cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4239509
title: Supplementary Material for: Bubble CPAP Support after Discontinuation of Mechanical Ventilation Protects Rat Lungs with Ventilator-Induced Lung Injury

description: <b><i>Background:</i></b> Bubble continuous positive airway pressure (BCPAP) has been used in neonates with respiratory distress for decades, but its lung-protective effect and underlying mechanism has not been investigated. <b><i>Objectives:</i></b> To test the hypothesis that BCPAP use after extubation decreases lung injury and that alterations to lung nitric oxide synthase (NOS) 3 expression may be one of the underlying mechanisms. <b><i>Methods:</i></b> We compared gas exchange, lung injury severity, and lung NOS expression among rats with ventilator-induced lung injury (VILI) treated with either BCPAP or spontaneous breathing. After high tidal volume ventilation for 30 min, the rats were randomly divided to three groups: a control group underwent spontaneous breathing (n = 7), and two BCPAP groups were treated with the bubble technique with either a 2.5-mm-diameter (n = 7) or a 5.5-mm-diameter (n = 7) expiratory limb for 2 h. <b><i>Results:</i></b> The bubble technique (2.5 and 5.5 mm diameter combined) resulted in a significantly higher PaO<sub>2</sub>, decreased alveolar protein levels (1.01 vs. 1.43 mg/kg, p &lt; 0.05), a lower lung injury score (3.87 vs. 4.86, p &lt; 0.05), and decreased NOS3 expression (1.99 vs. 3.32, p &lt; 0.05) compared to spontaneous breathing in the control group. BCPAP with a 2.5-mm-diameter and with a 5.5-mm-diameter expiratory limb was not different with regard to gas exchange, alveolar protein levels, and lung injury scores, but there was a trend for lower NOS3 expression in the 5.5-mm group (1.41 vs. 2.56, p = 0.052). <b><i>Conclusions:</i></b> BCPAP decreases lung injury in rats with VILI after stopping mechanical ventilation. Attenuation of lung NOS3 expression may be one of the underlying mechanisms.
DOI: 10.6084/m9.figshare.4239500
title: Supplementary Material for: Cotton Wool Spots after Anti-Vascular Endothelial Growth Factor Therapy for Macular Edema Associated with Central Retinal Vein Occlusion

description: <b><i>Purpose:</i></b> To report a case series, whereby we encountered a transient increase in retinal cotton wool spots (CWS) following anti-vascular endothelial growth factor (anti-VEGF) therapy for the treatment of macular edema secondary to central retinal vein occlusion (CRVO). <b><i>Methods:</i></b> Eighteen eyes were treated with intravitreal aflibercept (IVA), and 5 were treated with intravitreal ranibizumab (IVR). Fundus photographs obtained 1 month after initial IVA or IVR injections were retrospectively evaluated for the presence of CWS. <b><i>Results:</i></b> Twenty-one (91.3%) patients had the following systemic diseases: hypertension, diabetes mellitus without retinopathy, dyslipidemia, or chronic renal failure requiring dialysis. One month after treatment, reduced macular edema was observed in 21 (91.3%) eyes. Initial injections facilitated complete resolution in 14 eyes, and CWS gradually became fainter with additional injections. <b><i>Conclusion:</i></b> Some eyes with CRVO-related macular edema can show a transient increase in CWS after initial anti-VEGF therapy; however, macular edema, retinal hemorrhage, and visual acuity were improved in almost every case.
DOI: 10.15131/shef.data.4239497
title: RICON 2016 - Introduction and Programme

description: <b>Research & Innovation Supporters' Conference – 14 June 2016. The Octagon Centre, University of Sheffield.</b><br>On 14 June 2016 we ran a one-day conference in the Octagon Centre that was designed specifically for professionals who support research and/or innovation activities – for professionals based in academic departments, in faculties, in Professional Services and in research centres and institutes.<br><br>Documents includedConference LogoHistory of the Research and Innovation Supporters' ConferenceConference ProgrammeKeynote speakers at the R&I Supporters' Conference 2016Exhibitors ListGuidelines for submission<br><br>The full programme of events can also be found here.<br>See also the RICOM (Research and Innovation Community) website and Google community, RICOMmunity.<br><br>
DOI: 10.15131/shef.data.4239497.v1
title: RICON 2016 - Introduction and Programme

description: <b>Research & Innovation Supporters' Conference – 14 June 2016. The Octagon Centre, University of Sheffield.</b><br>On 14 June 2016 we ran a one-day conference in the Octagon Centre that was designed specifically for professionals who support research and/or innovation activities – for professionals based in academic departments, in faculties, in Professional Services and in research centres and institutes.<br><br>Documents includedConference LogoHistory of the Research and Innovation Supporters' ConferenceConference ProgrammeKeynote speakers at the R&I Supporters' Conference 2016Exhibitors ListGuidelines for submission<br><br>The full programme of events can also be found here.<br>See also the RICOM (Research and Innovation Community) website and Google community, RICOMmunity.<br><br>
DOI: 10.6084/m9.figshare.4239467
title: Supplementary Material for: Genome-Wide STAT3 Binding Analysis after Histone Deacetylase Inhibition Reveals Novel Target Genes in Dendritic Cells

description: STAT3 is a master transcriptional regulator that plays an important role in the induction of both immune activation and immune tolerance in dendritic cells (DCs). The transcriptional targets of STAT3 in promoting DC activation are becoming increasingly understood; however, the mechanisms underpinning its role in causing DC suppression remain largely unknown. To determine the functional gene targets of STAT3, we compared the genome-wide binding of STAT3 using ChIP sequencing coupled with gene expression microarrays to determine STAT3-dependent gene regulation in DCs after histone deacetylase (HDAC) inhibition. HDAC inhibition boosted the ability of STAT3 to bind to distinct DNA targets and regulate gene expression. Among the top 500 STAT3 binding sites, the frequency of canonical motifs was significantly higher than that of noncanonical motifs. Functional analysis revealed that after treatment with an HDAC inhibitor, the upregulated STAT3 target genes were those that were primarily the negative regulators of proinflammatory cytokines and those in the IL-10 signaling pathway. The downregulated STAT3-dependent targets were those involved in immune effector processes and antigen processing/presentation. The expression and functional relevance of these genes were validated. Specifically, functional studies confirmed that the upregulation of IL-10Ra by STAT3 contributed to the suppressive function of DCs following HDAC inhibition.
DOI: 10.6084/m9.figshare.4239455
title: Field data from Eliminating incident subtraction in diffraction tomography

description: Incident and scattered field data for all cases in paper
DOI: 10.6084/m9.figshare.4239455.v1
title: Field data from Eliminating incident subtraction in diffraction tomography

description: Incident and scattered field data for all cases in paper
DOI: 10.6084/m9.figshare.4239452
title: The aDoctor Project

description: Code smells are symptoms of poor design solutions applied by programmers during the development of software systems. While the research community devoted a lot of effort in studying and devising approaches for detecting the traditional code smells defined by Fowler, a little knowledge and support is available for an emerging category of Mobile app code smells. Specifically, Reimann et al. recently proposed a new catalogue of Android-specific code smells that may threat the maintainability and the efficiency of Android applications. Existing tools working in the context of Mobile apps provide limited support and, more importantly, are not available for developers interested in monitoring the quality of their apps. To overcome these limitations, we propose a fully automated tool, coined as aDoctor , able to identify 15 Android-specific code smells from the catalogue by Reimann et al. An empirical study conducted on the source code of 18 Android applications reveal that the proposed tool is highly performant and reaches, on average, 98% of precision and 98% of recall. We made aDoctor publicly available.
DOI: 10.6084/m9.figshare.4239449
title: Villanueva-Cañas_etal_transcript_asemblies.tar.gz

description: Compressed file (.tar.gz) that contains the sequences of transcripts assembled from RNA-Seq data for different mammalian species. There are two types of files, novel.fa refers to transcripts that did not map to the gene annotations and annotated.fa to transcripts of already annotated genes. The data has been used in the publication Villanueva-Cañas et al. The uncompressed files occupy about 15 Gb.<br><br>
DOI: 10.6084/m9.figshare.4239449.v1
title: Villanueva-Cañas_etal_transcript_asemblies.tar.gz

description: Compressed file (.tar.gz) that contains the sequences of transcripts assembled from RNA-Seq data for different mammalian species. There are two types of files, novel.fa refers to transcripts that did not map to the gene annotations and annotated.fa to transcripts of already annotated genes. The data has been used in the publication Villanueva-Cañas et al. The uncompressed files occupy about 15 Gb.<br><br>
DOI: 10.6084/m9.figshare.4239440
title: Villanueva-Cañas_etal_families_sequences

description: Compressed file (.tar.gz) that contains the protein sequences for all gene families generated in the publication Villanueva-Cañas et al. Uncompressing the file will generates a folder with subfolders for the families in each node. It occupies ~7.1 Mb.<br>
DOI: 10.6084/m9.figshare.4239440.v1
title: Villanueva-Cañas_etal_families_sequences

description: Compressed file (.tar.gz) that contains the protein sequences for all gene families generated in the publication Villanueva-Cañas et al. Uncompressing the file will generates a folder with subfolders for the families in each node. It occupies ~7.1 Mb.<br>
DOI: 10.6084/m9.figshare.4239431
title: Villanueva-Cañas_etal_RNA-Seq_samples

description: File with information on the RNA-Seq datasets used to perform de novo transcript assembly for 30 different mammalian species from the publication Villanueva-Cañas et al. <br>
DOI: 10.6084/m9.figshare.4239431.v1
title: Villanueva-Cañas_etal_RNA-Seq_samples

description: File with information on the RNA-Seq datasets used to perform de novo transcript assembly for 30 different mammalian species from the publication Villanueva-Cañas et al. <br>
DOI: 10.6084/m9.figshare.4239413
title: Table S1 from The influence of wing morphology upon the dispersal, geographical distributions and diversification of the Corvides (Aves; Passeriformes)

description: New species are sometimes known to arise as a consequence of the dispersal and establishment of populations in new areas. It has nevertheless been difficult to demonstrate an empirical link between rates of dispersal and diversification, partly because dispersal abilities are challenging to quantify. Here, using wing morphology as a proxy for dispersal ability, we assess this relationship among the global radiation of corvoid birds. We found that species distributions are associated with wing shape. Widespread species (occurring on both islands and continents), and those that are migratory, exhibit wing morphologies better adapted to long-distance flight compared with sedentary continental or insular forms. Habitat preferences also strongly predict wing form, with species that occur in canopies and/or areas of sparse vegetation possessing dispersive morphologies. By contrast, we found no significant differences in diversification rates among either the migratory or habitat classifications, but species distributed in island settings diversify at higher rates than those found on continents. This latter finding may reflect the elevated dispersal capabilities of widespread taxa, facilitating the radiation of these lineages across insular areas. However, as the correlations between wing morphology and diversification rates were consistently weak throughout our dataset, this suggests that historical patterns of diversification are not particularly well reflected by present-day wing morphology.
DOI: 10.6084/m9.figshare.4239407
title: Table S2 from The influence of wing morphology upon the dispersal, geographical distributions and diversification of the Corvides (Aves; Passeriformes)

description: New species are sometimes known to arise as a consequence of the dispersal and establishment of populations in new areas. It has nevertheless been difficult to demonstrate an empirical link between rates of dispersal and diversification, partly because dispersal abilities are challenging to quantify. Here, using wing morphology as a proxy for dispersal ability, we assess this relationship among the global radiation of corvoid birds. We found that species distributions are associated with wing shape. Widespread species (occurring on both islands and continents), and those that are migratory, exhibit wing morphologies better adapted to long-distance flight compared with sedentary continental or insular forms. Habitat preferences also strongly predict wing form, with species that occur in canopies and/or areas of sparse vegetation possessing dispersive morphologies. By contrast, we found no significant differences in diversification rates among either the migratory or habitat classifications, but species distributed in island settings diversify at higher rates than those found on continents. This latter finding may reflect the elevated dispersal capabilities of widespread taxa, facilitating the radiation of these lineages across insular areas. However, as the correlations between wing morphology and diversification rates were consistently weak throughout our dataset, this suggests that historical patterns of diversification are not particularly well reflected by present-day wing morphology.
DOI: 10.6084/m9.figshare.4239413.v1
title: Table S1 from The influence of wing morphology upon the dispersal, geographical distributions and diversification of the Corvides (Aves; Passeriformes)

description: New species are sometimes known to arise as a consequence of the dispersal and establishment of populations in new areas. It has nevertheless been difficult to demonstrate an empirical link between rates of dispersal and diversification, partly because dispersal abilities are challenging to quantify. Here, using wing morphology as a proxy for dispersal ability, we assess this relationship among the global radiation of corvoid birds. We found that species distributions are associated with wing shape. Widespread species (occurring on both islands and continents), and those that are migratory, exhibit wing morphologies better adapted to long-distance flight compared with sedentary continental or insular forms. Habitat preferences also strongly predict wing form, with species that occur in canopies and/or areas of sparse vegetation possessing dispersive morphologies. By contrast, we found no significant differences in diversification rates among either the migratory or habitat classifications, but species distributed in island settings diversify at higher rates than those found on continents. This latter finding may reflect the elevated dispersal capabilities of widespread taxa, facilitating the radiation of these lineages across insular areas. However, as the correlations between wing morphology and diversification rates were consistently weak throughout our dataset, this suggests that historical patterns of diversification are not particularly well reflected by present-day wing morphology.
DOI: 10.6084/m9.figshare.4239404
title: Villanueva-Cañas_etal_families

description: File with information on the mammalian-specific gene families from the publication Villanueva-Cañas et al. It provides protein sequence identifiers as well as the number of species and proteins in each family. It also contains information on the transcripts with significant sequence similarity among novel assembled transcripts obtained from RNA-Seq data.<br>
DOI: 10.6084/m9.figshare.4239407.v1
title: Table S2 from The influence of wing morphology upon the dispersal, geographical distributions and diversification of the Corvides (Aves; Passeriformes)

description: New species are sometimes known to arise as a consequence of the dispersal and establishment of populations in new areas. It has nevertheless been difficult to demonstrate an empirical link between rates of dispersal and diversification, partly because dispersal abilities are challenging to quantify. Here, using wing morphology as a proxy for dispersal ability, we assess this relationship among the global radiation of corvoid birds. We found that species distributions are associated with wing shape. Widespread species (occurring on both islands and continents), and those that are migratory, exhibit wing morphologies better adapted to long-distance flight compared with sedentary continental or insular forms. Habitat preferences also strongly predict wing form, with species that occur in canopies and/or areas of sparse vegetation possessing dispersive morphologies. By contrast, we found no significant differences in diversification rates among either the migratory or habitat classifications, but species distributed in island settings diversify at higher rates than those found on continents. This latter finding may reflect the elevated dispersal capabilities of widespread taxa, facilitating the radiation of these lineages across insular areas. However, as the correlations between wing morphology and diversification rates were consistently weak throughout our dataset, this suggests that historical patterns of diversification are not particularly well reflected by present-day wing morphology.
DOI: 10.6084/m9.figshare.4239404.v2
title: Villanueva-Cañas_etal_families

description: File with information on the mammalian-specific gene families from the publication Villanueva-Cañas et al. It provides protein sequence identifiers as well as the number of species and proteins in each family. It also contains information on the transcripts with significant sequence similarity among novel assembled transcripts obtained from RNA-Seq data.<br>
DOI: 10.6084/m9.figshare.4239404.v1
title: Villanueva-Cañas_etal_families

description: File with information on the mammalian-specific gene families from the publication Villanueva-Cañas et al. It provides protein sequence identifiers as well as the number of species and proteins in each family. It also contains information on the transcripts with significant sequence similarity among novel assembled transcripts obtained from RNA-Seq data.<br>
DOI: 10.6084/m9.figshare.4239365
title: fMRI_reasoning

description: fMRI data for a reasoning task
DOI: 10.6084/m9.figshare.4239365.v1
title: fMRI_reasoning

description: fMRI data for a reasoning task
DOI: 10.6084/m9.figshare.4239314
title: OIKOS Compensating for delayed hatching reduces offspring immune response and increases life-history costs

description: Dataset from paper "Compensating for delayed hatching reduces offspring immune response and increases life-history costs", published in OIKOS
DOI: 10.6084/m9.figshare.4239314.v1
title: OIKOS Compensating for delayed hatching reduces offspring immune response and increases life-history costs

description: Dataset from paper "Compensating for delayed hatching reduces offspring immune response and increases life-history costs", published in OIKOS
DOI: 10.6084/m9.figshare.4239311
title: Biochemical characterization of the medaka (<i>Oryzias latipes</i>) orthologue for mammalian tissue-type transglutaminase (TG2)

description: Transglutaminase is an enzyme family responsible for post-translational modification such as protein cross-linking and the attachment of primary amine and/or deamidation of glutamine-residue in proteins. Medaka (<i>Oryzias latipes</i>), a recently established model fish, has similar functional proteins to those characterized in mammals. Previously, we found the apparent orthologues that correspond to human transglutaminases in medaka. In this study, regarding the medaka orthologue of human tissue-type transglutaminase (OlTGT), recombinant protein was expressed in an active form in bacteria cultured at low temperature. Using the recombinant protein, we biochemically characterized the enzymatic activity and also obtained a monoclonal antibody that specifically recognized OlTGT. Immunochemical analysis revealed that OlTGT was not expressed ubiquitously, unlike its mammalian orthologue, but in primarily limited tissues such as the eye, brain, spinal cord, and gas gland.
DOI: 10.6084/m9.figshare.4239260
title: Size-assortative mating and arm loss in the wild shallow-water octopus <i>Abdopus</i> sp. (Cephalopoda: Octopodidae)

description: The ability to autotomise and regenerate body parts as a means of escaping predation or renewing damaged tissues has evolved in several animal groups. Some octopuses belonging to the genus <i>Abdopus</i> are known for a high frequency of arm loss and their capacity to regenerate arms. I investigated the mating behaviour and the incidence of arm loss in a shallow-water <i>Abdopus</i> sp. in the wild. Mating occurred at night and at low tide. The male octopus tracked and copulated by repeatedly stretching the hectocotylised arm into the female’s mantle cavity during mating bouts, mostly while the mated female actively moved to forage at the same time. Relatively smaller males adopted sneaking tactics in which they stayed around a mating pair and sometimes gained opportunistic copulations with the female. A significant positive relationship between the body weights of the male and female in each mating pair was detected. Moreover, the proportion of sneaker males that had lost at least one arm prior to mating and their number of lost arms per individual were significantly higher than those of paired males. These results suggest that male arm loss in <i>Abdopus</i> sp. may directly or indirectly influence male competition over females and mating success, resulting in a positive size association between members of a mating pair. This finding would be important when considering the life-history strategies of octopuses.
DOI: 10.6084/m9.figshare.4239260.v1
title: Size-assortative mating and arm loss in the wild shallow-water octopus <i>Abdopus</i> sp. (Cephalopoda: Octopodidae)

description: The ability to autotomise and regenerate body parts as a means of escaping predation or renewing damaged tissues has evolved in several animal groups. Some octopuses belonging to the genus <i>Abdopus</i> are known for a high frequency of arm loss and their capacity to regenerate arms. I investigated the mating behaviour and the incidence of arm loss in a shallow-water <i>Abdopus</i> sp. in the wild. Mating occurred at night and at low tide. The male octopus tracked and copulated by repeatedly stretching the hectocotylised arm into the female’s mantle cavity during mating bouts, mostly while the mated female actively moved to forage at the same time. Relatively smaller males adopted sneaking tactics in which they stayed around a mating pair and sometimes gained opportunistic copulations with the female. A significant positive relationship between the body weights of the male and female in each mating pair was detected. Moreover, the proportion of sneaker males that had lost at least one arm prior to mating and their number of lost arms per individual were significantly higher than those of paired males. These results suggest that male arm loss in <i>Abdopus</i> sp. may directly or indirectly influence male competition over females and mating success, resulting in a positive size association between members of a mating pair. This finding would be important when considering the life-history strategies of octopuses.
DOI: 10.6084/m9.figshare.4239239
title: Experiment-1&2.xlsx

description: Data for paper "Prosody predicts contest outcome in non-verbal dialogs"<br>
DOI: 10.6084/m9.figshare.4239239.v1
title: Experiment-1&2.xlsx

description: Data for paper "Prosody predicts contest outcome in non-verbal dialogs"<br>