nils-herrmann/clean_scirepeval huggingface dataset:
Morphological and kinematic basis of the hummingbird flight stroke: scaling of flight muscle transmission ratio
Venue: Proceedings of The Royal Society B: Biological Sciences

Hummingbirds (Trochilidae) are widely known for their insect-like flight strokes characterized by high wing beat frequency, small muscle strains and a highly supinated wing orientation during upstroke that allows for lift production in both halves of the stroke cycle. Here, we show that hummingbirds achieve these functional traits within the limits imposed by a vertebrate endoskeleton and muscle physiology by accentuating a wing inversion mechanism found in other birds and using long-axis rotational movement of the humerus. In hummingbirds, long-axis rotation of the humerus creates additional wing translational movement, supplementing that produced by the humeral elevation and depression movements of a typical avian flight stroke. This adaptation increases the wing-to-muscle-transmission ratio, and is emblematic of a widespread scaling trend among flying animals whereby wing-to-muscle-transmission ratio varies inversely with mass, allowing animals of vastly different sizes to accommodate aerodynamic, biomechanical and physiological constraints on muscle-powered flapping flight.
Cnidocyst structure and the biomechanics of discharge.
Venue: Toxicon

The cnidocyst is the defining organelle of the cnidarians, used for capture of prey and defense. It consists of a cylindrical capsule, which releases a long tubule upon triggering. Cnidocysts develop inside a giant post-Golgi vesicle by a sequential accumulation of proteins from the Golgi apparatus. Traditionally three types of cnidocysts are distinguished: nematocysts, spirocysts, and ptychocysts. Here we focus on nematocysts, the prototypic cnidocyst and by far most diverse group of cnidocysts in this phylum. The mature nematocyst capsule comprises a collagenous polymer with remarkable biophysical properties, able to withstand an osmotic pressure of 150 bar. Release of the capsule and discharge is probably initiated by classical exocytosis. High-speed studies revealed the kinetics of discharge to be as short as 700 ns, generating an acceleration of 5,400,000 x g and a pressure of 7.7 GPa at the site of impact of the spines onto the prey. Thus nematocysts comprise a powerful molecular spring mechanism releasing energy stored in the wall polymer in the nanosecond time range. During the last few years, genomic, biochemical and structural studies have helped to unravel the molecular composition of the nematocyst supra-structure. Here we summarize these findings and present an integrative view of mechanical and molecular aspects that have shaped the nematocyst during evolution.
Abscission and dehiscence in the squirting cucumber, Ecballium elaterium. Regulation by ethylene
Venue: Botany

When treated with ethylene, mature fruits of the squirting cucumber (Ecballium elaterium (L.) A. Rich) abscind and dehisce prematurely. Abscission of male flowers is also accelerated by ethylene. Visible signs of senescence, a rise in ethylene production, and reduced carbon dioxide production always precede abscission or dehiscence in untreated fruits and flowers. The amounts of diffusible cellulase increase in tissues on both sides of the fruit abscission zone after exposure to ethylene. Anatomical features of this abscission zone are described.The leaves of Ecballium do not abscind although the blade and petiole produce large amounts of ethylene at senescence, nor do they separate when ethylene is supplied. Ethylene treatment of attached fruit peduncles accelerates their rate of elongation in the growing zone below the apical hook. The regulation of growth and abscission in these organs is discussed.
The effect of individual variation on the structure and function of interaction networks in harvester ants
Venue: Journal of the Royal Society Interface

Social insects exhibit coordinated behaviour without central control. Local interactions among individuals determine their behaviour and regulate the activity of the colony. Harvester ants are recruited for outside work, using networks of brief antennal contacts, in the nest chamber closest to the nest exit: the entrance chamber. Here, we combine empirical observations, image analysis and computer simulations to investigate the structure and function of the interaction network in the entrance chamber. Ant interactions were distributed heterogeneously in the chamber, with an interaction hot-spot at the entrance leading further into the nest. The distribution of the total interactions per ant followed a right-skewed distribution, indicating the presence of highly connected individuals. Numbers of ant encounters observed positively correlated with the duration of observation. Individuals varied in interaction frequency, even after accounting for the duration of observation. An ant's interaction frequency was explained by its path shape and location within the entrance chamber. Computer simulations demonstrate that variation among individuals in connectivity accelerates information flow to an extent equivalent to an increase in the total number of interactions. Individual variation in connectivity, arising from variation among ants in location and spatial behaviour, creates interaction centres, which may expedite information flow.
Mechanisms in Failure Prevention of Bio-Materials and Bio-Structures
Venue: Mechanics of Advanced Materials and Structures

Nature is replete with examples of layered-structure materials that are evolved through billions of years to provide high performance. Insect elytra (a portion of the exoskeleton) have evoked worldwide research attention and are believed to serve as fuselages and wings of natural aircraft. This work focuses on the relationship between structure, mechanical behavior, and failure mechanisms of the elytra. We report a failure-mode-optimization (FMO) mechanism that can explain elytra's mechanical behaviors. We show initial evidence that this mechanism makes bio-structures of low-strength materials strong and ductile that can effectively resist shear forces and crack growth. A bio-inspired design of a joint by using the FMO mechanism has been proved by experiments to have a potential to increase the interface shear strength as high as about 2.5 times. The FMO mechanism, which is based on the new concept of property-structure synergetic coupling proposed in this work, offer some thoughts to deal with the notoriously difficult problem of interface strength and to reduce catastrophic failure events.
Molecular nanosprings in spider capture-silk threads
Venue: Nature Materials

Spider capture silk is a natural material that outperforms almost any synthetic material in its combination of strength and elasticity. The structure of this remarkable material is still largely unknown, because spider-silk proteins have not been crystallized. Capture silk is the sticky spiral in the webs of orb-weaving spiders. Here we are investigating specifically the capture spiral threads from Araneus, an ecribellate orb-weaving spider. The major protein of these threads is flagelliform protein, a variety of silk fibroin. We present models for molecular and supramolecular structures of flagelliform protein, derived from amino acid sequences, force spectroscopy (molecular pulling) and stretching of bulk capture web. Pulling on molecules in capture-silk fibres from Araneus has revealed rupture peaks due to sacrificial bonds, characteristic of other self-healing biomaterials. The overall force changes are exponential for both capture-silk molecules and intact strands of capture silk.
Comparative overwintering physiology of Alaska and Indiana populations of the beetle Cucujus clavipes (Fabricius): roles of antifreeze proteins, polyols, dehydration and diapause
Venue: The Journal of Experimental Biology

The beetle Cucujus clavipes is found in North America over a broad latitudinal range from North Carolina (latitude ∼35°N) to near tree line in the Brooks Range in Alaska (latitude, ∼67°30′ N). The cold adaptations of populations from northern Indiana (∼41°45′ N) and Alaska were compared and, as expected, the supercooling points (the temperatures at which they froze) of these freeze-avoiding insects were significantly lower in Alaska insects. Both populations produce glycerol, but the concentrations in Alaska larvae were much higher than in Indiana insects (∼2.2 and 0.5 mol l–1, respectively). In addition, both populations produce antifreeze proteins. Interestingly, in the autumn both populations have the same approximate level of hemolymph thermal hysteresis, indicative of antifreeze protein activity, suggesting that they synthesize similar amounts of antifreeze protein. A major difference is that the Alaska larvae undergo extreme dehydration in winter wherein water content decreases from 63–65% body water (1.70–1.85 g H2O g–1 dry mass) in summer to 28–40% body water (0.40–0.68 g H2O g–1 dry mass) in winter. These 2.5–4.6-fold reductions in body water greatly increase the concentrations of antifreeze in the Alaska insects. Glycerol concentrations would increase to 7–10 mol l–1 while thermal hysteresis increased to nearly 13°C (the highest ever measured in any organism) in concentrated hemolymph. By contrast, Indiana larvae do not desiccate in winter. The Alaska population also undergoes a diapause while insects from Indiana do not. The result of these, and likely additional, adaptations is that while the mean winter supercooling points of Indiana larvae were approximately –23°C, those of Alaska larvae were –35 to– 42°C, and at certain times Alaska C. clavipes did not freeze when cooled to –80°C.
Diffractive hygrochromic effect in the cuticle of the hercules beetle Dynastes hercules
Venue: New Journal of Physics

The elytra from dry specimens of the hercules beetle, Dynastes hercules appear khaki-green in a dry atmosphere and turn black passively under high humidity levels. New scanning electron images, spectrophotometric measurements and physical modelling are used to unveil the mechanism of this colouration switch. The visible dry-state greenish colouration originates from a widely open porous layer located 3 μm below the cuticle surface. The structure of this layer is three-dimensional, with a network of filamentary strings, arranged in layers parallel to the cuticle surface and stiffening an array of strong cylindrical pillars oriented normal to the surface. Unexpectedly, diffraction plays a significant role in the broadband colouration of the cuticle in the dry state. The backscattering caused by this layer disappears when water infiltrates the structure and weakens the refractive index differences.
Gamma-aminobutyrate: defense against invertebrate pests?
Venue: Trends in Plant Science

Gamma-aminobutyrate (GABA) is a ubiquitous four-carbon, non-protein amino acid. In plants, stress-induced GABA accumulation is well documented. However, the role(s) of GABA accumulation is contentious. In this Opinion article, we argue that wounding due to herbivory and crawling by insect larvae causes rapid GABA accumulation via the disruption of cellular compartmentation and the release of the acidic vacuolar contents to the cytosol. The activity of glutamate decarboxylase, the cytosolic enzyme responsible for GABA synthesis, has an acidic pH optimum. Subsequent GABA ingestion has a plant defense function by directly acting on GABA-regulated invertebrate neuromuscular junctions. Plants with an enhanced GABA-producing capacity reduce herbivory by invertebrate pests. These findings suggest that GABA accumulation is a rapidly deployed, local resistance mechanism that constitutes a first line of defense in deterring herbivory.
Light transmission in window-leaved plants
Venue: Botany

Window-leaved plants are succulent plants which possess areas of clear epidermis on their leaves. The underlying water storage tissue is transparent to allow light penetration to the internal chlorenchyma. The most highly evolved window-leaved plants with the most transparent tissue grow completely underground in desert regions. Only the rounded leaf tips are level with the soil surface and directly exposed to incident light. Light transmission curves were measured using live windows of five species of plants from three families (Liliaceae, Piperaceae, Mesembryanthemaceae). These results suggest that subterranean window leaves may be limited to a relatively short effective maximum length because of light absorption by the tissues involved. Scanning electron micrographs (SEM) of these plants show considerable differences in surface structure which may help to modulate incident light. Comparisons with related Mesembryanthemaceae illustrate that a complex series of adaptations have been developed to allow un...
Lactobacillus fermentum RC-14 inhibits Staphylococcus aureus infection of surgical implants in rats.
Venue: The Journal of Infectious Diseases

Staphylococcus aureus is a common cause of community and hospital-acquired infections. Moreover, the clinical impact of S. aureus is on the rise because of the global increase in the incidence of multidrug-resistant strains and its growing prevalence as a major cause of surgical infections. As a result, there is a pressing need to identify new antistaphylococcal agents and preventative strategies that will help in the management of these types of infections. This report describes the successful use of a probiotic, Lactobacillus fermentum RC-14, and its secreted biosurfactant to inhibit surgical implant infections caused by S. aureus. L. fermentum RC-14 and its secreted biosurfactant both significantly inhibited S. aureus infection and bacteria adherence to surgical implants.
A test of whether economy or nutrition determines fecal sac ingestion in nesting corvids
Venue: The Condor

Parent birds of many species eat the fecal sacs produced by their nestlings. Two hypotheses have been proposed to explain why the parents ingest, rather than simply remove the sacs. (1) The parental nutrition hypothesis proposes that the parent benefits energetically or nutritionally from ingesting the sacs (Morton 1979, Gluck 1988); and (2) the economic disposal hypothesis postulates that parents incur some costs from eating waste products, but the cost of eating them is less than the benefits gained from being allowed to remain at the nest (Hurd et al. 1991). Behavioral data on nesting Florida Scrub Jays (Aphelocoma c. coerulescens) and American Crows (Corvus brachyrhynchos) support the parental nutrition, and not the economic disposal hypothesis. In both species, when two parents were present at the production of fecal sacs, the most nutritionally stressed parent, the female, ate significantly more sacs than her mate. On occasions where one adult left the nest immediately after fecal sac production and one remained, the departing adult was not more likely to dispose of the sac in either species. In neither species was a departing adult more likely to carry of a fecal sac than eat it
THE ANT‐PLANTS MYRMECODIA AND HYDNOPHYTUM (RUBIACEAE), AND THE RELATIONSHIPS BETWEEN THEIR MORPHOLOGY, ANT OCCUPANTS, PHYSIOLOGY AND ECOLOGY
Venue: New Phytologist

The history of investigation of the ant-plants is briefly reviewed and the external morphology of the plants described. Within Papua New Guinea ant-plants are abundant in open-canopied environments and less common but more diverse in rain forest. They also occur terrestrially above 2400 m. Initial tuber development was found to be similar that described by Treub (1883). Later cavities are formed by successive, increasingly complex phellogens. In certain Myrmecodia spp. later cavities are differentiated into regions with distinct surface characteristics, shapes and positions. Cavities in Hydnophytum are simpler in shape but sometimes differentiated in other ways. The anatomy of the cavity surfaces, especially the putative absorption sites ('warts') is described. 
 
The ant Iridomyrmex cordatus, which is common in ant-plants in other regions, is found in ant-plants in open habitats in Papua New Guinea, but is replaced by I. cf. scrutator in rain forest and above 2000 m. Two fungi, known also from ant-plants in Java (Miehe, 1911a), occur in the cavities of ant-plants throughout Papua New Guinea. Arthrocladium sp. Papend. grows on cavity surfaces where ant faecal material is present and the other (an unidentified Monilialine fungus) is parasitic on smooth, clean surfaces. The former is most common and the latter almost confined to Myrmecodia spp. occupied by Iridomyrmex cordatus. 
 
Experiments suggested that both Hydnophytum under artificial conditions and Myrmecodia under field conditions grow better in the presence than absence of Iridomyrmex cordatus and that the stimulus might be that of minerals supplied by the ants. Radioisotopes in both organic and inorganic compounds fed to I. cordatus were deposited preferentially by the ants on the warted cavity surfaces where ant faecal material was present, and were absorbed by the plants. In the discussion it is argued that the plant/ant relationship has had a considerable influence on both the ecology and evolution of the plants, but that this varies in different species.
The mound-building termite Macrotermes michaelseni as an ecosystem engineer
Venue: Journal of Tropical Ecology

Many organisms create or alter resource flows that affect the com- position and spatial arrangement of current and future organismal diversity. The phenomenon called ecosystem engineering is considered with a case study of the mound building termite Macrotermes michaelseni. It is argued that this species acts as an ecosystem engineer across a range of spatial scales, from alteration of local infiltration rates to the creation of landscape mosaics, and that its impacts accrue because of the initiation of biophysical processes that often include feedback mech- anisms. These changes to resource flows are likely to persist for long periods and constrain the biological structure of the habitat. The value of ecosystem engineer- ing is discussed as a holistic way of understanding the complexity of tropical ecology.
The exploitation of mutualisms
Venue: Ecology Letters

Mutualisms (interspecific cooperative interactions) are ubiquitously exploited by organisms that obtain the benefits mutualists offer, while delivering no benefits in return. The natural history of these exploiters is well-described, but relatively little effort has yet been devoted to analysing their ecological or evolutionary significance for mutualism. Exploitation is not a unitary phenomenon, but a set of loosely related phenomena: exploiters may follow mixed strategies or pure strategies at either the species or individual level, may or may not be derived from mutualists, and may or may not inflict significant costs on mutualisms. The evolutionary implications of these different forms of exploitation, especially the threats they pose to the stability of mutualism, have as yet been minimally explored. Studies of this issue are usually framed in terms of a “temptation to defect” that generates a destabilizing conflict of interest between partners. I argue that this idea is in fact rather inappropriate for interpreting most observed forms of exploitation in mutualisms. I suggest several alternative and testable ideas for how mutualism can persist in the face of exploitation.
Respiration by buried echidnas Tachyglossus aculeatus
Venue: The Journal of Experimental Biology

Short-beaked echidnas have an impressive ability to submerge completely into soil or sand and remain there, cryptic, for long periods. This poses questions about how they manage their respiration, cut off from a free flow of gases. We measured the gradient in oxygen partial pressure (PO2) away from the snouts of buried echidnas and oxygen consumption (V̇O2) in five individuals under similar conditions, in two substrates with different air-filled porosities (fa). A theoretical diffusion model indicated that diffusion alone was insufficient to account for the flux of oxygen required to meet measured rates of V̇O2. However, it was noticed that echidnas often showed periodic movements of the anterior part of the body, as if such movements were a deliberate effort to flush the tidal air space surrounding their nostrils. These `flushing movements' were subsequently found to temporarily increase the levels of interstitial oxygen in the soil around the head region. Flushing movements were more frequent while V̇O2 was higher during the burrowing process, and also in substrate with lower fa. We conclude that oxygen supply to buried echidnas is maintained by diffusion through the soil augmented by periodic flushing movements, which ventilate the tidal airspace that surrounds the nostrils.
Bill sweeping in the spoonbill, Platalea leucordia: evidence for a hydrodynamic function
Venue: Animal Behaviour

(Aves: Platalea spp., Ciconiiformes) characteristically feed by wading in shallow water and rhythmically sweeping their submerged and partially opened bills in an arc. This bill sweeping contrasts with the direct grasp, strike or stab employed by related species (storks, Ciconiidae; herons, Ardeidae) for similar prey (crustaceans, fish). A related feature of spoonbills is the shape of the bill: both upper and lower mandibles are dorso-ventrally flattened, the upper mandible being convex in cross section while the lower is tucked in, to result in an almost flat surface. The bill is wide throughout and broadens at the distal end. The hypothesis presented here is that spoonbills use their broad, flattened bills and lateral sweeping to shed a vortex off the tip of the bill that results in hydrodynamic suction on the bottom, which disturbs and moves prey. To achieve this the bill is used as a hydrofoil. The analysis predicts, and experimental results show that (1) in feeding, the tip of the bill is kept close to the bottom, (2) there is an inverse relationship between bill immersion depth and sweeping speed, and (3) bill sweeping over submerged prey results in the prey being lifted into the water column. This is the first reported case of an avian bill being used as a hydrofoil.
Differential Response to Circularly Polarized Light by the Jewel Scarab Beetle Chrysina gloriosa
Venue: The American Naturalist

Circularly polarized light is rare in the terrestrial environment, and cuticular reflections from scarab beetles are one of the few natural sources. Chrysina gloriosa LeConte 1854, a scarab beetle found in montane juniper forests of the extreme southwestern United States and northern Mexico, are camouflaged in juniper foliage; however, when viewed with right circularly polarizing filters, the beetles exhibit a stark black contrast. Given the polarization‐specific changes in the appearance of C. gloriosa, we hypothesized that C. gloriosa can detect circularly polarized light. We tested for phototactic response and differential flight orientation of C. gloriosa toward different light stimuli. Chrysina gloriosa exhibited (a) positive phototaxis, (b) differential flight orientation between linear and circularly polarized light stimuli of equal intensities, and (c) discrimination between circularly polarized and unpolarized lights of different intensities consistent with a model of circular polarization sensitivity based on a quarter‐wave plate. These results demonstrate that C. gloriosa beetles respond differentially to circularly polarized light. In contrast, Chrysina woodi Horn 1885, a close relative with reduced circularly polarized reflection, exhibited no phototactic discrimination between linear and circularly polarized light. Circularly polarized sensitivity may allow C. gloriosa to perceive and communicate with conspecifics that remain cryptic to predators, reducing indirect costs of communication.