nils-herrmann/clean_scirepeval huggingface dataset:
Evidence for self-cleaning in gecko setae.
Venue: Proceedings of the National Academy of Sciences of the United States of America

A tokay gecko can cling to virtually any surface and support its body mass with a single toe by using the millions of keratinous setae on its toe pads. Each seta branches into hundreds of 200-nm spatulae that make intimate contact with a variety of surface profiles. We showed previously that the combined surface area of billions of spatulae maximizes van der Waals interactions to generate large adhesive and shear forces. Geckos are not known to groom their feet yet retain their stickiness for months between molts. How geckos manage to keep their feet clean while walking about with sticky toes has remained a puzzle until now. Although self-cleaning by water droplets occurs in plant and animal surfaces, no adhesive has been shown to self-clean. In the present study, we demonstrate that gecko setae are a self-cleaning adhesive. Geckos with dirty feet recovered their ability to cling to vertical surfaces after only a few steps. Self-cleaning occurred in arrays of setae isolated from the gecko. Contact mechanical models suggest that self-cleaning occurs by an energetic disequilibrium between the adhesive forces attracting a dirt particle to the substrate and those attracting the same particle to one or more spatulae. We propose that the property of self-cleaning is intrinsic to the setal nanostructure and therefore should be replicable in synthetic adhesive materials in the future.
Ontogenetic changes in tracheal structure facilitate deep dives and cold water foraging in adult leatherback sea turtles
Venue: The Journal of Experimental Biology

Adult leatherbacks are large animals (300–500 kg), overlapping in size with marine pinniped and cetacean species. Unlike marine mammals, they start their aquatic life as 40–50 g hatchlings, so undergo a 10,000-fold increase in body mass during independent existence. Hatchlings are limited to the tropics and near-surface water. Adults, obligate predators on gelatinous plankton, encounter cold water at depth (<1280 m) or high latitude and are gigantotherms that maintain elevated core body temperatures in cold water. This study shows that there are great ontogenetic changes in tracheal structure related to diving and exposure to cold. Hatchling leatherbacks have a conventional reptilian tracheal structure with circular cartilaginous rings interspersed with extensive connective tissue. The adult trachea is an almost continuous ellipsoidal cartilaginous tube composed of interlocking plates, and will collapse easily in the upper part of the water column during dives, thus avoiding pressure-related structural and physiological problems. It is lined with an extensive, dense erectile vascular plexus that will warm and humidify cold inspired air and possibly retain heat on expiration. A sub-luminal lymphatic plexus is also present. Mammals and birds have independently evolved nasal turbinates to fulfil such a respiratory thermocontrol function; for them, turbinates are regarded as diagnostic of endothermy. This is the first demonstration of a turbinate equivalent in a living reptile.
Experimental and theoretical quantification of the development of damage in fatigue tests of bone and antler.
Venue: Journal of Biomechanics

This study concerns the development of damage (as measured by a reduction in elastic modulus) in two kinds of bones differing considerably in their degrees of mineralisation: laminar bone from bovine femur and osteonal bone from red deer antler. Antler bone is much tougher than 'ordinary' bone and its failure properties have been investigated in: (i) monotonic tensile tests and (ii) creep rupture experiments. Tensile fatigue is another way of examining how damage develops in bone. The development of damage in the present fatigue tests was non-linear with the cycle number, the degree of non-linearity was dependent on the level of stress and followed a clearly different course for bone and antler. Antler was a more damage-tolerant material, being able to achieve a reduction in the final modulus of elasticity, just prior to failure, three times greater than 'ordinary' bone. The evolution of damage is quantified by an empirical and a graphical method and by the use of Continuum Damage Mechanics (CDM) expressions. The CDM method shows important conditions, found in antler, but not in bone, that seen necessary for achieving stable fractures and consequently producing very tough materials.
Structural design of the minute clypeasteroid echinoid Echinocyamus pusillus
Venue: Royal Society Open Science

The clypeasteroid echinoid skeleton is a multi-plated, light-weight shell construction produced by biomineralization processes. In shell constructions, joints between individual elements are considered as weak points, yet these echinoid skeletons show an extensive preservation potential in both Recent and fossil environments. The remarkable strength of the test is achieved by skeletal reinforcement structures and their constructional layouts. Micro-computed tomography and scanning electron microscopy are used for microstructural and volumetric analyses of the echinoid's skeleton. It is shown that strengthening mechanisms act on different hierarchical levels from the overall shape of the skeleton to skeletal interlocking. The tight-fitting and interlocking plate joints lead to a shell considered to behave as a monolithic structure. The plate's architecture features distinct regions interpreted as a significant load-transferring system. The internal support system follows the segmentation of the remaining skeleton, where sutural layout and stereom distribution are designed for effective load transfer. The structural analysis of the multi-plated, yet monolithic skeleton of Echinocyamus pusillus reveals new aspects of the micro-morphology and its structural relevance for the load-bearing behaviour. The analysed structural principles allow E. pusillus to be considered as a role model for the development of multi-element, light-weight shell constructions.
Attractive and defensive functions of the ultraviolet pigments of a flower (Hypericum calycinum)
Venue: Proceedings of the National Academy of Sciences of the United States of America

The flower of Hypericum calycinum, which appears uniformly yellow to humans, bears a UV pattern, presumably visible to insects. Two categories of pigments, flavonoids and dearomatized isoprenylated phloroglucinols (DIPs), are responsible for the UV demarcations of this flower. Flavonoids had been shown previously to function as floral UV pigments, but DIPs had not been demonstrated to serve in that capacity. We found the DIPs to be present in high concentration in the anthers and ovarian wall of the flower, suggesting that the compounds also serve in defense. Indeed, feeding tests done with one of the DIPs (hypercalin A) showed the compound to be deterrent and toxic to a caterpillar (Utetheisa ornatrix). The possibility that floral UV pigments fulfill both a visual and a defensive function had not previously been contemplated. DIPs may also serve for protection of female reproductive structures in other plants, for example in hops (Humulus lupulus). The DIPs of hops are put to human use as bitter flavoring agents and preservatives in beer.
Fungal Aquaporins in Ectomycorrhizal Root Water Transport
Venue: Frontiers in Plant Science

Ectomycorrhizal fungi influence root water transport of host plants. To delineate the exact mechanisms of how fungal partner alters root water relations, it is important to understand the functions of fungal transmembrane water channels, i.e., aquaporins, the key component in the symplastic pathways. In this paper, we discussed what roles the fungal aquaporins may play in root water transport. We also highlighted the opportunities of using integrated approaches to address rising questions in future hotspots of aquaporin and root water relations research.
Conical Epidermal Cells Allow Bees to Grip Flowers and Increase Foraging Efficiency
Venue: Current Biology

The plant surface is by default flat, and development away from this default is thought to have some function of evolutionary advantage. Although the functions of many plant epidermal cells have been described, the function of conical epidermal cells, a defining feature of petals in the majority of insect-pollinated flowers, has not. The location and frequency of conical cells have led to speculation that they play a role in attracting animal pollinators. Snapdragon (Antirrhinum) mutants lacking conical cells have been shown to be discriminated against by foraging bumblebees. Here we investigated the extent to which a difference in petal surface structure influences pollinator behavior through touch-based discrimination. To isolate touch-based responses, we used both biomimetic replicas of petal surfaces and isogenic Antirrhinum lines differing only in petal epidermal cell shape. We show that foraging bumblebees are able to discriminate between different surfaces via tactile cues alone. We find that bumblebees use color cues to discriminate against flowers that lack conical cells--but only when flower surfaces are presented at steep angles, making them difficult to manipulate. This facilitation of physical handling is a likely explanation for the prevalence of conical epidermal petal cells in most flowering plants.
THE CALCAREOUS EGG CAPSULE OF THE PATAGONIAN NEOGASTROPOD ODONTOCYMBIOLA MAGELLANICA: MORPHOLOGY, SECRETION AND MINERALOGY
Venue: Journal of Molluscan Studies

Odontocymbiola magellanica is the only known South American volutid gastropod that deposits calcareous egg capsules. The spawn is moulded and fixed to flat or convex surfaces by the female’s ventral pedal gland, during an hours-long process in which the female adopts a stereotyped posture and appears nonreactive to most external stimuli. Microscopically, the different cells of the ventral pedal gland show features suggesting their participation in the secretion of both the organic matrix and the calcium component of the calcareous layer. The latter consists mainly of numerous spherspherulites that are packed together around cylindrical, septated spaces which traverse the spherspherulitic layer and attach to the membranous layers surrounding the capsule cavity. These septated spaces should ensure permeability of the capsule wall, which is necessary for gas exchange and excretion by the embryo. The calcareous layer is made of high-magnesium calcite, a calcium carbonate polymorph in which Ca is partially substituted by Mg in the calcite lattice. Mg substitution is thought to confer a greater crack resistance to the mineral; it is found in many invertebrates, but apparently has not been reported before in molluscs. Odontocymbiola magellanica is a long-lived species, investing heavily in its egg capsules.
Extreme resistance of bdelloid rotifers to ionizing radiation
Venue: Proceedings of the National Academy of Sciences of the United States of America

Rotifers of class Bdelloidea are common invertebrate animals with highly unusual characteristics, including apparently obligate asexuality, the ability to resume reproduction after desiccation at any life stage, and a paucity of transposable genetic elements of types not prone to horizontal transmission. We find that bdelloids are also extraordinarily resistant to ionizing radiation (IR). Reproduction of the bdelloids Adineta vaga and Philodina roseola is much more resistant to IR than that of Euchlanis dilatata, a rotifer belonging to the desiccation-intolerant and facultatively sexual class Monogononta, and all other animals for which we have found relevant data. By analogy with the desiccation- and radiation-resistant bacterium Deinococcus radiodurans, we suggest that the extraordinary radiation resistance of bdelloid rotifers is a consequence of their evolutionary adaptation to survive episodes of desiccation encountered in their characteristic habitats and that the damage incurred in such episodes includes DNA breakage that is repaired upon rehydration. Such breakage and repair may have maintained bdelloid chromosomes as colinear pairs and kept the load of transposable genetic elements low and may also have contributed to the success of bdelloid rotifers in avoiding the early extinction suffered by most asexuals.
Energy storage and synchronisation of hind leg movements during jumping in planthopper insects (Hemiptera, Issidae)
Venue: The Journal of Experimental Biology

The hind legs of Issus (Hemiptera, Issidae) move in the same plane underneath the body, an arrangement that means they must also move synchronously to power jumping. Moreover, they move so quickly that energy must be stored before a jump and then released suddenly. High speed imaging and analysis of the mechanics of the proximal joints of the hind legs show that mechanical mechanisms ensure both synchrony of movements and energy storage. The hind trochantera move first in jumping and are synchronised to within 30 μs. Synchrony is achieved by mechanical interactions between small protrusions from each trochantera which fluoresce bright blue under specific wavelengths of ultra-violet light and which touch at the midline when the legs are cocked before a jump. In dead Issus, a depression force applied to a cocked hind leg, or to the tendon of its trochanteral depressor muscle causes a simultaneous depression of both hind legs. The protrusion of the hind leg that moves first nudges the other hind leg so that both move synchronously. Contractions of the trochanteral depressor muscles that precede a jump bend the metathoracic pleural arches of the internal skeleton. Large areas of these bow-shaped structures fluoresce bright blue in ultraviolet light, and the intensity of this fluorescence depends on the pH of the bathing saline. These are key signatures of the rubber-like protein resilin. The remainder of a pleural arch consists of stiff cuticle. Bending these composite structures stores energy and their recoil powers jumping.
Rain-, wind-, and touch-induced expression of calmodulin and calmodulin-related genes in Arabidopsis
Venue: Cell

In response to water spray, subirrigation, wind, touch, wounding, or darkness, Arabidopsis regulates the expression of at least four touch-induced (TCH) genes. Ten to thirty minutes after stimulation, mRNA levels increase up to 100-fold. Arabidopsis plants stimulated by touch develop shorter petioles and bolts. This developmental response is known as thigmomorphogenesis. TCH 1 cDNA encodes the putative Arabidopsis calmodulin differing in one amino acid from wheat calmodulin. Sequenced regions of TCH 2 and TCH 3 contain 44% and 70% amino acid identities to calmodulin, respectively. The regulation of this calmodulin-related gene family in Arabidopsis suggests that calcium ions and calmodulin are involved in transduction of signals from the environment, enabling plants to sense and respond to environmental changes.
Non-smooth morphologies of typical plant leaf surfaces and their anti-adhesion effects
Venue: Journal of Bionic Engineering

The micromorphologies of surfaces of several typical plant leaves were investigated by scanning electron microscopy(SEM). Different non-smooth surface characteristics were described and classified. The hydrophobicity and anti-adhesion of non-smooth leaf surfaces were quantitatively measured. Results show that the morphology of epidermal cells and the morphology and distribution density of epicuticular wax directly affect the hydrophobicity and anti-adhesion. The surface with uniformly distributed convex units shows the best anti-adhesion, and the surface with regularly arranged trellis units displays better anti-adhesion. In contrast, the surface with randomly distributed hair units performs relatively bad anti-adhesion. The hydrophobic models of papilla-ciliary and fold-setal non-smooth surfaces were set up to determine the impacts of geometric parameters on the hydrophobicity. This study may provide an insight into surface machine molding and apparent morphology design for biomimetics engineering.
FISH MUCUS: IN SITU MEASUREMENTS OF POLYMER DRAG REDUCTION
Venue: The Biological Bulletin

The external layer of mucus on fish was investigated as a drag reducing polymer. Comparing velocity profiles for water flow over rainbow trout (Salmo gairdneri) and wax models of trout with and without hydrodynamically smooth surfaces revealed that the integumental mucous secretion can significantly reduce the rate of momentum transfer through the boundary layer. The difference in momentum transfer is expressed as a reduction in friction drag and discussed in view of the overall drag experienced by fish.
Passive radiative cooling below ambient air temperature under direct sunlight
Venue: Nature

Cooling is a significant end-use of energy globally and a major driver of peak electricity demand. Air conditioning, for example, accounts for nearly fifteen per cent of the primary energy used by buildings in the United States. A passive cooling strategy that cools without any electricity input could therefore have a significant impact on global energy consumption. To achieve cooling one needs to be able to reach and maintain a temperature below that of the ambient air. At night, passive cooling below ambient air temperature has been demonstrated using a technique known as radiative cooling, in which a device exposed to the sky is used to radiate heat to outer space through a transparency window in the atmosphere between 8 and 13 micrometres. Peak cooling demand, however, occurs during the daytime. Daytime radiative cooling to a temperature below ambient of a surface under direct sunlight has not been achieved because sky access during the day results in heating of the radiative cooler by the Sun. Here, we experimentally demonstrate radiative cooling to nearly 5 degrees Celsius below the ambient air temperature under direct sunlight. Using a thermal photonic approach, we introduce an integrated photonic solar reflector and thermal emitter consisting of seven layers of HfO2 and SiO2 that reflects 97 per cent of incident sunlight while emitting strongly and selectively in the atmospheric transparency window. When exposed to direct sunlight exceeding 850 watts per square metre on a rooftop, the photonic radiative cooler cools to 4.9 degrees Celsius below ambient air temperature, and has a cooling power of 40.1 watts per square metre at ambient air temperature. These results demonstrate that a tailored, photonic approach can fundamentally enable new technological possibilities for energy efficiency. Further, the cold darkness of the Universe can be used as a renewable thermodynamic resource, even during the hottest hours of the day.
A nonprotein thermal hysteresis-producing xylomannan antifreeze in the freeze-tolerant Alaskan beetle Upis ceramboides
Venue: Proceedings of the National Academy of Sciences of the United States of America

Thermal hysteresis (TH), a difference between the melting and freezing points of a solution that is indicative of the presence of large-molecular-mass antifreezes (e.g., antifreeze proteins), has been described in animals, plants, bacteria, and fungi. Although all previously described TH-producing biomolecules are proteins, most thermal hysteresis factors (THFs) have not yet been structurally characterized, and none have been characterized from a freeze-tolerant animal. We isolated a highly active THF from the freeze-tolerant beetle, Upis ceramboides, by means of ice affinity. Amino acid chromatographic analysis, polyacrylamide gel electrophoresis, UV-Vis spectrophotometry, and NMR spectroscopy indicated that the THF contained little or no protein, yet it produced 3.7 ± 0.3 °C of TH at 5 mg/ml, comparable to that of the most active insect antifreeze proteins. Compositional and structural analyses indicated that this antifreeze contains a β-mannopyranosyl-(1→4) β-xylopyranose backbone and a fatty acid component, although the lipid may not be covalently linked to the saccharide. Consistent with the proposed structure, treatment with endo-β-(1→4)xylanase ablated TH activity. This xylomannan is the first TH-producing antifreeze isolated from a freeze-tolerant animal and the first in a new class of highly active THFs that contain little or no protein.
How ants use quorum sensing to estimate the average quality of a fluctuating resource
Venue: Scientific Reports

We show that one of the advantages of quorum-based decision-making is an ability to estimate the average value of a resource that fluctuates in quality. By using a quorum threshold, namely the number of ants within a new nest site, to determine their choice, the ants are in effect voting with their feet. Our results show that such quorum sensing is compatible with homogenization theory such that the average value of a new nest site is determined by ants accumulating within it when the nest site is of high quality and leaving when it is poor. Hence, the ants can estimate a surprisingly accurate running average quality of a complex resource through the use of extraordinarily simple procedures.
Desaturation of exhaled air in camels
Venue: Proceedings of The Royal Society B: Biological Sciences

We have found that camels can reduce the water loss due to evaporation from the respiratory tract in two ways: (1) by decreasing the temperature of the exhaled air and (2) by removal of water vapour from this air, resulting in the exhalation of air at less than 100% relative humidity (r. h.). Camels were kept under desert conditions and deprived of drinking water. In the daytime the exhaled air was at or near body core temperature, while in the cooler night exhaled air was at or near ambient air temperature. In the daytime the exhaled air was fully saturated, but at night its humidity might fall to approximately 75% r. h. The combination of cooling and desaturation can provide a saving of water of 60% relative to exhalation of saturated air at body temperature. The mechanism responsible for cooling of the exhaled air is a simple heat exchange between the respiratory air and the surfaces of the nasal passageways. On inhalation these surfaces are cooled by the air passing over them, and on exhalation heat from the exhaled air is given off to these cooler surfaces. The mechanism responsible for desaturation of the air appears to depend on the hygroscopic properties of the nasal surfaces when the camel is dehydrated. The surfaces give off water vapour during inhalation and take up water from the respiratory air during exhalation. We have used a simple mechanical model to demonstrate the effectiveness of this mechanism.