nils-herrmann/clean_scirepeval huggingface dataset:
The biology of extinct and extant sawfish (Batoidea: Sclerorhynchidae and Pristidae)
Venue: Reviews in Fish Biology and Fisheries

Sclerorhynchids (extinct sawfishes, Batoidea), pristids (extant sawfish, Batoidea) and pristiophorids (sawsharks, Squalomorphi) are the three elasmobranch families that possess an elongated rostrum with lateral teeth. Sclerorhynchids are the extinct sawfishes of the Cretaceous period, which reached maximum total lengths of 100 cm. The morphology of their rostral teeth is highly variable. Pristid sawfish occur circumtropically and can reach maximum total lengths of around 700 cm. All pristid species are globally endangered due to their restricted habitat inshore. Pristiophorid sawsharks are small sharks of maximum total lengths below 150 cm, which occur in depths of 70–900 m. Close examination of the morphology of pectoral fin basals and the internal structure of the rostrum reveals that sclerorhynchids and pristids evolved independently from rhinobatids, whereas pristiophorids are squalomorph sharks. The elongation of the rostrum may be an adaptation for feeding, as all marine vertebrate taxa that possess this structure are said to use it in the context of feeding.
Micronanostructures of the scales on a mosquito's legs and their role in weight support.
Venue: Physical Review E

We show here that the mosquito cannot only give rise to a higher water-supporting force than the water strider if the ratio of the water-supporting force to the body weight of the insect itself is compared, but also can safely take off or land on the water surface, and also can attach on any solid surface like the fly. We found that the mosquito's legs are covered by numerous scales consisting of the uniform microscale longitudinal ridges (nanoscale thickness and microscale spacing between) and nanoscale cross ribs (nanoscale thickness and spacing between). Such special delicate microstructure and/or nanostructure on the leg surface give a water contact angle of approximately 153 degrees and give a surprising high water-supporting ability. It was found that the water-supporting force of a single leg of the mosquito is about 23 times the body weight of the mosquito, compared with a water strider's leg giving a water-supporting force of about 15 times the body weight of the insect.
Mechanisms of membrane fusion: disparate players and common principles
Venue: Nature Reviews Molecular Cell Biology

Membrane fusion can occur between cells, between different intracellular compartments, between intracellular compartments and the plasma membrane and between lipid-bound structures such as viral particles and cellular membranes. In order for membranes to fuse they must first be brought together. The more highly curved a membrane is, the more fusogenic it becomes. We discuss how proteins, including SNAREs, synaptotagmins and viral fusion proteins, might mediate close membrane apposition and induction of membrane curvature to drive diverse fusion processes. We also highlight common principles that can be derived from the analysis of the role of these proteins.
A spider that feeds indirectly on vertebrate blood by choosing female mosquitoes as prey.
Venue: Proceedings of the National Academy of Sciences of the United States of America

Spiders do not feed directly on vertebrate blood, but a small East African jumping spider (Salticidae), Evarcha culicivora, feeds indirectly on vertebrate blood by choosing as preferred prey female mosquitoes that have had recent blood meals. Experiments show that this spider can identify its preferred prey by sight alone and by odor alone. When presented with two types of size-matched motionless lures, E. culicivora consistently chose blood-fed female mosquitoes in preference to nonmosquito prey, male mosquitoes, and sugar-fed female mosquitoes (i.e., females that had not been feeding on blood). When the choice was between mosquitoes of different sizes (both blood- or both sugar-fed), small juveniles chose the smaller prey, whereas adults and larger juveniles chose the larger prey. However, preference for blood took precedence over preference for size (i.e., to get a blood meal, small individuals took prey that were larger than the preferred size, and larger individuals took prey that were smaller than the preferred size). When presented with odor from two prey types, E. culicivora approached the odor from blood-fed female mosquitoes significantly more often the odor of the prey that were not carrying blood.
Correlation between aquaporin and water permeability in response to vasotocin, hydrin and β-adrenergic effectors in the ventral pelvic skin of the tree frog Hyla japonica
Venue: The Journal of Experimental Biology

The ventral pelvic skin of the tree frog Hyla japonica expresses two kinds of arginine vasotocin (AVT)-stimulated aquaporins (AQP-h2 and AQP-h3), which affect the capacity of the frog's skin to absorb water. As such, it can be used as a model system for analyzing the molecular mechanisms of water permeability. We investigated AQP dynamics and water permeability in the pelvic skin of H. japonica following challenge with AVT, hydrins (intermediate peptides of pro-AVT) and β-adrenergic effectors. In the in vivo experiment, both AQP-h2 and AQP-h3 proteins were translocated to the apical plasma membrane in the principal cells of the first-reacting cell (FRC) layer in the pelvic skin following challenge with AVT, hydrin 1 and hydrin 2, thereby increasing the water permeability of the pelvic skin. The β-adrenergic receptor agonist isoproterenol (IP) and its anatagonist propranolol (PP) in combination with AVT or hydrins were used as challenge in the in vitro experiment. IP increased water permeability whereas PP inhibited it, and both events were well correlated with the translocation of the AQPs to the apical membrane. In the PP+AVT-treated skins, labels for AQP-h2 and AQP-h3 were differentially visible among the principal cells; the apical plasma membrane of some cells was labeled while others were not, indicating that the response of PP or AVT is different from cell to cell. These results provide morphological evidence that the principal cells of the FRC layers may have two kinds of receptors: a V2 receptor and β-adrenergic receptor.
Nest ‘moulting’ in the ant Temnothorax albipennis

Venue: Animal Behaviour

We showed how super-organisms, here ant colonies, modify their home according to their increasing or decreasing space requirements. The ontogeny of wall building by colonies of the ant Temnothorax albipennis involves discontinuous rebuilding events that are reminiscent of moulting in insects. Here for the first time we manipulated worker density by changing nest cavity size instead of worker number, thus avoiding accidentally shifting the balance of workers with different propensities for building tasks. Our results suggest for the first time that history influences wall building in ants when worker density decreases (e.g. with colony diminution) as well as when it increases (e.g. with colony growth) as shown by earlier work. Furthermore, we found that ants used a greater number of the larger building blocks (big sand grains) both after cavity expansion and, more surprisingly, also after cavity contraction. The pattern of nest ‘moulting’ we experimentally manipulated and analysed should provide insights into possible trade-offs between the various functions and structural properties of the nest that these animals may have to optimize.
A Cultured Greigite-Producing Magnetotactic Bacterium in a Novel Group of Sulfate-Reducing Bacteria
Venue: Science

The crystal structure of biomineralized magnetic nanocrystals depends on environmental and genetic factors. Magnetotactic bacteria contain magnetosomes—intracellular, membrane-bounded, magnetic nanocrystals of magnetite (Fe3O4) or greigite (Fe3S4)—that cause the bacteria to swim along geomagnetic field lines. We isolated a greigite-producing magnetotactic bacterium from a brackish spring in Death Valley National Park, California, USA, strain BW-1, that is able to biomineralize greigite and magnetite depending on culture conditions. A phylogenetic comparison of BW-1 and similar uncultured greigite- and/or magnetite-producing magnetotactic bacteria from freshwater to hypersaline habitats shows that these organisms represent a previously unknown group of sulfate-reducing bacteria in the Deltaproteobacteria. Genomic analysis of BW-1 reveals the presence of two different magnetosome gene clusters, suggesting that one may be responsible for greigite biomineralization and the other for magnetite.
Renewable fluid dynamic energy derived from aquatic animal locomotion.
Venue: Bioinspiration & Biomimetics

Aquatic animals swimming in isolation and in groups are known to extract energy from the vortices in environmental flows, significantly reducing muscle activity required for locomotion. A model for the vortex dynamics associated with this phenomenon is developed, showing that the energy extraction mechanism can be described by simple criteria governing the kinematics of the vortices relative to the body in the flow. In this way, we need not make direct appeal to the fluid dynamics, which can be more difficult to evaluate than the kinematics. Examples of these principles as exhibited in swimming fish and existing energy conversion devices are described. A benefit of the developed framework is that the potentially infinite-dimensional parameter space of the fluid-structure interaction is reduced to a maximum of eight combinations of three parameters. The model may potentially aid in the design and evaluation of unsteady aero- and hydrodynamic energy conversion systems that surpass the Betz efficiency limit of steady fluid dynamic energy conversion systems.
Nanoscale design of snake skin for reptation locomotions via friction anisotropy.
Venue: Journal of Biomechanics

Multi-mode scanning probe microscopy is employed to investigate the nanostructure of dermal samples from three types of snakes. Sophisticated friction modifying nanostructures are described. These include an ordered microfibrillar array that can function to achieve mission adaptable friction characteristics. Significant reduction of adhesive forces in the contact areas caused by the 'double-ridge' nanoscale microfibrillar geometry provides ideal conditions for sliding in forward direction with minimum adhesive forces and friction. Low surface adhesion in these local contact points may reduce local wear and skin contamination by environmental debris. The highly asymmetric, 'pawl-like' profile of the microfibrillar ends with radius of curvature 20-40 nm induces friction anisotropy in forward backward motions and serves as an effective stopper for backward motion preserving low friction for forward motion. The system of continuous micropores penetrating through the snake skin may serve as a delivery system for lubrication/anti-adhesive lipid mixture that provides for boundary lubrication of snake skins.
Teacher tree: The evolution of notch shape optimization from complex to simple
Venue: Engineering Fracture Mechanics

Shape optimization of engineering components following the design rules of nature was started in the late eighties in the Karlsruhe Research Centre. The key idea was the natural observation that trees care by load-adaptive growth to maintain a uniform stress distribution at their surface. This means also that high stress peaks (notch stresses) are avoided as potential failure points. The computer simulation of this adaptive growth has been called Computer Aided Optimization (CAO). CAO is based on the use of the Finite-Element-Method (FEM). The present paper shows how 15 years after the CAO-method drastic simplifications are available. So notch shape optimization in many cases can be done without the FEM-codes, with a pocket calculator or even simpler with a graphic method.
Plant green-island phenotype induced by leaf-miners is mediated by bacterial symbionts
Venue: Proceedings of The Royal Society B: Biological Sciences

The life cycles of many organisms are constrained by the seasonality of resources. This is particularly true for leaf-mining herbivorous insects that use deciduous leaves to fuel growth and reproduction even beyond leaf fall. Our results suggest that an intimate association with bacterial endosymbionts might be their way of coping with nutritional constraints to ensure successful development in an otherwise senescent environment. We show that the phytophagous leaf-mining moth Phyllonorycter blancardella (Lepidoptera) relies on bacterial endosymbionts, most likely Wolbachia, to manipulate the physiology of its host plant resulting in the ‘green-island’ phenotype—photosynthetically active green patches in otherwise senescent leaves—and to increase its fitness. Curing leaf-miners of their symbiotic partner resulted in the absence of green-island formation on leaves, increased compensatory larval feeding and higher insect mortality. Our results suggest that bacteria impact green-island induction through manipulation of cytokinin levels. This is the first time, to our knowledge, that insect bacterial endosymbionts have been associated with plant physiology.
The biomechanics of Cornus canadensis stamens are ideal for catapulting pollen vertically
Venue: Functional Ecology

1 
Rapid movements in fungi and plants have evolved in different species to facilitate the dispersal of spores and seeds. The mechanisms of action can differ among species, but the effectiveness of these movements has rarely, if ever, been tested. Here we show through a quantitative biomechanical analysis that the stamens of Cornus canadensis L. (bunchberry) are ideal for catapulting pollen vertically at high speeds. 
 
2 
We develop a biomechanical model to describe the explosive launch of pollen from the flowers of bunchberry. The model determines the equation of motion for the stamens based only on the morphology and measurements of the parts of the stamens. To measure the motion of the stamens to compare with our model, we analysed individual frames of a video taken at 10 000 fps. 
 
3 
The thecae of adjacent stamens dehisce in bud so that the stomia face each other, retaining pollen between neighbouring anthers. As the flowers open, pollen is accelerated vertically as long as the thecae remain in contact. Pollen is released only when the anthers move horizontally and separate. 
 
4 
The observed motion of the stamens matches the results from our model through release of the pollen. The model reveals that pollen release (horizontal movement of the anthers) occurs only after the vertical speed is at its maximum. Thus, for this particular catapult mechanism, the morphology of the stamens is optimal for launching light, dry pollen straight upwards at high speed. Pollen launched vertically at high speed both enhances insect pollination by helping to making pollen stick on visiting insects, and also allows for successful wind pollination by propelling pollen into the air column. Seed set by inflorescences in pollinator-exclosure cages further supports the ability of this flower to use wind as a pollination mechanism.
Cartilage aggrecan can undergo self-adhesion.
Venue: Biophysical Journal

Here it is reported that aggrecan, the highly negatively charged macromolecule in the cartilage extracellular matrix, undergoes Ca(2+)-mediated self-adhesion after static compression even in the presence of strong electrostatic repulsion in physiological-like solution conditions. Aggrecan was chemically end-attached onto gold-coated planar silicon substrates and gold-coated microspherical atomic force microscope probe tips (end radius R approximately 2.5 mum) at a density ( approximately 40 mg/mL) that simulates physiological conditions in the tissue ( approximately 20-80 mg/mL). Colloidal force spectroscopy was employed to measure the adhesion between opposing aggrecan monolayers in NaCl (0.001-1.0 M) and NaCl + CaCl(2) (] = 0.15 M, [Ca(2+)] = 0 - 75 mM) aqueous electrolyte solutions. Aggrecan self-adhesion was found to increase with increasing surface equilibration time upon compression (0-30 s). Hydrogen bonding and physical entanglements between the chondroitin sulfate-glycosaminoglycan side chains are proposed as important factors contributing to aggrecan self-adhesion. Self-adhesion was found to significantly increase with decreasing bath ionic strength (and hence, electrostatic double-layer repulsion), as well as increasing Ca(2+) concentration due to the additional ion-bridging effects. It is hypothesized that aggrecan self-adhesion, and the macromolecular energy dissipation that results from this self-adhesion, could be important factors contributing to the self-assembled architecture and integrity of the cartilage extracellular matrix in vivo.
Surface structure and frictional properties of the skin of the Amazon tree boa Corallus hortulanus (Squamata, Boidae)
Venue: Journal of Comparative Physiology A-neuroethology Sensory Neural and Behavioral Physiology

The legless locomotion of snakes requires specific adaptations of their ventral scales to maintain friction force in different directions. The skin microornamentation of the snake Corallus hortulanus was studied by means of scanning electron microscopy and the friction properties of the skin were tested on substrates of different roughness. Skin samples from various parts of the body (dorsal, lateral, ventral) were compared. Dorsal and lateral scales showed similar, net-like microornamentation and similar friction coefficients. Average friction coefficients for dorsal and lateral scales on the epoxy resin surfaces were 0.331 and 0.323, respectively. In contrast, ventral scales possess ridges running parallel to the longitudinal body axis. They demonstrated a significantly lower friction coefficient compared to both dorsal and lateral scales (0.191 on average). In addition, ventral scales showed frictional anisotropy comparing longitudinal and perpendicular direction of the ridges. This study clearly demonstrates that different skin microstructure is responsible for different frictional properties in different body regions.
Quantitative microstructural studies of the armor of the marine threespine stickleback (Gasterosteus aculeatus).
Venue: Journal of Structural Biology

In this study, a quantitative investigation of the microstructure and composition of field-caught marine Gasterosteus aculeatus (threespine stickleback) armor is presented, which provides useful phylogenetic information and insights into biomechanical function. Micro-computed tomography (microCT) was employed to create full three-dimensional images of the dorsal spines and basal plate, lateral plates, pelvic girdle and spines and to assess structural and compositional properties such as the spatial distribution of thickness (approximately 100-300 microm), the heterogeneous cross-sectional geometry (centrally thickened), plate-to-plate juncture and overlap (approximately 50% of the plate width), and bone mineral density (634-748 HA/cm(3)). The convolution of plate geometry in conjunction with plate-to-plate overlap allows a relatively constant armor thickness to be maintained throughout the assembly, promoting spatially homogeneous protection and thereby avoiding weakness at the armor unit interconnections. Plate-to-plate junctures act to register and join the plates while permitting compliance in sliding and rotation in selected directions. Mercury porosimetry was used to determine the pore size distribution and volume percent porosity of the lateral plates (20-35 vol.%) and spines (10-15 vol.%). SEM and microCT revealed a porous, sandwich-like cross-section beneficial for bending stiffness and strength at minimum weight. Back-scattered electron microscopy and energy dispersive X-ray analysis were utilized to quantify the weight percent mineral content (58-68%). Scanning electron microscopy and surface profilometry were used to characterize the interior and exterior surface topography (tubercles) of the lateral plates. The results obtained in this study are discussed in the context of mechanical function, performance, fitness, and survivability.
Foldable structures and the natural design of pollen grains
Venue: Proceedings of the National Academy of Sciences of the United States of America

Upon release from the anther, pollen grains of angiosperm flowers are exposed to a dry environment and dehydrate. To survive this process, pollen grains possess a variety of physiological and structural adaptations. Perhaps the most striking of these adaptations is the ability of the pollen wall to fold onto itself to prevent further desiccation. Roger P. Wodehouse coined the term harmomegathy for this folding process in recognition of the critical role it plays in the survival of the pollen grain. There is still, however, no quantitative theory that explains how the structure of the pollen wall contributes to harmomegathy. Here we demonstrate that simple geometrical and mechanical principles explain how wall structure guides pollen grains toward distinct folding pathways. We found that the presence of axially elongated apertures of high compliance is critical for achieving a predictable and reversible folding pattern. Moreover, the intricate sculpturing of the wall assists pollen closure by preventing mirror buckling of the surface. These results constitute quantitative structure-function relationships for pollen harmomegathy and provide a framework to elucidate the functional significance of the very diverse pollen morphologies observed in angiosperms.
Aggressive pharmacological treatment for reversing malignant bowel obstruction.
Venue: Journal of Pain and Symptom Management

Early and intensive pharmacological treatment not only may reduce gastrointestinal symptoms but also reverse malignant bowel obstruction. Fifteen consecutive advanced cancer patients with inoperable bowel obstruction received a combination of drugs including metoclopramide, octreotide, dexamethasone and an initial bolus of amidotrizoato. Recovery of intestinal transit was reported within 1-5 days in fourteen patients, who continued this treatment without presenting symptoms of bowel obstruction until death. This case series establishes that the combination of propulsive and antisecretive agents can act synergistically to allow a fast recovery of bowel transit without inducing unpleasant colic. It suggests that the most important mechanism in these circumstances is functional and can be reversible, if an aggressive treatment is initiated early before fecal impaction and edema render bowel obstruction irreversible.
Erosion resistance of bionic functional surfaces inspired from desert scorpions.
Venue: Langmuir

In this paper, a bionic method is presented to improve the erosion resistance of machine components. Desert scorpion (Androctonus australis) is a typical animal living in sandy deserts, and may face erosive action of blowing sand at a high speed. Based on the idea of bionics and biologic experimental techniques, the mechanisms of the sand erosion resistance of desert scorpion were investigated. Results showed that the desert scorpions used special microtextures such as bumps and grooves to construct the functional surfaces to achieve the erosion resistance. In order to understand the erosion resistance mechanisms of such functional surfaces, the combination of computational and experimental research were carried out in this paper. The Computational Fluid Dynamics (CFD) method was applied to predict the erosion performance of the bionic functional surfaces. The result demonstrated that the microtextured surfaces exhibited better erosion resistance than the smooth surfaces. The further erosion tests indicated that the groove surfaces exhibited better erosion performance at 30° injection angle. In order to determine the effect of the groove dimensions on the erosion resistance, regression analysis of orthogonal multinomials was also performed under a certain erosion condition, and the regression equation between the erosion rate and groove distance, width, and height was established.