PyBEAM: A Bayesian approach to parameter inference for a wide class of binary evidence accumulation models.

Many decision-making theories are encoded in a class of processes known as evidence accumulation models (EAM). These assume that noisy evidence stochastically accumulates until a set threshold is reached, triggering a decision. One of the most successful and widely used of this class is the Diffusion Decision Model (DDM). The DDM however is limited in scope and does not account for processes such as evidence leakage, changes of evidence, or time varying caution. More complex EAMs can encode a wider array of hypotheses, but are currently limited by computational challenges. In this work, we develop the Python package PyBEAM (Bayesian Evidence Accumulation Models) to fill this gap. Toward this end, we develop a general probabilistic framework for predicting the choice and response time distributions for a general class of binary decision models. In addition, we have heavily computationally optimized this modeling process and integrated it with PyMC, a widely used Python package for Bayesian parameter estimation. This 1) substantially expands the class of EAM models to which Bayesian methods can be applied, 2) reduces the computational time to do so, and 3) lowers the entry fee for working with these models. Here we demonstrate the concepts behind this methodology, its application to parameter recovery for a variety of models, and apply it to a recently published data set to demonstrate its practical use.

Cortical tension initiates the positive feedback loop between cadherin and F-actin.

Adherens junctions physically link two cells at their contact interface via extracellular binding between cadherin molecules and intracellular interactions between cadherins and the actin cytoskeleton. Cadherin and actomyosin cytoskeletal dynamics are regulated reciprocally by mechanical and chemical signals, which subsequently determine the strength of cell-cell adhesions and the emergent organization and stiffness of the tissues they form. However, an understanding of the integrated system is lacking. We present a new mechanistic computational model of intercellular junction maturation in a cell doublet to investigate the mechanochemical cross talk that regulates adherens junction formation and homeostasis. The model couples a two-dimensional lattice-based simulation of cadherin dynamics with a reaction-diffusion representation of the reorganising actomyosin network through its regulation by Rho signalling at the intracellular junction. We demonstrate that local immobilization of cadherin induces cluster formation in a cis-less-dependent manner. We then recapitulate the process of cell-cell contact formation. Our model suggests that cortical tension applied on the contact rim can explain the ring distribution of cadherin and actin filaments (F-actin) on the cell-cell contact of the cell doublet. Furthermore, we propose and test the hypothesis that cadherin and F-actin interact like a positive feedback loop, which is necessary for formation of the ring structure. Different patterns of cadherin distribution were observed as an emergent property of disturbances of this positive feedback loop. We discuss these findings in light of available experimental observations on underlying mechanisms related to cadherin/F-actin binding and the mechanical environment.

A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development.

During early mammalian embryo development, a small number of cells make robust fate decisions at particular spatial locations in a tight time window to form inner cell mass (ICM), and later epiblast (Epi) and primitive endoderm (PE). While recent single-cell transcriptomics data allows scrutinization of heterogeneity of individual cells, consistent spatial and temporal mechanisms the early embryo utilize to robustly form the Epi/PE layers from ICM remain elusive. Here we build a multiscale three-dimensional model for mammalian embryo to recapitulate the observed patterning process from zygote to late blastocyst. By integrating the spatiotemporal information reconstructed from multiple single-cell transcriptomic datasets, the data-informed modeling analysis suggests two major processes critical to the formation of Epi/PE layers: a selective cell-cell adhesion mechanism (via EphA4/EphrinB2) for fate-location coordination and a temporal attenuation mechanism of cell signaling (via Fgf). Spatial imaging data and distinct subsets of single-cell gene expression data are then used to validate the predictions. Together, our study provides a multiscale framework that incorporates single-cell gene expression datasets to analyze gene regulations, cell-cell communications, and physical interactions among cells in complex geometries at single-cell resolution, with direct application to late-stage development of embryogenesis.

Surface-bound hydroxyl radical-dominated degradation of sulfamethoxazole in the amorphous FeOOH/ peroxymonosulfate system: The key role of amorphous structure enhancing electron transfer.

In this study, activation of peroxymonosulfate (PMS) by amorphous FeOOH to degrade sulfamethoxazole (SMX) was investigated. The amorphous FeOOH showed a better performance in the decomposition of PMS and the degradation of SMX than the crystallized α-FeOOH and ß-FeOOH. The quenching experiments and EPR measurements suggested that the mechanism of PMS activation by amorphous FeOOH was mainly the surface-bound radicals (●OH and SO4●-). Basically, the surface-bound ●OH radicals were the dominate reactive oxide species in this system, which were mainly generated via the decomposition of amorphous FeOOH-PMS complexes. The degradation of SMX was significantly inhibited with the presence of H2PO4-, and this adverse impact was negligibly affected by the increase of H2PO4- concentration, implying that the inhibition of SMX degradation was caused by competitive adsorption. Consequently, the Fe-OH bonds on the amorphous FeOOH were proposed as the reactive sites for forming amorphous FeOOH-PMS complexes. Besides, the amorphous FeOOH showed a better performance in the degradation of SMX in the acid conditions than that in the base conditions due to the surface charge of amorphous FeOOH. More importantly, the reduction efficiency of Fe(III) was significantly enhanced due to the excellent conductivity of amorphous FeOOH.

Biophysical Models of PAR Cluster Transport by Cortical Flow in C. elegans Early Embryogenesis.

The clustering of membrane-bound proteins facilitates their transport by cortical actin flow in early Caenorhabditis elegans embryo cell polarity. PAR-3 clustering is critical for this process, yet the biophysical processes that couple protein clusters to cortical flow remain unknown. We develop a discrete, stochastic agent-based model of protein clustering and test four hypothetical models for how clusters may interact with the flow. Results show that the canonical way to assess transport characteristics from single-particle tracking data used thus far in this area, the Péclet number, is insufficient to distinguish these hypotheses and that all models can account for transport characteristics quantified by this measure. However, using this model, we demonstrate that these different cluster-cortex interactions may be distinguished using a different metric, namely the scalar projection of cluster displacement on to the flow displacement vector. Our results thus provide a testable way to use existing single-particle tracking data to test how endogenous protein clusters may interact with the cortical flow to localize during polarity establishment. To facilitate this investigation, we also develop both improved simulation and semi-analytic methodologies to quantify motion summary statistics (e.g., Péclet number and scalar projection) for these stochastic models as a function of biophysical parameters.

4-Sodium phenyl butyric acid has both efficacy and counter-indicative effects in the treatment of Col4a1 disease.

Mutations in the collagen genes COL4A1 and COL4A2 cause Mendelian eye, kidney and cerebrovascular disease including intracerebral haemorrhage (ICH), and common collagen IV variants are a risk factor for sporadic ICH. COL4A1 and COL4A2 mutations cause endoplasmic reticulum (ER) stress and basement membrane (BM) defects, and recent data suggest an association of ER stress with ICH due to a COL4A2 mutation. However, the potential of ER stress as a therapeutic target for the multi-systemic COL4A1 pathologies remains unclear. We performed a preventative oral treatment of Col4a1 mutant mice with the chemical chaperone phenyl butyric acid (PBA), which reduced adult ICH. Importantly, treatment of adult mice with the established disease also reduced ICH. However, PBA treatment did not alter eye and kidney defects, establishing tissue-specific outcomes of targeting Col4a1-derived ER stress, and therefore this treatment may not be applicable for patients with eye and renal disease. While PBA treatment reduced ER stress and increased collagen IV incorporation into BMs, the persistence of defects in BM structure and reduced ability of the BM to withstand mechanical stress indicate that PBA may be counter-indicative for pathologies caused by matrix defects. These data establish that treatment for COL4A1 disease requires a multipronged treatment approach that restores both ER homeostasis and matrix defects. Alleviating ER stress is a valid therapeutic target for preventing and treating established adult ICH, but collagen IV patients will require stratification based on their clinical presentation and mechanism of their mutations.

Simple Rho GTPase Dynamics Generate a Complex Regulatory Landscape Associated with Cell Shape.

Migratory cells exhibit a variety of morphologically distinct responses to their environments that manifest in their cell shape. Some protrude uniformly to increase substrate contacts, others are broadly contractile, some polarize to facilitate migration, and yet others exhibit mixtures of these responses. Prior studies have identified a discrete collection of shapes that the majority of cells display and demonstrated that activity levels of the cytoskeletal regulators Rac1 and RhoA GTPase regulate those shapes. Here, we use computational modeling to assess whether known GTPase dynamics can give rise to a sufficient diversity of spatial signaling states to explain the observed shapes. Results show that the combination of autoactivation and mutually antagonistic cross talk between GTPases, along with the conservative membrane binding, generates a wide array of distinct homogeneous and polarized regulatory phenotypes that arise for fixed model parameters. From a theoretical perspective, these results demonstrate that simple GTPase dynamics can generate complex multistability in which six distinct stable steady states (three homogeneous and three polarized) coexist for a fixed set of parameters, each of which naturally maps to an observed morphology. From a biological perspective, although we do not explicitly model the cytoskeleton or resulting cell morphologies, these results, along with prior literature linking GTPase activity to cell morphology, support the hypothesis that GTPase signaling dynamics can generate the broad morphological characteristics observed in many migratory cell populations. Further, the observed diversity may be the result of cells populating a complex morphological landscape generated by GTPase regulation rather than being the result of intrinsic cell-cell variation. These results demonstrate that Rho GTPases may have a central role in regulating the broad characteristics of cell shape (e.g., expansive, contractile, polarized, etc.) and that shape heterogeneity may be (at least partly) a reflection of the rich signaling dynamics regulating the cytoskeleton rather than intrinsic cell heterogeneity.

Membrane Tension Can Enhance Adaptation to Maintain Polarity of Migrating Cells.

Migratory cells are known to adapt to environments that contain wide-ranging levels of chemoattractant. Although biochemical models of adaptation have been previously proposed, here, we discuss a different mechanism based on mechanosensing, in which the interaction between biochemical signaling and cell tension facilitates adaptation. We describe and analyze a model of mechanochemical-based adaptation coupling a mechanics-based physical model of cell tension coupled with the wave-pinning reaction-diffusion model for Rac GTPase activity. The mathematical analysis of this model, simulations of a simplified one-dimensional cell geometry, and two-dimensional finite element simulations of deforming cells reveal that as a cell protrudes under the influence of high stimulation levels, tension-mediated inhibition of Rac signaling causes the cell to polarize even when initially overstimulated. Specifically, tension-mediated inhibition of Rac activation, which has been experimentally observed in recent years, facilitates this adaptation by countering the high levels of environmental stimulation. These results demonstrate how tension-related mechanosensing may provide an alternative (and potentially complementary) mechanism for cell adaptation.

Microtubules Regulate Localization and Availability of Insulin Granules in Pancreatic Beta Cells.

Two key prerequisites for glucose-stimulated insulin secretion (GSIS) in ß cells are the proximity of insulin granules to the plasma membrane and their anchoring or docking to the plasma membrane (PM). Although recent evidence has indicated that both of these factors are altered in the context of diabetes, it is unclear what regulates localization of insulin granules and their interactions with the PM within single cells. Here, we demonstrate that microtubule (MT)-motor-mediated transport dynamics have a critical role in regulating both factors. Super-resolution imaging shows that whereas the MT cytoskeleton resembles a random meshwork in the cells' interior, MTs near the cell surface are preferentially aligned with the PM. Computational modeling suggests two consequences of this alignment. First, this structured MT network preferentially withdraws granules from the PM. Second, the binding and transport of insulin granules by MT motors prevents their stable anchoring to the PM. These findings suggest the MT cytoskeleton may negatively regulate GSIS by both limiting the amount of insulin proximal to the PM and preventing or breaking interactions between the PM and the remaining nearby insulin granules. These results predict that altering MT network structure in ß cells can be used to tune GSIS. Thus, our study points to the potential of an alternative therapeutic strategy for diabetes by targeting specific MT regulators.

Mechanochemical feedback underlies coexistence of qualitatively distinct cell polarity patterns within diverse cell populations.

Cell polarization and directional cell migration can display random, persistent, and oscillatory dynamic patterns. However, it is not clear whether these polarity patterns can be explained by the same underlying regulatory mechanism. Here, we show that random, persistent, and oscillatory migration accompanied by polarization can simultaneously occur in populations of melanoma cells derived from tumors with different degrees of aggressiveness. We demonstrate that all of these patterns and the probabilities of their occurrence are quantitatively accounted for by a simple mechanism involving a spatially distributed, mechanochemical feedback coupling the dynamically changing extracellular matrix (ECM)-cell contacts to the activation of signaling downstream of the Rho-family small GTPases. This mechanism is supported by a predictive mathematical model and extensive experimental validation, and can explain previously reported results for diverse cell types. In melanoma, this mechanism also accounts for the effects of genetic and environmental perturbations, including mutations linked to invasive cell spread. The resulting mechanistic understanding of cell polarity quantitatively captures the relationship between population variability and phenotypic plasticity, with the potential to account for a wide variety of cell migration states in diverse pathological and physiological conditions.

A parameter recovery assessment of time-variant models of decision-making.

Evidence accumulation models have been one of the most dominant modeling frameworks used to study rapid decision-making over the past several decades. These models propose that evidence accumulates from the environment until the evidence for one alternative reaches some threshold, typically associated with caution, triggering a response. However, researchers have recently begun to reconsider the fundamental assumptions of how caution varies with time. In the past, it was typically assumed that levels of caution are independent of time. Recent investigations have however suggested the possibility that levels of caution decrease over time and that this strategy provides more efficient performance under certain conditions. Our study provides the first comprehensive assessment of this newer class of models accounting for time-varying caution to determine how robustly their parameters can be estimated. We assess five overall variants of collapsing threshold/urgency signal models based on the diffusion decision model, linear ballistic accumulator model, and urgency gating model frameworks. We find that estimation of parameters, particularly those associated with caution/urgency modulation are most robust for the linearly collapsing threshold diffusion model followed by an urgency-gating model with a leakage process. All other models considered, particularly those with ballistic accumulation or nonlinear thresholds, are unable to recover their own parameters adequately, making their usage in parameter estimation contexts questionable.

Subdiffusive Dynamics Lead to Depleted Particle Densities near Cellular Borders.

It has long been known that the complex cellular environment leads to anomalous motion of intracellular particles. At a gross level, this is characterized by mean-squared displacements that deviate from the standard linear profile. Statistical analysis of particle trajectories has helped further elucidate how different characteristics of the cellular environment can introduce different types of anomalousness. A significant majority of this literature has, however, focused on characterizing the properties of trajectories that do not interact with cell borders (e.g., cell membrane or nucleus). Numerous biological processes ranging from protein activation to exocytosis, however, require particles to be near a membrane. This study investigates the consequences of a canonical type of subdiffusive motion, fractional Brownian motion, and its physical analog, generalized Langevin equation dynamics, on the spatial localization of particles near reflecting boundaries. Results show that this type of subdiffusive motion leads to the formation of significant zones of depleted particle density near boundaries and that this effect is independent of the specific model details encoding those dynamics. Rather, these depletion layers are a natural and robust consequence of the anticorrelated nature of motion increments that is at the core of fractional Brownian motion (or alternatively generalized Langevin equation) dynamics. If such depletion zones are present, it would be of profound importance given the wide array of signaling and transport processes that occur near membranes. If not, that would suggest our understanding of this type of anomalous motion may be flawed. Either way, this result points to the need to further investigate the consequences of anomalous particle motions near cell borders from both theoretical and experimental perspectives.

Enhancing the functionality of a microscale bioreactor system as an industrial process development tool for mammalian perfusion culture.

Without a scale-down model for perfusion, high resource demand makes cell line screening or process development challenging, therefore, potentially successful cell lines or perfusion processes are unrealized and their ability untapped. We present here the refunctioning of a high-capacity microscale system that is typically used in fed-batch process development to allow perfusion operation utilizing in situ gravity settling and automated sampling. In this low resource setting, which involved routine perturbations in mixing, pH and dissolved oxygen concentrations, the specific productivity and the maximum cell concentration were higher than 3.0 × 106 mg/cell/day and 7 × 10 7 cells/ml, respectively, across replicate microscale perfusion runs conducted at one vessel volume exchange per day. A comparative analysis was conducted at bench scale with vessels operated in perfusion mode utilizing a cell retention device. Neither specific productivity nor product quality indicated by product aggregation (6%) was significantly different across scales 19 days after inoculation, thus demonstrating this setup to be a suitable and reliable platform for evaluating the performance of cell lines and the effect of process parameters, relevant to perfusion mode of culturing.

Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach.

Calcium/calmodulin-dependent protein kinase II (CaMKII) holoenzymes play a critical role in decoding Ca2+ signals in neurons. Understanding how this occurs has been the focus of numerous studies including many that use models. However, CaMKII is notoriously difficult to simulate in detail because of its multi-subunit nature, which causes a combinatorial explosion in the number of species that must be modeled. To study the Ca2+-calmodulin-CaMKII reaction network with detailed kinetics while including the effect of diffusion, we have customized an existing stochastic particle-based simulator, Smoldyn, to manage the problem of combinatorial explosion. With this new method, spatial and temporal aspects of the signaling network can be studied without compromising biochemical details. We used this new method to examine how calmodulin molecules, both partially loaded and fully loaded with Ca2+, choose pathways to interact with and activate CaMKII under various Ca2+ input conditions. We found that the dependence of CaMKII phosphorylation on Ca2+ signal frequency is intrinsic to the network kinetics and the activation pattern can be modulated by the relative amount of Ca2+ to calmodulin and by the rate of Ca2+ diffusion. Depending on whether Ca2+ influx is saturating or not, calmodulin molecules could choose different routes within the network to activate CaMKII subunits, resulting in different frequency dependence patterns. In addition, the size of the holoenzyme produces a subtle effect on CaMKII activation. The more extended the subunits are organized, the easier for calmodulin molecules to access and activate the subunits. The findings suggest that particular intracellular environmental factors such as crowding and calmodulin availability can play an important role in decoding Ca2+ signals and can give rise to distinct CaMKII activation patterns in dendritic spines, Ca2+ channel nanodomains and cytoplasm.

Fine Tuning: Effects of Post-Translational Modification on Hsp70 Chaperones.

The discovery of heat shock proteins shaped our view of protein folding in the cell. Since their initial discovery, chaperone proteins were identified in all domains of life, demonstrating their vital and conserved functional roles in protein homeostasis. Chaperone proteins maintain proper protein folding in the cell by utilizing a variety of distinct, characteristic mechanisms to prevent aberrant intermolecular interactions, prevent protein aggregation, and lower entropic costs to allow for protein refolding. Continued study has found that chaperones may exhibit alternative functions, including maintaining protein folding during endoplasmic reticulum (ER) import and chaperone-mediated degradation, among others. Alternative chaperone functions are frequently controlled by post-translational modification, in which a given chaperone can switch between functions through covalent modification. This review will focus on the Hsp70 class chaperones and their Hsp40 co-chaperones, specifically highlighting the importance of post-translational control of chaperones. These modifications may serve as a target for therapeutic intervention in the treatment of diseases of protein misfolding and aggregation.

Sexual Trauma Screening for Men and Women: Examining the Construct Validity of a Two-Item Screen.

The Veterans Health Administration (VHA), the largest integrated healthcare system in the United States, has conducted universal screening for military sexual trauma (MST) to facilitate MST-related care since 2002. VHA defines MST as sexual assault or repeated, threatening sexual harassment that occurred during military service. Evidence of construct validity, the degree to which the screen is measuring what it purports to measure (i.e., MST), was examined using the 23-item Sexual Experiences Questionnaire-Department of Defense (SEQ-DoD). Results showed individuals who endorsed no SEQ-DoD items screened MST negative. Those who had experienced more SEQ-DoD behaviors with greater frequency, and across all four SEQ-DoD domains, were more likely to screen MST positive. Findings were similar for men and women. These findings contribute to the validity evidence for the VHA MST screen.

Parallel probability density approximation.

Probability density approximation (PDA) is a nonparametric method of calculating probability densities. When integrated into Bayesian estimation, it allows researchers to fit psychological processes for which analytic probability functions are unavailable, significantly expanding the scope of theories that can be quantitatively tested. PDA is, however, computationally intensive, requiring large numbers of Monte Carlo simulations in order to attain good precision. We introduce Parallel PDA (pPDA), a highly efficient implementation of this method utilizing the Armadillo C++ and CUDA C libraries to conduct millions of model simulations simultaneously in graphics processing units (GPUs). This approach provides a practical solution for rapidly approximating probability densities with high precision. In addition to demonstrating this method, we fit a piecewise linear ballistic accumulator model (Holmes, Trueblood, & Heathcote, 2016) to empirical data. Finally, we conducted simulation studies to investigate various issues associated with PDA and provide guidelines for pPDA applications to other complex cognitive models.

Intramuscular triglyceride synthesis: importance in muscle lipid partitioning in humans.

Intramuscular triglyceride (IMTG) concentration is elevated in insulin-resistant individuals and was once thought to promote insulin resistance. However, endurance-trained athletes have equivalent concentration of IMTG compared with individuals with type 2 diabetes, and have very low risk of diabetes, termed the "athlete's paradox." We now know that IMTG synthesis is positively related to insulin sensitivity, but the exact mechanisms for this are unclear. To understand the relationship between IMTG synthesis and insulin sensitivity, we measured IMTG synthesis in obese control subjects, endurance-trained athletes, and individuals with type 2 diabetes during rest, exercise, and recovery. IMTG synthesis rates were positively related to insulin sensitivity, cytosolic accumulation of DAG, and decreased accumulation of C18:0 ceramide and glucosylceramide. Greater rates of IMTG synthesis in athletes were not explained by alterations in FFA concentration, DGAT1 mRNA expression, or protein content. IMTG synthesis during exercise in Ob and T2D indicate utilization as a fuel despite unchanged content, whereas IMTG concentration decreased during exercise in athletes. mRNA expression for genes involved in lipid desaturation and IMTG synthesis were increased after exercise and recovery. Further, in a subset of individuals, exercise decreased cytosolic and membrane di-saturated DAG content, which may help explain insulin sensitization after acute exercise. These data suggest IMTG synthesis rates may influence insulin sensitivity by altering intracellular lipid localization, and decreasing specific ceramide species that promote insulin resistance.

Multiple boli arterial spin labeling for high signal-to-noise rodent brain perfusion imaging.

PURPOSE: A systematic method is proposed for optimizing a promising preclinical arterial spin labeling (ASL) sequence based on the use of a train of adiabatic radiofrequency pulses labeling successive boli of blood water. METHODS: The sequence optimization is performed and evaluated using brain imaging experiments in mice and in rats. It involves the investigation of several parameters, ranging from the number of adiabatic pulses and labeling duration to the properties of the adiabatic hyperbolic secant pulses (ie, amplitude and frequency modulation). RESULTS: Species-dependent parameters are identified, allowing for robust fast optimization protocols to be introduced. The resulting optimized multiple boli ASL (mbASL) sequence provides with significantly higher average signal-to-noise ratios (SNR) per voxel volume than currently encountered in ASL studies (278 mm-3 in mice and 172 mm-3 in rats). Comparing with the commonly used flow-sensitive alternating inversion recovery technique (FAIR), mbASL-to-FAIR SNR ratios reach 203% for mice and 725% for rats. CONCLUSION: When properly optimized, mbASL can offer a robust, high SNR ASL alternative for rodent brain perfusion studies Magn Reson Med 79:1020-1030, 2018. © 2017 International Society for Magnetic Resonance in Medicine.