cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4781188
title: Software Engineering Arousal (SEA) Lexicon

description: Please cite the paper: <br><br>Mika V. Mäntylä, Nicole Novielli, Filippo Lanubile, Maëlick Claes, Miikka Kuutila, "Bootstrapping a Lexicon for Emotional Arousal in Software Engineering", 14th International Conference on Mining Software Repositories (MSR 2017), 20-21 May 2017, Buenos Aires, Argentina, pp 1-5
DOI: 10.6084/m9.figshare.4781200.v1
title: PONE-D-16-45371_Data_Fig3B

description: Quantification of prometaphase duration as observed in the live-cell imaging in control (siCtrl), KBP-, Kif15- or KBP/Kif15-silenced cells. Prometaphase was defined as the time needed for cells to progress from NEBD till anaphase onset. Time in min.
DOI: 10.6084/m9.figshare.4781161
title: Supplementary Material for: Do Listeners Store in Memory a Speaker’s Habitual Utterance-Final Phonation Type?

description: Earlier studies report systematic differences across speakers in the occurrence of utterance-final irregular phonation; the work reported here investigated whether human listeners remember this speaker-specific information and can access it when necessary (a prerequisite for using this cue in speaker recognition). Listeners personally familiar with the voices of the speakers were presented with pairs of speech samples: one with the original and the other with transformed final phonation type. Asked to select the member of the pair that was closer to the talker’s voice, most listeners tended to choose the unmanipulated token (even though they judged them to sound essentially equally natural). This suggests that utterance-final pitch period irregularity is part of the mental representation of individual speaker voices, although this may depend on the individual speaker and listener to some extent.
DOI: 10.6084/m9.figshare.4781140
title: Supplementary Material for: A Non-Human Primate BAC Resource to Study Interchromosomal Segmental Duplications

description: Segmental duplications (SDs) are involved in the reshaping and evolutionary development of primate genome architecture. Their intrinsic property to promote genomic instability facilitates genome rearrangements, thereby contributing to karyotype diversity in primates. However, comparative analyses of SDs based on whole-genome shotgun assemblies of primate genomes may lead to a distorted view of their evolutionary dynamics as this method will incorrectly assemble or simply not represent these regions. Therefore high-quality sequences of chromosomally assigned SDs are indispensable for unraveling the amplification and dispersal pattern of SDs during primate evolution. Here, we use an updated version of the ancestral duplicon state of the non-palindromic SDs of all 4 human Y-chromosome euchromatin/heterochromatin transition regions to perform a survey of duplicons genome-wide across 7 primate species. By adjusting experimental conditions to the mean nucleotide sequence divergence to human we identified 11,075 BAC clones carrying primate orthologs or paralogs of human Y chromosome-derived duplicons. Preliminary results indicate lineage-specific amplification of duplicons in prosimians and gibbons. This BAC-based framework represents the first complete set of a defined number of duplicons over 60 million years of primate evolution. Comparative sequence analysis of this genetic resource can contribute to our deeper understanding of the impact of segmental duplications on primate genome evolution.
DOI: 10.6084/m9.figshare.4781149
title: Supplementary Material for: Bioinformatic Analyses of Transmembrane Transport: Novel Software for Deducing Protein Phylogeny, Topology, and Evolution

description: During the past decade, we have experienced a revolution in the biological sciences resulting from the flux of information generated by genome-sequencing efforts. Our understanding of living organisms, the metabolic processes they catalyze, the genetic systems encoding cellular protein and stable RNA constituents, and the pathological conditions caused by some of these organisms has greatly benefited from the availability of complete genomic sequences and the establishment of comprehensive databases. Many research institutes around the world are now devoting their efforts largely to genome sequencing, data collection and data analysis. In this review, we summarize tools that are in routine use in our laboratory for characterizing transmembrane transport systems. Applications of these tools to specific transporter families are presented. Many of the computational approaches described should be applicable to virtually all classes of proteins and RNA molecules.
DOI: 10.6084/m9.figshare.4781224.v1
title: Clostridium difficile Manuka honey biofilm formation Results.xlsx

description: Raw data
DOI: 10.6084/m9.figshare.4781095
title: Supplementary Material for: Intranasal Administration of CpG Induces a Rapid and Transient Cytokine Response Followed by Dendritic and Natural Killer Cell Activation and Recruitment in the Mouse Lung

description: CpG-containing oligodeoxynucleotides are potent mucosal adjuvants and effective as stand-alone treatment of respiratory infections in mice. Although CpG is also used as a type 1 helper immunomodulator in the treatment of asthma and allergic disease, immune modulation following intranasal application has not been fully characterized yet. Using a B-type CpG, we monitored RNA expression profiles, cytokine production and cellular activation in lung tissue and bronchoalveolar lavages ex vivo and cytokine production of purified cell populations in vitro. CpG triggered the upregulation of many transcripts, including interferon response genes and proinflammatory cytokine genes, between 3 h and 4 days. Overlapping subsets of these cytokine proteins were induced in vitro in purified CD11c+ cells, B cells and alveolar macrophages from the lung, thus identifying these cells as direct targets of CpG. While lung B cells strongly respond to CpG in vitro, less activation is found ex vivo, suggesting efficient CpG sequestering or rapid B cell migration after activation. In contrast, a type II alveolar epithelial cell line did not respond to CpG in vitro. We noted selective recruitment of plasmacytoid dendritic cells (DCs) into the lung tissue, and of conventional DCs and natural killer (NK) cells into the lung tissue and bronchoalveolar space. Furthermore, CpG induced activation of intrapulmonary DCs, NK and T cells. We hypothesize that CpG-linked adjuvanticity and clearance of respiratory pathogens are mediated by two major mechanisms: transient induction of the interferon pathway limiting microbial survival and selective recruitment of DCs and NK cells, which allows for better adaptive responses.
DOI: 10.6084/m9.figshare.4781149.v1
title: Supplementary Material for: Bioinformatic Analyses of Transmembrane Transport: Novel Software for Deducing Protein Phylogeny, Topology, and Evolution

description: During the past decade, we have experienced a revolution in the biological sciences resulting from the flux of information generated by genome-sequencing efforts. Our understanding of living organisms, the metabolic processes they catalyze, the genetic systems encoding cellular protein and stable RNA constituents, and the pathological conditions caused by some of these organisms has greatly benefited from the availability of complete genomic sequences and the establishment of comprehensive databases. Many research institutes around the world are now devoting their efforts largely to genome sequencing, data collection and data analysis. In this review, we summarize tools that are in routine use in our laboratory for characterizing transmembrane transport systems. Applications of these tools to specific transporter families are presented. Many of the computational approaches described should be applicable to virtually all classes of proteins and RNA molecules.
DOI: 10.6084/m9.figshare.4781095.v1
title: Supplementary Material for: Intranasal Administration of CpG Induces a Rapid and Transient Cytokine Response Followed by Dendritic and Natural Killer Cell Activation and Recruitment in the Mouse Lung

description: CpG-containing oligodeoxynucleotides are potent mucosal adjuvants and effective as stand-alone treatment of respiratory infections in mice. Although CpG is also used as a type 1 helper immunomodulator in the treatment of asthma and allergic disease, immune modulation following intranasal application has not been fully characterized yet. Using a B-type CpG, we monitored RNA expression profiles, cytokine production and cellular activation in lung tissue and bronchoalveolar lavages ex vivo and cytokine production of purified cell populations in vitro. CpG triggered the upregulation of many transcripts, including interferon response genes and proinflammatory cytokine genes, between 3 h and 4 days. Overlapping subsets of these cytokine proteins were induced in vitro in purified CD11c+ cells, B cells and alveolar macrophages from the lung, thus identifying these cells as direct targets of CpG. While lung B cells strongly respond to CpG in vitro, less activation is found ex vivo, suggesting efficient CpG sequestering or rapid B cell migration after activation. In contrast, a type II alveolar epithelial cell line did not respond to CpG in vitro. We noted selective recruitment of plasmacytoid dendritic cells (DCs) into the lung tissue, and of conventional DCs and natural killer (NK) cells into the lung tissue and bronchoalveolar space. Furthermore, CpG induced activation of intrapulmonary DCs, NK and T cells. We hypothesize that CpG-linked adjuvanticity and clearance of respiratory pathogens are mediated by two major mechanisms: transient induction of the interferon pathway limiting microbial survival and selective recruitment of DCs and NK cells, which allows for better adaptive responses.
DOI: 10.6084/m9.figshare.4781140.v1
title: Supplementary Material for: A Non-Human Primate BAC Resource to Study Interchromosomal Segmental Duplications

description: Segmental duplications (SDs) are involved in the reshaping and evolutionary development of primate genome architecture. Their intrinsic property to promote genomic instability facilitates genome rearrangements, thereby contributing to karyotype diversity in primates. However, comparative analyses of SDs based on whole-genome shotgun assemblies of primate genomes may lead to a distorted view of their evolutionary dynamics as this method will incorrectly assemble or simply not represent these regions. Therefore high-quality sequences of chromosomally assigned SDs are indispensable for unraveling the amplification and dispersal pattern of SDs during primate evolution. Here, we use an updated version of the ancestral duplicon state of the non-palindromic SDs of all 4 human Y-chromosome euchromatin/heterochromatin transition regions to perform a survey of duplicons genome-wide across 7 primate species. By adjusting experimental conditions to the mean nucleotide sequence divergence to human we identified 11,075 BAC clones carrying primate orthologs or paralogs of human Y chromosome-derived duplicons. Preliminary results indicate lineage-specific amplification of duplicons in prosimians and gibbons. This BAC-based framework represents the first complete set of a defined number of duplicons over 60 million years of primate evolution. Comparative sequence analysis of this genetic resource can contribute to our deeper understanding of the impact of segmental duplications on primate genome evolution.
DOI: 10.6084/m9.figshare.4781224.v2
title: Clostridium difficile Manuka honey biofilm formation Results.xlsx

description: Raw data
DOI: 10.6084/m9.figshare.4781086
title: Supplementary Material for: Effects of a Supplementation of n-3 Polyunsaturated Fatty Acids with or without Fish Gelatin on Gene Expression in Peripheral Blood Mononuclear Cells in Obese, Insulin-Resistant Subjects

description: <em>Aim:</em> To investigate gene expression changes in peripheral blood mononuclear cells (PBMCs) following an n-3 polyunsaturated fatty acid (PUFA) and n-3 PUFA plus fish gelatin (+FG) supplementation. <i>Methods:</i> A transcriptome comparison of 8-week supplementation with n-3 PUFA and n-3 PUFA+FG was carried out in PBMCs of 16 obese insulin-resistant subjects. <i>Results:</i> Erythrocyte n-3 PUFA concentration increased and plasma triglycerides decreased significantly without altering inflammatory parameters after both supplementations. n-3 PUFA supplementation changed the expression of 805 genes, whereas n-3 PUFA+FG supplementation altered the expression of 184 genes. Three genes were commonly changed: fatty acid desaturase 1, free fatty acid receptor 3, and ectodysplasin. Pathway analyses indicate changes in gene expression via the nuclear receptor peroxisome proliferator-activated receptor α pathway after both supplementations. Further, the extent of modifications in the expression of genes implicated in the inflammatory pathways – the oxidative stress response mediated by nuclear factor (erythroid-derived 2)-like 2, nuclear transcription factor ĸB, oxidative stress, and hypoxia-inducible factor signaling – was different after each supplementation. <i>Conclusion:</i> Although n-3 PUFA and n-3 PUFA+FG supplementations have a distinct impact on gene expression levels, the consequences on biochemical parameters and metabolic pathways were comparable after both supplementations.
DOI: 10.6084/m9.figshare.4781089
title: Supplementary Material for: A Cost-Effective Statistical Method to Correct for Differential Genotype Misclassification When Performing Case-Control Genetic Association

description: <i>Background/Aims:</i> There is a growing interest regarding the effect of differential misclassification on power and type I error rate in genome-wide association studies. We present an extension of a previously published test statistic: the likelihood ratio test allowing for errors (<i>LRT</i><sub><i>AE</i></sub>). This test uses double-sample information on a subset of individuals to increase power for genetic association in the presence of nondifferential misclassification. <i>Methods:</i>We extend the original <i>LRT</i><sub><i>AE</i></sub> by allowing for differential genotype misclassification between case and control populations. We label this new statistic as <i>LRT</i><sup>D</sup><sub><i>A</i></sub><sup>M</sup><sub><i>E </i></sub>. We test the performance of this statistic with data simulated under differential misclassification specifications and two different types of genetic models: null and power. For simulations using the null model, we specify that there is no difference between case and control genotype frequencies before the introduction of errors. For simulations under power, we consider three modes of inheritance: dominant, multiplicative, and recessive. <i>Results:</i> We show that the <i>LRT</i><sup>D</sup><sub><i>A</i></sub><sup>M</sup><sub><i>E </i></sub>, with p values computed using permutation, maintains a correct type I error rate under the null model after the introduction of differential genotyping errors. Also, we find that as little as 10 to 15% of double-sampled genotype data is needed to achieve this effect. Aside from a few situations (particularly recessive mode of inheritance simulations) the <i>LRT</i><sup>D</sup><sub><i>A</i></sub><sup>M</sup><sub><i>E </i></sub> version that calculates p values through permutation requires 15 to 20% double sampling to maintain an 80% power for a 0.05 significance level and approximately 20% double sampling for a 0.01 significance level.
DOI: 10.25387/g3.12845840
title: Supplemental Material for Ahn et al., 2020

description: Supplementary figure and tables
DOI: 10.6084/m9.figshare.4781086.v1
title: Supplementary Material for: Effects of a Supplementation of n-3 Polyunsaturated Fatty Acids with or without Fish Gelatin on Gene Expression in Peripheral Blood Mononuclear Cells in Obese, Insulin-Resistant Subjects

description: <em>Aim:</em> To investigate gene expression changes in peripheral blood mononuclear cells (PBMCs) following an n-3 polyunsaturated fatty acid (PUFA) and n-3 PUFA plus fish gelatin (+FG) supplementation. <i>Methods:</i> A transcriptome comparison of 8-week supplementation with n-3 PUFA and n-3 PUFA+FG was carried out in PBMCs of 16 obese insulin-resistant subjects. <i>Results:</i> Erythrocyte n-3 PUFA concentration increased and plasma triglycerides decreased significantly without altering inflammatory parameters after both supplementations. n-3 PUFA supplementation changed the expression of 805 genes, whereas n-3 PUFA+FG supplementation altered the expression of 184 genes. Three genes were commonly changed: fatty acid desaturase 1, free fatty acid receptor 3, and ectodysplasin. Pathway analyses indicate changes in gene expression via the nuclear receptor peroxisome proliferator-activated receptor α pathway after both supplementations. Further, the extent of modifications in the expression of genes implicated in the inflammatory pathways – the oxidative stress response mediated by nuclear factor (erythroid-derived 2)-like 2, nuclear transcription factor ĸB, oxidative stress, and hypoxia-inducible factor signaling – was different after each supplementation. <i>Conclusion:</i> Although n-3 PUFA and n-3 PUFA+FG supplementations have a distinct impact on gene expression levels, the consequences on biochemical parameters and metabolic pathways were comparable after both supplementations.
DOI: 10.6084/m9.figshare.4781071
title: Asthma control in London secondary school children

description: <i>Objective</i>: The asthma control test (ACT) is a validated tool for assessing control in asthmatic children aged 12 years and older. Using the ACT, we sought to assess asthma control and knowledge in London secondary school children. <i>Methods</i>: Secondary schools in London, UK, participated in this study. Children with doctor-diagnosed asthma were invited to complete an online questionnaire that included the ACT and questions about asthma. Suboptimal asthma control was defined as an ACT score of ≤ 19 out of a maximum score of 25. Data are summarised as median and interquartile range (IQR), and were analysed by either Mann-Whitney test, or chi-square test. A <i>p</i> value of &lt; 0.05 was considered significant. <i>Results</i>: A total of 799 children completed the questionnaire; 689 (86.2%) were included for analysis. Suboptimal asthma control was reported by 49.6% of students. Over a third (42.4%) of students prescribed a short-acting β2-agonist inhaler felt uncomfortable using it at school, and 29.2% (<i>n</i> = 173) reported not using this inhaler when wheezy. 56.4% (<i>n</i> = 220) of those with regular inhaled corticosteroids did not take them as prescribed, and 41.7% did not know what this inhaler was for. Suboptimal control was associated with a greater proportion of students reporting that they were ‘somewhat’, ‘hardly’ or ‘not at all’ comfortable using inhalers at school (52.7% vs 29.1%, <i>p</i> &lt; 0.01) and outside school (22.8% vs. 14.8%, <i>p</i> &lt; 0.01). <i>Conclusions</i>: Suboptimal asthma control and poor asthma knowledge are common in London schoolchildren.
DOI: 10.6084/m9.figshare.4781071.v1
title: Asthma control in London secondary school children

description: <i>Objective</i>: The asthma control test (ACT) is a validated tool for assessing control in asthmatic children aged 12 years and older. Using the ACT, we sought to assess asthma control and knowledge in London secondary school children. <i>Methods</i>: Secondary schools in London, UK, participated in this study. Children with doctor-diagnosed asthma were invited to complete an online questionnaire that included the ACT and questions about asthma. Suboptimal asthma control was defined as an ACT score of ≤ 19 out of a maximum score of 25. Data are summarised as median and interquartile range (IQR), and were analysed by either Mann-Whitney test, or chi-square test. A <i>p</i> value of &lt; 0.05 was considered significant. <i>Results</i>: A total of 799 children completed the questionnaire; 689 (86.2%) were included for analysis. Suboptimal asthma control was reported by 49.6% of students. Over a third (42.4%) of students prescribed a short-acting β2-agonist inhaler felt uncomfortable using it at school, and 29.2% (<i>n</i> = 173) reported not using this inhaler when wheezy. 56.4% (<i>n</i> = 220) of those with regular inhaled corticosteroids did not take them as prescribed, and 41.7% did not know what this inhaler was for. Suboptimal control was associated with a greater proportion of students reporting that they were ‘somewhat’, ‘hardly’ or ‘not at all’ comfortable using inhalers at school (52.7% vs 29.1%, <i>p</i> &lt; 0.01) and outside school (22.8% vs. 14.8%, <i>p</i> &lt; 0.01). <i>Conclusions</i>: Suboptimal asthma control and poor asthma knowledge are common in London schoolchildren.
DOI: 10.6084/m9.figshare.4781089.v1
title: Supplementary Material for: A Cost-Effective Statistical Method to Correct for Differential Genotype Misclassification When Performing Case-Control Genetic Association

description: <i>Background/Aims:</i> There is a growing interest regarding the effect of differential misclassification on power and type I error rate in genome-wide association studies. We present an extension of a previously published test statistic: the likelihood ratio test allowing for errors (<i>LRT</i><sub><i>AE</i></sub>). This test uses double-sample information on a subset of individuals to increase power for genetic association in the presence of nondifferential misclassification. <i>Methods:</i>We extend the original <i>LRT</i><sub><i>AE</i></sub> by allowing for differential genotype misclassification between case and control populations. We label this new statistic as <i>LRT</i><sup>D</sup><sub><i>A</i></sub><sup>M</sup><sub><i>E </i></sub>. We test the performance of this statistic with data simulated under differential misclassification specifications and two different types of genetic models: null and power. For simulations using the null model, we specify that there is no difference between case and control genotype frequencies before the introduction of errors. For simulations under power, we consider three modes of inheritance: dominant, multiplicative, and recessive. <i>Results:</i> We show that the <i>LRT</i><sup>D</sup><sub><i>A</i></sub><sup>M</sup><sub><i>E </i></sub>, with p values computed using permutation, maintains a correct type I error rate under the null model after the introduction of differential genotyping errors. Also, we find that as little as 10 to 15% of double-sampled genotype data is needed to achieve this effect. Aside from a few situations (particularly recessive mode of inheritance simulations) the <i>LRT</i><sup>D</sup><sub><i>A</i></sub><sup>M</sup><sub><i>E </i></sub> version that calculates p values through permutation requires 15 to 20% double sampling to maintain an 80% power for a 0.05 significance level and approximately 20% double sampling for a 0.01 significance level.
DOI: 10.25387/g3.12845840.v1
title: Supplemental Material for Ahn et al., 2020

description: Supplementary figure and tables