cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4248767.v1
title: Autolysosome biogenesis and developmental senescence are regulated by both Spns1 and v-ATPase

description: Spns1 (Spinster homolog 1 [<i>Drosophila</i>]) in vertebrates, as well as Spin (Spinster) in <i>Drosophila</i>, is a hypothetical lysosomal H<sup>+</sup>-carbohydrate transporter, which functions at a late stage of macroautophagy (hereafter autophagy). The Spin/Spns1 defect induces aberrant autolysosome formation that leads to developmental senescence in the embryonic stage and premature aging symptoms in adulthood. However, the molecular mechanism by which loss of Spin/Spns1 leads to the specific pathogenesis remains to be elucidated. Using chemical, genetic and CRISPR/Cas9-mediated genome-editing approaches in zebrafish, we investigated and determined a mechanism that suppresses embryonic senescence as well as autolysosomal impairment mediated by Spns1 deficiency. Unexpectedly, we found that a concurrent disruption of the vacuolar-type H<sup>+</sup>-ATPase (v-ATPase) subunit gene, <i>atp6v0ca</i> (ATPase, H<sup>+</sup> transporting, lysosomal, V0 subunit ca) led to suppression of the senescence induced by the Spns1 defect, whereas the sole loss of Atp6v0ca led to senescent embryos similar to the single <i>spns1</i> mutation. Moreover, we discovered that the combined stable defect seen in the presence of both the <i>spns1</i> and <i>atp6v0ca</i> mutant genes still subsequently induced premature autophagosome-lysosome fusion marked by insufficient acidity, while extending developmental life span, compared with the solely mutated <i>spns1</i> defect. Our data suggest that Spns1 and the v-ATPase orchestrate proper autolysosomal biogenesis with optimal acidification that is critically linked to developmental senescence and survival.
DOI: 10.17608/k6.auckland.4248656
title: figures6and7EJP.ipynb

description: jupyter notebook to create the figures of our EJP article on earthquake location with school seismograms.
DOI: 10.17608/k6.auckland.4248656.v2
title: figures6and7EJP.ipynb

description: jupyter notebook to create the figures of our EJP article on earthquake location with school seismograms.
DOI: 10.6084/m9.figshare.4246982
title: Test-retest reliability of scotopic full-field electroretinograms in rabbits

description: Scotopic ERG values (a-wave (N1) and b-wave (P1) amplitudes and peak times across a wide range of stimulus strengths in New Zealand White rabbits.“ allDataTestRetest.xlsx” contains the data, the other files are R scripts to load and generate the various analysis findings and figures.
DOI: 10.6084/m9.figshare.4246745
title: Objectives and design of BLEEDS: a cohort study to identify new risk factors and predictors for major bleeding during treatment with vitamin K antagonists

description: Data used in the article 'Objectives and design of BLEEDS: a cohort study to identify new risk factors and predictors for major bleeding during treatment with vitamin K antagonists' published in Plos One
DOI: 10.6084/m9.figshare.4246718
title: Abundance and Characterization of Perfect Microsatellites on the Cattle Y Chromosome

description: Microsatellites or simple sequence repeats (SSRs) are found in most organisms and play an important role in genomic organization and function. To characterize the abundance of SSRs (1-6 base-pairs [bp]) on the cattle Y chromsome, the relative frequency and density of perfect or uninterrupted SSRs based on the published Y chromosome sequence were examined. A total of 17,273 perfect SSRs were found, with total length of 324.78 kb, indicating that approximately 0.75% of the cattle Y chromosome sequence (43.30 Mb) comprises perfect SSRs, with an average length of 18.80 bp. The relative frequency and density were 398.92 loci/Mb and 7500.62 bp/Mb, respectively. The proportions of the six classes of perfect SSRs were highly variable on the cattle Y chromosome. Mononucleotide repeats had a total number of 8073 (46.74%) and an average length of 15.45 bp, and were the most abundant SSRs class, while the percentages of di-, tetra-, tri-, penta-, and hexa-nucleotide repeats were 22.86%, 11.98%, 11.58%, 6.65%, and 0.19%, respectively. Different classes of SSRs varied in their repeat number, with the highest being 42 for dinucleotides. Results reveal that repeat categories A, AC, AT, AAC, AGC, GTTT, CTTT, ATTT, and AACTG predominate on the Y chromosome. This study provides insight into the organization of cattle Y chromosome repetitive DNA, as well as information useful for developing more polymorphic cattle Y-chromosome-specific SSRs.
DOI: 10.6084/m9.figshare.4246718.v1
title: Abundance and Characterization of Perfect Microsatellites on the Cattle Y Chromosome

description: Microsatellites or simple sequence repeats (SSRs) are found in most organisms and play an important role in genomic organization and function. To characterize the abundance of SSRs (1-6 base-pairs [bp]) on the cattle Y chromsome, the relative frequency and density of perfect or uninterrupted SSRs based on the published Y chromosome sequence were examined. A total of 17,273 perfect SSRs were found, with total length of 324.78 kb, indicating that approximately 0.75% of the cattle Y chromosome sequence (43.30 Mb) comprises perfect SSRs, with an average length of 18.80 bp. The relative frequency and density were 398.92 loci/Mb and 7500.62 bp/Mb, respectively. The proportions of the six classes of perfect SSRs were highly variable on the cattle Y chromosome. Mononucleotide repeats had a total number of 8073 (46.74%) and an average length of 15.45 bp, and were the most abundant SSRs class, while the percentages of di-, tetra-, tri-, penta-, and hexa-nucleotide repeats were 22.86%, 11.98%, 11.58%, 6.65%, and 0.19%, respectively. Different classes of SSRs varied in their repeat number, with the highest being 42 for dinucleotides. Results reveal that repeat categories A, AC, AT, AAC, AGC, GTTT, CTTT, ATTT, and AACTG predominate on the Y chromosome. This study provides insight into the organization of cattle Y chromosome repetitive DNA, as well as information useful for developing more polymorphic cattle Y-chromosome-specific SSRs.
DOI: 10.6084/m9.figshare.4246706
title: Epigenetic changes as prognostic predictors in endometrial carcinomas

description: Endometrial carcinoma is one of the most frequent gynecological malignancies of the female. The diagnostic and prognostic markers for the high-risk subgroups with unfavorable prognosis are under intense debate worldwide, and, therefore, the aim of this study was to identify new potential DNA methylation markers for the high-risk groups. We used the Illumina Infinium HumanMethylation450 BeadChip to analyze the DNA methylation pattern and investigated its association with clinicopathological features important for defining the high-risk (FIGO-grade 3) and low-risk (FIGO-grade 1) groups of patients with endometrial cancer (n = 31 and n = 39, respectively). We identified specific DNA methylation signature in high-risk endometrial tumors, and potential molecular biomarker genes (<i>TBX2, CHST11</i>, and <i>NID2</i>) associated with unfavorable clinical predictive and prognostic factors.
DOI: 10.6084/m9.figshare.4246706.v1
title: Epigenetic changes as prognostic predictors in endometrial carcinomas

description: Endometrial carcinoma is one of the most frequent gynecological malignancies of the female. The diagnostic and prognostic markers for the high-risk subgroups with unfavorable prognosis are under intense debate worldwide, and, therefore, the aim of this study was to identify new potential DNA methylation markers for the high-risk groups. We used the Illumina Infinium HumanMethylation450 BeadChip to analyze the DNA methylation pattern and investigated its association with clinicopathological features important for defining the high-risk (FIGO-grade 3) and low-risk (FIGO-grade 1) groups of patients with endometrial cancer (n = 31 and n = 39, respectively). We identified specific DNA methylation signature in high-risk endometrial tumors, and potential molecular biomarker genes (<i>TBX2, CHST11</i>, and <i>NID2</i>) associated with unfavorable clinical predictive and prognostic factors.
DOI: 10.6084/m9.figshare.4246694
title: Territorial black-capped chickadee males respond faster to high- than to low-frequency songs in experimentally elevated noise conditions

description: This is the data for the manuscript: Territorial black-capped chickadee males respond faster to high- than to low-frequency songs in experimentally elevated noise conditions<br><b><br>Metadata as follows:<br><br></b>Each row corresponds to a single playback trial. Two rows constitutes a paired playback dyad.<br><b>ID</b> - ID of focal male<br><b>region</b> - region where playback was performed (van = Vancouver; kel = Kelowna; que = Quesnel; prg = Prince George)<br><b>hab</b> - Urbanization index (see LaZerte et al. 2017 DOI: 10.1007/s11252-017-0652-7)<br><b>spl</b> - Sound Pressure level in dB(Z) measured after each trial<br><b>spl_scale</b> - SPL centered around zero<br><b>treatment</b> - Contrast category including playback order and stimulus type<br><b>pb_freq_c</b> - Which stimulus type was presented (Categorical frequency)<br><b>pb_order</b> - Order of stimuli presentation<br><b>pb_freq</b> - Dominant frequency of bee-note in stimulus in kHz<br><b>pb_file </b>- File name of the playback stimulus<br><b>start_dist</b> - Starting distance in meters of the focal male<br><b>first_rxn</b> - Response, latency to first response<br><b>PC1_dist</b> - Response, PC1 Approach and stay close<br><b>PC2_song</b> - Response, PC2 Sing more<br><b>time_0_10</b> - Contribution to PCs, Time spent &lt; 10m from speaker<br><b>time_10_20</b> - Contribution to PCs, Time spent between 10 and 20m from speaker<br><b>time_20_100</b> - Contribution to PCs, Time spent &gt; 20m from speaker<br><b>latency_dist_min</b> - Contribution to PCs, Latency (s) to minimum distance from speaker<br><b>dist_min</b> - Contribution to PCs, Minimum distance from speaker<br><b>total_song</b> - Contribution to PCs, Total songs sung during trial<br>
DOI: 10.6084/m9.figshare.4246706.v2
title: Epigenetic changes as prognostic predictors in endometrial carcinomas

description: Endometrial carcinoma is one of the most frequent gynecological malignancies of the female. The diagnostic and prognostic markers for the high-risk subgroups with unfavorable prognosis are under intense debate worldwide, and, therefore, the aim of this study was to identify new potential DNA methylation markers for the high-risk groups. We used the Illumina Infinium HumanMethylation450 BeadChip to analyze the DNA methylation pattern and investigated its association with clinicopathological features important for defining the high-risk (FIGO-grade 3) and low-risk (FIGO-grade 1) groups of patients with endometrial cancer (n = 31 and n = 39, respectively). We identified specific DNA methylation signature in high-risk endometrial tumors, and potential molecular biomarker genes (<i>TBX2, CHST11</i>, and <i>NID2</i>) associated with unfavorable clinical predictive and prognostic factors.
DOI: 10.6084/m9.figshare.4246706.v3
title: Epigenetic changes as prognostic predictors in endometrial carcinomas

description: Endometrial carcinoma is one of the most frequent gynecological malignancies of the female. The diagnostic and prognostic markers for the high-risk subgroups with unfavorable prognosis are under intense debate worldwide, and, therefore, the aim of this study was to identify new potential DNA methylation markers for the high-risk groups. We used the Illumina Infinium HumanMethylation450 BeadChip to analyze the DNA methylation pattern and investigated its association with clinicopathological features important for defining the high-risk (FIGO-grade 3) and low-risk (FIGO-grade 1) groups of patients with endometrial cancer (n = 31 and n = 39, respectively). We identified specific DNA methylation signature in high-risk endometrial tumors, and potential molecular biomarker genes (<i>TBX2, CHST11</i>, and <i>NID2</i>) associated with unfavorable clinical predictive and prognostic factors.
DOI: 10.6084/m9.figshare.4246694.v1
title: Territorial black-capped chickadee males respond faster to high- than to low-frequency songs in experimentally elevated noise conditions

description: This is the data for the manuscript: Territorial black-capped chickadee males respond faster to high- than to low-frequency songs in experimentally elevated noise conditions<br><b><br>Metadata as follows:<br><br></b>Each row corresponds to a single playback trial. Two rows constitutes a paired playback dyad.<br><b>ID</b> - ID of focal male<br><b>region</b> - region where playback was performed (van = Vancouver; kel = Kelowna; que = Quesnel; prg = Prince George)<br><b>hab</b> - Urbanization index (see LaZerte et al. 2017 DOI: 10.1007/s11252-017-0652-7)<br><b>spl</b> - Sound Pressure level in dB(Z) measured after each trial<br><b>spl_scale</b> - SPL centered around zero<br><b>treatment</b> - Contrast category including playback order and stimulus type<br><b>pb_freq_c</b> - Which stimulus type was presented (Categorical frequency)<br><b>pb_order</b> - Order of stimuli presentation<br><b>pb_freq</b> - Dominant frequency of bee-note in stimulus in kHz<br><b>pb_file </b>- File name of the playback stimulus<br><b>start_dist</b> - Starting distance in meters of the focal male<br><b>first_rxn</b> - Response, latency to first response<br><b>PC1_dist</b> - Response, PC1 Approach and stay close<br><b>PC2_song</b> - Response, PC2 Sing more<br><b>time_0_10</b> - Contribution to PCs, Time spent &lt; 10m from speaker<br><b>time_10_20</b> - Contribution to PCs, Time spent between 10 and 20m from speaker<br><b>time_20_100</b> - Contribution to PCs, Time spent &gt; 20m from speaker<br><b>latency_dist_min</b> - Contribution to PCs, Latency (s) to minimum distance from speaker<br><b>dist_min</b> - Contribution to PCs, Minimum distance from speaker<br><b>total_song</b> - Contribution to PCs, Total songs sung during trial<br>
DOI: 10.17045/sthlmuni.4246691
title: Dataset of ASE and genomic predictors from Capsella grandiflora

description: The dataset includes all the information used to assess the importance of genomic predictors on allele specific expression in Capsella grandiflora. The description of the predictors can be found in the Steige et al 2017 PNAS .
DOI: 10.17045/sthlmuni.4246691.v1
title: Dataset of ASE and genomic predictors from Capsella grandiflora

description: The dataset includes all the information used to assess the importance of genomic predictors on allele specific expression in Capsella grandiflora. The description of the predictors can be found in the Steige et al 2017 PNAS .
DOI: 10.6084/m9.figshare.4246667
title: Fig 4a 1 from The influence of closed brine pockets and permeable brine channels on the thermo-elastic properties of saline ice

description: A model of the thermo-elastic behaviour of saline ice is formulated, and model solutions describing thermo-elastic waves (TEW) propagating into a half-space of the ice are investigated. The model is based on a proposal that saline ice is a matrix, which encompasses both closed brine pockets and permeable channels filled with brine. Experiments on the thermal expansion of saline ice samples, and on TEW in saline ice, have been performed in the cold laboratories of the University Centre in Svalbard and in University College London. The experimental data are compared with theoretical conclusions. The experimental data support our hypothesis that the brine in saline ice is divided between closed pockets and open, permeable channels.
DOI: 10.6084/m9.figshare.4246664
title: Fig 4b from The influence of closed brine pockets and permeable brine channels on the thermo-elastic properties of saline ice

description: A model of the thermo-elastic behaviour of saline ice is formulated, and model solutions describing thermo-elastic waves (TEW) propagating into a half-space of the ice are investigated. The model is based on a proposal that saline ice is a matrix, which encompasses both closed brine pockets and permeable channels filled with brine. Experiments on the thermal expansion of saline ice samples, and on TEW in saline ice, have been performed in the cold laboratories of the University Centre in Svalbard and in University College London. The experimental data are compared with theoretical conclusions. The experimental data support our hypothesis that the brine in saline ice is divided between closed pockets and open, permeable channels.
DOI: 10.6084/m9.figshare.4246664.v1
title: Fig 4b from The influence of closed brine pockets and permeable brine channels on the thermo-elastic properties of saline ice

description: A model of the thermo-elastic behaviour of saline ice is formulated, and model solutions describing thermo-elastic waves (TEW) propagating into a half-space of the ice are investigated. The model is based on a proposal that saline ice is a matrix, which encompasses both closed brine pockets and permeable channels filled with brine. Experiments on the thermal expansion of saline ice samples, and on TEW in saline ice, have been performed in the cold laboratories of the University Centre in Svalbard and in University College London. The experimental data are compared with theoretical conclusions. The experimental data support our hypothesis that the brine in saline ice is divided between closed pockets and open, permeable channels.
DOI: 10.6084/m9.figshare.4246655
title: Fig 3b from The influence of closed brine pockets and permeable brine channels on the thermo-elastic properties of saline ice

description: A model of the thermo-elastic behaviour of saline ice is formulated, and model solutions describing thermo-elastic waves (TEW) propagating into a half-space of the ice are investigated. The model is based on a proposal that saline ice is a matrix, which encompasses both closed brine pockets and permeable channels filled with brine. Experiments on the thermal expansion of saline ice samples, and on TEW in saline ice, have been performed in the cold laboratories of the University Centre in Svalbard and in University College London. The experimental data are compared with theoretical conclusions. The experimental data support our hypothesis that the brine in saline ice is divided between closed pockets and open, permeable channels.
DOI: 10.6084/m9.figshare.4246652
title: Fig 10a from The influence of closed brine pockets and permeable brine channels on the thermo-elastic properties of saline ice

description: A model of the thermo-elastic behaviour of saline ice is formulated, and model solutions describing thermo-elastic waves (TEW) propagating into a half-space of the ice are investigated. The model is based on a proposal that saline ice is a matrix, which encompasses both closed brine pockets and permeable channels filled with brine. Experiments on the thermal expansion of saline ice samples, and on TEW in saline ice, have been performed in the cold laboratories of the University Centre in Svalbard and in University College London. The experimental data are compared with theoretical conclusions. The experimental data support our hypothesis that the brine in saline ice is divided between closed pockets and open, permeable channels.
DOI: 10.6084/m9.figshare.4246655.v1
title: Fig 3b from The influence of closed brine pockets and permeable brine channels on the thermo-elastic properties of saline ice

description: A model of the thermo-elastic behaviour of saline ice is formulated, and model solutions describing thermo-elastic waves (TEW) propagating into a half-space of the ice are investigated. The model is based on a proposal that saline ice is a matrix, which encompasses both closed brine pockets and permeable channels filled with brine. Experiments on the thermal expansion of saline ice samples, and on TEW in saline ice, have been performed in the cold laboratories of the University Centre in Svalbard and in University College London. The experimental data are compared with theoretical conclusions. The experimental data support our hypothesis that the brine in saline ice is divided between closed pockets and open, permeable channels.
DOI: 10.6084/m9.figshare.4246652.v1
title: Fig 10a from The influence of closed brine pockets and permeable brine channels on the thermo-elastic properties of saline ice

description: A model of the thermo-elastic behaviour of saline ice is formulated, and model solutions describing thermo-elastic waves (TEW) propagating into a half-space of the ice are investigated. The model is based on a proposal that saline ice is a matrix, which encompasses both closed brine pockets and permeable channels filled with brine. Experiments on the thermal expansion of saline ice samples, and on TEW in saline ice, have been performed in the cold laboratories of the University Centre in Svalbard and in University College London. The experimental data are compared with theoretical conclusions. The experimental data support our hypothesis that the brine in saline ice is divided between closed pockets and open, permeable channels.
DOI: 10.6084/m9.figshare.4246646
title: Fig 4a 2 from The influence of closed brine pockets and permeable brine channels on the thermo-elastic properties of saline ice

description: A model of the thermo-elastic behaviour of saline ice is formulated, and model solutions describing thermo-elastic waves (TEW) propagating into a half-space of the ice are investigated. The model is based on a proposal that saline ice is a matrix, which encompasses both closed brine pockets and permeable channels filled with brine. Experiments on the thermal expansion of saline ice samples, and on TEW in saline ice, have been performed in the cold laboratories of the University Centre in Svalbard and in University College London. The experimental data are compared with theoretical conclusions. The experimental data support our hypothesis that the brine in saline ice is divided between closed pockets and open, permeable channels.
DOI: 10.6084/m9.figshare.4246643
title: Processing Code from Gait control in a soft robot by sensing interactions with the environment using self-deformation

description: All animals use mechanosensors to help them move in complex and changing environments. With few exceptions, these sensors are embedded in soft tissues that deform in normal use such that sensory feedback results from the interaction of an animal with its environment. Useful information about the environment is expected to be embedded in the mechanical responses of the tissues during movements. To explore how such sensory information can be used to control movements, we have developed a soft-bodied crawling robot inspired by a highly tractable animal model, the tobacco hornworm <i>Manduca sexta</i>. This robot uses deformations of its body to detect changes in friction force on the substrate. This information is used to provide local sensory feedback for coupled oscillators that control the robot's locomotion. The validity of the control strategy is demonstrated with both simulation and a highly deformable three-dimensionally printed soft robot. The results show that very simple oscillators are able to generate propagating waves and crawling/inching locomotion through the interplay of deformation in different body parts in a fully decentralized manner. Additionally, we confirmed numerically and experimentally that the gait pattern can switch depending on the surface contact points. These results are expected to help in the design of adaptable, robust locomotion control systems for soft robots and also suggest testable hypotheses about how soft animals use sensory feedback.