nils-herrmann/clean_scirepeval huggingface dataset:
Optimal design of microfluidic networks using biologically inspired principles
Venue: Microfluidics and Nanofluidics

From the earliest of times, Man has sought to replicate ideas that have evolved naturally in plants and animals. Understanding and extracting these “natural” design strategies has opened up a whole new field of research known as biomimetics. Designs formulated using biologically inspired principles range from novel surface treatments that mimic physiological processes to geometrical optimization for improving the performance of a system. In this paper, we will show how biomimetic principles based on the laws that govern biological vascular trees can be used to design artificial microfluidic distribution systems. The study focuses specifically on microfluidic manifolds composed of constant-depth rectangular- or trapezoidal-sectioned channels, as these geometries can readily be fabricated using standard micro-fabrication techniques. We will show that it is possible to introduce a prescribed element of flow control into the system by carefully selecting the branching parameter that governs the change in channel dimension at each bifurcation.
An Acidic Matrix Protein, Pif, Is a Key Macromolecule for Nacre Formation
Venue: Science

Making Mother of Pearl Nacre is an iridescent layer of calcium carbonate lining the inside of shells of marine mollusks and is commonly known as “mother of pearl.” It is composed of layers of uniformly oriented crystals of aragonite (a metastable form of calcium carbonate) separated by layers of organic matrix. How the ordered structure of aragonite layers is achieved has been unclear. Suzuki et al. (p. 1388, published online 13 August 2009; see the Perspective by Kröger) identified two acidic matrix proteins (Pif 97 and Pif 80) that regulate nacre formation in the Japanese pearl oyster. The proteins appear to form a complex in which Pif 80 binds to aragonite and Pif 97 binds to other macromolecules in the organic matrix. A matrix protein is identified that regulates nacre formation in the Japanese pearl oyster. The mollusk shell is a hard tissue consisting of calcium carbonate crystals and an organic matrix. The nacre of the shell is characterized by a stacked compartment structure with a uniformly oriented c axis of aragonite crystals in each compartment. Using a calcium carbonate–binding assay, we identified an acidic matrix protein, Pif, in the pearl oyster Pinctada fucata that specifically binds to aragonite crystals. The Pif complementary DNA (cDNA) encoded a precursor protein, which was posttranslationally cleaved to produce Pif 97 and Pif 80. The results from immunolocalization, a knockdown experiment that used RNA interference, and in vitro calcium carbonate crystallization studies strongly indicate that Pif regulates nacre formation.
The weak interfaces within tough natural composites: experiments on three types of nacre.
Venue: Journal of The Mechanical Behavior of Biomedical Materials

Mineralization is a typical strategy used in natural materials to achieve high stiffness and hardness for structural functions such as skeletal support, protection or predation. High mineral content generally leads to brittleness, yet natural materials such as bone, mollusk shells or glass sponge achieve relatively high toughness considering the weakness of their constituents through intricate microstructures. In particular, nanometers thick organic interfaces organized in micro-architectures play a key role in providing toughness by various processes including crack deflection, crack bridging or energy dissipation. While these interfaces are critical in these materials, their composition, structure and mechanics is often poorly understood. In this work we focus on nacre, one of the most impressive hard biological materials in terms of toughness. We performed interfacial fracture tests on chevron notched nacre samples from three different species: red abalone, top shell and pearl oyster. We found that the intrinsic toughness of the interfaces is indeed found to be extremely low, in the order of the toughness of the mineral inclusions themselves. Such low toughness is required for the cracks to follow the interfaces, and to deflect and circumvent the mineral tablets. This result highlights the efficacy of toughening mechanisms in natural materials, turning low-toughness inclusions and interfaces into high-performance composites. We found that top shell nacre displayed the highest interfacial toughness, because of higher surface roughness and a more resilient organic material, and also through extrinsic toughening mechanisms including crack deflection, crack bridging and process zone. In the context of biomimetics, the main implication of this finding is that the interface in nacre-like composite does not need to be tough; the extensibility or ductility of the interfaces may be more important than their strength and toughness to produce toughness at the macroscale.
Keeping cool: Enhanced optical reflection and radiative heat dissipation in Saharan silver ants
Venue: Science

Keeping cool Silver ants inhabit one of the hottest and driest environments on Earth, the Saharan sands, where most insects shrivel and die moments after contact. Shi et al. show that the triangular shape of the silver hairs that cover their bodies enables this existence. The hairs both increase the reflection of near-infrared rays and dissipate heat from the ants' bodies, even under full sun conditions. Evolution's simple solution to intense heat management in this species could lead to better designs for passive cooling of human-produced objects. Science, this issue p. 298 Silver hairs on Saharan ants facilitate both reflection and dissipation of intense heat. Saharan silver ants, Cataglyphis bombycina, forage under extreme temperature conditions in the African desert. We show that the ants’ conspicuous silvery appearance is created by a dense array of triangular hairs with two thermoregulatory effects. They enhance not only the reflectivity of the ant’s body surface in the visible and near-infrared range of the spectrum, where solar radiation culminates, but also the emissivity of the ant in the mid-infrared. The latter effect enables the animals to efficiently dissipate heat back to the surroundings via blackbody radiation under full daylight conditions. This biological solution for a thermoregulatory problem may lead to the development of biomimetic coatings for passive radiative cooling of objects.
Flight of a samara, Alsomitra macrocarpa
Venue: Journal of Theoretical Biology

The steady gliding flight of samples of Alsomitra macrocarpa samara was filmed and analysed. By using the observed data, the flight performance of the samara was made clear. The lift-to-drag ratio or the gliding ratio was about 3 ∼ 4 and the rate of descent was 0·3 ∼ 0·7 m/sec, which was smaller than those of other rotary seeds. The flight was so stable that samples were seen to take their optimal trimmed angle of attack with a value between the maximum gliding ratio and the minimum rate of descent. The aerodynamic function of the husk for the distribution of the seeds was also revealed by making wind tunnel tests of the husk.
Plant and lichen colonization in an asbestos mine: Spontaneous bioattenuation limits air dispersion of fibres
Venue: Plant Biosystems

Plant and lichen phytosociological studies describe the different dynamic stages of colonization. This approach has been applied to the Balangero asbestos mine, the most important of Western Europe up to 1990, which is a potential source for the air-dispersion of carcinogenic fibres. Vegetation relevés and maps have shown that plants and lichens develop spontaneously on the asbestos-rich substrates. Early colonization stages with low-covering hyperaccumulators, such as Thlaspi sylvium and Minuartia laricifolia, and with Thymus alpestris and T. cfr. humifusus, are followed, some decades later, by mature plant communities, which completely cover the asbestos-rich debris, thereby limiting the dispersion of fibres. Lichen colonization, even when limited to low covering early stages with pioneer crustose species, such as Scoliciosporum umbrinum and Candelariella vitellina, and young foliose thalli of Xanthoparmelia tinctina, is important whenever asbestos veins are exposed on serpentinite blocks and walls. Plants and lichens can be considered as bioattenuation (spontaneous bioremediation) agents in ecological recovery.
The characterization, replication and testing of dermal denticles of Scyliorhinus canicula for physical mechanisms of biofouling prevention.
Venue: Bioinspiration & Biomimetics

There is a current need to develop novel non-toxic antifouling materials. The mechanisms utilized by marine organisms to prevent fouling of external surfaces are of interest in this regard. Biomimicry of these mechanisms and the ability to transfer the antifouling characteristics of these surfaces to artificial surfaces are a highly attractive prospect to those developing antifouling technologies. In order to achieve this, the mechanisms responsible for any antifouling ability must be elucidated from the study of the natural organism and the critical surface parameters responsible for fouling reduction. Dermal denticles of members of the shark family have been speculated to possess some natural, as yet unidentified antifouling mechanism related to the physical presence of denticles. In this study, the dermal denticles of one particular member of the slow-swimming sharks, Scyliorhinus canicula were characterized and it was found that a significant natural variation in denticle dimensions exists in this species. The degree of denticle surface contamination was quantified on denticles at various locations and it was determined that the degree of contamination of the dorsal surface of denticles varies with the position on the shark body. In addition, we successfully produced synthetic sharkskin samples using the real skin as a template. Testing of the produced synthetic skin in field conditions resulted in significant differences in material attachment on surfaces exhibiting denticles of different dimensions.
Responses of single neurons in the olfactory bulbs of rabbits, dogs, and cats to X-rays
Venue: Cellular and Molecular Life Sciences

Die durch Röntgenstrahlen (1 R/sec) erzeugten elektrischen Impulse einzelner Nervenzellen der Geruchszwiebel wurden in narkotisierten Katzen, Kaninchen und Hunden gemessen. Als typische Reaktion wurde eine kurzfristige Erhöhung der elektrischen Impulse gefunden. Somit sind die von Röntgenstrahlen ausgelösten elektrischen Impulse des Geruchsystems kein artspezifisches, sondern vielmehr ein allgemeines Phänomen.
Fuel-Powered Artificial Muscles
Venue: Science

Artificial muscles and electric motors found in autonomous robots and prosthetic limbs are typically battery-powered, which severely restricts the duration of their performance and can necessitate long inactivity during battery recharge. To help solve these problems, we demonstrated two types of artificial muscles that convert the chemical energy of high–energy-density fuels to mechanical energy. The first type stores electrical charge and uses changes in stored charge for mechanical actuation. In contrast with electrically powered electrochemical muscles, only half of the actuator cycle is electrochemical. The second type of fuel-powered muscle provides a demonstrated actuator stroke and power density comparable to those of natural skeletal muscle and generated stresses that are over a hundred times higher.
Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation.
Venue: Molecular Cell

Tardigrades are microscopic animals that survive a remarkable array of stresses, including desiccation. How tardigrades survive desiccation has remained a mystery for more than 250 years. Trehalose, a disaccharide essential for several organisms to survive drying, is detected at low levels or not at all in some tardigrade species, indicating that tardigrades possess potentially novel mechanisms for surviving desiccation. Here we show that tardigrade-specific intrinsically disordered proteins (TDPs) are essential for desiccation tolerance. TDP genes are constitutively expressed at high levels or induced during desiccation in multiple tardigrade species. TDPs are required for tardigrade desiccation tolerance, and these genes are sufficient to increase desiccation tolerance when expressed in heterologous systems. TDPs form non-crystalline amorphous solids (vitrify) upon desiccation, and this vitrified state mirrors their protective capabilities. Our study identifies TDPs as functional mediators of tardigrade desiccation tolerance, expanding our knowledge of the roles and diversity of disordered proteins involved in stress tolerance.
BIRD ACTIVITY AND SEED DISPERSAL OF A TROPICAL WET FOREST TREE
Venue: Ecology

Feeding assemblages of birds were observed throughout a fruiting season at a Costa Rican population of the rain forest tree Casearia corymbosa in order to distinguish effective dispersal agents from visitors which used arils for food without dispersing seeds. This system is of special interest because the tree fruits during an annual period of fruit scarcity in a forest characterized by high proportions of animal-dispersed plants and obligate frugivores. Results show that the Masked Tityra (Tityra semifasciata) is an effective dispersal agent of seeds of this tree because it: (1) regurgitates viable seeds, (2) is a common and regular visitor throughout the season, (3) has high feeding rates, (4) removes seeds from the vicinity of the parent tree before processing them, and (5) depends on this rather than other plants fruiting at the same time. Twenty-one other visitors were deficient dispersers, although some depended heavily on fruit of this tree for food. Two parrots (Amazona autumnalis and Amazona farinosa) preclude dispersal by strip- ping arils with their bills and dropping all seeds in situ. Fourteen species are occasional visitors. Five visitors (Ramphastos sulfuratus, Ramphastos swainsonii, Pteroglossus torquatus, Myiozetetes similis, and Myiozetetes granadensis) process seeds undamaged and are sometimes numerically abun- dant, but are absent part of the season and tend to regurgitate seeds in situ. Because fruiting activity of this tree occurs during annual scarcity, it represents a pivotal species in the community. Three obligate frugivores, including one effective disperser and two fruit thieves, depend almost entirely on it for food for periods of 2-6 wk. I hypothesize that extinction of this plant at this site would lead to disappearance of these birds, and would almost certainly depress recruitment of other species of trees for which they serve as dispersal agents at other times of the year.
Inferring the rules of interaction of shoaling fish
Venue: Proceedings of the National Academy of Sciences of the United States of America

Collective motion, where large numbers of individuals move synchronously together, is achieved when individuals adopt interaction rules that determine how they respond to their neighbors’ movements and positions. These rules determine how group-living animals move, make decisions, and transmit information between individuals. Nonetheless, few studies have explicitly determined these interaction rules in moving groups, and very little is known about the interaction rules of fish. Here, we identify three key rules for the social interactions of mosquitofish (Gambusia holbrooki): (i) Attraction forces are important in maintaining group cohesion, while we find only weak evidence that fish align with their neighbor’s orientation; (ii) repulsion is mediated principally by changes in speed; (iii) although the positions and directions of all shoal members are highly correlated, individuals only respond to their single nearest neighbor. The last two of these rules are different from the classical models of collective animal motion, raising new questions about how fish and other animals self-organize on the move.
A new pollination system: dung-beetle pollination discovered in Orchidantha inouei (Lowiaceae, Zingiberales) in Sarawak, Malaysia.
Venue: American Journal of Botany

Lowiaceae, a family of the Zingiberales, comprise 11 species in the single genus Orchidantha. Here we present the first report on the pollination of Lowiaceae and describe a new system of dung-beetle pollination from Sarawak, Borneo. Orchidantha inouei has a zygomorphic flower located just above the ground. Observations revealed that the plant is visited frequently and is pollinated by scarabaeid dung beetles, mainly members of the genus Onthophagus. All four species of Onthophagus collected on O. inouei have also been caught using traps baited with dung or carrion in Borneo. Onthophagus was presumably attracted to the dung-like odor of the flower. Pollination of O. inouei is different from other examples of beetle pollination in that its flower provides neither reward nor protected space. Dung beetles are excellent at following a particular dung scent. Orchidantha is the only genus that includes species lacking floral nectar. It is interesting that this deception pollination using dung beetles was found in Zingiberales, in which all known species have mutual and specialized relationships with their long-distance, but costly, pollinators-bees, birds, and bats.
Expanding dialogues: from natural autoinducers to non-natural analogues that modulate quorum sensing in Gram-negative bacteria.
Venue: Chemical Society Reviews

Bacteria are capable of "communicating" their local population densities via a process termed quorum sensing (QS). Gram-negative bacteria use N-acylated l-homoserine lactones (AHLs), in conjunction with their cognate LuxR-type receptors, as their primary signalling circuit for QS. In this critical review, we examine AHL signalling in Gram-negative bacteria with a primary focus on the design of non-natural AHLs, their structure-activity relationships, and their application in chemical biological approaches to study QS (72 references).
Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors
Venue: Nature

One of the central aims of ecology is to identify mechanisms that maintain biodiversity. Numerous theoretical models have shown that competing species can coexist if ecological processes such as dispersal, movement, and interaction occur over small spatial scales. In particular, this may be the case for non-transitive communities, that is, those without strict competitive hierarchies. The classic non-transitive system involves a community of three competing species satisfying a relationship similar to the children's game rock–paper–scissors, where rock crushes scissors, scissors cuts paper, and paper covers rock. Such relationships have been demonstrated in several natural systems. Some models predict that local interaction and dispersal are sufficient to ensure coexistence of all three species in such a community, whereas diversity is lost when ecological processes occur over larger scales. Here, we test these predictions empirically using a non-transitive model community containing three populations of Escherichia coli. We find that diversity is rapidly lost in our experimental community when dispersal and interaction occur over relatively large spatial scales, whereas all populations coexist when ecological processes are localized.
Floral volatiles controlling ant behaviour
Venue: Functional Ecology

Ants show complex interactions with plants, both facultative and mutualistic, ranging from grazers through seed predators and dispersers to herders of some herbivores and guards against others. But ants are rarely pollinators, and their visits to flowers may be detrimental to plant fitness. 2. Plants therefore have various strategies to control ant distributions, and restrict them to foliage rather than flowers. These 'filters' may involve physical barriers on or around flowers, or 'decoys and bribes' sited on the foliage (usually extrafloral nectaries - EFNs). Alternatively, volatile organic compounds (VOCs) are used as signals to control ant behaviour, attracting ants to leaves and/or deterring them from functional flowers. Some of the past evidence that flowers repel ants by VOCs has been equivocal and we describe the shortcomings of some experimental approaches, which involve behavioural tests in artificial conditions. 3. We review our previous study of myrmecophytic acacias, which used in situ experiments to show that volatiles derived from pollen can specifically and transiently deter ants during dehiscence, the effects being stronger in ant-guarded species and more effective on resident ants, both in African and Neotropical species. In these plants, repellence involves at least some volatiles that are known components of ant alarm pheromones, but are not repellent to beneficial bee visitors. 4. We also present new evidence of ant repellence by VOCs in temperate flowers, which is usually pollen-based and active on common European ants. We use these data to indicate that across a wide range of plants there is an apparent trade-off in ant-controlling filter strategies between the use of defensive floral volatiles and the alternatives of decoying EFNs or physical barriers.
Scaling and mechanics of carnivoran footpads reveal the principles of footpad design
Venue: Journal of the Royal Society Interface

In most mammals, footpads are what first strike ground with each stride. Their mechanical properties therefore inevitably affect functioning of the legs; yet interspecific studies of the scaling of locomotor mechanics have all but neglected the feet and their soft tissues. Here we determine how contact area and stiffness of footpads in digitigrade carnivorans scale with body mass in order to show how footpads’ mechanical properties and size covary to maintain their functional integrity. As body mass increases across several orders of magnitude, we find the following: (i) foot contact area does not keep pace with increasing body mass; therefore pressure increases, placing footpad tissue of larger animals potentially at greater risk of damage; (ii) but stiffness of the pads also increases, so the tissues of larger animals must experience less strain; and (iii) total energy stored in hindpads increases slightly more than that in the forepads, allowing additional elastic energy to be returned for greater propulsive efficiency. Moreover, pad stiffness appears to be tuned across the size range to maintain loading regimes in the limbs that are favourable for long-bone remodelling. Thus, the structural properties of footpads, unlike other biological support-structures, scale interspecifically through changes in both geometry and material properties, rather than geometric proportions alone, and do so with consequences for both maintenance and operation of other components of the locomotor system.
Scale morphology and flexibility in the shortfin mako Isurus oxyrinchus and the blacktip shark Carcharhinus limbatus
Venue: Physics of Fluids; Philosophical Transactions of the Royal Society A; Bioinspiration & Biomimetics; Journal of Morphology; The Journal of Experimental Biology; Journal of Fish Biology

Cover illustration. The shortfin mako Isurus oxyrinchus is perhaps the fastest swimming shark. The modified scales on the lateral flank of the shark are highly flexible and are believed to erect during rapid swimming. Erection of the flank scales and resulting drag reduction is hypothesized to be passively driven by localized flow patterns over the skin. The cover image, “Mako Moon”, is courtesy of Don Ray of donrayart.com. See Motta et al.,  in this issue of the Journal of Morphology.