nils-herrmann/clean_scirepeval huggingface dataset:
Elastic modulus of tree frog adhesive toe pads
Venue: Journal of Comparative Physiology A-neuroethology Sensory Neural and Behavioral Physiology

Previous work using an atomic force microscope in nanoindenter mode indicated that the outer, 10- to 15-μm thick, keratinised layer of tree frog toe pads has a modulus of elasticity equivalent to silicone rubber (5–15 MPa) (Scholz et al. 2009), but gave no information on the physical properties of deeper structures. In this study, micro-indentation is used to measure the stiffness of whole toe pads of the tree frog, Litoria caerulea. We show here that tree frog toe pads are amongst the softest of biological structures (effective elastic modulus 4–25 kPa), and that they exhibit a gradient of stiffness, being stiffest on the outside. This stiffness gradient results from the presence of a dense network of capillaries lying beneath the pad epidermis, which probably has a shock absorbing function. Additionally, we compare the physical properties (elastic modulus, work of adhesion, pull-off force) of the toe pads of immature and adult frogs.
Thermal Energy Exchange Model and Water Loss of a Barrel Cactus, Ferocactus acanthodes.
Venue: Plant Physiology

The influences of various diurnal stomatal opening patterns, spines, and ribs on the stem surface temperature and water economy of a CAM succulent, the barrel cactus Ferocactus acanthodes, were examined using an energy budget model. To incorporate energy exchanges by shortwave and longwave irradiation, latent heat, conduction, and convection as well as the heat storage in the massive stem, the plant was subdivided into over 100 internal and external regions in the model. This enabled the average surface temperature to be predicted within 1 C of the measured temperature for both winter and summer days.Reducing the stem water vapor conductance from the values observed in the field to zero caused the average daily stem surface temperature to increase only 0.7 C for a winter day and 0.3 C for a summer day. Thus, latent heat loss does not substantially reduce stem temperature. Although the surface temperatures averaged 18 C warmer for the summer day than for the winter day for a plant 41 cm tall, the temperature dependence of stomatal opening caused the simulated nighttime water loss rates to be about the same for the 2 days.Spines moderated the amplitude of the diurnal temperature changes of the stem surface, since the daily variation was 17 C for the winter day and 25 C for the summer day with spines compared with 23 C and 41 C, respectively, in their simulated absence. Ribs reduced the daytime temperature rise by providing 54% more area for convective heat loss than for a smooth circumscribing surface. In a simulation where both spines and ribs were eliminated, the daytime average surface temperature rose by 5 C.
Optimal Predator Risk Assessment by the Sonar-Jamming Arctiine Moth Bertholdia trigona
Venue: PLOS ONE

Nearly all animals face a tradeoff between seeking food and mates and avoiding predation. Optimal escape theory holds that an animal confronted with a predator should only flee when benefits of flight (increased survival) outweigh the costs (energetic costs, lost foraging time, etc.). We propose a model for prey risk assessment based on the predator's stage of attack. Risk level should increase rapidly from when the predator detects the prey to when it commits to the attack. We tested this hypothesis using a predator – the echolocating bat – whose active biosonar reveals its stage of attack. We used a prey defense – clicking used for sonar jamming by the tiger moth Bertholdia trigona– that can be readily studied in the field and laboratory and is enacted simultaneously with evasive flight. We predicted that prey employ defenses soon after being detected and targeted, and that prey defensive thresholds discriminate between legitimate predatory threats and false threats where a nearby prey is attacked. Laboratory and field experiments using playbacks of ultrasound signals and naturally behaving bats, respectively, confirmed our predictions. Moths clicked soon after bats detected and targeted them. Also, B. trigona clicking thresholds closely matched predicted optimal thresholds for discriminating legitimate and false predator threats for bats using search and approach phase echolocation – the period when bats are searching for and assessing prey. To our knowledge, this is the first quantitative study to correlate the sensory stimuli that trigger defensive behaviors with measurements of signals provided by predators during natural attacks in the field. We propose theoretical models for explaining prey risk assessment depending on the availability of cues that reveal a predator's stage of attack.
Two chemosensory receptors together mediate carbon dioxide detection in Drosophila
Venue: Nature

Blood-feeding insects, including the malaria mosquito Anopheles gambiae, use highly specialized and sensitive olfactory systems to locate their hosts. This is accomplished by detecting and following plumes of volatile host emissions, which include carbon dioxide (CO2). CO2 is sensed by a population of olfactory sensory neurons in the maxillary palps of mosquitoes and in the antennae of the more genetically tractable fruitfly, Drosophila melanogaster. The molecular identity of the chemosensory CO2 receptor, however, remains unknown. Here we report that CO2-responsive neurons in Drosophila co-express a pair of chemosensory receptors, Gr21a and Gr63a, at both larval and adult life stages. We identify mosquito homologues of Gr21a and Gr63a, GPRGR22 and GPRGR24, and show that these are co-expressed in A. gambiae maxillary palps. We show that Gr21a and Gr63a together are sufficient for olfactory CO2-chemosensation in Drosophila. Ectopic expression of Gr21a and Gr63a together confers CO2 sensitivity on CO2-insensitive olfactory neurons, but neither gustatory receptor alone has this function. Mutant flies lacking Gr63a lose both electrophysiological and behavioural responses to CO2. Knowledge of the molecular identity of the insect olfactory CO2 receptors may spur the development of novel mosquito control strategies designed to take advantage of this unique and critical olfactory pathway. This in turn could bolster the worldwide fight against malaria and other insect-borne diseases.
The aerodynamics of insect flight
Venue: The Journal of Experimental Biology

The flight of insects has fascinated physicists and biologists for more than a century. Yet, until recently, researchers were unable to rigorously quantify the complex wing motions of flapping insects or measure the forces and flows around their wings. However, recent developments in high-speed videography and tools for computational and mechanical modeling have allowed researchers to make rapid progress in advancing our understanding of insect flight. These mechanical and computational fluid dynamic models, combined with modern flow visualization techniques, have revealed that the fluid dynamic phenomena underlying flapping flight are different from those of non-flapping, 2-D wings on which most previous models were based. In particular, even at high angles of attack, a prominent leading edge vortex remains stably attached on the insect wing and does not shed into an unsteady wake, as would be expected from non-flapping 2-D wings. Its presence greatly enhances the forces generated by the wing, thus enabling insects to hover or maneuver. In addition, flight forces are further enhanced by other mechanisms acting during changes in angle of attack, especially at stroke reversal, the mutual interaction of the two wings at dorsal stroke reversal or wing–wake interactions following stroke reversal. This progress has enabled the development of simple analytical and empirical models that allow us to calculate the instantaneous forces on flapping insect wings more accurately than was previously possible. It also promises to foster new and exciting multi-disciplinary collaborations between physicists who seek to explain the phenomenology, biologists who seek to understand its relevance to insect physiology and evolution, and engineers who are inspired to build micro-robotic insects using these principles. This review covers the basic physical principles underlying flapping flight in insects, results of recent experiments concerning the aerodynamics of insect flight, as well as the different approaches used to model these phenomena.
No shot in the dark: myxozoans chemically detect fresh fish.
Venue: International Journal for Parasitology

This work reports the discovery of an hitherto unknown chemical recognition trait enabling a parasitic life cycle in aquatic habitats. We believe this is the first record of a natural, host-derived chemical molecule identified as a recognition cue for the phylum Myxozoa. The actinospores of these parasites attach to fish hosts via polar filaments that are extruded upon mechanical stimulation after preceding recognition of a chemical trigger contained in surface mucus. Our goal was to identify this signal. We separated compounds from a purified active fraction derived from trout mucus by a novel HPLC method. By subsequent nuclear magnetic resonance analysis of distinct components and testing in bioassays we elicited stimulation of polar filament discharge and sporoplasm emission in actinospores of three myxozoan spp., Myxobolus cerebralis, Myxobolus pseudodispar and Henneguya nuesslini, by the free nucleosides inosine, 2'-deoxyinosine and guanosine. These nucleosides also activated sporoplasm emission. Nucleosides appear to be appropriate cues for rapid host recognition by the waterborne parasite stages since they are continuously released into surface mucus. The recognition mechanism is not specific for susceptible host species, at least in the myxozoan spp. examined. In addition, a novel function of nucleobase derivatives as semiochemicals was uncovered and a wider impact of this molecule class in parasite recognition systems and aquatic chemical ecology is predicted. The relevance for disease prevention and cell culturing remains to be explored.
A study of mucus from the solitary coral Fungia fungites (Scleractinia: Fungiidae) in relation to photobiological UV adaptation
Venue: Marine Biology

The ultraviolet (UV)-absorbance spectrum (300 to 360 nm) of mucus obtained from Fungia fungites (L. 1758, collected in Tahiti in 1991) after being exposed to air for up to 5 min was measured, and UV-absorbing compounds were demonstrated to be present in the mucus, with a peak at 332 nm. The concentration of these UV-absorbing compounds was at a maximum in the first 2 min of secretion and decreased thereafter. Concentration was significantly related to the weight of the coral. Also, as corals were adapted to bathymetric levels of UV radiation, mucus concentration of UV-absorbing compounds decreased significantly with increasing depth.
Fish Exploiting Vortices Decrease Muscle Activity
Venue: Science

Fishes moving through turbulent flows or in formation are regularly exposed to vortices. Although animals living in fluid environments commonly capture energy from vortices, experimental data on the hydrodynamics and neural control of interactions between fish and vortices are lacking. We used quantitative flow visualization and electromyography to show that trout will adopt a novel mode of locomotion to slalom in between experimentally generated vortices by activating only their anterior axial muscles. Reduced muscle activity during vortex exploitation compared with the activity of fishes engaged in undulatory swimming suggests a decrease in the cost of locomotion and provides a mechanism to understand the patterns of fish distributions in schools and riverine environments.
Skeletal Muscle: A Brief Review of Structure and Function
Venue: Calcified Tissue International

Skeletal muscle is one of the most dynamic and plastic tissues of the human body. In humans, skeletal muscle comprises approximately 40 % of total body weight and contains 50–75 % of all body proteins. In general, muscle mass depends on the balance between protein synthesis and degradation and both processes are sensitive to factors such as nutritional status, hormonal balance, physical activity/exercise, and injury or disease, among others. In this review, we discuss the various domains of muscle structure and function including its cytoskeletal architecture, excitation-contraction coupling, energy metabolism, and force and power generation. We will limit the discussion to human skeletal muscle and emphasize recent scientific literature on single muscle fibers.
Tropic failure of Phyllactinia corylea contributes to the mildew resistance of mulberry genotypes
Venue: Mycopathologia

Different mulberry genotypes show great variation in their resistance to the powdery mildew Phyllactinia corylea. Conidial germination and hyphal growth of P. corylea on the leaf surface of two susceptible mulberry genotypes, viz., Kanva 2 (K2) and Victory 1 (V1) varieties of Morus indica, and on two resistant species, viz., M. laevigata and M. serrata were studied by scanning electron microscopy. Conidial germination and growth of germ tubes were normal on all the leaves. The hyphae of P. coryleaidentify stomata on host leaves by their topographical features to produce the stomatopodia precisely over them. The holes and/or the grooves of stomata appear to provide the signals for the initiation of stomatopodia and similar structures are erratically developed over many local depressions or grooves on leaf surface. The abaxial surface of K2 leaf is smooth without prominent undulations of epidermal cell surface, and the stomata are flush with the leaf surface. Although successful penetration is also achieved on V1 leaf, its slightly undulated surface occasionally provides inaccurate tropic signals to the hyphae, inducing the development of stomatopodia away from the stomata. The leaf surfaces of M. laevigata and M. serrata are very rough with highly sculptured cuticle and abundant epidermal outgrowths. Stomata mostly remain sunken or hidden amidst the cuticular ornamentations and the hyphae fail to recognise the precise signals from them. As the surface architecture of the leaves provides many immense sources of tropic signals, stomatopodia are often produced over local depressions or grooves. In these cases the fungus fails to penetrate the leaf, does not develop beyond 24 h and penetration is rarely achieved on the leaves of the resistant plants. The study indicates that the stimulatory effect of the leaf surface topography of resistant varieties misleads the pathogen from successful penetration, thus contributing to the plant's resistance.
Correlating Nanostructures with Function: Structural Colors on the Wings of a Malaysian Bee
Venue: THE THIRD NANOSCIENCE AND NANOTECHNOLOGY SYMPOSIUM 2010 (NNSB2010)

Structural colours refer to colours generated by nanostructures, with the characteristic dimension of the structures on the wavelength of the visible light (i.e., some hundreds of nanometers). Examples for structural colours are the colours of CDs and DVDs, the colours of soap bubbles or oil films on water (thin films), or the colours of certain butterfly wings (e.g., photonic crystals). Recently, we located a Malaysian bee with iridescent structural coloration on its wings. The generation of the colouration is still unknown, and there is no respective scientific literature available. This study presents the first AFM experiments related to the structural coloration of the carpenter bee wing. First attempts to investigate the nanostructures of the wing were performed with non‐contact atomic force microscopy (AFM, Park Systems XE‐100), using a Silicon nitride cantilever with a spring constant of 40 N/m and a resonance frequency of 300.000 kHz. The AFM scans reveal three layers with structures with a diamet...
Sneeze to leave: African wild dogs (Lycaon pictus) use variable quorum thresholds facilitated by sneezes in collective decisions
Venue: Proceedings of The Royal Society B: Biological Sciences

In despotically driven animal societies, one or a few individuals tend to have a disproportionate influence on group decision-making and actions. However, global communication allows each group member to assess the relative strength of preferences for different options among their group-mates. Here, we investigate collective decisions by free-ranging African wild dog packs in Botswana. African wild dogs exhibit dominant-directed group living and take part in stereotyped social rallies: high energy greeting ceremonies that occur before collective movements. Not all rallies result in collective movements, for reasons that are not well understood. We show that the probability of rally success (i.e. group departure) is predicted by a minimum number of audible rapid nasal exhalations (sneezes), within the rally. Moreover, the number of sneezes needed for the group to depart (i.e. the quorum) was reduced whenever dominant individuals initiated rallies, suggesting that dominant participation increases the likelihood of a rally's success, but is not a prerequisite. As such, the ‘will of the group’ may override dominant preferences when the consensus of subordinates is sufficiently great. Our findings illustrate how specific behavioural mechanisms (here, sneezing) allow for negotiation (in effect, voting) that shapes decision-making in a wild, socially complex animal society.
Dynamics of Drying in Phenolically Tanned Materials
Venue: Journal of Bionic Engineering

The cuticle of a maggot goes through a mechanical transition when it dries, increasing in stiffness by about an order of magnitude (e.g. from 0.5 GPa to 5 GPa) as the water content drops from about 1 g/g (weight of water per unit dry weight) to 0.4 g/g. Thus stiffness represents the loss of freezable water and is more or less diagnostic of a material stabilized by hydrogen bonds. Further loss in water results in a smaller increase in stiffness. In natural systems the water content is controlled by the addition of phenolic residues, resulting in tanning or sclerotisation, which drives the matrix components towards co-operative interaction and makes the material permanently waterproof.
Plant-bacteria partnerships for the remediation of hydrocarbon contaminated soils.
Venue: Chemosphere

Plant-bacteria partnerships have been extensively studied and applied to improve crop yield. In addition to their application in agriculture, a promising field to exploit plant-bacteria partnerships is the remediation of soil and water polluted with hydrocarbons. Application of effective plant-bacteria partnerships for the remediation of hydrocarbons depend mainly on the presence and metabolic activities of plant associated rhizo- and endophytic bacteria possessing specific genes required for the degradation of hydrocarbon pollutants. Plants and their associated bacteria interact with each other whereby plant supplies the bacteria with a special carbon source that stimulates the bacteria to degrade organic contaminants in the soil. In return, plant associated-bacteria can support their host plant to overcome contaminated-induced stress responses, and improve plant growth and development. In addition, plants further get benefits from their associated-bacteria possessing hydrocarbon-degradation potential, leading to enhanced hydrocarbon mineralization and lowering of both phytotoxicity and evapotranspiration of volatile hydrocarbons. A better understanding of plant-bacteria partnerships could be exploited to enhance the remediation of hydrocarbon contaminated soils in conjunction with sustainable production of non-food crops for biomass and biofuel production.
How snapping shrimp snap: through cavitating bubbles.
Venue: Science

The snapping shrimp (Alpheus heterochaelis) produces a loud snapping sound by an extremely rapid closure of its snapper claw. One of the effects of the snapping is to stun or kill prey animals. During the rapid snapper claw closure, a high-velocity water jet is emitted from the claw with a speed exceeding cavitation conditions. Hydrophone measurements in conjunction with time-controlled high-speed imaging of the claw closure demonstrate that the sound is emitted at the cavitation bubble collapse and not on claw closure. A model for the bubble dynamics based on a Rayleigh-Plesset-type equation quantitatively accounts for the time dependence of the bubble radius and for the emitted sound.
Underwater locomotion in a terrestrial beetle: combination of surface de-wetting and capillary forces
Venue: Proceedings of The Royal Society B: Biological Sciences

For the first time, we report the remarkable ability of the terrestrial leaf beetle Gastrophysa viridula to walk on solid substrates under water. These beetles have adhesive setae on their feet that produce a secretory fluid having a crucial role in adhesion on land. In air, adhesion is produced by capillary forces between the fluid-covered setae and the substrate. In general, capillary forces do not contribute to adhesion under water. However, our observations showed that these beetles may use air bubbles trapped between their adhesive setae to walk on flooded, inclined substrata or even under water. Beetle adhesion to hydrophilic surfaces under water was lower than that in air, whereas adhesion to hydrophobic surfaces under water was comparable to that in air. Oil-covered hairy pads had a pinning effect, retaining the air bubbles on their feet. Bubbles in contact with the hydrophobic substrate de-wetted the substrate and produced capillary adhesion. Additional capillary forces are generated by the pad's liquid bridges between the foot and the substrate. Inspired by this idea, we designed an artificial silicone polymer structure with underwater adhesive properties.
Hierarchical assembly of the siliceous skeletal lattice of the hexactinellid sponge Euplectella aspergillum.
Venue: Journal of Structural Biology

Despite its inherent mechanical fragility, silica is widely used as a skeletal material in a great diversity of organisms ranging from diatoms and radiolaria to sponges and higher plants. In addition to their micro- and nanoscale structural regularity, many of these hard tissues form complex hierarchically ordered composites. One such example is found in the siliceous skeletal system of the Western Pacific hexactinellid sponge, Euplectella aspergillum. In this species, the skeleton comprises an elaborate cylindrical lattice-like structure with at least six hierarchical levels spanning the length scale from nanometers to centimeters. The basic building blocks are laminated skeletal elements (spicules) that consist of a central proteinaceous axial filament surrounded by alternating concentric domains of consolidated silica nanoparticles and organic interlayers. Two intersecting grids of non-planar cruciform spicules define a locally quadrate, globally cylindrical skeletal lattice that provides the framework onto which other skeletal constituents are deposited. The grids are supported by bundles of spicules that form vertical, horizontal and diagonally ordered struts. The overall cylindrical lattice is capped at its upper end by a terminal sieve plate and rooted into the sea floor at its base by a flexible cluster of barbed fibrillar anchor spicules. External diagonally oriented spiral ridges that extend perpendicular to the surface further strengthen the lattice. A secondarily deposited laminated silica matrix that cements the structure together additionally reinforces the resulting skeletal mass. The mechanical consequences of each of these various levels of structural complexity are discussed.