Velocity-based movement modeling for individual and population level inference.
Ontology highlight
ABSTRACT:
SUBMITTER: Hanks EM
PROVIDER: S-EPMC3154913 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Recent advances in probabilistic pragmatics have achieved considerable success in modeling speakers' and listeners' pragmatic reasoning as probabilistic inference. However, these models are usually applied to population-level data, and so implicitly suggest a homogeneous population without individual differences. Here we investigate potential individual differences in Theory-of-Mind related depth of pragmatic reasoning in so-called reference games that require drawing ad hoc Quantity implicatures of varying complexity. We show by Bayesian model comparison that a model that assumes a heterogenous population is a better predictor of our data, especially for comprehension. We discuss the implications for the treatment of individual differences in probabilistic models of language use.
| S-EPMC4858259 | biostudies-literature
Project description:We derive a new method to estimate the age specific incidence of an infection with a differential mortality, using individual level infection status data from successive surveys. The method consists of a) an SI-type model to express the incidence rate in terms of the prevalence and its derivatives as well as the difference in mortality rate, and b) a maximum likelihood approach to estimate the prevalence and its derivatives. Estimates can in principle be obtained for any chosen age and time, and no particular assumptions are made about the epidemiological or demographic context. This is in contrast with earlier methods for estimating incidence from prevalence data, which work with aggregated data, and the aggregated effect of demographic and epidemiological rates over the time interval between prevalence surveys. Numerical simulation of HIV epidemics, under the presumption of known excess mortality due to infection, shows improved control of bias and variance, compared to previous methods. Our analysis motivates for a) effort to be applied to obtain accurate estimates of excess mortality rates as a function of age and time among HIV infected individuals and b) use of individual level rather than aggregated data in order to estimate HIV incidence rates at times between two prevalence surveys.
| S-EPMC3440384 | biostudies-literature
Project description:We report Cytopath, a method for trajectory inference that takes advantage of transcriptional activity information from the RNA velocity of single cells to perform trajectory inference. Cytopath performs this task by defining a Markov chain model, simulating an ensemble of possible differentiation trajectories, and constructing a consensus trajectory. We show that Cytopath can recapitulate the topological and molecular characteristics of the differentiation process under study. In our analysis, we include differentiation trajectories with varying bifurcated, circular, convergent, and mixed topologies studied in single-snapshot as well as time-series single-cell RNA sequencing experiments. We demonstrate the capability to reconstruct differentiation trajectories, assess the association of RNA velocity-based pseudotime with actually elapsed process time, and identify drawbacks in current state-of-the art trajectory inference approaches.
| S-EPMC9795361 | biostudies-literature
Project description:Individual Level Models (ILMs), a new class of models, are being applied to infectious epidemic data to aid in the understanding of the spatio-temporal dynamics of infectious diseases. These models are highly flexible and intuitive, and can be parameterised under a Bayesian framework via Markov chain Monte Carlo (MCMC) methods. Unfortunately, this parameterisation can be difficult to implement due to intense computational requirements when calculating the full posterior for large, or even moderately large, susceptible populations, or when missing data are present. Here we detail a methodology that can be used to estimate parameters for such large, and/or incomplete, data sets. This is done in the context of a study of the UK 2001 foot-and-mouth disease (FMD) epidemic.
| S-EPMC4578172 | biostudies-literature
Project description:The history of human population size is important for understanding human evolution. Various studies have found evidence for a founder event (bottleneck) in East Asian and European populations, associated with the human dispersal out-of-Africa event around 60 thousand years (kyr) ago. However, these studies have had to assume simplified demographic models with few parameters, and they do not provide a precise date for the start and stop times of the bottleneck. Here, with fewer assumptions on population size changes, we present a more detailed history of human population sizes between approximately ten thousand and a million years ago, using the pairwise sequentially Markovian coalescent model applied to the complete diploid genome sequences of a Chinese male (YH), a Korean male (SJK), three European individuals (J. C. Venter, NA12891 and NA12878 (ref. 9)) and two Yoruba males (NA18507 (ref. 10) and NA19239). We infer that European and Chinese populations had very similar population-size histories before 10-20 kyr ago. Both populations experienced a severe bottleneck 10-60 kyr ago, whereas African populations experienced a milder bottleneck from which they recovered earlier. All three populations have an elevated effective population size between 60 and 250 kyr ago, possibly due to population substructure. We also infer that the differentiation of genetically modern humans may have started as early as 100-120 kyr ago, but considerable genetic exchanges may still have occurred until 20-40 kyr ago.
| S-EPMC3154645 | biostudies-literature
Project description:Our species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a population over time, conditioned on different pathways for the transmission of information between individuals. From these data, we obtain theoretical expectations for a range of statistics commonly used to capture population-level characteristics (e.g. the degree of cultural diversity). Consistent with previous theoretical work, our results show that the patterns observed at the level of groups are rooted in the interplay between the transmission pathways and the age structure of the population. We also explore whether, and under what conditions, the different pathways can be distinguished based on their group-level signatures, in an effort to establish theoretical limits to inference. Our results show that the temporal dynamic of cultural change over time retains a stronger signature than the cultural composition of the population at a specific point in time. Overall, the results suggest a shift in focus from identifying the one individual-level process that likely produced the observed data to excluding those that likely did not. We conclude by discussing the implications for empirical studies of human cultural evolution.
| S-EPMC5627126 | biostudies-literature
Project description:Ocean acidification is predicted to have detrimental effects on many marine organisms and ecological processes. Despite growing evidence for direct impacts on specific species, few studies have simultaneously considered the effects of ocean acidification on individuals (e.g. consequences for energy budgets and resource partitioning) and population level demographic processes. Here we show that ocean acidification increases energetic demands on gastropods resulting in altered energy allocation, i.e. reduced shell size but increased body mass. When scaled up to the population level, long-term exposure to ocean acidification altered population demography, with evidence of a reduction in the proportion of females in the population and genetic signatures of increased variance in reproductive success among individuals. Such increased variance enhances levels of short-term genetic drift which is predicted to inhibit adaptation. Our study indicates that even against a background of high gene flow, ocean acidification is driving individual- and population-level changes that will impact eco-evolutionary trajectories.
| S-EPMC4731747 | biostudies-literature
Project description:Socioeconomic status is an important determinant of health, the measurement of which is of great significance to population health research. However, individual-level socioeconomic factors are absent from much health administrative data, resulting in widespread use of area-level measures in their place. This study aims to clarify the role of individual- and area-level socioeconomic status in Ontario, Canada, through comparison of income measures. Using data from four cycles (2005-2012) of the Canadian Community Health Survey, we assessed concordance between individual- and area-level income quintiles using percent agreement and Kappa statistics. Individual-level characteristics were compared at baseline. Cumulative adult premature mortality was calculated for 5-years following interview. Rates were calculated separately for area-level and individual-level income, and jointly for each combination of income groups. Multivariable negative binomial models were fit to estimate associations between area- and individual-level income quintile and premature mortality after adjustment for basic demographics (age, sex, interview cycle) and key risk factors (alcohol, smoking, physical activity, and body mass index). Agreement between individual- and area-level income measures was low. Kappa statistics for same and similar (i.e. ±1 quintile) measures were 0.11 and 0.48, indicating low and moderate agreement, respectively. Socioeconomic disparities in premature mortality were greater for individual-level income than area-level income. When rates were stratified by both area- and individual-level income quintiles simultaneously, individual-level income gradients persisted within each area-level income group. The association between income and premature mortality was significant for both measures, including after full adjustment. Area-level socioeconomic status is an inappropriate proxy for missing individual-level data. The low agreement between area- and individual-level income measures and differences in demographic profile indicate that the two socioeconomic status measures do not capture the same population groups. However, our findings demonstrate that both individual- and area-level income measures are associated with premature mortality, and describe unique socioeconomic inequities.
| S-EPMC7013127 | biostudies-literature
Project description:We tested the hypothesis that the degree of adaptation to highly focused sprint training at opposite ends of the sprint Force-Velocity (FV) spectrum would be associated with initial sprint FV profile in rugby athletes. Training-induced changes in sprint FV profiles were computed before and after an eight-week in-season resisted or assisted sprint training protocol, including a three-week taper. Professional male rugby players (age: 18.9 ± 1.0 years; body height: 1.9 ± 0.0 m; body mass: 88.3 ± 10.0 kg) were divided into two groups based on their initial sprint FV profiles: 1) Heavy sled training (RESISTED, N = 9, velocity loss 70-80%), and 2) assisted acceleration training (ASSISTED, N = 12, velocity increase 5-10%). A total of 16 athletes were able to finish all required measurements and sessions. According to the hypothesis, a significant correlation was found between initial sprint FV profile and relative change in sprint FV profile (RESISTED: r = -0.95, p < 0.01, ASSISTED: r = -0.79, p < 0.01). This study showed that initial FV properties influence the degree of mechanical response when training at different ends of the FV spectrum. Practitioners should consider utilizing the sprint FV profile to improve the individual effectiveness of resisted and assisted sprint training programs in high-level rugby athletes.
| S-EPMC7281595 | biostudies-literature
Project description:BACKGROUND: The allele frequency spectrum (AFS) consists of counts of the number of single nucleotide polymorphism (SNP) loci with derived variants present at each given frequency in a sample. Multiple approaches have recently been developed for parameter estimation and calculation of model likelihoods based on the joint AFS from two or more populations. We conducted a simulation study of one of these approaches, implemented in the Python module δaδi, to compare parameter estimation and model selection accuracy given different sample sizes under one- and two-population models. RESULTS: Our simulations included a variety of demographic models and two parameterizations that differed in the timing of events (divergence or size change). Using a number of SNPs reasonably obtained through next-generation sequencing approaches (10,000 - 50,000), accurate parameter estimates and model selection were possible for models with more ancient demographic events, even given relatively small numbers of sampled individuals. However, for recent events, larger numbers of individuals were required to achieve accuracy and precision in parameter estimates similar to that seen for models with older divergence or population size changes. We quantify i) the uncertainty in model selection, using tools from information theory, and ii) the accuracy and precision of parameter estimates, using the root mean squared error, as a function of the timing of demographic events, sample sizes used in the analysis, and complexity of the simulated models. CONCLUSIONS: Here, we illustrate the utility of the genome-wide AFS for estimating demographic history and provide recommendations to guide sampling in population genomics studies that seek to draw inference from the AFS. Our results indicate that larger samples of individuals (and thus larger AFS) provide greater power for model selection and parameter estimation for more recent demographic events.
| S-EPMC4269862 | biostudies-other