nils-herrmann/clean_scirepeval huggingface dataset:
Role of multiple, adjustable toes in distributed control shown by sideways wall-running in geckos
Venue: Proceedings of The Royal Society B: Biological Sciences

Remarkable progress has been made characterizing one of nature's most integrated, hierarchical structures––the fibrillar adhesive system of geckos. Nonetheless, we lack an understanding of how multiple toes coordinate to facilitate geckos' acrobatic locomotion. Here, we tested the control function of gecko toes by running them on vertical substrates varying in orientation, friction and roughness. Sideways wall-running geckos realigned the toes of their top feet upward to resist gravity. Toe contact area was not compromised, but redistributed. Geckos aligned all toes upward to resist slipping when encountering low-friction patches during sideways wall-running. Negotiation of intermittent slippery strips showed an increased contribution of particular toes to compensate for toes that lost adhesion. Increasing substrate roughness using discrete rods perpendicular to sideways locomotion resulted in geckos bending and/or rotating toes to conform to and even grasp the rods, with potential forces more than five times body weight. Geckos increase their effectiveness of manoeuvrability in demanding environments by taking advantage of the distributed control afforded by multiple toes. Our findings provide insight on biological attachment and offer inspiration to advance gecko-inspired robotics and other biomimetic applications.
Dynamics and stability of running on rough terrains
Venue: Royal Society Open Science

Stability of running on rough terrain depends on the propagation of perturbations due to the ground. We consider stability within the sagittal plane and model the dynamics of running as a two-dimensional body with alternating aerial and stance phases. Stance is modelled as a passive, impulsive collision followed by an active, impulsive push-off that compensates for collisional losses. Such a runner has infinitely many strategies to maintain periodic gaits on flat ground. However, these strategies differ in how perturbations due to terrain unevenness are propagated. Instabilities manifest as tumbling (orientational instability) or failing to maintain a steady speed (translational instability). We find that open-loop strategies that avoid sensory feedback are sufficient to maintain stability on step-like terrains with piecewise flat surfaces that randomly vary in height. However, these open-loop runners lose orientational stability on rough terrains whose slope also varies randomly. The orientational instability is significantly mitigated by minimizing the tangential collision, which typically requires sensory information and anticipatory strategies such as leg retraction. By analysing the propagation of perturbations, we derive a single dimensionless parameter that governs stability. This parameter provides guidelines for the design and control of both biological and robotic runners.
Nature's forms are frilly, flexible, and functional.
Venue: European Physical Journal E

A ubiquitous motif in nature is the self-similar hierarchical buckling of a thin lamina near its margins. This is seen in leaves, flowers, fungi, corals, and marine invertebrates. We investigate this morphology from the perspective of non-Euclidean plate theory. We identify a novel type of defect, a branch-point of the normal map, that allows for the generation of such complex wrinkling patterns in thin elastic hyperbolic surfaces, even in the absence of stretching. We argue that branch points are the natural defects in hyperbolic sheets, they carry a topological charge which gives them a degree of robustness, and they can influence the overall morphology of a hyperbolic surface without concentrating elastic energy. We develop a theory for branch points and investigate their role in determining the mechanical response of hyperbolic sheets to weak external forces.
Plant-pollinator interactions between generalists persist over time and space.
Venue: Ecology

Generalist species are the linchpins of networks, as they are important for maintaining network structure and function. Previous studies have shown that interactions between generalists tend to occur consistently across years and sites. However, the link between temporal and spatial interaction persistence across scales remains unclear. To address this gap, we collected data on plant-pollinator interactions throughout the flowering period for five years across six plots in a subalpine meadow in the Rocky Mountains. We found that interactions between generalists tended to persist more in time and space such that interactions near the network core were more frequently recorded across years, within seasons, and among plots. We posit that species' tolerance of environmental variation across time and space plays a key role in generalization by regulating spatiotemporal overlap with interaction partners. Our results imply a role of spatiotemporal environmental variation in organizing species interactions, marrying niche concepts that emphasize species environmental constraints and their community role.
Total Synthesis and Target Identification of the Curcusone Diterpenes.
Venue: Journal of the American Chemical Society

The curcusone natural products are complex diterpenes featuring a characteristic [6-7-5] tricyclic carbon skeleton similar to the daphnane and tigliane diterpenes. Among them, curcusones A-D demonstrated potent anticancer activity against a broad spectrum of human cancer cell lines. Prior to this study, no total synthesis of the curcusones was achieved and their anticancer mode of action remained unknown. Herein, we report our synthetic and chemoproteomics studies of the curcusone diterpenes which culminate in the first total synthesis of several curcusone natural products and identification of BRCA1-associated ATM activator 1 (BRAT1) as a cellular target. Our efficient synthesis is highly convergent, builds upon cheap and abundant starting materials, features a thermal [3,3]-sigmatropic rearrangement and a novel FeCl3-promoted cascade reaction to rapidly construct the critical cycloheptadienone core of the curcusones, and led us to complete the first total synthesis of curcusones A and B in only 9 steps, C and D in 10 steps, and dimericursone A in 12 steps. The chemical synthesis of dimericursone A from curcusones C and D provided direct evidence to support the proposed Diels-Alder dimerization and cheletropic elimination biosynthetic pathway. Using an alkyne-tagged probe molecule, BRAT1, an important but previously "undruggable" oncoprotein, was identified as a key cellular target via chemoproteomics. We further demonstrate for the first time that BRAT1 can be inhibited by curcusone D, resulting in impaired DNA damage response, reduced cancer cell migration, potentiated activity of the DNA damaging drug etoposide, and other phenotypes similar to BRAT1 knockdown.
Extreme strength observed in limpet teeth
Venue: Journal of the Royal Society Interface

The teeth of limpets exploit distinctive composite nanostructures consisting of high volume fractions of reinforcing goethite nanofibres within a softer protein phase to provide mechanical integrity when rasping over rock surfaces during feeding. The tensile strength of discrete volumes of limpet tooth material measured using in situ atomic force microscopy was found to range from 3.0 to 6.5 GPa and was independent of sample size. These observations highlight an absolute material tensile strength that is the highest recorded for a biological material, outperforming the high strength of spider silk currently considered to be the strongest natural material, and approaching values comparable to those of the strongest man-made fibres. This considerable tensile strength of limpet teeth is attributed to a high mineral volume fraction of reinforcing goethite nanofibres with diameters below a defect-controlled critical size, suggesting that natural design in limpet teeth is optimized towards theoretical strength limits.
Wave-slope soaring of the brown pelican
Venue: Movement ecology

From the laboratory at Scripps Institution of Oceanography, it is common to see the brown pelican ( Pelecanus occidentalis ) traveling along the crests of ocean waves just offshore of the surf-zone. When flying in this manner, the birds can travel long distances without flapping, centimeters above the ocean’s surface. Here we derive a theoretical framework for assessing the energetic savings related to this behavior, ‘wave-slope soaring,’ in which an organism in flight takes advantage of localized updrafts caused by traveling ocean surface gravity waves.  The energy cost of steady, constant altitude flight in and out of ground effect are analyzed as controls. Potential flow theory is used to quantify the ocean wave-induced wind associated with near-shoaling, weakly nonlinear, shallow water ocean surface gravity waves moving through an atmosphere initially at rest. Using perturbation theory and the Green’s function for Laplace’s equation in 2D with Dirichlet boundary conditions, we obtain integrals for the horizontal and vertical components of the wave-induced wind in a frame of reference moving with the wave. Wave-slope soaring flight is then analyzed using an energetics-based approach for waves under a range of ocean conditions and the body plan of P. occidentalis.  For ground effect flight, we calculate a ∼15 - 25% reduction in cost of transport as compared with steady, level flight out of ground effect. When wave-slope soaring is employed at flight heights ∼2m in typical ocean conditions (2m wave height, 15s period), we calculate 60-70% reduction in cost of transport as compared with flight in ground effect. A relatively small increase in swell amplitude or decrease in flight height allows up to 100% of the cost of transport to be offset by wave-slope soaring behavior.  The theoretical development presented here suggests there are energy savings associated with wave-slope soaring. Individual brown pelicans may significantly decrease their cost of transport utilizing this mode of flight under typical ocean conditions. Thus wave-slope soaring may provide fitness benefit to these highly mobile organisms that depend on patchy prey distribution over large home ranges.
Map-like use of Earth’s magnetic field in sharks
Venue: Current Biology

Migration is common in marine animals,1-5 and use of the map-like information of Earth's magnetic field appears to play an important role.2,6-9 While sharks are iconic migrants10-12 and well known for their sensitivity to electromagnetic fields,13-20 whether this ability is used for navigation is unresolved.14,17,21,22 We conducted magnetic displacement experiments on wild-caught bonnetheads (Sphyrna tiburo) and show that magnetic map cues can elicit homeward orientation. We further show that use of a magnetic map to derive positional information may help explain aspects of the genetic structure of bonnethead populations in the northwest Atlantic.23-26 These results offer a compelling explanation for the puzzle of how migratory routes and population structure are maintained in marine environments, where few physical barriers limit movements of vagile species.
Repeated evolution of underwater rebreathing in diving Anolis lizards
Venue: Current Biology

Air-based respiration limits the use of aquatic environments by ancestrally terrestrial animals. To overcome this challenge, diving arthropods have evolved to respire without resurfacing using air held between their cuticle and surrounding water.1-4 Inspired by natural history observations in Haiti (unpublished data) and Costa Rica,5,6 we conducted experiments documenting routine air-based underwater respiration in several distantly related semi-aquatic Anolis lizard species. Semi-aquatic anoles live along neotropical streams and frequently dive for refuge or food,7-12 remaining underwater for up to 18 min. While submerged, these lizards iteratively expire and re-inspire narial air bubbles-underwater "rebreathing." Rebreathed air is used in respiration, as the partial pressure of oxygen in the bubbles decreases with experimental submersion time in living anoles, but not in mechanical controls. Non-aquatic anoles occasionally rebreathe when submerged but exhibit more rudimentary rebreathing behaviors. Anole rebreathing is facilitated by a thin air layer (i.e., a "plastron," sensu Brocher13) supported by the animal's rugose skin upon submergence. We suggest that hydrophobic skin, which we observed in all sampled anoles,14,15 may have been exaptative, facilitating the repeated evolution of specialized rebreathing in species that regularly dive. Phylogenetic analyses strongly suggest that specialized rebreathing is adaptive for semi-aquatic habitat specialists. Air-based rebreathing may enhance dive performance by incorporating dead space air from the buccal cavity or plastron into the lungs, facilitating clearance of carbon dioxide, or allowing uptake of oxygen from surrounding water (i.e., a "physical gill" mechanism4,16).
Eggshell membrane biomaterial as a platform for applications in materials science.
Venue: Acta Biomaterialia

Eggshell membrane (ESM) is a unique biomaterial, which is generally considered as waste. However, it has extraordinary properties which can be utilized in various fields and its potential applications are therefore now being widely studied. The first part of this review focuses on the chemical composition and morphology of ESM. The main areas of ESM application are discussed in the second part. These applications include its utilization as a biotemplate for the synthesis of nanoparticles; as a sorbent of heavy metals, organics, dyes, sulfonates and fluorides; as the main component of biosensors; in medicine; and various other applications. For each area of interest, a detailed literature survey is given.
The structure and mechanics of Moso bamboo material
Venue: Journal of the Royal Society Interface

Although bamboo has been used structurally for millennia, there is currently increasing interest in the development of renewable and sustainable structural bamboo products (SBPs). These SBPs are analogous to wood products such as plywood, oriented strand board and glue-laminated wood. In this study, the properties of natural Moso bamboo (Phyllostachys pubescens) are investigated to further enable the processing and design of SBPs. The radial and longitudinal density gradients in bamboo give rise to variations in the mechanical properties. Here, we measure the flexural properties of Moso bamboo in the axial direction, along with the compressive strengths in the axial and transverse directions. Based on the microstructural variations (observed with scanning electron microscopy) and extrapolated solid cell wall properties of bamboo, we develop models, which describe the experimental results well. Compared to common North American construction woods loaded along the axial direction, Moso bamboo is approximately as stiff and substantially stronger, in both flexure and compression but denser. This work contributes to critical knowledge surrounding the microstructure and mechanical properties of bamboo, which are vital to the engineering and design of sustainable SBPs.
Neurophysiological coordination of duet singing
Venue: Proceedings of the National Academy of Sciences of the United States of America

Cooperation, turn taking, and other social behaviors often depend on temporal coordination between individuals. How brains use sensory cues from participants to synchronize performances is not known. We examined the interactions between sensory cues and motor activity in the brains of female and male plain-tailed wrens that rapidly take turns to produce a duet that sounds as if a single bird is singing. We made simultaneous neurophysiological recordings from the brains of pairs of awake, duetting wrens. We discovered that inhibition driven by auditory feedback from the partner alternated with the premotor activity used by each individual to produce its own vocalizations. These data show how sensory feedback links the brains of cooperating animals through the modulation of motor circuits. Coordination of behavior for cooperative performances often relies on linkages mediated by sensory cues exchanged between participants. How neurophysiological responses to sensory information affect motor programs to coordinate behavior between individuals is not known. We investigated how plain-tailed wrens (Pheugopedius euophrys) use acoustic feedback to coordinate extraordinary duet performances in which females and males rapidly take turns singing. We made simultaneous neurophysiological recordings in a song control area “HVC” in pairs of singing wrens at a field site in Ecuador. HVC is a premotor area that integrates auditory feedback and is necessary for song production. We found that spiking activity of HVC neurons in each sex increased for production of its own syllables. In contrast, hearing sensory feedback produced by the bird’s partner decreased HVC activity during duet singing, potentially coordinating HVC premotor activity in each bird through inhibition. When birds sang alone, HVC neurons in females but not males were inhibited by hearing the partner bird. When birds were anesthetized with urethane, which antagonizes GABAergic (γ-aminobutyric acid) transmission, HVC neurons were excited rather than inhibited, suggesting a role for GABA in the coordination of duet singing. These data suggest that HVC integrates information across partners during duets and that rapid turn taking may be mediated, in part, by inhibition.
Mammalian enteral ventilation ameliorates respiratory failure
Venue: Med

Several aquatic organisms such as loaches have evolved unique intestinal breathing mechanisms to survive under extensive hypoxia. To date, it is highly controversial whether such capability can be adapted in mammalian species as another site for gas exchange. Here, we report the advent of the intestinal breathing phenomenon in mammalians by exploiting EVA (enteral ventilation via anus).  Two different modes of EVA were investigated in an experimental model of respiratory failure: intra-rectal oxygen O2 gas ventilation (g-EVA) or liquid ventilation (l-EVA) with oxygenated perfluorocarbon. After induction of type 1 respiratory failure, we analyzed the effectiveness of g-EVA and I-EVA in mouse and pig, followed by preclinical safety analysis in rat.  Both intra-rectal O2 gas and oxygenated liquid delivery were shown to provide vital rescue of experimental models of respiratory failure, improving survival, behavior, and systemic O2 level. A rodent and porcine model study confirmed the tolerable and repeatable features of an enema-like l-EVA procedure with no major signs of complications.  EVA has proven effective in mammalians such that it oxygenated systemic circulation and ameliorated respiratory failure. Due to the proven safety of perfluorochemicals in clinics, EVA potentially provides an adjunctive means of oxygenation for patients under respiratory distress conditions.  This work is funded by the Research Program on Emerging and Re-emerging Infectious Diseases, Research Projects on COVID-19 (JP20fk0108278, 20fk0108506h0001), from the Japan Agency for Medical Research and Development (AMED), to T.T.; Strategic Promotion for Practical Application of Innovative Medical Technology, Seeds A (A145), to T.T.; and KAKENHI 19K22657, to T.C.-Y. This research is partially supported by the AMED Translational Research Program; Strategic Promotion for Practical Application of Innovative Medical Technology (TR-SPRINT), to T.C.-Y.; and AMED JP18bm0704025h0001 (Program for Technological Innovation of Regenerative Medicine), to T.T.
Phytohormone-dependent plant defense signaling orchestrated by oral bacteria of the herbivore Spodoptera litura.
Venue: New Phytologist

A vast array of herbivorous arthropods live with symbiotic microorganisms. However, little is known about the nature and functional mechanism of bacterial effects on plant defense responses towards herbivores. We explored the role of microbes present in extracts of oral secretion (OS) isolated from larvae of Spodoptera litura, a generalist herbivore, in phytohormone signaling-dependent defense responses in Arabidopsis thaliana (arabidopsis). In response to mechanical damage (MD) with application of bacteria-free OS (OS- ) prepared by sterilization or filtration of OS, arabidopsis leaves exhibited enhanced de novo synthesis of oxylipins, and induction of transcript levels of the responsible genes, in comparison to those in leaves with MD + non-sterilized OS (OS+ ), indicating that OS bacteria serve as suppressors of these genes. By contrast, de novo synthesis/signaling of salicylic acid and signaling of abscisic acid were enhanced by OS bacteria. These signaling networks were cross-regulated by each other. Meta-analysis of OS bacteria identified 70 bacterial strains. Among them was Staphylococcus epidermidis, an anaerobic staphylococcus that was shown to contribute to the suppression/manipulation of phytohormone-dependent plant defense signaling. The presence of OS bacteria was consequently beneficial for S. litura larvae hosted by Brassicaceae.
Self-adaptive and efficient propulsion of Ray sperms at different viscosities enabled by heterogeneous dual helixes
Venue: Proceedings of the National Academy of Sciences of the United States of America

For decades, the propulsion of sperms has been traditionally attributed to the beating or rotating of the soft tails. However, this work disclosed an unusual swimming model of Ray sperms whose propulsion is from not only the helical tail but also the unique spiral head (i.e., the head can contribute ∼31% of the force in propulsion). Such a propulsion mechanism provides Ray sperms with high adaptability to large environmental viscosities along with advantages in linearity, straightness, and efficiency. This study expands our knowledge on the microorganisms’ motion and provides inspirations for engineering design. We disclose a peculiar rotational propulsion mechanism of Ray sperms enabled by its unusual heterogeneous dual helixes with a rigid spiral head and a soft tail, named Heterogeneous Dual Helixes (HDH) model for short. Different from the conventional beating propulsion of sperm, the propulsion of Ray sperms is from both the rotational motion of the soft helical tail and the rigid spiral head. Such heterogeneous dual helical propulsion style provides the Ray sperm with high adaptability in viscous solutions along with advantages in linearity, straightness, and bidirectional motion. This HDH model is further corroborated by a miniature swimming robot actuated via a rigid spiral head and a soft tail, which demonstrates similar superiorities over conventional ones in terms of adaptability and efficiency under the same power input. Such findings expand our knowledge on microorganisms’ motion, motivate further studies on natural fertilization, and inspire engineering designs.
Antlers - Evolution, development, structure, composition, and biomechanics of an outstanding type of bone.
Venue: Bone

Antlers are bony appendages of deer that undergo periodic regeneration from the top of permanent outgrowths (the pedicles) of the frontal bones. Of the "less familiar" bone types whose study was advocated by John Currey to gain a better understanding of structure-function relationships of mineralized tissues and organs, antlers were of special interest to him. The present review summarizes our current knowledge about the evolution, development, structure, mineralization, and biomechanics of antlers and how their formation is affected by environmental factors like nutrition. Furthermore, the potential role of antlers as a model in bone biology and several fields of biomedicine as well as their use as a monitoring tool in environmental studies are discussed.