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349 results for “Viability”
Data from: Evaluating population viability and efficacy of conservation management using integrated population models
Predicting population responses to environmental conditions or management scenarios is a fundamental challenge for conservation. Proper consideration of demographic, environmental and parameter uncertainties is essential for projecting population trends and optimal conservation strategies. We developed a coupled integrated population model-Bayesian population viability analysis to assess the (1) impact of demographic rates (survival, fecundity, immigration) on past population dynamics; (2) population viability 10 years into the future; and (3) efficacy of possible management strategies for the federally endangered Great Lakes piping plover Charadrius melodus population. Our model synthesizes long-term population survey, nest monitoring and mark–resight data, while accounting for multiple sources of uncertainty. We incorporated latent abundance of eastern North American merlins Falco columbarius, a primary predator of adult plovers, as a covariate on adult survival via a parallel state-space model, accounting for the influence of an imperfectly observed process (i.e. predation pressure) on population viability. Mean plover abundance increased from 18 pairs in 1993 to 75 pairs in 2016, but annual population growth (math formula) was projected to be 0.95 (95% CI 0.72–1.12), suggesting a potential decline to 67 pairs within 10 years. Without accounting for an expanding merlin population, we would have concluded that the plover population was projected to increase (math formula = 1.02; 95% CI 0.94–1.09) to 91 pairs by 2026. We compared four conservation scenarios: (1) no proposed management; (2) increased control of chick predators (e.g. Corvidae, Laridae, mammals); (3) increased merlin control; and (4) simultaneous chick predator and merlin control. Compared to the null scenario, chick predator control reduced quasi-extinction probability from 11.9% to 8.7%, merlin control more than halved (3.5%) the probability and simultaneous control reduced quasi-extinction probability to 2.6%. Synthesis and applications. Piping plover recovery actions should consider systematic predator control, rather than current ad hoc protocols, especially given the predicted increase in regional merlin abundance. This approach of combining integrated population models with Bayesian population viability analysis to identify limiting components of the population cycle and evaluate alternative management strategies for conservation decision-making shows great utility for aiding recovery of threatened populations.
Data and scripts to reproduce figures from "Ocean warming threatens the viability of 60% of Antarctic ice shelves"
<p>This is the formatted data related to the paper "Ocean warming threatens the viability of 60% of Antarctic ice shelves".</p> <p>Main data used to produce the main figures:<br>> bayesian_weights_davison_varying_combined_2300_withoutGISS.nc: Bayesian weights used in the computation of weighted likelihoods and averages considering all simulations going to 2300 - used in the main study<br>> all_fluxes_br_withoutGISS.nc: all fluxes forming the ice-shelf mass balance propagated across the different dimensions of uncertainty (CMIP models, basal melt parameterisations, bed plasticities)<br>> hydrofracturing_limits_new.nc: File containing the percentiles of reaching the hydrofracturing criterion</p> <p>Files needed to compute the weights:<br>> area_isf_greene22.nc: ice-shelf area used in Davison et al. 23 (from <a href="https://doi.org/10.1038/s41586-022-05037-w">Greene et al. 2022</a>)<br>> varying_conditions_davison23.nc: Ice-shelf mass budget fluxes from 1997 on from <a href="https://doi.org/10.1126/sciadv.adi0186">Davison et al. 2023</a><br>> steadystate_davison23.nc: Ice-shelf mass budget fluxes from the steady state from <a href="https://doi.org/10.1126/sciadv.adi0186">Davison et al. 2023</a></p> <p>Geometric information:<br>> gridarea_ISMIP6_AIS_4000m_grid.nc: File containing area of grid cells<br>> Mask_Iceshelf_4km_IMBIE_withNisf.nc: Mask used to define the location of the different ice shelves, based on <a href="https://zenodo.org/records/15863352">Caillet et al. 2025 </a><br>> BedMachine_4km_slope_info_bedrock_draft_latlon_oneFRIS.nc: Geometric information needed for neural network parameterisation, inferred using the <a href="https://github.com/ClimateClara/multimelt">multimelt package</a><br>> BedMachinev2_4km_isf_masks_and_info_and_distance_oneFRIS.nc: Geometric information needed for different computations, inferred using the <a href="https://github.com/ClimateClara/multimelt">multimelt package</a><br>> ano_choice_NEMOorISMIP_withoutGISS.nc: file recording which T and S profiles should be taken, either ISMIP climatology or NEMO hindcast, depending on their difference to the reference mass balance</p> <p>Data for analysis only until 2100:<br>> bayesian_weights_davison_varying_combined_withoutGISS.nc: Bayesian weights used in the computation of weighted likelihoods and averages considering all simulations going to 2100 (see Extended Data Fig. 5)</p> <p>Additional files needed for the additional analysis on other plausible geometries: <br>> ElmerIce_4km_2100isf_masks_and_info_and_distance_oneFRIS.nc: Geometric information needed for different computations for the 2100 ice-sheet geometry<br>> ElmerIce_4km_2100_slope_info_bedrock_draft_latlon_oneFRIS.nc: Geometric information needed for neural network parameterisation for the 2100 ice-sheet geometry<br>> ElmerIce_4km_2150isf_masks_and_info_and_distance_oneFRIS.nc: Geometric information needed for different computations for the 2150 ice-sheet geometry<br>> ElmerIce_4km_2150_slope_info_bedrock_draft_latlon_oneFRIS.nc: Geometric information needed for neural network parameterisation for the 2150 ice-sheet geometry<br>> all_fluxes_br_withoutGISS_ElmerIcegeo2100.nc: all fluxes forming the ice-shelf mass balance propagated across the different dimensions of uncertainty (CMIP models, basal melt parameterisations, bed plasticities) for the 2100 ice-sheet geometry<br>> all_fluxes_br_withoutGISS_ElmerIcegeo2150.nc: all fluxes forming the ice-shelf mass balance propagated across the different dimensions of uncertainty (CMIP models, basal melt parameterisations, bed plasticities) for the 2150 ice-sheet geometry<br><br>The scripts are explained in the associated README in scripts_paper_iceshelf_viability.zip. You can also find them here: https://github.com/ClimateClara/scripts_paper_iceshelf_viability<br><br>Here is a summary of the README:</p> <p>- Figure 2 and 3 were done with /notebooks_for_figures/timeseries_nb_viable_isf_withoutGISS_withhydrofrac_calving0.ipynb and /notebooks_for_figures/2D_subplots_viability_proba_withoutGISS_calving0.ipynb<br>- Figure 4 was done with /notebooks_for_figures/2D_subplots_viability_proba_withoutGISS_calving0.ipynb<br>- Figure 5 was done with /notebooks_for_figures/timeseries_nb_viable_isf_withoutGISS_withhydrofrac_calving0.ipynb and notebooks_for_figures/2D_subplots_viability_proba_onlyhydrofrac.ipynb</p> <p>- Extended Data Figures 1 to 4 were done with /notebooks_for_figures/plot_mass_fluxes.ipynb<br>- Extended Data Figure 5 was done with /notebooks_for_figures/timeseries_nb_viable_isf_withoutGISS_withhydrofrac_calving0.ipynb<br>- Extended Data Figure 6 was done with /notebooks_for_figures/timeseries_nb_viable_isf_withoutGISS_withhydrofrac.ipynb and /notebooks_for_figures/2D_subplots_viability_proba.ipynb<br>- Extended Data Figure 7 was done with /notebooks_for_figures/2D_subplots_viability_proba.ipynb<br>- Extended Data Figure 8 was done with /notebooks_for_figures/timeseries_nb_viable_isf_withoutGISS_withhydrofrac_ElmerIcegeometries.ipynb and /notebooks_for_figures/2D_subplots_viability_proba_withoutGISS_ElmerIcegeometries.ipynb<br>- Extended Data Figures 10 to 12 were done with /notebooks_for_figures/histo_weights_new.ipynb</p> <p>In the folder 'notebooks_for_datapreparation', you will find a few scripts to prepare the data. These are not as detailed and not meant to be run out of the box but permit to give insight into the practical application of the methods described in the paper. For potential inspiration of similar work :)<br>For the hydrofracturing calculations we refer to `Jourdain et al. 2025 <https://doi.org/10.5194/tc-19-1641-2025>`_ and the associated scripts: https://doi.org/10.5281/zenodo.13756240 and https://doi.org/10.5281/zenodo.15003864.</p>
Data for: Tracking hybrid viability across life-stages in a natural avian contact zone
<p><span>Hybrid inviability is an important post-zygotic reproductive barrier between species, but emerging signs of reduced viability can be difficult to study across the lifespan of natural hybrids.</span><span> We use a combination of long-term monitoring, extra-pair paternity and mitochondrial DNA identification in a natural hybrid zone of <em>Ficedula </em>flycatchers to detect emerging signs of intrinsic hybrid inviability across their entire lifespan. We evaluate possible evidence of Darwin's corollary to Haldane's rule, predicting asymmetries in inviability between hybrids resulting from reciprocal crosses, due to incompatible genetic factors with sex-specific inheritance patterns. We found higher hatching failure among mixed-species pairs, possibly indicating early developmental impairments associated with specific parental genetic combinations. Adult hybrids had a higher basal mortality rate than both parental species, and different age-specific mortality trajectories. There were signs of differences in age-independent mortality rates between the reciprocal hybrid crosses: hybrids with a pied flycatcher mother experienced slightly increased mortality later in life. Using an exceptional dataset with many natural hybrids tracked across life stages, we provide evidence for several emerging signs of reduced hybrid viability. Incompatibilities between alleles located on autosomes and uniparentally inherited factors such Z-linked and/or mitochondrial genes are strong candidates underlying intrinsic hybrid dysfunction in this system.</span></p>
Extracellular Vesicles from Pneumocystis carinii-infected rats impair fungal viability but are dispensable for macrophage functions
<p><em>Pneumocystis</em> spp. are host obligate fungal pathogens that can cause severe pneumonia in mammals and rely heavily on their host for essential nutrients. The lack of a sustainable <em>in vitro</em> culture system poses challenges in understanding their metabolism and the acquisition of essential nutrients from host lungs remains unexplored.</p> <p>Transmission electron micrographs show Extracellular Vesicles (EVs) are found near <em>Pneumocystis</em>spp. within the lung. We hypothesized that EVs transport essential nutrients to the fungi during infection. To investigate this, EVs from <em>P. carinii</em>- and <em>P. murina-</em>infected rodents were biochemically and functionally characterized. These EVs contained host proteins involved in cellular, metabolic, and immune processes as well as proteins with homologs found in other fungal EV proteomes, indicating <em>Pneumocystis</em> may release EVs. Notably, EV uptake by<em> P. carinii</em> indicated their potential involvement in nutrient acquisition and indicated a possibility for using engineered EVs for efficient therapeutic delivery. However, EVs added to <em>P. carinii</em> <em>in vitro</em>, did not show increased growth or viability, implying that additional nutrients or factors are necessary to support their metabolic requirements. Exposure of macrophages to EVs increased proinflammatory cytokine levels but did not affect macrophages' ability to kill or phagocytose <em>P. carinii</em>. These findings provide vital insights into <em>P. carinii</em> and host EV interactions, yet the mechanisms underlying <em>P. carinii</em>'s survival in the lung remain uncertain. These studies are the first to isolate, characterize, and functionally assess EVs from <em>Pneumocystis</em>-infected rodents, promising to enhance our understanding of host-pathogen dynamics and therapeutic potential.</p>
Supplemental information for: Inhibition of CSF1R and KIT with pexidartinib reduces inflammatory signaling and cell viability in endometriosis
<p>Endometriosis is a common and debilitating disease, affecting ~170 million women worldwide. Affected patients have limited therapeutic options such as hormonal suppression or surgical excision of the lesions, though therapies are often not completely curative. Targeting receptor tyrosine-kinases (RTKs) could provide a nonhormonal treatment option for endometriosis. We determined that two RTKs, Macrophage colony stimulating factor receptor (CSF1R) and Mast/stem cell growth factor receptor KIT (KIT), are overexpressed in endometriotic lesions and could be novel nonhormonal therapeutic targets for endometriosis. The kinase activity of CSF1R and KIT is suppressed by pexidartinib, a small molecule inhibitor that was recently approved by the US Food and Drug Administration (FDA). Using immunohistochemistry, we detected CSF1R and KIT in endometriotic tissues obtained from peritoneal lesions, colorectal lesions, and endometriomas. Specifically, we show that KIT is localized to the epithelium of the lesions, while CSF1R is expressed in the stroma and macrophages of the endometriotic lesions. Given the high epithelial expression of CSF1R and KIT, 12Z endometriotic epithelial cells were used to evaluate the efficacy of dual CSF1R and KIT inhibition with pexidartinib. We found that pexidartinib suppressed activation in 12Z cells of JNK, STAT3 and AKT signaling pathways, which control key pro-inflammatory and survival networks within the cell. Using quantitative real time PCR, we determined that pexidartinib suppressed interleukin 8 (<em>IL8) </em>and cyclin D1 (<em>CCND1) </em>expression<em>.</em> Lastly, we demonstrated that pexidartinib decreased cell growth and viability.<em> </em>Overall, these results indicate that pexidartinib-mediated CSF1R and KIT inhibition reduces pro-inflammatory signaling and cell viability in endometriosis.</p>
Mendelian gene identification through mouse embryo viability screening
<p>Supplementary files to support a manuscript entitled "Mendelian gene identification through mouse embryo viability screening"</p>
Opt2Q Example cell_viability_calibration_results
<p>A model of apoptosis (aEARM) was calibrated to published cell viability data using PyDREAM. The posterior sample for the model parameters and log-posterior traces are included as .npy files. The .txt files show the Gelman Rubin metric for each of the model parameters. The data was generated using https://github.com/LoLab-VU/aEARM_cell_viability_calibration</p>
Cryopreservation and transplantation of common carp spermatogonia - spermatogonia viability dataset
<p><strong>Dataset of spermatogonia viability assessment from optimization of cryopreservation and vitrification protocols.</strong></p>
Optimisation of viability assay for DIPG patient-derived cell lines
<p>Evaluation of the efficacy of M4K compounds in DIPG patient-derived cell lines is essential before any promising compounds can be further tested in mouse xenograft models. This approach can aid in narrowing down clinical compound candidates and reduce the time, resources and animal sacrifice needed downstream.</p> <p>A robust and efficient readout for the changes in the viability of the DIPG cells needs to be established before it can be used to evaluate the M4K compounds. In addition, the amount of cells to be seeded at the beginning of the experiment has to be optimised to avoid overcrowding and starvation of the cells after extended culture times. Overcrowding and starvation will lead to increased cell death and prevent accurate estimation of the potency of M4K compounds (EC50).</p>
Evaluating the effect of 8 M4K compounds on the viability of DIPG patient-derived cells (SU-DIPG-VI, HSJD-DIPG-007 and SU-DIPG-IV)
<p>Viability assay using Celltiter Glo kit has been chosen as the main method for evaluating the efficacy of ALK2 inhibitors on DIPG patient-derived cells due to its robustness. As a pilot experiment, 8 ALK2 inhibitors with differing potencies were chosen and evaluated in 3 DIPG patient-derived cell lines (one with wild-type ALK2 and two with mutant ALK2).</p>
Fig. 1 in Effect of temperature and egg laying depths on giant African land snail (Gastropoda: Achatinidae) viability
Fig. 1. Percent mortality of Lissachatina fulica at different temperature extremes.
Fig. 2 in Effect of temperature and egg laying depths on giant African land snail (Gastropoda: Achatinidae) viability
Fig. 2. Percent hatch and emergence of Lissachatina fulica from different soil depths.
Data from: Antineoplastic Nature of WWOX in Glioblastoma Is Mainly a Consequence of Reduced Cell Viability and Invasion
<p>Supporting data for the article "Antineoplastic Nature of WWOX in Glioblastoma Is Mainly a Consequence of Reduced Cell Viability and Invasion ", published in Biology (DOI: <span>10.3390/biology12030465</span>).</p>
Vortex input files -- Linking habitat and population viability analysis models of a metapopulation of Florida scrub-jays
<p>Vortex input files for manuscript "<span>Linking </span><span><span>habitat and population viability analysis models to account for <span>vegetation dynamics, habitat fragmentation, and social behavior of a metapopulation of Florida scrub-jays</span></span></span>" by R. C. Lacy, D. B. Breininger, et al. </p>
Black spruce seed availability and viability after fire, Northwest Territories, Canada
<p>Context : Black spruce ( Picea mariana ) is an important conifer in boreal North American that develops a semi-serotinous, aerial seedbank and releases a pulse of seeds after fire. Variation in post-fire seed rain has important consequences for black spruce regeneration and stand composition.</p> <p>Aims : We explore the possible effects of changes in fire regime on the abundance and viability of black spruce seeds following a very large wildfire season in the Northwest Territories, Canada (NWT).</p> <p>Methods: We measured post-fire seed rain over two years at 25 black sprucedominated sites and evaluated drivers of stand characteristics and environmental conditions on total black spruce seed rain and viability.</p> <p>Results : We found a positive relationship between black spruce basal area and total seed rain. However, at high basal areas this increasing rate of seed rain was not maintained. Viable seed rain was greater in stands that were older, closer to unburned edges, and where canopy combustion was less severe. Finally, we demonstrated positive relationships between seed rain and seedling establishment, confirming our measures of seed rain were key drivers of post-fire forest regeneration.</p> <p>Conclusion: These results suggest that black spruce recruitment after fire may be reduced with projected increases in fire activity.</p>
Diversity of Reproductive Characters, Reproductive Capacity, and Viability of Agave Seeds
<p>Raw data of morphological variables of reproductive characters of Agave landraces used for the production of pulque in 10 localities of Tlaxcala. These data were used to analyze and describe the morphological diversity of these varieties.</p>
Determining the Viability a Lozenge Dosage for Probiotics
ClinicalTrials.gov study NCT06819761. IPD Sharing: NO. Countries: 1. Publications: 10.
Range-wide population viability analyses reveal high sensitivity to wildflower harvesting in extreme environments
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Supplemental information for: Inhibition of CSF1R and KIT with pexidartinib reduces inflammatory signaling and cell viability in endometriosis
Open the record for dataset details and reuse information.
Data from: Reproductive losses due to climate change-induced earlier flowering are not the primary threat to plant population viability in a perennial herb
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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