cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8203577
title: Altered microRNA expression profiles in large offspring syndrome and Beckwith-Wiedemann syndrome

description: The use of assisted reproductive technologies (ART) can induce a congenital overgrowth condition in humans and ruminants, namely Beckwith-Wiedemann syndrome (BWS) and large offspring syndrome (LOS), respectively. Shared phenotypes and epigenotypes have been found between BWS and LOS. We have observed global misregulation of transcripts in bovine foetuses with LOS. microRNAs (miRNAs) are important post-transcriptional gene expression regulators. We hypothesize that there is miRNA misregulation in LOS and that this misregulation is shared with BWS. In this study, small RNA sequencing was conducted to investigate miRNA expression profiles in bovine and human samples. We detected 407 abundant known miRNAs and predicted 196 putative miRNAs from the bovine sequencing results and identified 505 abundant miRNAs in human tongue. Differentially expressed miRNAs (DE-miRNAs) were identified between control and LOS groups in all tissues analysed as well as between BWS and control human samples. DE-miRNAs were detected from several miRNA clusters including DLK1-DIO3 genomic imprinted cluster in LOS and BWS. DNA hypermethylation was associated with downregulation of miRNAs in the DLK1-DIO3. mRNA targets of the DE-miRNAs were predicted and signalling pathways associated with control of organ size (including the Hippo signalling pathway), cell proliferation, apoptosis, cell survival, cell cycle, and cell adhesion were found to be enriched with these genes. Yes associated protein 1 (YAP1) is the core effector of the Hippo signalling pathway, and increased level of active (non-phosphorylated) YAP1 protein was detected in skeletal muscle of LOS foetuses. Overall, our data provide evidence of miRNA misregulation in LOS and BWS.
DOI: 10.6084/m9.figshare.8203583.v1
title: variance.mat

description: The dataset is the basis of our analysis of correlated gene expression (CGE) in the developing mouse brain.
DOI: 10.6084/m9.figshare.8203577.v1
title: Altered microRNA expression profiles in large offspring syndrome and Beckwith-Wiedemann syndrome

description: The use of assisted reproductive technologies (ART) can induce a congenital overgrowth condition in humans and ruminants, namely Beckwith-Wiedemann syndrome (BWS) and large offspring syndrome (LOS), respectively. Shared phenotypes and epigenotypes have been found between BWS and LOS. We have observed global misregulation of transcripts in bovine foetuses with LOS. microRNAs (miRNAs) are important post-transcriptional gene expression regulators. We hypothesize that there is miRNA misregulation in LOS and that this misregulation is shared with BWS. In this study, small RNA sequencing was conducted to investigate miRNA expression profiles in bovine and human samples. We detected 407 abundant known miRNAs and predicted 196 putative miRNAs from the bovine sequencing results and identified 505 abundant miRNAs in human tongue. Differentially expressed miRNAs (DE-miRNAs) were identified between control and LOS groups in all tissues analysed as well as between BWS and control human samples. DE-miRNAs were detected from several miRNA clusters including DLK1-DIO3 genomic imprinted cluster in LOS and BWS. DNA hypermethylation was associated with downregulation of miRNAs in the DLK1-DIO3. mRNA targets of the DE-miRNAs were predicted and signalling pathways associated with control of organ size (including the Hippo signalling pathway), cell proliferation, apoptosis, cell survival, cell cycle, and cell adhesion were found to be enriched with these genes. Yes associated protein 1 (YAP1) is the core effector of the Hippo signalling pathway, and increased level of active (non-phosphorylated) YAP1 protein was detected in skeletal muscle of LOS foetuses. Overall, our data provide evidence of miRNA misregulation in LOS and BWS.
DOI: 10.6084/m9.figshare.8203538
title: Block-matrix-based approach for the hybrid vehicle routing problem with fuzzy travel time and transportation type selection

description: This study proposes a novel model for the vehicle routing problem that considers transportation type selection between milk-run and cross-dock strategies under uncertain environment with fuzzy travel time to derive an optimal transportation plan. Furthermore, a novel block-matrix-based approach for the transportation type selection to explore optimal transportation plans in an intuitive, reasonable, effective, and efficient form is presented. An extended biogeography-based optimization (BBO) algorithm is proposed to effectively derive a transportation plan with the optimal degree of plant satisfaction by extending the operators of migration and mutation, and introducing a novel self-adaptive mutation rate, as well as a secondary mutation operator.
DOI: 10.6084/m9.figshare.8203538.v1
title: Block-matrix-based approach for the hybrid vehicle routing problem with fuzzy travel time and transportation type selection

description: This study proposes a novel model for the vehicle routing problem that considers transportation type selection between milk-run and cross-dock strategies under uncertain environment with fuzzy travel time to derive an optimal transportation plan. Furthermore, a novel block-matrix-based approach for the transportation type selection to explore optimal transportation plans in an intuitive, reasonable, effective, and efficient form is presented. An extended biogeography-based optimization (BBO) algorithm is proposed to effectively derive a transportation plan with the optimal degree of plant satisfaction by extending the operators of migration and mutation, and introducing a novel self-adaptive mutation rate, as well as a secondary mutation operator.
DOI: 10.6084/m9.figshare.8203529.v1
title: Block-matrix-based approach for the hybrid vehicle routing problem with fuzzy travel time and transportation type selection

description: This study proposes a novel model for the vehicle routing problem that considers transportation type selection between milk-run and cross-dock strategies under uncertain environment with fuzzy travel time to derive an optimal transportation plan. Furthermore, a novel block-matrix-based approach for the transportation type selection to explore optimal transportation plans in an intuitive, reasonable, effective, and efficient form is presented. An extended biogeography-based optimization (BBO) algorithm is proposed to effectively derive a transportation plan with the optimal degree of plant satisfaction by extending the operators of migration and mutation, and introducing a novel self-adaptive mutation rate, as well as a secondary mutation operator.
DOI: 10.6084/m9.figshare.8203469
title: Table 1 with all data used in the comparative analyses from The evolution of infanticide by females in mammals

description: In most mammalian species, females regularly interact with kin, which is expected to reduce aggressive competitive behaviour among females. It may thus be difficult to understand why infanticide by females has been reported in numerous species and is sometimes perpetrated by groupmates. Here, we investigate the evolutionary determinants of infanticide by females by combining a quantitative analysis of the taxonomic distribution of infanticide with a qualitative synthesis of the circumstances of infanticidal attacks in published reports. Our results show that female infanticide is widespread across mammals and varies in relation to social organization and life history, being more frequent where females breed in groups and have intense bouts of high reproductive output. Specifically, female infanticide occurs where the proximity of conspecific offspring directly threatens the killer's reproductive success by limiting access to critical resources for her dependent progeny, including food, shelters, care or a social position. By contrast, infanticide is not immediately modulated by the degree of kinship among females, and females occasionally sacrifice closely related infants. Our findings suggest that the potential direct fitness rewards of gaining access to reproductive resources have a stronger influence on the expression of female aggression than the indirect fitness costs of competing against kin.This article is part of the theme issue ‘The evolution of female-biased kinship in humans and other mammals’.
DOI: 10.6084/m9.figshare.8203469.v1
title: Table 1 with all data used in the comparative analyses from The evolution of infanticide by females in mammals

description: In most mammalian species, females regularly interact with kin, which is expected to reduce aggressive competitive behaviour among females. It may thus be difficult to understand why infanticide by females has been reported in numerous species and is sometimes perpetrated by groupmates. Here, we investigate the evolutionary determinants of infanticide by females by combining a quantitative analysis of the taxonomic distribution of infanticide with a qualitative synthesis of the circumstances of infanticidal attacks in published reports. Our results show that female infanticide is widespread across mammals and varies in relation to social organization and life history, being more frequent where females breed in groups and have intense bouts of high reproductive output. Specifically, female infanticide occurs where the proximity of conspecific offspring directly threatens the killer's reproductive success by limiting access to critical resources for her dependent progeny, including food, shelters, care or a social position. By contrast, infanticide is not immediately modulated by the degree of kinship among females, and females occasionally sacrifice closely related infants. Our findings suggest that the potential direct fitness rewards of gaining access to reproductive resources have a stronger influence on the expression of female aggression than the indirect fitness costs of competing against kin.This article is part of the theme issue ‘The evolution of female-biased kinship in humans and other mammals’.
DOI: 10.6084/m9.figshare.8203463
title: Table 2 with all data used in the population analyses from The evolution of infanticide by females in mammals

description: In most mammalian species, females regularly interact with kin, which is expected to reduce aggressive competitive behaviour among females. It may thus be difficult to understand why infanticide by females has been reported in numerous species and is sometimes perpetrated by groupmates. Here, we investigate the evolutionary determinants of infanticide by females by combining a quantitative analysis of the taxonomic distribution of infanticide with a qualitative synthesis of the circumstances of infanticidal attacks in published reports. Our results show that female infanticide is widespread across mammals and varies in relation to social organization and life history, being more frequent where females breed in groups and have intense bouts of high reproductive output. Specifically, female infanticide occurs where the proximity of conspecific offspring directly threatens the killer's reproductive success by limiting access to critical resources for her dependent progeny, including food, shelters, care or a social position. By contrast, infanticide is not immediately modulated by the degree of kinship among females, and females occasionally sacrifice closely related infants. Our findings suggest that the potential direct fitness rewards of gaining access to reproductive resources have a stronger influence on the expression of female aggression than the indirect fitness costs of competing against kin.This article is part of the theme issue ‘The evolution of female-biased kinship in humans and other mammals’.
DOI: 10.6084/m9.figshare.8203463.v1
title: Table 2 with all data used in the population analyses from The evolution of infanticide by females in mammals

description: In most mammalian species, females regularly interact with kin, which is expected to reduce aggressive competitive behaviour among females. It may thus be difficult to understand why infanticide by females has been reported in numerous species and is sometimes perpetrated by groupmates. Here, we investigate the evolutionary determinants of infanticide by females by combining a quantitative analysis of the taxonomic distribution of infanticide with a qualitative synthesis of the circumstances of infanticidal attacks in published reports. Our results show that female infanticide is widespread across mammals and varies in relation to social organization and life history, being more frequent where females breed in groups and have intense bouts of high reproductive output. Specifically, female infanticide occurs where the proximity of conspecific offspring directly threatens the killer's reproductive success by limiting access to critical resources for her dependent progeny, including food, shelters, care or a social position. By contrast, infanticide is not immediately modulated by the degree of kinship among females, and females occasionally sacrifice closely related infants. Our findings suggest that the potential direct fitness rewards of gaining access to reproductive resources have a stronger influence on the expression of female aggression than the indirect fitness costs of competing against kin.This article is part of the theme issue ‘The evolution of female-biased kinship in humans and other mammals’.
DOI: 10.6084/m9.figshare.8203394
title: R4R_BoF_Results.xlsx

description: This spreadsheet contains the results of the modelling session.Columns include the following:RID: the unique role idTitle: the unique role titleService: the service under which the role was categorised.Capability: the aggregation of roles as a service/capability (left blank for those roles deemed not eResearch).CID: the capability id.<br>
DOI: 10.6084/m9.figshare.8203415.v2
title: Bat Recording Manager v8.n

description: This program provides a management system for your library of bat (or other) recordings. It can be flexible in its approach but is primarily designed to work with libraries stored and analysed according to a particular protocol which is described below.<br>The program has four main ‘views’. The default view lists all recording sessions, with details of the currently selected session. Sessions can be added or edited manually or deleted from the database. Similarly individual recordings within the session can be added, edited or deleted.<br>The program assumes that the recordings are of bat calls, and incorporates a reference list of bat species, which can also be modified by the user. This reference list also defines a set of ‘tags’ which can be used when analysing recordings to indicate the presence of each species.<br>Recordings may also be displayed ‘by bat species’. In this case the defined species are listed and the recording sessions and recordings which detected the selected species are shown.<br>An ‘Import’ page allows recording sessions which have been analysed using Audacity to be imported into the database. A single folder containing a set of recordings may be imported or a selection of folders can be imported sequentially.Analyse and Import mode allows interaction with Audacity or Kaleidoscope Light for rapid sequential analysis of recording files.The program also provides report generation in a number of formats, storage of screen capture images during analysis, and the ability to replay portions of recordings at reduced speed or in heterodyne (tuned bat detector) mode.This setup file incorporates .NET 4.7.2 and Audacity 2.3.2 which will be installed automatically if required. The Audacity installation will not affect any pre-existing installations. Kaleidoscope interaction requires that Kaleidoscope is installed to C:<br>v8.0 builds on version 7.3 (see other figshare project) but updates to .NET 4.72 and provides virtualized data access for faster loading in some situations.<br>v8.0.7111 completes the conversion to Visual Studio 2019 and .NET 4.72 with extensive refactoring and code tidying using Resharper. Source code is now available from GitHub.https://github.com/jathalls/BatRecordingManager_v8.n<br>
DOI: 10.6084/m9.figshare.8203373
title: Developmental Science 2019 Data DS-08-18-0411-SI

description: SPSS dataset
DOI: 10.6084/m9.figshare.8203415.v1
title: Bat Recording Manager v8.n

description: This program provides a management system for your library of bat (or other) recordings. It can be flexible in its approach but is primarily designed to work with libraries stored and analysed according to a particular protocol which is described below.<br>The program has four main ‘views’. The default view lists all recording sessions, with details of the currently selected session. Sessions can be added or edited manually or deleted from the database. Similarly individual recordings within the session can be added, edited or deleted.<br>The program assumes that the recordings are of bat calls, and incorporates a reference list of bat species, which can also be modified by the user. This reference list also defines a set of ‘tags’ which can be used when analysing recordings to indicate the presence of each species.<br>Recordings may also be displayed ‘by bat species’. In this case the defined species are listed and the recording sessions and recordings which detected the selected species are shown.<br>An ‘Import’ page allows recording sessions which have been analysed using Audacity to be imported into the database. A single folder containing a set of recordings may be imported or a selection of folders can be imported sequentially.Analyse and Import mode allows interaction with Audacity or Kaleidoscope Light for rapid sequential analysis of recording files.The program also provides report generation in a number of formats, storage of screen capture images during analysis, and the ability to replay portions of recordings at reduced speed or in heterodyne (tuned bat detector) mode.This setup file incorporates .NET 4.7.2 and Audacity 2.3.2 which will be installed automatically if required. The Audacity installation will not affect any pre-existing installations. Kaleidoscope interaction requires that Kaleidoscope is installed to C:<br>v8.0 builds on version 7.3 (see other figshare project) but updates to .NET 4.72 and provides virtualized data access for faster loading in some situations.
DOI: 10.6084/m9.figshare.8203358
title: Code scripts_Instances_Plots.rar

description: This folder contains code scripts, tested instances, figures, and results of the various computational studies that are conducted in the paper titled “Online Optimization of First-responder Routes in Disaster Response Logistics“ with authors Davood Shiri and F. Sibel Salman, submitted to the IBM Journal of Research and Development. The computational experiments are performed over four different type of networks: (1) a two-dimensional 32*32 grid network which is uniformly weighted, (2) multiple randomly generated Euclidean networks, (3) road network of the Gulf Coast area of the United States taken from the literature, (4) Istanbul city networks taken from the literature.
DOI: 10.6084/m9.figshare.8203355
title: Democratically deficient, yet responsive? How politicization facilitates responsiveness in the European Union

description: This article examines the thermostatic responsiveness of EU public policy. It inquires into the conditions under which EU policy decisions are responsive to wavering public demands for policy change and how European citizens in turn respond to policy change. The main argument holds that the <i>politicization</i> of EU policy processes facilitates both public and policy responsiveness. My expectations are tested based on a novel database containing information on 15 EU policy issues (2010–2016). The analyses draw from panel data based on Eurobarometer polls and a large-scale content analysis of 5887 media statements in eight European news outlets. The results demonstrate that under politicized conditions, the adoption of EU policy decisions is preceded by increased public support and followed by decreased public support for EU policy change. The facilitating role of politicization is primarily triggered by the mobilization of civil society groups, while media salience and polarization are less consequential for responsiveness.
DOI: 10.6084/m9.figshare.8203355.v1
title: Democratically deficient, yet responsive? How politicization facilitates responsiveness in the European Union

description: This article examines the thermostatic responsiveness of EU public policy. It inquires into the conditions under which EU policy decisions are responsive to wavering public demands for policy change and how European citizens in turn respond to policy change. The main argument holds that the <i>politicization</i> of EU policy processes facilitates both public and policy responsiveness. My expectations are tested based on a novel database containing information on 15 EU policy issues (2010–2016). The analyses draw from panel data based on Eurobarometer polls and a large-scale content analysis of 5887 media statements in eight European news outlets. The results demonstrate that under politicized conditions, the adoption of EU policy decisions is preceded by increased public support and followed by decreased public support for EU policy change. The facilitating role of politicization is primarily triggered by the mobilization of civil society groups, while media salience and polarization are less consequential for responsiveness.
DOI: 10.6084/m9.figshare.8203355.v3
title: Democratically deficient, yet responsive? How politicization facilitates responsiveness in the European Union

description: This article examines the thermostatic responsiveness of EU public policy. It inquires into the conditions under which EU policy decisions are responsive to wavering public demands for policy change and how European citizens in turn respond to policy change. The main argument holds that the <i>politicization</i> of EU policy processes facilitates both public and policy responsiveness. My expectations are tested based on a novel database containing information on 15 EU policy issues (2010–2016). The analyses draw from panel data based on Eurobarometer polls and a large-scale content analysis of 5887 media statements in eight European news outlets. The results demonstrate that under politicized conditions, the adoption of EU policy decisions is preceded by increased public support and followed by decreased public support for EU policy change. The facilitating role of politicization is primarily triggered by the mobilization of civil society groups, while media salience and polarization are less consequential for responsiveness.
DOI: 10.6084/m9.figshare.8203355.v2
title: Democratically deficient, yet responsive? How politicization facilitates responsiveness in the European Union

description: This article examines the thermostatic responsiveness of EU public policy. It inquires into the conditions under which EU policy decisions are responsive to wavering public demands for policy change and how European citizens in turn respond to policy change. The main argument holds that the <i>politicization</i> of EU policy processes facilitates both public and policy responsiveness. My expectations are tested based on a novel database containing information on 15 EU policy issues (2010–2016). The analyses draw from panel data based on Eurobarometer polls and a large-scale content analysis of 5887 media statements in eight European news outlets. The results demonstrate that under politicized conditions, the adoption of EU policy decisions is preceded by increased public support and followed by decreased public support for EU policy change. The facilitating role of politicization is primarily triggered by the mobilization of civil society groups, while media salience and polarization are less consequential for responsiveness.