nils-herrmann/clean_scirepeval huggingface dataset:
Coral Skeletons Defend against Ultraviolet Radiation
Venue: PLOS ONE

Many coral reef organisms are photosynthetic or have evolved in tight symbiosis with photosynthetic symbionts. As such, the tissues of reef organisms are often exposed to intense solar radiation in clear tropical waters and have adapted to trap and harness photosynthetically active radiation (PAR). High levels of ultraviolet radiation (UVR) associated with sunlight, however, represent a potential problem in terms of tissue damage.  By measuring UVR and PAR reflectance from intact and ground bare coral skeletons we show that the property of calcium carbonate skeletons to absorb downwelling UVR to a significant extent, while reflecting PAR back to the overlying tissue, has biological advantages. We placed cnidarians on top of bare skeletons and a UVR reflective substrate and showed that under ambient UVR levels, UVR transmitted through the tissues of cnidarians placed on top of bare skeletons were four times lower compared to their counterparts placed on a UVR reflective white substrate. In accordance with the lower levels of UVR measured in cnidarians on top of coral skeletons, a similar drop in UVR damage to their DNA was detected. The skeletons emitted absorbed UVR as yellow fluorescence, which allows for safe dissipation of the otherwise harmful radiation.  Our study presents a novel defensive role for coral skeletons and reveals that the strong UVR absorbance by the skeleton can contribute to the ability of corals, and potentially other calcifiers, to thrive under UVR levels that are detrimental to most marine life.
Self-propelled dropwise condensate on superhydrophobic surfaces.
Venue: Physical Review Letters

In conventional dropwise condensation on a hydrophobic surface, the condensate drops must be removed by external forces for continuous operation. This Letter reports continuous dropwise condensation spontaneously occurring on a superhydrophobic surface without any external forces. The spontaneous drop removal results from the surface energy released upon drop coalescence, which leads to a surprising out-of-plane jumping motion of the coalesced drops at a speed as high as 1 m/s. The jumping follows an inertial-capillary scaling and gives rise to a micrometric average diameter at steady state.
Salt allocation during leaf development and leaf fall in mangroves
Venue: Trees-structure and Function

By taking samples along individual branches and measuring leaf size, thickness and Na+ and K+ concentrations, we have shown in Bruguiera cylindrica, Avicennia rumphiana and Avicennia marina that there are two phases of salt accumulation by leaves. This is confirmed by re-analysis of published data for other species. The first phase is a rapid increase in leaf content as it grows from bud to maturity; the second is a slower but continuous change in quantity in the leaf, via changes in ion concentration and/or in leaf thickening. Leaf thickening must not be overlooked in estimating changes in leaf contents with age. Generally, leaf Na+ content increases significantly, and K+ content falls slightly. Mangrove leaves thus continue as sinks for Na+ throughout their lifetime. At the end of a leaf's life, just before abscission, no burst of salt accumulation has been found. Yellow, senescent leaves do not have higher Na+ than old green ones. We point out that leaf drop involves losing both salt and biomass, not just salt, and hence does not reduce the salt concentration in the plant. We conclude that leaf drop is not a salt excretion mechanism, but is simply the point in time at which the leaf ceases to accumulate salt. Using a simple model, the contribution to salt accumulation of slowly accumulated Na+ by mature leaves has been calculated. For B. cylindrica, the most extensively studied species, 60% of the salt in the leaf is accumulated slowly in the mature phase, thus more than during the initial phase of rapid expansion growth. The limited data suggest that gland-bearing species show smaller changes in mature leaf Na+ content than do gland-less species.
Serotonin Mediates Behavioral Gregarization Underlying Swarm Formation in Desert Locusts
Venue: Science

Desert locusts, Schistocerca gregaria, show extreme phenotypic plasticity, transforming between a little-seen solitarious phase and the notorious swarming gregarious phase depending on population density. An essential tipping point in the process of swarm formation is the initial switch from strong mutual aversion in solitarious locusts to coherent group formation and greater activity in gregarious locusts. We show here that serotonin, an evolutionarily conserved mediator of neuronal plasticity, is responsible for this behavioral transformation, being both necessary if behavioral gregarization is to occur and sufficient to induce it. Our data demonstrate a neurochemical mechanism linking interactions between individuals to large-scale changes in population structure and the onset of mass migration.
Grip and detachment of locusts on inverted sandpaper substrates.
Venue: Bioinspiration & Biomimetics

Locusts (Locusta migratoria manilensis) are characterized by their strong flying and grasping ability. Research on the grasping mechanism and behaviour of locusts on sloping substrates plays an important role in elucidating the mechanics of hexapod locomotion. Data on the maximum angles of slope at which locusts can grasp stably (critical angles of detachment) were obtained from high-speed video recordings at 215 fps. The grasping forces were collected by using two sensors, in situations where all left legs were standing on one and the right legs on the other sensor plate. These data were used to illustrate the grasping ability of locusts on slopes with varying levels of roughness. The grasping morphologies of locusts' bodies and tarsi were observed, and the surface roughness as well as diameters of their claw tips was measured under a microscope to account for the grasping mechanism of these insects on the sloping substrate. The results showed that the claw tips and part of the pads were in contact with the inverted substrate when the mean particle diameter was in the range of 15.3-40.5 µm. The interaction between pads and substrates may improve the stability of contact, and claw tips may play a key role in keeping the attachment reliable. A model was developed to explain the significant effects of the relative size of claw tips and mean particle diameter on grasping ability as well as the observed increase in lateral force (2.09-4.05 times greater than the normal force during detachment) with increasing slope angle, which indicates that the lateral force may be extremely important in keeping the contact reliable. This research lays the groundwork for the probable design and development of biomimetic robotics.
On the electrical conductivity of microbial nanowires and biofilms
Venue: Energy and Environmental Science

Dissimilatory metal-reducing bacteria (DMRB), such as Geobacter and Shewanella spp., occupy a distinct metabolic niche in which they acquire energy by coupling oxidation of organic fuels with reduction of insoluble extracellular electron acceptors (i.e., minerals). Their unique extracellular electron transfer (EET) capabilities extend to reduction of anodes (electrodes maintained at sufficiently positive potentials) on which they form persistent, electric current generating biofilms. One hypothesis describing the mechanism of EET by Geobacter and Shewanella spp. involves superexchange in which electrons are conducted by a succession of electron transfer reactions among redox proteins associated with the outer cell membranes, aligned along pilus-like filaments (e.g.pili), and/or throughout the extracellular matrix. Here we present theory, previously developed to describe superexchange within abiotic redox polymers, to describe superexchange within DMRB biofilms grown on anodes. We show that this theory appears to apply to recent ex situ measurements of electrical conductivity by individual pilus-like filaments of S. oneidensis MR-1 and G. sulfurreducensDL1, referred to as microbial nanowires. Microbial nanowires have received much recent attention because they are thought by some to impart electrical conductivity to DMRB biofilms and because of the prospect of microbe-produced conductive nanomaterials. We also show that this theory appears to apply to preliminary in situ demonstration of electrical conductivity of an anode-grown G. sulfurreducensDL1 biofilm. Based on these results we suggest a role for nanowires of S. oneidensis and G. sulfurreducens in biofilm conductivity.
Adaptive evolution of threonine deaminase in plant defense against insect herbivores
Venue: Proceedings of the National Academy of Sciences of the United States of America

Gene duplication is a major source of plant chemical diversity that mediates plant–herbivore interactions. There is little direct evidence, however, that novel chemical traits arising from gene duplication reduce herbivory. Higher plants use threonine deaminase (TD) to catalyze the dehydration of threonine (Thr) to α-ketobutyrate and ammonia as the committed step in the biosynthesis of isoleucine (Ile). Cultivated tomato and related Solanum species contain a duplicated TD paralog (TD2) that is coexpressed with a suite of genes involved in herbivore resistance. Analysis of TD2-deficient tomato lines showed that TD2 has a defensive function related to Thr catabolism in the gut of lepidopteran herbivores. During herbivory, the regulatory domain of TD2 is removed by proteolysis to generate a truncated protein (pTD2) that efficiently degrades Thr without being inhibited by Ile. We show that this proteolytic activation step occurs in the gut of lepidopteran but not coleopteran herbivores, and is catalyzed by a chymotrypsin-like protease of insect origin. Analysis of purified recombinant enzymes showed that TD2 is remarkably more resistant to proteolysis and high temperature than the ancestral TD1 isoform. The crystal structure of pTD2 provided evidence that electrostatic interactions constitute a stabilizing feature associated with adaptation of TD2 to the extreme environment of the lepidopteran gut. These findings demonstrate a role for gene duplication in the evolution of a plant defense that targets and co-opts herbivore digestive physiology.
Biochemical analysis of elastic and rigid cuticles of Cirsium horridulum
Venue: Planta

The cuticle is a complex structure of soluble lipids, lipid polymers and polysaccharides. In addition to its functions to reduce water loss and provide a protective barrier, its mechanical properties may be significant to plant growth and development. We investigated the cuticle of Cirsium horridulum Michx. because of its involvement in the thigmonastic contraction of staminal filaments. The staminal filaments and portions of the style are surrounded by a highly elastic cuticle in contrast to the rigid cuticle of the corolla and leaves. Our aim was to determine if the biochemical composition affected the elasticity of the cuticle. We discovered that the ratio of carbohydrates to lipids is 1:7 in floral parts but 2:1 in leaf cuticle. Esterified cutin components represented about 80% of the cuticle and di-hydroxyhexadecanoic acids were the major monomers of cutin, regardless of origin. The cutin of elastic tissues is characterized by a higher content of tri-hydroxy monomers than the cutin of rigid tissues. The data suggest that hydroxyl groups enhance the hydrophilic character of the cuticle and contribute to cuticular elasticity.
Surface Tension Transport of Prey by Feeding Shorebirds: The Capillary Ratchet
Venue: Science

The variability of bird beak morphology reflects diverse foraging strategies. One such feeding mechanism in shorebirds involves surface tension–induced transport of prey in millimetric droplets: By repeatedly opening and closing its beak in a tweezering motion, the bird moves the drop from the tip of its beak to its mouth in a stepwise ratcheting fashion. We have analyzed the subtle physical mechanism responsible for drop transport and demonstrated experimentally that the beak geometry and the dynamics of tweezering may be tuned to optimize transport efficiency. We also highlight the critical dependence of the capillary ratchet on the beak's wetting properties, thus making clear the vulnerability of capillary feeders to surface pollutants.
Adaptive aerial righting during the escape dropping of wingless pea aphids
Venue: Current Biology

Pea aphids ( Acyrthosiphon pisum ) are small sap-sucking insects that live on plants in colonies containing mostly wingless individuals. They often escape predators, parasitoids and grazing mammalian herbivores by dropping off the plant [1,2], avoiding immediate danger but exposing themselves to ground predators, starvation and desiccation . We show here that dropping pea aphids land on their legs, regardless of their initial orientation on the plant (like a defenestrated cat), by rotating their body during the fall. This righting ability is intriguing, as wingless aphids have no specialized structures for maneuvering in mid-air. Instead, they assume a stereotypic posture which is aerodynamically stable only when the aphids fall right-side up. Consequently, the body passively rotates to the stable upright orientation, improving the chance of clinging to leaves encountered on the way down and lowering the danger of reaching the ground.
Stratum corneum keratin structure, function, and formation: the cubic rod-packing and membrane templating model.
Venue: Journal of Investigative Dermatology

A new model for stratum corneum keratin structure, function, and formation is presented. The structural and functional part of the model, which hereafter is referred to as "the cubic rod-packing model", postulates that stratum corneum keratin intermediate filaments are arranged according to a cubic-like rod-packing symmetry with or without the presence of an intracellular lipid membrane with cubic-like symmetry enveloping each individual filament. The new model could account for (i) the cryo-electron density pattern of the native corneocyte keratin matrix, (ii) the X-ray diffraction patterns, (iii) the swelling behavior, and (iv) the mechanical properties of mammalian stratum corneum. The morphogenetic part of the model, which hereafter is referred to as "the membrane templating model", postulates the presence in cellular space of a highly dynamic small lattice parameter (<30 nm) membrane structure with cubic-like symmetry, to which keratin is associated. It further proposes that membrane templating, rather than spontaneous self-assembly, is responsible for keratin intermediate filament formation and dynamics. The new model could account for (i) the cryo-electron density patterns of the native keratinocyte cytoplasmic space, (ii) the characteristic features of the keratin network formation process, (iii) the dynamic properties of keratin intermediate filaments, (iv) the close lipid association of keratin, (v) the insolubility in non-denaturating buffers and pronounced polymorphism of keratin assembled in vitro, and (vi) the measured reduction in cell volume and hydration level between the stratum granulosum and stratum corneum. Further, using cryo-transmission electron microscopy on native, fully hydrated, vitreous epidermis we show that the subfilametous keratin electron density pattern consists, both in corneocytes and in viable keratinocytes, of one axial subfilament surrounded by an undetermined number of peripheral subfilaments forming filaments with a diameter of approximately 8 nm.
Mushrooms as Rainmakers: How Spores Act as Nuclei for Raindrops
Venue: PLOS ONE

Millions of tons of fungal spores are dispersed in the atmosphere every year. These living cells, along with plant spores and pollen grains, may act as nuclei for condensation of water in clouds. Basidiospores released by mushrooms form a significant proportion of these aerosols, particularly above tropical forests. Mushroom spores are discharged from gills by the rapid displacement of a droplet of fluid on the cell surface. This droplet is formed by the condensation of water on the spore surface stimulated by the secretion of mannitol and other hygroscopic sugars. This fluid is carried with the spore during discharge, but evaporates once the spore is airborne. Using environmental electron microscopy, we have demonstrated that droplets reform on spores in humid air. The kinetics of this process suggest that basidiospores are especially effective as nuclei for the formation of large water drops in clouds. Through this mechanism, mushroom spores may promote rainfall in ecosystems that support large populations of ectomycorrhizal and saprotrophic basidiomycetes. Our research heightens interest in the global significance of the fungi and raises additional concerns about the sustainability of forests that depend on heavy precipitation.
Geographical Variation in Bill Size across Bird Species Provides Evidence for Allen’s Rule
Venue: The American Naturalist

Allen’s rule proposes that the appendages of endotherms are smaller, relative to body size, in colder climates, in order to reduce heat loss. Empirical support for Allen’s rule is mainly derived from occasional reports of geographical clines in extremity size of individual species. Interspecific evidence is restricted to two studies of leg proportions in seabirds and shorebirds. We used phylogenetic comparative analyses of 214 bird species to examine whether bird bills, significant sites of heat exchange, conform to Allen’s rule. The species comprised eight diverse taxonomic groups—toucans, African barbets, Australian parrots, estrildid finches, Canadian galliforms, penguins, gulls, and terns. Across all species, there were strongly significant relationships between bill length and both latitude and environmental temperature, with species in colder climates having significantly shorter bills. Patterns supporting Allen’s rule in relation to latitudinal or altitudinal distribution held within all groups except the finches. Evidence for a direct association with temperature was found within four groups (parrots, galliforms, penguins, and gulls). Support for Allen’s rule in leg elements was weaker, suggesting that bird bills may be more susceptible to thermoregulatory constraints generally. Our results provide the strongest comparative support yet published for Allen’s rule and demonstrate that thermoregulation has been an important factor in shaping the evolution of bird bills.
Morphological variations of Macrocystis pyrifera in the Falkland Islands in relation to environment and season
Venue: Marine Biology

Some morphological characteristics of the giant kelp Macrocystis pyrifera in the Falkland Islands were studied from December 1985 until March 1987 in a shallow and relatively sheltered coastal zone and from December 1985 until January 1987 in a deeper offshore field exposed to swells. Seasonal fluctuations in lamina wet weight, density and form as well as pneumatocyst wet weight form and stipe density (i.e., wet weight per unit length) paralleled fluctuations in frond wet weight. Morphological differences between canopies of the giant kelp in the coastal zone and the offshore bed were probably mainly due to differences in water movement and depth between the two sites. Laminae and pneumatocysts of submersed-frond sites had different shapes than those of canopy-forming portions of fronds at the same sites, and their internodes were longer.
Distributed graph coloring: an approach based on the calling behavior of Japanese tree frogs
Venue: Swarm Intelligence

Graph coloring—also known as vertex coloring—considers the problem of assigning colors to the nodes of a graph such that adjacent nodes do not share the same color. The optimization version of the problem concerns the minimization of the number of colors used. In this paper we deal with the problem of finding valid graphs colorings in a distributed way, that is, by means of an algorithm that only uses local information for deciding the color of the nodes. The algorithm proposed in this paper is inspired by the calling behavior of Japanese tree frogs. Male frogs use their calls to attract females. Interestingly, groups of males that are located near each other desynchronize their calls. This is because female frogs are only able to correctly localize male frogs when their calls are not too close in time. The proposed algorithm makes use of this desynchronization behavior for the assignment of different colors to neighboring nodes. We experimentally show that our algorithm is very competitive with the current state of the art, using different sets of problem instances and comparing to one of the most competitive algorithms from the literature.
The Advantages of a Tapered Whisker
Venue: PLOS ONE

The role of facial vibrissae (whiskers) in the behavior of terrestrial mammals is principally as a supplement or substitute for short-distance vision. Each whisker in the array functions as a mechanical transducer, conveying forces applied along the shaft to mechanoreceptors in the follicle at the whisker base. Subsequent processing of mechanoreceptor output in the trigeminal nucleus and somatosensory cortex allows high accuracy discriminations of object distance, direction, and surface texture. The whiskers of terrestrial mammals are tapered and approximately circular in cross section. We characterize the taper of whiskers in nine mammal species, measure the mechanical deflection of isolated felid whiskers, and discuss the mechanics of a single whisker under static and oscillatory deflections. We argue that a tapered whisker provides some advantages for tactile perception (as compared to a hypothetical untapered whisker), and that this may explain why the taper has been preserved during the evolution of terrestrial mammals.
Hyperacute directional hearing in a microscale auditory system
Venue: Nature

The physics of sound propagation imposes fundamental constraints on sound localization: for a given frequency, the smaller the receiver, the smaller the available cues. Thus, the creation of nanoscale acoustic microphones with directional sensitivity is very difficult. The fly Ormia ochracea possesses an unusual ‘ear’ that largely overcomes these physical constraints; attempts to exploit principles derived from O. ochracea for improved hearing aids are now in progress. Here we report that O. ochracea can behaviourally localize a salient sound source with a precision equal to that of humans. Despite its small size and minuscule interaural cues, the fly localizes sound sources to within 2° azimuth. As the fly's eardrums are less than 0.5 mm apart, localization cues are around 50 ns. Directional information is represented in the auditory system by the relative timing of receptor responses in the two ears. Low-jitter, phasic receptor responses are pooled to achieve hyperacute timecoding. These results demonstrate that nanoscale/microscale directional microphones patterned after O. ochracea have the potential for highly accurate directional sensitivity, independent of their size. Notably, in the fly itself this performance is dependent on a newly discovered set of specific coding strategies employed by the nervous system.