nils-herrmann/clean_scirepeval huggingface dataset:
The structure of the cushions in the feet of African elephants (Loxodonta africana)
Venue: Journal of Anatomy

The uniquely designed limbs of the African elephant, Loxodonta africana, support the weight of the largest terrestrial animal. Besides other morphological peculiarities, the feet are equipped with large subcutaneous cushions which play an important role in distributing forces during weight bearing and in storing or absorbing mechanical forces. Although the cushions have been discussed in the literature and captive elephants, in particular, are frequently affected by foot disorders, precise morphological data are sparse. The cushions in the feet of African elephants were examined by means of standard anatomical and histological techniques, computed tomography (CT) and magnetic resonance imaging (MRI). In both the forelimb and the hindlimb a 6th ray, the prepollex or prehallux, is present. These cartilaginous rods support the metacarpal or metatarsal compartment of the cushions. None of the rays touches the ground directly. The cushions consist of sheets or strands of fibrous connective tissue forming larger metacarpal/metatarsal and digital compartments and smaller chambers which were filled with adipose tissue. The compartments are situated between tarsal, metatarsal, metacarpal bones, proximal phalanges or other structures of the locomotor apparatus covering the bones palmarly/plantarly and the thick sole skin. Within the cushions, collagen, reticulin and elastic fibres are found. In the main parts, vascular supply is good and numerous nerves course within the entire cushion. Vater–Pacinian corpuscles are embedded within the collagenous tissue of the cushions and within the dermis. Meissner corpuscles are found in the dermal papillae of the foot skin. The micromorphology of elephant feet cushions resembles that of digital cushions in cattle or of the foot pads in humans but not that of digital cushions in horses. Besides their important mechanical properties, foot cushions in elephants seem to be very sensitive structures.
A comparative study of piscine defense: The scales of Arapaima gigas, Latimeria chalumnae and Atractosteus spatula.
Venue: Journal of The Mechanical Behavior of Biomedical Materials

We compare the characteristics of the armored scales of three large fish, namely the Arapaima gigas (arapaima), Latimeria chalumnae (coelacanth), and Atractosteus spatula (alligator gar), with specific focus on their unique structure-mechanical property relationships and their specialized ability to provide protection from predatory pressures, with the ultimate goal of providing bio-inspiration for manmade materials. The arapaima has flexible and overlapping cycloid scales which consist of a tough Bouligand-type arrangement of collagen layers in the base and a hard external mineralized surface, protecting it from piranha, a predator with extremely sharp teeth. The coelacanth has overlapping elasmoid scales that consist of adjacent Bouligand-type pairs, forming a double-twisted Bouligand-type structure. The collagenous layers are connected by collagen fibril struts which significantly contribute to the energy dissipation, so that the scales have the capability to defend from predators such as sharks. The alligator gar has inflexible articulating ganoid scales made of a hard and highly mineralized enamel-like outer surface and a tough dentine-like bony base, which resist powerful bite forces of self-predation and attack by alligators. The structural differences between the three scales correspond with the attack of their predators, and show refined mechanisms which may be imitated and incorporated into superior bioinspired and biomimetic designs that are specialized to resist specific modes of predation.
Soil immune responses
Venue: Science

Soil microbiomes may be harnessed for plant health Soil microorganisms are central to the provision of food, feed, fiber, and medicine. Engineering of soil microbiomes may promote plant growth and plant health, thus contributing to food security and agricultural sustainability (1, 2). However, little is known about most soil microorganisms and their impact on plant health. Disease-suppressive soils offer microbiome-mediated protection of crop plants against infections by soil-borne pathogens. Understanding of the microbial consortia and mechanisms involved in disease suppression may help to better manage plants while reducing fertilizer and pesticide inputs.
Distribution of unique red feather pigments in parrots
Venue: Biology Letters

In many birds, red, orange and yellow feathers are coloured by carotenoid pigments, but parrots are an exception. For over a century, biochemists have known that parrots use an unusual set of pigments to produce their rainbow of plumage colours, but their biochemical identity has remained elusive until recently. Here, we use high-performance liquid chromatography to survey the pigments present in the red feathers of 44 species of parrots representing each of the three psittaciform families. We found that all species used the same suite of five polyenal lipochromes (or psittacofulvins) to colour their plumage red, indicating that this unique system of pigmentation is remarkably conserved evolutionarily in parrots. Species with redder feathers had higher concentrations of psittacofulvins in their plumage, but neither feather colouration nor historical relatedness predicted the ratios in which the different pigments appeared. These polyenes were absent from blood at the time when birds were replacing their colourful feathers, suggesting that parrots do not acquire red plumage pigments from the diet, but instead manufacture them endogenously at growing feathers.
Crosslinking Lessons From Biology: Enlisting Enzymes for Macromolecular Assembly
Venue: Journal of Adhesion

Biology is well known for its use of linear polymers to perform sophisticated functions. Nucleic acids store and process genetic information, while proteins perform recognition, transport, and catalytic functions. Biology also employs polymers (especially proteins and polysaccharides) to perform mechanical functions and there are several examples in which biology covalently crosslinks polymers to confer elasticity and strength. In some cases, the crosslinking enzymes have attracted attention as a simple and safe means for macromolecular processing in vitro. Here, we review recent research with two enzymes, tyrosinase and microbial transglutaminase, that are being examined for a variety of applications.
Flow-dependent porosity and other biomechanical properties of mysticete baleen
Venue: The Journal of Experimental Biology

Despite its vital function in a highly dynamic environment, baleen is typically assumed to be a static material. Its biomechanical and material properties have not previously been explored. Thus I tested sections of baleen from bowhead whales, Balaena mysticetus, and humpback whales, Megaptera novaeangliae, alone or in groups representing miniature ‘racks’, in a flow tank through which water and buoyant particles circulated with variable flow velocity. Kinematic sequences were recorded through an endoscopic camera or viewing window. One set of experiments investigated particle capture; another series analyzed biomechanical behavior, including fringe spacing, movement and interaction. Baleen fringe porosity directly correlates, in a mostly linear fashion, with velocity of incident water flow. However, undulation and interaction of fringes (especially of bowheads) at higher flow velocities can decrease porosity. Fringe porosity depends on distance from the baleen plate. Porosity also varies, with fringe length, by position along the length of an individual plate. Plate orientation, which varied from 0 to 90 deg relative to water flow, is crucial in fringe spacing and particle capture. At all flow velocities, porosity is lowest with plates aligned parallel to water flow. Turbulence introduced when plates rotate perpendicular to flow (as in cross-flow filtration) increases fringe interaction, so that particles more easily strike fringes yet more readily dislodge. Baleen of bowhead whales, which feed by continuous ram filtration, differs biomechanically from that of humpbacks, which use intermittent lunge filtration. The longer, finer fringes of bowhead baleen readily form a mesh-like mat, especially at higher flow velocities, to trap tiny particles.
Odorant-Binding Proteins from a Primitive Termite
Venue: Journal of Chemical Ecology

Hitherto, odorant-binding proteins (OBPs) have been identified from insects belonging to more highly evolved insect orders (Lepidoptera, Coleoptera, Diptera, Hymenoptera, and Hemiptera), whereas only chemosensory proteins have been identified from more primitive species, such as orthopteran and phasmid species. Here, we report for the first time the isolation and cloning of odorant-binding proteins from a primitive termite species, the dampwood termite, Zootermopsis nevadensis nevadensis (Isoptera: Termopsidae). A major antennae-specific protein was detected by native PAGE along with four other minor proteins, which were also absent in the extract from control tissues (hindlegs). Multiple cDNA cloning led to the full characterization of the major antennae-specific protein (ZnevOBP1) and to the identification of two other antennae-specific cDNAs, encoding putative odorant-binding proteins (ZnevOBP2 and ZnevOBP3). N-terminal amino acid sequencing of the minor antennal bands and cDNA cloning showed that olfaction in Z. n. nevadensis may involve multiple odorant-binding proteins. Database searches suggest that the OBPs from this primitive termite are homologues of the pheromone-binding proteins from scarab beetles and antennal-binding proteins from moths.
The hummingbird tongue is a fluid trap, not a capillary tube
Venue: Proceedings of the National Academy of Sciences of the United States of America

Hummingbird tongues pick up a liquid, calorie-dense food that cannot be grasped, a physical challenge that has long inspired the study of nectar-transport mechanics. Existing biophysical models predict optimal hummingbird foraging on the basis of equations that assume that fluid rises through the tongue in the same way as through capillary tubes. We demonstrate that the hummingbird tongue does not function like a pair of tiny, static tubes drawing up floral nectar via capillary action. Instead, we show that the tongue tip is a dynamic liquid-trapping device that changes configuration and shape dramatically as it moves in and out of fluids. We also show that the tongue–fluid interactions are identical in both living and dead birds, demonstrating that this mechanism is a function of the tongue structure itself, and therefore highly efficient because no energy expenditure by the bird is required to drive the opening and closing of the trap. Our results rule out previous conclusions from capillarity-based models of nectar feeding and highlight the necessity of developing a new biophysical model for nectar intake in hummingbirds. Our findings have ramifications for the study of feeding mechanics in other nectarivorous birds, and for the understanding of the evolution of nectarivory in general. We propose a conceptual mechanical explanation for this unique fluid-trapping capacity, with far-reaching practical applications (e.g., biomimetics).
Nacre from mollusk shells: a model for high-performance structural materials.
Venue: Bioinspiration & Biomimetics

Nacre is the iridescent layer found inside a large number of mollusk shells. This natural composite has a very high mineral content, which makes it hard and stiff. However it is the toughness of nacre which is the most impressive: it is three orders of magnitude tougher than the mineral it is made of. No manmade composite material can boast such amplification in toughness, and for this reason nacre has become a biomimetic model material. The mineral in nacre comes in the form of microscopic polygonal tablets, which have the ability to 'slide' on one another in large numbers when the material is loaded in tension. This key mechanism makes nacre a quasi-ductile material, which in turn greatly increases its toughness and makes it damage tolerant. Numerous 'artificial nacres' were developed in the past but none of them can truly duplicate the remarkable mechanism of tablet sliding. In this work selected structural features of nacre were implemented in a PMMA-based composite, which for the first time could replicate the collective tablet sliding mechanism. This material demonstrates that the powerful toughening mechanism operating in natural nacre can be duplicated and harnessed in engineering materials.
Solar-powered sea slugs. Mollusc/algal chloroplast symbiosis.
Venue: Plant Physiology

Solar-powered “leaves that crawl”? This description of photosynthetic sea slugs (adapted from Bill Rudman [[www.austmus.gov.au/seaslugs/solarpow.htm][1]] and Robert Trench [1975]) aptly describes the symbiotic association that occurs between certain molluscan sea slugs and algal chloroplasts.
The Great Silk Alternative: Multiple Co-Evolution of Web Loss and Sticky Hairs in Spiders
Venue: PLOS ONE

Spiders are the most important terrestrial predators among arthropods. Their ecological success is reflected by a high biodiversity and the conquest of nearly every terrestrial habitat. Spiders are closely associated with silk, a material, often seen to be responsible for their great ecological success and gaining high attention in life sciences. However, it is often overlooked that more than half of all Recent spider species have abandoned web building or never developed such an adaptation. These species must have found other, more economic solutions for prey capture and retention, compensating the higher energy costs of increased locomotion activity. Here we show that hairy adhesive pads (scopulae) are closely associated with the convergent evolution of a vagrant life style, resulting in highly diversified lineages of at least, equal importance as the derived web building taxa. Previous studies often highlighted the idea that scopulae have the primary function of assisting locomotion, neglecting the fact that only the distal most pads (claw tufts) are suitable for those purposes. The former observations, that scopulae are used in prey capture, are largely overlooked. Our results suggest the scopulae evolved as a substitute for silk in controlling prey and that the claw tufts are, in most cases, a secondary development. Evolutionary trends towards specialized claw tufts and their composition from a low number of enlarged setae to a dense array of slender ones, as well as the secondary loss of those pads are discussed further. Hypotheses about the origin of the adhesive setae and their diversification throughout evolution are provided.
Blood-Squirting Variability in Horned Lizards (Phrynosoma)
Venue: Copeia

Variability within the genus Phrynosoma in the occurrence of ocular-sinus blood-squirting, reportedly a defense used in canid encounters, is reviewed from the literature. Six species have been reported to squirt blood, and seven species remain unreported. Five of the latter species were tested in dog trials; one exhibited blood-squirting (Phrynosoma hernandesi), one exhibited precursor behaviors but failed to squirt blood (Phrynosoma ditmarsi), and three yielded negative results (Phrynosoma mcallii, Phrynosoma modestum, and Phrynosoma platyrhinos). Instances of blood-squirting in response to human encounters were collected and largely support the negative results for the three species P. mcallii, P. modestum, and P. platyrhinos. A phylogeny of blood-squirting and nonblood-squirting species is presented with blood-squirting being plesiomorphic in the genus and the synapomorphic condition of nonsquirting species being restricted to a single clade of P. mcallii-modestum-platyrhinos. The possibility of P. douglasii independently evolving an autapomorphic condition remains unresolved. Dog trials with 40 adult Phrynosoma cornutum were conducted to determine influences of body size and sex on squirt frequency and blood mass expelled, as well as to examine aspects of the potential physiological cost of the defense. In 153 trials, 85% of all lizards squirted in at least one trial, 82% squirted in more than one trial, and two lizards squirted daily over the seven-day trial period. Initial body mass positively correlated with the total number of squirts/individual (r2 = 0.28; P < 0.001) and the number of days a lizard continued squirting (r2 = 0.63; P < 0.01). Number of squirts/individual/day declined over the seven-day trial period (r2 = 0.20; P < 0.05). Cumulative mass loss for individual lizards attributable to blood-squirting averaged 0.7 ± 0.8 g (2.0 ± 2.0% body mass), with a high of 2.8 g (6.8% body mass). In addition, juvenile P. cornutum and P. hernandesi were shown to squirt blood in dog trials, illustrating the early developmental onset of the behavior.
Drag reduction by air release promotes fast ascent in jumping emperor penguins—a novel hypothesis
Venue: Marine Ecology Progress Series

To jump out of water onto sea ice, emperor penguins must achieve sufficient underwa- ter speed to overcome the influence of gravity when they leave the water. The relevant combination of density and kinematic viscosity of air is much lower than for water. Injection of air into boundary layers ('air lubrication') has been used by engineers to speed movement of vehicles (ships, torpedoes) through sea water. Analysis of published and unpublished underwater film leads us to present a hypothesis that free-ranging emperor penguins employ air lubrication in achieving high, probably maximal, underwater speeds (mean ± SD: 5.3 ± 1.01 m s -1 ), prior to jumps. Here we show evidence that penguins dive to 15 to 20 m with air in their plumage and that this compressed air is released as the birds subsequently ascend whilst maintaining depressed feathers. Fine bubbles emerge continu- ously from the entire plumage, forming a smooth layer over the body and generating bubbly wakes behind the penguins. In several hours of film of hundreds of penguins, none were seen to swim rapidly upwards without bubbly wakes. Penguins descend and swim horizontally at about 2 m s -1 ; from simple physical models and calculations presented, we hypothesize that a significant proportion of the enhanced ascent speed is due to air lubrication reducing frictional and form drag, that buoyancy forces alone cannot explain the observed speeds, and that cavitation plays no part in bubble formation.
Rheum palaestinum (desert rhubarb), a self-irrigating desert plant
Venue: Naturwissenschaften

The rare plant Rheum palaestinum (Polygonaceae) is a perennial hemicryptophyte that grows during the rainy winter in desert mountainous areas in Israel and Jordan that receive an average annual rainfall of ca. 75 mm. It produces between one and four large round leaves that are tightly attached to the ground and form large rosettes of up to 1 m2. These leaves differ markedly from the typical small leaves of most desert plants. Moreover, they have a unique 3D morphology resembling a scaled-down mountainous area with well-developed steep drainage systems, raising the question which selective agents were involved in their evolution. We propose that the large leaves collect rainwater that then infiltrates the soil surrounding the root. We measured the seasonal course of leaf growth, examined the area of wet soil surrounding the root after actual and simulated rain, and modeled the water harvesting capacity using the plant leaf area and the weekly precipitation. We show that even in the slightest rains, water flows above the veins to the leaf’s base where it irrigates the vertical root. A typical plant harvests more than 4,100 cm3 of water per year, and enjoys a water regime of about 427 mm/year, equivalent to the water supply in a Mediterranean climate. This is the first example of self-irrigation by large leaves in a desert plant, creating a leaf-made mini oasis.
Convergent evolution in mechanical design of lamnid sharks and tunas
Venue: Nature

The evolution of ‘thunniform’ body shapes in several different groups of vertebrates, including whales, ichthyosaurs and several species of large pelagic fishes supports the view that physical and hydromechanical demands provided important selection pressures to optimize body design for locomotion during vertebrate evolution. Recognition of morphological similarities between lamnid sharks (the most well known being the great white and the mako) and tunas has led to a general expectation that they also have converged in their functional design; however, no quantitative data exist on the mechanical performance of the locomotor system in lamnid sharks. Here we examine the swimming kinematics, in vivo muscle dynamics and functional morphology of the force-transmission system in a lamnid shark, and show that the evolutionary convergence in body shape and mechanical design between the distantly related lamnids and tunas is much more than skin deep; it extends to the depths of the myotendinous architecture and the mechanical basis for propulsive movements. We demonstrate that not only have lamnids and tunas converged to a much greater extent than previously known, but they have also developed morphological and functional adaptations in their locomotor systems that are unlike virtually all other fishes.
Neutralization of lethality and proteolytic activities of Malayan pit viper (Calloselasma rhodostoma) venom with North American Virginia opossum (Didelphis virginiana) serum.
Venue: Toxicon

Malayan pit viper (Calloselasma rhodostoma) envenomation is a major health problem in South East Asia. During envenomation, venom components mainly affect the hemostatic system. The sera from the North American Virginia opossums (Didelphis virginiana) were able to neutralize the venom of the Malayan pit viper. These natural inhibitors could be explored as potential therapeutics against envenomations of a variety of venomous snake species in different geographical habitats.
Heat transfer through penguin feathers
Venue: Journal of Theoretical Biology

Morphological measurements of penguin feathers are used to construct a thermal model of heat transfer through the coat. Assuming uniform distribution of the feathers and their associated afterfeathers, it is possible to model heat transfer through the coat of the penguin using standard theory. It is shown that convection does not occur in the coat of the penguin and that radiative heat loss is minimized. The theory predicts a thermal conductivity of 2.38 W m(-2)K(-1)which compares well with an empirically measured value of 1.93 W m(-2)K(-1).
Organisms as ecosystem engineers
Venue: Oikos

Interactions between organisms are a major determinant of the distribution and abundance of species. Ecology textbooks (e.g., Ricklefs 1984, Krebs 1985, Begon et al. 1990) summarise these important interactions as intra- and interspecific competition for abiotic and biotic resources, predation, parasitism and mutualism. Conspicuously lacking from the list of key processes in most text books is the role that many organisms play in the creation, modification and maintenance of habitats. These activities do not involve direct trophic interactions between species, but they are nevertheless important and common. The ecological literature is rich in examples of habitat modification by organisms, some of which have been extensively studied (e.g. Thayer 1979, Naiman et al. 1988).