Negation-triggered inferences are universal across human languages. Hearing \"This is not X\" should logically lead to the inference that all elements other than X constitute possible alternatives. However, not all logically possible alternatives are equally accessible in the real world. To qualify as a plausible alternative, it must share with the negated element as many similarities as possible, and the most plausible one is often from the same taxonomic category as the negated element. The current article reports on two experiments that investigated the development of preschool children\'s ability to infer plausible alternatives triggered by negation. Experiment 1 showed that in a context where children were required to determine the most plausible alternative to the negated element, the 3-, 4- and 5-year-olds, exhibited a robust preference for the taxonomic associates. Experiment 2 further demonstrated that the 3-, 4- and 5-year-olds considered all the complement set members as equally possible alternatives in a context where they were not explicitly required to evaluate the plausibility of different candidates. Taken together, our findings reveal interesting developmental continuity in preschool children\'s ability to make inferences about plausible alternatives triggered by negation. We discuss the potential semantic and pragmatic factors that contribute to children\'s emerging awareness of typical alternatives triggered by negative expressions.

Determining gene regulatory network (GRN) structure is a central problem in biology, with a variety of inference methods available for different types of data. For a widely prevalent and challenging use case, namely single-cell gene expression data measured after intervention at multiple time points with unknown joint distributions, there is only one known specifically developed method, which does not fully utilize the rich information contained in this data type. We develop an inference method for the GRN in this case, netWork infErence by covariaNce DYnamics, dubbed WENDY. The core idea of WENDY is to model the dynamics of the covariance matrix, and solve this dynamics as an optimization problem to determine the regulatory relationships. To evaluate its effectiveness, we compare WENDY with other inference methods using synthetic data and experimental data. Our results demonstrate that WENDY performs well across different data sets.

The COVID-19 pandemic demonstrated the key role that epidemiology and modelling play in analysing infectious threats and supporting decision making in real-time. Motivated by the unprecedented volume and breadth of data generated during the pandemic, we review modern opportunities for analysis to address questions that emerge during a major modern epidemic. Following the broad chronology of insights required - from understanding initial dynamics to retrospective evaluation of interventions, we describe the theoretical foundations of each approach and the underlying intuition. Through a series of case studies, we illustrate real life applications, and discuss implications for future work.

Dominance refers to the effect of a heterozygous genotype relative to that of the two homozygous genotypes. The degree of dominance of mutations for fitness can have a profound impact on how deleterious and beneficial mutations change in frequency over time as well as on the patterns of linked neutral genetic variation surrounding such selected alleles. Since dominance is such a fundamental concept, it has received immense attention throughout the history of population genetics. Early work from Fisher, Wright, and Haldane focused on understanding the conceptual basis for why dominance exists. More recent work has attempted to test these theories and conceptual models by estimating dominance effects of mutations. However, estimating dominance coefficients has been notoriously challenging and has only been done in a few species in a limited number of studies. In this review, we first describe some of the early theoretical and conceptual models for understanding the mechanisms for the existence of dominance. Second, we discuss several approaches used to estimate dominance coefficients and summarize estimates of dominance coefficients. We note trends that have been observed across species, types of mutations, and functional categories of genes. By comparing estimates of dominance coefficients for different types of genes, we test several hypotheses for the existence of dominance. Lastly, we discuss how dominance influences the dynamics of beneficial and deleterious mutations in populations and how the degree of dominance of deleterious mutations influences the impact of inbreeding on fitness.

Informal educational opportunities such as visits to museums, aquariums, and zoos support children\'s semantic knowledge gain. Most research focuses on outcomes of direct learning, such as factual recall. The extent to which children engage in productive memory processes such as inferential reasoning and self-derivation through memory integration is not yet well understood. We assessed 8- to 9-year-old children\'s performance on tests of direct (e.g., fact recall) and productive (e.g., inference, integration) learning from virtual museum exhibits. We also examined the influence of children\'s involvement on learning outcomes, through measuring within-exhibit dyadic conversation and post-exhibit reflection. Children performed successfully on all three tests of learning; fact recall was the most accessible and self-derivation was the least. Both within and post-exhibit involvement predicted overall learning outcomes; within-exhibit conversational phrases predicted self-derivation performance in particular. The current work provides novel insights into mechanisms that support children\'s informal learning.

Edge servers frequently manage their own offline digital twin (DT) services, in addition to caching online digital twin services. However, current research often overlooks the impact of offline caching services on memory and computation resources, which can hinder the efficiency of online service task processing on edge servers. In this study, we concentrated on service caching and task offloading within a collaborative edge computing system by emphasizing the integrated quality of service (QoS) for both online and offline edge services. We considered the resource usage of both online and offline services, along with incoming online requests. To maximize the overall QoS utility, we established an optimization objective that rewards the throughput of online services while penalizing offline services that miss their soft deadlines. We formulated this as a utility maximization problem, which was proven to be NP-hard. To tackle this complexity, we reframed the optimization problem as a Markov decision process (MDP) and introduced a joint optimization algorithm for service caching and task offloading by leveraging the deep Q-network (DQN). Comprehensive experiments revealed that our algorithm enhanced the utility by at least 14.01% compared with the baseline algorithms.

Measuring the fitnesses of genetic variants is a fundamental objective in evolutionary biology. A standard approach for measuring microbial fitnesses in bulk involves labeling a library of genetic variants with unique sequence barcodes, competing the labeled strains in batch culture, and using deep sequencing to track changes in the barcode abundances over time. However, idiosyncratic properties of barcodes can induce nonuniform amplification or uneven sequencing coverage that causes some barcodes to be over- or under-represented in samples. This systematic bias can result in erroneous read count trajectories and misestimates of fitness. Here, we develop a computational method, named REBAR (Removing the Effects of Bias through Analysis of Residuals), for inferring the effects of barcode processing bias by leveraging the structure of systematic deviations in the data. We illustrate this approach by applying it to two independent data sets, and demonstrate that this method estimates and corrects for bias more accurately than standard proxies, such as GC-based corrections. REBAR mitigates bias and improves fitness estimates in high-throughput assays without introducing additional complexity to the experimental protocols, with potential applications in a range of experimental evolution and mutation screening contexts.

The modality is an important topic for modelling. Using parametric models is an efficient way when real data set shows trimodality. In this paper, we propose a new class of trimodal probability distributions, that is, probability distributions that have up to three modes. Trimodality itself is achieved by applying a proper transformation to density function of certain continuous probability distributions. At first, we obtain preliminary results for an arbitrary density function g ( x ) and, next, we focus on the Gaussian case, studying trimodal Gaussian model more deeply. The Gaussian distribution is applied to produce the trimodal form of Gaussian known as normal distribution. The tractability of analytical expression of normal distribution and properties of the trimodal normal distribution are important reasons why we choose normal distribution. Furthermore, the existing distributions should be improved to be capable of modelling efficiently when there exists a trimodal form in a data set. After new density function is proposed, estimating its parameters is important. Since Mathematica 12.0 software has optimization tools and important modelling techniques, computational steps are performed using this software. The bootstrapped form of real data sets are applied to show the modelling ability of the proposed distribution when real data sets show trimodality.

Viral impacts on microbial populations depend on interaction phenotypes-including viral traits spanning the adsorption rate, latent period, and burst size. The latent period is a key viral trait in lytic infections. Defined as the time from viral adsorption to viral progeny release, the latent period of bacteriophage is conventionally inferred via one-step growth curves in which the accumulation of free virus is measured over time in a population of infected cells. Developed more than 80 years ago, one-step growth curves do not account for cellular-level variability in the timing of lysis, potentially biasing inference of viral traits. Here, we use nonlinear dynamical models to understand how individual-level variation of the latent period impacts virus-host dynamics. Our modeling approach shows that inference of the latent period via one-step growth curves is systematically biased-generating estimates of shorter latent periods than the underlying population-level mean. The bias arises because variability in lysis timing at the cellular level leads to a fraction of early burst events, which are interpreted, artefactually, as an earlier mean time of viral release. We develop a computational framework to estimate latent period variability from joint measurements of host and free virus populations. Our computational framework recovers both the mean and variance of the latent period within simulated infections including realistic measurement noise. This work suggests that reframing the latent period as a distribution to account for variability in the population will improve the study of viral traits and their role in shaping microbial populations.IMPORTANCEQuantifying viral traits-including the adsorption rate, burst size, and latent period-is critical to characterize viral infection dynamics and develop predictive models of viral impacts across scales from cells to ecosystems. Here, we revisit the gold standard of viral trait estimation-the one-step growth curve-to assess the extent to which assumptions at the core of viral infection dynamics lead to ongoing and systematic biases in inferences of viral traits. We show that latent period estimates obtained via one-step growth curves systematically underestimate the mean latent period and, in turn, overestimate the rate of viral killing at population scales. By explicitly incorporating trait variability into a dynamical inference framework that leverages both virus and host time series, we provide a practical route to improve estimates of the mean and variance of viral traits across diverse virus-microbe systems.

OBJECTIVE: Gene Regulatory Network (GRN) inference is a fundamental task in biology and medicine, as it enables a deeper understanding of the intricate mechanisms of gene expression present in organisms. This bioinformatics problem has been addressed in the literature through multiple computational approaches. Techniques developed for inferring from expression data have employed Bayesian networks, ordinary differential equations (ODEs), machine learning, information theory measures and neural networks, among others. The diversity of implementations and their respective customization have led to the emergence of many tools and multiple specialized domains derived from them, understood as subsets of networks with specific characteristics that are challenging to detect a priori. This specialization has introduced significant uncertainty when choosing the most appropriate technique for a particular dataset. This proposal, named MO-GENECI, builds upon the basic idea of the previous proposal GENECI and optimizes consensus among different inference techniques, through a carefully refined multi-objective evolutionary algorithm guided by various objective functions, linked to the biological context at hand.
METHODS: MO-GENECI has been tested on an extensive and diverse academic benchmark of 106 gene regulatory networks from multiple sources and sizes. The evaluation of MO-GENECI compared its performance to individual techniques using key metrics (AUROC and AUPR) for gene regulatory network inference. Friedman\'s statistical ranking provided an ordered classification, followed by non-parametric Holm tests to determine statistical significance.
RESULTS: MO-GENECI\'s Pareto front approximation facilitates easy selection of an appropriate solution based on generic input data characteristics. The best solution consistently emerged as the winner in all statistical tests, and in many cases, the median precision solution showed no statistically significant difference compared to the winner.
CONCLUSIONS: MO-GENECI has not only demonstrated achieving more accurate results than individual techniques, but has also overcome the uncertainty associated with the initial choice due to its flexibility and adaptability. It is shown intelligently to select the most suitable techniques for each case. The source code is hosted in a public repository at GitHub under MIT license: https://github.com/AdrianSeguraOrtiz/MO-GENECI. Moreover, to facilitate its installation and use, the software associated with this implementation has been encapsulated in a Python package available at PyPI: https://pypi.org/project/geneci/.