nils-herrmann/clean_scirepeval huggingface dataset:
Alternation between attachment mechanisms by limpets in the field
Venue: Journal of Experimental Marine Biology and Ecology

The attachment mechanism used by limpets in the rocky, wave-swept intertidal zone of California was determined during high tide and low tide. The two mechanisms that limpets are known to use, suction and glue-like adhesion, were distinguished by measuring the limpets' attachment forces in shear and by staining for glue-like residues where the limpets had been attached. The results show that ≈ 73% of limpets at high tide use suction, while the rest use glue-like adhesion. Conversely, ≈ 75% of limpets at low tide use glue-like adhesion, while the rest use suction. The normal tenacity of limpets was also measured at high and low tide. The mean tenacity at high tide was significantly less than that at low tide. From these data it was estimated that the mean tenacity of glue-like adhesion is ≈ 0.23 MN·m−2 and the mean tenacity of suction adhesion is ≈ 0.09 MN·m−2. It is hypothesized that the cycle of alternating attachment mechanisms is linked to the limpets foraging cycles.
A mechanical analysis of woodpecker drumming and its application to shock-absorbing systems.
Venue: Bioinspiration & Biomimetics

A woodpecker is known to drum the hard woody surface of a tree at a rate of 18 to 22 times per second with a deceleration of 1200 g, yet with no sign of blackout or brain damage. As a model in nature, a woodpecker is studied to find clues to develop a shock-absorbing system for micromachined devices. Its advanced shock-absorbing mechanism, which cannot be explained merely by allometric scaling, is analyzed in terms of endoskeletal structures. In this analysis, the head structures (beak, hyoid, spongy bone, and skull bone with cerebrospinal fluid) of the golden-fronted woodpecker, Melanerpes aurifrons, are explored with x-ray computed tomography images, and their shock-absorbing mechanism is analyzed with a mechanical vibration model and an empirical method. Based on these analyses, a new shock-absorbing system is designed to protect commercial micromachined devices from unwanted high-g and high-frequency mechanical excitations. The new shock-absorbing system consists of close-packed microglasses within two metal enclosures and a viscoelastic layer fastened by steel bolts, which are biologically inspired from a spongy bone contained within a skull bone encompassed with the hyoid of a woodpecker. In the experimental characterizations using a 60 mm smoothbore air-gun, this bio-inspired shock-absorbing system shows a failure rate of 0.7% for the commercial micromachined devices at 60 000 g, whereas a conventional hard-resin method yields a failure rate of 26.4%, thus verifying remarkable improvement in the g-force tolerance of the commercial micromachined devices.
Nanopatterned protein microrings from a diatom that direct silica morphogenesis
Venue: Proceedings of the National Academy of Sciences of the United States of America

Diatoms are eukaryotic microalgae that produce species-specifically structured cell walls made of SiO2 (silica). Formation of the intricate silica structures of diatoms is regarded as a paradigm for biomolecule-controlled self-assembly of three-dimensional, nano- to microscale-patterned inorganic materials. Silica formation involves long-chain polyamines and phosphoproteins (silaffins and silacidins), which are readily soluble in water, and spontaneously form dynamic supramolecular assemblies that accelerate silica deposition and influence silica morphogenesis in vitro. However, synthesis of diatom-like silica structure in vitro has not yet been accomplished, indicating that additional components are required. Here we describe the discovery and intracellular location of six novel proteins (cingulins) that are integral components of a silica-forming organic matrix (microrings) in the diatom Thalassiosira pseudonana. The cingulin-containing microrings are specifically associated with girdle bands, which constitute a substantial part of diatom biosilica. Remarkably, the microrings exhibit protein-based nanopatterns that closely resemble characteristic features of the girdle band silica nanopatterns. Upon the addition of silicic acid the microrings become rapidly mineralized in vitro generating nanopatterned silica replicas of the microring structures. A silica-forming organic matrix with characteristic nanopatterns was also discovered in the diatom Coscinodiscus wailesii, which suggests that preassembled protein-based templates might be general components of the cellular machinery for silica morphogenesis in diatoms. These data provide fundamentally new insight into the molecular mechanisms of biological silica morphogenesis, and may lead to the development of self-assembled 3D mineral forming protein scaffolds with designed nanopatterns for a host of applications in nanotechnology.
Non-wetting wings and legs of the cranefly aided by fine structures of the cuticle
Venue: The Journal of Experimental Biology

Non-wetting surfaces are imperative to the survival of terrestrial and semi-aquatic insects as they afford resistance to wetting by rain and other liquid surfaces that insects may encounter. Thus, there is an evolutionary pay-off for these insects to adopt hydrophobic technologies, especially on contacting surfaces such as legs and wings. The cranefly is a weak flier, with many species typically found in wet/moist environments where they lay eggs. Water droplets placed on this insect's wings will spontaneously roll off the surface. In addition, the insect can stand on water bodies without its legs penetrating the water surface. The legs and wings of this insect possess thousands of tiny hairs with intricate surface topographies comprising a series of ridges running longitudinally along the long axis of the hair fibre. Here we demonstrate that this fine hair structure enhances the ability of the hairs to resist penetration into water bodies.
A finite element simulation scheme for biological muscular hydrostats.
Venue: Journal of Theoretical Biology

An explicit finite element scheme is developed for biological muscular hydrostats such as squid tentacles, octopus arms and elephant trunks. The scheme is implemented by embedding muscle fibers in finite elements. In any given element, the fiber orientation can be assigned arbitrarily and multiple muscle directions can be simulated. The mechanical stress in each muscle fiber is the sum of active and passive parts. The active stress is taken to be a function of activation state, muscle fiber shortening velocity and fiber strain; while the passive stress depends only on the strain. This scheme is tested by simulating extension of a squid tentacle during prey capture; our numerical predictions are in close correspondence with existing experimental results. It is shown that the present finite element scheme can successfully simulate more complex behaviors such as torsion of a squid tentacle and the bending behavior of octopus arms or elephant trunks.
Reconstruction and Regulation of the Central Catabolic Pathway in the Thermophilic Propionate-Oxidizing Syntroph Pelotomaculum thermopropionicum
Venue: Journal of Bacteriology

Obligate anaerobic bacteria fermenting volatile fatty acids in syntrophic association with methanogenic archaea share the intermediate bottleneck step in organic-matter decomposition. These organisms (called syntrophs) are biologically significant in terms of their growth at the thermodynamic limit and are considered to be the ideal model to address bioenergetic concepts. We conducted genomic and proteomic analyses of the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum to obtain the genetic basis for its central catabolic pathway. Draft sequencing and subsequent targeted gap closing identified all genes necessary for reconstructing its propionate-oxidizing pathway (i.e., methylmalonyl coenzyme A pathway). Characteristics of this pathway include the following. (i) The initial two steps are linked to later steps via transferases. (ii) Each of the last three steps can be catalyzed by two different types of enzymes. It was also revealed that many genes for the propionate-oxidizing pathway, except for those for propionate coenzyme A transferase and succinate dehydrogenase, were present in an operon-like cluster and accompanied by multiple promoter sequences and a putative gene for a transcriptional regulator. Proteomic analysis showed that enzymes in this pathway were up-regulated when grown on propionate; of these enzymes, regulation of fumarase was the most stringent. We discuss this tendency of expression regulation based on the genetic organization of the open reading frame cluster. Results suggest that fumarase is the central metabolic switch controlling the metabolic flow and energy conservation in this syntroph.
Chemistry-Specific Interfacial Forces Between Barnacle (Semibalanus Balanoides) Cyprid Footprint Proteins and Chemically Functionalised AFM Tips
Venue: Journal of Adhesion

Cypris larvae of the barnacle Semibalanus balanoides leave proteinaceous footprints on surfaces during pre-settlement exploration. These footprints are considered to mediate temporary adhesion of cyprids to substrata and, as such, represent a crucial first step in the colonization of man-made surfaces by barnacles, a process known as biofouling. Interest in this system also stems from the potential for a synthetic reversible adhesion system, based on the strategy used by cyprids. Cyprid footprints were probed using atomic force microscopy (AFM) and nanomechanical data relating to interfacial adhesion forces were correlated with AFM tip chemistry. Commercial Si3N4-tips and chemically functionalized CH3-tips were chosen to mimic the interactions of cyprid footprints with hydrophilic and hydrophobic surfaces, respectively. Force-extension curves of protein bundles picked up by AFM tips exhibited a characteristic saw-tooth appearance for both types of tip, but demonstrated clear differences relating to pull-off force and pull-off length, based on tip chemistry. Additional (∼6 nN) interfacial adhesion forces between −CH3 functionalized tips and footprints were assigned to hydrophobic interactions. Footprint proteins adhered with greater tenacity to the hydrophobic tip. This may suggest conformational change and denaturing of the protein which would facilitate hydrophobic interaction by enhancing contact forces between −CH3 functionalized tips and hydrophobic groups in the footprint molecule(s). Neither tip removed proteins from the −NH2 substratum suggesting that specific chemical interactions, rather than simple wetting phenomena, govern the adhesion of footprint proteins to that surface.
Coordinated ventilation and spiracle activity produce unidirectional airflow in the hissing cockroach, Gromphadorhina portentosa
Venue: The Journal of Experimental Biology

Insects exchange respiratory gases via an extensive network of tracheal vessels that open to the surface of the body through spiracular valves. Although gas exchange is known to increase with the opening of these spiracles, it is not clear how this event relates to gas flow through the tracheal system. We examined the relationship between respiratory airflow and spiracle activity in a ventilating insect, the hissing cockroach, Gromphadorhina portentosa, to better understand the complexity of insect respiratory function. Using simultaneous video recordings of multiple spiracular valves, we found that abdominal spiracles open and close in unison during periods of ventilation. Additionally, independent recordings of CO2 release from the abdominal and thoracic regions and observations of hyperoxic tracer gas movement indicate that air is drawn into the thoracic spiracles and expelled from the abdominal spiracles. Our video recordings suggest that this unidirectional flow is driven by abdominal contractions that occur when the abdominal spiracles open. The spiracles then close as the abdomen relaxes and fills with air from the thorax. Therefore, the respiratory system of the hissing cockroach functions as a unidirectional pump through the coordinated action of the spiracles and abdominal musculature. This mechanism may be employed by a broad diversity of large insects that respire by active ventilation.
A water-borne adhesive modeled after the sandcastle glue of P. californica.
Venue: Macromolecular Bioscience

Polyacrylate glue protein analogs of the glue secreted by Phragmatopoma californica, a marine polycheate, were synthesized with phosphate, primary amine, and catechol sidechains with molar ratios similar to the natural glue proteins. Aqueous mixtures of the mimetic polyelectrolytes condensed into liquid complex coacervates around neutral pH. Wet cortical bone specimens bonded with the coacervates, oxidatively crosslinked through catechol sidechains, had bond strengths nearly 40% of the strength of a commercial cyanoacrylate. The unique material properties of complex coacervates may be ideal for development of clinically useful adhesives and other biomaterials.
Convergence of specialised behaviour, eye movements and visual optics in the sandlance (Teleostei) and the chameleon (Reptilia)
Venue: Current Biology

Chameleons have a number of unusual, highly specialised visual features, including telescopic visual optics with a reduced lens power, wide separation of the eye's nodal point from the axis of rotation, a deep-pit fovea, rapid pre-calculated strikes for prey based on monocular depth judgements (including focus), and a complex pattern of partially independent alternating eye movements. The same set of features has been acquired independently by a teleost, the sandlance Limnichthyes fasciatus. Despite its underwater lifestyle, this fish displays visual behaviour and rapid strikes for prey that are remarkably similar to those of the chameleon . In a direct comparison of the two species, we have revealed other, previously unsuspected, similarities, such as corneal accommodation, which was unknown in teleosts, as well as bringing together, for the first time, data collected from both species. The sandlance is the only teleost, among thousands studied, that has corneal refraction, corneal accommodation and reduced lens power, as well as sharing the other specialised optical features seen in chameleons. The independent eye movement pattern in the sandlance is also unusual and similar to that of the chameleon. The selection pressures that have produced this remarkable example of convergence may relate to common visual constraints in the life styles of these two phylogenetically disparate species.
Biophysics of catch bonds.
Venue: Annual Review of Biophysics

Receptor-ligand bonds strengthened by tensile mechanical force are referred to as catch bonds. This review examines experimental data and biophysical theory to analyze why mechanical force prolongs the lifetime of these bonds rather than shortens the lifetime by pulling the ligand out of the binding pocket. Although many mathematical models can explain catch bonds, experiments using structural variants have been more helpful in determining how catch bonds work. The underlying mechanism has been worked out so far only for the bacterial adhesive protein FimH. This protein forms catch bonds because it is allosterically activated when mechanical force pulls an inhibitory domain away from the ligand-binding domain. Other catch bond-forming proteins, including blood cell adhesion proteins called selectins and the motor protein myosin, show evidence of allosteric regulation between two domains, but it remains unclear if this is related to their catch bond behavior.
Butenolides from plant-derived smoke: natural plant-growth regulators with antagonistic actions on seed germination.
Venue: Journal of Natural Products

Smoke plays an intriguing role in promoting the germination of seeds of many species following a fire. Recently, a bicyclic compound containing a condensed butenolide moiety, 3-methyl-2H-furo[2,3-c]pyran-2-one (1), was reported as a potent germination promoter from plant-derived smoke. In this study, a related butenolide, 3,4,5-trimethylfuran-2(5H)-one (2), which inhibits germination and significantly reduces the effect of 1 when applied simultaneously, was also isolated from plant-derived smoke. The interaction of these compounds with opposing actions on seed germination may have important ecological implications in a post-fire environment and could be useful molecules for understanding the events involved in breaking seed dormancy and promoting seed germination.
Ballistic tongue projection in chameleons maintains high performance at low temperature
Venue: Proceedings of the National Academy of Sciences of the United States of America

Environmental temperature impacts the physical activity and ecology of ectothermic animals through its effects on muscle contractile physiology. Sprinting, swimming, and jumping performance of ectotherms decreases by at least 33% over a 10 °C drop, accompanied by a similar decline in muscle power. We propose that ballistic movements that are powered by recoil of elastic tissues are less thermally dependent than movements that rely on direct muscular power. We found that an elastically powered movement, ballistic tongue projection in chameleons, maintains high performance over a 20 °C range. Peak velocity and power decline by only 10%–19% with a 10 °C drop, compared to >42% for nonelastic, muscle-powered tongue retraction. These results indicate that the elastic recoil mechanism circumvents the constraints that low temperature imposes on muscle rate properties and thereby reduces the thermal dependence of tongue projection. We propose that organisms that use elastic recoil mechanisms for ecologically important movements such as feeding and locomotion may benefit from an expanded thermal niche.
Should the wind disturbance patterns observed in natural forests be mimicked in planted forests in the British uplands
Venue: Forestry

Recent developments in UK forestry policy require the adoption of management practices that maintain and improve the biodiversity of managed forests. One approach is to use natural disturbance in unmanaged forests as a template for setting the scale, frequency and pattern of forest operations in managed forests. This review considers the relevance of this approach for conifer plantations in upland Britain. The dynamics of British planted forests are compared with the disturbance dynamics of analogous natural forests with particular reference to disturbance by strong winds. Western hemlock‐Sitka spruce (Tsuga heterophylla‐Picea sitchensis) forests in the Pacific North-west of North America and particularly South-east Alaska provide the most promising comparison. There are few reports on disturbance in these forests, but the regime includes both gap-phase and stand replacement dynamics due to wind. However, the landscape proportion and pattern of resulting structural types are not well defined. The dynamics of planted forests in Britain are dominated by rotational patch clearfelling which results in regular stand replacement and little possibility of the stands developing beyond the stage of stem exclusion towards old-growth. The pattern and timing of felling is driven by economic and visual amenity considerations rather than by an attempt to mimic natural disturbance patterns. Moreover, the structural complexity and remnant elements (such as deadwood, large trees, vegetation patches) left after large scale disturbance are rarely found after conventional timber harvesting. The authors conclude that natural wind disturbance regimes have potential as a reference point for management in British upland forests but at present are not relevant as a model to mimic explicitly. This is because the biodiversity benefits of adopting a ‘natural’ approach in planted forests are unclear compared with management guided by other criteria such as rarity. Furthermore, the spatial and temporal pattern to be mimicked is not sufficiently well understood. Improved knowledge could inform decisions on the scale and distribution of harvesting across a landscape, and modify silvicultural operations to create and maintain the structures and patterns associated with natural disturbance. However, further research is needed to quantify the spatial and temporal characteristics of wind disturbance in upland forests in Britain and in natural forests elsewhere.
The Mechanics of the Flower Stem of the Sedge Carex acutiformis
Venue: Annals of Botany

The mechanics of the triangular stems of Carex acutiformis was investigated by subjecting sections to bending and torsional tests. The stem was rigid in bending, being stiffened peripherally by lignified material around the vascular bundles, but because of its triangular shape it was vulnerable to local buckling. Despite being and narrow the stem was able to support the seed head, though it sagged appreciably towards the tip. In contrast the stem had very low torsional rigidity, both because of its triangular shape because the strands of lignified material were isolated from each other. In its lowland habitat this allows the drooping stem to twist away from the light winds, so reducing drag and the chances of self-fertilization. This method of reconfiguring is not possible in the shorter, stiffer mountain sedges which must withstand higher winds; many therefore have more circular stems which will be more efficient at resisting bending.
Biologically Induced Reduction in Symmetry: A Study of Crystal Texture of Calcitic Sponge Spicules
Venue: Chemistry: A European Journal

Organisms can exert a remark- able degree of control over crystal growth. One way of achieving this is by the ad- sorption of specialized macromolecules on specific planes of the growing crystals. With continued growth of the crystal, the macromolecules are incorporated inside the crystal bulk. Their presence does not change the crystal structure, but creates discontinuities in the perfect lattice. Here we study in detail three unusual cases of reduction in symmetry at the level of crys- tal domain shapes, induced by this con- trolled intercalation. We examined sponge spicules, which are single crystals of Mg- bearing calcite. They were specifically chosen for this study, because their mor- phologies do not reflect the hexagonal symmetry of calcite. Their crystal textures (coherence lengths and angular spreads) were characterized by high-resolution X- ray diffraction with well-collimated syn- chrotron radiation. The results are com- pared to analogous studies of synthetic calcite and Mg-bearing calcite. In all the selected spicules reduction in symmetry is observed in the coherence lengths among symmetry-related crystallographic direc- tions. The reconstructed shapes of the do- mains of perfect structure closely match the specific spicule morphologies. The synthetic crystals show no such reduction in symmetry. Although the manner by which such exquisite control is achieved is not known, we envisage it involving a combination of oriented nucleation with either physical or stereochemically driven adsorption.