cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4009887.v1
title: Supplementary Table 3. Power analysis results from Chemical communication is not sufficient to explain reproductive inhibition in the bumblebee <i>Bombus impatiens</i>

description: Reproductive division of labour is a hallmark of eusociality, but disentangling the underlying proximate mechanisms can be challenging. In bumblebees, workers isolated from the queen can activate their ovaries and lay haploid, male eggs. We investigated if volatile, contact, visual or behavioural cues produced by the queen or brood mediate reproductive dominance in <i>Bombus impatiens.</i> Exposure to queen-produced volatiles, brood-produced volatiles and direct contact with pupae did not reduce worker ovary activation: only direct contact with the queen could reduce ovary activation. We evaluated behaviour, physiology and gene expression patterns in workers that were reared in chambers with all stages of brood and a free queen, caged queen (where workers could contact the queen, but the queen was unable to initiate interactions) or no queen. Workers housed with a caged queen or no queen fully activated their ovaries, whereas ovary activation in workers housed with a free queen was completely inhibited. The caged queen marginally reduced worker aggression and expression of an aggression-associated gene relative to queenless workers. Thus, queen-initiated behavioural interactions appear necessary to establish reproductive dominance. Queen-produced chemical cues may function secondarily in a context-specific manner to augment behavioural cues, as reliable or honest signal.
DOI: 10.6084/m9.figshare.4009890.v1
title: Figure 5 raw data. The raw values for each shear metric within the instrumented and control arteries of each mouse from Influence of shear stress magnitude and direction on atherosclerotic plaque composition

description: The precise flow characteristics that promote different atherosclerotic plaque types remain unclear. We previously developed a blood flow-modifying cuff for ApoE<sup>−/−</sup> mice that induces the development of advanced plaques with vulnerable and stable features upstream and downstream of the cuff, respectively. Herein, we sought to test the hypothesis that changes in flow magnitude promote formation of the upstream (vulnerable) plaque, whereas altered flow direction is important for development of the downstream (stable) plaque. We instrumented ApoE<sup>−/−</sup> mice (<i>n</i> = 7) with a cuff around the left carotid artery and imaged them with micro-CT (39.6 µm resolution) eight to nine weeks after cuff placement. Computational fluid dynamics was then performed to compute six metrics that describe different aspects of atherogenic flow in terms of wall shear stress magnitude and/or direction. In a subset of four imaged animals, we performed histology to confirm the presence of advanced plaques and measure plaque length in each segment. Relative to the control artery, the region upstream of the cuff exhibited changes in shear stress magnitude only (<i>p</i> p
DOI: 10.7910/dvn/v1rjpf/wowvvw
title: ykc20161113_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hriyvf
title: ykc20161112_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/6u1uzd
title: ykc20160707_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4009875
title: Measurement of the wettabily of a kinorhynch body: Measured values of each specimen and each condition from Does the kinorhynch have a hydrophobic body surface? Measurement of the wettability of a meiobenthic metazoan

description: The body surface of aquatic invertebrates is generally thought to be hydrophilic to prevent the attachment of air bubbles. In contrast, some interstitial invertebrates, such as kinorhynchs and some crustaceans, have a hydrophobic body surface: they are often trapped at the water surface when the sediment in which they reside is mixed with air and water. Here, we directly measured the wettability of the body surface of the kinorhynch <i>Echinoderes komatsui</i>, using a microscopic contact angle meter. The intact body surface of live specimens was not hydrophobic, but the head was less hydrophilic. Furthermore, washing with seawater significantly decreased the wettability of the body surface, but a hydrophilic surface was recovered after a 1 h incubation in seawater. We believe that the hydrophobic cuticle of the kinorhynch has a hydrophilic coat that is readily exfoliated by disturbance. Ultrastructural observations supported the presence of a mucus-like coating on the cuticle. Regulation of wettability is crucial to survival in a shallow, fluctuating habitats for microscopic organisms and may also contribute to expansion of the dispersal range of these animals.
DOI: 10.7910/dvn/v1rjpf/0uepqt
title: ykc20160701_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4009875.v1
title: Measurement of the wettabily of a kinorhynch body: Measured values of each specimen and each condition from Does the kinorhynch have a hydrophobic body surface? Measurement of the wettability of a meiobenthic metazoan

description: The body surface of aquatic invertebrates is generally thought to be hydrophilic to prevent the attachment of air bubbles. In contrast, some interstitial invertebrates, such as kinorhynchs and some crustaceans, have a hydrophobic body surface: they are often trapped at the water surface when the sediment in which they reside is mixed with air and water. Here, we directly measured the wettability of the body surface of the kinorhynch <i>Echinoderes komatsui</i>, using a microscopic contact angle meter. The intact body surface of live specimens was not hydrophobic, but the head was less hydrophilic. Furthermore, washing with seawater significantly decreased the wettability of the body surface, but a hydrophilic surface was recovered after a 1 h incubation in seawater. We believe that the hydrophobic cuticle of the kinorhynch has a hydrophilic coat that is readily exfoliated by disturbance. Ultrastructural observations supported the presence of a mucus-like coating on the cuticle. Regulation of wettability is crucial to survival in a shallow, fluctuating habitats for microscopic organisms and may also contribute to expansion of the dispersal range of these animals.
DOI: 10.7910/dvn/v1rjpf/v4ye62
title: ykc20170810_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4009860
title: Dataset 1 from Zebrafish response to a robotic replica in three dimensions

description: As zebrafish emerge as a species of choice for the investigation of biological processes, a number of experimental protocols are being developed to study their social behaviour. While live stimuli may elicit varying response in focal subjects owing to idiosyncrasies, tiredness and circadian rhythms, video stimuli suffer from the absence of physical input and rely only on two-dimensional projections. Robotics has been recently proposed as an alternative approach to generate physical, customizable, effective and consistent stimuli for behavioural phenotyping. Here, we contribute to this field of investigation through a novel four-degree-of-freedom robotics-based platform to manoeuvre a biologically inspired three-dimensional-printed replica. The platform enables three-dimensional motions as well as body oscillations to mimic zebrafish locomotion. In a series of experiments, we demonstrate the differential role of the visual stimuli associated with the biologically inspired replica and its three-dimensional motion. Three-dimensional tracking and information-theoretic tools are complemented to quantify the interaction between zebrafish and the robotic stimulus. Live subjects displayed a robust attraction towards the moving replica, and such attraction was lost when controlling for its visual appearance or motion. This effort is expected to aid zebrafish behavioural phenotyping, by offering a novel approach to generate physical stimuli moving in three dimension.
DOI: 10.7910/dvn/v1rjpf/abogi9
title: ykc20160205_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4009860.v1
title: Dataset 1 from Zebrafish response to a robotic replica in three dimensions

description: As zebrafish emerge as a species of choice for the investigation of biological processes, a number of experimental protocols are being developed to study their social behaviour. While live stimuli may elicit varying response in focal subjects owing to idiosyncrasies, tiredness and circadian rhythms, video stimuli suffer from the absence of physical input and rely only on two-dimensional projections. Robotics has been recently proposed as an alternative approach to generate physical, customizable, effective and consistent stimuli for behavioural phenotyping. Here, we contribute to this field of investigation through a novel four-degree-of-freedom robotics-based platform to manoeuvre a biologically inspired three-dimensional-printed replica. The platform enables three-dimensional motions as well as body oscillations to mimic zebrafish locomotion. In a series of experiments, we demonstrate the differential role of the visual stimuli associated with the biologically inspired replica and its three-dimensional motion. Three-dimensional tracking and information-theoretic tools are complemented to quantify the interaction between zebrafish and the robotic stimulus. Live subjects displayed a robust attraction towards the moving replica, and such attraction was lost when controlling for its visual appearance or motion. This effort is expected to aid zebrafish behavioural phenotyping, by offering a novel approach to generate physical stimuli moving in three dimension.
DOI: 10.6084/m9.figshare.4009857
title: Dataset 2 from Zebrafish response to a robotic replica in three dimensions

description: As zebrafish emerge as a species of choice for the investigation of biological processes, a number of experimental protocols are being developed to study their social behaviour. While live stimuli may elicit varying response in focal subjects owing to idiosyncrasies, tiredness and circadian rhythms, video stimuli suffer from the absence of physical input and rely only on two-dimensional projections. Robotics has been recently proposed as an alternative approach to generate physical, customizable, effective and consistent stimuli for behavioural phenotyping. Here, we contribute to this field of investigation through a novel four-degree-of-freedom robotics-based platform to manoeuvre a biologically inspired three-dimensional-printed replica. The platform enables three-dimensional motions as well as body oscillations to mimic zebrafish locomotion. In a series of experiments, we demonstrate the differential role of the visual stimuli associated with the biologically inspired replica and its three-dimensional motion. Three-dimensional tracking and information-theoretic tools are complemented to quantify the interaction between zebrafish and the robotic stimulus. Live subjects displayed a robust attraction towards the moving replica, and such attraction was lost when controlling for its visual appearance or motion. This effort is expected to aid zebrafish behavioural phenotyping, by offering a novel approach to generate physical stimuli moving in three dimension.
DOI: 10.7910/dvn/v1rjpf/3rjlru
title: ykc20160127_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ohtjyc
title: ykc20160615_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4009857.v1
title: Dataset 2 from Zebrafish response to a robotic replica in three dimensions

description: As zebrafish emerge as a species of choice for the investigation of biological processes, a number of experimental protocols are being developed to study their social behaviour. While live stimuli may elicit varying response in focal subjects owing to idiosyncrasies, tiredness and circadian rhythms, video stimuli suffer from the absence of physical input and rely only on two-dimensional projections. Robotics has been recently proposed as an alternative approach to generate physical, customizable, effective and consistent stimuli for behavioural phenotyping. Here, we contribute to this field of investigation through a novel four-degree-of-freedom robotics-based platform to manoeuvre a biologically inspired three-dimensional-printed replica. The platform enables three-dimensional motions as well as body oscillations to mimic zebrafish locomotion. In a series of experiments, we demonstrate the differential role of the visual stimuli associated with the biologically inspired replica and its three-dimensional motion. Three-dimensional tracking and information-theoretic tools are complemented to quantify the interaction between zebrafish and the robotic stimulus. Live subjects displayed a robust attraction towards the moving replica, and such attraction was lost when controlling for its visual appearance or motion. This effort is expected to aid zebrafish behavioural phenotyping, by offering a novel approach to generate physical stimuli moving in three dimension.
DOI: 10.7910/dvn/v1rjpf/6bau4m
title: ykc20160815_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/atytw5
title: ykc20161128_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.4009842
title: The original gene expression data including four tissue from The role of three heat shock protein genes in the immune response to <i>Aeromonas hydrophila</i> challenge in marbled eel, <i>Anguilla marmorata</i>

description: Heat shock proteins (HSPs) are highly conserved molecular chaperones that play critical roles in both innate and adaptive immune. However, little information about <i>hsps</i> from marbled eel, <i>Anguilla marmorata</i> is known. In this study, the full-length <i>Amhsp90</i> (2527 bp), <i>Amhsp70</i> (2443 bp) and <i>Amhsc70</i> (2247 bp) were first cloned from <i>A. marmorata</i>, using rapid amplification of cDNA ends, containing open reading frames with 2181, 1932 and 1950 bp in length, and encoding proteins with 726, 643 and 649 amino acids, respectively. The deduced amino acid sequences of three <i>Amhsps</i> shared a high homology similarity with other migratory fish. Real-time fluorescent quantitative-PCR was used to evaluate tissue-specific distribution and mRNA expression levels of three <i>Amhsps</i> subjected to the infection with <i>Aeromonas hydrophila</i>. The mRNA expression of three <i>Amhsps</i> in eight tested tissues, including liver, heart, muscle, gill, spleen, kidney, brain and intestine tissues of juvenile <i>A. marmorata</i> was evaluated to reveal the major expression distribution in liver, intestine, muscle and heart. After pathogen challenge treatments, mRNA transcriptions of three <i>Amhsps</i> revealed a significant regulation at various time points in the same tissue. All these findings suggest that <i>Amhsps</i> may be involved in the immune response in <i>A. marmorata</i>.
DOI: 10.15156/bio/sh117723.07fu
title: SH117723.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh117724.07fu
title: SH117724.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh117725.07fu
title: SH117725.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh117726.07fu
title: SH117726.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh117727.07fu
title: SH117727.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh117728.07fu
title: SH117728.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh117729.07fu
title: SH117729.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh117730.07fu
title: SH117730.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.