Sunday, April 14, 2024

 

When Waddington meets Helmholtz: EPR-Net for constructing the potential landscapes of complex non-equilibrium systems



SCIENCE CHINA PRESS
Constructing energy landscapes through enhanced EPR workflow. 

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(A) THE PRIMARY OBJECTIVE IS TO CONSTRUCT THE ENERGY LANDSCAPE DEFINED THROUGH THE STEADY-STATE DISTRIBUTION OF THE SYSTEM. (B) CONSTRUCTING THE HIGH-DIMENSIONAL ENERGY LANDSCAPE USING THE EPR FRAMEWORK WITH PRIMITIVE VARIABLES. (C) CONSTRUCTING THE DIMENSIONALITY-REDUCED ENERGY LANDSCAPE USING EPR WITH PRESCRIBED REDUCED VARIABLES.

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CREDIT: ©SCIENCE CHINA PRESS




The concept of Waddington landscape, originally proposed by British developmental biologist Conrad Hal Waddington in 1957, has been influential in describing the dynamical evolution of cellular development. Waddington's metaphor of a ball rolling down a hill to represent cell differentiation has been widely adopted in epigenetics and developmental biology. However, quantitative characterization of these landscapes, particularly for high-dimensional systems, remains a challenging problem in computational biology.

Led by Professor Tiejun Li (from Peking University) and Dr. Wei Zhang (from Freie Universität Berlin and Zuse Institute Berlin), together with Yue Zhao (first author, PhD student from Peking University), the study introduces EPR-Net, a deep learning method that effectively tackles this challenge.                

This method leverages the unique mathematical insight that the negative gradient of Waddington landscape corresponds to an extended Helmholtz decomposition in the context of non-equilibrium systems. This insight, closely related to the entropy production rate (EPR) in statistical physics, is a breakthrough that has not be recognized previously.

The research team demonstrates the power of EPR-Net through its application to various biological models, including those exhibiting multiple stable points, limit cycles, and strange attractors. Enhanced EPR-Net, an extension of the method, is also introduced. The study showcases the effectiveness of enhanced EPR on benchmark problems and its superiority over other methods. It also provides a unified framework to address landscape construction, dimensionality reduction, and problems with variable coefficients.

EPR-Net offers computational efficiency, eliminates the need for boundary conditions, and provides a clear physical interpretation that links directly to the entropy production rate in statistical physics.

To address the challenge of visualizing high-dimensional landscapes, the researchers also developed a dimensionality reduction strategy using EPR-Net. This strategy has been applied to study an 8-dimensional limit cycle system, where it gives accurate projections which not only closely match the system’s equilibrium distribution but also reveal new delicate structures not observed before.

“EPR-Net, with its elegant mathematical foundation and convex structure, promises to be an effective strategy for constructing energy landscape functions of high-dimensional NESS systems." The researchers conclude. "We are currently exploring further extensions and applications of the method. We feel exciting because this powerful method has the potential to improve our understanding of many complex NESS systems by visualizing their potential landscapes."

See the article:

EPR-Net: constructing a non-equilibrium potential landscape via a variational force projection formulation

https://doi.org/10.1093/nsr/nwae052


(a) and (b) show the projected energy landscapes of an 8-dimensional limit cycle system, while (c) reveals the detailed structure of a small potential well outside the limit cycle, corresponding to a stable spiral point.

CREDIT

©Science China Press

 

Surprising role of female sex pheromone in crop pest: new biocontrol possibilities?



INRAE - NATIONAL RESEARCH INSTITUTE FOR AGRICULTURE, FOOD AND ENVIRONMENT
African cotton moth 

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AFRICAN COTTON MOTH

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CREDIT: INRAE - MICHEL RENOU




In animals, social interactions can have a pronounced influence on circadian rhythm, such as helping to regulate the timing of rest. For the circadian clock to function effectively, it must be entrained by local day-night cycles, a process that employs cues such as light and temperature.

 

Researchers at INRAE have been exploring how sociosexual interactions can modulate circadian rhythm. Elemental social interactions remain essential even in solitary animal species, such as the African cotton moth, Spodoptera littoralis. The latter is an agricultural pest whose caterpillars attack maize and legume crops. Adults live just 7 to 8 days, and thus adult males devote themselves exclusively to mating.

 

While studying S. littoralis, researchers observed that the circadian rhythm of males changed in the presence of females. Males can perceive female pheromones even across very long distances. Thus, females can remotely modulate the circadian rhythm of males such that the sexes are in synchrony during periods of mating, which favours reproductive success.

 

In S. littoralis, the pheromone gland synthesises diverse chemical compounds, but only one, (Z,E)-9,11-tetradecadienyl acetate (i.e., Z9E11-14Ac), can attract males. When males are exposed to Z9E11-14Ac, their circadian rhythms are altered, even in broad daylight. This result is the first of its kind: never before in a solitary animal species has a sociosexual interaction been shown to affect the circadian clock, let alone surpass light in its entrainment effects. The study’s discovery paves the way for new research into circadian synchronisation, including in mammals.

 

The black cutworm, Agrotis ipsilon, is a close relative of S. littoralis and exhibits a significant degree of niche overlap. Interestingly, while pheromones from A. ipsilon can modulate male circadian rhythm in S. littoralis, the two species do not mate.

 

The researchers are exploring how their findings can inform the development of biocontrol[1]practices targeting S. littoralis. The idea is that, since females do not respond strongly to their own pheromones, males could be exposed to pheromones in the morning (i.e., outside of the natural chemical communication window), which would modify their circadian rhythm for the day. As a result, the two sexes would be out of sync and less likely to meet and mate.

 


[1] A pillar of agroecology, biocontrol methods utilise knowledge about natural interactions among species to protect crops against pests and diseases.

CURSE MAGICK

After being insulted, writing down your feelings on paper then getting rid of it reduces anger



NAGOYA UNIVERSITY
Figure 1 

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PHYSICALLY DISPOSING OF A PIECE OF PAPER CONTAINING YOUR ANGRY THOUGHTS IN A SHREDDER (LEFT) EFFECTIVELY NEUTRALIZES THE ANGER, WHEREAS PUTTING IT IN A PLASTIC BOX (RIGHT) DOES NOT.

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CREDIT: YUTA KANAYA




A research group in Japan has discovered that writing down one's reaction to a negative incident on a piece of paper and then shredding it or throwing it away reduces feelings of anger. 

 

“We expected that our method would suppress anger to some extent,” lead researcher Nobuyuki Kawai said. “However, we were amazed that anger was eliminated almost entirely.” 

 

This research is important because controlling anger at home and in the workplace can reduce negative consequences in our jobs and personal lives. Unfortunately, many anger management techniques proposed by specialists lack empirical research support. They can also be difficult to recall when angry.  

 

The results of this study, published in Scientific Reports, are the culmination of years of previous research on the association between the written word and anger reduction. It builds on work showing how interactions with physical objects can control a person’s mood. 

 

For their project, Kawai and his graduate student Yuta Kanaya, both at the Graduate School of Informatics, Nagoya University, asked participants to write brief opinions about important social problems, such as whether smoking in public should be outlawed. They then told them that a doctoral student at Nagoya University would evaluate their writing.  

 

However, the doctoral students doing the evaluation were plants. Regardless of what the participants wrote, the evaluators scored them low on intelligence, interest, friendliness, logic, and rationality. To really drive home the point, the doctoral students also wrote the same insulting comment: “I cannot believe an educated person would think like this. I hope this person learns something while at the university”.  

 

After handing out these negative comments, the researchers asked the participants to write their thoughts on the feedback, focusing on what triggered their emotions. Finally, one group of participants was told to either dispose of the paper they wrote in a trash can or keep it in a file on their desk. A second group was told to destroy the document in a shredder or put it in a plastic box.  

 

The students were then asked to rate their anger after the insult and after either disposing of or keeping the paper. As expected, all participants reported a higher level of anger after receiving insulting comments. However, the anger levels of the individuals who discarded their paper in the trash can or shredded it returned to their initial state after disposing of the paper. Meanwhile, the participants who held on to a hard copy of the insult experienced only a small decrease in their overall anger.  

 

Kawai imagines using his research to help businesspeople who find themselves in stressful situations. “This technique could be applied in the moment by writing down the source of anger as if taking a memo and then throwing it away when one feels angry in a business situation,” he explained.  

 

Along with its practical benefits, this discovery may shed light on the origins of the Japanese cultural tradition known as hakidashisara (hakidashi refers to the purging or spitting out of something, and sara refers to a dish or plate) at the Hiyoshi shrine in Kiyosu, Aichi Prefecture, just outside of Nagoya. Hakidashisara is an annual festival where people smash small discs representing things that make them angry. Their findings may explain the feeling of relief that participants report after leaving the festival.

 

When and how does touch make a difference?


Psychology



RUHR-UNIVERSITY BOCHUM

Julian Packheiser 

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JULIAN PACKHEISER AND HIS COLLEAGUES HAVE ANALYSED OVER 130 STUDIES ON THE SUBJECT OF TOUCH.

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CREDIT: RUB, MARQUARD




Touch can do a lot of good – so far, so good. But to what extent do humans benefit from it? How much touch is allowed? Who should touch and where? When we experience physical contact – does it even have to be with another human? A research team from Bochum, Duisburg-Essen and Amsterdam analyzed over 130 international studies with around 10,000 participants to answer these questions. The researchers proved that what touch really does is alleviate pain, depression and anxiety. While frequent touching has a particularly beneficial effect, there’s indication that the touch doesn’t have to last long. The effect is enhanced by contact of skin on skin. Most notably, touch administered by objects such as social robots, heavy blankets and body pillows also showed a demonstrable effect. The team published their findings in the journal Nature Human Behavior from April, 8, 2024.

With infants, touch should be administered by the parents

“We were aware of the importance of touch as a health intervention,” says Dr. Julian Packheiser from the Institute of Cognitive Neuroscience at Ruhr University Bochum. “But despite many studies, it remained unclear how to use it optimally, what effects can be expected specifically and what the influencing factors are.” Following the comprehensive meta-analysis, the team was able to answer many of these questions.

Both adults and infants benefit from touch. “In the case of infants, it’s important that it is the parents who administer the touch; their touch is more effective than that of a care professional,” points out Dr. Helena Hartmann from the University of Duisburg-Essen. “In adults, however, we found there was no difference between people our volunteers were familiar with and a nursing professional.” The greatest effect of touch on adults was demonstrated by the many studies conducted on the mental state of the participants. According to these studies, pain, depression and anxiety decreased significantly. Touch also had a positive effect on cardiovascular factors such as blood pressure and heart rate, but the effect was less pronounced.

Even a brief hug makes a difference

A longer duration of touch, which averaged 20 minutes in the studies, did not significantly affect the outcome. “It’s not true that the longer the touch, the better,” summarizes Julian Packheiser. Shorter but more frequent touching proved to be more beneficial. “It doesn’t have to be a long expensive massage,” says the researcher. “Even a short hug has a positive impact.” The researchers were surprised by the positive effect of touch administered by objects. Social robots, stuffed animals, body pillows and other such items performed less well than humans when it came to mental health factors, but still showed a measurable positive effect.

“This led us to the conclusion that consensual touch improves the well-being of patients in clinical scenarios and healthy people alike,” says Julian Packheiser. “So, if you feel like hugging family or friends – don’t hold back, as long as the other person gives their consent.”

Still many questions left unanswered

For the researchers, this raises many more questions about the potential of touch interventions for public health. For example, it remained unclear in the studies which quality the touch had for the people experiencing it. Another unresolved question is whether affective touch has a different effect than instrumental touch, such as hair washing by a hairdresser or exams performed by a physician. The role of touching animals has also not yet been sufficiently researched, nor have cultural differences between different communities.