nils-herrmann/clean_scirepeval huggingface dataset:
The hydrodynamic function of shark skin and two biomimetic applications
Venue: The Journal of Experimental Biology

It has long been suspected that the denticles on shark skin reduce hydrodynamic drag during locomotion, and a number of man-made materials have been produced that purport to use shark-skin-like surface roughness to reduce drag during swimming. But no studies to date have tested these claims of drag reduction under dynamic and controlled conditions in which the swimming speed and hydrodynamics of shark skin and skin-like materials can be quantitatively compared with those of controls lacking surface ornamentation or with surfaces in different orientations. We use a flapping foil robotic device that allows accurate determination of the self-propelled swimming (SPS) speed of both rigid and flexible membrane-like foils made of shark skin and two biomimetic models of shark skin to measure locomotor performance. We studied the SPS speed of real shark skin, a silicone riblet material with evenly spaced ridges and a Speedo® ‘shark skin-like’ swimsuit fabric attached to rigid flat-plate foils and when made into flexible membrane-like foils. We found no consistent increase in swimming speed with Speedo® fabric, a 7.2% increase with riblet material, whereas shark skin membranes (but not rigid shark skin plates) showed a mean 12.3% increase in swimming speed compared with the same skin foils after removing the denticles. Deformation of the shark skin membrane is thus crucial to the drag-reducing effect of surface denticles. Digital particle image velocimetry (DPIV) of the flow field surrounding moving shark skin foils shows that skin denticles promote enhanced leading-edge suction, which might have contributed to the observed increase in swimming speed. Shark skin denticles might thus enhance thrust, as well as reduce drag.
Microbial degradation of petroleum hydrocarbons in a polluted tropical stream
Venue: World Journal of Microbiology & Biotechnology

SummaryCrude oil degradation was observed in water samples from three sites along the course of a polluted stream in Lagos, Nigeria. Consistent increase and decrease in the total viable counts (TVCs) of indigenous organisms occurred in the test and control experiments, respectively. Enrichments of the water samples with crude oil resulted in the isolation of nine bacteria belonging to seven genera. A mixed culture was developed from the assemblage of the nine species. The defined microbial consortium utilized a wide range of pure HCs including cycloalkane and aromatic HCs. Utilization of crude oil and petroleum cuts, i.e., kerosene and diesel resulted in an increase in TVC (till day 10) concomitant with decreases in pH and residual oil concentration. Crude oil, diesel and kerosene were degraded by 88, 85 and 78%, respectively, in 14 days. Substrate uptake studies with axenic cultures showed that growth was not sustainable on either cyclohexane or aromatics while degradation of the petroleum fractions fell below 67% in spite of extended incubation period (20 day). From the GC analysis of recovered oil, while reductions in peaks of n-alkane fractions and in biomarkers namely n-C17/pristane and n-C18/phytane ratios were observed in culture fluids of pure strains, complete removal of all the HC components of kerosene, diesel and crude oil including the isoprenoids was obtained with the consortium within 14 days.
Hygromorphs: from pine cones to biomimetic bilayers
Venue: Journal of the Royal Society Interface

We consider natural and artificial hygromorphs, objects that respond to environmental humidity by changing their shape. Using the pine cone as an example that opens when dried and closes when wet, we quantify the geometry, mechanics and dynamics of closure and opening at the cell, tissue and organ levels, building on our prior structural knowledge. A simple scaling theory allows us to quantify the hysteretic dynamics of opening and closing. We also show how simple bilayer hygromorphs of paper and polymer show similar behaviour that can be quantified via a theory which couples fluid transport in a porous medium and evaporative flux to mechanics and geometry. Our work unifies varied observations of natural hygromorphs and suggests interesting biomimetic analogues, which we illustrate using an artificial flower with a controllable blooming and closing response.
Revisiting the organohalogens associated with 1979-samples of Brazilian bees (Eufriesea purpurata).
Venue: Science of The Total Environment

Brazilian bees of the species Eufriesea purpurata are known to tolerate very high concentrations of DDT. As reported in the literature, these bees have suffered no harm from as much as 2 mg/bee, which is in the per-cent range of the body weight. In 1979, individuals of E. purpurata were captured as they collected DDT from walls of remote, rural houses in Brazil. Reported herein are quantities and identities of DDT, DDT metabolites, and other organohalogen compounds in four samples of bees stored since 1979. The concentrations of DDT (sum of p,p'-DDT, -DDE, and -DDD) ranged from 23 to 314 microg/bee which is up to twelve fold higher than the LD(50) value of DDT in the honey bee (Apis mellifera) but significantly lower than the no-effect concentration in E. purpurata. Enantioselective determination confirmed the presence of racemic o,p'-DDT in the four individual samples. GC/ECNI-MS investigation resulted in the detection of low amounts (<1 microg/bee) of PCA, lindane, and chlordane. At higher retention times four unknown compounds were detected with a proposed molecular ion at m/z 498, a non-aromatic hydrocarbon backbone along with the presence of eight chlorine substituents. Neither the structure nor the origin of these compounds could be determined. Considering where and when the bees were collected and considering the biology and ecology of the euglossine bees themselves, we propose that the four unknowns are natural products and, as such, are the most highly chlorinated natural compounds yet discovered.
Teaching in tandem-running ants
Venue: Nature

The ant Temnothorax albipennis uses a technique known as tandem running to lead another ant from the nest to food —with signals between the two ants controlling both the speed and course of the run. Here we analyse the results of this communication and show that tandem running is an example of teaching, to our knowledge the first in a non-human animal, that involves bidirectional feedback between teacher and pupil. This behaviour indicates that it could be the value of information, rather than the constraint of brain size, that has influenced the evolution of teaching.
How tussocks structure sedge meadow vegetation
Venue: Wetlands

Carex stricta dominates sedge meadows in southern Wisconsin, USA. In contrast with invasive species that dominate as monotypes, C. stricta supports a diversity of co-occurring species by forming tussocks. Concerns about diversity loss and the potential to restore species-rich tussocks led us to ask how tussocks foster high species richness and affect composition. Our study of 181 tussocks at three sites showed that tussocks structure sedge meadow vegetation by adding both surface area and micro-habitats. Tussocks, which average 15–25 cm tall, increase surface area of an otherwise flat plot by 40%. Species richness was positively correlated with tussock size, but the patterns differed among sites. At a site where water was deep, tussock height was the best predictor of richness; at two other sites, surface area and circumference were the best predictors. Micro-habitats differed in conditions and species composition: tussock tops were high in light, variable in temperature, and high in litter cover. Tussock sides had less litter but more moss; off-tussock areas tended to be aquatic. Of the 56 taxa found, 34 showed significant affinities for one or more micro-habitats. Of these, four species occurred primarily on tops, several extended from tops to lower levels, seven aquatic taxa preferred areas off-tussocks, and one species specialized in tussock sides. Over the 2004 growing season, species richness increased in an additive process, from 35 species in May to 56 in September 2004. Cover of litter and moss increased and bare surface decreased with season, but only seven of the 34 taxa with micro-site preferences expanded their distributions as the September drawdown exposed the off-tussock micro-habitat. We conclude that tussocks enhance species richness in three ways, by increasing surface area, by providing multiple micro-habitats, and by undergoing seasonal changes in composition. Our detailed data on plant-diversity support by large tussocks form a benchmark for tussock meadow conservation, as well as a target for restoration of degraded meadows.
Xyloglucan endo-transglycosylase (XET) functions in gelatinous layers of tension wood fibers in poplar--a glimpse into the mechanism of the balancing act of trees.
Venue: Plant and Cell Physiology

Tension wood is a specialized tissue of deciduous trees that functions in bending woody stems to optimize their position in space. Tension wood fibers that develop on one side of the stem have an increased potency to shrink compared with fibers on the opposite side, thus creating a bending moment. It is believed that the gelatinous (G) cell wall layer containing almost pure cellulose of tension wood fibers is pivotal to their shrinking. By analyzing saccharide composition and linkage in isolated G-layers of poplar, we found that they contain some matrix components in addition to cellulose, of which xyloglucan is the most abundant. Xyloglucan, xyloglucan endo-transglycosylase (XET) activity and xyloglucan endo-transglycosylase/hydrolase (XTH) gene products were detected in developing G-layers by labeling using CCRC-M1 monoclonal antibody, in situ incorporation of XXXG-SR and the polyclonal antibody to poplar PttXET16-34, respectively, indicating that xyloglucan is incorporated into the G-layer during its development. Moreover, several XTH transcripts were altered and were generally up-regulated in developing tension wood compared with normal wood. In mature G-fibers, XTH gene products were detected in the G-layers while the XET activity was evident in the adjacent S(2) wall layer. We propose that XET activity is essential for G-fiber shrinking by repairing xyloglucan cross-links between G- and S(2)-layers and thus maintaining their contact. Surprisingly, XTH gene products and XET activity persisted in mature G-fibers for several years, suggesting that the enzyme functions after cell death repairing the cross-links as they are being broken during the shrinking process.
Pigment chemistry: The red sweat of the hippopotamus
Venue: Nature

Within a few minutes of perspiration, the colourless, viscous sweat of the hippopotamus gradually turns red, and then brown as the pigment polymerizes. Here we isolate and characterize the pigments responsible for this colour reaction. The unstable red and orange pigments turn out to be non-benzenoid aromatic compounds that are unexpectedly acidic and have antibiotic as well as sunscreen activity.
The Kármán gait: novel body kinematics of rainbow trout swimming in a vortex street
Venue: The Journal of Experimental Biology

Most fishes commonly experience unsteady flows and hydrodynamic perturbations during their lifetime. In this study, we provide evidence that rainbow trout Oncorhynchus mykiss voluntarily alter their body kinematics when interacting with vortices present in the environment that are not self-generated. To demonstrate this, we measured axial swimming kinematics in response to changes in known hydrodynamic wake characteristics. We compared trout swimming in the Kármán street behind different diameter cylinders (2.5 and 5 cm) at two flow speeds (2.5 and 4.5 L s-1, where L is total body length) to trout swimming in the free stream and in the cylinder bow wake. Trout swimming behind cylinders adopt a distinctive, previously undescribed pattern of movement in order to hold station, which we term the Kármán gait. During this gait, body amplitudes and curvatures are much larger than those of trout swimming at an equivalent flow velocity in the absence of a cylinder. Tail-beat frequency is not only lower than might be expected for a trout swimming in the reduced flow behind a cylinder, but also matches the vortex shedding frequency of the cylinder. Therefore, in addition to choosing to be in the slower flow velocity offered behind a cylinder (drafting), trout are also altering their body kinematics to synchronize with the shed vortices (tuning), using a mechanism that may not involve propulsive locomotion. This behavior is most distinctive when cylinder diameter is large relative to fish length. While tuning, trout have a longer body wavelength than the prescribed wake wavelength, indicating that only certain regions of the body may need to be oriented in a consistent manner to the oncoming vortices. Our results suggest that fish can capture energy from vortices generated by the environment to maintain station in downstream flow. Interestingly, trout swimming in front of a cylinder display lower tail-beat amplitudes and body wave speeds than trout subjected to any of the other treatments, implying that the bow wake may be the most energetically favorable region for a fish to hold station near a cylinder.
The captured launch of a ballistospore.
Venue: Mycologia

Ballistospore discharge is a feature of 30000 species of mushrooms, basidiomycete yeasts and pathogenic rusts and smuts. The biomechanics of discharge may involve an abrupt change in the center of mass associated with the coalescence of Buller's drop and the spore. However this process occurs so rapidly that the launch of the ballistospore has never been visualized. Here we report ultra high-speed video recordings of the earliest events of spore dispersal using the yeast Itersonilia perplexans and the distantly related jelly fungus Auricularia auricula. Images taken at camera speeds of up to 100,000 frames/ s demonstrate that ballistospore discharge does involve the coalescence of Buller's drop and the spore. Recordings of I. perplexans demonstrate that although coalescence may result from the directed collapse of Buller's drop onto the spore, it also may involve the movement of the spore toward the drop. The release of surface tension at coalescence provides the energy and directional momentum to propel the drop and spore away from the fungus. Analyses show that ballistospores launch into the air at initial accelerations in excess of 10,000 g. There is no known analog of this micromechanical process in animals, plants or bacteria, but the recent development of a surface tension motor may mimic the fungal biology described here.
Dynamic mechanical properties of the tissue-engineered matrix associated with individual chondrocytes.
Venue: Journal of Biomechanics

The success of cell-based tissue engineering approaches in restoring biological function will be facilitated by a comprehensive fundamental knowledge of the temporal evolution of the structure and properties of the newly synthesized matrix. Here, we quantify the dynamic oscillatory mechanical behavior of the engineered matrix associated with individual chondrocytes cultured in vitro for up to 28 days in alginate scaffolds. The magnitude of the complex modulus (|E*|) and phase shift (delta) were measured in culture medium using Atomic Force Microscopy (AFM)-based nanoindentation in response to an imposed oscillatory deformation (amplitude approximately 5nm) as a function of frequency (f=1-316Hz), probe tip geometry (2.5microm radius sphere and 50nm radius square pyramid), and in the absence and presence of growth factors (GF, insulin growth factor-1, IGF-1, and osteogenic protein-1, OP-1). |E*| for all conditions increased nonlinearly with frequency dependence approximately f(1/2) and ranged between approximately 1 and 25kPa. This result, along with theoretical calculations of the characteristic poroelastic relaxation frequency, f(p), (approximately 50-90Hz) suggested that this time-dependent behavior was governed primarily by fluid flow-dependent poroelasticity, rather than flow-independent viscoelastic processes associated with the solid matrix. |E*(f)| increased, (f) decreased, and the hydraulic permeability, k, decreased with time in culture and with growth factor treatment. This trend of a more elastic-like response was thought to be associated with increased macromolecular biosynthesis, density, and a more mature matrix structure/organization.
Hydromechanics and biology
Venue: Biophysics of Structure and Mechanism

SummaryTo exemplify relations between biology and hydrodynamics the Reynolds number range and the effects of viscosity and inertia in swimming and flying organisms is discussed. Comparing water beetles and penguins it is shown, that the technical drag coefficient is an adequate means to describe flow adaptation in animals. Compared to technical systems, especially the penguins' drag coefficient is astonishingly low. Furthermore, the question, why comparatively thick bodies in penguins and dolphins show rather low drag is discussed. Distributed boundary layer damping in dolphins and secretion of special high molecular slimes in fishes help to keep flow characteristics laminar. As an example of one easily understood thrust mechanism, the drag inducing pair of rowing legs in water beetles is morphologically and hydrodynamically analysed. Fish swimming is discussed as a locomotion principle using lift components. Thrust generation by the moving tail fin of a fish is analysed in detail. Coming back to the influence if Reynolds number, it is finally shown, how very small, bristle bearing swimming legs and wings of insects make use of viscosity effects for locomotion.
Biomimicking of animal quills and plant stems: natural cylindrical shells with foam cores
Venue: Materials Science and Engineering: C

Thin walled cylindrical shell structures are widespread in nature: examples include porcupine quills, hedgehog spines and plant stems. All have an outer shell of almost fully dense material supported by a low density, cellular core. In nature, all are loaded in some combination of axial compression and bending: failure is typically by buckling. Natural structures are often optimized. Here we have investigated and characterized the morphology of several natural tubular structures. Mechanical models recently developed to analyze the elastic buckling of a thin cylindrical shell supported by a soft elastic core (G.N. Karam and L.J. Gibson, Elastic buckling of cylindrical shells with elastic cores, I: Analysis,  1994 , G.N. Karam and L.J. Gibson, Elastic buckling of cylindrical shells with elastic cores, II: Experiments, submitted to Int. J. Solids Structures, 1994 ) were used to study the mechanical efficiency of these natural structures. It was found that natural structures are often more mechanically efficient than equivalent weight hollow cylinders. Biomimicking of natural cylindrical shell structures may offer the potential to increase the mechanical efficiency of engineering structures.
Microbial Biosynthesis of Alkanes
Venue: Science

Toward Alkane Synthesis Alkanes are major components of fossil fuels, and synthesis of alkanes remains a challenge in the conversion of renewable raw materials to fuels. Even though diverse organisms synthesize alkanes, synthesis pathways have remained elusive. Now Schirmer et al. (p. 559) describe an alkane biosynthesis pathway in cyanobacteria that converts intermediates of fatty acid metabolism to alkanes and alkenes. Heterologous expression of the biosynthetic genes resulted in production of alkanes in Escherichia coli. This pathway is likely to be a valuable tool in the production of biofuels. Alkane biosynthesis genes were identified in cyanobacteria and engineered into Escherichia coli for recombinant hydrocarbon production. Alkanes, the major constituents of gasoline, diesel, and jet fuel, are naturally produced by diverse species; however, the genetics and biochemistry behind this biology have remained elusive. Here we describe the discovery of an alkane biosynthesis pathway from cyanobacteria. The pathway consists of an acyl–acyl carrier protein reductase and an aldehyde decarbonylase, which together convert intermediates of fatty acid metabolism to alkanes and alkenes. The aldehyde decarbonylase is related to the broadly functional nonheme diiron enzymes. Heterologous expression of the alkane operon in Escherichia coli leads to the production and secretion of C13 to C17 mixtures of alkanes and alkenes. These genes and enzymes can now be leveraged for the simple and direct conversion of renewable raw materials to fungible hydrocarbon fuels.
Lung ventilation in salamanders and the evolution of vertebrate air-breathing mechanisms
Venue: Biological Journal of The Linnean Society

Functional analysis of lung ventilation in salamanders combined with historical analysis of respiratory pumps provides new perspectives on the evolution of breathing mechanisms in vertebrates. Lung ventilation in the aquatic salamander Necturus maculosus was examined by means of cineradiography, measurement of buccal and pleuroperitoneal cavity pressures, and electromyography of hypaxial musculature. In deoxygenated water Necturus periodically rises to the surface, opens its mouth, expands its buccal cavity to draw in fresh air, exhales air from the lungs, closes its mouth, and then compresses its buccal cavity and pumps air into the lungs. Thus Necturus produces only two buccal movements per breath: one expansion and one compression. Necturus shares the use of this two-stroke buccal pump with lungfishes, frogs and other salamanders. The ubiquitous use of this system by basal sarcopterygians is evidence that a two-stroke buccal pump is the primitive lung ventilation mechanism for sarcopterygian vertebrates. In contrast, basal actinopterygian fishes use a four-stroke buccal pump. In these fishes the buccal cavity expands to fill with expired air, compresses to expel the pulmonary air, expands to fill with fresh air, and then compresses for a second time to pump air into the lungs. Whether the sarcopterygian two-stroke buccal pump and the actinopterygian four-stroke buccal pump arose independently, whether both are derived from a single, primitive osteichthyian breathing mechanism, or whether one might be the primitive pattern and the other derived, cannot be determined Although Necturus and lungfishes both use a two-stroke buccal pump, they differ in their expiration mechanics. Unlike a lungfish (Protopterus), Necturus exhales by contracting a portion of its hypaxial trunk musculature (the m. transversus abdominis) to increase pleuroperitoneal pressure. The occurrence of this same expiratory mechanism in amniotes is evidence that the use of hypaxial musculature for expiration, but not for inspiration, is a primitive tetrapod feature. From this observation we hypothesize that aspiration breathing may have evolved in two stages: initially, from pure buccal pumping to the use of trunk musculature for exhalation but not for inspiration (as in Necturus); and secondarily, to the use of trunk musculature for both exhalation and inhalation by costal aspiration (as in amniotes).
Bamboo-inspired optimal design for functionally graded hollow cylinders
Venue: PLOS ONE

The optimal distribution of the reinforcing fibers for stiffening hollow cylindrical composites is explored using the linear elasticity theory. The spatial distribution of the vascular bundles in wild bamboo, a nature-designed functionally graded material, is the basis for the design. Our results suggest that wild bamboos maximize their flexural rigidity by optimally regulating the radial gradation of their vascular bundle distribution. This fact provides us with a plant-mimetic design principle that enables the realization of high-stiffness and lightweight cylindrical composites.