cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7539239.v1
title: Nexus file used to run phylogenetic analysis from Burgess shale fossils shed light on the agnostid problem

description: Agnostids (agnostinids and eodiscinids) are a widespread and biostratigraphically important group of Cambro-Ordovician euarthropods whose evolutionary affinities have been highly controversial. Their dumbbell-shaped calcified tergum was traditionally suggested to unite them with trilobites, but agnostinids have alternatively been interpreted as stem-crustaceans, based on Orsten larval material from the Cambrian of Sweden. We describe exceptionally preserved soft tissues from mature individuals of the agnostinids <i>Peronopsis</i> and <i>Ptychagnostus</i> from the middle Cambrian (Wuliuan Stage) Burgess Shale (Walcott Quarry and Marble Canyon, British Columbia, Canada), facilitating the testing of alternative hypotheses. The digestive tract includes conspicuous ramifying cephalic diverticulae. The cephalon carries one pair of elongate spinous antennules projecting to the front, two pairs of appendages with terminal setose, oar-like exopods, and three pairs of presumably biramous appendages with endopods sporting club-shaped exites. The trunk bears five appendage pairs, at least the first two of which are similar to the posteriormost cephalic pairs. A head with six appendiferous segments contrasts strikingly with the four known in trilobites and five typical of mandibulates. Our phylogenetic analysis retrieves agnostinids as the sister group to ‘polymeroid’ trilobites, implying that crustacean-like morphologies evolved homoplastically and highlighting the variability in segmental composition of the artiopodan head. Our study supports a nektobenthic lifestyle for agnostinids and emphasizes the importance of Burgess Shale-type fossils in resolving the affinities of problematic biomineralizing taxa.
DOI: 10.6084/m9.figshare.7539248
title: Stretcher3Dmodel from Embryonic stem cells become functionally sensitive to mechanical stress upon exit from naive pluripotency.

description: Stem cell fate decisions are driven by a broad array of signals, both chemical and mechanical. Although much progress has been made in our understanding of the impact of chemical signals on cell fate choice, much less is known about the role and influence of mechanical signalling, particularly in embryonic stem (ES) cells. Many studies use substrates with different stiffness to study mechanical signalling, but changing substrate stiffness can induce secondary effects which are difficult to disentangle from the direct effects of forces/mechanical signals. To probe the direct impact of mechanical stress on cells, we developed an adaptable cell substrate stretcher to exert specific, reproducible forces on cells. Using this device to test the response of ES cells to tensile strain, we found that cells experienced a transient influx of calcium followed by an upregulation of the so-called immediate and early genes. On longer timescales, however, ES cells in naive pluripotent conditions were largely insensitive to mechanical stress. Nonetheless, as ES cells exited the ground state, their susceptibility to mechanical signals increased, resulting in broad transcriptional changes. Our findings suggest that exit from naive pluripotency is unaffected by mechanical signals, but that these signals could become important during the next stage of lineage specification. A better understanding of this process could improve our understanding of cell fate choice in early development and improve protocols for differentiation guided by mechanical cues.
DOI: 10.6084/m9.figshare.7539248.v2
title: Stretcher3Dmodel from Embryonic stem cells become functionally sensitive to mechanical stress upon exit from naive pluripotency.

description: Stem cell fate decisions are driven by a broad array of signals, both chemical and mechanical. Although much progress has been made in our understanding of the impact of chemical signals on cell fate choice, much less is known about the role and influence of mechanical signalling, particularly in embryonic stem (ES) cells. Many studies use substrates with different stiffness to study mechanical signalling, but changing substrate stiffness can induce secondary effects which are difficult to disentangle from the direct effects of forces/mechanical signals. To probe the direct impact of mechanical stress on cells, we developed an adaptable cell substrate stretcher to exert specific, reproducible forces on cells. Using this device to test the response of ES cells to tensile strain, we found that cells experienced a transient influx of calcium followed by an upregulation of the so-called immediate and early genes. On longer timescales, however, ES cells in naive pluripotent conditions were largely insensitive to mechanical stress. Nonetheless, as ES cells exited the ground state, their susceptibility to mechanical signals increased, resulting in broad transcriptional changes. Our findings suggest that exit from naive pluripotency is unaffected by mechanical signals, but that these signals could become important during the next stage of lineage specification. A better understanding of this process could improve our understanding of cell fate choice in early development and improve protocols for differentiation guided by mechanical cues.
DOI: 10.6084/m9.figshare.7539248.v1
title: Stretcher3Dmodel from Embryonic stem cells become functionally sensitive to mechanical stress upon exit from naive pluripotency

description: Stem cell fate decisions are driven by a broad array of signals, both chemical and mechanical. Although much progress has been made in our understanding of the impact of chemical signals on cell fate choice, much less is known about the role and influence of mechanical signalling, particularly in embryonic stem (ES) cells. Many studies use substrates with different stiffness to study mechanical signalling, but changing substrate stiffness can induce secondary effects which are difficult to disentangle from the direct effects of forces/mechanical signals. To probe the direct impact of mechanical stress on cells, we developed an adaptable cell substrate stretcher to exert specific, reproducible forces on cells. Using this device to test the response of ES cells to tensile strain, we found that cells experienced a transient influx of calcium followed by an upregulation of the so-called immediate and early genes. On longer timescales, however, ES cells in naive pluripotent conditions were largely insensitive to mechanical stress. Nonetheless, as ES cells exited the naive state, their susceptibility to mechanical signals increased, resulting in broad transcriptional changes. Our findings suggest that exit from naive pluripotency is unaffected by mechanical signals, but that these signals could become important during the next stage of lineage specification. A better understanding of this process could improve our understanding of cell fate choice in early development and improve protocols for differentiation guided by mechanical cues.
DOI: 10.6084/m9.figshare.7583834
title: Uniform Pulloff Data from Spatially variant microstructured adhesive with one-way friction.

description: Preload force and pulloff force direction and magnitude for tests on uniform adhesive materials.
DOI: 10.6084/m9.figshare.7583831
title: Spatially Variant Pulloff Data from Spatially variant microstructured adhesive with one-way friction.

description: Preload force and friction magnitude for tests on spatially variant adhesive materials.
DOI: 10.6084/m9.figshare.7583834.v2
title: Uniform Pulloff Data from Spatially variant microstructured adhesive with one-way friction.

description: Preload force and pulloff force direction and magnitude for tests on uniform adhesive materials.
DOI: 10.6084/m9.figshare.7583831.v2
title: Spatially Variant Pulloff Data from Spatially variant microstructured adhesive with one-way friction.

description: Preload force and friction magnitude for tests on spatially variant adhesive materials.
DOI: 10.6084/m9.figshare.7583840
title: ANSYS Simulation Data from Spatially variant microstructured adhesive with one-way friction.

description: Geometric parameters and extracted tip displacement and forces for ANSYS simulations.
DOI: 10.6084/m9.figshare.7583834.v1
title: Uniform Pulloff Data from Spatially variant microstructured adhesive with one-way friction

description: Preload force and pulloff force direction and magnitude for tests on uniform adhesive materials.
DOI: 10.6084/m9.figshare.7583831.v1
title: Spatially Variant Pulloff Data from Spatially variant microstructured adhesive with one-way friction

description: Preload force and friction magnitude for tests on spatially variant adhesive materials.
DOI: 10.6084/m9.figshare.7583837
title: Wedge Stiffness Model Data from Spatially variant microstructured adhesive with one-way friction.

description: Compressive and shear force data as a function of applied compressive displacement.
DOI: 10.6084/m9.figshare.7583840.v2
title: ANSYS Simulation Data from Spatially variant microstructured adhesive with one-way friction.

description: Geometric parameters and extracted tip displacement and forces for ANSYS simulations.
DOI: 10.6084/m9.figshare.7583837.v2
title: Wedge Stiffness Model Data from Spatially variant microstructured adhesive with one-way friction.

description: Compressive and shear force data as a function of applied compressive displacement.
DOI: 10.6084/m9.figshare.7583840.v1
title: ANSYS Simulation Data from Spatially variant microstructured adhesive with one-way friction

description: Geometric parameters and extracted tip displacement and forces for ANSYS simulations.
DOI: 10.6084/m9.figshare.7583837.v1
title: Wedge Stiffness Model Data from Spatially variant microstructured adhesive with one-way friction

description: Compressive and shear force data as a function of applied compressive displacement.
DOI: 10.6084/m9.figshare.7610729
title: Yilmaz et al._data_ESM from Distributed plasticity in ant visual pathways following colour learning.

description: Data files supporting the paper
DOI: 10.6084/m9.figshare.7610729.v2
title: Yilmaz et al._data_ESM from Distributed plasticity in ant visual pathways following colour learning.

description: Data files supporting the paper
DOI: 10.6084/m9.figshare.7610729.v1
title: Yilmaz et al._data_ESM from Distributed plasticity in ant visual pathways following colour learning

description: Data files supporting the paper
DOI: 10.6084/m9.figshare.7611083
title: Table S1: list of analyzed species from Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life.

description: Species sequenced and analyzed in this study, including new and publicly available data.
DOI: 10.6084/m9.figshare.7611083.v2
title: Table S1: list of analyzed species from Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life.

description: Species sequenced and analyzed in this study, including new and publicly available data.
DOI: 10.6084/m9.figshare.7611083.v1
title: Table S1: list of analyzed species from Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life

description: Species sequenced and analyzed in this study, including new and publicly available data.
DOI: 10.5281/zenodo.4090961
title: Subjective Test Dataset and Meta-data-based Models for 360° Streaming Video Quality

description: During the last years, the number of 360° videos available for streaming has rapidly increased, leading to the<br> need for 360° streaming video quality assessment. In this paper, we report and publish results of three subjective 360° video<br> quality tests, with conditions used to reflect real-world bitrates and resolutions including 4K, 6K and 8K, resulting in 64 stimuli<br> each for the first two tests and 63 for the third. As playout device we used the HTC Vive for the first and HTC Vive Pro<br> for the remaining two tests. Video-quality ratings were collected using the 5-point Absolute Category Rating scale. The 360°<br> dataset provided with the paper contains the links of the used source videos, the raw subjective scores, video-related meta-data,<br> head rotation data and Simulator Sickness Questionnaire results per stimulus and per subject to enable reproducibility of the<br> provided results. Moreover, we use our dataset to compare the performance of state-of-the-art full-reference quality metrics such<br> as VMAF, PSNR, SSIM, ADM2, WS-PSNR and WS-SSIM. Out of all metrics, VMAF was found to show the highest correlation<br> with the subjective scores. Further, we evaluated a center-cropped version of VMAF ("VMAF-cc") that showed to provide a similar<br> performance as the full VMAF. In addition to the dataset and the objective metric evaluation, we propose two new video-quality<br> prediction models, a bitstream meta-data-based model and a hybrid no-reference model using bitrate, resolution and pixel<br> information of the video as input. The new lightweight models provide similar performance as the full-reference models while<br> enabling fast calculations.
DOI: 10.6084/m9.figshare.7613180
title: Crater_Expt1_AdultData.csv from Male sexual signal predicts phenotypic plasticity in offspring: implications for the evolution of plasticity and local adaptation.

description: In a rapidly changing world, understanding the processes that influence a population's ability to respond to natural selection is critical for identifying how to preserve biodiversity. Two such processes are phenotypic plasticity and sexual selection. Whereas plasticity can facilitate local adaptation, sexual selection potentially impedes local adaptation, especially in rapidly changing or variable environments. Here we hypothesize that, when females preferentially choose males that sire plastic offspring, sexual selection can actually facilitate local adaptation to variable or novel environments by promoting the evolution of adaptive plasticity. We tested this hypothesis by evaluating whether male sexual signals could indicate plasticity in their offspring and, concomitantly, their offspring's ability to produce locally adapted phenotypes. Using spadefoot toads (<i>Spea multiplicata</i>) as our experimental system, we show that a male sexual signal predicts plasticity in his offspring's resource-use morphology. Specifically, faster-calling males (which are preferred by females) produce more plastic offspring; such plasticity, in turn, enables these males' offspring to respond adaptively to the spadefoots’ highly variable environment. The association between a preferred male signal and adaptive plasticity in his offspring suggests that female mate choice can favour the evolution and maintenance of phenotypic plasticity and thereby foster adaptation to a variable environment.This article is part of the theme issue ‘The role of plasticity in phenotypic adaptation to rapid environmental change’.
DOI: 10.6084/m9.figshare.7613183
title: PO2_Expt2.csv from Male sexual signal predicts phenotypic plasticity in offspring: implications for the evolution of plasticity and local adaptation.

description: In a rapidly changing world, understanding the processes that influence a population's ability to respond to natural selection is critical for identifying how to preserve biodiversity. Two such processes are phenotypic plasticity and sexual selection. Whereas plasticity can facilitate local adaptation, sexual selection potentially impedes local adaptation, especially in rapidly changing or variable environments. Here we hypothesize that, when females preferentially choose males that sire plastic offspring, sexual selection can actually facilitate local adaptation to variable or novel environments by promoting the evolution of adaptive plasticity. We tested this hypothesis by evaluating whether male sexual signals could indicate plasticity in their offspring and, concomitantly, their offspring's ability to produce locally adapted phenotypes. Using spadefoot toads (<i>Spea multiplicata</i>) as our experimental system, we show that a male sexual signal predicts plasticity in his offspring's resource-use morphology. Specifically, faster-calling males (which are preferred by females) produce more plastic offspring; such plasticity, in turn, enables these males' offspring to respond adaptively to the spadefoots’ highly variable environment. The association between a preferred male signal and adaptive plasticity in his offspring suggests that female mate choice can favour the evolution and maintenance of phenotypic plasticity and thereby foster adaptation to a variable environment.This article is part of the theme issue ‘The role of plasticity in phenotypic adaptation to rapid environmental change’.
DOI: 10.5281/zenodo.4090960
title: Subjective Test Dataset and Meta-data-based Models for 360° Streaming Video Quality

description: During the last years, the number of 360° videos available for streaming has rapidly increased, leading to the<br> need for 360° streaming video quality assessment. In this paper, we report and publish results of three subjective 360° video<br> quality tests, with conditions used to reflect real-world bitrates and resolutions including 4K, 6K and 8K, resulting in 64 stimuli<br> each for the first two tests and 63 for the third. As playout device we used the HTC Vive for the first and HTC Vive Pro<br> for the remaining two tests. Video-quality ratings were collected using the 5-point Absolute Category Rating scale. The 360°<br> dataset provided with the paper contains the links of the used source videos, the raw subjective scores, video-related meta-data,<br> head rotation data and Simulator Sickness Questionnaire results per stimulus and per subject to enable reproducibility of the<br> provided results. Moreover, we use our dataset to compare the performance of state-of-the-art full-reference quality metrics such<br> as VMAF, PSNR, SSIM, ADM2, WS-PSNR and WS-SSIM. Out of all metrics, VMAF was found to show the highest correlation<br> with the subjective scores. Further, we evaluated a center-cropped version of VMAF ("VMAF-cc") that showed to provide a similar<br> performance as the full VMAF. In addition to the dataset and the objective metric evaluation, we propose two new video-quality<br> prediction models, a bitstream meta-data-based model and a hybrid no-reference model using bitrate, resolution and pixel<br> information of the video as input. The new lightweight models provide similar performance as the full-reference models while<br> enabling fast calculations.
DOI: 10.6084/m9.figshare.7613174
title: Crater_Expt1.csv from Male sexual signal predicts phenotypic plasticity in offspring: implications for the evolution of plasticity and local adaptation.

description: In a rapidly changing world, understanding the processes that influence a population's ability to respond to natural selection is critical for identifying how to preserve biodiversity. Two such processes are phenotypic plasticity and sexual selection. Whereas plasticity can facilitate local adaptation, sexual selection potentially impedes local adaptation, especially in rapidly changing or variable environments. Here we hypothesize that, when females preferentially choose males that sire plastic offspring, sexual selection can actually facilitate local adaptation to variable or novel environments by promoting the evolution of adaptive plasticity. We tested this hypothesis by evaluating whether male sexual signals could indicate plasticity in their offspring and, concomitantly, their offspring's ability to produce locally adapted phenotypes. Using spadefoot toads (<i>Spea multiplicata</i>) as our experimental system, we show that a male sexual signal predicts plasticity in his offspring's resource-use morphology. Specifically, faster-calling males (which are preferred by females) produce more plastic offspring; such plasticity, in turn, enables these males' offspring to respond adaptively to the spadefoots’ highly variable environment. The association between a preferred male signal and adaptive plasticity in his offspring suggests that female mate choice can favour the evolution and maintenance of phenotypic plasticity and thereby foster adaptation to a variable environment.This article is part of the theme issue ‘The role of plasticity in phenotypic adaptation to rapid environmental change’.
DOI: 10.6084/m9.figshare.7613180.v2
title: Crater_Expt1_AdultData.csv from Male sexual signal predicts phenotypic plasticity in offspring: implications for the evolution of plasticity and local adaptation.

description: In a rapidly changing world, understanding the processes that influence a population's ability to respond to natural selection is critical for identifying how to preserve biodiversity. Two such processes are phenotypic plasticity and sexual selection. Whereas plasticity can facilitate local adaptation, sexual selection potentially impedes local adaptation, especially in rapidly changing or variable environments. Here we hypothesize that, when females preferentially choose males that sire plastic offspring, sexual selection can actually facilitate local adaptation to variable or novel environments by promoting the evolution of adaptive plasticity. We tested this hypothesis by evaluating whether male sexual signals could indicate plasticity in their offspring and, concomitantly, their offspring's ability to produce locally adapted phenotypes. Using spadefoot toads (<i>Spea multiplicata</i>) as our experimental system, we show that a male sexual signal predicts plasticity in his offspring's resource-use morphology. Specifically, faster-calling males (which are preferred by females) produce more plastic offspring; such plasticity, in turn, enables these males' offspring to respond adaptively to the spadefoots’ highly variable environment. The association between a preferred male signal and adaptive plasticity in his offspring suggests that female mate choice can favour the evolution and maintenance of phenotypic plasticity and thereby foster adaptation to a variable environment.This article is part of the theme issue ‘The role of plasticity in phenotypic adaptation to rapid environmental change’.
DOI: 10.6084/m9.figshare.7613177
title: rstb20180179_si_004.csv from Male sexual signal predicts phenotypic plasticity in offspring: implications for the evolution of plasticity and local adaptation.

description: In a rapidly changing world, understanding the processes that influence a population's ability to respond to natural selection is critical for identifying how to preserve biodiversity. Two such processes are phenotypic plasticity and sexual selection. Whereas plasticity can facilitate local adaptation, sexual selection potentially impedes local adaptation, especially in rapidly changing or variable environments. Here we hypothesize that, when females preferentially choose males that sire plastic offspring, sexual selection can actually facilitate local adaptation to variable or novel environments by promoting the evolution of adaptive plasticity. We tested this hypothesis by evaluating whether male sexual signals could indicate plasticity in their offspring and, concomitantly, their offspring's ability to produce locally adapted phenotypes. Using spadefoot toads (<i>Spea multiplicata</i>) as our experimental system, we show that a male sexual signal predicts plasticity in his offspring's resource-use morphology. Specifically, faster-calling males (which are preferred by females) produce more plastic offspring; such plasticity, in turn, enables these males' offspring to respond adaptively to the spadefoots’ highly variable environment. The association between a preferred male signal and adaptive plasticity in his offspring suggests that female mate choice can favour the evolution and maintenance of phenotypic plasticity and thereby foster adaptation to a variable environment.This article is part of the theme issue ‘The role of plasticity in phenotypic adaptation to rapid environmental change’.