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954 results for “survival data”
Data from: Survival of the feces: does a nematode lungworm adaptively manipulate the behavior of its cane toad host?
Parasites can enhance their fitness by modifying the behavior of their hosts in ways that increase rates of production and transmission of parasite larvae. We used an antihelminthic drug to experimentally alter infections of lungworms (Rhabdias pseudosphaerocephala) in cane toads (Rhinella marina). We then compared subsequent behaviors of dewormed toads versus toads that retained infections. Both in the laboratory and in the field, the presence of parasites induced hosts to select higher body temperatures (thereby increasing rates of lungworm egg production), to defecate in moister sites, and to produce feces with higher moisture content (thereby enhancing survival of larvae shed in feces). Because those behavioral modifications enhance rather than decrease parasite fitness, they are likely to have arisen as adaptive manipulations of host behavior rather than as host adaptations to combat infection or as nonadaptive consequences of infection on host physiology. However, the mechanisms by which lungworms alter cane toad thermal preference and defecation are not known. Although many examples of host manipulation by parasites involve intermediate hosts facilitating their own demise, our findings indicate that manipulation of definitive hosts can be as subtle as when and where to defecate.
Data from: Maternal effects influence phenotypes and survival during early life stages in an aquatic turtle
Offspring phenotypic variation can be substantially influenced by non-genetic factors such as maternal effects, which ultimately can influence organismal fitness. For oviparous organisms that lack parental care, oviposition-site choice and egg size are maternal effects that can greatly affect offspring traits. Yet, few studies examine the consequences of these traits in the wild. We manipulated the contents of natural painted turtle nests such that offspring spent two life stages (incubation and hibernation) in either maternally-selected nest sites or randomly-selected nest sites, and quantified treatment differences in environmental parameters and offspring phenotypes. Additionally, we tracked the fates of individual eggs and hatchlings, which allowed us to quantify the strength and form of selection acting on egg size during incubation and, for the first time, body size during hibernation. Maternally-selected nest sites were warmer and produced offspring that were longer and hatched earlier than their siblings emerging from cooler, randomly-selected nests. Treatments did not affect any measured traits during hibernation. We detected no selection on egg size during the incubation stage, but significant linear selection favoring larger hatchlings during hibernation. Our results suggest that nest-site choice allows mothers to partially control the environment of their incubating eggs, but is less effective at controlling hatchling environments during hibernation. Additionally, we provide novel support for the "bigger-is-better" hypothesis in turtles by showing a positive relationship between size and survival during the hibernation stage.
Data from: Experimental evolution of Legionella pneumophila in mouse macrophages leads to strains with altered determinants of environmental survival
The Gram-negative bacterium, Legionella pneumophila, is a protozoan parasite and accidental intracellular pathogen of humans. We propose a model in which host cycling through multiple protozoan hosts in the environment holds L. pneumophila in a state of evolutionary stasis as a broad host-range pathogen. Using an experimental evolution approach, we tested this hypothesis by restricting L. pneumophila to growth within mouse macrophages for hundreds of generations. Whole-genome resequencing and high-throughput genotyping identified several parallel adaptive mutations and population dynamics that led to improved replication within macrophages. Based on these results, we provide a detailed view of the population dynamics of an experimentally evolving bacterial population, punctuated by frequent instances of transient clonal interference and selective sweeps. Non-synonymous point mutations in the flagellar regulator, fleN, resulted in increased uptake and broadly increased replication in both macrophages and amoebae. Mutations in multiple steps of the lysine biosynthesis pathway were also independently isolated, resulting in lysine auxotrophy and reduced replication in amoebae. These results demonstrate that under laboratory conditions, host restriction is sufficient to rapidly modify L. pneumophila fitness and host range. We hypothesize that, in the environment, host cycling prevents L. pneumophila host-specialization by maintaining pathways that are deleterious for growth in macrophages and other hosts.
Data from: The survival-reproduction association becomes stronger when conditions are good
Positive covariations between survival and reproductive performance (S-R covariation) are generally interpreted in the context of fixed or dynamic demographic heterogeneity (i.e., persistent differences between individuals, or dynamic variation in resource acquisition), but the processes underlying covariations are still unknown. We used multi-event modelling to investigate how environmental and individual features influence S-R covariation patterns in a long-lived seabird, the Monteiro's storm-petrel (Oceanodroma monteiroi). Our analysis reveals that a strong positive association between individual breeding success and subsequent survival occurs only when conditions are favourable to reproduction (in favourable years, in high quality nests and in nest-faithful breeders). This finding reflects differences in the main causes of breeding failure and mortality under favourable and unfavourable conditions, which in turn lead to distinct patterns of S-R covariation. We suggest, in particular, that resource-related sources of demographic heterogeneity do not generate a strong S-R covariation, in contrast to hidden and unpredictable sources of variation.
METEOROLOGICAL AND AGRICULTURAL DROUGHT RISK ASSESSMENT VIA KAPLAN-MEIER SURVIVABILITY ESTIMATOR SUPPLEMENTARY DATA
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Data for: Food Web Structure Significantly Affects the Body Condition and Survival of an Amphibian Intraguild Predator
<p>Data for upcoming publication</p>
Data associated with "Survival outcomes are associated with genomic instability in luminal breast cancers".
<p>Data utilised in <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245042">Survival outcomes are associated with genomic instability in luminal breast cancers</a>.</p>
Data from: Temporal factors and distance to human settlement affect nest survival of the endangered Yellow-headed Parrot in Belize, Central America
<p>The endangered Yellow-headed Parrot (<em>Amazona oratrix</em>) has experienced a considerable reduction in abundance and distribution. Identifying natural and anthropogenic causes of nest failure is a critical step towards developing conservation actions that increase nest survival. In this study, we examined daily nest survival in relation to temporal, habitat and anthropogenic factors, as well as nest site properties. We monitored nests (<em>n </em>= 124) across six study sites in Belize during 2017 and 2018 and independently modeled the effects of predation, abandonment and poaching on daily nest survival rates. Overall, the estimated cumulative nest survival probability was 0.18 (95% CI = 0.12 – 0.25). Predation was the main cause of nest failure, followed by abandonment and poaching. Our results showed that nest predation and abandonment usually occurred early in the nesting cycle. Day within the nesting season negatively influenced daily survival for abandoned nests and had a quadratic effect on survival for poached nests.<strong> </strong>Poaching events occurred at a specific date range later in the season, with nests farther from the nearest human settlement having higher daily survival. Findings from this study highlight the additive mortality effect that nest poaching is having on Yellow-headed Parrot populations in Belize and show that managers can anticipate the timing and location of nests most vulnerable to poaching.<span> </span></p>
Data assessing survival variation between capture methods in white-tailed deer
<p>Understanding what variables affect ungulate neonate survival is imperative to successful conservation and management of the species. Predation is commonly cited as a cause-specific source of mortality and ecological covariates often influence neonate survival. However, variation in survival estimates related to capture methodology has been documented with opportunistically captured neonates generally displaying greater survival than those captured via aid of vaginal implant transmitters (VITs), likely because of increased left truncation observed in the opportunistically captured datasets. Our goal was to assess if 3- and 6-month survival estimates varied by capture method while simultaneously assessing if capture method affected model selection and interpretation of ecological covariates for white-tailed deer neonates captured from three study sites from 2014 to 2015 in North Dakota and South Dakota, USA. We found survival varied by capture method for 3-month neonate survival with opportunistically captured neonates displaying up to 26% greater survival than their counterparts captured via VITs; however, this relationship was not present for 6-month survival. We also found model selection and subsequent interpretation of ecological covariates varied when analyzing datasets comprised of neonates captured via VITs, neonates captured opportunistically, and all neonates combined regardless of capture method. When interpreting results from our VIT only analysis for 3-month survival, we found survival varied by three time intervals and was lowest in the first two weeks of life. Capture method did not affect 6-month survival, which was most influenced by total precipitation occurring during 3 – 8 weeks of a neonate's life and percent canopy cover found at a neonate's capture site. Our results support previous research that capture method must be accounted for when deriving survival estimates for ungulate neonates as it can impact derived estimates and subsequent interpretation of results. </p>
Survival and growth data for tree species planted to reforest degraded tropical peat swamp forests and functional trait data for peat swamp forest species across Southeast Asia
<p>Degraded tropical peat swamp forests are harsh environments so difficult to restore. Evidence from past restoration projects can inform selection of species for planting. As part of a systematic review, we collated and synthesised survival and growth monitoring data on trees planted in degraded tropical peat swamp forests across Southeast Asia. A key aim of the systematic review and meta-analysis was to determine which tree species survive best when planted to restore tropical peat swamp forests. We also investigated the impact of seedling and site treatments and climatic conditions (El Niño-Southern Oscillation) on tree seedling survival and growth and the potential to use plant functional traits to predict survival and growth. </p> <p>Full methodological details of the systematic review, including: search strategy, article screening and inclusion criteria, critical appraisal of screened articles, data processing and data analysis can be found in the published article and supporting information stated below.</p> <p>Smith SW, Rahman NEB, Harrison ME, Shiodera S, Giesen W, Lampela M, Wardle DA, Chong KY, Randi A, Wijedasa LS, Teo PY, Fatimah, YA, Teng NT, Joanne YKQ, Alam MJ, Brugues Sintes P, Darusman T, Graham LLB, Katoppo DR, Kojima K, Kusin K, Lestari DP, Metali F, Morrogh-Bernard HC, Nahor MB, Napitupulu RRP, Nasir D, Nath TK, Nilus R, Norisada M, Rachmanadi D, Rachmat HH, Ripoll Capilla B, Salahuddin, Santosa PB, Sukri RS, Tay B, Tuah W, Wedeux, BMM, Yamanoshita T, Yokoyama EY, Yuwati TW, Lee JSH. Tree species that ‘live slow, die older’ enhance tropical peat swamp restoration: evidence from a systematic review. <em>Journal of Applied Ecology. </em>DOI:<a href="https://doi.org/10.1111/1365-2664.14232">10.1111/1365-2664.14232</a></p> <p>In this data repository, we have uploaded the following data used in the meta-analysis to generate the findings presented in the systematic review, specifically:</p> <ul> <li>Screening sheets of eligible articles across languages (English, Indonesian, Japanese and German) read in detailed by multiple authors on the review</li> <li>Survival monitoring data, including predicted half-life (duration until 50% mortality) derived from functional line-fitting</li> <li>Height monitoring data, including standardized relative growth rates (cm × cm<sup>-1 </sup>month<sup>-1</sup>) derived from functional line-fitting</li> <li>Plant functional traits, selected leaf nutrient contents and wood densities for those species used in the functional trait analyses</li> </ul> <p>Each data file has an associated meta-data file explaining the column headers and variables. Please note, data contributors from some studies wished to retain control over access to their monitoring data, but are willing to share this data on request. The relevant study-site code those studies used in the analyses in our systematic review can be found in the meta-data sheets. Details given include study-site code (used in the systematic review), site name and location, author name(s), author contact email(s). All these details have been provided with permission from relevant data contributor co-author(s). </p>
ESMO-GROW checklist for the publication PD-1/PD-L1 blockade plus abnobaViscum® therapy is associated with improved survival in advanced or metastasized NSCLC patients, a real-world data registry study according to the ESMO-GROW criteria
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Data from: Can recombinant human thrombomodulin increase survival among patients with severe septic-induced disseminated intravascular coagulation: a single-centre, open-label, randomised controlled trial
Objective: To determine whether treatment with recombinant human thrombomodulin (rhTM) increases survival among severe septic patients with sepsis-induced disseminated intravascular coagulation (DIC) Design: Single-center, open-label, randomized controlled trial Setting: Single tertiary hospital Participant: 92 severe septic patients with sepsis-induced DIC Interventions: Patients with DIC scores ≥4, as defined by the Japanese Association of Acute Medicine, were diagnosed with DIC. Randomization was performed by the envelope method. The treatment group (rhTM group, n = 47) was intravenously treated with rhTM within 24 h of admission (day 0), and the control group (n = 45) did not receive any anti-coagulants, except in cases of deep venous thrombosis and pulmonary embolism. Primary and secondary measurements: Data were collected on days 0 (admission), 1, 2, 3, 5, 7, and 10. The primary outcome was survival at 28 and 90 days. The secondary endpoints comprised changes in DIC scores, platelet counts, D-dimer, antithrombin III (ATIII), and C-reactive protein (CRP) levels, and Sequential Organ Failure Assessment (SOFA) scores. All analyses were conducted on an intent-to-treat basis. Main Results: The 28-day survival rates were 84 and 83% in the control and rhTM groups, respectively (p = 0.745, log rank test). The 90-day survival rates were 73% and 72% in the control and rhTM groups, respectively (p = 0.94, log rank test). Meanwhile, the rates of recovery from DIC (<4) were significantly higher in the rhTM group than in the control group (p = 0.001, log rank test). Relative change from baseline of D-dimer levels were significantly lower in the rhTM group than in the control group, on day 3 and 5. Conclusion: rhTM treatment decreased D-dimer levels and facilitated DIC recovery in severe septic patients with sepsis-induced DIC. However, the treatment did not improve survival in this cohort.
Gene alterations, clinical informations and survival data of gliomas with/without corpus callosum involvement
<p>The raw dataset of this study contained the gene alterations, clinical informations and survival data of glioma patients. Gene alterations data were obtained by Next-generation DNA sequencing of glioma samples of patients. Clinical informations were obtained from Electronic medical records and follow-up. The survival data were obtained by follow-up of patients. In order to explore gene alterations and their correlation with the survival of glioblastoma (GBM) of corpus callosum (CC) involvement (ccGBM), this dataset was analyzed in detail. A total of<b> </b>30 ccGBM and 88 non-ccGBM were finally included. The ccGBM had higher incidence of <i>PDGFRA </i>(33.3% versus 9.1%, P=0.004) alterations than non-ccGBM. <i>PDGFRA </i>amplification (<i>PDGFRAamp</i>, 33.3% versus 9.1%, P=0.004) and missense mutation (<i>PDGFRAmut</i>, 20.0% versus 3.4%, P=0.011) both had higher incidence in ccGBM than in non-ccGBM. <i>PDGFRA </i>alteration was significantly associated with the occurrence of ccGBM (OR=4.91 [95%CI: 1.55-15.52], P=0.007). The ccGBM of <i>PDGFRAamp </i>achieved shorter median PFS (8.6 versus 13.5 months, P=0.025) and OS (12.4 versus 17.9 months, P=0.022) than non-ccGBM of <i>PDGFRAnon-amp</i>. The ccGBM of <i>PDGFRAamp</i> combined with <i>PDGFRAmut</i> (<i>PDGFRAamp-mut</i>)<i> </i>had shorter median PFS (7.6 versus 8.9 months, P=0.022) and OS (9.6 versus 17.8 months, P=0.006) than non-ccGBM of <i>PDGFRA</i> wild type and non-amplification (<i>PDGFRA-w, non-amp</i>). Compared to ccGBM of <i>PDGFRA-w, non-amp</i>, the ccGBM of <i>PDGFRAamp</i> and <i>PDGFRAamp-mut </i>both had shorter median PFS and OS (P<0.05). Hazard ratios (HRs) of <i>PDGFRAamp</i> for PFS and OS of ccGBM were 3.08 (95%CI: 1.02-9.35, P=0.047) and 5.07 (95%CI: 1.52-16.89, P=0.008) respectively, HRs of <i>PDGFRAamp-mut </i>for PFS and OS were 13.16 (95%CI: 3.19-54.40, P<0.001) and 16.36 (95%CI: 2.66-100.70, P=0.003) respectively. The <i>PDGFRA </i>alterations is significantly associated with the occurrence and poor prognosis of ccGBM.</p>
Data from: Delayed transmission selects for increased survival of vesicular stomatitis virus
Life-history theory predicts that traits for survival and reproduction cannot be simultaneous maximized in evolving populations. For this reason, in obligate parasites such as infectious viruses, selection for improved between-host survival during transmission may lead to evolution of decreased within-host reproduction. We tested this idea using experimental evolution of RNA virus populations, passaged under differing transmission times in the laboratory. A single ancestral genotype of Vesicular Stomatitis Virus (VSV), a negative-sense RNA Rhabdovirus, was used to found multiple virus lineages evolved in either ordinary 24-hour cell-culture passage, or in delayed passages of 48 hours. After 30 passages (120 generations of viral evolution), we observed that delayed transmission selected for improved extracellular survival, which traded-off with lowered viral fecundity (slower exponential population growth, and smaller mean plaque size). To further examine the confirmed evolutionary trade-off, we obtained consensus whole-genome sequences of evolved virus populations, to infer phenotype-genotype associations. Results implied that increased virus survival did not occur via convergence; rather, improved virion stability was gained via independent mutations in various VSV structural proteins. Our study suggests that RNA viruses can evolve different molecular solutions for enhanced survival despite their limited genetic architecture, but suffer generalized reproductive trade-offs that limit overall fitness gains.
Data from: Elevated salinity blocks pathogen transmission and improves host survival for a globally pandemic disease: implications for amphibian translocations
1. Emerging infectious diseases are one of the greatest threats to global biodiversity. Chytridiomycosis in amphibians is perhaps the most extreme example of this phenomenon known to science. Translocations are increasingly used to fight disease-induced extinctions. However, many programs fail because disease is still present or subsequently establishes in the translocation environment. There is a need for studies in real-world scenarios to test whether environmental manipulation could improve survival in populations by generating unfavourable environmental conditions for pathogens. Reintroductions of amphibians impacted by chytridiomycosis into environments where the disease persists provide a scenario where this paradigm can be tested. 2. We tested the hypothesis that manipulating environmental salinity in outdoor mesocosms under near identical environmental conditions applying in a nearby translocation program for an endangered amphibian, would improve survival and determine the mechanisms involved. 160 infected and 288 uninfected, captive-bred, juvenile frogs were released into 16 outdoor mesocosms in which salinity was controlled (high or low salinity treatment). The experiment was run for 25 weeks from the mid-austral winter to the mid-austral summer of 2013 in a temperate coastal environment, Australia. 3. Increasing salinity from ca. 0.5 ppt to 3.5 - 4.5 ppt reduced pathogen transmission between infected and uninfected animals, resulting in significantly reduced mortality in elevated salt mesocosms (0.13, high salt versus 0.23, low salt survival at 23 weeks). Increasing water temperature associated with season (from mean 13oC to 25oC) eventually cleared all surviving animals of the pathogen. 4. Synthesis and applications. We identified a mechanism by which environmental salinity can protect amphibian hosts from chytridomycosis by reducing disease transmission rates and conclude that manipulating environmental salinity in landscapes where chytrid-affected amphibians are currently translocated could improve the probability of population persistence for hundreds of species. More broadly, we provide support for the paradigm that environmental manipulation can be used to mitigate the impact of emerging infectious diseases.18-Sep-2017
Data from: In situ glacial survival maintains high genetic diversity of Mussaenda kwangtungensis on continental islands in subtropical China
<p>Generally, island populations are predicted to have less genetic variation than their mainland relatives. However, there has been exceptions, indicating that the relationships were impacted by several factors, e.g historical processes. In the present study, we chose a group of subtropical islands located in South China as the study system, which are quite younger and much closer to the mainland than most of the previous studied island systems, to test the hypothesis that<i> in situ</i> glacial survival contributes to high levels of genetic diversity in island populations. We conducted a comparison of genetic variation between 12 island and 11 nearby mainland populations of <i>Mussaenda kwangtungensis</i> using eleven nuclear microsatellite and three chloroplast markers, evaluated effects of the island area and distance to mainland on genetic diversity of island populations, and simulated the potential distribution over the past by ecological niche modelling, together with the genetic data to detect the role of islands during the glacial periods. The island populations displayed comparable levels of genetic diversity and differentiation with mainland populations, overall high levels of unique polymorphisms, and the greatest values of specific within-population genetic diversity. No significant correlation was detected between genetic diversity of island populations and distance to mainland, as well as area of islands, except that allelic richness was significantly positively correlated with the area of islands. Nuclear microsatellites revealed two main clusters, largely corresponding to islands and inland populations, which divergence dated to a time of island formation by ABC analysis. Ecological Niche Modelling predicted a highly climatic suitability on islands during the Last Glacial Maximum (LGM). Our results suggest that the islands have acted as refugia during the LGM and highlight the role of <i>in situ</i> glacial survival in maintaining high levels of genetic diversity of <i>M. kwangtungensis</i> in continental islands of subtropical China.</p>
Data from: Identification and validation of a novel immune-related signature associated with macrophages and CD8 T cell infiltration predicting overall survival for hepatocellular carcinoma
<p><b>Background:</b> Although the effects of macrophages and CD8 T cell infiltration on clinical outcomes have been widely reported, the association between immunity-associated gene with them for hepatocellular carcinoma (HCC) remains unclear.</p> <p><b>Materials and methods: </b>The ssGSEA served for quantifying the macrophages as well as CD8 T cell infiltration in the HCC samples obtained from TCGA database. Kaplan-Meier(KM) survival assay was used to determine the associations between macrophages and CD8 T cell infiltration with OS. LASSO Cox regressive method assisted in developing an immune gene signature as well as building a risk score. The performance was evaluated by the time-dependent ROC together with the KM survival analysis. The ICGC database were adopted for external verification. CIBERSORT was applied to the correlation analysis on the immune-related signature and the immunocyte infiltration. GSEA were employed exploring the underlying molecular mechanisms.</p> <p><b>Results:</b> Increased CD8+ T cell infiltration was associated with longer OS, whereas a greater infiltration of macrophages was related to shorter OS. There were 398 differential expression genes (DEGs) between the high- and low infiltration groups with the "edgeR" package. A prognostic signature consisted of 10 immune genes was built in TCGA and examined in ICGC. The uniform cutoff (0.927) was adopted for separating sufferers into the high-risk(HR) and low-risk(LR) groups. The ROC curves revealed that the AUC data for this signature predicting 1,2,3,4 and 5 year were all above 0.7 in both TCGA and ICGC cohort and patients in the HR<sub> </sub>group exhibited evidently weaker prognostic results compared with the LR group. The HR<sub> </sub>group presented evidently greater Tregs and Macrophage M0 relative to the LR group, whereas the LR group saw the enrichment of CD8 T cells.</p> <p><b>Conclusion:</b> The immune signature associated with macrophages as well as CD8 T cell infiltration has reliable prognostic and predictive value for HCC patients.</p>
Data from: Spermidine dietary supplementation and polyamines level in reference to survival and lifespan of honey bees
<p>File containing raw data about publication.</p>
Data from: Family network size and survival across the lifespan of female macaques
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Data from: Socially selected ornaments and fitness: signals of fighting ability in paper wasps are positively associated with survival, reproductive success, and rank
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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.