nils-herrmann/clean_scirepeval huggingface dataset:
Defense by foot adhesion in a beetle (Hemisphaerota cyanea).
Venue: Proceedings of the National Academy of Sciences of the United States of America

The beetle Hemisphaerota cyanea (Chrysomelidae; Cassidinae) responds to disturbance by activating a tarsal adhesion mechanism by which it secures a hold on the substrate. Its tarsi are oversized and collectively bear some 60,000 adhesive bristles, each with two terminal pads. While walking, the beetle commits but a small fraction of the bristles to contact with the substrate. But when assaulted, it presses its tarsi flatly down, thereby touching ground with all or nearly all of the bristles. Once so adhered, it can withstand pulling forces of up to 0.8 g ( approximately 60 times its body mass) for 2 min, and of higher magnitudes, up to >3 g, for shorter periods. Adhesion is secured by a liquid, most probably an oil. By adhering, the beetle is able to thwart attacking ants, given that it is able to cling more persistently than the ant persists in its assault. One predator, the reduviid Arilus cristatus, is able to feed on the beetle, possibly because by injecting venom it prevents the beetle from maintaining its tarsal hold.
From three-dimensional weavings to swollen corneocytes
Venue: Journal of the Royal Society Interface

A novel technique to generate three-dimensional Euclidean weavings, composed of close-packed, periodic arrays of one-dimensional fibres, is described. Some of these weavings are shown to dilate by simple shape changes of the constituent fibres (such as fibre straightening). The free volume within a chiral cubic example of a dilatant weaving, the ideal conformation of the G129 weaving related to the Σ+ rod packing, expands more than fivefold on filament straightening. This remarkable three-dimensional weaving, therefore, allows an unprecedented variation of packing density without loss of structural rigidity and is an attractive design target for materials. We propose that the G129 weaving (ideal Σ+ weaving) is formed by keratin fibres in the outermost layer of mammalian skin, probably templated by a folded membrane.
Smart Swarms of Bacteria-Inspired Agents with Performance Adaptable Interactions
Venue: PLOS Computational Biology

Collective navigation and swarming have been studied in animal groups, such as fish schools, bird flocks, bacteria, and slime molds. Computer modeling has shown that collective behavior of simple agents can result from simple interactions between the agents, which include short range repulsion, intermediate range alignment, and long range attraction. Here we study collective navigation of bacteria-inspired smart agents in complex terrains, with adaptive interactions that depend on performance. More specifically, each agent adjusts its interactions with the other agents according to its local environment – by decreasing the peers' influence while navigating in a beneficial direction, and increasing it otherwise. We show that inclusion of such performance dependent adaptable interactions significantly improves the collective swarming performance, leading to highly efficient navigation, especially in complex terrains. Notably, to afford such adaptable interactions, each modeled agent requires only simple computational capabilities with short-term memory, which can easily be implemented in simple swarming robots.
Resisting Antimicrobial Resistance: Lessons from Fungus Farming Ants.
Venue: Trends in Ecology and Evolution

Attine ants use antimicrobials produced by commensal bacteria to inhibit parasites on their fungal gardens. However, in this agricultural system, antimicrobial use does not lead to overwhelming resistance, as is typical in clinical settings. Mixtures of continually evolving antimicrobial variants could support these dynamics.
Orange/lemon-scented beetles: opposite enantiomers of limonene as major constituents in the defensive secretion of related carabids
Venue: Naturwissenschaften

The major constituent in the pygidial gland defensive fluid of the carabid beetle Ardistomis schaumii is (R)-(+)-limonene, whereas that of Semiardistomis puncticollis is (S)-(−)-limonene. This was an unanticipated result, since it is not very common to find the opposite enantiomers of the same compound among the secondary metabolites of related species. Moreover, the glandular liquid of A. schaumii contains 1,8-cineole, and that of S. puncticollis has β-pinene, β-phellandrene, sabinene, and p-cymene. Of about 500 carabid species that have been chemically investigated, this is the first report of the presence of such complex mixtures of monoterpenes in their defensive secretions.
Wet mammals shake at tuned frequencies to dry
Venue: Journal of the Royal Society Interface

In cold wet weather, mammals face hypothermia if they cannot dry themselves. By rapidly oscillating their bodies, through a process similar to shivering, furry mammals can dry themselves within seconds. We use high-speed videography and fur particle tracking to characterize the shakes of 33 animals (16 animals species and five dog breeds), ranging over four orders of magnitude in mass from mice to bears. We here report the power law relationship between shaking frequency f and body mass M to be f ∼ M−0.22, which is close to our prediction of f ∼ M−0.19 based upon the balance of centrifugal and capillary forces. We also observe a novel role for loose mammalian dermal tissue: by whipping around the body, it increases the speed of drops leaving the animal and the ensuing dryness relative to tight dermal tissue.
Electrical signals control wound healing through phosphatidylinositol-3-OH kinase-γ and PTEN
Venue: Nature

Wound healing is essential for maintaining the integrity of multicellular organisms. In every species studied, disruption of an epithelial layer instantaneously generates endogenous electric fields, which have been proposed to be important in wound healing. The identity of signalling pathways that guide both cell migration to electric cues and electric-field-induced wound healing have not been elucidated at a genetic level. Here we show that electric fields, of a strength equal to those detected endogenously, direct cell migration during wound healing as a prime directional cue. Manipulation of endogenous wound electric fields affects wound healing in vivo. Electric stimulation triggers activation of Src and inositol–phospholipid signalling, which polarizes in the direction of cell migration. Notably, genetic disruption of phosphatidylinositol-3-OH kinase-γ (PI(3)Kγ) decreases electric-field-induced signalling and abolishes directed movements of healing epithelium in response to electric signals. Deletion of the tumour suppressor phosphatase and tensin homolog (PTEN) enhances signalling and electrotactic responses. These data identify genes essential for electrical-signal-induced wound healing and show that PI(3)Kγ and PTEN control electrotaxis.
Draculin, the anticoagulant factor in vampire bat saliva, is a tight-binding, noncompetitive inhibitor of activated factor X.
Venue: Biochimica et Biophysica Acta

The kinetic mechanism of action of Draculin on activated Factor X (FXa) is established. Draculin inhibits activated Factor X within seconds of incubation at near equimolar concentration (2-6 times on molar basis). Fitting the data to the equation for a tight-binding inhibitor gives a value for K(i)(K(d)) = 14.8+/-1.5 nM. The formation of the Draculin-FXa complex can be explained by a two-step mechanism, where for the first, reversible step, k(on) = 1.117 (+/- 0.169, S.E.M.) x 10(6) M(-1)s(-1) and k(off) = 15.388 (+/- 1.672) x 10(-3) s(-1), while for the second, irreversible step, which is concentration-independent, k(2) = 0.072 s(-1). K(d) obtained from k(off)/k(on) = 13.76 nM. Lineweaver-Burk plot shows a noncompetitive behavior. This noncompetitive mode of inhibition of Draculin is supported by the observation that Draculin, at concentrations giving complete inhibition, does not impair binding of p-aminobenzamidine to FXa. Moreover, under the same conditions, Draculin induces <14% decrease of the fluorescence intensity of the p-aminobenzamidine-FXa complex. We conclude that Draculin is a noncompetitive, tight-binding inhibitor of FXa, a characteristic so far unique amongst natural FXa inhibitors.
A method for characterizing and mimicking forest canopy gaps caused by different disturbances
Venue: Forest Science

Forest canopy gaps are measurable indicators of past small-scale disturbances. These disturbances can impact forest stand dynamics in ways that help maintain and enhance many ecosystem values. Impacts are commonly assessed using timber production metrics based on average stand values, but metrics based on smaller scales are needed to assess impacts on nontimber resources. In this study, we developed a multivariate method of quantitatively characterizing individual canopy gaps in Douglas-fir/grand fir stands in the Blue Mountains of eastern Oregon. We then established a reference or target range of variability by profiling gaps according to numbers of snags, downed logs, gap size and shape, and recolonizing vegetation. Cluster analysis, multidimensional scaling, and classification trees were used with these profiles to quantify similarity among individual gaps. Gaps fell into four groups, which could be interpreted as three ecologically functional groups on the basis of their role in stand development. Gaps caused by the same agents commonly fell within the same functional group: (1) flooding, logging, spruce budworm, and windfall cause stand level impacts that reset the stand development sequence; (2) bark beetles, tree fall, and root diseases cause within stand impacts that altered the rate of stand development; and (3) stem decay and dwarf mistletoe, and, under some circumstances, all disturbance agents, could kill trees yet have no impact on stand development except create space into which neighboring trees expand. We present a simple test to monitor how gaps change with silvicultural manipulations. Results indicate that this method offers (1) a way to systematically guide silvicultural manipulations aimed at mimicking natural disturbances at the canopy gap scale, and (2) a way to monitor the effectiveness of such silvicultural treatments and management actions using gap-based silviculture prescriptions.
Hardness in arthropod exoskeletons in the absence of transition metals.
Venue: Acta Biomaterialia

The arthropod cuticle is a remarkable and versatile biological material commonly composed of chitin and proteins. Lessons can be learned from the way it is adapted to fit its functions. The larval jewel beetle, Pseudotaenia frenchi, demonstrates hardness in the cutting edge of the mandibles in excess of the mineralized carapace of stone crabs and compares favourably with some stainless steels. Yet this is a form of cuticle which is devoid of transition metals or mineralization. In seeming contradiction, the similarly dark coloured adult beetle mandibles contain the transition metal manganese, but are significantly softer. Energy dispersive X-ray analysis and infrared spectroscopy have been used to investigate the differences in composition of mandible cuticle of the adult and larval beetles.
A Biological Screw in a Beetle’s Leg
Venue: Science

Joints on the legs of weevils form a functional screw-and-nut system. The coxa-trochanteral joints on the legs of the weevil Trigonopterus oblongus (Pascoe) work as a biological screw-and-nut system. The apical portions of the coxae closely resemble nuts with well-defined inner threads covering 345°. The corresponding trochanters have perfectly compatible external spiral threads of 410°.
Calcium Carbonate in Termite Mounds
Venue: Nature

THE presence of appreciable quantities of calcium carbonate in termite mounds on non-calcareous soil has intrigued pedologists for many years. Milne6, for example, found a termite mound with 7% calcium carbonate and estimated that it contained about 2 t of calcium carbonate excluding the hard limestone (53% CaCO3) base of the mound. The soil below the base of a termite mound may also be calcareous. The soil underneath one termite mound in an area of non-calcareous soil was found to have a mean of 1.7% calcium carbonate to a depth of 6 m, or about 20 t of calcium carbonate9.
Growth, geometry, and mechanics of a blooming lily
Venue: Proceedings of the National Academy of Sciences of the United States of America

Despite the common use of the blooming metaphor, its floral inspiration remains poorly understood. Here we study the physical process of blooming in the asiatic lily Lilium casablanca. Our observations show that the edges of the petals wrinkle as the flower opens, suggesting that differential growth drives the deployment of these laminar shell-like structures. We use a combination of surgical manipulations and quantitative measurements to confirm this hypothesis and provide a simple theory for this change in the shape of a doubly curved thin elastic shell subject to differential growth across its planform. Our experiments and theory overturn previous hypotheses that suggest that blooming is driven by differential growth of the inner layer of the petals and in the midrib by providing a qualitatively different paradigm that highlights the role of edge growth. This functional morphology suggests new biomimetic designs for deployable structures using boundary or edge actuation rather than the usual bulk or surface actuation.
Frequency specificity of vibration dependent discharge of nematocysts in sea anemones.
Venue: Journal of Experimental Zoology

Hair bundles on tentacles of sea anemones are similar to vertebrate hair bundles in terms of structure and function. Anemone hair bundles are involved in regulating discharge of nematocysts, "stinging capsules," used to capture prey. N-acetylated sugars from the prey including N-acetylneuraminic acid (NANA) induce hair bundles to elongate while shifting vibration dependent discharge of nematocysts to lower frequencies matching prey movements. In the present study, we find that vibration dependent discharge of nematocysts exhibits sharp frequency discrimination to within one Hz. Testing at one-Hz intervals over the range of frequencies spanning 1-75 Hz, we find that seven of these are stimulatory in seawater alone. A total of twenty-six frequencies are stimulatory in the presence of NANA. Stimulatory frequencies in NANA are lower than those in seawater alone. We find that antagonists of ryanodine receptors including ryanodine, procaine and tetracaine shift discharge to lower frequencies. Fluorescently tagged ryanodine labels numerous small loci in the apical cytoplasm of supporting cells. We propose that calcium induced calcium release (CICR) via ryanodine receptors may sharpen frequency specificity and/or cause shortening of hair bundles to shift frequency specificity to higher frequencies.
Sag-Mediated Modulated Tension in Terebellid Tentacles Exposed to Flow.
Venue: The Biological Bulletin

The long, compliant feeding tentacles of the terebellid polychaete Eupolymnia heterobranchia not only stretch out over a sandflat substratum but also extend into flow. Tentacles suspended perpendicular to flow responded to increasing velocity by increasing their sag. An analysis of tension in these tentacles, mathematically analogous to that applicable to suspension bridges, shows that sagging permits the tentacles to avoid increases in tension that would otherwise occur as flow increases. Force modulation was achieved by active muscular control rather than by passive material properties. Although these tentacles would certainly break in the experimental flows if they did not sag, the low tension achieved suggests that some other reason, such as limitations on the adherence of cilia and mucus, accounts for the level of tension observed. Because drag is maximum on tentacles oriented perpendicular to flow, reorientation of tentacles, either by sagging or by dangling parallel to flow, additionally reduces tension by reducing drag. Theoretical estimates of drag on tentacles oriented parallel to flow show that they are never in danger of being broken. Drag is sufficient, however, to assist in passive extension of tentacles. While reorientation is a common mode of drag reduction among marine organisms, sagging represents a novel mechanism of mediating structural forces resulting from flow.
Structural Design and Biomechanics of Friction-Based Releasable Attachment Devices in Insects1
Venue: Integrative and Comparative Biology

Many systems, located on different parts of the body, involve surfaces with particular frictional properties. Such systems evolved to attach parts of the body to each other, or to attach an insect to the substratum by providing fast and reversible attachment/detachment. Among these systems, there are some that deal with predefined surfaces, and others, in which one surface remains unpredictable. The first type of system occurs, for example, in wing-locking devices and head-arresting systems and is called probabilistic fasteners. The second type is mainly represented by insect attachment pads of two alternative designs: hairy and smooth. The relationship between surface patterns and/or mechanical properties of materials of contact pairs results in two main working principles of the frictional devices: mechanical interlocking, or maximization of the contact area. We give an overview of the functional design of two main groups of friction-based attachment devices in insects: probabilistic fasteners and attachment pads.
Dynamics of leg muscle function in tammar wallabies (M. eugenii) during level versus incline hopping
Venue: The Journal of Experimental Biology

The goal of our study was to examine whether the in vivo force-length behavior, work and elastic energy savings of distal muscle-tendon units in the legs of tammar wallabies (Macropus eugenii) change during level versus incline hopping. To address this question, we obtained measurements of muscle activation (via electromyography), fascicle strain (via sonomicrometry) and muscle-tendon force (via tendon buckles) from the lateral gastrocnemius (LG) and plantaris (PL) muscles of tammar wallabies trained to hop on a level and an inclined (10°, 17.4% grade) treadmill at two speeds (3.3 m s-1 and 4.2 m s-1). Similar patterns of muscle activation, force and fascicle strain were observed under both level and incline conditions. This also corresponded to similar patterns of limb timing and movement (duty factor, limb contact time and hopping frequency). During both level and incline hopping, the LG and PL exhibited patterns of fascicle stretch and shortening that yielded low levels of net fascicle strain [LG: level, -1.0±4.6% (mean ± s.e.m.) vs incline, 0.6±4.5%; PL: level, 0.1±1.0% vs incline, 0.4±1.6%] and muscle work (LG: level, -8.4±8.4 J kg-1 muscle vs incline, -6.8±7.5 J kg-1 muscle; PL: level, -2.0±0.6 J kg-1 muscle vs incline, -1.4±0.7 J kg-1 muscle). Consequently, neither muscle significantly altered its contractile dynamics to do more work during incline hopping. Whereas electromyographic (EMG) phase, duration and intensity did not differ for the LG, the PL exhibited shorter but more intense periods of activation, together with reduced EMG phase (P<0.01), during incline versus level hopping. Our results indicate that design for spring-like tendon energy savings and economical muscle force generation is key for these two distal muscle-tendon units of the tammar wallaby, and the need to accommodate changes in work associated with level versus incline locomotion is achieved by more proximal muscles of the limb.
Ultra-fast underwater suction traps
Venue: Proceedings of The Royal Society B: Biological Sciences

Carnivorous aquatic Utricularia species catch small prey animals using millimetre-sized underwater suction traps, which have fascinated scientists since Darwin's early work on carnivorous plants. Suction takes place after mechanical triggering and is owing to a release of stored elastic energy in the trap body accompanied by a very fast opening and closing of a trapdoor, which otherwise closes the trap entrance watertight. The exceptional trapping speed—far above human visual perception—impeded profound investigations until now. Using high-speed video imaging and special microscopy techniques, we obtained fully time-resolved recordings of the door movement. We found that this unique trapping mechanism conducts suction in less than a millisecond and therefore ranks among the fastest plant movements known. Fluid acceleration reaches very high values, leaving little chance for prey animals to escape. We discovered that the door deformation is morphologically predetermined, and actually performs a buckling/unbuckling process, including a complete trapdoor curvature inversion. This process, which we predict using dynamical simulations and simple theoretical models, is highly reproducible: the traps are autonomously repetitive as they fire spontaneously after 5–20 h and reset actively to their ready-to-catch condition.
Increased Food and Ecosystem Security via Perennial Grains
Venue: Science

Perennial grains hold promise, especially for marginal landscapes or with limited resources where annual versions struggle. Despite doubling of yields of major grain crops since the 1950s, more than one in seven people suffer from malnutrition (1). Global population is growing; demand for food, especially meat, is increasing; much land most suitable for annual crops is already in use; and production of nonfood goods (e.g., biofuels) increasingly competes with food production for land (2). The best lands have soils at low or moderate risk of degradation under annual grain production but make up only 12.6% of global land area (16.5 million km2) (3). Supporting more than 50% of world population is another 43.7 million km2 of marginal lands (33.5% of global land area), at high risk of degradation under annual grain production but otherwise capable of producing crops (3). Global food security depends on annual grains—cereals, oilseeds, and legumes—planted on almost 70% of croplands, which combined supply a similar portion of human calories (4, 5). Annual grain production, though, often compromises essential ecosystem services, pushing some beyond sustainable boundaries (5). To ensure food and ecosystem security, farmers need more options to produce grains under different, generally less favorable circumstances than those under which increases in food security were achieved this past century. Development of perennial versions of important grain crops could expand options.