Publications by authors named "Frank T D"

58 Publications

COVID-19 interventions in some European countries induced bifurcations stabilizing low death states against high death states: An eigenvalue analysis based on the order parameter concept of synergetics.

Authors:
T D Frank

Chaos Solitons Fractals 2020 Nov 11;140:110194. Epub 2020 Aug 11.

Dept of Psychology and Dept of Physics, University of Connecticut, Storrs, CT, 06269, USA.

Taking a dynamical systems perspective, COVID-19 infections are assumed to spread out in a human population via an instability. Conversely, government interventions to reduce the spread of the disease and the number of fatalities may induce a bifurcation that stabilizes a desirable state with low numbers of COVID-19 cases and associated deaths. The key characteristic feature of an infection dynamical system in this context is the eigenvalue that determines the stability of the states under consideration and is known in synergetics as the order parameter eigenvalue. Using a SEIR-like infection disease model, the relevant order parameter and its eigenvalue are determined. A three stage methodology is proposed to track and estimate the eigenvalue through time. The method is applied to COVID-19 infection data reported from 20 European countries during the period of January 1, 2020 to June 15. It is shown that in 15 out of the 20 countries the eigenvalue switched its sign suggesting that during the reporting period an intervention bifurcation took place that stabilized the desirable low death state. It is shown that the eigenvalue analysis also allows for a ranking of countries by the degree of the stability of the infection-free state. For the investigated countries, Ireland was found to exhibit the most stable infection-free state. Finally, a six point classification scheme is suggested with groups 5 and 6 including countries that failed to stabilize the desirable infection-free low death state. In doing so, tools for assessing the effectiveness of government interventions are provided that are at the heart of bifurcation theory, in general, and synergetics, in particular.
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http://dx.doi.org/10.1016/j.chaos.2020.110194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418651PMC
November 2020

Grasp Affordances in Bistable Perception of the Necker Cube.

Nonlinear Dynamics Psychol Life Sci 2020 Apr;24(2):143-157

University of Connecticut, Storrs, CT.

Stimulus-response compatibility effects illustrate the mutual depen-dence of perception and action processes. Ellis and Tucker (2000) showed that object identification was facilitated when the response required a grip that was compatible with the stimulus. In the current study, we extend grip-compatibility effects to perception of the Necker cube. Participants reported the perceived orientation of a Necker cube by orienting a hand-held cube into a compatible or an incompatible position. Participants in the incompatible condition were quickly attracted to the FRB (front-side right bottom) percept, consistent with previous work. However, participants in the compatible condition showed an extended period of metastability, switching between the two perceptual states about equally. A second experiment replicated these results and showed that a control condition in which responses were made with a key press produced intermediate levels of metastability. These results are interpreted in terms of the dynamics of bistable perception.
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April 2020

Embodied gestalts: Unstable visual phenomena become stable when they are stimuli for competitive action selection.

Atten Percept Psychophys 2019 Oct;81(7):2330-2342

University of Connecticut, Storrs, CT, USA.

An animal's environment is rich with affordances. Different possible actions are specified by visual information while competing for dominance over neural dynamics. Affordance competition models account for this in terms of winner-takes-all cross-inhibition dynamics. Multistable phenomena also reveal how the visual system deals with ambiguity. Their key property is spontaneous instability, in forms such as alternating dominance in binocular rivalry. Theoretical models of self-inhibition or self-organized instability posit that the instability is tied to some kind of neural adaptation and that its functional significance is to enable flexible perceptual transitions. We hypothesized that the two perspectives are interlinked. Spontaneous instability is an intrinsic property of perceptual systems, but it is revealed when they are stripped from the constraints of possibilities for action. To test this, we compared a multistable gestalt phenomenon against its embodied version and estimated the neural adaptation and competition parameters of an affordance transition dynamic model. Wertheimer's (Zeitschrift fur Psychologie 61, 161-265, 1912) optimal (β) and pure (φ) forms of apparent motion from a stroboscopic point-light display were endowed with action relevance by embedding the display in a visual object-tracking task. Thus, each mode was complemented by its action, because each perceptual mode uniquely enabled different ways of tracking the target. Perceptual judgment of the traditional apparent motion exhibited spontaneous instabilities, in the form of earlier switching when the frame rate was changed stepwise. In contrast, the embodied version exhibited hysteresis, consistent with affordance transition studies. Consistent with our predictions, the parameter for competition between modes in the affordance transition model increased, and the parameter for self-inhibition vanished.
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http://dx.doi.org/10.3758/s13414-019-01868-4DOI Listing
October 2019

Age and pattern of the southern high-latitude continental end-Permian extinction constrained by multiproxy analysis.

Nat Commun 2019 01 23;10(1):385. Epub 2019 Jan 23.

Isotope Geology Laboratory, Boise State University, 1910 University Drive, Boise, ID, 83725-1535, USA.

Past studies of the end-Permian extinction (EPE), the largest biotic crisis of the Phanerozoic, have not resolved the timing of events in southern high-latitudes. Here we use palynology coupled with high-precision CA-ID-TIMS dating of euhedral zircons from continental sequences of the Sydney Basin, Australia, to show that the collapse of the austral Permian Glossopteris flora occurred prior to 252.3 Ma (~370 kyrs before the main marine extinction). Weathering proxies indicate that floristic changes occurred during a brief climate perturbation in a regional alluvial landscape that otherwise experienced insubstantial change in fluvial style, insignificant reorganization of the depositional surface, and no abrupt aridification. Palaeoclimate modelling suggests a moderate shift to warmer summer temperatures and amplified seasonality in temperature across the EPE, and warmer and wetter conditions for all seasons into the Early Triassic. The terrestrial EPE and a succeeding peak in Ni concentration in the Sydney Basin correlate, respectively, to the onset of the primary extrusive and intrusive phases of the Siberian Traps Large Igneous Province.
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http://dx.doi.org/10.1038/s41467-018-07934-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344581PMC
January 2019

A cluster phase analysis for collective behavior in team sports.

Hum Mov Sci 2018 Jun 5;59:96-111. Epub 2018 Apr 5.

Center for the Ecological Study of Perception and Action, Department of Psychological Sciences, University of Connecticut, United States. Electronic address:

Collective behavior can be defined as the ability of humans to coordinate with others through a complex environment. Sports offer exquisite examples of this dynamic interplay, requiring decision making and other perceptual-cognitive skills to adjust individual decisions to the team self-organization and vice versa. Considering players of a team as periodic phase oscillators, synchrony analyses can be used to model the coordination of a team. Nonetheless, a main limitation of current models is that collective behavior is context independent. In other words, players on a team can be highly synchronized without this corresponding to a meaningful coordination dynamics relevant to the context of the game. Considering these issues, the aim of this study was to develop a method of analysis sensitive to the context for evidence-based measures of collective behavior.
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http://dx.doi.org/10.1016/j.humov.2018.03.013DOI Listing
June 2018

Increasing isoniazid preventive therapy uptake in an HIV program in rural Papua New Guinea.

Public Health Action 2017 Sep;7(3):193-198

Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA.

Tuberculosis (TB) is the leading cause of death among people living with the human immunodeficiency virus (PLHIV) in Papua New Guinea. Despite a policy for isoniazid preventive therapy (IPT) among PLHIV, implementation has been slow. We prospectively evaluated a standardized guided screening process, including TB diagnostic support, to increase IPT initiation in adult PLHIV on antiretro-viral treatment. The guided process included a paper-based IPT screening tool that prompted review of patient history and TB symptoms and sputum analysis by smear microscopy and Xpert MTB/RIF. Chest X-ray was performed at the provider's discretion. We quantified the yield of this guided process on IPT initiation and detection of TB and rifampicin resistance, and examined the contributions of each diagnostic modality. Among 532 patients, TB was ruled out and IPT initiated in 450 (84%). TB was diagnosed and treatment was started in 82 (15%) patients. Xpert detected rifampicin resistance in one of 21 patients (5%, 95%CI 0.24-21.3) with a positive Xpert result. All TB cases were diagnosed by chest X-ray and/or Xpert. No cases were diagnosed by sputum smear alone. A standardized guided process, including TB diagnostic support, successfully enabled IPT initiation and identified a large burden of undetected TB.
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http://dx.doi.org/10.5588/pha.17.0011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676994PMC
September 2017

Correlations Between Hysteretic Categorical and Continuous Judgments of Perceptual Stimuli Supporting a Unified Dynamical Systems Approach to Perception.

Authors:
S Kim T D Frank

Perception 2018 Jan 24;47(1):44-66. Epub 2017 Sep 24.

Center for the Ecological Study of Perception and Action, 7712 University of Connecticut , Storrs, CT, USA; Department of Physics, University of Connecticut, Storrs, CT, USA.

We report from two variants of a figure-ground experiment that is known in the literature to involve a bistable perceptual domain. The first variant was conducted as a two-alternative forced-choice experiment and in doing so tested participants on a categorical measurement scale. The second variant involved a Likert scale measure that was considered to represent a continuous measurement scale. The two variants were conducted as a single within-subjects experiment. Measures of bistability operationalized in terms of hysteresis size scores showed significant positive correlations across the two response conditions. The experimental findings are consistent with a dualistic interpretation of self-organizing perceptual systems when they are described on a macrolevel by means of so-called amplitude equations. This is explicitly demonstrated for a Lotka-Volterra-Haken amplitude equation model of task-related brain activity. As a by-product, the proposed dynamical systems perspective also sheds new light on the anchoring problem of producing numerical, continuous judgments.
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http://dx.doi.org/10.1177/0301006617731047DOI Listing
January 2018

Early Initiation of Breastfeeding Among Maya Mothers in the Western Highlands of Guatemala: Practices and Beliefs.

J Hum Lact 2017 Nov 20;33(4):781-789. Epub 2017 Jan 20.

1 Duke Global Health Institute, Duke University, Durham, NC, USA.

Background: Guatemala exhibits the sixth highest rate of child stunting worldwide, and stunting disproportionately affects Guatemala indigenous communities. In a country struggling to combat this result of malnutrition, early child nutrition is especially critical. Specifically, early initiation of breastfeeding is important for the development of newborn infants. Understanding beliefs and practices related to early initiation of breastfeeding in Maya Guatemala may provide an avenue to guide nutrition interventions in indigenous communities. Research aim: This study aimed to determine major beliefs and practices associated with early initiation of breastfeeding among Maya mothers in Lake Atitlán, Guatemala.

Methods: As part of a larger study to assess child nutrition in the Lake Atitlán region, we created a series of semistructured interview questions to document breastfeeding practices and beliefs among mothers. We conducted and audio-recorded in-person interviews that were translated from Kaqchikel, the local language, to Spanish by a community assistant.

Results: We conducted 178 interviews with mothers; 76% practiced early initiation. Early initiation was associated with the village and complementary feeding practices. Mothers held a variety of beliefs about the value of colostrum, and these beliefs were associated with the village. Mothers who held negative beliefs toward colostrum were more likely to delay breastfeeding initiation.

Conclusion: Although most Maya mothers practice early initiation, the intervillage disparity in breastfeeding practices demonstrates a need to geographically focus breastfeeding interventions. Our novel insights into the breastfeeding beliefs among Maya mothers will serve as a guide to structure culturally competent breastfeeding education interventions in indigenous communities.
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http://dx.doi.org/10.1177/0890334416682729DOI Listing
November 2017

Reaction kinetics of the jasmonate-isoleucine complex formation during wound-induced plant defense responses: A model-based re-analysis of published data.

J Plant Physiol 2016 Nov 23;206:103-113. Epub 2016 Sep 23.

Center for the Ecological Study of Perception and Action, University of Connecticut, 406 Babbidge Road, Storrs, CT 06269, USA; Department of Physics, University of Connecticut, 2152 Hillside Road, Storrs, CT 06269, USA. Electronic address:

Three studies were considered in which jasmonate-isoleucine levels were observed for several hours after plant wounding. The data from these studies were fitted to a first order kinetical model describing jasmonate-isoleucine complex formation and dissociation. It was found that the model could explain up to 97 percent of the variations in the data sets. In general, the data re-analysis confirmed that the protein-protein interactions involved in the biosynthesis and dissociation of the jasmonate-isoleucine complex are fast relative to the dynamics of the jasmonate levels themselves. Moreover, the data re-analysis supported the notion that transgenic plant manipulations affecting the defense-responses in plants not only affect the jasmonate-isoleucine levels indirectly by affecting jasmonate levels during plant responses. Rather, it seems that transgenic plant manipulations affect kinetic rate parameters of the jasmonate-isoleucine complex formation and dissociation reactions. In addition to these general findings, several specific conclusions for the three experimental studies were obtained.
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http://dx.doi.org/10.1016/j.jplph.2016.09.003DOI Listing
November 2016

Body-scaled perception is subjected to adaptation when repetitively judging opportunities for grasping.

Exp Brain Res 2016 09 24;234(9):2731-43. Epub 2016 May 24.

Center for the Ecological Study of Perception and Action, University of Connecticut, 406 Babbidge Rd., Unit 1020, Storrs, CT, 06269-1020, USA.

Experimental evidence is given that the perceptual system adapts to repetitive task execution in a perceptual two-choice judgment task. Participants were tested with respect to their perception of opportunities for plank grasping. Participants had to report whether planks were perceived as objects being graspable with either one hand or two hands. When the plank size was gradually increased and subsequently decreased, transitions from one hand judgments to two hands judgments and vice versa were observed. Analysis of the transition scores revealed that the perceptual judgments were body-scaled, as it is known in the literature. However, judgments were also found to be context dependent. Judgment transition scores were affected in a systematic way by the kind of and the number of previously made judgments. The latter quantitative impact was observed in three related experiments and suggests that perceptual judgments about opportunities for action adapt to task repetition. Overall, the experimental findings are consistent with the predictions of a dynamical systems model, which assumes that perceptual judgments are emergent properties of a self-organizing process that involves inhibitory top-down feedback.
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http://dx.doi.org/10.1007/s00221-016-4677-6DOI Listing
September 2016

Three-factor models versus time series models: quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data.

Math Med Biol 2017 06;34(2):177-191

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

Signal integration determines cell fate on the cellular level, affects cognitive processes and affective responses on the behavioural level, and is likely to be involved in psychoneurobiological processes underlying mood disorders. Interactions between stimuli may subjected to time effects. Time-dependencies of interactions between stimuli typically lead to complex cell responses and complex responses on the behavioural level. We show that both three-factor models and time series models can be used to uncover such time-dependencies. However, we argue that for short longitudinal data the three factor modelling approach is more suitable. In order to illustrate both approaches, we re-analysed previously published short longitudinal data sets. We found that in human embryonic kidney 293 cells cells the interaction effect in the regulation of extracellular signal-regulated kinase (ERK) 1 signalling activation by insulin and epidermal growth factor is subjected to a time effect and dramatically decays at peak values of ERK activation. In contrast, we found that the interaction effect induced by hypoxia and tumour necrosis factor-alpha for the transcriptional activity of the human cyclo-oxygenase-2 promoter in HEK293 cells is time invariant at least in the first 12-h time window after stimulation. Furthermore, we applied the three-factor model to previously reported animal studies. In these studies, memory storage was found to be subjected to an interaction effect of the beta-adrenoceptor agonist clenbuterol and certain antagonists acting on the alpha-1-adrenoceptor / glucocorticoid-receptor system. Our model-based analysis suggests that only if the antagonist drug is administer in a critical time window, then the interaction effect is relevant.
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http://dx.doi.org/10.1093/imammb/dqw001DOI Listing
June 2017

Affordance-based perception-action dynamics: A model of visually guided braking.

Psychol Rev 2016 Apr 15;123(3):305-23. Epub 2016 Feb 15.

Center for the Ecological Study of Perception and Action, Department of Psychological Sciences, University of Connecticut.

Behavioral dynamics is a framework for understanding adaptive behavior as arising from the self-organizing interaction between animal and environment. The methods of nonlinear dynamics provide a language for describing behavior that is both stable and flexible. Behavioral dynamics has been criticized for ignoring the animal's sensitivity to its own capabilities, leading to the development of an alternative framework: affordance-based control. Although it is theoretically sound and empirically motivated, affordance-based control has resisted characterization in terms of nonlinear dynamics. Here, we provide a dynamical description of affordance-based control, extending behavioral dynamics to meet its criticisms. We propose a general modeling strategy consistent with both theories. We use visually guided braking as a representative behavior and construct a novel dynamical model. This model demonstrates the possibility of understanding visually guided action as respecting the limits of the actor's capabilities, while still being guided by informational variables associated with desired states of affairs. In addition to such "hard" constraints on behavior, our framework allows for the influence of "soft" constraints such as preference and comfort, opening a new area of inquiry in perception-action dynamics.
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http://dx.doi.org/10.1037/rev0000029DOI Listing
April 2016

On a Fitzhugh-Nagumo type model for the pulse-like jasmonate defense response in plants.

Math Biosci 2016 Mar 13;273:80-90. Epub 2016 Jan 13.

Center for the Ecological Study of Perception and Action, University of Connecticut, 406 Babbidge Road, Storrs, CT 06269, USA; Department of Physics, University of Connecticut, 2152 Hillside Road, Storrs, CT 06269, USA. Electronic address:

A mechanistic model of the Fitzhugh-Nagumo type is proposed for the pulse-like jasmonate response in plants. The model is composed of a bistable signaling pathway coupled to a negative feedback loop. The bistable signaling pathway describes a recently discovered positive feedback loop involving jasmonate and the MYC2 transcription factor regulating promoter activity during plant defense. The negative feedback loop is assumed to reflect a second jasmonate-dependent signaling pathway that is also used for ethylene signaling. The impact of the negative feedback loop is to destroy the high-level jasmonate fixed-point of the bistable jasmonate/MYC2 module. As a result, the high-level state becomes a ghost attractor and the jasmonate defense response becomes pulse-like.
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http://dx.doi.org/10.1016/j.mbs.2016.01.001DOI Listing
March 2016

Front waves in the early RNA world: The Schlögl model and the logistic growth model.

Authors:
T D Frank

J Theor Biol 2016 Mar 29;392:62-8. Epub 2015 Dec 29.

Center for the Ecological Study of Perception and Action, University of Connecticut, 406 Babbidge Road, Storrs, CT 06269, USA. Electronic address:

Front wave solutions of nonlinear reaction-diffusion models describing the spatio-temporal growth of RNA populations in the early RNA world are discussed. A two-variable model for RNA enzymes and enzyme complex molecules as well as single-variable models obtained via adiabatic elimination of the complex molecules are considered. In both models, the focus is on enzyme diffusion in one spatial dimension, assuming that the diffusion of complex molecules can be neglected. It is shown that one of the single-variable models corresponds to a Schlögl model of front propagation. In general, for the single-variable models it is found that front speed corresponds to the minimal speed of traveling fronts. In contrast, the two-variable model exhibits even slower front propagation. Front propagation might be an important factor in competitive evolutionary processes in the early RNA world.
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http://dx.doi.org/10.1016/j.jtbi.2015.11.027DOI Listing
March 2016

Perception adapts via top-down regulation to task repetition: A Lotka-Volterra-Haken modeling analysis of experimental data.

Authors:
T D Frank

J Integr Neurosci 2016 Mar 18;15(1):67-79. Epub 2015 Dec 18.

1 Center for the Ecological Study of Perception and Action, Department of Psychology, University of Connecticut, 406 Babbidge Road, Storrs, CT 06269, USA.

Two experiments are reported in which participants perceived different physical quantities: size and speed. The perceptual tasks were performed in the context of motor performance problems. Participants perceived the size of objects in order to grasp the objects single handed or with both hands. Likewise, participants perceived the speed of a moving treadmill in order to control walking or running at that speed. In both experiments, the perceptual tasks were repeatedly performed by the participants while the to-be-perceived quantity was gradually varied from small to large objects (Experiment 1) and from low to high speeds (Experiment 2). Hysteresis with negative sign was found when participants were not allowed to execute the motor component, that is, when the execution stage was decoupled from the planning stage. No such effect was found in the control condition, when participants were allowed to execute the motor action. Using a Lotka-Volterra-Haken model for two competing neural populations, it is argued that the observations are consistent with the notion that the repetitions induce an adaptation effect of the perceptual system via top-down regulation. Moreover, the amount of synaptic modulation involved in the adaptation is estimated from participant data.
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http://dx.doi.org/10.1142/S0219635216500059DOI Listing
March 2016

On the Interplay between Order Parameter Dynamics and System Parameter Dynamics in Human Perceptual-Cognitive-Behavioral Systems.

Authors:
T D Frank

Nonlinear Dynamics Psychol Life Sci 2015 Apr;19(2):111-46

University of Connecticut, Storrs, CT.

Previous research has demonstrated that perceiving, thinking, and acting are human activities that correspond to self-organized patterns. The emergence of such patterns can be completely described in terms of the dynamics of the pattern amplitudes, which are referred to as order parameters. The patterns emerge at bifurcations points when certain system parameters internal and external to a human agent exceed critical values. At issue is how one might study the order parameter dynamics for sequences of consecutive, emergent perceptual, cognitive, or behavioral activities. In particular, these activities may in turn impact the system parameters that have led to the emergence of the activities in the first place. This interplay between order parameter dynamics and system parameter dynamics is discussed in general and formulated in mathematical terms. Previous work that has made use of this two-tiered framework of order parameter and system parameter dynamics are briefly addressed. As an application, a model for perception under functional fixedness is presented. Finally, it is argued that the phenomena that emerge in this framework and can be observed when human agents perceive, think, and act are just as likely to occur in pattern formation systems of the inanimate world. Consequently, these phenomena do not necessarily have a neurophysiological basis but should instead be understood from the perspective of the theory of self-organization.
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April 2015

Interplay between order-parameter and system parameter dynamics: considerations on perceptual-cognitive-behavioral mode-mode transitions exhibiting positive and negative hysteresis and on response times.

J Biol Phys 2015 Jun 3;41(3):257-92. Epub 2015 Mar 3.

Center for the Ecological Study of Perception and Action, Department of Psychology, University of Connecticut, 406 Babbidge Road, Unit 1020, Storrs, CT, 06269, USA,

A mathematical model is presented for the emergence of perceptual-cognitive-behavioral modes in psychophysical experiments in which participants are confronted with two alternatives. The model is based on the theory of self-organization and, in particular, the order parameter concept such that the emergence of a mode is conceptualized as an instability leading to the emergence of an appropriately defined order parameter. The order parameter model is merged with a second model that describes adaptation in terms of a system parameter dynamics. It is shown that the two-component model predicts hysteretic mode-mode transitions when control parameters are increased or decreased beyond critical values. The two-component model can account for both positive and negative hysteresis effects due to the interaction between order parameter and system parameter dynamics. Moreover, the model-based analysis reveals that response time curves look rather flat when response times are relatively decoupled from the mode-mode transition phenomenon. In general, response time curves exhibit a peaked close to the mode-mode transition point. In this context, the possibility is discussed that such peaked response time curves belong to the class of critical phenomena of self-organizing systems. In order to illustrate the relevance of peaked response time curves for future research and research reported in the past, results from a perceptual judgment experiment are reported, in which participants judged their ability to stand on a tilted slope for various angles of inclination. Response time curves were found that exhibited a peak around the mode-mode-transition points between "yes" and "no" responses.
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http://dx.doi.org/10.1007/s10867-015-9378-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456489PMC
June 2015

Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gate.

Cell Mol Life Sci 2015 Jun 20;72(12):2431-43. Epub 2015 Feb 20.

Systems Biology Ireland, University College Dublin, Dublin 4, Ireland.

Cyclooxygenase 2 (COX2), a key regulatory enzyme of the prostaglandin/eicosanoid pathway, is an important target for anti-inflammatory therapy. It is highly induced by pro-inflammatory cytokines in a Nuclear factor kappa B (NFκB)-dependent manner. However, the mechanisms determining the amplitude and dynamics of this important pro-inflammatory event are poorly understood. Furthermore, there is significant difference between human and mouse COX2 expression in response to the inflammatory stimulus tumor necrosis factor alpha (TNFα). Here, we report the presence of a molecular logic AND gate composed of two NFκB response elements (NREs) which controls the expression of human COX2 in a switch-like manner. Combining quantitative kinetic modeling and thermostatistical analysis followed by experimental validation in iterative cycles, we show that the human COX2 expression machinery regulated by NFκB displays features of a logic AND gate. We propose that this provides a digital, noise-filtering mechanism for a tighter control of expression in response to TNFα, such that a threshold level of NFκB activation is required before the promoter becomes active and initiates transcription. This NFκB-regulated AND gate is absent in the mouse COX2 promoter, most likely contributing to its differential graded response in promoter activity and protein expression to TNFα. Our data suggest that the NFκB-regulated AND gate acts as a novel mechanism for controlling the expression of human COX2 to TNFα, and its absence in the mouse COX2 provides the foundation for further studies on understanding species-specific differential gene regulation.
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http://dx.doi.org/10.1007/s00018-015-1850-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4439527PMC
June 2015

Non-equilibrium thermodynamical description of rhythmic motion patterns of active systems: a canonical-dissipative approach.

Biosystems 2015 Feb 22;128:26-36. Epub 2015 Jan 22.

Center for the Ecological Study of Perception and Action, Department of Psychology, University of Connecticut, 406 Babbidge Road, Storrs, CT 06269, USA. Electronic address:

We derive explicit expressions for the non-equilibrium thermodynamical variables of a canonical-dissipative limit cycle oscillator describing rhythmic motion patterns of active systems. These variables are statistical entropy, non-equilibrium internal energy, and non-equilibrium free energy. In particular, the expression for the non-equilibrium free energy is derived as a function of a suitable control parameter. The control parameter determines the Hopf bifurcation point of the deterministic active system and describes the effective pumping of the oscillator. In analogy to the equilibrium free energy of the Landau theory, it is shown that the non-equilibrium free energy decays as a function of the control parameter. In doing so, a similarity between certain equilibrium and non-equilibrium phase transitions is pointed out. Data from an experiment on human rhythmic movements is presented. Estimates for pumping intensity as well as the thermodynamical variables are reported. It is shown that in the experiment the non-equilibrium free energy decayed when pumping intensity was increased, which is consistent with the theory. Moreover, pumping intensities close to zero could be observed at relatively slow intended rhythmic movements. In view of the Hopf bifurcation underlying the limit cycle oscillator model, this observation suggests that the intended limit cycle movements were actually more similar to trajectories of a randomly perturbed stable focus.
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http://dx.doi.org/10.1016/j.biosystems.2015.01.002DOI Listing
February 2015

Deep-water microbialites of the Mesoproterozoic Dismal Lakes Group: microbial growth, lithification, and implications for coniform stromatolites.

Geobiology 2015 Jan 29;13(1):15-32. Epub 2014 Oct 29.

Geology Department, Gustavus Adolphus College, St. Peter, MN, USA.

Offshore facies of the Mesoproterozoic Sulky Formation, Dismal Lakes Group, arctic Canada, preserve microbialites with unusual morphology. These microbialites grew in water depths greater than several tens of meters and correlate with high-relief conical stromatolites of the more proximal September Lake reef complex. The gross morphology of these microbial facies consists of ridge-like vertical supports draped by concave-upward, subhorizontal elements, resulting in tent-shaped cuspate microbialites with substantial primary void space. Morphological and petrographic analyses suggest a model wherein penecontemporaneous upward growth of ridge elements and development of subhorizontal draping elements initially resulted in a buoyantly supported, unlithified microbial form. Lithification began via precipitation within organic elements during microbialite growth. Mineralization either stabilized or facilitated collapse of initially neutrally buoyant microbialite forms. Microbial structures and breccias were then further stabilized by precipitation of marine herringbone cement. During late-stage diagenesis, remaining void space was occluded by ferroan dolomite cement. Cuspate microbialites are most similar to those found in offshore facies of Neoarchean carbonate platforms and to unlithified, buoyantly supported microbial mats in modern ice-covered Antarctic lakes. We suggest that such unusual microbialite morphologies are a product of the interaction between motile and non-motile communities under nutrient-limiting conditions, followed by early lithification, which served to preserve the resultant microbial form. The presence of marine herringbone cement, commonly associated with high dissolved inorganic carbon (DIC), low O2 conditions, also suggests growth in association with reducing environments at or near the seafloor or in conjunction with a geochemical interface. Predominance of coniform stromatolite forms in the Proterozoic--across a variety of depositional environments--may thus reflect a combination of heterogeneous nutrient distribution, potentially driven by variable redox conditions, and an elevated carbonate saturation state, which permits preservation of these unusual microbialite forms.
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http://dx.doi.org/10.1111/gbi.12114DOI Listing
January 2015

Symmetry and order parameter dynamics of the human odometer.

Biol Cybern 2015 Feb 9;109(1):63-73. Epub 2014 Sep 9.

Center for the Ecological Study of Perception and Action, Department of Psychology, University of Connecticut, Storrs, CT, USA,

Bipedal gaits have been classified on the basis of the group symmetry of the minimal network of identical differential equations (alias cells) required to model them. Primary bipedal gaits (e.g., walk, run) are characterized by dihedral symmetry, whereas secondary bipedal gaits (e.g., gallop-walk, gallop- run) are characterized by a lower, cyclic symmetry. This fact has been used in tests of human odometry (e.g., Turvey et al. in P Roy Soc Lond B Biol 276:4309-4314, 2009, J Exp Psychol Hum Percept Perform 38:1014-1025, 2012). Results suggest that when distance is measured and reported by gaits from the same symmetry class, primary and secondary gaits are comparable. Switching symmetry classes at report compresses (primary to secondary) or inflates (secondary to primary) measured distance, with the compression and inflation equal in magnitude. The present research (a) extends these findings from overground locomotion to treadmill locomotion and (b) assesses a dynamics of sequentially coupled measure and report phases, with relative velocity as an order parameter, or equilibrium state, and difference in symmetry class as an imperfection parameter, or detuning, of those dynamics. The results suggest that the symmetries and dynamics of distance measurement by the human odometer are the same whether the odometer is in motion relative to a stationary ground or stationary relative to a moving ground.
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http://dx.doi.org/10.1007/s00422-014-0627-1DOI Listing
February 2015

Partner testing, linkage to care, and HIV-free survival in a program to prevent parent-to-child transmission of HIV in the Highlands of Papua New Guinea.

Glob Health Action 2014 27;7:24995. Epub 2014 Aug 27.

Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA.

Background: To eliminate new pediatric HIV infections, interventions that facilitate adherence, including those that minimize stigma, enhance social support, and mitigate the influence of poverty, will likely be required in addition to combination antiretroviral therapy (ART). We examined the relationship between partner testing and infant outcome in a prevention of parent-to-child transmission of HIV program, which included a family-centered case management approach and a supportive environment for partner disclosure and testing.

Design: We analyzed routinely collected data for women and infants who enrolled in the parent-to-child transmission of HIV program at Goroka Family Clinic, Eastern Highlands Provincial Hospital, Papua New Guinea, from 2007 through 2011.

Results: Two hundred and sixty five women were included for analysis. Of these, 226 (85%) had a partner, 127 (56%) of whom had a documented HIV test. Of the 102 HIV-infected partners, 81 (79%) had been linked to care. In adjusted analyses, we found a significantly higher risk of infant death, infant HIV infection, or loss to follow-up among mother-infant pairs in which the mother reported having no partner or a partner who was not tested or had an unknown testing status. In a second multivariable analysis, infants born to women with more time on ART or who enrolled in the program in later years experienced greater HIV-free survival.

Conclusions: In a program with a patient-oriented and family-centered approach to prevent vertical HIV transmission, the majority of women's partners had a documented HIV test and, if positive, linkage to care. Having a tested partner was associated with program retention and HIV-free survival for infants. Programs aiming to facilitate diagnosis disclosure, partner testing, and linkage to care may contribute importantly to the elimination of pediatric HIV.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149744PMC
http://dx.doi.org/10.3402/gha.v7.24995DOI Listing
May 2015

Balance affects prism adaptation: evidence from the latent aftereffect.

Exp Brain Res 2013 Dec 26;231(4):425-32. Epub 2013 Sep 26.

Department of Psychology, Center for the Ecological Study of Perception and Action, University of Connecticut, 406 Babbidge Road, Storrs, CT, 06269-1020, USA,

In prism adaptation experiments, the effect on throwing to a target is reduced (primary aftereffect is smaller) when the throwing condition with prisms removed (first test phase) is different from the throwing condition with prisms (the training phase). The missing adaptation, however, can be revealed through further testing (second test phase) in which the throwing condition during training is fully reinstated. We studied throwing underhand to a target flush with the floor. During training, participants wore left-shifting prism glasses while standing on the floor (Group 1) or on a balance board (Groups 2 and 3). Tests 1 and 2 following training involved the same underhand throwing. For Group 2, Test 1 was on the balance board and Test 2 on the ground; for Group 3, the order was reversed; and for Group 1, both tests were on the ground. The Group 3 Test 1 aftereffect was smaller, and the Test 2 aftereffect was larger than the respective tests for Groups 1 and 2, with the aftereffect sum the same for all three groups. A parallel was noted between prism adaptation and implicit memory: whether given training (study) conditions lead to better or poorer persistence of adaptation (memory performance) at test depends on the fit between the conditions at test relative to the conditions at training (study). In the general memory case, those conditions will involve nonobvious contributors to memory performance, analogous to the support for upright standing in the adaptation of the visual system to prismatic distortion investigated in the present research.
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http://dx.doi.org/10.1007/s00221-013-3707-xDOI Listing
December 2013

Negative hysteresis in the behavioral dynamics of the affordance "graspable".

Atten Percept Psychophys 2013 Jul;75(5):1075-91

Department of Psychology, Marymount University, 2807 North Glebe Road, Arlington, VA 22207, USA.

One commonly perceives whether a visible object will afford grasping with one hand or with both hands. In experiments in which differently sized objects of a fixed type are presented, the transition from using one of these manual modes to the other depends on the ratio of object size to hand span and on the presentation sequence, with size increasing versus decreasing. Conventional positive hysteresis (i.e., a larger transition ratio for the increasing sequence) can be accommodated by the order parameter dynamics that typify self-organizing systems (Lopresti-Goodman, Turvey, and Frank, Attention, Perception, & Psychophysics 73:1948-1965, 2011). Here we identified and addressed conditions of unconventional negative hysteresis (i.e., a larger transition ratio for the decreasing sequence). They suggest a second control parameter in the self-organization of affordance perception, one that is seemingly regulated by inhibitory dynamics occurring in the agent-task-environment system. Our experimental results and modeling extend the investigation of affordance perception within dynamical systems theory.
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http://dx.doi.org/10.3758/s13414-013-0437-xDOI Listing
July 2013

Measuring group synchrony: a cluster-phase method for analyzing multivariate movement time-series.

Front Physiol 2012 19;3:405. Epub 2012 Oct 19.

Department of Psychology, Center for Cognition, Action, and Perception, University of Cincinnati Cincinnati, OH, USA.

A new method for assessing group synchrony is introduced as being potentially useful for objectively determining degree of group cohesiveness or entitativity. The cluster-phase method of Frank and Richardson (2010) was used to analyze movement data from the rocking chair movements of six-member groups who rocked their chairs while seated in a circle facing the center. In some trials group members had no information about others' movements (their eyes were shut) or they had their eyes open and gazed at a marker in the center of the group. As predicted, the group level synchrony measure was able to distinguish between situations where synchrony would have been possible and situations where it would be impossible. Moreover, other aspects of the analysis illustrated how the cluster phase measures can be used to determine the type of patterning of group synchrony, and, when integrated with multi-level modeling, can be used to examine individual-level differences in synchrony and dyadic level synchrony as well.
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http://dx.doi.org/10.3389/fphys.2012.00405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475977PMC
October 2012

Capturing and quantifying the dynamics of valenced emotions and valenced events of the organism-environment system.

Nonlinear Dynamics Psychol Life Sci 2012 Oct;16(4):397-427

University of Connecticut, Storrs, CT, USA.

The events we encounter and the emotions we experience are valenced-they are positively or negatively charged. Although these occurrences seem to be distributed irregularly throughout the day, the two experiments presented here reveal systematicity in the temporal dynamics of affective experience using a variety of time-series analyses. In Experiment 1, participants used a portable button to respond to event valence (the positive or negative charge of an event in the environment) or affective valence (one's positive or negative feeling at the time of responding). This methodology yields signed response durations, indexing the valence and intensity of an occurrence, and inter-response intervals, indexing their distribution. These measures revealed that valenced occurrences are correlated with both temporally proximal and remote occurrences. Experiment 2 validated the methodology employed in Experiment 1 using artificial, laboratory-created event structures. Implications of dynamical approaches to understanding emotion are discussed.
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October 2012

Unifying mass-action kinetics and Newtonian mechanics by means of Nambu brackets.

Authors:
T D Frank

J Biol Phys 2011 Sep 17;37(4):375-85. Epub 2011 Jun 17.

We demonstrate that elementary biochemical reactions defined by mass-action kinetics satisfy a particular Nambu structure. To this end, we express biochemical reaction equations in terms of Nambu brackets and certain ω-factors. The ω-factors account for the fact that mass-action kinetics exhibits in general flow fields with finite divergence. The proposed approach by means of Nambu brackets and ω-factors unifies divergence freeflow fields of Newtonian mechanics and flow fields with finite divergence of mass-action kinetics.
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http://dx.doi.org/10.1007/s10867-011-9230-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169697PMC
September 2011

Catching transcriptional regulation by thermostatistical modeling.

Phys Biol 2012 Aug 7;9(4):045007. Epub 2012 Aug 7.

Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.

Gene expression is frequently regulated by multiple transcription factors (TFs). Thermostatistical methods allow for a quantitative description of interactions between TFs, RNA polymerase and DNA, and their impact on the transcription rates. We illustrate three different scales of the thermostatistical approach: the microscale of TF molecules, the mesoscale of promoter energy levels and the macroscale of transcriptionally active and inactive cells in a cell population. We demonstrate versatility of combinatorial transcriptional activation by exemplifying logic functions, such as AND and OR gates. We discuss a metric for cell-to-cell transcriptional activation variability known as Fermi entropy. Suitability of thermostatistical modeling is illustrated by describing the experimental data on transcriptional induction of NFκB and the c-Fos protein.
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http://dx.doi.org/10.1088/1478-3975/9/4/045007DOI Listing
August 2012

Human odometry verifies the symmetry perspective on bipedal gaits.

J Exp Psychol Hum Percept Perform 2012 Aug 16;38(4):1014-25. Epub 2012 Apr 16.

Center for the Ecological Study of Perception and Action, Unit 1020, 406 Babbidge Rd., University of Connecticut, Storrs, CT 06269-1020.

Bipedal gaits have been classified on the basis of the group symmetry of the minimal network of identical differential equations (alias cells) required to model them. Primary gaits are characterized by dihedral symmetry, whereas secondary gaits are characterized by a lower, cyclic symmetry. This fact was used in a test of human odometry. Results suggest that when distance is measured and reported by gaits from the same symmetry class, primary and secondary gaits are comparable. Switching symmetry classes at report compresses (primary to secondary) or inflates (secondary to primary) measured distance, with the compression and inflation equal in magnitude. Lessons are drawn from modeling the dynamics of behaviors executed in parallel (e.g., interlimb coordination) to model the dynamics of human odometry, in which the behaviors are executed sequentially. The major observations are characterized in terms of a dynamics of sequentially coupled measure and report phases, with relative velocity as an order parameter, or equilibrium state, and difference in symmetry class as an imperfection parameter, or detuning, of that dynamic.
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http://dx.doi.org/10.1037/a0027853DOI Listing
August 2012

Versatility of cooperative transcriptional activation: a thermodynamical modeling analysis for greater-than-additive and less-than-additive effects.

PLoS One 2012 10;7(4):e34439. Epub 2012 Apr 10.

Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.

We derive a statistical model of transcriptional activation using equilibrium thermodynamics of chemical reactions. We examine to what extent this statistical model predicts synergy effects of cooperative activation of gene expression. We determine parameter domains in which greater-than-additive and less-than-additive effects are predicted for cooperative regulation by two activators. We show that the statistical approach can be used to identify different causes of synergistic greater-than-additive effects: nonlinearities of the thermostatistical transcriptional machinery and three-body interactions between RNA polymerase and two activators. In particular, our model-based analysis suggests that at low transcription factor concentrations cooperative activation cannot yield synergistic greater-than-additive effects, i.e., DNA transcription can only exhibit less-than-additive effects. Accordingly, transcriptional activity turns from synergistic greater-than-additive responses at relatively high transcription factor concentrations into less-than-additive responses at relatively low concentrations. In addition, two types of re-entrant phenomena are predicted. First, our analysis predicts that under particular circumstances transcriptional activity will feature a sequence of less-than-additive, greater-than-additive, and eventually less-than-additive effects when for fixed activator concentrations the regulatory impact of activators on the binding of RNA polymerase to the promoter increases from weak, to moderate, to strong. Second, for appropriate promoter conditions when activator concentrations are increased then the aforementioned re-entrant sequence of less-than-additive, greater-than-additive, and less-than-additive effects is predicted as well. Finally, our model-based analysis suggests that even for weak activators that individually induce only negligible increases in promoter activity, promoter activity can exhibit greater-than-additive responses when transcription factors and RNA polymerase interact by means of three-body interactions. Overall, we show that versatility of transcriptional activation is brought about by nonlinearities of transcriptional response functions and interactions between transcription factors, RNA polymerase and DNA.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0034439PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3323628PMC
October 2012