Control of stochastic and induced switching in biophysical networks

Noise caused by fluctuations at the molecular level is a fundamental part of intracellular processes. While the response of biological systems to noise has been studied extensively, there has been limited understanding of how to exploit it to induce a desired cell state. Here we present a scalable, quantitative method based on the Freidlin-Wentzell action to predict and control noise-induced switching between different states in genetic networks that, conveniently, can also control transitions between stable states in the absence of noise. We apply this methodology to models of cell differentiation and show how predicted manipulations of tunable factors can induce lineage changes, and further utilize it to identify new candidate strategies for cancer therapy in a cell death pathway model. This framework offers a systems approach to identifying the key factors for rationally manipulating biophysical dynamics, and should also find use in controlling other classes of noisy complex networks.Comment: A ready-to-use code package implementing the method described here is available from the authors upon reques

Tandem androgenic and psychological shifts in male reproductive effort following a manipulated “win” or “loss” in a sporting competition

© 2018, The Author(s). Male-male competition is involved in inter- and intrasexual selection, with both endocrine and psychological factors presumably contributing to reproductive success in human males. We examined relationships among men’s naturally occurring testosterone, their self-perceived mate value (SPMV), self-esteem, sociosexuality, and expected likelihood of approaching attractive women versus situations leading to child involvement. We then monitored changes in these measures in male rowers (N = 38) from Cambridge, UK, following a manipulated “win” or “loss” as a result of an indoor rowing contest. Baseline results revealed that men with heightened testosterone and SPMV values typically had greater inclinations toward engaging in casual sexual relationships and a higher likelihood of approaching attractive women in a hypothetical social situation. As anticipated, both testosterone and SPMV increased following a manipulated “victory” and were associated with heightened sociosexuality, and increased expectations toward approaching attractive women versus individuals who would involve them in interacting with children after the race. SPMV and self-esteem appeared to mediate some of the effects of testosterone on post-race values. These findings are considered in the broader context of individual trade-offs between mating and parental effort and a model of the concurrent and dynamic androgenic and psychological influences contributing to male reproductive effort and success

A Repeated Measures Experiment of Green Exercise to Improve Self-Esteem in UK School Children

Exercising in natural, green environments creates greater improvements in adult's self-esteem than exercise undertaken in urban or indoor settings. No comparable data are available for children. The aim of this study was to determine whether so called 'green exercise' affected changes in self-esteem; enjoyment and perceived exertion in children differently to urban exercise. We assessed cardiorespiratory fitness (20 m shuttle-run) and self-reported physical activity (PAQ-A) in 11 and 12 year olds (n = 75). Each pupil completed two 1.5 mile timed runs, one in an urban and another in a rural environment. Trials were completed one week apart during scheduled physical education lessons allocated using a repeated measures design. Self-esteem was measured before and after each trial, ratings of perceived exertion (RPE) and enjoyment were assessed after completing each trial. We found a significant main effect (F (1,74), = 12.2, p<0.001), for the increase in self-esteem following exercise but there was no condition by exercise interaction (F (1,74), = 0.13, p = 0.72). There were no significant differences in perceived exertion or enjoyment between conditions. There was a negative correlation (r = -0.26, p = 0.04) between habitual physical activity and RPE during the control condition, which was not evident in the green exercise condition (r = -0.07, p = 0.55). Contrary to previous studies in adults, green exercise did not produce significantly greater increases in self-esteem than the urban exercise condition. Green exercise was enjoyed more equally by children with differing levels of habitual physical activity and has the potential to engage less active children in exercise. © 2013 Reed et al

Effects of relaxation interventions during pregnancy on maternal mental health, and pregnancy and newborn outcomes:A systematic review and meta-analysis

BACKGROUND: Stress during pregnancy is detrimental to maternal health, pregnancy and birth outcomes and various preventive relaxation interventions have been developed. This systematic review and meta-analysis aimed to evaluate their effectiveness in terms of maternal mental health, pregnancy and birth outcomes.METHOD: The protocol for this review is published on PROSPERO with registration number CRD42020187443. A systematic search of major databases was conducted. Primary outcomes were maternal mental health problems (stress, anxiety, depression), and pregnancy (gestational age, labour duration, delivery mode) and birth outcomes (birth weight, Apgar score, preterm birth). Randomized controlled trials or quasi-experimental studies were eligible. Meta-analyses using a random-effects model was conducted for outcomes with sufficient data. For other outcomes a narrative review was undertaken.RESULT: We reviewed 32 studies comprising 3,979 pregnant women aged 18 to 40 years. Relaxation interventions included yoga, music, Benson relaxation, progressive muscle relaxation (PMR), deep breathing relaxation (BR), guided imagery, mindfulness and hypnosis. Intervention duration ranged from brief experiment (~10 minutes) to 6 months of daily relaxation. Meta-analyses showed relaxation therapy reduced maternal stress (-4.1 points; 95% Confidence Interval (CI): -7.4, -0.9; 9 trials; 1113 participants), anxiety (-5.04 points; 95% CI: -8.2, -1.9; 10 trials; 1965 participants) and depressive symptoms (-2.3 points; 95% CI: -3.4, -1.3; 7 trials; 733 participants). Relaxation has also increased offspring birth weight (80 g, 95% CI: 1, 157; 8 trials; 1239 participants), explained by PMR (165g, 95% CI: 100, 231; 4 trials; 587 participants) in sub-group analysis. In five trials evaluating maternal physiological responses, relaxation therapy optimized blood pressure, heart rate and respiratory rate. Four trials showed relaxation therapy reduced duration of labour. Apgar score only improved significantly in two of six trials. One of three trials showed a significant increase in birth length, and one of three trials showed a significant increase in gestational age. Two of six trials examining delivery mode showed significantly increased spontaneous vaginal delivery and decreased instrumental delivery or cesarean section following a relaxation intervention.DISCUSSION: We found consistent evidence for beneficial effects of relaxation interventions in reducing maternal stress, improving mental health, and some evidence for improved maternal physiological outcomes. In addition, we found a positive effect of relaxation interventions on birth weight and inconsistent effects on other pregnancy or birth outcomes. High quality adequately powered trials are needed to examine impacts of relaxation interventions on newborns and offspring health outcomes.CONCLUSION: In addition to benefits for mothers, relaxation interventions provided during pregnancy improved birth weight and hold some promise for improving newborn outcomes; therefore, this approach strongly merits further research.</p

Moving the needle: Employing deep reinforcement learning to push the boundaries of coarse-grained vaccine models

Highly mutable infectious disease pathogens (hm-IDPs) such as HIV and influenza evolve faster than the human immune system can contain them, allowing them to circumvent traditional vaccination approaches and causing over one million deaths annually. Agent-based models can be used to simulate the complex interactions that occur between immune cells and hm-IDP-like proteins (antigens) during affinity maturation&mdash;the process by which antibodies evolve. Compared to existing experimental approaches, agent-based models offer a safe, low-cost, and rapid route to study the immune response to vaccines spanning a wide range of design variables. However, the highly stochastic nature of affinity maturation and vast sequence space of hm-IDPs render brute force searches intractable for exploring all pertinent vaccine design variables and the subset of immunization protocols encompassed therein. To address this challenge, we employed deep reinforcement learning to drive a recently developed agent-based model of affinity maturation to focus sampling on immunization protocols with greater potential to improve the chosen metrics of protection, namely the broadly neutralizing antibody (bnAb) titers or fraction of bnAbs produced. Using this approach, we were able to coarse-grain a wide range of vaccine design variables and explore the relevant design space. Our work offers new testable insights into how vaccines should be formulated to maximize protective immune responses to hm-IDPs and how they can be minimally tailored to account for major sources of heterogeneity in human immune responses and various socioeconomic factors. Our results indicate that the first 3 to 5 immunizations, depending on the metric of protection, should be specially tailored to achieve a robust protective immune response, but that beyond this point further immunizations require only subtle changes in formulation to sustain a durable bnAb response. &nbsp;</p

Spin chirality on a two-dimensional frustrated lattice

The collective behavior of interacting magnetic moments can be strongly influenced by the topology of the underlying lattice. In geometrically frustrated spin systems, interesting chiral correlations may develop that are related to the spin arrangement on triangular plaquettes. We report a study of the spin chirality on a two-dimensional geometrically frustrated lattice. Our new chemical synthesis methods allow us to produce large single crystal samples of KFe3(OH)6(SO4)2, an ideal Kagome lattice antiferromagnet. Combined thermodynamic and neutron scattering measurements reveal that the phase transition to the ordered ground-state is unusual. At low temperatures, application of a magnetic field induces a transition between states with different non-trivial spin-textures.Comment: 7 pages, 4 figure

Variable strength of forest stand attributes and weather conditions on the questing activity of Ixodes ricinus ticks over years in managed forests

Given the ever-increasing human impact through land use and climate change on the environment, we crucially need to achieve a better understanding of those factors that influence the questing activity of ixodid ticks, a major disease-transmitting vector in temperate forests. We investigated variation in the relative questing nymph densities of Ixodes ricinus in differently managed forest types for three years (2008–2010) in SW Germany by drag sampling. We used a hierarchical Bayesian modeling approach to examine the relative effects of habitat and weather and to consider possible nested structures of habitat and climate forces. The questing activity of nymphs was considerably larger in young forest successional stages of thicket compared with pole wood and timber stages. Questing nymph density increased markedly with milder winter temperatures. Generally, the relative strength of the various environmental forces on questing nymph density differed across years. In particular, winter temperature had a negative effect on tick activity across sites in 2008 in contrast to the overall effect of temperature across years. Our results suggest that forest management practices have important impacts on questing nymph density. Variable weather conditions, however, might override the effects of forest management practices on the fluctuations and dynamics of tick populations and activity over years, in particular, the preceding winter temperatures. Therefore, robust predictions and the detection of possible interactions and nested structures of habitat and climate forces can only be quantified through the collection of long-term data. Such data are particularly important with regard to future scenarios of forest management and climate warming

Influence of next-nearest-neighbor electron hopping on the static and dynamical properties of the 2D Hubbard model

Comparing experimental data for high temperature cuprate superconductors with numerical results for electronic models, it is becoming apparent that a hopping along the plaquette diagonals has to be included to obtain a quantitative agreement. According to recent estimations the value of the diagonal hopping $t'$ appears to be material dependent. However, the values for $t'$ discussed in the literature were obtained comparing theoretical results in the weak coupling limit with experimental photoemission data and band structure calculations. The goal of this paper is to study how $t'$ gets renormalized as the interaction between electrons, $U$, increases. For this purpose, the effect of adding a bare diagonal hopping $t'$ to the fully interacting two dimensional Hubbard model Hamiltonian is investigated using numerical techniques. Positive and negative values of $t'$ are analyzed. Spin-spin correlations, $n(\bf{k})$, $\langle n\rangle$ vs $\mu$, and local magnetic moments are studied for values of $U/t$ ranging from 0 to 6, and as a function of the electronic density. The influence of the diagonal hopping in the spectral function $A(\bf{k},\omega)$ is also discussed, and the changes in the gap present in the density of states at half-filling are studied. We introduce a new criterion to determine probable locations of Fermi surfaces at zero temperature from $n(\bf{k})$ data obtained at finite temperature. It appears that hole pockets at ${\bf{k}}=(\pi/2,\pi/2)$ may be induced for negative $t'$ while a positive $t'$ produces similar features at ${\bf{k}}=(\pi,0)$ and $(0,\pi)$. Comparisons with the standard 2D Hubbard ($t'=0$) model indicate that a negative $t'$ hopping amplitude appears to be dynamically generated. In general, we conclude that it is very dangerous to extract a bare parameter of the Hamiltonian $(t')$ from PES data whereComment: 9 pages (RevTex 3.0), 12 figures (postscript), files packed with uufile

A biophysical model of cell adhesion mediated by immunoadhesin drugs and antibodies

A promising direction in drug development is to exploit the ability of natural killer cells to kill antibody-labeled target cells. Monoclonal antibodies and drugs designed to elicit this effect typically bind cell-surface epitopes that are overexpressed on target cells but also present on other cells. Thus it is important to understand adhesion of cells by antibodies and similar molecules. We present an equilibrium model of such adhesion, incorporating heterogeneity in target cell epitope density and epitope immobility. We compare with experiments on the adhesion of Jurkat T cells to bilayers containing the relevant natural killer cell receptor, with adhesion mediated by the drug alefacept. We show that a model in which all target cell epitopes are mobile and available is inconsistent with the data, suggesting that more complex mechanisms are at work. We hypothesize that the immobile epitope fraction may change with cell adhesion, and we find that such a model is more consistent with the data. We also quantitatively describe the parameter space in which binding occurs. Our results point toward mechanisms relating epitope immobility to cell adhesion and offer insight into the activity of an important class of drugs.Comment: 13 pages, 5 figure

A pair of temperate sub-Neptunes transiting the star EPIC 212737443

We report the validation of a new planetary system around the K3 star EPIC 212737443 using a combination of K2 photometry, follow-up high resolution imaging and spectroscopy. The system consists of two sub-Neptune sized transiting planets with radii of 2.6R⊕, and 2.7R⊕, with orbital periods of 13.6 days and 65.5 days, equilibrium temperatures of 536 K and 316 K respectively. In the context of validated K2 systems, the outer planet has the longest precisely measured orbital period, as well as the lowest equilibrium temperature for a planet orbiting a star of spectral type earlier than M. The two planets in this system have a mutual Hill radius of ΔRH = 36, larger than most other known transiting multi-planet systems, suggesting the existence of another (possibly non-transiting) planet, or that the system is not maximally packed