nils-herrmann/clean_scirepeval huggingface dataset:
Mechanism of Closure of the Aortic Valve
Venue: Nature

THE human aortic valve consists of three cusps made of relatively inelastic, muscle-free material about 0.15 mm thick. It opens and shuts about once a second, and withstands a pressure difference of 100 mm of mercury when closed. It usually functions for 70 yr without failure, and works so efficiently that very little blood is regurgitated at each pulse. In order to support this large pressure difference, the cusps must close simultaneously in all operating conditions and should not touch the wall of the aorta, for considerable reversed flow would then be required to close the valve. This action suggests a fluid dynamic control mechanism which positions the cusps away from the wall of the aorta, so that the slightest reversed flow will close the valve.
Superhydrophobic and superhydrophilic plant surfaces: an inspiration for biomimetic materials
Venue: Philosophical Transactions of the Royal Society A

The diversity of plant surface structures, evolved over 460 million years, has led to a large variety of highly adapted functional structures. The plant cuticle provides structural and chemical modifications for surface wetting, ranging from superhydrophilic to superhydrophobic. In this paper, the structural basics of superhydrophobic and superhydrophilic plant surfaces and their biological functions are introduced. Wetting in plants is influenced by the sculptures of the cells and by the fine structure of the surfaces, such as folding of the cuticle, or by epicuticular waxes. Hierarchical structures in plant surfaces are shown and further types of plant surface structuring leading to superhydrophobicity and superhydrophilicity are presented. The existing and potential uses of superhydrophobic and superhydrophilic surfaces for self-cleaning, drag reduction during moving in water, capillary liquid transport and other biomimetic materials are shown.
Localized fluidization burrowing mechanics of Ensis directus
Venue: The Journal of Experimental Biology

Muscle measurements of Ensis directus, the Atlantic razor clam, indicate that the organism only has sufficient strength to burrow a few centimeters into the soil, yet razor clams burrow to over 70 cm. In this paper, we show that the animal uses the motions of its valves to locally fluidize the surrounding soil and reduce burrowing drag. Substrate deformations were measured using particle image velocimetry (PIV) in a novel visualization system that enabled us to see through the soil and watch E. directus burrow in situ. PIV data, supported by soil and fluid mechanics theory, show that contraction of the valves of E. directus locally fluidizes the surrounding soil. Particle and fluid mixtures can be modeled as a Newtonian fluid with an effective viscosity based on the local void fraction. Using these models, we demonstrate that E. directus is strong enough to reach full burrow depth in fluidized soil, but not in static soil. Furthermore, we show that the method of localized fluidization reduces the amount of energy required to reach burrow depth by an order of magnitude compared with penetrating static soil, and leads to a burrowing energy that scales linearly with depth rather than with depth squared.
Small molecules that modulate quorum sensing and control virulence in Pseudomonas aeruginosa.
Venue: Journal of Organic Chemistry

Bacteria use small molecule signals to access their local population densities in a process called quorum sensing (QS). Once a threshold signal concentration is reached, and therefore a certain number of bacteria have assembled, bacteria use QS to change gene expression levels and initiate behaviors that benefit the group. These group processes play central roles in both bacterial virulence and symbiosis and can have significant impacts on human health, agriculture, and the environment. The dependence of QS on small molecule signals has inspired organic chemists to design non-native molecules that can intercept these signals and thereby perturb bacterial group behaviors. The opportunistic pathogen Pseudomonas aeruginosa has been the target of many of these efforts due to its prevalence in human infections. P. aeruginosa uses at least two N-acyl l-homoserine lactone signals and three homologous LuxR-type receptors to initiate a range of pathogenic behaviors at high cell densities, including biofilm formation and the production of an arsenal of virulence factors. This perspective highlights recent chemical efforts to modulate LuxR-type receptor activity in P. aeruginosa and offers insight into the development of receptor-specific ligands as potential antivirulence strategies.
Structural coloration in nature
Venue: RSC Advances

's color has three main sources: pigments, structural colors and bioluminescence. Structural color is a special one, which is the color produced by micro- or nano-structures, and is bright and dazzling. The most common mechanisms of structural colors are film interference, diffraction grating, scattering and photonic crystals. Biological colors are mainly derived from film interference, which includes thin-film and multi-film interference. The diffraction grating mechanism is found in, for example, seed shrimp, mollusk Haliotis Glabra and the Hibiscus trionum flower. Scattering includes coherent and incoherent scattering. Well-known examples of coherent scattering include colors produced by brilliant iridescent butterfly wing scales and avian feather barbules, such as the peacock's tail. Examples of colors produced by photonic crystal structures include opal in beetles and iridescent spines in the sea mouse. Coloration changes occur through structural changes for camouflage, predation, signal communication and sex choice. This paper presents an overview of lessons from nature and various relevant mechanisms. Examples of bioinspired fabrication methods and applications are also presented in this paper.
The functional morphology of the petioles of the banana, Musa textilis.
Venue: Journal of Experimental Botany

Bananas are among the largest herbs in the world and their lightweight petioles hold up huge leaves. This study examined how the petioles manage to achieve adequate rigidity to do this, while allowing extensive and reversible reconfiguration in high winds. Morphological and anatomical examination of the petioles and leaves of Musa textilis suggested how these two apparently incompatible abilities are achieved. The hollow U-shaped section of the petiole and the longitudinal strengthening elements in its outer skin give it adequate rigidity, while its ventral curvature help support the leaf without the need for thick lateral veins. These features, however, also allow the petiole to reconfigure by twisting away from the wind, while the leaf can fold away. In addition, two sets of internal structures, longitudinal partitions and transverse stellate parenchyma plates, help prevent dorsoventral flattening, allowing the petiole to flex further away from the wind without buckling. These ideas were tested and verified by a range of mechanical tests. Simple four-point-bending and torsion tests showed that the petioles are indeed far more compliant in torsion than in bending. Axial bending tests and crushing tests showed that petioles could be flexed twice as far and were four times as resistant to dorsoventral flattening when intact than when the internal tissue is removed. The banana petiole, therefore, seems to be an excellent example of natural integrated mechanical design.
Assessment of the Phytotoxic Potential of m-Tyrosine in Laboratory Soil Bioassays
Venue: Journal of Chemical Ecology

The significance of soil-allelochemical interactions was addressed in this paper through studies conducted with m-tyrosine, an amino acid analogue and a potent plant growth inhibitor, in a series of laboratory assays performed in field soil or growth media. The studies were performed as a basis for further evaluation of m-tyrosine activity in field soils containing living plant roots. Here, we examined the role of common soil amendments, including ammonium nitrate fertilizer and activated carbon, in overcoming plant growth inhibition in soils in a laboratory setting by using lettuce as a sensitive indicator of plant toxicity. The phytotoxicity of m-tyrosine was not influenced significantly by soil N amendment; however, when significant amounts of activated carbon were added to the soil medium, growth inhibition in treated lettuce seedlings was strongly reduced. Soil texture did not influence the bioavailability or activity of m-tyrosine, as activity in high organic growth media was similar to that of sand and soil mixtures. Similar to other purported allelochemicals, soil persistence of m-tyrosine was limited, with a predicted half life of less than 1 day in soil in a controlled laboratory setting. Rapid degradation of this molecule likely was due to microbial activity but degradation did not appear to be influenced significantly by soil N amendment. Given the observed activity of m-tyrosine in soil and growth media on seedling growth, potential may exist for development of m-tyrosine as a soil applied herbicide if formulations can be stabilized under soil conditions.
Iron-Clad Fibers: A Metal-Based Biological Strategy for Hard Flexible Coatings
Venue: Science

Mussel Fibers While it is possible to make strong fibers or threads from organic materials, most suffer from high wear abrasion. Marine mussels attach themselves to rocky seashores using a series of byssal threads. Despite the constant rubbing caused by the motion of the tides, the threads show high wear resistance. Harrington et al. (p. 216, published online 4 March; see the Perspective by Messersmith) now find that the threads are protected by a proteinaceous outer cuticle that is rich in the amino acid 3,4-dihydroxyphenylalanine (dopa), which is known to be a strong adhesive. The cuticle is also rich in metal ions, primarily Fe3+. The dopa-metal crosslinks helped to form the tough outer coating. Marine mussel byssal threads have an outer coating in which proteins are linked to metal ions. The extensible byssal threads of marine mussels are shielded from abrasion in wave-swept habitats by an outer cuticle that is largely proteinaceous and approximately fivefold harder than the thread core. Threads from several species exhibit granular cuticles containing a protein that is rich in the catecholic amino acid 3,4-dihydroxyphenylalanine (dopa) as well as inorganic ions, notably Fe3+. Granular cuticles exhibit a remarkable combination of high hardness and high extensibility. We explored byssus cuticle chemistry by means of in situ resonance Raman spectroscopy and demonstrated that the cuticle is a polymeric scaffold stabilized by catecholato-iron chelate complexes having an unusual clustered distribution. Consistent with byssal cuticle chemistry and mechanics, we present a model in which dense cross-linking in the granules provides hardness, whereas the less cross-linked matrix provides extensibility.
The cellulose system in viscin from mistletoe berries
Venue: Cellulose

The cellulose system of the viscous fibrous cellulosic polysaccharide (viscan) in the viscin tissue of the European mistletoe, Viscum album L., was analyzed by chemical and physicochemical techniques including sugar analysis, optical and transmission electron microscopy, X-ray and electron diffraction together with solid state CP/MAS 13C-NMR spectroscopy. The results confirmed that in the elongated thin viscin cells, the cellulose microfibrils (having a diameter of around 3 nm) were tightly coiled with their axes perpendicular to the long axis of the cell. Upon stretching these cells became deformed by more than a hundred fold. In such a deformation, the cellulose microfibrils became unwound to be perfectly aligned along the stretching direction. Based on solid-state CP/MAS 13C-NMR spectroscopic analysis of the viscin tissue, it was found that its cellulose consisted of Iα and Iβ polymorphs in the ratio 1:1.
Comparison of IR thermography and thermocouple measurement of heat loss from rabbit pinna.
Venue: American Journal of Physiology-regulatory Integrative and Comparative Physiology

The temperature of the pinnae of male New Zealand White rabbits was measured by use of infrared thermography. At ambient temperatures of 15, 20, and 25 degrees C, the average pinna temperatures were 23.0, 28.7, and 36.2 degrees C, respectively. From these temperatures, average heat loss from the total pinna surface area was calculated to be 2.8, 3.3, and 4.4 W, respectively. Preoptic temperature changes also affect the vasomotor state of the rabbit. At an ambient temperature of 20 degrees C, cooling the preoptic area of the rabbit by approximately 1 degree C resulted in an average pinna temperature of 26.5 degrees C and a heat loss of 2.4 W. Heating the preoptic area by approximately 1 degree C resulted in an average pinna temperature of 33.5 degrees C and a heat loss of 5.4 W. Finally, pinna temperatures were measured by use of a thermocouple and infrared thermography simultaneously. When the pinnae were vasodilated, the thermocouple measurements were consistently higher than the pinna surface temperatures measured thermographically. When the pinnae were vasoconstricted, the thermocouple measurements were consistently lower than the pinna surface temperatures measured thermographically. The discrepancy between the two methods of measurement is discussed.
The salvinia paradox: superhydrophobic surfaces with hydrophilic pins for air retention under water.
Venue: Advanced Materials

[*] Prof. W. Barthlott, S. Wiersch, Dr. H. F. Bohn Nees-Institut für Biodiversität der Pflanzen Rheinische Friedrich-Wilhelms-Universität Meckenheimer Allee 170, 53115 Bonn (Germany) E-mail: barthlott@uni-bonn.de Prof. Th. Schimmel, Dr. M. Barczewski, Dr. S. Walheim, A. Weis, A. Kaltenmaier Institute of Applied Physics and Center for Functional Nanostructures (CFN) University of Karlsruhe Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe (Germany) Institute of Nanotechnology and Center for Functional Nanostructures (CFN) Forschungszentrum Karlsruhe Karlsruhe Institute of Technology (KIT) 76021 Karlsruhe (Germany) E-mail: thomas.schimmel@physik.uni-karlsruhe.de Prof. K. Koch Biologie und Nanobiotechnologie Hochschule Rhein-Waal Landwehr 4, 47533 Kleve (Germany)
Current issues in the evolutionary ecology of ant-plant symbioses.
Venue: New Phytologist

Ant-plant symbioses involve plants that provide hollow structures specialized for housing ants and often food to ants. In return, the inhabiting ants protect plants against herbivores and sometimes provide them with nutrients. Here, we review recent advances in ant-plant symbioses, focusing on three areas. First, the nutritional ecology of plant-ants, which is based not only on plant-derived food rewards, but also on inputs from other symbiotic partners, in particular fungi and possibly bacteria. Food and protection are the most important 'currencies' exchanged between partners and they drive the nature and evolution of the relationships. Secondly, studies of conflict and cooperation in ant-plant symbioses have contributed key insights into the evolution and maintenance of mutualism, particularly how partner-mediated feedbacks affect the specificity and stability of mutualisms. There is little evidence that mutualistic ants or plants are under selection to cheat, but the costs and benefits of ant-plant interactions do vary with environmental factors, making them vulnerable to natural or anthropogenic environmental change. Thus, thirdly, ant-plant symbioses should be considered good models for investigating the effects of global change on the outcome of mutualistic interactions.
Viscosin-like lipopeptides from frog skin bacteria inhibit Aspergillus fumigatus and Batrachochytrium dendrobatidis detected by imaging mass spectrometry and molecular networking
Venue: Scientific Reports

Amphibian populations worldwide have declined and in some cases become extinct due to chytridiomycosis, a pandemic disease caused by the fungus Batrachochytrium dendrobatidis; however, some species have survived these fungal epidemics. Previous studies have suggested that the resistance of these species is due to the presence of cutaneous bacteria producing antifungal metabolites. As our understanding of these metabolites is still limited, we assessed the potential of such compounds against human-relevant fungi such as Aspergillus. In this work we isolated 201 bacterial strains from fifteen samples belonging to seven frog species collected in the highlands of Panama and tested them against Aspergillus fumigatus. Among the 29 bacterial isolates that exhibited antifungal activity, Pseudomonas cichorii showed the greatest inhibition. To visualize the distribution of compounds and identify them in the inhibition zone produced by P. cichorii, we employed MALDI imaging mass spectrometry (MALDI IMS) and MS/MS molecular networking. We identified viscosin and massetolides A, F, G and H in the inhibition zone. Furthermore, viscosin was isolated and evaluated in vitro against A. fumigatus and B. dendrobatidis showing MIC values of 62.50 µg/mL and 31.25 µg/mL, respectively. This is the first report of cyclic depsipeptides with antifungal activity isolated from frog cutaneous bacteria.
Adaptive Advantages of Cooperative Courtship for Subordinate Male Lance‐Tailed Manakins
Venue: The American Naturalist

Male lance‐tailed manakins (Chiroxiphia lanceolata) cooperate in complex courtship displays, but the dominant (alpha) partner monopolizes mating opportunities. This raises the question of why subordinates (betas) cooperate. Three nonexclusive hypotheses explain the adaptive basis of helping behavior by subordinate males: cooperation may increase (1) subordinates’ immediate reproductive success, (2) the reproductive success of close relatives, or (3) subordinates’ chances of future reproduction. I demonstrated that beta males rarely sired chicks and were unrelated to their alpha partners but received delayed direct benefits from cooperation; betas had an increased probability of becoming an alpha when compared to males that had not been betas. To investigate the mechanism by which betas attain these adaptive benefits, I examined betas’ success in replacing their alpha partners both in natural turnover events and when alphas were experimentally removed. Beta males did not consistently inherit alpha roles in the same territories where they served their beta tenure, arguing that queuing for status does not fully explain the benefits of cooperation for betas. Instead, betas may be apprenticing to develop effective and appropriate displays that enhance their subsequent success as alphas. Complex social affiliations appear to mediate selective pressure for cooperation in this species.
The use of waggle dance information by honey bees throughout their foraging careers
Venue: Behavioral Ecology and Sociobiology

We studied the extent to which worker honey bees acquire information from waggle dances throughout their careers as foragers. Small groups of foragers were monitored from time of orientation flights to time of death and all in-hive behaviors relating to foraging were recorded. In the context of a novice forager finding her first food source, 60% of the bees relied, at least in part, on acquiring information from waggle dances (being recruited) rather than searching independently (scouting). In the context of an experienced forager whose foraging has been interrupted, 37% of the time the bees resumed foraging by following waggle dances (being reactivated) rather than examining the food source on their own (inspecting). And in the context of an experienced forager engaged in foraging, 17% of the time the bees initiated a foraging trip by following a waggle dance. Such dance following was observed much more often after an unsuccessful than after a successful foraging trip. Successful foragers often followed dances just briefly, perhaps to confirm that the kind of flowers they had been visiting were still yielding forage. Overall, waggle dance following for food discovery accounted for 12–25% of all interactions with dancers (9% by novice foragers and 3–16% by experienced foragers) whereas dance following for reactivation and confirmation accounted for the other 75–88% (26% for reactivation and 49–62% for confirmation). We conclude that foragers make extensive use of the waggle dance not only to start work at new, unfamiliar food sources but also to resume work at old, familiar food sources.
Sensitivity to dimethyl sulphide suggests a mechanism for olfactory navigation by seabirds
Venue: Biology Letters

Petrels, albatrosses and other procellariiform seabirds have an excellent sense of smell, and routinely navigate over the world's oceans by mechanisms that are not well understood. These birds travel thousands of kilometres to forage on ephemeral prey patches at variable locations, yet they can quickly and efficiently find their way back to their nests on remote islands to provision chicks, even with magnetic senses experimentally disrupted. Over the seemingly featureless ocean environment, local emissions of scents released by phytoplankton reflect bathymetric features such as shelf breaks and seamounts. These features suggest an odour landscape that may provide birds with orientation cues. We have previously shown that concentrated experimental deployments of one such compound, dimethyl sulphide (DMS), attracts procellariiforms at sea, suggesting that some species can use it as a foraging cue. Here we present the first physiological demonstration that an Antarctic seabird can detect DMS at biogenic levels. We further show that birds can use DMS as an orientation cue in a non-foraging context within a concentration range that they might naturally encounter over the ocean.
Cell-cell communication in Gram-negative bacteria.
Venue: Molecular BioSystems

Over the last decade or so, a wealth of research has established that bacteria communicate with one another using small molecules. These signals enable the individuals in a population to coordinate their behaviour. In the case of pathogens, this behaviour may include decisions such as when to attack a host organism or form a biofilm. Consequently, such signalling systems are excellent targets for the development of new antibacterial therapies. In this review, we assess how Gram-negative bacteria use small molecules for cell-cell communication, and discuss the main approaches that have been developed to interfere with it.