Approximate Bayesian computational methods to estimate the strength of divergent selection in population genomics models.

Statistical estimation of parameters in large models of evolutionary processes is often too computationally inefficient to pursue using exact model likelihoods, even with single-nucleotide polymorphism (SNP) data, which offers a way to reduce the size of genetic data while retaining relevant information. Approximate Bayesian Computation (ABC) to perform statistical inference about parameters of large models takes the advantage of simulations to bypass direct evaluation of model likelihoods. We develop a mechanistic model to simulate forward-in-time divergent selection with variable migration rates, modes of reproduction (sexual, asexual), length and number of migration-selection cycles.

Controlling Recombination to Evolve Bacteriophages.

Recombination among different phages sometimes facilitates their ability to grow on new hosts. Protocols to direct the evolution of phage host range, as might be used in the application of phage therapy, would then benefit from including steps to enable recombination. Applying mathematical and computational models, in addition to experiments using phages T3 and T7, we consider ways that a protocol may influence recombination levels.

Mathematical model for IL-2-based cancer immunotherapy.

A basic mathematical model for IL-2-based cancer immunotherapy is proposed and studied. Our analysis shows that the outcome of therapy is mainly determined by three parameters, the relative death rate of CD4 T cells, the relative death rate of CD8 T cells, and the dose of IL-2 treatment. Minimal equilibrium tumor size can be reached with a large dose of IL-2 in the case that CD4 T cells die out.

Confinement tonicity on epidemic spreading.

Emerging and re-emerging pathogens are latent threats in our society with the risk of killing millions of people worldwide, without forgetting the severe economic and educational backlogs. From COVID-19, we learned that self isolation and quarantine restrictions (confinement) were the main way of protection till availability of vaccines. However, abrupt lifting of social confinement would result in new waves of new infection cases and high death tolls.

A far-ultraviolet-driven photoevaporation flow observed in a protoplanetary disk.

Most low-mass stars form in stellar clusters that also contain massive stars, which are sources of far-ultraviolet (FUV) radiation. Theoretical models predict that this FUV radiation produces photodissociation regions (PDRs) on the surfaces of protoplanetary disks around low-mass stars, which affects planet formation within the disks. We report James Webb Space Telescope and Atacama Large Millimeter Array observations of a FUV-irradiated protoplanetary disk in the Orion Nebula.

Application of elastic net regression for modeling COVID-19 sociodemographic risk factors.

Objectives: COVID-19 has been at the forefront of global concern since its emergence in December of 2019. Determining the social factors that drive case incidence is paramount to mitigating disease spread. We gathered data from the Social Vulnerability Index (SVI) along with Democratic voting percentage to attempt to understand which county-level sociodemographic metrics had a significant correlation with case rate for COVID-19.

A stochastic framework for evaluating CAR T cell therapy efficacy and variability.

Based on a deterministic and stochastic process hybrid model, we use white noises to account for patient variabilities in treatment outcomes, use a hyperparameter to represent patient heterogeneity in a cohort, and construct a stochastic model in terms of Ito stochastic differential equations for testing the efficacy of three different treatment protocols in CAR T cell therapy. The stochastic model has three ergodic invariant measures which correspond to three unstable equilibrium solutions of the deterministic system, while the ergodic invariant measures are attractors under some conditions for tumor growth. As the stable dynamics of the stochastic system reflects long-term outcomes of the therapy, the transient dynamics provide chances of cure in short-term.

A physiologically enhanced muscle spindle model: using a Hill-type model for extrafusal fibers as template for intrafusal fibers.

The muscle spindle is an essential proprioceptor, significantly involved in sensing limb position and movement. Although biological spindle models exist for years, the gold-standard for motor control in biomechanics are still sensors built of homogenized spindle output models due to their simpler combination with neuro-musculoskeletal models. Aiming to improve biomechanical simulations, this work establishes a more physiological model of the muscle spindle, aligned to the advantage of easy integration into large-scale musculoskeletal models.

Emerging porcine Enterovirus G infections, epidemiological, complete genome sequencing, evolutionary and risk factor analysis in India.

The current study reports the in-depth analysis of the epidemiology, risk factors, and molecular characterization of a complete genome of Enterovirus G (EV-G) isolated from Indian pigs. We analysed several genes of EV-G isolates collected from various provinces in India, using phylogenetic analysis, recombination detection, SimPlot, and selection pressure analyses. Our analysis of 534 porcine faecal samples revealed that 11.

Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability.

Background: Computational methods of predicting protein stability changes upon missense mutations are invaluable tools in high-throughput studies involving a large number of protein variants. However, they are limited by a wide variation in accuracy and difficulty of assessing prediction uncertainty. Using a popular computational tool, FoldX, we develop a statistical framework that quantifies the uncertainty of predicted changes in protein stability.

Stochastic dynamics of human papillomavirus delineates cervical cancer progression.

Starting from a deterministic model, we propose and study a stochastic model for human papillomavirus infection and cervical cancer progression. Our analysis shows that the chronic infection state as random variables which have the ergodic invariant probability measure is necessary for progression from infected cell population to cervical cancer cells. It is shown that small progression rate from infected cells to precancerous cells and small microenvironmental noises associated with the progression rate and viral infection help to establish such chronic infection states.

Threshold photoelectron spectroscopy and dissociative photoionization of benzonitrile.

The threshold photoionization and dissociative ionization of benzonitrile (CHCN) were studied using double imaging photoelectron photoion coincidence (PEPICO) spectroscopy at the Vacuum Ultraviolet (VUV) beamline of the Swiss Light Source (SLS). The threshold photoelectron spectrum was recorded from 9.6 to 12.

Estimating County Level Health Indicators Using Spatial Microsimulation.

Given the importance of understanding health outcomes at fine spatial scales, iterative proportional fitting (IPF), a form of small area estimation, was applied to a fixed number of health-related variables (obesity, overweight, diabetes) taken from regionalized 2019 survey responses (n = 5474) from the Idaho Behavioral Risk Factor Surveillance System (BRFSS). Using associated county-level American Community Survey (ACS) census data, a set of constraints, which included age categorization, race, sex, and education level, were used to create county-level weighting matrices for each variable, for each of the seven (7) Idaho public health districts. Using an optimized modeling construction technique, we identified significant constraints and grouping splits for each variable/region, resulting in estimates that were internally and externally validated.

Cooperative mechanisms underlie differences in myocardial contractile dynamics between large and small mammals.

Ca2+ binding to troponin C (TnC) and myosin cross-bridge binding to actin act in a synergistic cooperative manner to modulate myocardial contraction and relaxation. The responsiveness of the myocardial thin filament to the activating effects of Ca2+ and myosin cross-bridge binding has been well-characterized in small mammals (e.g.

Noise resilient exceptional-point voltmeters enabled by oscillation quenching phenomena.

Exceptional point degeneracies (EPD) of linear non-Hermitian systems have been recently utilized for hypersensitive sensing. This proposal exploits the sublinear response that the degenerate frequencies experience once the system is externally perturbed. The enhanced sensitivity, however, might be offset by excess (fundamental and/or technical) noise.

Coordination of Mercury(II) in Water Promoted over Hydrolysis in Solvated Clusters [Hg(HO)]: Insights from Relativistic Effects and Free Energy Analysis.

Understanding the nature of the interaction between mercury(II) ions, Hg, and water molecules is crucial to describe the stability and chemical behavior of structures formed during solvation, as well as the conditions that favor the Hg coordination or inducing water hydrolysis. In our study, we explored exhaustively the potential energy surface of Hg with up to six water molecules. We analyzed electronic and Gibbs free energies, binding, and nuclear magnetic resonance parameters.

Contrastive Metric Learning for Lithium Super-ionic Conductor Screening.

High-performance Li-ion battery significantly impacts modern society, and materials with high conductivity play critical roles in battery development. Machine learning (ML) technologies have rapidly changed the field in recent years. However, it is still challenging to predict the high conductors directly due to the lack of validated conductor samples.

Atomistic Molecular Insights into Angiotensin-(1-7) Interpeptide Interactions.

Angiotensin-(1-7) is an endogenous peptide known for its vasoprotective, antioxidant, and anti-inflammatory effects, making it a promising therapeutic candidate for various clinical conditions. However, the peptide exhibits pH-dependent physical instability in aqueous solutions, and a comprehensive atomistic study elucidating this behavior and its implications is currently lacking. Therefore, we performed all-atom molecular dynamics simulations to investigate the early formation of angiotensin-(1-7) oligomeric aggregates under different conditions: acidic and neutral pH-like conditions, physiological and high ionic strength, and high and low peptide concentrations.

Spatial Modeling of Sociodemographic Risk for COVID-19 Mortality.

In early 2020, the Coronavirus Disease 19 (COVID-19) rapidly spread across the United States (US), exhibiting significant geographic variability. While several studies have examined the predictive relationships of differing factors on COVID-19 deaths, few have looked at spatiotemporal variation at refined geographic scales. The objective of this analysis is to examine this spatiotemporal variation in COVID-19 deaths with respect to association with socioeconomic, health, demographic, and political factors.

Modeling the effects of Prophylactic behaviors on the spread of SARS-CoV-2 in West Africa.

Various general and individual measures have been implemented to limit the spread of SARS-CoV-2 since its emergence in China. Several phenomenological and mechanistic models have been developed to inform and guide health policy. Many of these models ignore opinions about certain control measures, although various opinions and attitudes can influence individual actions.

Dysfunctional neuro-muscular mechanisms explain gradual gait changes in prodromal spastic paraplegia.

Background: In Hereditary Spastic Paraplegia (HSP) type 4 (SPG4) a length-dependent axonal degeneration in the cortico-spinal tract leads to progressing symptoms of hyperreflexia, muscle weakness, and spasticity of lower extremities. Even before the manifestation of spastic gait, in the prodromal phase, axonal degeneration leads to subtle gait changes. These gait changes - depicted by digital gait recording - are related to disease severity in prodromal and early-to-moderate manifest SPG4 participants.

Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae.

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects.

Assessment of the Environmental Impacts of a Localized Food System and Food Waste Reduction in a Water-Scarce Region Using Diet Optimization Models.

Despite growing interest in fresh local produce across the United States, scaling up local agricultural development might impose new environmental pressures on increasingly scarce water and land resources in specific localities. Drawing upon the case of the Palouse of the US Inland Northwest, this study evaluates land and water footprints of local foods along with food waste reduction in a water-scarce region. We used both non-robust and robust diet-optimization techniques to estimate the minimum amounts of irrigation water necessary to grow foods locally and to satisfy the local population's caloric or nutrition needs.

Topological data analysis of antibody dynamics of severe and non-severe patients with COVID-19.

The COVID-19 pandemic is a significant public health threat with unanswered questions regarding the immune system's role in the disease's severity level. Here, based on antibody kinetic data of severe and non-severe COVID-19 patients, topological data analysis (TDA) highlights that severity is not binary. However, there are differences in the shape of antibody responses that further classify COVID-19 patients into non-severe, severe, and intermediate cases of severity.

Hopf bifurcation without parameters in deterministic and stochastic modeling of cancer virotherapy, part II.

In part II, we analyze our stochastic model which incorporates microenvironmental noises and uncertainties related to immune responses. Outcomes of the therapy in our model are largely determined by the infectivity constant, the infection value, and stochastic relative immune clearance rates. The infection value is a universal critical value for immune-free ergodic invariant probability measures and persistence in all cases.