Characterizing unsuccessful animal adoptions: age and breed predict the likelihood of return, reasons for return and post-return outcomes.
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ABSTRACT:
SUBMITTER: Powell L
PROVIDER: S-EPMC8044234 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:DNA methylation is a reaction that results in the formation of 5-methylcytosine when a methyl group is added to the cytosine’s C5 position. As organisms age, DNA methylation patterns change in a reproducible fashion. This phenomenon has established DNA methylation as a valuable biomarker in aging studies. Epigenetic clocks based on weighted combinations of methylation sites have been developed to accurately predict the age of an individual from their methylome. However, many epigenetic clocks, particularly those that utilize penalized regression, model the changes in methylation linearly with age. Moreover, these models, which use methylation levels as features, are not robust to missing data and do not account for the count-based nature of bisulfite sequence data. Additionally, the models are generally not interpretable. To overcome these challenges, we present BayesAge, an extension of the previously developed scAge approach that was developed for the analysis of single cell DNA methylation datasets. BayesAge utilizes maximum likelihood estimation (MLE) to infer ages, models count data using binomial distributions, and uses LOWESS smoothing to capture the non-linear dynamics between methylation and age. Our approach is designed for use with bulk bisulfite sequencing datasets. BayesAge outperforms scAge in several respects. Specifically, BayesAge’s age residuals are not age associated, thus providing a less biased representation of epigenetic age variation across populations. Moreover, BayesAge enables the estimation of error bounds on age inference and, when run on downsampled data, its coefficient of determination between predicted and actual ages surpasses both scAge and penalized regression.
2024-03-20 | GSE261769 | GEO
Project description:BayesAge: A Maximum Likelihood Algorithm To Predict Epigenetic Age
| PRJNA1088825 | ENA
Project description:Predicting breed-specific environmental suitability has been problematic in livestock production. Native breeds have low productivity but are thought to be more robust to perform under local conditions than exotic breeds. Attempts to introduce genetically improved exotic breeds are generally unsuccessful, mainly due to the antagonistic environmental conditions. Knowledge of the environmental conditions that are shaping the breed would be needed to determine its suitability to different locations. Here, we present a methodology to predict the suitability of breeds for different agro-ecological zones using Geographic Information Systems tools and predictive habitat distribution models. This methodology was tested on the current distribution of two introduced chicken breeds in Ethiopia: the Koekoek, originally from South Africa, and the Fayoumi, originally from Egypt. Cross-validation results show this methodology to be effective in predicting breed suitability for specific environmental conditions. Furthermore, the model predicts suitable areas of the country where the breeds could be introduced. The specific climatic parameters that explained the potential distribution of each of the breeds were similar to the environment from which the breeds originated. This novel methodology finds application in livestock programs, allowing for a more informed decision when designing breeding programs and introduction programs, and increases our understanding of the role of the environment in livestock productivity.
| S-EPMC6582082 | biostudies-other
Project description:The gaze of other dogs and humans is informative for dogs, but it has not been explored which factors predict face-directed attention. We used image presentations of unfamiliar human and dog heads, facing the observer (portrait) or facing away (profile), and measured looking time responses. We expected dog portraits to be aversive, human portraits to attract interest, and tested dogs of different sex, skull length and breed function, which in previous work had predicted human-directed attention. Dog portraits attracted longer looking times than human profiles. Mesocephalic dogs looked at portraits longer than at profiles, independent of the species in the image. Overall, brachycephalic dogs and dogs of unspecified breed function (such as mixed breeds) displayed the longest looking times. Among the latter, females observed the images for longer than males, which is in line with human findings on sex differences in processing faces. In a subsequent experiment, we tested whether dog portraits functioned as threatening stimuli. We hypothesized that dogs will avoid food rewards or approach them more slowly in the presence of a dog portrait, but found no effect of image type. In general, older dogs took longer to approach food placed in front of the images and mesocephalic dogs were faster than dogs of other skull length types. The results suggest that short-headed dogs are more attentive to faces, while sex and breed function predict looking times through complex interactions.
| S-EPMC6112419 | biostudies-literature
Project description:BackgroundMany studies on low back pain (LBP) have identified prognostic factors, but prediction models for use in secondary health care are not available. The purpose of this cohort study, based on a randomised clinical study, was to identify risk factors for unsuccessful return to work (U-RTW) in sick-listed LBP patients with or without radiculopathy and to validate a prediction model for U-RTW.Methods325 sick-listed LBP patients with or without radiculopathy were included in an intervention study and followed for one year. Afterwards, 117 other LBP patients were recruited similarly, included in a validation study and also followed for one year. All patients were subjected to identical procedures and interventions and received a brief intervention by the same rehabilitation doctor and physiotherapist. Half of them received case manager guidance within a multidisciplinary setting. At baseline, they completed a questionnaire and went through a clinical low-back examination. Sciatica was investigated by magnetic resonance imaging (MRI). U-RTW was registered in a national database both initially and at 1-year.ResultsNeither initial U-RTW (24.0%) nor one-year U-RTW (38.2%) were statistically significantly different in the two intervention groups nor in patients with and without radiculopathy. Multivariate logistic regression analysis identified two clinical and five psychosocial baseline predictors for one-year U-RTW (primary outcome). The clinical predictors included pain score (back+leg pain) and side-flexion. The five psychosocial predictors included 'bodily distress' 'low expectations of RTW', 'blaming the work for pain', 'no home ownership' and 'drinking alcohol less than once/month'. These predictors were not statistically significantly different in patients with and without radiculopathy, and they also predicted initial U-RTW (secondary outcome). Obesity and older age were only supplementary predictors in patients with radiculopathy. A prediction model was established and tested in the validation study group. The model predicted one-year U-RWT in patients with intermediate and high risk, but only partially in patients with low risk. The model predicted all three risk categories in initial U-RTW.ConclusionsA prediction model combining baseline clinical and psychosocial risk factors predicted patients with low, intermediate and high risk for unsuccessful return to work, both initially and at 1-year.
| S-EPMC3663778 | biostudies-literature
Project description:Although memory recall is known to be reduced with normal aging, little is known about the patterns of brain activity that accompany these recall failures. By assessing faulty memory, we can identify the brain regions engaged during retrieval attempts in the absence of successful memory and determine the impact of aging on this functional activity. We used functional magnetic resonance imaging to examine age differences in brain activity associated with memory failure in three memory retrieval tasks: autobiographical (AM), episodic (EM) and semantic (SM). Compared to successful memory retrieval, both age groups showed more activity when they failed to recall a memory in regions consistent with the salience network (SLN), a brain network also associated with non-memory errors. Both groups also showed strong functional coupling among SLN regions during incorrect trials and in intrinsic patterns of functional connectivity. In comparison to young adults, older adults demonstrated (1) less activity within the SLN during unsuccessful AM trials; (2) weaker intrinsic functional connectivity between SLN nodes and dorsolateral prefrontal cortex; and (3) less differentiation of SLN functional connectivity during incorrect trials across memory conditions. These results suggest that the SLN is engaged during recall failures, as it is for non-memory errors, which may be because errors in general have particular salience for adapting behavior. In older adults, the dedifferentiation of functional connectivity within the SLN across memory conditions and the reduction of functional coupling between it and prefrontal cortex may indicate poorer inter-network communication and less flexible use of cognitive control processes, either while retrieval is attempted or when monitoring takes place after retrieval has failed. This article is part of a Special Issue entitled SI: Memory & Aging.
| S-EPMC4898958 | biostudies-literature
Project description:ObjectiveTo determine factors that influence sperm recovery after T-associated infertility.DesignClinical retrospective study.SettingAcademic male-infertility urology clinic.Patient(s)Sixty-six men who presented with infertility after T use.Intervention(s)T cessation and combination high-dose hCG and selective estrogen modulator (SERM) therapy.Main outcome measure(s)Whether patients successfully achieved or failed to achieve a total motile count (TMC) of greater than 5 million sperm within 12 months of T cessation and initiation of therapy.Result(s)A TMC of greater than 5 million sperm was achieved by 46 men (70%). Both increased age and duration of T use directly correlated with time to sperm recovery at both 6 and 12 months of hCG/SERM therapy. Age more consistently limited sperm recovery, while duration of T use had less influence at 12 months than at 6 months. Only 64.8% of azoospermic men achieved a TMC greater than 5 million sperm at 12 months, compared with 91.7% of cryptozoospermic men, yet this did not predict a failure of sperm recovery.Conclusion(s)Increasing age and duration of T use significantly reduce the likelihood of recovery of sperm in the ejaculate, based on a criterion of a TMC of 5 million sperm, at 6 and 12 months. Physicians should be cautious in pursuing long-term T therapy, particularly in men who still desire fertility. Using these findings, physicians can counsel men regarding the likelihood of recovery of sperm at 6 and 12 months.
| S-EPMC5292276 | biostudies-literature
Project description:BackgroundVector-borne disease transmission is dependent on the many nuances of the contact event between infectious and susceptible hosts. Virus acquisition from a viremic human to a susceptible mosquito is often assumed to be nearly perfect and almost always uniform across the infectious period. Dengue transmission models that have previously addressed variability in human to vector transmission dynamics do not account for the variation in infectiousness of a single individual, and subsequent infection of naïve mosquitoes. Understanding the contribution of this variability in human infectiousness is especially important in the context of introduction events where an infected individual carries the virus into a population of competent vectors. Furthermore, it could affect the ability to detect an epidemic (and the timing of detection) following introduction.MethodsWe constructed a stochastic, compartmental model to describe the heterogeneity of human viremia and calculate the probability of a successful introduction, taking into account the viremia level (and thus acquisition potential) of the index case on, and after, the day of introduction into a susceptible population and varying contact rates between the human and mosquito populations. We then compared the results of this model with those generated by a simpler model that has the same average infectiousness but only a single infectious class.ResultsWe found that the infectivity of the index case as well as the contact rate affected the probability of emergence, but that contact rate had the most significant effect. We also found that the interaction between contact rate and the infectiousness of the index case affected the time to detection relative to the peak of the epidemic curve. Additionally, when compared to our model that accounts for variable infectiousness, a model with a single infectious class underestimates the probability of emergence and transmission intensity.ConclusionUnderstanding the interplay between individual human heterogeneity of infectiousness and the rate of contact with the vector population will be important when predicting the likelihood, detection, and magnitude of an outbreak.
| S-EPMC4082489 | biostudies-literature
Project description:Glucocorticoid receptors (GRs) shuttle from the cytoplasm (cy) to the nucleus (nu) when bound with glucocorticoids (i.e. GR internalization) and alter transcriptional activity. GR activation within the fear circuit has been implicated in fear memory and post traumatic stress disorder (PTSD). However, no study to date has characterized GR internalization within the fear circuit during fear memory formation or examined how traumatic stress impacts this process. To address this, we assayed cy and nu GR levels at baseline and after auditory fear conditioning (FC) in the single prolonged stress (SPS) model of PTSD. Cy and nu GRs within the medial prefrontal cortex (mPFC), dorsal hippocampus (dHipp), ventral hippocampus (vHipp), and amygdala (AMY) were assayed using western blot. The distribution of GR in the cy and nu (at baseline and after FC) was varied across individual nodes of the fear circuit. At baseline, SPS enhanced cyGRs in the dHipp, but decreased cyGRs in the AMY. FC only enhanced GR internalization in the AMY and this effect was attenuated by SPS exposure. SPS also decreased cyGRs in the dHipp after FC. The results of this study suggests that GR internalization is varied across the fear circuit, which in turn suggests GR activation is selectively regulated within individual nodes of the fear circuit. The findings also suggest that changes in GR dynamics in the dHipp and AMY modulate the enhancing effect SPS has on fear memory persistence.
| S-EPMC6286002 | biostudies-literature
Project description:BACKGROUND:In many domains, scientists build complex simulators of natural phenomena that encode their hypotheses about the underlying processes. These simulators can be deterministic or stochastic, fast or slow, constrained or unconstrained, and so on. Optimizing the simulators with respect to a set of parameter values is common practice, resulting in a single parameter setting that minimizes an objective subject to constraints. RESULTS:We propose algorithms for post optimization posterior evaluation (POPE) of simulators. The algorithms compute and visualize all simulations that can generate results of the same or better quality than the optimum, subject to constraints. These optimization posteriors are desirable for a number of reasons among which are easy interpretability, automatic parameter sensitivity and correlation analysis, and posterior predictive analysis. Our algorithms are simple extensions to an existing simulation-based inference framework called approximate Bayesian computation. POPE is applied two biological simulators: a fast and stochastic simulator of stem-cell cycling and a slow and deterministic simulator of tumor growth patterns. CONCLUSIONS:POPE allows the scientist to explore and understand the role that constraints, both on the input and the output, have on the optimization posterior. As a Bayesian inference procedure, POPE provides a rigorous framework for the analysis of the uncertainty of an optimal simulation parameter setting.
| S-EPMC4545973 | biostudies-literature