nils-herrmann/clean_scirepeval huggingface dataset:
Encoding memory in tube diameter hierarchy of living flow network
Venue: Proceedings of the National Academy of Sciences of the United States of America

Simple organisms manage to thrive in complex environments. Having memory about the environment is key in taking informed decisions. Physarum polycephalum excels as a giant unicellular eukaryote, being even able to solve optimization problems despite the lack of a nervous system. Here, we follow experimentally the organism’s response to a nutrient source and find that memory about nutrient location is encoded in the morphology of the network-shaped organism. Our theoretical predictions in line with our observations unveil the mechanism behind memory encoding and demonstrate the P. polycephalum’s ability to read out previously stored information. The concept of memory is traditionally associated with organisms possessing a nervous system. However, even very simple organisms store information about past experiences to thrive in a complex environment—successfully exploiting nutrient sources, avoiding danger, and warding off predators. How can simple organisms encode information about their environment? We here follow how the giant unicellular slime mold Physarum polycephalum responds to a nutrient source. We find that the network-like body plan of the organism itself serves to encode the location of a nutrient source. The organism entirely consists of interlaced tubes of varying diameters. Now, we observe that these tubes grow and shrink in diameter in response to a nutrient source, thereby imprinting the nutrient’s location in the tube diameter hierarchy. Combining theoretical model and experimental data, we reveal how memory is encoded: a nutrient source locally releases a softening agent that gets transported by the cytoplasmic flows within the tubular network. Tubes receiving a lot of softening agent grow in diameter at the expense of other tubes shrinking. Thereby, the tubes’ capacities for flow-based transport get permanently upgraded toward the nutrient location, redirecting future decisions and migration. This demonstrates that nutrient location is stored in and retrieved from the networks’ tube diameter hierarchy. Our findings explain how network-forming organisms like slime molds and fungi thrive in complex environments. We here identify a flow networks’ version of associative memory—very likely of relevance for the plethora of living flow networks as well as for bioinspired design.
Sea stars generate downforce to stay attached to surfaces
Venue: Scientific Reports

Intertidal sea stars often function in environments with extreme hydrodynamic loads that can compromise their ability to remain attached to surfaces. While behavioral responses such as burrowing into sand or sheltering in rock crevices can help minimize hydrodynamic loads, previous work shows that sea stars also alter body shape in response to flow conditions. This morphological plasticity suggests that sea star body shape may play an important hydrodynamic role. In this study, we measured the fluid forces acting on surface-mounted sea star and spherical dome models in water channel tests. All sea star models created downforce, i.e., the fluid pushed the body towards the surface. In contrast, the spherical dome generated lift. We also used Particle Image Velocimetry (PIV) to measure the midplane flow field around the models. Control volume analyses based on the PIV data show that downforce arises because the sea star bodies serve as ramps that divert fluid away from the surface. These observations are further rationalized using force predictions and flow visualizations from numerical simulations. The discovery of downforce generation could explain why sea stars are shaped as they are: the pentaradial geometry aids attachment to surfaces in the presence of high hydrodynamic loads.
An improved artificial ecosystem optimization algorithm for optimal configuration of a hybrid PV/WT/FC energy system
Venue: alexandria engineering journal

This paper mainly focuses on the optimal design of a grid-dependent and off-grid hybrid renewable energy system (RES). This system consists of Photovoltaic (PV), Wind Turbine (WT) as well as Fuel Cell (FC) with hydrogen gas tank for storing the energy in the chemical form. The optimal components sizes of the proposed hybrid generating system are achieved using a novel metaheuristic optimization technique. This optimization technique, called Improved Artificial Ecosystem Optimization (IAEO), is proposed for enhancing the performance of the conventional Artificial Ecosystem Optimization (AEO) algorithm. The IAEO improves the convergence trends of the original AEO, gives the best minimum objective function, reaches the optimal solution after a few iterations numbers as well as reduces the falling into the local optima. The proposed IAEO algorithm for solving the multiobjective optimization problem of minimizing the Cost of Energy (COE), the reliability index presented by the Loss of Power Supply Probability (LPSP), and excess energy under the constraints are considered. The hybrid system is suggested to be located in Ataka region, Suez Gulf (latitude 30.0, longitude 32.5), Egypt, and the whole lifetime of the suggested case study is 25 years. To ensure the accurateness, stability, and robustness of the proposed optimization algorithm, it is examined on six different configurations, representing on-grid and off-grid hybrid RES. For all the studied cases the proposed IAEO algorithm outperforms the original AEO and generates the minimum value of the fitness function in less execution time. Furthermore, comprehensive statistical measurements are demonstrated to prove the effectiveness of the proposed algorithm. Also, the results obtained by the conventional AEO and IAEO are compared with those obtained by several well-known optimization algorithms, Particle Swarm Optimization (PSO), Salp Swarm Algorithm (SSA), and Grey Wolf Optimizer (GWO). Based on the obtained simulation results, the proposed IAEO has the best performance among other algorithms and it has successfully positioned itself as a competitor to novel algorithms for tackling the most complicated engineering problems.
How neurons exploit fractal geometry to optimize their network connectivity
Venue: Scientific Reports

We investigate the degree to which neurons are fractal, the origin of this fractality, and its impact on functionality. By analyzing three-dimensional images of rat neurons, we show the way their dendrites fork and weave through space is unexpectedly important for generating fractal-like behavior well-described by an ‘effective’ fractal dimension D. This discovery motivated us to create distorted neuron models by modifying the dendritic patterns, so generating neurons across wide ranges of D extending beyond their natural values. By charting the D-dependent variations in inter-neuron connectivity along with the associated costs, we propose that their D values reflect a network cooperation that optimizes these constraints. We discuss the implications for healthy and pathological neurons, and for connecting neurons to medical implants. Our automated approach also facilitates insights relating form and function, applicable to individual neurons and their networks, providing a crucial tool for addressing massive data collection projects (e.g. connectomes).
Meta-analysis of neural systems underlying placebo analgesia from individual participant fMRI data
Venue: Nature Communications

The brain systems underlying placebo analgesia are insufficiently understood. Here we performed a systematic, participant-level meta-analysis of experimental functional neuroimaging studies of evoked pain under stimulus-intensity-matched placebo and control conditions, encompassing 603 healthy participants from 20 (out of 28 eligible) studies. We find that placebo vs. control treatments induce small, widespread reductions in pain-related activity, particularly in regions belonging to ventral attention (including mid-insula) and somatomotor networks (including posterior insula). Behavioral placebo analgesia correlates with reduced pain-related activity in these networks and the thalamus, habenula, mid-cingulate, and supplementary motor area. Placebo-associated activity increases occur mainly in frontoparietal regions, with high between-study heterogeneity. We conclude that placebo treatments affect pain-related activity in multiple brain areas, which may reflect changes in nociception and/or other affective and decision-making processes surrounding pain. Between-study heterogeneity suggests that placebo analgesia is a multi-faceted phenomenon involving multiple cerebral mechanisms that differ across studies.
Cuttlefish exert self-control in a delay of gratification task
Venue: Proceedings of The Royal Society B: Biological Sciences

The ability to exert self-control varies within and across taxa. Some species can exert self-control for several seconds whereas others, such as large-brained vertebrates, can tolerate delays of up to several minutes. Advanced self-control has been linked to better performance in cognitive tasks and has been hypothesized to evolve in response to specific socio-ecological pressures. These pressures are difficult to uncouple because previously studied species face similar socio-ecological challenges. Here, we investigate self-control and learning performance in cuttlefish, an invertebrate that is thought to have evolved under partially different pressures to previously studied vertebrates. To test self-control, cuttlefish were presented with a delay maintenance task, which measures an individual's ability to forgo immediate gratification and sustain a delay for a better but delayed reward. Cuttlefish maintained delay durations for up to 50–130 s. To test learning performance, we used a reversal-learning task, whereby cuttlefish were required to learn to associate the reward with one of two stimuli and then subsequently learn to associate the reward with the alternative stimulus. Cuttlefish that delayed gratification for longer had better learning performance. Our results demonstrate that cuttlefish can tolerate delays to obtain food of higher quality comparable to that of some large-brained vertebrates.
Hide-and-seek strategies and post-contact immobility
Venue: Biology Letters

To understand why an animal might gain by playing dead, or more precisely, exhibit post-contact immobility (PCI), we consider the context in which this behaviour occurs. Is it, for example, a method by which a potential victim encourages a predator to direct its attention elsewhere? We investigate this possibility by using the marginal value theorem to analyse predator behaviour in the context of this defence strategy by potential prey. We consider two models. In the first, (random revisiting) the predator may return to sites it has already depleted within the patch. In the second, (systematic search) the predator goes only to new sites within the patch. The results of the two models are qualitatively extremely similar. We show that when prey occur in patches, PCI favours prey survival. Indeed, certain antlion larvae have PCI durations characterized by very long half-lives. These appear to be of such long durations that further increases would convey no substantial benefits in redirecting potential predators to other antlions within the patch and subsequently to other patches.
Lung mediated auditory contrast enhancement improves the Signal-to-noise ratio for communication in frogs
Venue: Current Biology

Environmental noise is a major source of selection on animal sensory and communication systems. The acoustic signals of other animals represent particularly potent sources of noise for chorusing insects, frogs, and birds, which contend with a multi-species analog of the human "cocktail party problem" (i.e., our difficulty following speech in crowds). However, current knowledge of the diverse adaptations that function to solve noise problems in nonhuman animals remains limited. Here, we show that a lung-to-ear sound transmission pathway in frogs serves a heretofore unknown noise-control function in vertebrate hearing and sound communication. Inflated lungs improve the signal-to-noise ratio for communication by enhancing the spectral contrast in received vocalizations in ways analogous to signal processing algorithms used in hearing aids and cochlear implants. Laser vibrometry revealed that the resonance of inflated lungs selectively reduces the tympanum's sensitivity to frequencies between the two spectral peaks present in conspecific mating calls. Social network analysis of continent-scale citizen science data on frog calling behavior revealed that the calls of other frog species in multi-species choruses can be a prominent source of environmental noise attenuated by the lungs. Physiological modeling of peripheral frequency tuning indicated that inflated lungs could reduce both auditory masking and suppression of neural responses to mating calls by environmental noise. Together, these data suggest an ancient adaptation for detecting sound via the lungs has been evolutionarily co-opted to create auditory contrast enhancement that contributes to solving a multi-species cocktail party problem.
Protective coloration of European vipers throughout the predation sequence
Venue: Animal Behaviour

Antipredator adaptations in the form of animal coloration are common and often multifunctional. European vipers (genus Vipera) have a characteristic dorsal zigzag pattern, which has been shown to serve as a warning signal to potential predators. At the same time, it has been suggested to decrease detection risk, and to cause a motion dazzle or flicker–fusion effect during movement. We tested these hypotheses by asking whether (1) the zigzag pattern decreases detection risk and (2) the detection is dependent on the base coloration (grey or brown) or the snake's posture (coiled, basking form or S-shaped, active form). Additionally, (3) we measured the fleeing speed of adders, Vipera berus, and calculated the flicker rate of the zigzag pattern, to see whether it is fast enough to cause a flicker–fusion effect against predators. Our results show that the zigzag pattern reduced detectability regardless of base coloration or posture of the snake. The brown zigzag morph was detected less often than the grey zigzag morph. The fleeing speed of adders appeared to be fast enough to induce a flicker–fusion effect for mammalian predators. However, it is unlikely to be fast enough to induce the flicker–fusion effect for raptors. Our findings highlight that the colour pattern of animals can be multifunctional. The same colour pattern that can decrease detection by predators can also serve as a warning function once detected, and potentially hinder capture during an attack.
Extreme autotomy and whole-body regeneration in photosynthetic sea slugs
Venue: Current Biology

Autotomy, the voluntary shedding of a body part, is common to distantly-related animals such as arthropods, gastropods, asteroids, amphibians, and lizards1,2. Autotomy is generally followed by regeneration of shed terminal body parts, such as appendages or tails. Here, we identify a new type of extreme autotomy in two species of sacoglossan sea slug (Mollusca: Gastropoda). Surprisingly, they shed the main body, including the whole heart, and regenerated a new body. In contrast, the shed body did not regenerate the head. These sacoglossans can incorporate chloroplasts from algal food into their cells to utilise for photosynthesis (kleptoplasty3), and we propose that this unique characteristic may facilitate survival after autotomy and subsequent regeneration.
Reflectin needs its intensity amplifier: Realizing the potential of tunable structural biophotonics
Venue: Applied Physics Letters

Underwater camouflage and communication in a family of recently evolved squids are controlled, in part, by the reflectin proteins, which regulate dynamic changes in the color and intensity of light reflected from intracellular Bragg reflectors and Mie scatterers. The reflectins act as a signal transducer, precisely tuning the dimensions and refractive index of the membrane-bounded structural reflectors containing them to an extent exactly proportional to neuronal signaling. This calibration between the activating signal and the output color and intensity of reflectance is governed by the physics of the liquid state of reflectin assemblies, which osmotically fine-tune the dimensions and refractive index of the membrane-bounded structural reflectors containing them. While thin-film or genetically engineered assemblies of reflectin deliver changes in the colors of reflection approximating those of the biological system (as do other proteins and polymers), none has delivered the signal-activated increase in the intensity of reflectance characteristic of the native system. The membrane envelopes (Bragg reflector lamellae and Mie-scattering vesicles) containing the reflectins apparently serve as amplifiers, functionally “impedance matched” to the range of tunable sizes of the reflectin assemblies; reflectin films or assemblies lacking such an amplifier fail to deliver signal-activated increases in reflectance intensity.
Hard to catch: experimental evidence supports evasive mimicry
Venue: Proceedings of The Royal Society B: Biological Sciences

Most research on aposematism has focused on chemically defended prey, but the signalling difficulty of capture remains poorly explored. Similar to classical Batesian and Müllerian mimicry related to distastefulness, such ‘evasive aposematism' may also lead to convergence in warning colours, known as evasive mimicry. A prime candidate group for evasive mimicry are Adelpha butterflies, which are agile insects and show remarkable colour pattern convergence. We tested the ability of naive blue tits to learn to avoid and generalize Adelpha wing patterns associated with the difficulty of capture and compared their response to that of birds that learned to associate the same wing patterns with distastefulness. Birds learned to avoid all wing patterns tested and generalized their aversion to other prey to some extent, but learning was faster with evasive prey compared to distasteful prey. Our results on generalization agree with longstanding observations of striking convergence in wing colour patterns among Adelpha species, since, in our experiments, perfect mimics of evasive and distasteful models were always protected during generalization and suffered the lowest attack rate. Moreover, generalization on evasive prey was broader compared to that on distasteful prey. Our results suggest that being hard to catch may deter predators at least as effectively as distastefulness. This study provides empirical evidence for evasive mimicry, a potentially widespread but poorly understood form of morphological convergence driven by predator selection.
A Graphic Way For Notch Shape Optimization
Venue: COMPARING DESIGN IN NATURE WITH SCIENCE AND ENGINEERING 2006

Many components have notches and notches are in the majority of cases the reason for failure. There are many options to reach a longer lifetime and a better utilisation of material. One method for the shape optimization of components, developed in Forschungszentrum Karlsruhe, uses the design rules of nature. During the last 15 years it has spread very well and proven itself in industry, especially in automotive engineering. The limits for using the CAO-method (Computer Aided Optimization) are more or less of an economic nature. So we need a method that allows optimization by everybody. Now a new pure graphical method has been found, which works without any FEM or optimization software. It is called the “Method of Tensile Triangles” and requires only a set square and a piece of paper to optimize the notch shape in an effective and simple way.
A controllable dual-catapult system inspired by the biomechanics of the dragonfly larvae’s predatory strike
Venue: Science Robotics

The independently loaded synchronized dual-catapult system of dragonfly larvae can serve as a model for bioinspired robotics. The biomechanics underlying the predatory strike of dragonfly larvae is not yet understood. Dragonfly larvae are aquatic ambush predators, capturing their prey with a strongly modified extensible mouthpart. The current theory of hydraulic pressure being the driving force of the predatory strike can be refuted by our manipulation experiments and reinterpretation of former studies. Here, we report evidence for an independently loaded synchronized dual-catapult system. To power the ballistic movement of a single specialized mouthpart, two independently loaded springs simultaneously release and actuate two separate joints in a kinematic chain. Energy for the movement is stored by straining an elastic structure at each joint and, possibly, the surrounding cuticle, which is preloaded by muscle contraction. As a proof of concept, we developed a bioinspired robotic model resembling the morphology and functional principle of the extensible mouthpart. Understanding the biomechanics of the independently loaded synchronized dual-catapult system found in dragonfly larvae can be used to control the extension direction and, thereby, thrust vector of a power-modulated robotic system.
Multimodal and multifunctional signaling? – Web reduction courtship behavior in a North American population of the false black widow spider
Venue: PLOS ONE

Males of widow spiders courting on the web of females engage in web-reduction behavior which entails excising a section of the web, bundling it up, and wrapping it with their silk. Males of the false black widow spider, Steatoda grossa, in European populations also produce stridulatory courtship sound which has not yet been studied in their invaded North American range. Working with a North American population of S. grossa, we tested the hypotheses that (1) web reduction by males renders webs less attractive to rival males; (2) deposition of silk by courting males has an inter-sexual (male-female) signal function that enhances their likelihood of copulation; and (3) stridulatory sound is a courtship signal of males. Testing anemotactic attraction of males in Y-tube olfactometer experiments revealed that reduced webs (indicative of a mated female) and intact webs (indicative of a virgin female) were equally attractive to males. Recording courtship behavior of males with either functional (silk-releasing) spinnerets or spinnerets experimentally occluded on the web of virgin females showed that males with functional spinnerets were more likely to copulate with the female they courted. Although males possess the stridulatory apparatus to produce courtship sound, they did not stridulate when courting or copulating on the web of females. Our data support the conclusion that web-reduction behavior of S. grossa males in their invaded North American range has no long-range effect on mate seeking males. Instead, web-reduction behavior has an inter-sexual signaling function that seems to be linked to functional spinnerets of the courting male. The signal produced by a male likely entails a volatile silk-borne pheromone, but may also embody a gauge of his endurance (the amount of time he engages in web reduction causing web vibrations).