The generalization-across-dimensions model applied to conditional temporal discrimination

Can simple choice conditional-discrimination choice be accounted for by recent quantitative models of combined stimulus and reinforcer control? In Experiment 1, two sets of five blackout durations, one using shorter intervals and one using longer intervals, conditionally signaled which subsequent choice response might provide food. In seven conditions, the distribution of blackout durations across the sets was varied. An updated version of the generalization-across-dimensions model nicely described the way that choice changed across durations. In Experiment 2, just two blackout durations acted as the conditional stimuli and the durations were varied over 10 conditions. The parameters of the model obtained in Experiment 1 failed adequately to predict choice in Experiment 2, but the model again fitted the data nicely. The failure to predict the Experiment 2 data from the Experiment 1 parameters occurred because in Experiment 1 differential control by reinforcer locations progressively decreased with blackout durations, whereas in Experiment 2 this control remained constant. These experiments extend the ability of the model to describe data from procedures based on concurrent schedules in which reinforcer ratios reverse at fixed times to those from conditional-discrimination procedures. Further research is needed to understand why control by reinforcer location differed between the two experiments.

A cell-based model for size control in the multiple fission alga Chlamydomonas reinhardtii

Understanding how population-size homeostasis emerges from stochastic individual cell behaviors remains a challenge in biology.1,2,3,4,5,6,7 The unicellular green alga Chlamydomonas reinhardtii (Chlamydomonas) proliferates using a multiple fission cell cycle, where a prolonged G1 phase is followed by n rounds of alternating division cycles (S/M) to produce 2n daughters. A "Commitment" sizer in mid-G1 phase ensures sufficient cell growth before completing the cell cycle. A mitotic sizer couples mother-cell size to division number (n) such that daughter size distributions are uniform regardless of mother size distributions. Although daughter size distributions were highly robust to altered growth conditions, ∼40% of daughter cells fell outside of the 2-fold range expected from a "perfect" multiple fission sizer.7,8 A simple intuitive power law model with stochastic noise failed to reproduce individual division behaviors of tracked single cells. Through additional iterative modeling, we identified an alternative modified threshold (MT) model, where cells need to cross a threshold greater than 2-fold their median starting size to become division-competent (i.e., Committed), after which their behaviors followed a power law model. The Commitment versus mitotic size threshold uncoupling in the MT model was likely a key pre-adaptation in the evolution of volvocine algal multicellularity. A similar experimental approach was used in size mutants mat3/rbr and dp1 that are, respectively, missing repressor or activator subunits of the retinoblastoma tumor suppressor complex (RBC). Both mutants showed altered relationships between Commitment and mitotic sizer, suggesting that RBC functions to decouple the two sizers.

Assessing policies to reduce adolescent overweight and obesity: Insights from a system dynamics model using data from the Health Behavior in School-Aged Children study

Adolescent overweight and obesity (AdOWOB) in Europe has proven to be a persistent and complex problem, and appropriate systems methods may help in evaluating potential policy options. This paper describes the development of a system dynamics model of AdOWOB as part of the EU-funded CO-CREATE project. The model was developed using literature and data from the Health Behavior in School-Aged Children (HBSC) study across 31 European countries. We identified 10 HBSC variables that were included as direct or indirect drivers of AdOWOB in the dynamic model, seven at the level of the individual, and three related to the social environment. The model was calibrated to 24 separate cases based on four gender and perceived wealth segments for each of the five CO-CREATE countries (The Netherlands, Norway, Poland, Portugal, and the UK) and for Europe overall. Out of 10 possible intervention points tested, exercise, fruit, life dissatisfaction, school pressure, and skipping breakfast were identified as the top five most influential ones across the 24 cases. These model-based priorities can be compared with the policy ideas suggested by the CO-CREATE adolescents.

Physicochemical models of protein-DNA binding with standard and modified base pairs

DNA-binding proteins play important roles in various cellular processes, but the mechanisms by which proteins recognize genomic target sites remain incompletely understood. Functional groups at the edges of the base pairs (bp) exposed in the DNA grooves represent physicochemical signatures. As these signatures enable proteins to form specific contacts between protein residues and bp, their study can provide mechanistic insights into protein-DNA binding. Existing experimental methods, such as X-ray crystallography, can reveal such mechanisms based on physicochemical interactions between proteins and their DNA target sites. However, the low throughput of structural biology methods limits mechanistic insights for selection of many genomic sites. High-throughput binding assays enable prediction of potential target sites by determining relative binding affinities of a protein to massive numbers of DNA sequences. Many currently available computational methods are based on the sequence of standard Watson-Crick bp. They assume that the contribution of overall binding affinity is independent for each base pair, or alternatively include dinucleotides or short k-mers. These methods cannot directly expand to physicochemical contacts, and they are not suitable to apply to DNA modifications or non-Watson-Crick bp. These variations include DNA methylation, and synthetic or mismatched bp. The proposed method, DeepRec, can predict relative binding affinities as function of physicochemical signatures and the effect of DNA methylation or other chemical modifications on binding. Sequence-based modeling methods are in comparison a coarse-grain description and cannot achieve such insights. Our chemistry-based modeling framework provides a path towards understanding genome function at a mechanistic level.

Hyperbolic discounting and exponentiated demand: Modeling demand for cigarettes in three dimensions

Behavioral economics has been a fruitful area of research in substance use. Mathematical descriptions of how individuals temporally discount the value of a commodity have been correlated with substance use and mathematical descriptions of drug consumption decreasing as a function of price (i.e., demand) predict maladaptive substance use. While there is a logical assumption that temporal factors affect demand for a drug, little has been done to merge these models. Thus, the purpose of this study was to combine models of discounting and demand, extending Howard Rachlin's work and contributions to novel areas of study. Data from 85 participants from Amazon Mechanical Turk (MTurk) who completed a hypothetical cigarette purchase task that included price of and delay to cigarettes were analyzed. Multilevel modeling was used to determine descriptive accuracy of combined additive and multiplicative models of discounting and demand. Of the discounting models used in conjunction with the exponentiated demand equation, the Rachlin hyperboloid best described the delay dimension of consumption. The multiplicative version of the Rachlin equation applied to both delay and price outperformed other models tested. Therefore, existing models of discounting and demand can be extended to modeling consumption data from complex multidimensional experimental arrangements.

Dynamic Tracking of State Anxiety via Multi-Modal Data and Machine Learning

Anxiety induction is widely used in the investigations of the mechanism and treatment of state anxiety. State anxiety is accompanied by immediate psychological and physiological responses. However, the existing state anxiety measurement, such as the commonly used state anxiety subscale of the State-Trait Anxiety Inventory, mainly relies on questionnaires with low temporal resolution. This study aims to develop a tracking model of state anxiety with high temporal resolution. To capture the dynamic changes of state anxiety levels, we induced the participants' state anxiety through exposure to aversive pictures or the risk of electric shocks and simultaneously recorded multi-modal data, including dimensional emotion ratings, electrocardiogram, and galvanic skin response. Using the paired self-reported state anxiety levels and multi-modal measures, we trained and validated machine learning models to predict state anxiety based on psychological and physiological features extracted from the multi-modal data. The prediction model achieved a high correlation between the predicted and self-reported state anxiety levels. This quantitative model provides fine-grained and sensitive measures of state anxiety levels for future affective brain-computer interaction and anxiety modulation studies.

Prediction of shiftworker alertness, sleep, and circadian phase using a model of arousal dynamics constrained by shift schedules and light exposure

STUDY OBJECTIVES

The study aimed to, for the first time, (1) compare sleep, circadian phase, and alertness of intensive care unit (ICU) nurses working rotating shifts with those predicted by a model of arousal dynamics; and (2) investigate how different environmental constraints affect predictions and agreement with data.

METHODS

The model was used to simulate individual sleep-wake cycles, urinary 6-sulphatoxymelatonin (aMT6s) profiles, subjective sleepiness on the Karolinska Sleepiness Scale (KSS), and performance on a Psychomotor Vigilance Task (PVT) of 21 ICU nurses working day, evening, and night shifts. Combinations of individual shift schedules, forced wake time before/after work and lighting, were used as inputs to the model. Predictions were compared to empirical data. Simulations with self-reported sleep as an input were performed for comparison.

RESULTS

All input constraints produced similar prediction for KSS, with 56%-60% of KSS scores predicted within ±1 on a day and 48%-52% on a night shift. Accurate prediction of an individual's circadian phase required individualized light input. Combinations including light information predicted aMT6s acrophase within ±1 h of the study data for 65% and 35%-47% of nurses on diurnal and nocturnal schedules. Minute-by-minute sleep-wake state overlap between the model and the data was between 81 ± 6% and 87 ± 5% depending on choice of input constraint.

CONCLUSIONS

The use of individualized environmental constraints in the model of arousal dynamics allowed for accurate prediction of alertness, circadian phase, and sleep for more than half of the nurses. Individual differences in physiological parameters will need to be accounted for in the future to further improve predictions.

Quantifying the regulatory role of individual transcription factors in Escherichia coli

Gene regulation often results from the action of multiple transcription factors (TFs) acting at a promoter, obscuring the individual regulatory effect of each TF on RNA polymerase (RNAP). Here we measure the fundamental regulatory interactions of TFs in E. coli by designing synthetic target genes that isolate individual TFs' regulatory effects. Using a thermodynamic model, each TF's regulatory interactions are decoupled from TF occupancy and interpreted as acting through (de)stabilization of RNAP and (de)acceleration of transcription initiation. We find that the contribution of each mechanism depends on TF identity and binding location; regulation immediately downstream of the promoter is insensitive to TF identity, but the same TFs regulate by distinct mechanisms upstream of the promoter. These two mechanisms are uncoupled and can act coherently, to reinforce the observed regulatory role (activation/repression), or incoherently, wherein the TF regulates two distinct steps with opposing effects.

Role of the Discriminator Sequence in the Supercoiling Sensitivity of Bacterial Promoters

DNA supercoiling acts as a global transcriptional regulator that contributes to the rapid transcriptional response of bacteria to many environmental changes. Although a large fraction of promoters from phylogenetically distant species respond to superhelical variations, the sequence or structural determinants of this behavior remain elusive. Here, we focus on the sequence of the "discriminator" element that was shown to modulate this response in several promoters. We develop a quantitative thermodynamic model of this regulatory effect, focusing on open complex formation during transcription initiation independently from promoter-specific regulatory proteins. We analyze previous and new expression data and show that the model predictions quantitatively match the in vitro and in vivo supercoiling response of selected promoters with mutated discriminator sequences. We then test the universality of this mechanism by a statistical analysis of promoter sequences from transcriptomes of phylogenetically distant bacteria under conditions of supercoiling variations (i) by gyrase inhibitors, (ii) by environmental stresses, or (iii) inherited in the longest-running evolution experiment. In all cases, we identify a robust and significant sequence signature in the discriminator region, suggesting that supercoiling-modulated promoter opening underpins a ubiquitous regulatory mechanism in the prokaryotic kingdom based on the fundamental mechanical properties of DNA and its basal interaction with RNA polymerase. IMPORTANCE In this study, we highlight the role of the discriminator as a global sensor of supercoiling variations and propose the first quantitative regulatory model of this principle, based on the specific step of promoter opening during transcription initiation. It defines the predictive rule by which DNA supercoiling quantitatively modulates the expression rate of bacterial promoters, depending on the G/C content of their discriminator and independently from promoter-specific regulatory proteins. This basal mechanism affects a wide range of species, which is tested by an extensive analysis of global high-throughput expression data. Altogether, ours results confirm and provide a quantitative framework for the long-proposed notion that the discriminator sequence is a significant determinant of promoter supercoiling sensitivity, underpinning the ubiquitous regulatory action of DNA supercoiling on the core transcriptional machinery, in particular in response to quick environmental changes.

A zero-bounded model of operant demand

Contemporary approaches for evaluating the demand for reinforcers use either the Exponential or the Exponentiated model of operant demand, both derived from the framework of Hursh and Silberberg (2008). This report summarizes the strengths and complications of this framework and proposes a novel implementation. This novel implementation incorporates earlier strengths and resolves existing shortcomings that are due to the use of a logarithmic scale for consumption. The Inverse Hyperbolic Sine (IHS) transformation is reviewed and evaluated as a replacement for the logarithmic scale in models of operant demand. Modeling consumption in the "log₁₀ -like" IHS scale reflects relative changes in consumption (as with a log scale) and accommodates a true zero bound (i.e., zero consumption values). The presence of a zero bound obviates the need for a separate span parameter (i.e., k) and the span of the model may be more simply defined by maximum demand at zero price (i.e., Q₀ ). Further, this reformulated model serves to decouple the exponential rate constant (i.e., α) from variations in span, thus normalizing the rate constant to the span of consumption in IHS units and permitting comparisons when spans vary. This model, called the Zero-bounded Exponential (ZBE), is evaluated using simulated and real-world data. The direct reinstatement ZBE model showed strong correspondence with empirical indicators of demand and with a normalization of α (ZBEn) across empirical data that varied in reinforcing efficacy (dose, time to onset of peak effects). Future directions in demand curve analysis are discussed with recommendations for additional replication and exploration of scales beyond the logarithm when accommodating zero consumption data.

The Problem of Coordination and the Pursuit of Structural Constraints in Psychology

Paul Meehl's famous critique detailed many of the problematic practices and conceptual confusions that stand in the way of meaningful theoretical progress in psychological science. By integrating many of Meehl's points, we argue that one of the reasons for the slow progress in psychology is the failure to acknowledge the problem of coordination. This problem arises whenever we attempt to measure quantities that are not directly observable but can be inferred from observable variables. The solution to this problem is far from trivial, as demonstrated by a historical analysis of thermometry. The key challenge is the specification of a functional relationship between theoretical concepts and observations. As we demonstrate, empirical means alone cannot determine this relationship. In the case of psychology, the problem of coordination has dramatic implications in the sense that it severely constrains our ability to make meaningful theoretical claims. We discuss several examples and outline some of the solutions that are currently available.

A Quantitative Modular Modeling Approach Reveals the Effects of Different A20 Feedback Implementations for the NF-kB Signaling Dynamics

Signaling pathways involve complex molecular interactions and are controled by non-linear regulatory mechanisms. If details of regulatory mechanisms are not fully elucidated, they can be implemented by different, equally reasonable mathematical representations in computational models. The study presented here focusses on NF-κB signaling, which is regulated by negative feedbacks via IκBα and A20. A20 inhibits NF-κB activation indirectly through interference with proteins that transduce the signal from the TNF receptor complex to activate the IκB kinase (IKK) complex. A number of pathway models has been developed implementing the A20 effect in different ways. We here focus on the question how different A20 feedback implementations impact the dynamics of NF-κB. To this end, we develop a modular modeling approach that allows combining previously published A20 modules with a common pathway core module. The resulting models are fitted to a published comprehensive experimental data set and therefore show quantitatively comparable NF-κB dynamics. Based on defined measures for the initial and long-term behavior we analyze the effects of a wide range of changes in the A20 feedback strength, the IκBα feedback strength and the TNFα stimulation strength on NF-κB dynamics. This shows similarities between the models but also model-specific differences. In particular, the A20 feedback strength and the TNFα stimulation strength affect initial and long-term NF-κB concentrations differently in the analyzed models. We validated our model predictions experimentally by varying TNFα concentrations applied to HeLa cells. These time course data indicate that only one of the A20 feedback models appropriately describes the impact of A20 on the NF-κB dynamics in this cell type.

Object-Displacement-Sensitive Visual Neurons Drive Freezing in Drosophila

Visual systems are often equipped with neurons that detect small moving objects, which may represent prey, predators, or conspecifics. Although the processing properties of those neurons have been studied in diverse organisms, links between the proposed algorithms and animal behaviors or circuit mechanisms remain elusive. Here, we have investigated behavioral function, computational algorithm, and neurochemical mechanisms of an object-selective neuron, LC11, in Drosophila. With genetic silencing and optogenetic activation, we show that LC11 is necessary for a visual object-induced stopping behavior in walking flies, a form of short-term freezing, and its activity can promote stopping. We propose a new quantitative model for small object selectivity based on the physiology and anatomy of LC11 and its inputs. The model accurately reproduces LC11 responses by pooling fast-adapting, tightly size-tuned inputs. Direct visualization of neurotransmitter inputs to LC11 confirmed the model conjectures about upstream processing. Our results demonstrate how adaptation can enhance selectivity for behaviorally relevant, dynamic visual features.

Dipole modeling of multispectral signal for detecting metallic biopsy markers during MRI-guided breast biopsy: a pilot study

PURPOSE

During MRI-guided breast biopsy, a metallic biopsy marker is deployed at the biopsy site to guide future interventions. Conventional MRI during biopsy cannot distinguish such markers from biopsy site air, and a post-biopsy mammogram is therefore performed to localize marker placement. The purpose of this pilot study is to develop dipole modeling of multispectral signal (DIMMS) as an MRI alternative to eliminate the cost, inefficiency, inconvenience, and ionizing radiation of a mammogram for biopsy marker localization.

METHODS

DIMMS detects and localizes the biopsy marker by fitting the measured multispectral imaging (MSI) signal to the MRI signal model and marker properties. MSI was performed on phantoms containing titanium biopsy markers and air to illustrate the clinical challenge that DIMMS addresses and on 20 patients undergoing MRI-guided breast biopsy to assess DIMMS feasibility for marker detection. DIMMS was compared to conventional MSI field map thresholding, using the post-procedure mammogram as the reference standard.

RESULTS

Biopsy markers were detected and localized in 20 of 20 cases using MSI with automated DIMMS post-processing (using a threshold of 0.7) and in 18 of 20 cases using MSI field mapping (using a threshold of 0.65 kHz).

CONCLUSION

MSI with DIMMS post-processing is a feasible technique for biopsy marker detection and localization during MRI-guided breast biopsy. With a 2-min MSI scan, DIMMS is a promising MRI alternative to the standard-of-care post-biopsy mammogram.

Comparative quantitative systems pharmacology modeling of anti-PCSK9 therapeutic modalities in hypercholesterolemia

Since the discovery of proprotein convertase subtilisin/kexin type 9 (PCSK9) as an attractive target in the treatment of hypercholesterolemia, multiple anti-PCSK9 therapeutic modalities have been pursued in drug development. The objective of this research is to set the stage for the quantitative benchmarking of two anti-PCSK9 pharmacological modality classes, monoclonal antibodies (mAbs) and small interfering RNA (siRNA). To this end, we developed an integrative mathematical model of lipoprotein homeostasis describing the dynamic interplay between PCSK9, LDL-cholesterol (LDL-C), VLDL-cholesterol, HDL-cholesterol (HDL-C), apoB, lipoprotein a [Lp(a)], and triglycerides (TGs). We demonstrate that LDL-C decreased proportionally to PCSK9 reduction for both mAb and siRNA modalities. At marketed doses, however, treatment with mAbs resulted in an additional ∼20% LDL-C reduction compared with siRNA. We further used the model as an evaluation tool and determined that no quantitative differences were observed in HDL-C, Lp(a), TG, or apoB responses, suggesting that the disruption of PCSK9 synthesis would provide no additional effects on lipoprotein-related biomarkers in the patient segment investigated. Predictive model simulations further indicate that siRNA therapies may reach reductions in LDL-C levels comparable to those achieved with mAbs if the current threshold of 80% PCSK9 inhibition via siRNA could be overcome.

Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity

Topoisomerase II (TOP2) relieves torsional stress by forming transient cleavage complex intermediates (TOP2ccs) that contain TOP2-linked DNA breaks (DSBs). While TOP2ccs are normally reversible, they can be "trapped" by chemotherapeutic drugs such as etoposide and subsequently converted into irreversible TOP2-linked DSBs. Here, we have quantified etoposide-induced trapping of TOP2ccs, their conversion into irreversible TOP2-linked DSBs, and their processing during DNA repair genome-wide, as a function of time. We find that while TOP2 chromatin localization and trapping is independent of transcription, it requires pre-existing binding of cohesin to DNA. In contrast, the conversion of trapped TOP2ccs to irreversible DSBs during DNA repair is accelerated 2-fold at transcribed loci relative to non-transcribed loci. This conversion is dependent on proteasomal degradation and TDP2 phosphodiesterase activity. Quantitative modeling shows that only two features of pre-existing chromatin structure-namely, cohesin binding and transcriptional activity-can be used to predict the kinetics of TOP2-induced DSBs.

Potentiality of Using Luojia1-01 Night-Time Light Imagery to Estimate Urban Community Housing Price-A Case Study in Wuhan, China

The first professional night-time light remote sensing satellite in China, Luojia1-01, has raised the resolution of night-time light data to 130 m, which provides a possibility for the study of small-scale night-time light. This paper is the first research on spatial analysis and quantitative modeling between night-time light intensity (NTLI) and community housing price (CHP) on a small scale by using the Luojia1-01 night-time light imagery. This paper takes Wuhan as the research area, CHP data obtained by web-crawler technology as the research object, combines Luojia1-01 data, and carries out spatial correlation analysis and quantitative modeling on a small scale for them. The experimental results show that there is a strong linear positive correlation between the NTLI and CHP based on geographically weighted regression (GWR), and the CHP data in Wuhan have obvious spatial non-stationarity. Moreover, the coupling mechanism between the NTLI and CHP is also revealed. We can conclude that there is potential for estimating the CHP by using Luojia1-01 night-time light imagery.

Effects of excitation angle strategy on quantitative analysis of hyperpolarized pyruvate

PURPOSE

Various excitation strategies have been proposed for dynamic imaging of hyperpolarized agents such as [1-¹³ C]-pyruvate, but the impact of these strategies on quantitative evaluation of signal evolution remains unclear. To better understand their relative performance, we compared the accuracy and repeatability of measurements made using variable excitation angle strategies and conventional constant excitation angle strategies.

METHODS

Signal evolution for constant and variable excitation angle schedules was simulated using a pharmacokinetic model of hyperpolarized pyruvate with 2 chemical pools and 2 physical compartments. Noisy synthetic data were then fit using the same pharmacokinetic model with the apparent chemical exchange term as an unknown, and fit results were compared with simulation parameters to determine accuracy and reproducibility.

RESULTS

Constant excitations and a variable excitation strategy that maximizes the HP lactate signal yielded data that supported quantitative analyses with similar accuracy and repeatability. Variable excitation angle strategies that were designed to produce a constant signal level resulted in lower signal and worse quantitative accuracy and repeatability, particularly for longer acquisition times.

CONCLUSIONS

These results suggest that either constant excitation angle or variable excitation angles that attempt to maximize total signal, as opposed to maintaining a constant signal level, are preferred for metabolic quantification using hyperpolarized pyruvate.

Data-driven quantitative modeling of bacterial active nematics

Active matter comprises individual units that convert energy into mechanical motion. In many examples, such as bacterial systems and biofilament assays, constituent units are elongated and can give rise to local nematic orientational order. Such "active nematics" systems have attracted much attention from both theorists and experimentalists. However, despite intense research efforts, data-driven quantitative modeling has not been achieved, a situation mainly due to the lack of systematic experimental data and to the large number of parameters of current models. Here, we introduce an active nematics system made of swarming filamentous bacteria. We simultaneously measure orientation and velocity fields and show that the complex spatiotemporal dynamics of our system can be quantitatively reproduced by a type of microscopic model for active suspensions whose important parameters are all estimated from comprehensive experimental data. This provides unprecedented access to key effective parameters and mechanisms governing active nematics. Our approach is applicable to different types of dense suspensions and shows a path toward more quantitative active matter research.

Landscape of Innovation for Cardiovascular Pharmaceuticals: From Basic Science to New Molecular Entities

PURPOSE

This study examines the complete timelines of translational science for new cardiovascular therapeutics from the initiation of basic research leading to identification of new drug targets through clinical development and US Food and Drug Administration (FDA) approval of new molecular entities (NMEs) based on this research.

METHODS

This work extends previous studies by examining the association between the growth of research on drug targets and approval of NMEs associated with these targets. Drawing on research on innovation in other technology sectors, where technological maturity is an important determinant in the success or failure of new product development, an analytical model was used to characterize the growth of research related to the known targets for all 168 approved cardiovascular therapeutics.

FINDINGS

Categorizing and mapping the technological maturity of cardiovascular therapeutics reveal that (1) there has been a distinct transition from phenotypic to targeted methods for drug discovery, (2) the durations of clinical and regulatory processes were significantly influenced by changes in FDA practice, and (3) the longest phase of the translational process was the time required for technology to advance from initiation of research to a statistically defined established point of technology maturation (mean, 30.8 years).

IMPLICATIONS

This work reveals a normative association between metrics of research maturation and approval of new cardiovascular therapeutics and suggests strategies for advancing translational science by accelerating basic and applied research and improving the synchrony between the maturation of this research and drug development initiatives.

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models

Transcription factors (TFs) achieve DNA‐binding specificity through contacts with functional groups of bases (base readout) and readout of structural properties of the double helix (shape readout). Currently, it remains unclear whether DNA shape readout is utilized by only a few selected TF families, or whether this mechanism is used extensively by most TF families. We resequenced data from previously published HT‐SELEX experiments, the most extensive mammalian TF–DNA binding data available to date. Using these data, we demonstrated the contributions of DNA shape readout across diverse TF families and its importance in core motif‐flanking regions. Statistical machine‐learning models combined with feature‐selection techniques helped to reveal the nucleotide position‐dependent DNA shape readout in TF‐binding sites and the TF family‐specific position dependence. Based on these results, we proposed novel DNA shape logos to visualize the DNA shape preferences of TFs. Overall, this work suggests a way of obtaining mechanistic insights into TF–DNA binding without relying on experimentally solved all‐atom structures.

Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle

Cells decide when, where, and to what level to express their genes by "computing" information from transcription factors (TFs) binding to regulatory DNA. How is the information contained in multiple TF-binding sites integrated to dictate the rate of transcription? The dominant conceptual and quantitative model is that TFs combinatorially recruit one another and RNA polymerase to the promoter by direct physical interactions. Here, we develop a quantitative framework to explore kinetic control, an alternative model in which combinatorial gene regulation can result from TFs working on different kinetic steps of the transcription cycle. Kinetic control can generate a wide range of analog and Boolean computations without requiring the input TFs to be simultaneously bound to regulatory DNA. We propose experiments that will illuminate the role of kinetic control in transcription and discuss implications for deciphering the cis-regulatory "code."

Target-based drug discovery for [Formula: see text]-globin disorders: drug target prediction using quantitative modeling with hybrid functional Petri nets

Recent molecular studies provide important clues into treatment of [Formula: see text]-thalassemia, sickle-cell anaemia and other [Formula: see text]-globin disorders revealing that increased production of fetal hemoglobin, that is normally suppressed in adulthood, can ameliorate the severity of these diseases. In this paper, we present a novel approach for drug prediction for [Formula: see text]-globin disorders. Our approach is centered upon quantitative modeling of interactions in human fetal-to-adult hemoglobin switch network using hybrid functional Petri nets. In accordance with the reverse pharmacology approach, we pose a hypothesis regarding modulation of specific protein targets that induce [Formula: see text]-globin and consequently fetal hemoglobin. Comparison of simulation results for the proposed strategy with the ones obtained for already existing drugs shows that our strategy is the optimal as it leads to highest level of [Formula: see text]-globin induction and thereby has potential beneficial therapeutic effects on [Formula: see text]-globin disorders. Simulation results enable verification of model coherence demonstrating that it is consistent with qPCR data available for known strategies and/or drugs.

Computational Framework for Modeling Multiple Noncooperative Transcription Factor Binding and Its Application to the Analysis of Nuclear Factor Kappa B Oscillatory Response

Recent studies have shown that regulation of many important genes is achieved with multiple transcription factor (TF) binding sites with low or no cooperativity. Additionally, noncooperative binding sites are gaining more and more importance in the field of synthetic biology. Here, we introduce a computational framework that can be applied to dynamical modeling and analysis of gene regulatory networks with multiple noncooperative TF binding sites. We propose two computational methods to be used within the framework, that is, average promoter state approximation and expression profiles based modeling. We demonstrate the application of the proposed framework on the analysis of nuclear factor kappa B (NF-κB) oscillatory response. We show that different promoter expression hypotheses in a combination with the number of TF binding sites drastically affect the dynamics of the observed system and should not be ignored in the process of quantitative dynamical modeling, as is usually the case in existent state-of-the-art computational analyses.

Alterations in Multi-Scale Cardiac Architecture in Association With Phosphorylation of Myosin Binding Protein-C

Background

The geometric organization of myocytes in the ventricular wall comprises the structural underpinnings of cardiac mechanical function. Cardiac myosin binding protein‐C (MYBPC3) is a sarcomeric protein, for which phosphorylation modulates myofilament binding, sarcomere morphology, and myocyte alignment in the ventricular wall. To elucidate the mechanisms by which MYBPC3 phospho‐regulation affects cardiac tissue organization, we studied ventricular myoarchitecture using generalized Q‐space imaging (GQI). GQI assessed geometric phenotype in excised hearts that had undergone transgenic (TG) modification of phospho‐regulatory serine sites to nonphosphorylatable alanines (MYBPC3^{AllP−/(t/t)}) or phospho‐mimetic aspartic acids (MYBPC3^AllP+/(t/t)).

Methods and Results

Myoarchitecture in the wild‐type (MYBPC3^WT) left‐ventricle (LV) varied with transmural position, with helix angles ranging from −90/+90 degrees and contiguous circular orientation from the LV mid‐myocardium to the right ventricle (RV). Whereas MYBPC3^AllP+/(t/t) hearts were not architecturally distinct from MYBPC3^WT, MYBPC3^{AllP−/(t/t)} hearts demonstrated a significant reduction in LV transmural helicity. Null MYBPC3^(t/t) hearts, as constituted by a truncated MYBPC3 protein, demonstrated global architectural disarray and loss in helicity. Electron microscopy was performed to correlate the observed macroscopic architectural changes with sarcomere ultrastructure and demonstrated that impaired phosphorylation of MYBPC3 resulted in modifications of the sarcomere aspect ratio and shear angle. The mechanical effect of helicity loss was assessed through a geometric model relating cardiac work to ejection fraction, confirming the mechanical impairments observed with echocardiography.

Conclusions

We conclude that phosphorylation of MYBPC3 contributes to the genesis of ventricular wall geometry, linking myofilament biology with multiscale cardiac mechanics and myoarchitecture.

Estimating cellular parameters through optimization procedures: elementary principles and applications

Construction of quantitative models is a primary goal of quantitative biology, which aims to understand cellular and organismal phenomena in a quantitative manner. In this article, we introduce optimization procedures to search for parameters in a quantitative model that can reproduce experimental data. The aim of optimization is to minimize the sum of squared errors (SSE) in a prediction or to maximize likelihood. A (local) maximum of likelihood or (local) minimum of the SSE can efficiently be identified using gradient approaches. Addition of a stochastic process enables us to identify the global maximum/minimum without becoming trapped in local maxima/minima. Sampling approaches take advantage of increasing computational power to test numerous sets of parameters in order to determine the optimum set. By combining Bayesian inference with gradient or sampling approaches, we can estimate both the optimum parameters and the form of the likelihood function related to the parameters. Finally, we introduce four examples of research that utilize parameter optimization to obtain biological insights from quantified data: transcriptional regulation, bacterial chemotaxis, morphogenesis, and cell cycle regulation. With practical knowledge of parameter optimization, cell and developmental biologists can develop realistic models that reproduce their observations and thus, obtain mechanistic insights into phenomena of interest.

Model-driven engineering of gene expression from RNA replicons

RNA replicons are an emerging platform for engineering synthetic biological systems. Replicons self-amplify, can provide persistent high-level expression of proteins even from a small initial dose, and, unlike DNA vectors, pose minimal risk of chromosomal integration. However, no quantitative model sufficient for engineering levels of protein expression from such replicon systems currently exists. Here, we aim to enable the engineering of multigene expression from more than one species of replicon by creating a computational model based on our experimental observations of the expression dynamics in single- and multireplicon systems. To this end, we studied fluorescent protein expression in baby hamster kidney (BHK-21) cells using a replicon derived from Sindbis virus (SINV). We characterized expression dynamics for this platform based on the dose-response of a single species of replicon over 50 h and on a titration of two cotransfected replicons expressing different fluorescent proteins. From this data, we derive a quantitative model of multireplicon expression and validate it by designing a variety of three-replicon systems, with profiles that match desired expression levels. We achieved a mean error of 1.7-fold on a 1000-fold range, thus demonstrating how our model can be applied to precisely control expression levels of each Sindbis replicon species in a system.

An electrocardiographic sign of ischemic preconditioning

Ischemic preconditioning is a form of intrinsic cardioprotection where an episode of sublethal ischemia protects against subsequent episodes of ischemia. Identifying a clinical biomarker of preconditioning could have important clinical implications, and prior work has focused on the electrocardiographic ST segment. However, the electrophysiology biomarker of preconditioning is increased action potential duration (APD) shortening with subsequent ischemic episodes, and APD shortening should primarily alter the T wave, not the ST segment. We translated findings from simulations to canine to patient models of preconditioning to test the hypothesis that the combination of increased [delta (Δ)] T wave amplitude with decreased ST segment elevation characterizes preconditioning. In simulations, decreased APD caused increased T wave amplitude with minimal ST segment elevation. In contrast, decreased action potential amplitude increased ST segment elevation significantly. In a canine model of preconditioning (9 mongrel dogs undergoing 4 ischemia-reperfusion episodes), ST segment amplitude increased more than T wave amplitude during the first ischemic episode [ΔT/ΔST slope = 0.81, 95% confidence interval (CI) 0.46-1.15]; however, during subsequent ischemic episodes the T wave increased significantly more than the ST segment (ΔT/ΔST slope = 2.43, CI 2.07-2.80) (P < 0.001 for interaction of occlusions 2 vs. 1). A similar result was observed in patients (9 patients undergoing 2 consecutive prolonged occlusions during elective percutaneous coronary intervention), with an increase in slope of ΔT/ΔST of 0.13 (CI -0.15 to 0.42) in the first occlusion to 1.02 (CI 0.31-1.73) in the second occlusion (P = 0.02). This integrated analysis of the T wave and ST segment goes beyond the standard approach to only analyze ST elevation, and detects cellular electrophysiology changes of preconditioning.

Implications of systemic dysfunction for the etiology of malignancy

The current approach to treatment in oncology is to replace the generally cytotoxic chemotherapies with pharmaceutical treatment which inactivates specific molecular targets associated with cancer development and progression. The goal is to limit cellular damage to pathways perceived to be directly responsible for the malignancy. Its underlying assumptions are twofold: (1) that individual pathways are the cause of malignancy; and (2) that the treatment objective should be destruction-either of the tumor or the dysfunctional pathway. However, the extent to which data actually support these assumptions has not been directly addressed. Accumulating evidence suggests that systemic dysfunction precedes the disruption of specific genetic/molecular pathways in most adult cancers and that targeted treatments such as kinase inhibitors may successfully treat one pathway while generating unintended changes to other, non-targeted pathways. This article discusses (1) the systemic basis of malignancy; (2) better profiling of pre-cancerous biomarkers associated with elevated risk so that preventive lifestyle modifications can be instituted early to revert high-risk epigenetic changes before tumors develop; (3) a treatment emphasis in early stage tumors that would target the restoration of systemic balance by strengthening the body's innate defense mechanisms; and (4) establishing better quantitative models of systems to capture adequate complexity for predictability at all stages of tumor progression.

Integrating experimentation and quantitative modeling to enhance discovery of Beta amyloid lowering therapeutics for Alzheimer's disease

Drug discovery can benefit from a proactive-knowledge-attainment philosophy which strategically integrates experimentation and pharmacokinetic/pharmacodynamic (PK/PD) modeling. Our programs for Alzheimer’s disease (AD) illustrate such an approach. Compounds that inhibit the generation of brain beta amyloid (Aβ), especially Aβ42, are being pursued as potential disease-modifying therapeutics. Complexities in the PK/Aβ relationship for these compounds have been observed and the data require an advanced approach for analysis. We established a semimechanistic PK/PD model that can describe the PK/Aβ data by accounting for Aβ generation and clearance. The modeling characterizes the in vivo PD (i.e., Aβ lowering) properties of compounds and generates insights about the salient biological systems. The learning from the modeling enables us to establish a framework for predicting in vivo Aβ lowering from in vitro parameters.

Metacognition in animals

Metacognition is thinking about thinking. There is considerable interest in developing animal models of metacognition to provide insight about the evolution of mind and a basis for investigating neurobiological mechanisms of cognitive impairments in people. Formal modeling of low-level (i.e., alternative) mechanisms has recently demonstrated that prevailing standards for documenting metacognition are inadequate. Indeed, low-level mechanisms are sufficient to explain data from existing methods. Consequently, an assessment of what is 'lost' (in terms of existing methods and data) necessitates the development of new, innovative methods for metacognition. Development of new methods may prompt the establishment of new standards for documenting metacognition.

Metacognition in animals: Trends and challenges

There is widespread agreement that metacognition is not demonstrated if alternative explanations account for putative meta-cognition data. However, there is less agreement on which studies are protected from alternative explanations. We have argued that existing experiments on uncertainty monitoring can be explained by low-level explanations without assuming metacognition (Crystal & Foote, 2009). The field would benefit from the development of accepted standards for what is required to produce a convincing example of metacognition in animals.

Prediction and measurement of an autoregulatory genetic module

The deduction of phenotypic cellular responses from the structure and behavior of complex gene regulatory networks is one of the defining challenges of systems biology. This goal will require a quantitative understanding of the modular components that constitute such networks. We pursued an integrated approach, combining theory and experiment, to analyze and describe the dynamics of an isolated genetic module, an in vivo autoregulatory gene network. As predicted by the model, temperature-induced protein destabilization led to the existence of two expression states, thus elucidating the trademark bistability of the positive feedback-network architecture. After sweeping the temperature, observed population distributions and coefficients of variation were in quantitative agreement with those predicted by a stochastic version of the model. Because model fluctuations originated from small molecule-number effects, the experimental validation underscores the importance of internal noise in gene expression. This work demonstrates that isolated gene networks, coupled with proper quantitative descriptions, can elucidate key properties of functional genetic modules. Such an approach could lead to the modular dissection of naturally occurring gene regulatory networks, the deduction of cellular processes such as differentiation, and the development of engineered cellular control.