cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3505586
title: Elevated intracellular pH appears in aged oocytes and causes oocyte aneuploidy associated with the loss of cohesion in mice

description: Increases in the aneuploidy rate caused by the deterioration of cohesion with increasing maternal age have been well documented. However, the molecular mechanism for the loss of cohesion in aged oocytes remains unknown. In this study, we found that intracellular pH (pH<sub>i</sub>) was elevated in aged oocytes, which might disturb the structure of the cohesin ring to induce aneuploidy. We observed for the first time that full-grown germinal vesicle (GV) oocytes displayed an increase in pH<sub>i</sub> with advancing age in CD1 mice. Furthermore, during the <i>in vitro</i> oocyte maturation process, the pH<sub>i</sub> was maintained at a high level, up to ∼7.6, in 12-month-old mice. Normal pH<sub>i</sub> is necessary to maintain protein localization and function. Thus, we put forward a hypothesis that the elevated oocyte pH<sub>i</sub> might be related to the loss of cohesion and the increased aneuploidy in aged mice. Through the <i>in vitro</i> alkalinization treatment of young oocytes, we observed that the increased pH<sub>i</sub> caused an increase in the aneuploidy rate and the sister inter-kinetochore (iKT) distance associated with the strength of cohesion and caused a decline in the cohesin subunit SMC3 protein level. Young oocytes with elevated pH<sub>i</sub> exhibited substantially the increase in chromosome misalignment.
DOI: 10.6084/m9.figshare.3505586.v1
title: Elevated intracellular pH appears in aged oocytes and causes oocyte aneuploidy associated with the loss of cohesion in mice

description: Increases in the aneuploidy rate caused by the deterioration of cohesion with increasing maternal age have been well documented. However, the molecular mechanism for the loss of cohesion in aged oocytes remains unknown. In this study, we found that intracellular pH (pH<sub>i</sub>) was elevated in aged oocytes, which might disturb the structure of the cohesin ring to induce aneuploidy. We observed for the first time that full-grown germinal vesicle (GV) oocytes displayed an increase in pH<sub>i</sub> with advancing age in CD1 mice. Furthermore, during the <i>in vitro</i> oocyte maturation process, the pH<sub>i</sub> was maintained at a high level, up to ∼7.6, in 12-month-old mice. Normal pH<sub>i</sub> is necessary to maintain protein localization and function. Thus, we put forward a hypothesis that the elevated oocyte pH<sub>i</sub> might be related to the loss of cohesion and the increased aneuploidy in aged mice. Through the <i>in vitro</i> alkalinization treatment of young oocytes, we observed that the increased pH<sub>i</sub> caused an increase in the aneuploidy rate and the sister inter-kinetochore (iKT) distance associated with the strength of cohesion and caused a decline in the cohesin subunit SMC3 protein level. Young oocytes with elevated pH<sub>i</sub> exhibited substantially the increase in chromosome misalignment.
DOI: 10.6084/m9.figshare.3505580
title: Asynchronous fate decisions at the single cell level collectively ensure a consistent lineage composition in the mouse blastocyst - Segmented images

description: Image stacks (TIFF sequences) showing the nuclear segmentation performed by MINS, overlaid on the nuclear staining channel (Hoechst, in grayscale). Individual nuclei were assigned a random color by MINS and an ID number that corresponds to the Cell_ID value in the corresponding data file (raw or corrected).
DOI: 10.6084/m9.figshare.3505580.v1
title: Segmented images for Saiz et al 2016

description: Image stacks (TIFF sequences) showing the nuclear segmentation performed by MINS, overlaid on the nuclear staining channel (Hoechst, in grayscale). Individual nuclei were assigned a random color by MINS and an ID number that corresponds to the Cell_ID value in the corresponding data file (raw or corrected).
DOI: 10.6084/m9.figshare.3505580.v2
title: Asynchronous fate decisions at the single cell level collectively ensure a consistent lineage composition in the mouse blastocyst - Segmented images

description: Image stacks (TIFF sequences) showing the nuclear segmentation performed by MINS, overlaid on the nuclear staining channel (Hoechst, in grayscale). Individual nuclei were assigned a random color by MINS and an ID number that corresponds to the Cell_ID value in the corresponding data file (raw or corrected).
DOI: 10.6084/m9.figshare.3505571
title: Asynchronous fate decisions at the single cell level collectively ensure a consistent lineage composition in the mouse blastocyst - Corrected data files

description: Data tables (in .csv format) for each embryo analyzed, after correcting for over- and under segmentation. Dead cells were eliminated and over- or under segmented cells were corrected as described in Saiz <i>et al</i>., (2016) <i>Journal of Visualized Experiments</i> and in Saiz <i>et al</i>., (2016) <i>Nature Communications. </i><br>File names correspond to the Embryo_ID variable and follow the format: Date_RegimeX_GroupNumber, where Date corresponds to the experimental date (in MMDDYY format), used for the file name in the images (both segmentation .tiff files and raw .lsm files), Regime corresponds to the treatment regime for that experiment (when applicable), the Group to the experimental group (Control or else) and the Number is a sequence given to differentiate embryos in that particular group and experiment.
DOI: 10.6084/m9.figshare.3505571.v2
title: Asynchronous fate decisions at the single cell level collectively ensure a consistent lineage composition in the mouse blastocyst - Corrected data files

description: Data tables (in .csv format) for each embryo analyzed, after correcting for over- and under segmentation. Dead cells were eliminated and over- or under segmented cells were corrected as described in Saiz <i>et al</i>., (2016) <i>Journal of Visualized Experiments</i> and in Saiz <i>et al</i>., (2016) <i>Nature Communications. </i><br>File names correspond to the Embryo_ID variable and follow the format: Date_RegimeX_GroupNumber, where Date corresponds to the experimental date (in MMDDYY format), used for the file name in the images (both segmentation .tiff files and raw .lsm files), Regime corresponds to the treatment regime for that experiment (when applicable), the Group to the experimental group (Control or else) and the Number is a sequence given to differentiate embryos in that particular group and experiment.
DOI: 10.6084/m9.figshare.3505571.v1
title: Corrected data files for Saiz et al 2016

description: Data tables (in .csv format) for each embryo analyzed, after correcting for over- and under segmentation. Dead cells were eliminated and over- or under segmented cells were corrected as described in Saiz <i>et al</i>., (2016) <i>Journal of Visualized Experiments</i> and in Saiz <i>et al</i>., (2016) <i>Nature Communications. </i><br>File names correspond to the Embryo_ID variable and follow the format: Date_RegimeX_GroupNumber, where Date corresponds to the experimental date (in MMDDYY format), used for the file name in the images (both segmentation .tiff files and raw .lsm files), Regime corresponds to the treatment regime for that experiment (when applicable), the Group to the experimental group (Control or else) and the Number is a sequence given to differentiate embryos in that particular group and experiment.
DOI: 10.6084/m9.figshare.3505565
title: Asynchronous fate decisions at the single cell level collectively ensure a consistent lineage composition in the mouse blastocyst - Raw data files.

description: Raw data tables (in .csv format) generated by MINS for each of the embryos analyzed. These tables are the original, uncorrected files, created by the segmentation algorithm.
DOI: 10.6084/m9.figshare.3505565.v2
title: Asynchronous fate decisions at the single cell level collectively ensure a consistent lineage composition in the mouse blastocyst - Raw data files.

description: Raw data tables (in .csv format) generated by MINS for each of the embryos analyzed. These tables are the original, uncorrected files, created by the segmentation algorithm.
DOI: 10.6084/m9.figshare.3505565.v1
title: Raw data files for Saiz et al 2016

description: Raw data tables (in .csv format) generated by MINS for each of the embryos analyzed. These tables are the original, uncorrected files, created by the segmentation algorithm.
DOI: 10.6084/m9.figshare.3505475
title: Sustainable geotourism using digital technologies along a rural georoute in Monsagro (Salamanca, Spain)

description: Rural geotourism looks at the natural resources of the territory as a means of promoting a specialized, educational, sustainable tourism. This is an increasingly sought-after activity. This paper presents a rural georoute across a high mountain village, highlighting the remarkable value of the geological heritage of biological trace fossils and physical sedimentary structures exposed on street pavements and façades of houses. A series of tourist georesources were created and implemented: educational and interpretive panels, videos, QR codes, geoapps and games, all of which promote and disseminate the exceptional geological content and the history of the earth through the use of new technologies (smartphones, ipod, etc.). All this is intended as a means to make geotourism a natural tourism, favoring experiences, whilst explaining the natural environment and its temporal and spatial dimensions, offering opportunities for socio-economic development and job creation in rural areas with problems of depopulation.
DOI: 10.6084/m9.figshare.3505475.v1
title: Sustainable geotourism using digital technologies along a rural georoute in Monsagro (Salamanca, Spain)

description: Rural geotourism looks at the natural resources of the territory as a means of promoting a specialized, educational, sustainable tourism. This is an increasingly sought-after activity. This paper presents a rural georoute across a high mountain village, highlighting the remarkable value of the geological heritage of biological trace fossils and physical sedimentary structures exposed on street pavements and façades of houses. A series of tourist georesources were created and implemented: educational and interpretive panels, videos, QR codes, geoapps and games, all of which promote and disseminate the exceptional geological content and the history of the earth through the use of new technologies (smartphones, ipod, etc.). All this is intended as a means to make geotourism a natural tourism, favoring experiences, whilst explaining the natural environment and its temporal and spatial dimensions, offering opportunities for socio-economic development and job creation in rural areas with problems of depopulation.
DOI: 10.6084/m9.figshare.3505454
title: Oligomerized backbone pilin helps piliated <i>Lactococcus lactis</i> to withstand shear flow

description: The present work focuses on the role of pili present at the cell surface of <i>Lactococcus lactis</i> in bacterial adhesion to abiotic (hydrophobic polystyrene) and biotic (mucin-coated polystyrene) surfaces. Native pili-displaying strains and isogenic derivatives in which pilins or sortase C structural genes had been modified were used. Surface physico-chemistry, morphology and shear-flow-induced detachment of lactococcal cells were evaluated. The involvement of pili in <i>L. lactis</i> adhesion was clearly demonstrated, irrespective of the surface characteristics (hydrophobic/hydrophilic, presence or not of specific binding sites). The accessory pilin, PilC, and the backbone pilin, PilB, were revealed to play a major role in adhesion, provided that the PilB was present in its polymerized form. Within the population fraction that remained attached to the surface under increasing shear flow, different association behaviors were observed, showing that pili could serve as anchoring sites thus hampering the effect of shear flow on cell orientation and detachment.
DOI: 10.6084/m9.figshare.3505454.v1
title: Oligomerized backbone pilin helps piliated <i>Lactococcus lactis</i> to withstand shear flow

description: The present work focuses on the role of pili present at the cell surface of <i>Lactococcus lactis</i> in bacterial adhesion to abiotic (hydrophobic polystyrene) and biotic (mucin-coated polystyrene) surfaces. Native pili-displaying strains and isogenic derivatives in which pilins or sortase C structural genes had been modified were used. Surface physico-chemistry, morphology and shear-flow-induced detachment of lactococcal cells were evaluated. The involvement of pili in <i>L. lactis</i> adhesion was clearly demonstrated, irrespective of the surface characteristics (hydrophobic/hydrophilic, presence or not of specific binding sites). The accessory pilin, PilC, and the backbone pilin, PilB, were revealed to play a major role in adhesion, provided that the PilB was present in its polymerized form. Within the population fraction that remained attached to the surface under increasing shear flow, different association behaviors were observed, showing that pili could serve as anchoring sites thus hampering the effect of shear flow on cell orientation and detachment.
DOI: 10.6084/m9.figshare.3505436.v1
title: Number of settling larvae - 24 hrs after dosing

description: The number of <i>Botrylloides violaceus</i> larvae settling on experimental plates 24 hours after larval dosing.
DOI: 10.6084/m9.figshare.3505436.v2
title: Data from: Propagule pressure and the invasibility of marine habitats

description: The number of <i>Botrylloides violaceus</i> larvae settling on experimental plates 24 hours and 56 days after larval dosing. Bare space on occupied community plates at the start of the experiment, analyzed using ImageJ.
DOI: 10.6084/m9.figshare.3505418.v1
title: Proportion of bare space on occupied community plates

description: Proportion of bare space on occupied community plates at the start of the experiment.
DOI: 10.6084/m9.figshare.3505418.v2
title: Proportion of bare space on occupied community plates

description: Proportion of bare space on occupied community plates at the start of the experiment.
DOI: 10.6084/m9.figshare.3505340
title: Evaluation of polylactic acid nanoparticles safety using Drosophila model

description: Cytotoxicity of nanoparticles and their sub-lethal effect on cell behavior and cell fate are a high topic of studies in the nanomaterial field. With an explosion of nanoparticle types (size, shape, polarity, stiffness, composition, etc.), Drosophila has become an attractive animal model for high throughput analysis of these nanocarriers in the drug delivery field with applications in cancer therapy, or simply to generate a fast and complete cytotoxic study of a peculiar nanoparticle. In respect to that, we have conducted an <i>in cellulo</i> study of poly(lactic acid) (PLA) nanoparticle cytotoxicity, and determined that near lethal nanoparticle doses, oxidative stress as well as P53 and ATP pathways may lead to cell cycle arrest at G1, and ultimately to cell death. Neither viability nor the development of Drosophila larvae are affected by the ingestion of PLA nanoparticles at sub-lethal concentrations. Drosophila will be a useful model to study PLA and PLA-modified nanoparticle toxicity, and nanoparticle fate after ingestion.
DOI: 10.6084/m9.figshare.3505340.v1
title: Evaluation of polylactic acid nanoparticles safety using Drosophila model

description: Cytotoxicity of nanoparticles and their sub-lethal effect on cell behavior and cell fate are a high topic of studies in the nanomaterial field. With an explosion of nanoparticle types (size, shape, polarity, stiffness, composition, etc.), Drosophila has become an attractive animal model for high throughput analysis of these nanocarriers in the drug delivery field with applications in cancer therapy, or simply to generate a fast and complete cytotoxic study of a peculiar nanoparticle. In respect to that, we have conducted an <i>in cellulo</i> study of poly(lactic acid) (PLA) nanoparticle cytotoxicity, and determined that near lethal nanoparticle doses, oxidative stress as well as P53 and ATP pathways may lead to cell cycle arrest at G1, and ultimately to cell death. Neither viability nor the development of Drosophila larvae are affected by the ingestion of PLA nanoparticles at sub-lethal concentrations. Drosophila will be a useful model to study PLA and PLA-modified nanoparticle toxicity, and nanoparticle fate after ingestion.
DOI: 10.6084/m9.figshare.12917252.v1
title: Is it possible to reduce geospatial mapping time by automating land survey field work?

description: Data related to paper submitted to Cartography and Geographic Information Science Journal
DOI: 10.6084/m9.figshare.3505334
title: Geotagged urban activity

description: As described in our paper, we have collected 11.5M checkins around the world that were publicly made available on twitter. Each of them is represented by a line of a CSV file `all_checkins.csv` containing the following values:<br><br>userId: a random number uniquely identifying a foursquare user<br>venueId: id of the venue where the checkin took place<br>timestamp: UTC timestamp of the checkins<br>timeZoneOffset: local offset from UTC in minutes<br><br>In total there are 2M venues in those checkins and while we can't provide too much information as per Foursquare policy (https://developer.foursquare.com/overview/venues#rules), the file `all_venues.csv` contains their location and category. Namely:<br>venueId: id of the venue<br>latitude,longitude: coordinates<br>categoryId: foursquare main category id for that venue (https://developer.foursquare.com/categorytree)<br><br>In addition, the script get_venues_info.py can be used to get the remaining up to date information.<br><br>
DOI: 10.6084/m9.figshare.3505334.v1
title: Geotagged urban activity

description: As described in our paper, we have collected 11.5M checkins around the world that were publicly made available on twitter. Each of them is represented by a line of a CSV file `all_checkins.csv` containing the following values:<br><br>userId: a random number uniquely identifying a foursquare user<br>venueId: id of the venue where the checkin took place<br>timestamp: UTC timestamp of the checkins<br>timeZoneOffset: local offset from UTC in minutes<br><br>In total there are 2M venues in those checkins and while we can't provide too much information as per Foursquare policy (https://developer.foursquare.com/overview/venues#rules), the file `all_venues.csv` contains their location and category. Namely:<br>venueId: id of the venue<br>latitude,longitude: coordinates<br>categoryId: foursquare main category id for that venue (https://developer.foursquare.com/categorytree)<br><br>In addition, the script get_venues_info.py can be used to get the remaining up to date information.<br><br>
DOI: 10.6084/m9.figshare.3505169
title: Assorted Shapefiles and Associated Data for Geographic Visualisations

description: This repository provides a number of shapefiles and associated files for the processing of shapefiles, for instance membership data.<br><br>US-FIPS-Codes.csv - provides a useful file for checking whether a US State/Region is a member of the contiguous USA.<br><br>
DOI: 10.6084/m9.figshare.3505169.v1
title: Assorted Shapefiles and Associated Data for Geographic Visualisations

description: This repository provides a number of shapefiles and associated files for the processing of shapefiles, for instance membership data.<br><br>US-FIPS-Codes.csv - provides a useful file for checking whether a US State/Region is a member of the contiguous USA.<br><br>
DOI: 10.6084/m9.figshare.3505163
title: Cyclic Fatigue Resistance and Force Generated by OneShape Instruments During Curved Canal Preparation

description: <b>Objectives:</b> To evaluate the cyclic fatigue resistance and the force generated by OneShape files during preparation of simulated curved canals. <b>Methods:</b> Six OneShape files (the test) and six ProTaper F2 files (the control) were subject to the bending ability test. Another thirty files of each type were used to prepare artificial canals (n=60), which were divided into 3 groups according to respective curvatures of the canals (30°, 60°, and 90°). The numbers of cycles to fatigue (NCF) as well as the positive and negative forces that were generated by files during canal preparation were recorded. The scanning electron microscopy was applied to detect the fracture surfaces. <b>Results:</b> Compared with ProTaper F2 files, the bending loads of OneShape files were significantly lower at deflections of 45°(<i>P</i> &lt; .05), 60° (<i>P</i> &lt; .05) and 75° (<i>P</i> &lt; .01). No significant difference was found at 30°. OneShape files presented a higher NCF in both 60° and 90° canals than the control (<i>P</i> &lt; .01). No significant difference of NCF was found between OneShape and ProTaper files in 30° canals. During the preparation of 30° canals by both files, the negative forces were dominant. With the increase of the curvature, more positive forces were observed. When the OneShape Files were compared with the control, significant different forces were found at D3 and D2 (<i>P</i> &lt; .05) in 30° canals, at D2 (<i>P</i> &lt; .05), D1 (<i>P</i> &lt; .01) and D0 (<i>P</i> &lt; .01) in 60° canals, and at D4 and D3 (<i>P</i> &lt; .01) in 90° canals. <b>Conclusions</b>：OneShape files possessed a reliable flexibility and cyclic fatigue resistance. According to the assessments of the forces generated by files, OneShape instruments performed in a more fatigue-resistant way during curved canal preparation, compared with the ProTaper F2 files.
DOI: 10.6084/m9.figshare.3505163.v1
title: Cyclic Fatigue Resistance and Force Generated by OneShape Instruments During Curved Canal Preparation

description: <b>Objectives:</b> To evaluate the cyclic fatigue resistance and the force generated by OneShape files during preparation of simulated curved canals. <b>Methods:</b> Six OneShape files (the test) and six ProTaper F2 files (the control) were subject to the bending ability test. Another thirty files of each type were used to prepare artificial canals (n=60), which were divided into 3 groups according to respective curvatures of the canals (30°, 60°, and 90°). The numbers of cycles to fatigue (NCF) as well as the positive and negative forces that were generated by files during canal preparation were recorded. The scanning electron microscopy was applied to detect the fracture surfaces. <b>Results:</b> Compared with ProTaper F2 files, the bending loads of OneShape files were significantly lower at deflections of 45°(<i>P</i> &lt; .05), 60° (<i>P</i> &lt; .05) and 75° (<i>P</i> &lt; .01). No significant difference was found at 30°. OneShape files presented a higher NCF in both 60° and 90° canals than the control (<i>P</i> &lt; .01). No significant difference of NCF was found between OneShape and ProTaper files in 30° canals. During the preparation of 30° canals by both files, the negative forces were dominant. With the increase of the curvature, more positive forces were observed. When the OneShape Files were compared with the control, significant different forces were found at D3 and D2 (<i>P</i> &lt; .05) in 30° canals, at D2 (<i>P</i> &lt; .05), D1 (<i>P</i> &lt; .01) and D0 (<i>P</i> &lt; .01) in 60° canals, and at D4 and D3 (<i>P</i> &lt; .01) in 90° canals. <b>Conclusions</b>：OneShape files possessed a reliable flexibility and cyclic fatigue resistance. According to the assessments of the forces generated by files, OneShape instruments performed in a more fatigue-resistant way during curved canal preparation, compared with the ProTaper F2 files.