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129 results for “survival analysis”
Data from: Individual differences in behaviour explain variation in survival: a meta-analysis
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Validation of Sepsis-3 using survival analysis and clinical evaluation of quick SOFA, SIRS, and burn-specific SIRS for sepsis in burn patients with suspected infection
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Body size predicts ant worker longevity: A hierarchical analysis of field and laboratory survival across phylogenetic lineages
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Capture histories of owls with covariates for survival analysis
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Data from: A meta-analysis of global avian survival across species and latitude
<p>Tropical birds are thought to be longer lived than many temperate species. We explored the idea of higher survival at tropical latitudes and whether extrinsic climate factors and intrinsic traits helped explain this pattern using a meta-analytical approach. The dataset consists of 949 estimates from 204 studies of avian survival from both New World and Old World biogeographical realms.</p>
Data from: Risk of potential pesticide use to honeybee and bumblebee survival and distribution: a country-wide analysis for The Netherlands
Aim: Bees play an important role in natural ecosystems and the world's food supply. In the past decades, bee abundance and diversity have declined globally. This has resulted in decreased pollination services for natural ecosystems and the agricultural sector at the field scale. One of the causes of the decline in bee abundance and diversity is the use of pesticides. Linking pesticide use, land use and bee presence could provide crucial insights into areas and pesticides that pose a significant threat to the abundance and diversity of bees. Obtaining actual figures of farmer pesticide use is rarely possible. Therefore, we designed a method to study the effects of potential pesticide use on the survival and distribution of honey- and bumblebees. Location: The Netherlands. Methods: A pesticide risk model was implemented incorporating a hazard quotient as the risk assessment. The number of allowed pesticide active ingredients per crop that could pose a risk to honeybees and bumblebees were linked to the Dutch crop parcel locations for 2015 and 2016. The potential pesticide risk maps were analyzed using honeybee colony survival and bumblebee presence data. Results: Non-significant negative effects of potential pesticide risk on honeybee colony survival and bumblebee presence were found. A significant negative effect of greenhouses was identified for both honeybees and bumblebees. The most important factors in the models predicting honeybee colony survival and bumblebee presence were urban land areas and natural grasslands respectively, both showing a positive effect. Main conclusions: Here, the first attempt to estimate and map pesticide risk to bees in the Netherlands in a country-wide manner is presented. The results could provide crucial high-resolution insights for bee conservation action and facilitate the increase of pollination services in natural ecosystems and the agricultural sector on a local and country-wide scale.
Data from: Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values and small sample sizes
Background: Plant survival is a key factor in forest dynamics and survival probabilities often vary across life stages. Studies specifically aimed at assessing tree survival are unusual and so data initially designed for other purposes often need to be used; such data are more likely to contain errors than data collected for this specific purpose. Results: We investigate the survival rates of ten tree species in a dataset designed to monitor growth rates. As some individuals were not included in the census at some time points we use capture-mark-recapture methods both to allow us to account for missing individuals, and to estimate relocation probabilities. Growth rates, size, and light availability were included as covariates in the model predicting survival rates. The study demonstrates that tree mortality is best described as constant between years and size-dependent at early life stages and size independent at later life stages for most species of UK hardwood. We have demonstrated that even with a twenty-year dataset it is possible to discern variability both between individuals and between species. Conclusions: Our work illustrates the potential utility of the method applied here for calculating plant population dynamics parameters in time replicated datasets with small sample sizes and missing individuals without any loss of sample size, and including explanatory covariates.
Data from: Survival analysis and classification methods for forest fire size
Factors affecting wildland-fire size distribution include weather, fuels, and fire suppression activities. We present a novel application of survival analysis to quantify the effects of these factors on a sample of sizes of lightning-caused fires from Alberta, Canada. Two events were observed for each fire: the size at initial assessment (by the first fire fighters to arrive at the scene) and the size at "being held" (a state when no further increase in size is expected). We developed a statistical classifier to try to predict cases where there will be a growth in fire size (i.e., the size at "being held" exceeds the size at initial assessment). Logistic regression was preferred over two alternative classifiers, with covariates consistent with similar past analyses. We conducted survival analysis on the group of fires exhibiting a size increase. A screening process selected three covariates: an index of fire weather at the day the fire started, the fuel type burning at initial assessment, and a factor for the type and capabilities of the method of initial attack. The Cox proportional hazards model performed better than three accelerated failure time alternatives. Both fire weather and fuel type were highly significant, with effects consistent with known fire behaviour. The effects of initial attack method were not statistically significant, but did suggest a reverse causality that could arise if fire management agencies were to dispatch resources based on a-priori assessment of fire growth potentials. We discuss how a more sophisticated analysis of larger data sets could produce unbiased estimates of fire suppression effect under such circumstances.
Data from: Grow where you thrive, or where only you can survive? An analysis of performance curve evolution in a clade with diverse habitat affinities
Performance curves are valuable tools for quantifying the fundamental niches of organisms and testing hypotheses about evolution, life history trade-offs, and the drivers of variation in species' distribution patterns. Here, we present a novel Bayesian method for characterizing performance curves that facilitates comparisons among species. We then use this model to quantify and compare the hydrological performance curves of 14 different taxa in the genus Lasthenia, an ecologically diverse clade of plants that collectively occupy a variety of habitats with unique hydrological features, including seasonally flooded wetlands called vernal pools. We conducted a growth chamber experiment to measure each taxon's fitness across five hydrological treatments that ranged from severe drought to extended flooding, and identified differences in hydrological performance curves that explain their associations with vernal pool and terrestrial habitats. Our analysis revealed that the distribution of vernal pool taxa in the field do not reflect their optimal hydrological environments: all taxa, regardless of habitat affinity, have highest fitness under similar hydrological conditions of saturated soil without submergence. We also found that a taxon's relative position across flood gradients within vernal pools is best predicted by the height of its performance curve. These results demonstrate the utility of our approach for generating insights into when and how performance curves evolve among taxa as they diversify into distinct environments. To facilitate its use, the modeling framework has been developed into an R package (https://github.com/silastittes/performr).
Data from: Short-term and medium-term survival of critically ill patients with solid tumours admitted to the intensive care unit: a retrospective analysis
Objectives: Patients with cancer frequently require unplanned admission to the Intensive Care Unit (ICU). Our objectives were to assess hospital and 180-day mortality in patients with a non-haematological malignancy and unplanned ICU admission, and to identify which factors present on admission were the best predictors of mortality. Design: Retrospective review of all patients with a diagnosis of solid tumours following unplanned admission to the ICU between 1st August 2008 and 31st July 2012. Setting: Single centre tertiary care hospital in London (UK) Participants: 300 adult patients with non-haematological solid tumours requiring unplanned admission to the ICU. Interventions: None Primary and secondary outcomes: Hospital and 180-day survival Results: 300 patients were admitted to the ICU (median age 66.5 years; 61.7% male). Survival to hospital discharge and 180-days were 69% and 47.8%, respectively. Greater number of failed organ systems on admission was associated with significantly worse hospital survival (p<0.001) but not with 180-day survival (p=0.24). In multivariate analysis, predictors of hospital mortality were the presence of metastases [odds ratio (OR 1.97), 95% confidence interval (CI) 1.08-3.59], Acute Physiology and Chronic Health Evaluation II (APACHE II) score (OR 1.07, 95% CI 1.01-1.13) and a Glasgow Coma Scale score <7 on admission to ICU (OR 5.21, 95% CI 1.65-16.43). Predictors of worse 180-day survival were the presence of metastases (OR 2.82, 95% CI 1.57-5.06), APACHE II score (OR 1.07, 95% CI 1.01-1.13) and sepsis (OR 1.92, 95% CI 1.09-3.38). Conclusions: Short and medium-term survival in patients with solid tumours admitted to ICU is better than previously reported, suggesting that the presence of cancer alone should not be a barrier to ICU admission.
Data from: Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan
Climatic changes have played major roles in plants' evolutionary history. Glacial oscillations have been particularly important, but some of their effects on plants' populations are poorly understood, including the numbers and locations of refugia in Asian warm temperate zones. In the present study, we investigated the demographic history of the broadleaved evergreen tree species Castanopsis sieboldii (Fagaceae) during the last glacial period in Japan. We used approximate Bayesian computation (ABC) for model comparison and parameter estimation for the demographic modelling using 27 EST associated microsatellites. We also performed the species distribution modelling (SDM). The results strongly support a demographic scenario that the Ryukyu Islands and the western parts in the main islands (Kyushu and western Shikoku) were derived from separate refugia and the eastern parts in the main islands and the Japan Sea groups were diverged from the western parts prior to the coldest stage of the Last Glacial Maximum (LGM). Our data indicate that multiple refugia survived at least one in the Ryukyu Islands, and the other three regions of the western and eastern parts and around the Japan Sea of the main islands of Japan during the LGM. The SDM analysis also suggests the potential habitats under LGM climate conditions were mainly located along the Pacific Ocean side of coastal region. Our ABC-based study helps efforts resolve the demographic history of a dominant species in warm temperate broadleaved forests during and after the last glacial period, which provides a basic model for future phylogeographical studies using this approach.
Exploring Factors Promoting Dependency Updates with Survival Time Analysis and Logistic Regression
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GNOSIS: an R Shiny app supporting cancer genomics survival analysis with cBioPortal
<p>GNOSIS Instructional videos.</p>
Survival analysis of DNA mutation motifs with penalized proportional hazards
<p>Output used to produce the tables and figures in the manuscript:</p> <p>Feng and Shaw, et al. (2017) Survival analysis of DNA mutation motifs with penalized proportional hazards. <em>Annals of Applied Statistics</em>, <em>under revision</em>.</p> <p><br> Preprint: <a href="http://arxiv.org/abs/1711.04057">http://arxiv.org/abs/1711.04057</a></p> <p>Package: <a href="http://github.com/matsengrp/samm">http://github.com/matsengrp/samm</a></p> <p> </p> <p>See README.md for more information.</p>
Data from: Leukocyte profiles are associated with longevity and survival, but not migratory effort: a comparative analysis of shorebirds
1. Assessment of leukocyte profiles has become an increasingly popular tool in the fields of ecology and ecophysiology. The ratio of heterophils to lymphocytes (H/L ratio) is of special utility, as it reflects physiological adaptation of an organism to cope either with an infection through injury (via heterophils) or a communicable disease (via lymphocytes). Thus, elevated H/L ratios may constitute an adaptation to risky environments (i.e. associated with high risk of injury). While intra-population variation in avian H/L ratio has been extensively studied, we are aware of no studies that linked this trait to life-history components at the inter-specific level. 2. We measured H/L ratio in over 400 shorebirds from 19 species during their autumn migration through Central Europe. Phylogenetically informed comparative methods were used to test whether H/L ratio was related to: i) annual survival and lifespan; ii) migratory effort, as measured with total migration distance and migratory energy reserves; and iii) confounding variables such as body size or breeding latitude. 3. A relatively strong phylogenetic signal and spatial phylogenetic autocorrelation indicated that most diversification in shorebird H/L ratios occurred relatively early in radiation of this group. 4. Comparative analysis gave strong support for the negative associations of H/L ratio with residual lifespan and annual survival. In contrast, we found no support for the effect of migratory behaviour on H/L ratios, suggesting that leukocyte profiles in shorebirds may not constitute an important physiological adaptation for long-distance migration. 5. Our study provided the first comparative evidence for a link between H/L ratios and important life-history traits in birds. Strong negative associations with annual survival and residual lifespan indicate that leukocyte profiles may form an adaptive basis for life-history strategies in birds.
Data for: When does early-life telomere length predict survival? A case study and meta-analysis
<p>Suboptimal conditions during development can shorten telomeres, the protective DNA caps on the end of chromosomes. Shorter early-life telomere length (TL) can indicate reduced somatic maintenance, leading to lower survival and shorter lifespan. However, despite some clear evidence, not all studies show a relationship between early-life TL and survival or lifespan, which may be due to differences in biology or study design (e.g., survival period measured). In superb fairy-wrens (<em>Malurus cyaneus</em>), we assessed whether early-life TL predicts mortality across different life-history stages (fledgling, juvenile, adult). However, in contrast to a similar study on a congener, early-life TL did not predict mortality across any life stage in this species. We then performed a meta-analysis including 32 effect sizes from 23 studies (15 birds and 3 mammals) to quantify the effect of early-life TL on mortality whilst taking into consideration potential sources of biological and methodological variation. Overall, the effect of early-life TL on mortality was significant, corresponding to a 15% reduction in mortality risk with each standard deviation increase in TL. However, the effect became weaker when correcting for publication bias. Contrary to our predictions, there was no evidence that effects of early-life TL on mortality varied with species lifespan or the period over which survival was measured. However, negative effects of early-life TL on mortality risk were pervasive throughout life. These results imply that effects of early-life TL on mortality are more likely context-dependent rather than age-dependent, although substantial power and publication bias issues highlight the need for more research.</p>
Survival Rate and Treatment Cost in Patients With Pancreatic Cancer: An Analysis Using NHIS Database and K-PaC Registry Focusing on Liposomal Irinotecan
ClinicalTrials.gov study NCT04984174. IPD Sharing: Not stated. Countries: 1. Publications: 7.
Extramedullary Acute Myeloid Leukemia (eAML): Retrospective Single Center Cohort Study, Clinicopathological, Molecular Analysis and Survival Outcomes
ClinicalTrials.gov study NCT05057299. IPD Sharing: NO. Countries: 1. Publications: 2.
Retrospective Analysis of Survival in Adult MRD Positive Acute Lymphoblastic Leukemia Patients
ClinicalTrials.gov study NCT02010931. IPD Sharing: Not stated. Countries: 8. Publications: 1.
Variability of Definitions for Survival Endpoints and Surrogate Properties for OS in Sarcoma Trials: a Meta-analysis
ClinicalTrials.gov study NCT02873923. IPD Sharing: NO. Countries: 0. Publications: 2.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
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.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.