@C74(CF3)<i>n</i> through <i>in situ</i> trifluoromethylation

description: xyz structure file of DFT optimised Gd@C74(CF3)3 molecule
DOI: 10.6084/m9.figshare.7057973.v1
title: Gd@C74

description: xyz structure file of DFT optimised Gd@C74 molecule
DOI: 10.6084/m9.figshare.7057970.v1
title: Gd@C74(CF3)3 from Isolation and structure determination of missing fullerenes Gd@C74(CF3)<i>n</i> through <i>in situ</i> trifluoromethylation

description: xyz structure file of DFT optimised Gd@C74(CF3)3 molecule
DOI: 10.6084/m9.figshare.7057961
title: Entropy data

description: Entropy data
DOI: 10.6084/m9.figshare.7057961.v3
title: Entropy data

description: Entropy data
DOI: 10.6084/m9.figshare.7057961.v2
title: Entropy data

description: Entropy data